Daily Papers

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

The parcellation of Cranial Nerves (CNs) serves as a crucial quantitative methodology for evaluating the morphological characteristics and anatomical pathways of specific CNs. Multi-modal CNs parcellation networks have achieved promising segmentation performance, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI. However, insufficient exploration of diffusion MRI information has led to low performance of existing multi-modal fusion. In this work, we propose a tractography-guided Dual-label Collaborative Learning Network (DCLNet) for multi-modal CNs parcellation. The key contribution of our DCLNet is the introduction of coarse labels of CNs obtained from fiber tractography through CN atlas, and collaborative learning with precise labels annotated by experts. Meanwhile, we introduce a Modality-adaptive Encoder Module (MEM) to achieve soft information swapping between structural MRI and diffusion MRI. Extensive experiments conducted on the publicly available Human Connectome Project (HCP) dataset demonstrate performance improvements compared to single-label network. This systematic validation underscores the effectiveness of dual-label strategies in addressing inherent ambiguities in CNs parcellation tasks.

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

Brain decoding, a pivotal field in neuroscience, aims to reconstruct stimuli from acquired brain signals, primarily utilizing functional magnetic resonance imaging (fMRI). Currently, brain decoding is confined to a per-subject-per-model paradigm, limiting its applicability to the same individual for whom the decoding model is trained. This constraint stems from three key challenges: 1) the inherent variability in input dimensions across subjects due to differences in brain size; 2) the unique intrinsic neural patterns, influencing how different individuals perceive and process sensory information; 3) limited data availability for new subjects in real-world scenarios hampers the performance of decoding models. In this paper, we present a novel approach, MindBridge, that achieves cross-subject brain decoding by employing only one model. Our proposed framework establishes a generic paradigm capable of addressing these challenges by introducing biological-inspired aggregation function and novel cyclic fMRI reconstruction mechanism for subject-invariant representation learning. Notably, by cycle reconstruction of fMRI, MindBridge can enable novel fMRI synthesis, which also can serve as pseudo data augmentation. Within the framework, we also devise a novel reset-tuning method for adapting a pretrained model to a new subject. Experimental results demonstrate MindBridge's ability to reconstruct images for multiple subjects, which is competitive with dedicated subject-specific models. Furthermore, with limited data for a new subject, we achieve a high level of decoding accuracy, surpassing that of subject-specific models. This advancement in cross-subject brain decoding suggests promising directions for wider applications in neuroscience and indicates potential for more efficient utilization of limited fMRI data in real-world scenarios. Project page: https://littlepure2333.github.io/MindBridge

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

We present MindEye, a novel fMRI-to-image approach to retrieve and reconstruct viewed images from brain activity. Our model comprises two parallel submodules that are specialized for retrieval (using contrastive learning) and reconstruction (using a diffusion prior). MindEye can map fMRI brain activity to any high dimensional multimodal latent space, like CLIP image space, enabling image reconstruction using generative models that accept embeddings from this latent space. We comprehensively compare our approach with other existing methods, using both qualitative side-by-side comparisons and quantitative evaluations, and show that MindEye achieves state-of-the-art performance in both reconstruction and retrieval tasks. In particular, MindEye can retrieve the exact original image even among highly similar candidates indicating that its brain embeddings retain fine-grained image-specific information. This allows us to accurately retrieve images even from large-scale databases like LAION-5B. We demonstrate through ablations that MindEye's performance improvements over previous methods result from specialized submodules for retrieval and reconstruction, improved training techniques, and training models with orders of magnitude more parameters. Furthermore, we show that MindEye can better preserve low-level image features in the reconstructions by using img2img, with outputs from a separate autoencoder. All code is available on GitHub.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

Holistic 3D modeling of molecularly defined brain structures is crucial for understanding complex brain functions. Emerging tissue profiling technologies enable the construction of a comprehensive atlas of the mammalian brain with sub-cellular resolution and spatially resolved gene expression data. However, such tera-scale volumetric datasets present significant computational challenges in understanding complex brain functions within their native 3D spatial context. Here, we propose the novel generative approach Tera-MIND, which can simulate Tera-scale Mouse braINs in 3D using a patch-based and boundary-aware Diffusion model. Taking spatial transcriptomic data as the conditional input, we generate virtual mouse brains with comprehensive cellular morphological detail at teravoxel scale. Through the lens of 3D gene-gene self-attention, we identify spatial molecular interactions for key transcriptomic pathways in the murine brain, exemplified by glutamatergic and dopaminergic neuronal systems. Importantly, these in-silico biological findings are consistent and reproducible across three tera-scale virtual mouse brains. Therefore, Tera-MIND showcases a promising path toward efficient and generative simulations of whole organ systems for biomedical research. Project website: http://musikisomorphie.github.io/Tera-MIND.html{https}

In this paper, we introduce Recon3DMind, an innovative task aimed at reconstructing 3D visuals from Functional Magnetic Resonance Imaging (fMRI) signals, marking a significant advancement in the fields of cognitive neuroscience and computer vision. To support this pioneering task, we present the fMRI-Shape dataset, which includes data from 14 participants and features 360-degree videos of 3D objects to enable comprehensive fMRI signal capture across various settings, thereby laying a foundation for future research. Furthermore, we propose MinD-3D, a novel and effective three-stage framework specifically designed to decode the brain's 3D visual information from fMRI signals, demonstrating the feasibility of this challenging task. The framework begins by extracting and aggregating features from fMRI frames through a neuro-fusion encoder, subsequently employs a feature bridge diffusion model to generate visual features, and ultimately recovers the 3D object via a generative transformer decoder. We assess the performance of MinD-3D using a suite of semantic and structural metrics and analyze the correlation between the features extracted by our model and the visual regions of interest (ROIs) in fMRI signals. Our findings indicate that MinD-3D not only reconstructs 3D objects with high semantic relevance and spatial similarity but also significantly enhances our understanding of the human brain's capabilities in processing 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

Reconstructing 3D visuals from functional Magnetic Resonance Imaging (fMRI) data, introduced as Recon3DMind in our conference work, is of significant interest to both cognitive neuroscience and computer vision. To advance this task, we present the fMRI-3D dataset, which includes data from 15 participants and showcases a total of 4768 3D objects. The dataset comprises two components: fMRI-Shape, previously introduced and accessible at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Shape, and fMRI-Objaverse, proposed in this paper and available at https://huggingface.co/datasets/Fudan-fMRI/fMRI-Objaverse. fMRI-Objaverse includes data from 5 subjects, 4 of whom are also part of the Core set in fMRI-Shape, with each subject viewing 3142 3D objects across 117 categories, all accompanied by text captions. This significantly enhances the diversity and potential applications of the dataset. Additionally, we propose MinD-3D, a novel framework designed to decode 3D visual information from fMRI signals. The framework first extracts and aggregates features from fMRI data using a neuro-fusion encoder, then employs a feature-bridge diffusion model to generate visual features, and finally reconstructs the 3D object using a generative transformer decoder. We establish new benchmarks by designing metrics at both semantic and structural levels to evaluate model performance. Furthermore, we assess our model's effectiveness in an Out-of-Distribution setting and analyze the attribution of the extracted features and the visual ROIs in fMRI signals. Our experiments demonstrate that MinD-3D not only reconstructs 3D objects with high semantic and spatial accuracy but also deepens our understanding of how human brain processes 3D visual information. Project page at: https://jianxgao.github.io/MinD-3D.

The diffusion MRI Neurite Exchange Imaging model offers a promising framework for probing gray matter microstructure by estimating parameters such as compartment sizes, diffusivities, and inter-compartmental water exchange time. However, existing protocols require long scan times. This study proposes a reduced acquisition scheme for the Connectome 2.0 scanner that preserves model accuracy while substantially shortening scan duration. We developed a data-driven framework using explainable artificial intelligence with a guided recursive feature elimination strategy to identify an optimal 8-feature subset from a 15-feature protocol. The performance of this optimized protocol was validated in vivo and benchmarked against the full acquisition and alternative reduction strategies. Parameter accuracy, preservation of anatomical contrast, and test-retest reproducibility were assessed. The reduced protocol yielded parameter estimates and cortical maps comparable to the full protocol, with low estimation errors in synthetic data and minimal impact on test-retest variability. Compared to theory-driven and heuristic reduction schemes, the optimized protocol demonstrated superior robustness, reducing the deviation in water exchange time estimates by over two-fold. In conclusion, this hybrid optimization framework enables viable imaging of neurite exchange in 14 minutes without loss of parameter fidelity. This approach supports the broader application of exchange-sensitive diffusion magnetic resonance imaging in neuroscience and clinical research, and offers a generalizable method for designing efficient acquisition protocols in biophysical parameter mapping.

Every day, the human brain processes an immense volume of visual information, relying on intricate neural mechanisms to perceive and interpret these stimuli. Recent breakthroughs in functional magnetic resonance imaging (fMRI) have enabled scientists to extract visual information from human brain activity patterns. In this study, we present an innovative method for decoding brain activity into meaningful images and captions, with a specific focus on brain captioning due to its enhanced flexibility as compared to brain decoding into images. Our approach takes advantage of cutting-edge image captioning models and incorporates a unique image reconstruction pipeline that utilizes latent diffusion models and depth estimation. We utilized the Natural Scenes Dataset, a comprehensive fMRI dataset from eight subjects who viewed images from the COCO dataset. We employed the Generative Image-to-text Transformer (GIT) as our backbone for captioning and propose a new image reconstruction pipeline based on latent diffusion models. The method involves training regularized linear regression models between brain activity and extracted features. Additionally, we incorporated depth maps from the ControlNet model to further guide the reconstruction process. We evaluate our methods using quantitative metrics for both generated captions and images. Our brain captioning approach outperforms existing methods, while our image reconstruction pipeline generates plausible images with improved spatial relationships. In conclusion, we demonstrate significant progress in brain decoding, showcasing the enormous potential of integrating vision and language to better understand human cognition. Our approach provides a flexible platform for future research, with potential applications in various fields, including neural art, style transfer, and portable devices.

Reconstructions of visual perception from brain activity have improved tremendously, but the practical utility of such methods has been limited. This is because such models are trained independently per subject where each subject requires dozens of hours of expensive fMRI training data to attain high-quality results. The present work showcases high-quality reconstructions using only 1 hour of fMRI training data. We pretrain our model across 7 subjects and then fine-tune on minimal data from a new subject. Our novel functional alignment procedure linearly maps all brain data to a shared-subject latent space, followed by a shared non-linear mapping to CLIP image space. We then map from CLIP space to pixel space by fine-tuning Stable Diffusion XL to accept CLIP latents as inputs instead of text. This approach improves out-of-subject generalization with limited training data and also attains state-of-the-art image retrieval and reconstruction metrics compared to single-subject approaches. MindEye2 demonstrates how accurate reconstructions of perception are possible from a single visit to the MRI facility. All code is available on GitHub.

The quest for human imitative AI has been an enduring topic in AI research since its inception. The technical evolution and emerging capabilities of the latest cohort of large language models (LLMs) have reinvigorated the subject beyond academia to the cultural zeitgeist. While recent NLP evaluation benchmark tasks test some aspects of human-imitative behaviour (e.g., BIG-bench's 'human-like behavior' tasks), few, if not none, examine creative problem solving abilities. Creative problem solving in humans is a well-studied topic in cognitive neuroscience with standardized tests that predominantly use the ability to associate (heterogeneous) connections among clue words as a metric for creativity. Exposure to misleading stimuli - distractors dubbed red herrings - impede human performance in such tasks via the fixation effect and Einstellung paradigm. In cognitive neuroscience studies, such fixations are experimentally induced by pre-exposing participants to orthographically similar incorrect words to subsequent word-fragments or clues. The popular British quiz show Only Connect's Connecting Wall segment essentially mimics Mednick's Remote Associates Test (RAT) formulation with built-in, deliberate red herrings, which makes it an ideal proxy dataset to explore and study fixation effect and Einstellung paradigm from cognitive neuroscience in LLMs. In addition to presenting the novel Only Connect Wall (OCW) dataset, we also report results from our evaluation of selected pre-trained language models and LLMs (including OpenAI's GPT series) on creative problem solving tasks like grouping clue words by heterogeneous connections, and identifying correct open knowledge domain connections in respective groups. The code and link to the dataset are available at https://github.com/TaatiTeam/OCW.

