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Dec 8

The Flaw of Averages: Quantifying Uniformity of Performance on Benchmarks

Benchmarks shape scientific conclusions about model capabilities and steer model development. This creates a feedback loop: stronger benchmarks drive better models, and better models demand more discriminative benchmarks. Ensuring benchmark reliability is therefore essential for trustworthy evaluation and meaningful progress. In this work, we study benchmark reliability from a distributional perspective and introduce benchmark harmony, which measures how uniformly a model's performance is distributed across the subdomains of a benchmark. We posit that high harmony is a desirable benchmark property, indicating that the aggregate metric reflects uniform competence across subdomains. Across 19 multiple-choice benchmarks and five model families, we map each benchmark onto a mean-variance plane of harmony computed across models, where high mean and low variance signal more reliable evaluation. Our analysis shows that less harmonious benchmarks can give misleading results, since overall accuracy may be disproportionately influenced by specific subdomains. For instance, ARC-Easy is overwhelmed by questions on Biological Concepts, overshadowing other critical subdomains such as Geography, Physics, Chemistry, and Environmental Science. By recommending that harmony should be reported alongside accuracy, we reframe evaluation from simple performance averages to a more robust, distributionally reliable measurement of performance.

  • 3 authors
·
Sep 29

Augmenting LLMs for General Time Series Understanding and Prediction

Time series data is fundamental to decision-making in many crucial domains including healthcare, finance, and environmental science. However, analyzing this data often requires incorporating unstructured contextual information, answering domain-specific questions, and generating natural language explanations -- capabilities that traditional time series models lack due to their inability to process text. While Large Language Models (LLMs) excel at contextual reasoning and knowledge integration, they struggle with numerical time series due to inefficient text-based representations and limited exposure to temporal data during pretraining. We address this gap by augmenting an LLM with specialized time series perception through a patch-based encoder-decoder architecture. We train this Time Series-augmented LLM (TsLLM) on a large corpus of over 2 million interleaved time series and text examples spanning diverse analysis tasks: forecasting with contextual information, time series question-answering, pattern explanation, classification with natural language outputs, and report generation. This training enables TsLLM to leverage both its language understanding and newly acquired temporal reasoning capabilities. While not designed to surpass specialized models on traditional benchmarks, TsLLM demonstrates strong performance on tasks requiring the integration of time series analysis with natural language -- capabilities that existing approaches cannot provide. Our work establishes a new paradigm for time series analysis that bridges numerical computation and natural language understanding, democratizing access to sophisticated temporal reasoning through natural language interaction.

  • 4 authors
·
Oct 1

AI Agent Behavioral Science

Recent advances in large language models (LLMs) have enabled the development of AI agents that exhibit increasingly human-like behaviors, including planning, adaptation, and social dynamics across diverse, interactive, and open-ended scenarios. These behaviors are not solely the product of the internal architectures of the underlying models, but emerge from their integration into agentic systems operating within specific contexts, where environmental factors, social cues, and interaction feedbacks shape behavior over time. This evolution necessitates a new scientific perspective: AI Agent Behavioral Science. Rather than focusing only on internal mechanisms, this perspective emphasizes the systematic observation of behavior, design of interventions to test hypotheses, and theory-guided interpretation of how AI agents act, adapt, and interact over time. We systematize a growing body of research across individual agent, multi-agent, and human-agent interaction settings, and further demonstrate how this perspective informs responsible AI by treating fairness, safety, interpretability, accountability, and privacy as behavioral properties. By unifying recent findings and laying out future directions, we position AI Agent Behavioral Science as a necessary complement to traditional model-centric approaches, providing essential tools for understanding, evaluating, and governing the real-world behavior of increasingly autonomous AI systems.

