Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset comprising Cell Painting features for 11,000 genes and 3,600 compounds, along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.
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Datasets and Benchmarks
Solar power is a critical source of renewable energy, offering significant potential to lower greenhouse gas emissions and mitigate climate change. However, the cloud induced-variability of solar radiation reaching the earth’s surface presents a challenge for integrating solar power into the grid (e.g., storage and backup management). The new generation of geostationary satellites such as GOES-16 has become an important data source for large-scale and high temporal frequency solar radiation forecasting. However, no machine-learning-ready dataset has integrated geostationary satellite data with fine-grained solar radiation information to support forecasting model development and benchmarking with consistent metrics. We present SolarCube, a new ML-ready benchmark dataset for solar radiation forecasting. SolarCube covers 19 study areas distributed over multiple continents: North America, South America, Asia, and Oceania. The dataset supports short (i.e., 30 minutes to 6 hours) and long-term (i.e., day-ahead or longer) solar radiation forecasting at both point-level (i.e., specific locations of monitoring stations) and area-level, by processing and integrating data from multiple sources, including geostationary satellite images, physics-derived solar radiation, and ground station observations from different monitoring networks over the globe. We also evaluated a set of forecasting models for point- and image-based time-series data to develop performance benchmarks under different testing scenarios. The dataset is available at https://doi.org/10.5281/zenodo.11498739. A Python library is available to conveniently generate different variations of the dataset based on user needs, along with baseline models at https://github.com/Ruohan-Li/SolarCube.
Datasets and Benchmarks
Binary analysis is a core component of many critical security tasks, including reverse engineering, malware analysis, and vulnerability detection. Manual analysis is often time-consuming, but identifying commonly-used or previously-seen functions can reduce the time it takes to understand a new file. However, given the complexity of assembly, and the NP-hard nature of determining function equivalence, this task is extremely difficult. Common approaches often use sophisticated disassembly and decompilation tools, graph analysis, and other expensive pre-processing steps to perform function similarity searches over some corpus. In this work, we identify a number of discrepancies between the current research environment and the underlying application need. To remedy this, we build a new benchmark, REFuSe-Bench, for binary function similarity detection consisting of high-quality datasets and tests that better reflect real-world use cases. In doing so, we address issues like data duplication and accurate labeling, experiment with real malware, and perform the first serious evaluation of ML binary function similarity models on Windows data. Our benchmark reveals that a new, simple baseline — one which looks at only the raw bytes of a function, and requires no disassembly or other pre-processing --- is able to achieve state-of-the-art performance in multiple settings. Our findings challenge conventional assumptions that complex models with highly-engineered features are being used to their full potential, and demonstrate that simpler approaches can provide significant value.
Datasets and Benchmarks
Machine learning based surrogate models offer researchers powerful tools for accelerating simulation-based workflows. However, as standard datasets in this space often cover small classes of physical behavior, it can be difficult to evaluate the efficacy of new approaches. To address this gap, we introduce the Well: a large-scale collection of datasets containing numerical simulations of a wide variety of spatiotemporal physical systems. The Well draws from domain experts and numerical software developers to provide 15TB of data across 16 datasets covering diverse domains such as biological systems, fluid dynamics, acoustic scattering, as well as magneto-hydrodynamic simulations of extra-galactic fluids or supernova explosions. These datasets can be used individually or as part of a broader benchmark suite. To facilitate usage of the Well, we provide a unified PyTorch interface for training and evaluating models. We demonstrate the function of this library by introducing example baselines that highlight the new challenges posed by the complex dynamics of the Well. The code and data is available at https://github.com/PolymathicAI/the_well.