Attention Deficit Hyperactive Disorder (ADHD) is a common behavioral problem affecting children. In this work, we investigate the automatic classification of ADHD subjects using the resting state Functional Magnetic Resonance Imaging (fMRI) sequences of the brain. We show that the brain can be modeled as a functional network, and certain properties of the networks differ in ADHD subjects from control subjects. We compute the pairwise correlation of brain voxels' activity over the time frame of the experimental protocol which helps to model the function of a brain as a network. Different network features are computed for each of the voxels constructing the network. The concatenation of the network features of all the voxels in a brain serves as the feature vector. Feature vectors from a set of subjects are then used to train a PCA-LDA (principal component analysis-linear discriminant analysis) based classifier. We hypothesized that ADHD-related differences lie in some specific regions of the brain and using features only from those regions is sufficient to discriminate ADHD and control subjects. We propose a method to create a brain mask that includes the useful regions only and demonstrate that using the feature from the masked regions improves classification accuracy on the test data set. We train our classifier with 776 subjects and test on 171 subjects provided by The Neuro Bureau for the ADHD-200 challenge. We demonstrate the utility of graph-motif features, specifically the maps that represent the frequency of participation of voxels in network cycles of length 3. The best classification performance (69.59%) is achieved using 3-cycle map features with masking. Our proposed approach holds promise in being able to diagnose and understand the disorder.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Early diagnosis of mild cognitive impairment (MCI) and subjective cognitive decline (SCD) utilizing multi-modal magnetic resonance imaging (MRI) is a pivotal area of research. While various regional and connectivity features from functional MRI (fMRI) and diffusion tensor imaging (DTI) have been employed to develop diagnosis models, most studies integrate these features without adequately addressing their alignment and interactions. This limits the potential to fully exploit the synergistic contributions of combined features and modalities. To solve this gap, our study introduces a novel Hierarchical Alignments and Hierarchical Interactions (HA-HI) method for MCI and SCD classification, leveraging the combined strengths of fMRI and DTI. HA-HI efficiently learns significant MCI- or SCD- related regional and connectivity features by aligning various feature types and hierarchically maximizing their interactions. Furthermore, to enhance the interpretability of our approach, we have developed the Synergistic Activation Map (SAM) technique, revealing the critical brain regions and connections that are indicative of MCI/SCD. Comprehensive evaluations on the ADNI dataset and our self-collected data demonstrate that HA-HI outperforms other existing methods in diagnosing MCI and SCD, making it a potentially vital and interpretable tool for early detection. The implementation of this method is publicly accessible at https://github.com/ICI-BCI/Dual-MRI-HA-HI.git.

Reconstructing images seen by people from their fMRI brain recordings provides a non-invasive window into the human brain. Despite recent progress enabled by diffusion models, current methods often lack faithfulness to the actual seen images. We present "Brain-IT", a brain-inspired approach that addresses this challenge through a Brain Interaction Transformer (BIT), allowing effective interactions between clusters of functionally-similar brain-voxels. These functional-clusters are shared by all subjects, serving as building blocks for integrating information both within and across brains. All model components are shared by all clusters & subjects, allowing efficient training with a limited amount of data. To guide the image reconstruction, BIT predicts two complementary localized patch-level image features: (i)high-level semantic features which steer the diffusion model toward the correct semantic content of the image; and (ii)low-level structural features which help to initialize the diffusion process with the correct coarse layout of the image. BIT's design enables direct flow of information from brain-voxel clusters to localized image features. Through these principles, our method achieves image reconstructions from fMRI that faithfully reconstruct the seen images, and surpass current SotA approaches both visually and by standard objective metrics. Moreover, with only 1-hour of fMRI data from a new subject, we achieve results comparable to current methods trained on full 40-hour recordings.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

Magnetic resonance imaging (MRI) is the standard modality to understand human brain structure and function in vivo (antemortem). Decades of research in human neuroimaging has led to the widespread development of methods and tools to provide automated volume-based segmentations and surface-based parcellations which help localize brain functions to specialized anatomical regions. Recently ex vivo (postmortem) imaging of the brain has opened-up avenues to study brain structure at sub-millimeter ultra high-resolution revealing details not possible to observe with in vivo MRI. Unfortunately, there has been limited methodological development in ex vivo MRI primarily due to lack of datasets and limited centers with such imaging resources. Therefore, in this work, we present one-of-its-kind dataset of 82 ex vivo T2w whole brain hemispheres MRI at 0.3 mm isotropic resolution spanning Alzheimer's disease and related dementias. We adapted and developed a fast and easy-to-use automated surface-based pipeline to parcellate, for the first time, ultra high-resolution ex vivo brain tissue at the native subject space resolution using the Desikan-Killiany-Tourville (DKT) brain atlas. This allows us to perform vertex-wise analysis in the template space and thereby link morphometry measures with pathology measurements derived from histology. We will open-source our dataset docker container, Jupyter notebooks for ready-to-use out-of-the-box set of tools and command line options to advance ex vivo MRI clinical brain imaging research on the project webpage.

Graph Transformers have recently been successful in various graph representation learning tasks, providing a number of advantages over message-passing Graph Neural Networks. Utilizing Graph Transformers for learning the representation of the brain functional connectivity network is also gaining interest. However, studies to date have underlooked the temporal dynamics of functional connectivity, which fluctuates over time. Here, we propose a method for learning the representation of dynamic functional connectivity with Graph Transformers. Specifically, we define the connectome embedding, which holds the position, structure, and time information of the functional connectivity graph, and use Transformers to learn its representation across time. We perform experiments with over 50,000 resting-state fMRI samples obtained from three datasets, which is the largest number of fMRI data used in studies by far. The experimental results show that our proposed method outperforms other competitive baselines in gender classification and age regression tasks based on the functional connectivity extracted from the fMRI data.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

The complete connectome of the Drosophila larva brain offers a unique opportunity to investigate whether biologically evolved circuits can support artificial intelligence. We convert this wiring diagram into a Biological Processing Unit (BPU), a fixed recurrent network derived directly from synaptic connectivity. Despite its modest size 3,000 neurons and 65,000 weights between them), the unmodified BPU achieves 98% accuracy on MNIST and 58% on CIFAR-10, surpassing size-matched MLPs. Scaling the BPU via structured connectome expansions further improves CIFAR-10 performance, while modality-specific ablations reveal the uneven contributions of different sensory subsystems. On the ChessBench dataset, a lightweight GNN-BPU model trained on only 10,000 games achieves 60% move accuracy, nearly 10x better than any size transformer. Moreover, CNN-BPU models with ~2M parameters outperform parameter-matched Transformers, and with a depth-6 minimax search at inference, reach 91.7% accuracy, exceeding even a 9M-parameter Transformer baseline. These results demonstrate the potential of biofidelic neural architectures to support complex cognitive tasks and motivate scaling to larger and more intelligent connectomes in future work.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

Image-to-fMRI encoding is important for both neuroscience research and practical applications. However, such "Brain-Encoders" have been typically trained per-subject and per fMRI-dataset, thus restricted to very limited training data. In this paper we propose a Universal Brain-Encoder, which can be trained jointly on data from many different subjects/datasets/machines. What makes this possible is our new voxel-centric Encoder architecture, which learns a unique "voxel-embedding" per brain-voxel. Our Encoder trains to predict the response of each brain-voxel on every image, by directly computing the cross-attention between the brain-voxel embedding and multi-level deep image features. This voxel-centric architecture allows the functional role of each brain-voxel to naturally emerge from the voxel-image cross-attention. We show the power of this approach to (i) combine data from multiple different subjects (a "Crowd of Brains") to improve each individual brain-encoding, (ii) quick & effective Transfer-Learning across subjects, datasets, and machines (e.g., 3-Tesla, 7-Tesla), with few training examples, and (iii) use the learned voxel-embeddings as a powerful tool to explore brain functionality (e.g., what is encoded where in the brain).

Multi-subject fMRI studies are challenging due to the high variability of both brain anatomy and functional brain topographies across participants. An effective way of aggregating multi-subject fMRI data is to extract a shared representation that filters out unwanted variability among subjects. Some recent work has implemented probabilistic models to extract a shared representation in task fMRI. In the present work, we improve upon these models by incorporating temporal information in the common latent structures. We introduce a new model, Shared Gaussian Process Factor Analysis (S-GPFA), that discovers shared latent trajectories and subject-specific functional topographies, while modelling temporal correlation in fMRI data. We demonstrate the efficacy of our model in revealing ground truth latent structures using simulated data, and replicate experimental performance of time-segment matching and inter-subject similarity on the publicly available Raider and Sherlock datasets. We further test the utility of our model by analyzing its learned model parameters in the large multi-site SPINS dataset, on a social cognition task from participants with and without schizophrenia.

Recently, there is an increasing interest in using artificial intelligence (AI) to automate aspects of the research process, or even autonomously conduct the full research cycle from idea generation, over data analysis, to composing and evaluation of scientific manuscripts. Examples of working AI scientist systems have been demonstrated for computer science tasks and running molecular biology labs. While some approaches aim for full autonomy of the scientific AI, others rather aim for leveraging human-AI teaming. Here, we address how to adapt such approaches for boosting Brain-Computer Interface (BCI) development, as well as brain research resp. neuroscience at large. We argue that at this time, a strong emphasis on human-AI teaming, in contrast to fully autonomous AI BCI researcher will be the most promising way forward. We introduce the collaborative workspaces concept for human-AI teaming based on a set of Janusian design principles, looking both ways, to the human as well as to the AI side. Based on these principles, we present ChatBCI, a Python-based toolbox for enabling human-AI collaboration based on interaction with Large Language Models (LLMs), designed for BCI research and development projects. We show how ChatBCI was successfully used in a concrete BCI project on advancing motor imagery decoding from EEG signals. Our approach can be straightforwardly extended to broad neurotechnological and neuroscientific topics, and may by design facilitate human expert knowledge transfer to scientific AI systems in general.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

In this work, we present a computing platform named digital twin brain (DTB) that can simulate spiking neuronal networks of the whole human brain scale and more importantly, a personalized biological brain structure. In comparison to most brain simulations with a homogeneous global structure, we highlight that the sparseness, couplingness and heterogeneity in the sMRI, DTI and PET data of the brain has an essential impact on the efficiency of brain simulation, which is proved from the scaling experiments that the DTB of human brain simulation is communication-intensive and memory-access intensive computing systems rather than computation-intensive. We utilize a number of optimization techniques to balance and integrate the computation loads and communication traffics from the heterogeneous biological structure to the general GPU-based HPC and achieve leading simulation performance for the whole human brain-scaled spiking neuronal networks. On the other hand, the biological structure, equipped with a mesoscopic data assimilation, enables the DTB to investigate brain cognitive function by a reverse-engineering method, which is demonstrated by a digital experiment of visual evaluation on the DTB. Furthermore, we believe that the developing DTB will be a promising powerful platform for a large of research orients including brain-inspiredintelligence, rain disease medicine and brain-machine interface.

Recent fMRI-to-image approaches mainly focused on associating fMRI signals with specific conditions of pre-trained diffusion models. These approaches, while producing high-quality images, capture only a limited aspect of the complex information in fMRI signals and offer little detailed control over image creation. In contrast, this paper proposes to directly modulate the generation process of diffusion models using fMRI signals. Our approach, NeuroPictor, divides the fMRI-to-image process into three steps: i) fMRI calibrated-encoding, to tackle multi-individual pre-training for a shared latent space to minimize individual difference and enable the subsequent cross-subject training; ii) fMRI-to-image cross-subject pre-training, perceptually learning to guide diffusion model with high- and low-level conditions across different individuals; iii) fMRI-to-image single-subject refining, similar with step ii but focus on adapting to particular individual. NeuroPictor extracts high-level semantic features from fMRI signals that characterizing the visual stimulus and incrementally fine-tunes the diffusion model with a low-level manipulation network to provide precise structural instructions. By training with over 60,000 fMRI-image pairs from various individuals, our model enjoys superior fMRI-to-image decoding capacity, particularly in the within-subject setting, as evidenced in benchmark datasets. Project page: https://jingyanghuo.github.io/neuropictor/.

