Daily Papers

The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures based on structure-contextualised modelling. The alignment enables free and bidirectional mappings between sequences and structures by utilising the flexible RNA modelling paradigm that supports versatile input and output modalities, i.e., sequence and/or structure as input/output. We implement RNA design and zero-shot secondary structure prediction as case studies to evaluate the Seq2Str and Str2Seq mapping capacity of OmniGenome. Results on the EternaV2 benchmark show that OmniGenome solved 74% of puzzles, whereas existing FMs only solved up to 3% of the puzzles due to the oversight of sequence-structure alignment. We leverage four comprehensive in-silico genome modelling benchmarks to evaluate performance across a diverse set of genome downstream tasks, where the results show that OmniGenome achieves state-of-the-art performance on RNA and DNA benchmarks, even without any training on DNA genomes.

Explicitly disentangling style and content in vision models remains challenging due to their semantic overlap and the subjectivity of human perception. Existing methods propose separation through generative or discriminative objectives, but they still face the inherent ambiguity of disentangling intertwined concepts. Instead, we ask: Can we bypass explicit disentanglement by learning to merge style and content invertibly, allowing separation to emerge naturally? We propose SCFlow, a flow-matching framework that learns bidirectional mappings between entangled and disentangled representations. Our approach is built upon three key insights: 1) Training solely to merge style and content, a well-defined task, enables invertible disentanglement without explicit supervision; 2) flow matching bridges on arbitrary distributions, avoiding the restrictive Gaussian priors of diffusion models and normalizing flows; and 3) a synthetic dataset of 510,000 samples (51 styles times 10,000 content samples) was curated to simulate disentanglement through systematic style-content pairing. Beyond controllable generation tasks, we demonstrate that SCFlow generalizes to ImageNet-1k and WikiArt in zero-shot settings and achieves competitive performance, highlighting that disentanglement naturally emerges from the invertible merging process.

Adapting generative models to specific domains presents an effective solution for satisfying specialized requirements. However, adapting to some complex domains remains challenging, especially when these domains require substantial paired data to capture the targeted distributions. Since unpaired data from a single modality, such as vision or language, is more readily available, we utilize the bidirectional mappings between vision and language learned by the unified generative model to enable training on unpaired data for domain adaptation. Specifically, we propose DoraCycle, which integrates two multimodal cycles: text-to-image-to-text and image-to-text-to-image. The model is optimized through cross-entropy loss computed at the cycle endpoints, where both endpoints share the same modality. This facilitates self-evolution of the model without reliance on annotated text-image pairs. Experimental results demonstrate that for tasks independent of paired knowledge, such as stylization, DoraCycle can effectively adapt the unified model using only unpaired data. For tasks involving new paired knowledge, such as specific identities, a combination of a small set of paired image-text examples and larger-scale unpaired data is sufficient for effective domain-oriented adaptation. The code will be released at https://github.com/showlab/DoraCycle.

Current evaluation paradigms for large language models (LLMs) represent a critical blind spot in AI research--relying on opaque numerical metrics that conceal fundamental limitations in spatial reasoning while providing no intuitive understanding of model capabilities. This deficiency creates a dangerous disconnect between reported performance and practical abilities, particularly for applications requiring physical world understanding. We introduce LTD-Bench, a breakthrough benchmark that transforms LLM evaluation from abstract scores to directly observable visual outputs by requiring models to generate drawings through dot matrices or executable code. This approach makes spatial reasoning limitations immediately apparent even to non-experts, bridging the fundamental gap between statistical performance and intuitive assessment. LTD-Bench implements a comprehensive methodology with complementary generation tasks (testing spatial imagination) and recognition tasks (assessing spatial perception) across three progressively challenging difficulty levels, methodically evaluating both directions of the critical language-spatial mapping. Our extensive experiments with state-of-the-art models expose an alarming capability gap: even LLMs achieving impressive results on traditional benchmarks demonstrate profound deficiencies in establishing bidirectional mappings between language and spatial concept--a fundamental limitation that undermines their potential as genuine world models. Furthermore, LTD-Bench's visual outputs enable powerful diagnostic analysis, offering a potential approach to investigate model similarity.