From Street Views to Urban Science: Discovering Road Safety Factors with Multimodal Large Language Models

Urban and transportation research has long sought to uncover statistically meaningful relationships between key variables and societal outcomes such as road safety, to generate actionable insights that guide the planning, development, and renewal of urban and transportation systems. However, traditional workflows face several key challenges: (1) reliance on human experts to propose hypotheses, which is time-consuming and prone to confirmation bias; (2) limited interpretability, particularly in deep learning approaches; and (3) underutilization of unstructured data that can encode critical urban context. Given these limitations, we propose a Multimodal Large Language Model (MLLM)-based approach for interpretable hypothesis inference, enabling the automated generation, evaluation, and refinement of hypotheses concerning urban context and road safety outcomes. Our method leverages MLLMs to craft safety-relevant questions for street view images (SVIs), extract interpretable embeddings from their responses, and apply them in regression-based statistical models. UrbanX supports iterative hypothesis testing and refinement, guided by statistical evidence such as coefficient significance, thereby enabling rigorous scientific discovery of previously overlooked correlations between urban design and safety. Experimental evaluations on Manhattan street segments demonstrate that our approach outperforms pretrained deep learning models while offering full interpretability. Beyond road safety, UrbanX can serve as a general-purpose framework for urban scientific discovery, extracting structured insights from unstructured urban data across diverse socioeconomic and environmental outcomes. This approach enhances model trustworthiness for policy applications and establishes a scalable, statistically grounded pathway for interpretable knowledge discovery in urban and transportation studies.

  • 7 authors
·
Jun 2

Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science

Intelligent agents powered by large language models (LLMs) have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines. While their capabilities are promising, they also introduce novel vulnerabilities that demand careful consideration for safety. However, there exists a notable gap in the literature, as there has been no comprehensive exploration of these vulnerabilities. This position paper fills this gap by conducting a thorough examination of vulnerabilities in LLM-based agents within scientific domains, shedding light on potential risks associated with their misuse and emphasizing the need for safety measures. We begin by providing a comprehensive overview of the potential risks inherent to scientific LLM agents, taking into account user intent, the specific scientific domain, and their potential impact on the external environment. Then, we delve into the origins of these vulnerabilities and provide a scoping review of the limited existing works. Based on our analysis, we propose a triadic framework involving human regulation, agent alignment, and an understanding of environmental feedback (agent regulation) to mitigate these identified risks. Furthermore, we highlight the limitations and challenges associated with safeguarding scientific agents and advocate for the development of improved models, robust benchmarks, and comprehensive regulations to address these issues effectively.

  • 13 authors
·
Feb 6, 2024

MassSpecGym: A benchmark for the discovery and identification of molecules

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

  • 30 authors
·
Oct 30, 2024

CharacterBox: Evaluating the Role-Playing Capabilities of LLMs in Text-Based Virtual Worlds

Role-playing is a crucial capability of Large Language Models (LLMs), enabling a wide range of practical applications, including intelligent non-player characters, digital twins, and emotional companions. Evaluating this capability in LLMs is challenging due to the complex dynamics involved in role-playing, such as maintaining character fidelity throughout a storyline and navigating open-ended narratives without a definitive ground truth. Current evaluation methods, which primarily focus on question-answering or conversational snapshots, fall short of adequately capturing the nuanced character traits and behaviors essential for authentic role-playing. In this paper, we propose CharacterBox, which is a simulation sandbox designed to generate situational fine-grained character behavior trajectories. These behavior trajectories enable a more comprehensive and in-depth evaluation of role-playing capabilities. CharacterBox consists of two main components: the character agent and the narrator agent. The character agent, grounded in psychological and behavioral science, exhibits human-like behaviors, while the narrator agent coordinates interactions between character agents and environmental changes. Additionally, we introduce two trajectory-based methods that leverage CharacterBox to enhance LLM performance. To reduce costs and facilitate the adoption of CharacterBox by public communities, we fine-tune two smaller models, CharacterNR and CharacterRM, as substitutes for GPT API calls, and demonstrate their competitive performance compared to advanced GPT APIs.