Decoding non-invasive brain recordings is pivotal for advancing our understanding of human cognition but faces challenges due to individual differences and complex neural signal representations. Traditional methods often require customized models and extensive trials, lacking interpretability in visual reconstruction tasks. Our framework integrates 3D brain structures with visual semantics using a Vision Transformer 3D. This unified feature extractor efficiently aligns fMRI features with multiple levels of visual embeddings, eliminating the need for subject-specific models and allowing extraction from single-trial data. The extractor consolidates multi-level visual features into one network, simplifying integration with Large Language Models (LLMs). Additionally, we have enhanced the fMRI dataset with diverse fMRI-image-related textual data to support multimodal large model development. Integrating with LLMs enhances decoding capabilities, enabling tasks such as brain captioning, complex reasoning, concept localization, and visual reconstruction. Our approach demonstrates superior performance across these tasks, precisely identifying language-based concepts within brain signals, enhancing interpretability, and providing deeper insights into neural processes. These advances significantly broaden the applicability of non-invasive brain decoding in neuroscience and human-computer interaction, setting the stage for advanced brain-computer interfaces and cognitive models.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

In this work, we present a network-specific approach for predicting brain responses to complex multimodal movies, leveraging the Yeo 7-network parcellation of the Schaefer atlas. Rather than treating the brain as a homogeneous system, we grouped the seven functional networks into four clusters and trained separate multi-subject, multi-layer perceptron (MLP) models for each. This architecture supports cluster-specific optimization and adaptive memory modeling, allowing each model to adjust temporal dynamics and modality weighting based on the functional role of its target network. Our results demonstrate that this clustered strategy significantly enhances prediction accuracy across the 1,000 cortical regions of the Schaefer atlas. The final model achieved an eighth-place ranking in the Algonauts Project 2025 Challenge, with out-of-distribution (OOD) correlation scores nearly double those of the baseline model used in the selection phase. Code is available at https://github.com/Corsi01/algo2025.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.

Due to the lack of paired samples and the low signal-to-noise ratio of functional MRI (fMRI) signals, reconstructing perceived natural images or decoding their semantic contents from fMRI data are challenging tasks. In this work, we propose, for the first time, a task-agnostic fMRI-based brain decoding model, BrainCLIP, which leverages CLIP's cross-modal generalization ability to bridge the modality gap between brain activity, image, and text. Our experiments demonstrate that CLIP can act as a pivot for generic brain decoding tasks, including zero-shot visual categories decoding, fMRI-image/text matching, and fMRI-to-image generation. Specifically, BrainCLIP aims to train a mapping network that transforms fMRI patterns into a well-aligned CLIP embedding space by combining visual and textual supervision. Our experiments show that this combination can boost the decoding model's performance on certain tasks like fMRI-text matching and fMRI-to-image generation. On the zero-shot visual category decoding task, BrainCLIP achieves significantly better performance than BraVL, a recently proposed multi-modal method specifically designed for this task. BrainCLIP can also reconstruct visual stimuli with high semantic fidelity and establishes a new state-of-the-art for fMRI-based natural image reconstruction in terms of high-level semantic features.

Functional magnetic resonance imaging (fMRI) is an indispensable tool in modern neuroscience, providing a non-invasive window into whole-brain dynamics at millimeter-scale spatial resolution. However, fMRI is constrained by issues such as high operation costs and immobility. With the rapid advancements in cross-modality synthesis and brain decoding, the use of deep neural networks has emerged as a promising solution for inferring whole-brain, high-resolution fMRI features directly from electroencephalography (EEG), a more widely accessible and portable neuroimaging modality. Nonetheless, the complex projection from neural activity to fMRI hemodynamic responses and the spatial ambiguity of EEG pose substantial challenges both in modeling and interpretability. Relatively few studies to date have developed approaches for EEG-fMRI translation, and although they have made significant strides, the inference of fMRI signals in a given study has been limited to a small set of brain areas and to a single condition (i.e., either resting-state or a specific task). The capability to predict fMRI signals in other brain areas, as well as to generalize across conditions, remain critical gaps in the field. To tackle these challenges, we introduce a novel and generalizable framework: NeuroBOLT, i.e., Neuro-to-BOLD Transformer, which leverages multi-dimensional representation learning from temporal, spatial, and spectral domains to translate raw EEG data to the corresponding fMRI activity signals across the brain. Our experiments demonstrate that NeuroBOLT effectively reconstructs unseen resting-state fMRI signals from primary sensory, high-level cognitive areas, and deep subcortical brain regions, achieving state-of-the-art accuracy with the potential to generalize across varying conditions and sites, which significantly advances the integration of these two modalities.

Deep neural networks trained on Functional Connectivity (FC) networks extracted from functional Magnetic Resonance Imaging (fMRI) data have gained popularity due to the increasing availability of data and advances in model architectures, including Graph Neural Network (GNN). Recent research on the application of GNN to FC suggests that exploiting the time-varying properties of the FC could significantly improve the accuracy and interpretability of the model prediction. However, the high cost of acquiring high-quality fMRI data and corresponding phenotypic labels poses a hurdle to their application in real-world settings, such that a model na\"ively trained in a supervised fashion can suffer from insufficient performance or a lack of generalization on a small number of data. In addition, most Self-Supervised Learning (SSL) approaches for GNNs to date adopt a contrastive strategy, which tends to lose appropriate semantic information when the graph structure is perturbed or does not leverage both spatial and temporal information simultaneously. In light of these challenges, we propose a generative SSL approach that is tailored to effectively harness spatio-temporal information within dynamic FC. Our empirical results, experimented with large-scale (>50,000) fMRI datasets, demonstrate that our approach learns valuable representations and enables the construction of accurate and robust models when fine-tuned for downstream tasks.

We present a new large-scale electroencephalography (EEG) dataset as part of the THINGS initiative, comprising over 1.6 million visual stimulus trials collected from 20 participants, and totaling more than twice the size of the most popular current benchmark dataset, THINGS-EEG2. Crucially, our data was recorded using a 32-channel consumer-grade wet electrode system costing ~$2.2k, around 27x cheaper than research-grade EEG systems typically used in cognitive neuroscience labs. Our work is one of the first open-source, large-scale EEG resource designed to closely reflect the quality of hardware that is practical to deploy in real-world, downstream applications of brain-computer interfaces (BCIs). We aim to explore the specific question of whether deep neural network-based BCI research and semantic decoding methods can be effectively conducted with such affordable systems, filling an important gap in current literature that is extremely relevant for future research. In our analysis, we not only demonstrate that decoding of high-level semantic information from EEG of visualized images is possible at consumer-grade hardware, but also that our data can facilitate effective EEG-to-Image reconstruction even despite significantly lower signal-to-noise ratios. In addition to traditional benchmarks, we also conduct analyses of EEG-to-Image models that demonstrate log-linear decoding performance with increasing data volume on our data, and discuss the trade-offs between hardware cost, signal fidelity, and the scale of data collection efforts in increasing the size and utility of currently available datasets. Our contributions aim to pave the way for large-scale, cost-effective EEG research with widely accessible equipment, and position our dataset as a unique resource for the democratization and development of effective deep neural models of visual cognition.

Fiber tractography is a cornerstone of neuroimaging, enabling the detailed mapping of the brain's white matter pathways through diffusion MRI. This is crucial for understanding brain connectivity and function, making it a valuable tool in neurological applications. Despite its importance, tractography faces challenges due to its complexity and susceptibility to false positives, misrepresenting vital pathways. To address these issues, recent strategies have shifted towards deep learning, utilizing supervised learning, which depends on precise ground truth, or reinforcement learning, which operates without it. In this work, we propose Tract-RLFormer, a network utilizing both supervised and reinforcement learning, in a two-stage policy refinement process that markedly improves the accuracy and generalizability across various data-sets. By employing a tract-specific approach, our network directly delineates the tracts of interest, bypassing the traditional segmentation process. Through rigorous validation on datasets such as TractoInferno, HCP, and ISMRM-2015, our methodology demonstrates a leap forward in tractography, showcasing its ability to accurately map the brain's white matter tracts.

Neural decoding, the process of understanding how brain activity corresponds to different stimuli, has been a primary objective in cognitive sciences. Over the past three decades, advancements in functional Magnetic Resonance Imaging and machine learning have greatly improved our ability to map visual stimuli to brain activity, especially in the visual cortex. Concurrently, research has expanded into decoding more complex processes like language and memory across the whole brain, utilizing techniques to handle greater variability and improve signal accuracy. We argue that "seeing" involves more than just mapping visual stimuli onto the visual cortex; it engages the entire brain, as various emotions and cognitive states can emerge from observing different scenes. In this paper, we develop algorithms to enhance our understanding of visual processes by incorporating whole-brain activation maps while individuals are exposed to visual stimuli. We utilize large-scale fMRI encoders and Image generative models pre-trained on large public datasets, which are then fine-tuned through Image-fMRI contrastive learning. Our models hence can decode visual experience across the entire cerebral cortex, surpassing the traditional confines of the visual cortex. We first compare our method with state-of-the-art approaches to decoding visual processing and show improved predictive semantic accuracy by 43%. A network ablation analysis suggests that beyond the visual cortex, the default mode network contributes most to decoding stimuli, in line with the proposed role of this network in sense-making and semantic processing. Additionally, we implemented zero-shot imagination decoding on an extra validation dataset, achieving a p-value of 0.0206 for mapping the reconstructed images and ground-truth text stimuli, which substantiates the model's capability to capture semantic meanings across various scenarios.

We address prevailing challenges of the brain-powered research, departing from the observation that the literature hardly recover accurate spatial information and require subject-specific models. To address these challenges, we propose UMBRAE, a unified multimodal decoding of brain signals. First, to extract instance-level conceptual and spatial details from neural signals, we introduce an efficient universal brain encoder for multimodal-brain alignment and recover object descriptions at multiple levels of granularity from subsequent multimodal large language model (MLLM). Second, we introduce a cross-subject training strategy mapping subject-specific features to a common feature space. This allows a model to be trained on multiple subjects without extra resources, even yielding superior results compared to subject-specific models. Further, we demonstrate this supports weakly-supervised adaptation to new subjects, with only a fraction of the total training data. Experiments demonstrate that UMBRAE not only achieves superior results in the newly introduced tasks but also outperforms methods in well established tasks. To assess our method, we construct and share with the community a comprehensive brain understanding benchmark BrainHub. Our code and benchmark are available at https://weihaox.github.io/UMBRAE.

White matter bundle segmentation is crucial for studying brain structural connectivity, neurosurgical planning, and neurological disorders. White Matter Segmentation remains challenging due to structural similarity in streamlines, subject variability, symmetry in 2 hemispheres, etc. To address these challenges, we propose TractoGPT, a GPT-based architecture trained on streamline, cluster, and fusion data representations separately. TractoGPT is a fully-automatic method that generalizes across datasets and retains shape information of the white matter bundles. Experiments also show that TractoGPT outperforms state-of-the-art methods on average DICE, Overlap and Overreach scores. We use TractoInferno and 105HCP datasets and validate generalization across dataset.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

In recent years, the intersection of Natural Language Processing (NLP) and public health has opened innovative pathways for investigating various domains, including chronic pain in textual datasets. Despite the promise of NLP in chronic pain, the literature is dispersed across various disciplines, and there is a need to consolidate existing knowledge, identify knowledge gaps in the literature, and inform future research directions in this emerging field. This review aims to investigate the state of the research on NLP-based interventions designed for chronic pain research. A search strategy was formulated and executed across PubMed, Web of Science, IEEE Xplore, Scopus, and ACL Anthology to find studies published in English between 2014 and 2024. After screening 132 papers, 26 studies were included in the final review. Key findings from this review underscore the significant potential of NLP techniques to address pressing challenges in chronic pain research. The past 10 years in this field have showcased the utilization of advanced methods (transformers like RoBERTa and BERT) achieving high-performance metrics (e.g., F1>0.8) in classification tasks, while unsupervised approaches like Latent Dirichlet Allocation (LDA) and k-means clustering have proven effective for exploratory analyses. Results also reveal persistent challenges such as limited dataset diversity, inadequate sample sizes, and insufficient representation of underrepresented populations. Future research studies should explore multimodal data validation systems, context-aware mechanistic modeling, and the development of standardized evaluation metrics to enhance reproducibility and equity in chronic pain research.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

Neuroimage processing tasks like segmentation, reconstruction, and registration are central to the study of neuroscience. Robust deep learning strategies and architectures used to solve these tasks are often similar. Yet, when presented with a new task or a dataset with different visual characteristics, practitioners most often need to train a new model, or fine-tune an existing one. This is a time-consuming process that poses a substantial barrier for the thousands of neuroscientists and clinical researchers who often lack the resources or machine-learning expertise to train deep learning models. In practice, this leads to a lack of adoption of deep learning, and neuroscience tools being dominated by classical frameworks. We introduce Neuralizer, a single model that generalizes to previously unseen neuroimaging tasks and modalities without the need for re-training or fine-tuning. Tasks do not have to be known a priori, and generalization happens in a single forward pass during inference. The model can solve processing tasks across multiple image modalities, acquisition methods, and datasets, and generalize to tasks and modalities it has not been trained on. Our experiments on coronal slices show that when few annotated subjects are available, our multi-task network outperforms task-specific baselines without training on the task.