Offline model-based optimization aims to maximize a black-box objective function with a static dataset of designs and their scores. In this paper, we focus on biological sequence design to maximize some sequence score. A recent approach employs bidirectional learning, combining a forward mapping for exploitation and a backward mapping for constraint, and it relies on the neural tangent kernel (NTK) of an infinitely wide network to build a proxy model. Though effective, the NTK cannot learn features because of its parametrization, and its use prevents the incorporation of powerful pre-trained Language Models (LMs) that can capture the rich biophysical information in millions of biological sequences. We adopt an alternative proxy model, adding a linear head to a pre-trained LM, and propose a linearization scheme. This yields a closed-form loss and also takes into account the biophysical information in the pre-trained LM. In addition, the forward mapping and the backward mapping play different roles and thus deserve different weights during sequence optimization. To achieve this, we train an auxiliary model and leverage its weak supervision signal via a bi-level optimization framework to effectively learn how to balance the two mappings. Further, by extending the framework, we develop the first learning rate adaptation module Adaptive-eta, which is compatible with all gradient-based algorithms for offline model-based optimization. Experimental results on DNA/protein sequence design tasks verify the effectiveness of our algorithm. Our code is available~https://anonymous.4open.science/r/BIB-ICLR2023-Submission/README.md{here.}

In this paper, we show that a binary latent space can be explored for compact yet expressive image representations. We model the bi-directional mappings between an image and the corresponding latent binary representation by training an auto-encoder with a Bernoulli encoding distribution. On the one hand, the binary latent space provides a compact discrete image representation of which the distribution can be modeled more efficiently than pixels or continuous latent representations. On the other hand, we now represent each image patch as a binary vector instead of an index of a learned cookbook as in discrete image representations with vector quantization. In this way, we obtain binary latent representations that allow for better image quality and high-resolution image representations without any multi-stage hierarchy in the latent space. In this binary latent space, images can now be generated effectively using a binary latent diffusion model tailored specifically for modeling the prior over the binary image representations. We present both conditional and unconditional image generation experiments with multiple datasets, and show that the proposed method performs comparably to state-of-the-art methods while dramatically improving the sampling efficiency to as few as 16 steps without using any test-time acceleration. The proposed framework can also be seamlessly scaled to 1024 times 1024 high-resolution image generation without resorting to latent hierarchy or multi-stage refinements.

Existing text-driven motion generation methods often treat synthesis as a bidirectional mapping between language and motion, but remain limited in capturing the causal logic of action execution and the human intentions that drive behavior. The absence of visual grounding further restricts precision and personalization, as language alone cannot specify fine-grained spatiotemporal details. We propose MoGIC, a unified framework that integrates intention modeling and visual priors into multimodal motion synthesis. By jointly optimizing multimodal-conditioned motion generation and intention prediction, MoGIC uncovers latent human goals, leverages visual priors to enhance generation, and exhibits versatile multimodal generative capability. We further introduce a mixture-of-attention mechanism with adaptive scope to enable effective local alignment between conditional tokens and motion subsequences. To support this paradigm, we curate Mo440H, a 440-hour benchmark from 21 high-quality motion datasets. Experiments show that after finetuning, MoGIC reduces FID by 38.6\% on HumanML3D and 34.6\% on Mo440H, surpasses LLM-based methods in motion captioning with a lightweight text head, and further enables intention prediction and vision-conditioned generation, advancing controllable motion synthesis and intention understanding. The code is available at https://github.com/JunyuShi02/MoGIC

Digital cameras transform sensor RAW readings into RGB images by means of their Image Signal Processor (ISP). Computational photography tasks such as image denoising and colour constancy are commonly performed in the RAW domain, in part due to the inherent hardware design, but also due to the appealing simplicity of noise statistics that result from the direct sensor readings. Despite this, the availability of RAW images is limited in comparison with the abundance and diversity of available RGB data. Recent approaches have attempted to bridge this gap by estimating the RGB to RAW mapping: handcrafted model-based methods that are interpretable and controllable usually require manual parameter fine-tuning, while end-to-end learnable neural networks require large amounts of training data, at times with complex training procedures, and generally lack interpretability and parametric control. Towards addressing these existing limitations, we present a novel hybrid model-based and data-driven ISP that builds on canonical ISP operations and is both learnable and interpretable. Our proposed invertible model, capable of bidirectional mapping between RAW and RGB domains, employs end-to-end learning of rich parameter representations, i.e. dictionaries, that are free from direct parametric supervision and additionally enable simple and plausible data augmentation. We evidence the value of our data generation process by extensive experiments under both RAW image reconstruction and RAW image denoising tasks, obtaining state-of-the-art performance in both. Additionally, we show that our ISP can learn meaningful mappings from few data samples, and that denoising models trained with our dictionary-based data augmentation are competitive despite having only few or zero ground-truth labels.