  • 8 authors
·
Dec 7, 2024

Diffusion Sequence Models for Enhanced Protein Representation and Generation

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language Models (pLMs) aim to unlock insights from the vast space of unlabeled protein sequences by learning rich, semantic representations from primary sequences via masked language modeling. However, these models typically exhibit limited generative capacity. In this work, we introduce the Diffusion Sequence Model (DSM), a novel pLM trained with masked diffusion to enable both high-quality representation learning and generative protein design. DSM builds upon the ESM2 architecture by incorporating a masked forward diffusion process inspired by the LLaDA framework. After training, DSM is capable of generating diverse, biomimetic sequences that align with expected amino acid compositions, secondary structures, and predicted functions, even with 90\% token corruption. Furthermore, DSM's learned representations match or exceed those of similarly sized pLMs on downstream tasks. We also introduce DSM(ppi), a variant fine-tuned to generate protein binders by attending to target sequences. We demonstrate DSM(ppi)'s effectiveness on the challenging Bench-tested Binder Benchmark (BenchBB), where both DSM and DSM(ppi) produce candidates with superior predicted binding affinity compared to known binders. Our results establish masked diffusion as a powerful paradigm for unifying protein representation and generation in a single framework.

  • 4 authors
·
Jun 9

Locate Anything on Earth: Advancing Open-Vocabulary Object Detection for Remote Sensing Community

Object detection, particularly open-vocabulary object detection, plays a crucial role in Earth sciences, such as environmental monitoring, natural disaster assessment, and land-use planning. However, existing open-vocabulary detectors, primarily trained on natural-world images, struggle to generalize to remote sensing images due to a significant data domain gap. Thus, this paper aims to advance the development of open-vocabulary object detection in remote sensing community. To achieve this, we first reformulate the task as Locate Anything on Earth (LAE) with the goal of detecting any novel concepts on Earth. We then developed the LAE-Label Engine which collects, auto-annotates, and unifies up to 10 remote sensing datasets creating the LAE-1M - the first large-scale remote sensing object detection dataset with broad category coverage. Using the LAE-1M, we further propose and train the novel LAE-DINO Model, the first open-vocabulary foundation object detector for the LAE task, featuring Dynamic Vocabulary Construction (DVC) and Visual-Guided Text Prompt Learning (VisGT) modules. DVC dynamically constructs vocabulary for each training batch, while VisGT maps visual features to semantic space, enhancing text features. We comprehensively conduct experiments on established remote sensing benchmark DIOR, DOTAv2.0, as well as our newly introduced 80-class LAE-80C benchmark. Results demonstrate the advantages of the LAE-1M dataset and the effectiveness of the LAE-DINO method.

  • 8 authors
·
Aug 17, 2024 1

EcoVerse: An Annotated Twitter Dataset for Eco-Relevance Classification, Environmental Impact Analysis, and Stance Detection

Anthropogenic ecological crisis constitutes a significant challenge that all within the academy must urgently face, including the Natural Language Processing (NLP) community. While recent years have seen increasing work revolving around climate-centric discourse, crucial environmental and ecological topics outside of climate change remain largely unaddressed, despite their prominent importance. Mainstream NLP tasks, such as sentiment analysis, dominate the scene, but there remains an untouched space in the literature involving the analysis of environmental impacts of certain events and practices. To address this gap, this paper presents EcoVerse, an annotated English Twitter dataset of 3,023 tweets spanning a wide spectrum of environmental topics. We propose a three-level annotation scheme designed for Eco-Relevance Classification, Stance Detection, and introducing an original approach for Environmental Impact Analysis. We detail the data collection, filtering, and labeling process that led to the creation of the dataset. Remarkable Inter-Annotator Agreement indicates that the annotation scheme produces consistent annotations of high quality. Subsequent classification experiments using BERT-based models, including ClimateBERT, are presented. These yield encouraging results, while also indicating room for a model specifically tailored for environmental texts. The dataset is made freely available to stimulate further research.