The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particularly benefited: the use of deep learning models trained on large amounts of natural images has greatly improved its quality, and approaches that combine the diverse information contained in visual experiences have proliferated rapidly in recent years. In this technical paper, by taking advantage of the simple and generic framework that we proposed (Takagi and Nishimoto, CVPR 2023), we examine the extent to which various additional decoding techniques affect the performance of visual experience reconstruction. Specifically, we combined our earlier work with the following three techniques: using decoded text from brain activity, nonlinear optimization for structural image reconstruction, and using decoded depth information from brain activity. We confirmed that these techniques contributed to improving accuracy over the baseline. We also discuss what researchers should consider when performing visual reconstruction using deep generative models trained on large datasets. Please check our webpage at https://sites.google.com/view/stablediffusion-with-brain/. Code is also available at https://github.com/yu-takagi/StableDiffusionReconstruction.

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

Deep Learning (DL) in neuroimaging has become increasingly relevant for detecting neurological conditions and neurodegenerative disorders. One of the most predominant biomarkers in neuroimaging is represented by brain age, which has been shown to be a good indicator for different conditions, such as Alzheimer's Disease. Using brain age for weakly supervised pre-training of DL models in transfer learning settings has also recently shown promising results, especially when dealing with data scarcity of different conditions. On the other hand, anatomical information of brain MRIs (e.g. cortical thickness) can provide important information for learning good representations that can be transferred to many downstream tasks. In this work, we propose AnatCL, an anatomical foundation model for brain MRIs that i.) leverages anatomical information in a weakly contrastive learning approach, and ii.) achieves state-of-the-art performances across many different downstream tasks. To validate our approach we consider 12 different downstream tasks for the diagnosis of different conditions such as Alzheimer's Disease, autism spectrum disorder, and schizophrenia. Furthermore, we also target the prediction of 10 different clinical assessment scores using structural MRI data. Our findings show that incorporating anatomical information during pre-training leads to more robust and generalizable representations. Pre-trained models can be found at: https://github.com/EIDOSLAB/AnatCL.

In this study, we present a technique that spans multi-scale views (global scale -- meaning brain network-level and local scale -- examining each individual ROI that constitutes the network) applied to resting-state fMRI volumes. Deep learning based classification is utilized in understanding neurodegeneration. The novelty of the proposed approach lies in utilizing two extreme scales of analysis. One branch considers the entire network within graph-analysis framework. Concurrently, the second branch scrutinizes each ROI within a network independently, focusing on evolution of dynamics. For each subject, graph-based approach employs partial correlation to profile the subject in a single graph where each ROI is a node, providing insights into differences in levels of participation. In contrast, non-linear analysis employs recurrence plots to profile a subject as a multichannel 2D image, revealing distinctions in underlying dynamics. The proposed approach is employed for classification of a cohort of 50 healthy control (HC) and 50 Mild Cognitive Impairment (MCI), sourced from ADNI dataset. Results point to: (1) reduced activity in ROIs such as PCC in MCI (2) greater activity in occipital in MCI, which is not seen in HC (3) when analysed for dynamics, all ROIs in MCI show greater predictability in time-series.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

In the past five years, the use of generative and foundational AI systems has greatly improved the decoding of brain activity. Visual perception, in particular, can now be decoded from functional Magnetic Resonance Imaging (fMRI) with remarkable fidelity. This neuroimaging technique, however, suffers from a limited temporal resolution (approx0.5 Hz) and thus fundamentally constrains its real-time usage. Here, we propose an alternative approach based on magnetoencephalography (MEG), a neuroimaging device capable of measuring brain activity with high temporal resolution (approx5,000 Hz). For this, we develop an MEG decoding model trained with both contrastive and regression objectives and consisting of three modules: i) pretrained embeddings obtained from the image, ii) an MEG module trained end-to-end and iii) a pretrained image generator. Our results are threefold: Firstly, our MEG decoder shows a 7X improvement of image-retrieval over classic linear decoders. Second, late brain responses to images are best decoded with DINOv2, a recent foundational image model. Third, image retrievals and generations both suggest that high-level visual features can be decoded from MEG signals, although the same approach applied to 7T fMRI also recovers better low-level features. Overall, these results, while preliminary, provide an important step towards the decoding -- in real-time -- of the visual processes continuously unfolding within the human brain.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Brain extraction and removal of skull artifacts from magnetic resonance images (MRI) is an important preprocessing step in neuroimaging analysis. There are many tools developed to handle human fMRI images, which could involve manual steps for verifying results from brain segmentation that makes it time consuming and inefficient. In this study, we will use the segment anything model (SAM), a freely available neural network released by Meta[4], which has shown promising results in many generic segmentation applications. We will analyze the efficiency of SAM for neuroimaging brain segmentation by removing skull artifacts. The results of the experiments showed promising results that explore using automated segmentation algorithms for neuroimaging without the need to train on custom medical imaging dataset.

White matter tract segmentation is crucial for studying brain structural connectivity and neurosurgical planning. However, segmentation remains challenging due to issues like class imbalance between major and minor tracts, structural similarity, subject variability, symmetric streamlines between hemispheres etc. To address these challenges, we propose TractoEmbed, a modular multi-level embedding framework, that encodes localized representations through learning tasks in respective encoders. In this paper, TractoEmbed introduces a novel hierarchical streamline data representation that captures maximum spatial information at each level i.e. individual streamlines, clusters, and patches. Experiments show that TractoEmbed outperforms state-of-the-art methods in white matter tract segmentation across different datasets, and spanning various age groups. The modular framework directly allows the integration of additional embeddings in future works.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Modern language models can process inputs across diverse languages and modalities. We hypothesize that models acquire this capability through learning a shared representation space across heterogeneous data types (e.g., different languages and modalities), which places semantically similar inputs near one another, even if they are from different modalities/languages. We term this the semantic hub hypothesis, following the hub-and-spoke model from neuroscience (Patterson et al., 2007) which posits that semantic knowledge in the human brain is organized through a transmodal semantic "hub" which integrates information from various modality-specific "spokes" regions. We first show that model representations for semantically equivalent inputs in different languages are similar in the intermediate layers, and that this space can be interpreted using the model's dominant pretraining language via the logit lens. This tendency extends to other data types, including arithmetic expressions, code, and visual/audio inputs. Interventions in the shared representation space in one data type also predictably affect model outputs in other data types, suggesting that this shared representations space is not simply a vestigial byproduct of large-scale training on broad data, but something that is actively utilized by the model during input processing.

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors.

Reconstructing 3D human appearance from a single image is crucial for achieving holographic communication and immersive social experiences. However, this remains a challenge for existing methods, which typically rely on multi-camera setups or are limited to offline operations. In this paper, we propose R^2Human, the first approach for real-time inference and rendering of photorealistic 3D human appearance from a single image. The core of our approach is to combine the strengths of implicit texture fields and explicit neural rendering with our novel representation, namely Z-map. Based on this, we present an end-to-end network that performs high-fidelity color reconstruction of visible areas and provides reliable color inference for occluded regions. To further enhance the 3D perception ability of our network, we leverage the Fourier occupancy field to reconstruct a detailed 3D geometry, which serves as a prior for the texture field generation and provides a sampling surface in the rendering stage. Experiments show that our end-to-end method achieves state-of-the-art performance on both synthetic data and challenging real-world images and even outperforms many offline methods. The project page is available for research purposes at http://cic.tju.edu.cn/faculty/likun/projects/R2Human.

We present SAM4EM, a novel approach for 3D segmentation of complex neural structures in electron microscopy (EM) data by leveraging the Segment Anything Model (SAM) alongside advanced fine-tuning strategies. Our contributions include the development of a prompt-free adapter for SAM using two stage mask decoding to automatically generate prompt embeddings, a dual-stage fine-tuning method based on Low-Rank Adaptation (LoRA) for enhancing segmentation with limited annotated data, and a 3D memory attention mechanism to ensure segmentation consistency across 3D stacks. We further release a unique benchmark dataset for the segmentation of astrocytic processes and synapses. We evaluated our method on challenging neuroscience segmentation benchmarks, specifically targeting mitochondria, glia, and synapses, with significant accuracy improvements over state-of-the-art (SOTA) methods, including recent SAM-based adapters developed for the medical domain and other vision transformer-based approaches. Experimental results indicate that our approach outperforms existing solutions in the segmentation of complex processes like glia and post-synaptic densities. Our code and models are available at https://github.com/Uzshah/SAM4EM.

Modelling the complex spatiotemporal patterns of large-scale brain dynamics is crucial for neuroscience, but traditional methods fail to capture the rich structure in modalities such as magnetoencephalography (MEG). Recent advances in deep learning have enabled significant progress in other domains, such as language and vision, by using foundation models at scale. Here, we introduce MEG-GPT, a transformer based foundation model that uses time-attention and next time-point prediction. To facilitate this, we also introduce a novel data-driven tokeniser for continuous MEG data, which preserves the high temporal resolution of continuous MEG signals without lossy transformations. We trained MEG-GPT on tokenised brain region time-courses extracted from a large-scale MEG dataset (N=612, eyes-closed rest, Cam-CAN data), and show that the learnt model can generate data with realistic spatio-spectral properties, including transient events and population variability. Critically, it performs well in downstream decoding tasks, improving downstream supervised prediction task, showing improved zero-shot generalisation across sessions (improving accuracy from 0.54 to 0.59) and subjects (improving accuracy from 0.41 to 0.49) compared to a baseline methods. Furthermore, we show the model can be efficiently fine-tuned on a smaller labelled dataset to boost performance in cross-subject decoding scenarios. This work establishes a powerful foundation model for electrophysiological data, paving the way for applications in computational neuroscience and neural decoding.

Multimodal functional neuroimaging enables systematic analysis of brain mechanisms and provides discriminative representations for brain-computer interface (BCI) decoding. However, its acquisition is constrained by high costs and feasibility limitations. Moreover, underrepresentation of specific groups undermines fairness of BCI decoding model. To address these challenges, we propose a unified representation framework for multimodal functional neuroimaging via generative artificial intelligence (AI). By mapping multimodal functional neuroimaging into a unified representation space, the proposed framework is capable of generating data for acquisition-constrained modalities and underrepresented groups. Experiments show that the framework can generate data consistent with real brain activity patterns, provide insights into brain mechanisms, and improve performance on downstream tasks. More importantly, it can enhance model fairness by augmenting data for underrepresented groups. Overall, the framework offers a new paradigm for decreasing the cost of acquiring multimodal functional neuroimages and enhancing the fairness of BCI decoding models.

Deep neural networks have brought remarkable breakthroughs in medical image analysis. However, due to their data-hungry nature, the modest dataset sizes in medical imaging projects might be hindering their full potential. Generating synthetic data provides a promising alternative, allowing to complement training datasets and conducting medical image research at a larger scale. Diffusion models recently have caught the attention of the computer vision community by producing photorealistic synthetic images. In this study, we explore using Latent Diffusion Models to generate synthetic images from high-resolution 3D brain images. We used T1w MRI images from the UK Biobank dataset (N=31,740) to train our models to learn about the probabilistic distribution of brain images, conditioned on covariables, such as age, sex, and brain structure volumes. We found that our models created realistic data, and we could use the conditioning variables to control the data generation effectively. Besides that, we created a synthetic dataset with 100,000 brain images and made it openly available to the scientific community.

We present Brain Harmony (BrainHarmonix), the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (~ 14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: structure complements function - structural and functional modalities offer distinct yet synergistic insights into brain organization; function follows structure - brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

Working memory (WM), a fundamental cognitive process facilitating the temporary storage, integration, manipulation, and retrieval of information, plays a vital role in reasoning and decision-making tasks. Robust benchmark datasets that capture the multifaceted nature of WM are crucial for the effective development and evaluation of AI WM models. Here, we introduce a comprehensive Working Memory (WorM) benchmark dataset for this purpose. WorM comprises 10 tasks and a total of 1 million trials, assessing 4 functionalities, 3 domains, and 11 behavioral and neural characteristics of WM. We jointly trained and tested state-of-the-art recurrent neural networks and transformers on all these tasks. We also include human behavioral benchmarks as an upper bound for comparison. Our results suggest that AI models replicate some characteristics of WM in the brain, most notably primacy and recency effects, and neural clusters and correlates specialized for different domains and functionalities of WM. In the experiments, we also reveal some limitations in existing models to approximate human behavior. This dataset serves as a valuable resource for communities in cognitive psychology, neuroscience, and AI, offering a standardized framework to compare and enhance WM models, investigate WM's neural underpinnings, and develop WM models with human-like capabilities. Our source code and data are available at https://github.com/ZhangLab-DeepNeuroCogLab/WorM.