Datasets and Benchmarks
Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster preparedness and robust decision making amidst climate change. Yet, forecasting beyond the weather timescale is challenging because it deals with problems other than initial condition, including boundary interaction, butterfly effect, and our inherent lack of physical understanding. At present, existing benchmarks tend to have shorter forecasting range of up-to 15 days, do not include a wide range of operational baselines, and lack physics-based constraints for explainability. Thus, we propose ChaosBench, a challenging benchmark to extend the predictability range of data-driven weather emulators to S2S timescale. First, ChaosBench is comprised of variables beyond the typical surface-atmospheric ERA5 to also include ocean, ice, and land reanalysis products that span over 45 years to allow for full Earth system emulation that respects boundary conditions. We also propose physics-based, in addition to deterministic and probabilistic metrics, to ensure a physically-consistent ensemble that accounts for butterfly effect. Furthermore, we evaluate on a diverse set of physics-based forecasts from four national weather agencies as baselines to our data-driven counterpart such as ViT/ClimaX, PanguWeather, GraphCast, and FourCastNetV2. Overall, we find methods originally developed for weather-scale applications fail on S2S task: their performance simply collapse to an unskilled climatology. Nonetheless, we outline and demonstrate several strategies that can extend the predictability range of existing weather emulators, including the use of ensembles, robust control of error propagation, and the use of physics-informed models. Our benchmark, datasets, and instructions are available at https://leap-stc.github.io/ChaosBench.
Physical Models · Physics
We present DrivAerNet++, the largest and most comprehensive multimodal dataset for aerodynamic car design. DrivAerNet++ comprises 8,000 diverse car designs modeled with high-fidelity computational fluid dynamics (CFD) simulations. The dataset includes diverse car configurations such as fastback, notchback, and estateback, with different underbody and wheel designs to represent both internal combustion engines and electric vehicles. Each entry in the dataset features detailed 3D meshes, parametric models, aerodynamic coefficients, and extensive flow and surface field data, along with segmented parts for car classification and point cloud data. This dataset supports a wide array of machine learning applications including data-driven design optimization, generative modeling, surrogate model training, CFD simulation acceleration, and geometric classification. With more than 39 TB of publicly available engineering data, DrivAerNet++ fills a significant gap in available resources, providing high-quality, diverse data to enhance model training, promote generalization, and accelerate automotive design processes. Along with rigorous dataset validation, we also provide ML benchmarking results on the task of aerodynamic drag prediction, showcasing the breadth of applications supported by our dataset. This dataset is set to significantly impact automotive design and broader engineering disciplines by fostering innovation and improving the fidelity of aerodynamic evaluations. Dataset and code available at: https://github.com/Mohamedelrefaie/DrivAerNet
Datasets and Benchmarks
We present the `Multimodal Universe`, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, our dataset contains hundreds of millions of astronomical observations, constituting 100TB of multi-channel and hyper-spectral images, spectra, multivariate time series, as well as a wide variety of associated scientific measurements and metadata. In addition, we include a range of benchmark tasks representative of standard practices for machine learning methods in astrophysics. This massive dataset will enable the development of large multi-modal models specifically targeted towards scientific applications. All codes used to compile the dataset, and a description of how to access the data is available at https://github.com/MultimodalUniverse/MultimodalUniverse
Datasets and Benchmarks
We introduce Constrained Human-AI Cooperation (CHAIC), an inclusive embodied social intelligence challenge designed to test social perception and cooperation in embodied agents. In CHAIC, the goal is for an embodied agent equipped with egocentric observations to assist a human who may be operating under physical constraints—e.g., unable to reach high places or confined to a wheelchair—in performing common household or outdoor tasks as efficiently as possible. To achieve this, a successful helper must: (1) infer the human's intents and constraints by following the human and observing their behaviors (social perception), and (2) make a cooperative plan tailored to the human partner to solve the task as quickly as possible, working together as a team (cooperative planning). To benchmark this challenge, we create four new agents with real physical constraints and eight long-horizon tasks featuring both indoor and outdoor scenes with various constraints, emergency events, and potential risks. We benchmark planning- and learning-based baselines on the challenge and introduce a new method that leverages large language models and behavior modeling. Empirical evaluations demonstrate the effectiveness of our benchmark in enabling systematic assessment of key aspects of machine social intelligence. Our benchmark and code are publicly available at https://github.com/UMass-Foundation-Model/CHAIC.