  • 4 authors
·
Apr 7, 2024

SSL4Eco: A Global Seasonal Dataset for Geospatial Foundation Models in Ecology

With the exacerbation of the biodiversity and climate crises, macroecological pursuits such as global biodiversity mapping become more urgent. Remote sensing offers a wealth of Earth observation data for ecological studies, but the scarcity of labeled datasets remains a major challenge. Recently, self-supervised learning has enabled learning representations from unlabeled data, triggering the development of pretrained geospatial models with generalizable features. However, these models are often trained on datasets biased toward areas of high human activity, leaving entire ecological regions underrepresented. Additionally, while some datasets attempt to address seasonality through multi-date imagery, they typically follow calendar seasons rather than local phenological cycles. To better capture vegetation seasonality at a global scale, we propose a simple phenology-informed sampling strategy and introduce corresponding SSL4Eco, a multi-date Sentinel-2 dataset, on which we train an existing model with a season-contrastive objective. We compare representations learned from SSL4Eco against other datasets on diverse ecological downstream tasks and demonstrate that our straightforward sampling method consistently improves representation quality, highlighting the importance of dataset construction. The model pretrained on SSL4Eco reaches state of the art performance on 7 out of 8 downstream tasks spanning (multi-label) classification and regression. We release our code, data, and model weights to support macroecological and computer vision research at https://github.com/PlekhanovaElena/ssl4eco.

  • 7 authors
·
Apr 25

BioAnalyst: A Foundation Model for Biodiversity

The accelerating loss of biodiversity presents critical challenges for ecological research and conservation strategies. The preservation of biodiversity is paramount for maintaining ecological balance and ensuring the sustainability of ecosystems. However, biodiversity faces numerous threats, including habitat loss, climate change, and the proliferation of invasive species. Addressing these and other ecology-related challenges, both at local and global scales, requires comprehensive monitoring, predictive and conservation planning capabilities. Artificial Intelligence (AI) Foundation Models (FMs) have gained significant momentum in numerous scientific domains by leveraging vast datasets to learn general-purpose representations adaptable to various downstream tasks. This paradigm holds immense promise for biodiversity conservation. In response, we introduce BioAnalyst, the first Foundation Model tailored for biodiversity analysis and conservation planning. BioAnalyst employs a transformer-based architecture, pre-trained on extensive multi-modal datasets encompassing species occurrence records, remote sensing indicators, climate and environmental variables. BioAnalyst is designed for adaptability, allowing for fine-tuning of a range of downstream tasks, such as species distribution modelling, habitat suitability assessments, invasive species detection, and population trend forecasting. We evaluate the model's performance on two downstream use cases, demonstrating its generalisability compared to existing methods, particularly in data-scarce scenarios for two distinct use-cases, establishing a new accuracy baseline for ecological forecasting. By openly releasing BioAnalyst and its fine-tuning workflows to the scientific community, we aim to foster collaborative efforts in biodiversity modelling and advance AI-driven solutions to pressing ecological challenges.

  • 7 authors
·
Jul 11

GeoPlant: Spatial Plant Species Prediction Dataset

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

  • 10 authors
·
Aug 25, 2024

WHOI-Plankton- A Large Scale Fine Grained Visual Recognition Benchmark Dataset for Plankton Classification

Planktonic organisms are of fundamental importance to marine ecosystems: they form the basis of the food web, provide the link between the atmosphere and the deep ocean, and influence global-scale biogeochemical cycles. Scientists are increasingly using imaging-based technologies to study these creatures in their natural habit. Images from such systems provide an unique opportunity to model and understand plankton ecosystems, but the collected datasets can be enormous. The Imaging FlowCytobot (IFCB) at Woods Hole Oceanographic Institution, for example, is an in situ system that has been continuously imaging plankton since 2006. To date, it has generated more than 700 million samples. Manual classification of such a vast image collection is impractical due to the size of the data set. In addition, the annotation task is challenging due to the large space of relevant classes, intra-class variability, and inter-class similarity. Methods for automated classification exist, but the accuracy is often below that of human experts. Here we introduce WHOI-Plankton: a large scale, fine-grained visual recognition dataset for plankton classification, which comprises over 3.4 million expert-labeled images across 70 classes. The labeled image set is complied from over 8 years of near continuous data collection with the IFCB at the Martha's Vineyard Coastal Observatory (MVCO). We discuss relevant metrics for evaluation of classification performance and provide results for a traditional method based on hand-engineered features and two methods based on convolutional neural networks.