We introduce Brain-JEPA, a brain dynamics foundation model with the Joint-Embedding Predictive Architecture (JEPA). This pioneering model achieves state-of-the-art performance in demographic prediction, disease diagnosis/prognosis, and trait prediction through fine-tuning. Furthermore, it excels in off-the-shelf evaluations (e.g., linear probing) and demonstrates superior generalizability across different ethnic groups, surpassing the previous large model for brain activity significantly. Brain-JEPA incorporates two innovative techniques: Brain Gradient Positioning and Spatiotemporal Masking. Brain Gradient Positioning introduces a functional coordinate system for brain functional parcellation, enhancing the positional encoding of different Regions of Interest (ROIs). Spatiotemporal Masking, tailored to the unique characteristics of fMRI data, addresses the challenge of heterogeneous time-series patches. These methodologies enhance model performance and advance our understanding of the neural circuits underlying cognition. Overall, Brain-JEPA is paving the way to address pivotal questions of building brain functional coordinate system and masking brain activity at the AI-neuroscience interface, and setting a potentially new paradigm in brain activity analysis through downstream adaptation.

Deep-learning-based brain magnetic resonance imaging (MRI) reconstruction methods have the potential to accelerate the MRI acquisition process. Nevertheless, the scientific community lacks appropriate benchmarks to assess MRI reconstruction quality of high-resolution brain images, and evaluate how these proposed algorithms will behave in the presence of small, but expected data distribution shifts. The Multi-Coil Magnetic Resonance Image (MC-MRI) Reconstruction Challenge provides a benchmark that aims at addressing these issues, using a large dataset of high-resolution, three-dimensional, T1-weighted MRI scans. The challenge has two primary goals: 1) to compare different MRI reconstruction models on this dataset and 2) to assess the generalizability of these models to data acquired with a different number of receiver coils. In this paper, we describe the challenge experimental design, and summarize the results of a set of baseline and state of the art brain MRI reconstruction models. We provide relevant comparative information on the current MRI reconstruction state-of-the-art and highlight the challenges of obtaining generalizable models that are required prior to broader clinical adoption. The MC-MRI benchmark data, evaluation code and current challenge leaderboard are publicly available. They provide an objective performance assessment for future developments in the field of brain MRI reconstruction.

The deep neural nets of modern artificial intelligence (AI) have not achieved defining features of biological intelligence, including abstraction, causal learning, and energy-efficiency. While scaling to larger models has delivered performance improvements for current applications, more brain-like capacities may demand new theories, models, and methods for designing artificial learning systems. Here, we argue that this opportunity to reassess insights from the brain should stimulate cooperation between AI research and theory-driven computational neuroscience (CN). To motivate a brain basis of neural computation, we present a dynamical view of intelligence from which we elaborate concepts of sparsity in network structure, temporal dynamics, and interactive learning. In particular, we suggest that temporal dynamics, as expressed through neural synchrony, nested oscillations, and flexible sequences, provide a rich computational layer for reading and updating hierarchical models distributed in long-term memory networks. Moreover, embracing agent-centered paradigms in AI and CN will accelerate our understanding of the complex dynamics and behaviors that build useful world models. A convergence of AI/CN theories and objectives will reveal dynamical principles of intelligence for brains and engineered learning systems. This article was inspired by our symposium on dynamical neuroscience and machine learning at the 6th Annual US/NIH BRAIN Initiative Investigators Meeting.

In this paper, we introduce CineBrain, the first large-scale dataset featuring simultaneous EEG and fMRI recordings during dynamic audiovisual stimulation. Recognizing the complementary strengths of EEG's high temporal resolution and fMRI's deep-brain spatial coverage, CineBrain provides approximately six hours of narrative-driven content from the popular television series The Big Bang Theory for each of six participants. Building upon this unique dataset, we propose CineSync, an innovative multimodal decoding framework integrates a Multi-Modal Fusion Encoder with a diffusion-based Neural Latent Decoder. Our approach effectively fuses EEG and fMRI signals, significantly improving the reconstruction quality of complex audiovisual stimuli. To facilitate rigorous evaluation, we introduce Cine-Benchmark, a comprehensive evaluation protocol that assesses reconstructions across semantic and perceptual dimensions. Experimental results demonstrate that CineSync achieves state-of-the-art video reconstruction performance and highlight our initial success in combining fMRI and EEG for reconstructing both video and audio stimuli. Project Page: https://jianxgao.github.io/CineBrain.

Deciphering visual content from functional Magnetic Resonance Imaging (fMRI) helps illuminate the human vision system. However, the scarcity of fMRI data and noise hamper brain decoding model performance. Previous approaches primarily employ subject-specific models, sensitive to training sample size. In this paper, we explore a straightforward but overlooked solution to address data scarcity. We propose shallow subject-specific adapters to map cross-subject fMRI data into unified representations. Subsequently, a shared deeper decoding model decodes cross-subject features into the target feature space. During training, we leverage both visual and textual supervision for multi-modal brain decoding. Our model integrates a high-level perception decoding pipeline and a pixel-wise reconstruction pipeline guided by high-level perceptions, simulating bottom-up and top-down processes in neuroscience. Empirical experiments demonstrate robust neural representation learning across subjects for both pipelines. Moreover, merging high-level and low-level information improves both low-level and high-level reconstruction metrics. Additionally, we successfully transfer learned general knowledge to new subjects by training new adapters with limited training data. Compared to previous state-of-the-art methods, notably pre-training-based methods (Mind-Vis and fMRI-PTE), our approach achieves comparable or superior results across diverse tasks, showing promise as an alternative method for cross-subject fMRI data pre-training. Our code and pre-trained weights will be publicly released at https://github.com/YulongBonjour/See_Through_Their_Minds.

Image registration is the process of bringing different images into a common coordinate system - a technique widely used in various applications of computer vision, such as remote sensing, image retrieval, and, most commonly, medical imaging. Deep learning based techniques have been applied successfully to tackle various complex medical image processing problems, including medical image registration. Over the years, several image registration techniques have been proposed using deep learning. Deformable image registration techniques such as Voxelmorph have been successful in capturing finer changes and providing smoother deformations. However, Voxelmorph, as well as ICNet and FIRE, do not explicitly encode global dependencies (i.e. the overall anatomical view of the supplied image) and, therefore, cannot track large deformations. In order to tackle the aforementioned problems, this paper extends the Voxelmorph approach in three different ways. To improve the performance in case of small as well as large deformations, supervision of the model at different resolutions has been integrated using a multi-scale UNet. To support the network to learn and encode the minute structural co-relations of the given image-pairs, a self-constructing graph network (SCGNet) has been used as the latent of the multi-scale UNet - which can improve the learning process of the model and help the model to generalise better. And finally, to make the deformations inverse-consistent, cycle consistency loss has been employed. On the task of registration of brain MRIs, the proposed method achieved significant improvements over ANTs and VoxelMorph, obtaining a Dice score of 0.8013 \pm 0.0243 for intramodal and 0.6211 \pm 0.0309 for intermodal, while VoxelMorph achieved 0.7747 \pm 0.0260 and 0.6071 \pm 0.0510, respectively

Despite significant advances in large-scale text-to-image models, achieving hyper-realistic human image generation remains a desirable yet unsolved task. Existing models like Stable Diffusion and DALL-E 2 tend to generate human images with incoherent parts or unnatural poses. To tackle these challenges, our key insight is that human image is inherently structural over multiple granularities, from the coarse-level body skeleton to fine-grained spatial geometry. Therefore, capturing such correlations between the explicit appearance and latent structure in one model is essential to generate coherent and natural human images. To this end, we propose a unified framework, HyperHuman, that generates in-the-wild human images of high realism and diverse layouts. Specifically, 1) we first build a large-scale human-centric dataset, named HumanVerse, which consists of 340M images with comprehensive annotations like human pose, depth, and surface normal. 2) Next, we propose a Latent Structural Diffusion Model that simultaneously denoises the depth and surface normal along with the synthesized RGB image. Our model enforces the joint learning of image appearance, spatial relationship, and geometry in a unified network, where each branch in the model complements to each other with both structural awareness and textural richness. 3) Finally, to further boost the visual quality, we propose a Structure-Guided Refiner to compose the predicted conditions for more detailed generation of higher resolution. Extensive experiments demonstrate that our framework yields the state-of-the-art performance, generating hyper-realistic human images under diverse scenarios. Project Page: https://snap-research.github.io/HyperHuman/

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

Generating images from brain waves is gaining increasing attention due to its potential to advance brain-computer interface (BCI) systems by understanding how brain signals encode visual cues. Most of the literature has focused on fMRI-to-Image tasks as fMRI is characterized by high spatial resolution. However, fMRI is an expensive neuroimaging modality and does not allow for real-time BCI. On the other hand, electroencephalography (EEG) is a low-cost, non-invasive, and portable neuroimaging technique, making it an attractive option for future real-time applications. Nevertheless, EEG presents inherent challenges due to its low spatial resolution and susceptibility to noise and artifacts, which makes generating images from EEG more difficult. In this paper, we address these problems with a streamlined framework based on the ControlNet adapter for conditioning a latent diffusion model (LDM) through EEG signals. We conduct experiments and ablation studies on popular benchmarks to demonstrate that the proposed method beats other state-of-the-art models. Unlike these methods, which often require extensive preprocessing, pretraining, different losses, and captioning models, our approach is efficient and straightforward, requiring only minimal preprocessing and a few components. Code will be available after publication.

The human brain is a complex spiking neural network (SNN) that learns multimodal signals in a zero-shot manner by generalizing existing knowledge. Remarkably, the brain achieves this with minimal power consumption, using event-based signals that propagate within its structure. However, mimicking the human brain in neuromorphic hardware presents both hardware and software challenges. Hardware limitations, such as the slowdown of Moore's law and the von Neumann bottleneck, hinder the efficiency of digital computers. On the software side, SNNs are known for their difficult training, especially when learning multimodal signals. To overcome these challenges, we propose a hardware-software co-design that combines a fixed and random liquid state machine (LSM) SNN encoder with trainable artificial neural network (ANN) projections. The LSM is physically implemented using analogue resistive memory, leveraging the inherent stochasticity of resistive switching to generate random weights. This highly efficient and nanoscale in-memory computing approach effectively addresses the von Neumann bottleneck and the slowdown of Moore's law. The ANN projections are implemented digitally, allowing for easy optimization using contrastive loss, which helps to overcome the difficulties associated with SNN training. We experimentally implement this co-design on a 40nm 256Kb in-memory computing macro. We first demonstrate LSM-based event encoding through supervised classification and linear probing on the N-MNIST and N-TIDIGITS datasets.

Artificial intelligence (AI) has undergone a renaissance recently, making major progress in key domains such as vision, language, control, and decision-making. This has been due, in part, to cheap data and cheap compute resources, which have fit the natural strengths of deep learning. However, many defining characteristics of human intelligence, which developed under much different pressures, remain out of reach for current approaches. In particular, generalizing beyond one's experiences--a hallmark of human intelligence from infancy--remains a formidable challenge for modern AI. The following is part position paper, part review, and part unification. We argue that combinatorial generalization must be a top priority for AI to achieve human-like abilities, and that structured representations and computations are key to realizing this objective. Just as biology uses nature and nurture cooperatively, we reject the false choice between "hand-engineering" and "end-to-end" learning, and instead advocate for an approach which benefits from their complementary strengths. We explore how using relational inductive biases within deep learning architectures can facilitate learning about entities, relations, and rules for composing them. We present a new building block for the AI toolkit with a strong relational inductive bias--the graph network--which generalizes and extends various approaches for neural networks that operate on graphs, and provides a straightforward interface for manipulating structured knowledge and producing structured behaviors. We discuss how graph networks can support relational reasoning and combinatorial generalization, laying the foundation for more sophisticated, interpretable, and flexible patterns of reasoning. As a companion to this paper, we have released an open-source software library for building graph networks, with demonstrations of how to use them in practice.

Human brains respond to semantic features of presented stimuli with different neurons. It is then curious whether modern deep neural networks admit a similar behavior pattern. Specifically, this paper finds a small cluster of neurons in a diffusion model corresponding to a particular subject. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. A few steps of further fine-tuning can enhance the multi-concept capability, which may be the first to manage to generate up to four different subjects in a single image. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 values of the parameters, which reduces storage consumption by 90\% compared with previous subject-driven generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.