Geometric deep learning (GDL) has gained significant attention in scientific fields, for its proficiency in modeling data with intricate geometric structures. Yet, very few works have delved into its capability of tackling the distribution shift problem, a prevalent challenge in many applications.To bridge this gap, we propose GeSS, a comprehensive benchmark designed for evaluating the performance of GDL models in scientific scenarios with distribution shifts.Our evaluation datasets cover diverse scientific domains from particle physics, materials science to biochemistry, and encapsulate a broad spectrum of distribution shifts including conditional, covariate, and concept shifts. Furthermore, we study three levels of information access from the out-of-distribution (OOD) test data, including no OOD information, only unlabeled OOD data, and OOD data with a few labels. Overall, our benchmark results in 30 different experiment settings, and evaluates 3 GDL backbones and 11 learning algorithms in each setting. A thorough analysis of the evaluation results is provided, poised to illuminate insights for GDL researchers and domain practitioners who are to use GDL in their applications.
Datasets and Benchmarks
We introduce the **A**utoregressive **P**DE **E**mulator Benchmark (APEBench), a comprehensive benchmark suite to evaluate autoregressive neural emulators for solving partial differential equations. APEBench is based on JAX and provides a seamlessly integrated differentiable simulation framework employing efficient pseudo-spectral methods, enabling 46 distinct PDEs across 1D, 2D, and 3D. Facilitating systematic analysis and comparison of learned emulators, we propose a novel taxonomy for unrolled training and introduce a unique identifier for PDE dynamics that directly relates to the stability criteria of classical numerical methods. APEBench enables the evaluation of diverse neural architectures, and unlike existing benchmarks, its tight integration of the solver enables support for differentiable physics training and neural-hybrid emulators. Moreover, APEBench emphasizes rollout metrics to understand temporal generalization, providing insights into the long-term behavior of emulating PDE dynamics. In several experiments, we highlight the similarities between neural emulators and numerical simulators. The code is available at [github.com/tum-pbs/apebench](https://github.com/tum-pbs/apebench) and APEBench can be installed via `pip install apebench`.
SciInstruct: a Self-Reflective Instruction Annotated Dataset for Training Scientific Language Models
Datasets and Benchmarks
Large Language Models (LLMs) have shown promise in assisting scientific discovery. However, such applications are currently limited by LLMs' deficiencies in understanding intricate scientific concepts, deriving symbolic equations, and solving advanced numerical calculations. To bridge these gaps, we introduce SciInstruct, a suite of scientific instructions for training scientific language models capable of college-level scientific reasoning. Central to our approach is a novel self-reflective instruction annotation framework to address the data scarcity challenge in the science domain. This framework leverages existing LLMs to generate step-by-step reasoning for unlabelled scientific questions, followed by a process of self-reflective critic-and-revise. Applying this framework, we curated a diverse and high-quality dataset encompassing physics, chemistry, math, and formal proofs. We analyze the curated SciInstruct from multiple interesting perspectives (e.g., domain, scale, source, question type, answer length, etc.). To verify the effectiveness of SciInstruct, we fine-tuned different language models with SciInstruct, i.e., ChatGLM3 (6B and 32B), Llama3-8B-Instruct, and Mistral-7B: MetaMath, enhancing their scientific and mathematical reasoning capabilities, without sacrificing the language understanding capabilities of the base model. We release all codes and SciInstruct at https://github.com/THUDM/SciGLM.
Datasets and Benchmarks
Driving world models have gained increasing attention due to their ability to model complex physical dynamics. However, their superb modeling capability is yet to be fully unleashed due to the limited video diversity in current driving datasets. We introduce DrivingDojo, the first dataset tailor-made for training interactive world models with complex driving dynamics. Our dataset features video clips with a complete set of driving maneuvers, diverse multi-agent interplay, and rich open-world driving knowledge, laying a stepping stone for future world model development. We further define an action instruction following (AIF) benchmark for world models and demonstrate the superiority of the proposed dataset for generating action-controlled future predictions.