  • 4 authors
·
Oct 2, 2015

More than Carbon: Cradle-to-Grave environmental impacts of GenAI training on the Nvidia A100 GPU

The rapid expansion of AI has intensified concerns about its environmental sustainability. Yet, current assessments predominantly focus on operational carbon emissions using secondary data or estimated values, overlooking environmental impacts in other life cycle stages. This study presents the first comprehensive multi-criteria life cycle assessment (LCA) of AI training, examining 16 environmental impact categories based on detailed primary data collection of the Nvidia A100 SXM 40GB GPU. The LCA results for training BLOOM reveal that the use phase dominates 11 of 16 impact categories including climate change (96\%), while manufacturing dominates the remaining 5 impact categories including human toxicity, cancer (99\%) and mineral and metal depletion (85\%). For training GPT-4, the use phase dominates 10 of 16 impact categories, contributing about 96\% to both the climate change and resource use, fossils category. The manufacturing stage dominates 6 of 16 impact categories including human toxicity, cancer (94\%) and eutrophication, freshwater (81\%). Assessing the cradle-to-gate environmental impact distribution across the GPU components reveals that the GPU chip is the largest contributor across 10 of 16 of impact categories and shows particularly pronounced contributions to climate change (81\%) and resource use, fossils (80\%). While primary data collection results in modest changes in carbon estimates compared to database-derived estimates, substantial variations emerge in other categories. Most notably, minerals and metals depletion increases by 33\%, demonstrating the critical importance of primary data for non-carbon accounting. This multi-criteria analysis expands the Sustainable AI discourse beyond operational carbon emissions, challenging current sustainability narratives and highlighting the need for policy frameworks addressing the full spectrum of AI's environmental impact.

  • 8 authors
·
Aug 27

Using remotely sensed data for air pollution assessment

Air pollution constitutes a global problem of paramount importance that affects not only human health, but also the environment. The existence of spatial and temporal data regarding the concentrations of pollutants is crucial for performing air pollution studies and monitor emissions. However, although observation data presents great temporal coverage, the number of stations is very limited and they are usually built in more populated areas. The main objective of this work is to create models capable of inferring pollutant concentrations in locations where no observation data exists. A machine learning model, more specifically the random forest model, was developed for predicting concentrations in the Iberian Peninsula in 2019 for five selected pollutants: NO_2, O_3 SO_2, PM10, and PM2.5. Model features include satellite measurements, meteorological variables, land use classification, temporal variables (month, day of year), and spatial variables (latitude, longitude, altitude). The models were evaluated using various methods, including station 10-fold cross-validation, in which in each fold observations from 10\% of the stations are used as testing data and the rest as training data. The R^2, RMSE and mean bias were determined for each model. The NO_2 and O_3 models presented good values of R^2, 0.5524 and 0.7462, respectively. However, the SO_2, PM10, and PM2.5 models performed very poorly in this regard, with R^2 values of -0.0231, 0.3722, and 0.3303, respectively. All models slightly overestimated the ground concentrations, except the O_3 model. All models presented acceptable cross-validation RMSE, except the O_3 and PM10 models where the mean value was a little higher (12.5934 mu g/m^3 and 10.4737 mu g/m^3, respectively).

  • 3 authors
·
Feb 4, 2024

Effect Heterogeneity with Earth Observation in Randomized Controlled Trials: Exploring the Role of Data, Model, and Evaluation Metric Choice

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.