Artificial intelligence has made great strides in the last decade but still falls short of the human brain, the best-known example of intelligence. Not much is known of the neural processes that allow the brain to make the leap to achieve so much from so little beyond its ability to create knowledge structures that can be flexibly and dynamically combined, recombined, and applied in new and novel ways. This paper proposes a mathematical approach using graph theory and spectral graph theory, to hypothesize how to constrain these neural clusters of information based on eigen-relationships. This same hypothesis is hierarchically applied to scale up from the smallest to the largest clusters of knowledge that eventually lead to model building and reasoning.

Traditionally, theory and practice of Cognitive Control are linked via literature reviews by human domain experts. This approach, however, is inadequate to track the ever-growing literature. It may also be biased, and yield redundancies and confusion. Here we present an alternative approach. We performed automated text analyses on a large body of scientific texts to create a joint representation of tasks and constructs. More specifically, 385,705 scientific abstracts were first mapped into an embedding space using a transformers-based language model. Document embeddings were then used to identify a task-construct graph embedding that grounds constructs on tasks and supports nuanced meaning of the constructs by taking advantage of constrained random walks in the graph. This joint task-construct graph embedding, can be queried to generate task batteries targeting specific constructs, may reveal knowledge gaps in the literature, and inspire new tasks and novel hypotheses.

This article addresses the challenge of modeling the amplitude of spatially indexed low frequency fluctuations (ALFF) in resting state functional MRI as a function of cortical structural features and a multi-task coactivation network in the Adolescent Brain Cognitive Development (ABCD) Study. It proposes a generative model that integrates effects of spatially-varying inputs and a network-valued input using deep neural networks to capture complex non-linear and spatial associations with the output. The method models spatial smoothness, accounts for subject heterogeneity and complex associations between network and spatial images at different scales, enables accurate inference of each images effect on the output image, and allows prediction with uncertainty quantification via Monte Carlo dropout, contributing to one of the first Explainable AI (XAI) frameworks for heterogeneous imaging data. The model is highly scalable to high-resolution data without the heavy pre-processing or summarization often required by Bayesian methods. Empirical results demonstrate its strong performance compared to existing statistical and deep learning methods. We applied the XAI model to the ABCD data which revealed associations between cortical features and ALFF throughout the entire brain. Our model performed comparably to existing methods in predictive accuracy but provided superior uncertainty quantification and faster computation, demonstrating its effectiveness for large-scale neuroimaging analysis. Open-source software in Python for XAI is available.

In this paper, we introduce fastHDMI, a Python package designed for efficient variable screening in high-dimensional datasets, particularly neuroimaging data. This work pioneers the application of three mutual information estimation methods for neuroimaging variable selection, a novel approach implemented via fastHDMI. These advancements enhance our ability to analyze the complex structures of neuroimaging datasets, providing improved tools for variable selection in high-dimensional spaces. Using the preprocessed ABIDE dataset, we evaluate the performance of these methods through extensive simulations. The tests cover a range of conditions, including linear and nonlinear associations, as well as continuous and binary outcomes. Our results highlight the superiority of the FFTKDE-based mutual information estimation for feature screening in continuous nonlinear outcomes, while binning-based methods outperform others for binary outcomes with nonlinear probability preimages. For linear simulations, both Pearson correlation and FFTKDE-based methods show comparable performance for continuous outcomes, while Pearson excels in binary outcomes with linear probability preimages. A comprehensive case study using the ABIDE dataset further demonstrates fastHDMI's practical utility, showcasing the predictive power of models built from variables selected using our screening techniques. This research affirms the computational efficiency and methodological strength of fastHDMI, significantly enriching the toolkit available for neuroimaging analysis.

Blood vessel networks in the brain play a crucial role in stroke research, where understanding their topology is essential for analyzing blood flow dynamics. However, extracting detailed topological vessel network information from microscopy data remains a significant challenge, mainly due to the scarcity of labeled training data and the need for high topological accuracy. This work combines synthetic data generation with deep learning to automatically extract vessel networks as graphs from volumetric microscopy data. To combat data scarcity, we introduce a comprehensive pipeline for generating large-scale synthetic datasets that mirror the characteristics of real vessel networks. Our three-stage approach progresses from abstract graph generation through vessel mask creation to realistic medical image synthesis, incorporating biological constraints and imaging artifacts at each stage. Using this synthetic data, we develop a two-stage deep learning pipeline of 3D U-Net-based models for node detection and edge prediction. Fine-tuning on real microscopy data shows promising adaptation, improving edge prediction F1 scores from 0.496 to 0.626 by training on merely 5 manually labeled samples. These results suggest that automated vessel network extraction is becoming practically feasible, opening new possibilities for large-scale vascular analysis in stroke research.

Despite extensive standardization, diagnostic interviews for mental health disorders encompass substantial subjective judgment. Previous studies have demonstrated that EEG-based neural measures can function as reliable objective correlates of depression, or even predictors of depression and its course. However, their clinical utility has not been fully realized because of 1) the lack of automated ways to deal with the inherent noise associated with EEG data at scale, and 2) the lack of knowledge of which aspects of the EEG signal may be markers of a clinical disorder. Here we adapt an unsupervised pipeline from the recent deep representation learning literature to address these problems by 1) learning a disentangled representation using beta-VAE to denoise the signal, and 2) extracting interpretable features associated with a sparse set of clinical labels using a Symbol-Concept Association Network (SCAN). We demonstrate that our method is able to outperform the canonical hand-engineered baseline classification method on a number of factors, including participant age and depression diagnosis. Furthermore, our method recovers a representation that can be used to automatically extract denoised Event Related Potentials (ERPs) from novel, single EEG trajectories, and supports fast supervised re-mapping to various clinical labels, allowing clinicians to re-use a single EEG representation regardless of updates to the standardized diagnostic system. Finally, single factors of the learned disentangled representations often correspond to meaningful markers of clinical factors, as automatically detected by SCAN, allowing for human interpretability and post-hoc expert analysis of the recommendations made by the model.

This study introduces a parameter-efficient Hierarchical Spatial Temporal Network (HiSTN) specifically designed for the task of emotion classification using multi-channel electroencephalogram data. The network incorporates a graph hierarchy constructed from bottom-up at various abstraction levels, offering the dual advantages of enhanced task-relevant deep feature extraction and a lightweight design. The model's effectiveness is further amplified when used in conjunction with a proposed unique label smoothing method. Comprehensive benchmark experiments reveal that this combined approach yields high, balanced performance in terms of both quantitative and qualitative predictions. HiSTN, which has approximately 1,000 parameters, achieves mean F1 scores of 96.82% (valence) and 95.62% (arousal) in subject-dependent tests on the rarely-utilized 5-classification task problem from the DREAMER dataset. In the subject-independent settings, the same model yields mean F1 scores of 78.34% for valence and 81.59% for arousal. The adoption of the Sequential Top-2 Hit Rate (Seq2HR) metric highlights the significant enhancements in terms of the balance between model's quantitative and qualitative for predictions achieved through our approach when compared to training with regular one-hot labels. These improvements surpass 50% in subject-dependent tasks and 30% in subject-independent tasks. The study also includes relevant ablation studies and case explorations to further elucidate the workings of the proposed model and enhance its interpretability.

Understanding how humans conceptualize and categorize natural objects offers critical insights into perception and cognition. With the advent of Large Language Models (LLMs), a key question arises: can these models develop human-like object representations from linguistic and multimodal data? In this study, we combined behavioral and neuroimaging analyses to explore the relationship between object concept representations in LLMs and human cognition. We collected 4.7 million triplet judgments from LLMs and Multimodal LLMs (MLLMs) to derive low-dimensional embeddings that capture the similarity structure of 1,854 natural objects. The resulting 66-dimensional embeddings were stable, predictive, and exhibited semantic clustering similar to human mental representations. Remarkably, the dimensions underlying these embeddings were interpretable, suggesting that LLMs and MLLMs develop human-like conceptual representations of objects. Further analysis showed strong alignment between model embeddings and neural activity patterns in brain regions such as EBA, PPA, RSC, and FFA. This provides compelling evidence that the object representations in LLMs, while not identical to human ones, share fundamental similarities that reflect key aspects of human conceptual knowledge. Our findings advance the understanding of machine intelligence and inform the development of more human-like artificial cognitive systems.

Large Language Models (LLMs) demonstrate human-level or even superior language abilities, effectively modeling syntactic structures, yet the specific computational modules responsible remain unclear. A key question is whether LLM behavioral capabilities stem from mechanisms akin to those in the human brain. To address these questions, we introduce the Hierarchical Frequency Tagging Probe (HFTP), a tool that utilizes frequency-domain analysis to identify neuron-wise components of LLMs (e.g., individual Multilayer Perceptron (MLP) neurons) and cortical regions (via intracranial recordings) encoding syntactic structures. Our results show that models such as GPT-2, Gemma, Gemma 2, Llama 2, Llama 3.1, and GLM-4 process syntax in analogous layers, while the human brain relies on distinct cortical regions for different syntactic levels. Representational similarity analysis reveals a stronger alignment between LLM representations and the left hemisphere of the brain (dominant in language processing). Notably, upgraded models exhibit divergent trends: Gemma 2 shows greater brain similarity than Gemma, while Llama 3.1 shows less alignment with the brain compared to Llama 2. These findings offer new insights into the interpretability of LLM behavioral improvements, raising questions about whether these advancements are driven by human-like or non-human-like mechanisms, and establish HFTP as a valuable tool bridging computational linguistics and cognitive neuroscience. This project is available at https://github.com/LilTiger/HFTP.

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

Do machines and humans process language in similar ways? A recent line of research has hinted in the affirmative, demonstrating that human brain signals can be effectively predicted using the internal representations of language models (LMs). This is thought to reflect shared computational principles between LMs and human language processing. However, there are also clear differences in how LMs and humans acquire and use language, even if the final task they are performing is the same. Despite this, there is little work exploring systematic differences between human and machine language processing using brain data. To address this question, we examine the differences between LM representations and the human brain's responses to language, specifically by examining a dataset of Magnetoencephalography (MEG) responses to a written narrative. In doing so we identify three phenomena that, in prior work, LMs have been found to not capture well: emotional understanding, figurative language processing, and physical commonsense. By fine-tuning LMs on datasets related to these phenomena, we observe that fine-tuned LMs show improved alignment with human brain responses across these tasks. Our study implies that the observed divergences between LMs and human brains may stem from LMs' inadequate representation of these specific types of knowledge.

We present FOMO60K, a large-scale, heterogeneous dataset of 60,529 brain Magnetic Resonance Imaging (MRI) scans from 13,900 sessions and 11,187 subjects, aggregated from 16 publicly available sources. The dataset includes both clinical- and research-grade images, multiple MRI sequences, and a wide range of anatomical and pathological variability, including scans with large brain anomalies. Minimal preprocessing was applied to preserve the original image characteristics while reducing barriers to entry for new users. Accompanying code for self-supervised pretraining and finetuning is provided. FOMO60K is intended to support the development and benchmarking of self-supervised learning methods in medical imaging at scale.

Reconstructing human vision from brain activities has been an appealing task that helps to understand our cognitive process. Even though recent research has seen great success in reconstructing static images from non-invasive brain recordings, work on recovering continuous visual experiences in the form of videos is limited. In this work, we propose Mind-Video that learns spatiotemporal information from continuous fMRI data of the cerebral cortex progressively through masked brain modeling, multimodal contrastive learning with spatiotemporal attention, and co-training with an augmented Stable Diffusion model that incorporates network temporal inflation. We show that high-quality videos of arbitrary frame rates can be reconstructed with Mind-Video using adversarial guidance. The recovered videos were evaluated with various semantic and pixel-level metrics. We achieved an average accuracy of 85% in semantic classification tasks and 0.19 in structural similarity index (SSIM), outperforming the previous state-of-the-art by 45%. We also show that our model is biologically plausible and interpretable, reflecting established physiological processes.

Many AI models trained on natural images develop representations that resemble those of the human brain. However, the factors that drive this brain-model similarity remain poorly understood. To disentangle how the model, training and data independently lead a neural network to develop brain-like representations, we trained a family of self-supervised vision transformers (DINOv3) that systematically varied these different factors. We compare their representations of images to those of the human brain recorded with both fMRI and MEG, providing high resolution in spatial and temporal analyses. We assess the brain-model similarity with three complementary metrics focusing on overall representational similarity, topographical organization, and temporal dynamics. We show that all three factors - model size, training amount, and image type - independently and interactively impact each of these brain similarity metrics. In particular, the largest DINOv3 models trained with the most human-centric images reach the highest brain-similarity. This emergence of brain-like representations in AI models follows a specific chronology during training: models first align with the early representations of the sensory cortices, and only align with the late and prefrontal representations of the brain with considerably more training. Finally, this developmental trajectory is indexed by both structural and functional properties of the human cortex: the representations that are acquired last by the models specifically align with the cortical areas with the largest developmental expansion, thickness, least myelination, and slowest timescales. Overall, these findings disentangle the interplay between architecture and experience in shaping how artificial neural networks come to see the world as humans do, thus offering a promising framework to understand how the human brain comes to represent its visual world.

The process of reconstructing experiences from human brain activity offers a unique lens into how the brain interprets and represents the world. In this paper, we introduce a method for reconstructing music from brain activity, captured using functional magnetic resonance imaging (fMRI). Our approach uses either music retrieval or the MusicLM music generation model conditioned on embeddings derived from fMRI data. The generated music resembles the musical stimuli that human subjects experienced, with respect to semantic properties like genre, instrumentation, and mood. We investigate the relationship between different components of MusicLM and brain activity through a voxel-wise encoding modeling analysis. Furthermore, we discuss which brain regions represent information derived from purely textual descriptions of music stimuli. We provide supplementary material including examples of the reconstructed music at https://google-research.github.io/seanet/brain2music

A major goal of neuroscience is to understand brain computations during visual processing in naturalistic settings. A dominant approach is to use image-computable deep neural networks trained with different task objectives as a basis for linear encoding models. However, in addition to requiring tuning a large number of parameters, the linear encoding approach ignores the structure of the feature maps both in the brain and the models. Recently proposed alternatives have focused on decomposing the linear mapping to spatial and feature components but focus on finding static receptive fields for units that are applicable only in early visual areas. In this work, we employ the attention mechanism used in the transformer architecture to study how retinotopic visual features can be dynamically routed to category-selective areas in high-level visual processing. We show that this computational motif is significantly more powerful than alternative methods in predicting brain activity during natural scene viewing, across different feature basis models and modalities. We also show that this approach is inherently more interpretable, without the need to create importance maps, by interpreting the attention routing signal for different high-level categorical areas. Our approach proposes a mechanistic model of how visual information from retinotopic maps can be routed based on the relevance of the input content to different category-selective regions.

In neural decoding research, one of the most intriguing topics is the reconstruction of perceived natural images based on fMRI signals. Previous studies have succeeded in re-creating different aspects of the visuals, such as low-level properties (shape, texture, layout) or high-level features (category of objects, descriptive semantics of scenes) but have typically failed to reconstruct these properties together for complex scene images. Generative AI has recently made a leap forward with latent diffusion models capable of generating high-complexity images. Here, we investigate how to take advantage of this innovative technology for brain decoding. We present a two-stage scene reconstruction framework called ``Brain-Diffuser''. In the first stage, starting from fMRI signals, we reconstruct images that capture low-level properties and overall layout using a VDVAE (Very Deep Variational Autoencoder) model. In the second stage, we use the image-to-image framework of a latent diffusion model (Versatile Diffusion) conditioned on predicted multimodal (text and visual) features, to generate final reconstructed images. On the publicly available Natural Scenes Dataset benchmark, our method outperforms previous models both qualitatively and quantitatively. When applied to synthetic fMRI patterns generated from individual ROI (region-of-interest) masks, our trained model creates compelling ``ROI-optimal'' scenes consistent with neuroscientific knowledge. Thus, the proposed methodology can have an impact on both applied (e.g. brain-computer interface) and fundamental neuroscience.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Recently, Multimodal Large Language Models (MLLMs) have shown great promise in language-guided perceptual tasks such as recognition, segmentation, and object detection. However, their effectiveness in addressing visual cognition problems that require high-level reasoning is not well-established. One such challenge is abstract visual reasoning (AVR) -- the cognitive ability to discern relationships among patterns in a set of images and extrapolate to predict subsequent patterns. This skill is crucial during the early neurodevelopmental stages of children. Inspired by the AVR tasks in Raven's Progressive Matrices (RPM) and Wechsler Intelligence Scale for Children (WISC), we propose a new dataset MaRs-VQA and a new benchmark VCog-Bench containing three datasets to evaluate the zero-shot AVR capability of MLLMs and compare their performance with existing human intelligent investigation. Our comparative experiments with different open-source and closed-source MLLMs on the VCog-Bench revealed a gap between MLLMs and human intelligence, highlighting the visual cognitive limitations of current MLLMs. We believe that the public release of VCog-Bench, consisting of MaRs-VQA, and the inference pipeline will drive progress toward the next generation of MLLMs with human-like visual cognition abilities.

Visual neural decoding seeks to reconstruct or infer perceived visual stimuli from brain activity patterns, providing critical insights into human cognition and enabling transformative applications in brain-computer interfaces and artificial intelligence. Current approaches, however, remain constrained by the scarcity of high-quality stimulus-brain response pairs and the inherent semantic mismatch between neural representations and visual content. Inspired by perceptual variability and co-adaptive strategy of the biological systems, we propose a novel self-supervised architecture, named NeuroBridge, which integrates Cognitive Prior Augmentation (CPA) with Shared Semantic Projector (SSP) to promote effective cross-modality alignment. Specifically, CPA simulates perceptual variability by applying asymmetric, modality-specific transformations to both EEG signals and images, enhancing semantic diversity. Unlike previous approaches, SSP establishes a bidirectional alignment process through a co-adaptive strategy, which mutually aligns features from two modalities into a shared semantic space for effective cross-modal learning. NeuroBridge surpasses previous state-of-the-art methods under both intra-subject and inter-subject settings. In the intra-subject scenario, it achieves the improvements of 12.3% in top-1 accuracy and 10.2% in top-5 accuracy, reaching 63.2% and 89.9% respectively on a 200-way zero-shot retrieval task. Extensive experiments demonstrate the effectiveness, robustness, and scalability of the proposed framework for neural visual decoding.

Human intelligence, the most evident and accessible form of source of reasoning, hosted by biological hardware, has evolved and been refined over thousands of years, positioning itself today to create new artificial forms and preparing to self--design their evolutionary path forward. Beginning with the advent of foundation models, the rate at which human and artificial intelligence interact with each other has surpassed any anticipated quantitative figures. The close engagement led to both bits of intelligence to be impacted in various ways, which naturally resulted in complex confluences that warrant close scrutiny. In the sequel, we shall explore the interplay between human and machine intelligence, focusing on the crucial role humans play in developing ethical, responsible, and robust intelligent systems. We slightly delve into interesting aspects of implementation inspired by the mechanisms underlying neuroscience and human cognition. Additionally, we propose future perspectives, capitalizing on the advantages of symbiotic designs to suggest a human-centered direction for next-generation AI development. We finalize this evolving document with a few thoughts and open questions yet to be addressed by the broader community.

Synthesizing clinical evidence largely relies on systematic reviews of clinical trials and retrospective analyses from medical literature. However, the rapid expansion of publications presents challenges in efficiently identifying, summarizing, and updating clinical evidence. Here, we introduce TrialMind, a generative artificial intelligence (AI) pipeline for facilitating human-AI collaboration in three crucial tasks for evidence synthesis: study search, screening, and data extraction. To assess its performance, we chose published systematic reviews to build the benchmark dataset, named TrialReviewBench, which contains 100 systematic reviews and the associated 2,220 clinical studies. Our results show that TrialMind excels across all three tasks. In study search, it generates diverse and comprehensive search queries to achieve high recall rates (Ours 0.711-0.834 v.s. Human baseline 0.138-0.232). For study screening, TrialMind surpasses traditional embedding-based methods by 30% to 160%. In data extraction, it outperforms a GPT-4 baseline by 29.6% to 61.5%. We further conducted user studies to confirm its practical utility. Compared to manual efforts, human-AI collaboration using TrialMind yielded a 71.4% recall lift and 44.2% time savings in study screening and a 23.5% accuracy lift and 63.4% time savings in data extraction. Additionally, when comparing synthesized clinical evidence presented in forest plots, medical experts favored TrialMind's outputs over GPT-4's outputs in 62.5% to 100% of cases. These findings show the promise of LLM-based approaches like TrialMind to accelerate clinical evidence synthesis via streamlining study search, screening, and data extraction from medical literature, with exceptional performance improvement when working with human experts.

Modeling empathy is a complex endeavor that is rooted in interpersonal and experiential dimensions of human interaction, and remains an open problem within AI. Existing empathy datasets fall short in capturing the richness of empathy responses, often being confined to in-lab or acted scenarios, lacking longitudinal data, and missing self-reported labels. We introduce a new multimodal dataset for empathy during personal experience sharing: the EmpathicStories++ dataset (https://mitmedialab.github.io/empathic-stories-multimodal/) containing 53 hours of video, audio, and text data of 41 participants sharing vulnerable experiences and reading empathically resonant stories with an AI agent. EmpathicStories++ is the first longitudinal dataset on empathy, collected over a month-long deployment of social robots in participants' homes, as participants engage in natural, empathic storytelling interactions with AI agents. We then introduce a novel task of predicting individuals' empathy toward others' stories based on their personal experiences, evaluated in two contexts: participants' own personal shared story context and their reflections on stories they read. We benchmark this task using state-of-the-art models to pave the way for future improvements in contextualized and longitudinal empathy modeling. Our work provides a valuable resource for further research in developing empathetic AI systems and understanding the intricacies of human empathy within genuine, real-world settings.

Invasive brain-computer interfaces have garnered significant attention due to their high performance. The current intracranial stereoElectroEncephaloGraphy (sEEG) foundation models typically build univariate representations based on a single channel. Some of them further use Transformer to model the relationship among channels. However, due to the locality and specificity of brain computation, their performance on more difficult tasks, e.g., speech decoding, which demands intricate processing in specific brain regions, is yet to be fully investigated. We hypothesize that building multi-variate representations within certain brain regions can better capture the specific neural processing. To explore this hypothesis, we collect a well-annotated Chinese word-reading sEEG dataset, targeting language-related brain networks, over 12 subjects. Leveraging this benchmark dataset, we developed the Du-IN model that can extract contextual embeddings from specific brain regions through discrete codebook-guided mask modeling. Our model achieves SOTA performance on the downstream 61-word classification task, surpassing all baseline models. Model comparison and ablation analysis reveal that our design choices, including (i) multi-variate representation by fusing channels in vSMC and STG regions and (ii) self-supervision by discrete codebook-guided mask modeling, significantly contribute to these performances. Collectively, our approach, inspired by neuroscience findings, capitalizing on multi-variate neural representation from specific brain regions, is suitable for invasive brain modeling. It marks a promising neuro-inspired AI approach in BCI.

Artificial Intelligence (AI) can augment and sometimes even replace human cognition. Inspired by efforts to value human agency alongside productivity, we discuss the benefits of solving Citizen Science (CS) tasks with Hybrid Intelligence (HI), a synergetic mixture of human and artificial intelligence. Currently there is no clear framework or methodology on how to create such an effective mixture. Due to the unique participant-centered set of values and the abundance of tasks drawing upon both human common sense and complex 21st century skills, we believe that the field of CS offers an invaluable testbed for the development of HI and human-centered AI of the 21st century, while benefiting CS as well. In order to investigate this potential, we first relate CS to adjacent computational disciplines. Then, we demonstrate that CS projects can be grouped according to their potential for HI-enhancement by examining two key dimensions: the level of digitization and the amount of knowledge or experience required for participation. Finally, we propose a framework for types of human-AI interaction in CS based on established criteria of HI. This "HI lens" provides the CS community with an overview of several ways to utilize the combination of AI and human intelligence in their projects. It also allows the AI community to gain ideas on how developing AI in CS projects can further their own field.

Despite progress in perceptual tasks such as image classification, computers still perform poorly on cognitive tasks such as image description and question answering. Cognition is core to tasks that involve not just recognizing, but reasoning about our visual world. However, models used to tackle the rich content in images for cognitive tasks are still being trained using the same datasets designed for perceptual tasks. To achieve success at cognitive tasks, models need to understand the interactions and relationships between objects in an image. When asked "What vehicle is the person riding?", computers will need to identify the objects in an image as well as the relationships riding(man, carriage) and pulling(horse, carriage) in order to answer correctly that "the person is riding a horse-drawn carriage". In this paper, we present the Visual Genome dataset to enable the modeling of such relationships. We collect dense annotations of objects, attributes, and relationships within each image to learn these models. Specifically, our dataset contains over 100K images where each image has an average of 21 objects, 18 attributes, and 18 pairwise relationships between objects. We canonicalize the objects, attributes, relationships, and noun phrases in region descriptions and questions answer pairs to WordNet synsets. Together, these annotations represent the densest and largest dataset of image descriptions, objects, attributes, relationships, and question answers.

Representations from transformer-based unidirectional language models are known to be effective at predicting brain responses to natural language. However, most studies comparing language models to brains have used GPT-2 or similarly sized language models. Here we tested whether larger open-source models such as those from the OPT and LLaMA families are better at predicting brain responses recorded using fMRI. Mirroring scaling results from other contexts, we found that brain prediction performance scales log-linearly with model size from 125M to 30B parameter models, with ~15% increased encoding performance as measured by correlation with a held-out test set across 3 subjects. Similar log-linear behavior was observed when scaling the size of the fMRI training set. We also characterized scaling for acoustic encoding models that use HuBERT, WavLM, and Whisper, and we found comparable improvements with model size. A noise ceiling analysis of these large, high-performance encoding models showed that performance is nearing the theoretical maximum for brain areas such as the precuneus and higher auditory cortex. These results suggest that increasing scale in both models and data will yield incredibly effective models of language processing in the brain, enabling better scientific understanding as well as applications such as decoding.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

Over the past decade, predictive modeling of neural responses in the primate visual system has advanced significantly, largely driven by various DNN approaches. These include models optimized directly for visual recognition, cross-modal alignment through contrastive objectives, neural response prediction from scratch, and large language model embeddings.Likewise, different readout mechanisms, ranging from fully linear to spatial-feature factorized methods have been explored for mapping network activations to neural responses. Despite the diversity of these approaches, it remains unclear which method performs best across different visual regions. In this study, we systematically compare these approaches for modeling the human visual system and investigate alternative strategies to improve response predictions. Our findings reveal that for early to mid-level visual areas, response-optimized models with visual inputs offer superior prediction accuracy, while for higher visual regions, embeddings from LLMs based on detailed contextual descriptions of images and task-optimized models pretrained on large vision datasets provide the best fit. Through comparative analysis of these modeling approaches, we identified three distinct regions in the visual cortex: one sensitive primarily to perceptual features of the input that are not captured by linguistic descriptions, another attuned to fine-grained visual details representing semantic information, and a third responsive to abstract, global meanings aligned with linguistic content. We also highlight the critical role of readout mechanisms, proposing a novel scheme that modulates receptive fields and feature maps based on semantic content, resulting in an accuracy boost of 3-23% over existing SOTAs for all models and brain regions. Together, these findings offer key insights into building more precise models of the visual system.

Do brains and language models converge toward the same internal representations of the world? Recent years have seen a rise in studies of neural activations and model alignment. In this work, we review 25 fMRI-based studies published between 2023 and 2025 and explicitly confront their findings with two key hypotheses: (i) the Platonic Representation Hypothesis -- that as models scale and improve, they converge to a representation of the real world, and (ii) the Intermediate-Layer Advantage -- that intermediate (mid-depth) layers often encode richer, more generalizable features. Our findings provide converging evidence that models and brains may share abstract representational structures, supporting both hypotheses and motivating further research on brain-model alignment.

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

Reconstructing human dynamic vision from brain activity is a challenging task with great scientific significance. The difficulty stems from two primary issues: (1) vision-processing mechanisms in the brain are highly intricate and not fully revealed, making it challenging to directly learn a mapping between fMRI and video; (2) the temporal resolution of fMRI is significantly lower than that of natural videos. To overcome these issues, this paper propose a two-stage model named Mind-Animator, which achieves state-of-the-art performance on three public datasets. Specifically, during the fMRI-to-feature stage, we decouple semantic, structural, and motion features from fMRI through fMRI-vision-language tri-modal contrastive learning and sparse causal attention. In the feature-to-video stage, these features are merged to videos by an inflated Stable Diffusion. We substantiate that the reconstructed video dynamics are indeed derived from fMRI, rather than hallucinations of the generative model, through permutation tests. Additionally, the visualization of voxel-wise and ROI-wise importance maps confirms the neurobiological interpretability of our model.

With the widespread use of large language models (LLMs) in NLP tasks, researchers have discovered the potential of Chain-of-thought (CoT) to assist LLMs in accomplishing complex reasoning tasks by generating intermediate steps. However, human thought processes are often non-linear, rather than simply sequential chains of thoughts. Therefore, we propose Graph-of-Thought (GoT) reasoning, which models human thought processes not only as a chain but also as a graph. By representing thought units as nodes and connections between them as edges, our approach captures the non-sequential nature of human thinking and allows for a more realistic modeling of thought processes. Similar to Multimodal-CoT, we modeled GoT reasoning as a two-stage framework, generating rationales first and then producing the final answer. Specifically, we employ an additional graph-of-thoughts encoder for GoT representation learning and fuse the GoT representation with the original input representation through a gated fusion mechanism. We implement a GoT reasoning model on the T5 pre-trained model and evaluate its performance on a text-only reasoning task (GSM8K) and a multimodal reasoning task (ScienceQA). Our model achieves significant improvement over the strong CoT baseline with 3.41% and 5.08% on the GSM8K test set with T5-base and T5-large architectures, respectively. Additionally, our model boosts accuracy from 84.91% to 91.54% using the T5-base model and from 91.68% to 92.77% using the T5-large model over the state-of-the-art Multimodal-CoT on the ScienceQA test set. Experiments have shown that GoT achieves comparable results to Multimodal-CoT(large) with over 700M parameters, despite having fewer than 250M backbone model parameters, demonstrating the effectiveness of GoT.

Recent advances in learning multi-modal representation have witnessed the success in biomedical domains. While established techniques enable handling multi-modal information, the challenges are posed when extended to various clinical modalities and practical modalitymissing setting due to the inherent modality gaps. To tackle these, we propose an innovative Modality-prompted Heterogeneous Graph for Omnimodal Learning (GTP-4o), which embeds the numerous disparate clinical modalities into a unified representation, completes the deficient embedding of missing modality and reformulates the cross-modal learning with a graph-based aggregation. Specially, we establish a heterogeneous graph embedding to explicitly capture the diverse semantic properties on both the modality-specific features (nodes) and the cross-modal relations (edges). Then, we design a modality-prompted completion that enables completing the inadequate graph representation of missing modality through a graph prompting mechanism, which generates hallucination graphic topologies to steer the missing embedding towards the intact representation. Through the completed graph, we meticulously develop a knowledge-guided hierarchical cross-modal aggregation consisting of a global meta-path neighbouring to uncover the potential heterogeneous neighbors along the pathways driven by domain knowledge, and a local multi-relation aggregation module for the comprehensive cross-modal interaction across various heterogeneous relations. We assess the efficacy of our methodology on rigorous benchmarking experiments against prior state-of-the-arts. In a nutshell, GTP-4o presents an initial foray into the intriguing realm of embedding, relating and perceiving the heterogeneous patterns from various clinical modalities holistically via a graph theory. Project page: https://gtp-4-o.github.io/.

Insufficient data is a long-standing challenge for Brain-Computer Interface (BCI) to build a high-performance deep learning model. Though numerous research groups and institutes collect a multitude of EEG datasets for the same BCI task, sharing EEG data from multiple sites is still challenging due to the heterogeneity of devices. The significance of this challenge cannot be overstated, given the critical role of data diversity in fostering model robustness. However, existing works rarely discuss this issue, predominantly centering their attention on model training within a single dataset, often in the context of inter-subject or inter-session settings. In this work, we propose a hierarchical personalized Federated Learning EEG decoding (FLEEG) framework to surmount this challenge. This innovative framework heralds a new learning paradigm for BCI, enabling datasets with disparate data formats to collaborate in the model training process. Each client is assigned a specific dataset and trains a hierarchical personalized model to manage diverse data formats and facilitate information exchange. Meanwhile, the server coordinates the training procedure to harness knowledge gleaned from all datasets, thus elevating overall performance. The framework has been evaluated in Motor Imagery (MI) classification with nine EEG datasets collected by different devices but implementing the same MI task. Results demonstrate that the proposed frame can boost classification performance up to 16.7% by enabling knowledge sharing between multiple datasets, especially for smaller datasets. Visualization results also indicate that the proposed framework can empower the local models to put a stable focus on task-related areas, yielding better performance. To the best of our knowledge, this is the first end-to-end solution to address this important challenge.

Brain signal visualization has emerged as an active research area, serving as a critical interface between the human visual system and computer vision models. Although diffusion models have shown promise in analyzing functional magnetic resonance imaging (fMRI) data, including reconstructing high-quality images consistent with original visual stimuli, their accuracy in extracting semantic and silhouette information from brain signals remains limited. In this regard, we propose a novel approach, referred to as Controllable Mind Visual Diffusion Model (CMVDM). CMVDM extracts semantic and silhouette information from fMRI data using attribute alignment and assistant networks. Additionally, a residual block is incorporated to capture information beyond semantic and silhouette features. We then leverage a control model to fully exploit the extracted information for image synthesis, resulting in generated images that closely resemble the visual stimuli in terms of semantics and silhouette. Through extensive experimentation, we demonstrate that CMVDM outperforms existing state-of-the-art methods both qualitatively and quantitatively.

In this study, we aim to build up a model that can Segment Anything in radiology scans, driven by medical terminologies as Text prompts, termed as SAT. Our main contributions are three folds: (i) for dataset construction, we construct the first multi-modal knowledge tree on human anatomy, including 6502 anatomical terminologies; Then, we build up the largest and most comprehensive segmentation dataset for training, by collecting over 22K 3D medical image scans from72 segmentation datasets, across 497 classes, with careful standardization on both image scans and label space; (ii) for architecture design, we propose to inject medical knowledge into a text encoder via contrastive learning, and then formulate a universal segmentation model, that can be prompted by feeding in medical terminologies in text form; (iii) As a result, we have trained SAT-Nano (110M parameters) and SAT-Pro (447M parameters), demonstrating superior or comparable performance to 72 specialist models, i.e., nnU-Nets, U-Mamba or SwinUNETR, trained on each dataset/subsets. We validate SAT as a foundational segmentation model, with better generalization on external (cross-center) datasets, and can be further improved on specific tasks after fine-tuning adaptation. Comparing with state-of-the-art interactive segmentation model MedSAM, SAT demonstrate superior performance, scalability and robustness. We further compare SAT with BiomedParse, and observe SAT is significantly superior in both internal and external evaluation. Through extensive ablation study, we validate the benefit of domain knowledge on universal segmentation, especially on tail categories. As a use case, we demonstrate that SAT can act as a powerful out-of-the-box agent for large language models, enabling visual grounding in versatile application scenarios. All the data, codes, and models in this work have been released.

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

Closed-loop brain stimulation refers to capturing neurophysiological measures such as electroencephalography (EEG), quickly identifying neural events of interest, and producing auditory, magnetic or electrical stimulation so as to interact with brain processes precisely. It is a promising new method for fundamental neuroscience and perhaps for clinical applications such as restoring degraded memory function; however, existing tools are expensive, cumbersome, and offer limited experimental flexibility. In this article, we propose the Portiloop, a deep learning-based, portable and low-cost closed-loop stimulation system able to target specific brain oscillations. We first document open-hardware implementations that can be constructed from commercially available components. We also provide a fast, lightweight neural network model and an exploration algorithm that automatically optimizes the model hyperparameters to the desired brain oscillation. Finally, we validate the technology on a challenging test case of real-time sleep spindle detection, with results comparable to off-line expert performance on the Massive Online Data Annotation spindle dataset (MODA; group consensus). Software and plans are available to the community as an open science initiative to encourage further development and advance closed-loop neuroscience research.

Leading vision-language models (VLMs) are trained on general Internet content, overlooking scientific journals' rich, domain-specific knowledge. Training on specialty-specific literature could yield high-performance, task-specific tools, enabling generative AI to match generalist models in specialty publishing, educational, and clinical tasks. We created NeuroPubs, a multimodal dataset of 23,000 Neurosurgery Publications articles (134M words, 78K image-caption pairs). Using NeuroPubs, VLMs generated publication-ready graphical abstracts (70% of 100 abstracts) and board-style questions indistinguishable from human-written ones (54% of 89,587 questions). We used these questions to train CNS-Obsidian, a 34B-parameter VLM. In a blinded, randomized controlled trial, our model demonstrated non-inferiority to then state-of-the-art GPT-4o in neurosurgical differential diagnosis (clinical utility, 40.62% upvotes vs. 57.89%, p=0.1150; accuracy, 59.38% vs. 65.79%, p=0.3797). Our pilot study demonstrates how training generative AI models on specialty-specific journal content - without large-scale internet data - results in high-performance academic and clinical tools, enabling domain-tailored AI across diverse fields.