Datasets and Benchmarks
With the emergence of LLMs and their integration with other data modalities, multi-modal 3D perception attracts more attention due to its connectivity to the physical world and makes rapid progress. However, limited by existing datasets, previous works mainly focus on understanding object properties or inter-object spatial relationships in a 3D scene. To tackle this problem, this paper builds the first largest ever multi-modal 3D scene dataset and benchmark with hierarchical grounded language annotations, MMScan. It is constructed based on a top-down logic, from region to object level, from a single target to inter-target relationships, covering holistic aspects of spatial and attribute understanding. The overall pipeline incorporates powerful VLMs via carefully designed prompts to initialize the annotations efficiently and further involve humans' correction in the loop to ensure the annotations are natural, correct, and comprehensive. Built upon existing 3D scanning data, the resulting multi-modal 3D dataset encompasses 1.4M meta-annotated captions on 109k objects and 7.7k regions as well as over 3.04M diverse samples for 3D visual grounding and question-answering benchmarks. We evaluate representative baselines on our benchmarks, analyze their capabilities in different aspects, and showcase the key problems to be addressed in the future. Furthermore, we use this high-quality dataset to train state-of-the-art 3D visual grounding and LLMs and obtain remarkable performance improvement both on existing benchmarks and in-the-wild evaluation.
Datasets and Benchmarks
Fine urban change segmentation using multi-temporal remote sensing images is essential for understanding human-environment interactions in urban areas. Although there have been advances in high-quality land cover datasets that reveal the physical features of urban landscapes, the lack of fine-grained land use datasets hinders a deeper understanding of how human activities are distributed across landscapes and the impact of these activities on the environment, thus constraining proper technique development. To address this, we introduce FUSU, the first fine-grained land use change segmentation dataset for Fine-grained Urban Semantic Understanding. FUSU features the most detailed land use classification system to date, with 17 classes and 30 billion pixels of annotations. It includes bi-temporal high-resolution satellite images with 0.2-0.5 m ground sample distance and monthly optical and radar satellite time series, covering 847 km^2 across five urban areas in the southern and northern of China with different geographical features. The fine-grained land use pixel-wise annotations and high spatial-temporal resolution data provide a robust foundation for developing proper deep learning models to provide contextual insights on human activities and urbanization. To fully leverage FUSU, we propose a unified time-series architecture for both change detection and segmentation. We benchmark FUSU on various methods for several tasks. Dataset and code are available at: https://github.com/yuanshuai0914/FUSU.
Datasets and Benchmarks
Data-driven generative models have emerged as promising approaches towards achieving efficient mechanical inverse design. However, due to prohibitively high cost in time and money, there is still lack of open-source and large-scale benchmarks in this field. It is mainly the case for airfoil inverse design, which requires to generate and edit diverse geometric-qualified and aerodynamic-qualified airfoils following the multimodal instructions, \emph{i.e.,} dragging points and physical parameters. This paper presents the open-source endeavors in airfoil inverse design, \emph{AFBench}, including a large-scale dataset with 200 thousand airfoils and high-quality aerodynamic and geometric labels, two novel and practical airfoil inverse design tasks, \emph{i.e.,} conditional generation on multimodal physical parameters, controllable editing, and comprehensive metrics to evaluate various existing airfoil inverse design methods. Our aim is to establish \emph{AFBench} as an ecosystem for training and evaluating airfoil inverse design methods, with a specific focus on data-driven controllable inverse design models by multimodal instructions capable of bridging the gap between ideas and execution, the academic research and industrial applications. We have provided baseline models, comprehensive experimental observations, and analysis to accelerate future research. Our baseline model is trained on an RTX 3090 GPU within 16 hours. The codebase, datasets and benchmarks will be available at \url{https://hitcslj.github.io/afbench/}.
Computer Vision · Video Generation
We propose a novel text-to-video (T2V) generation benchmark, *ChronoMagic-Bench*, to evaluate the temporal and metamorphic knowledge skills in time-lapse video generation of the T2V models (e.g. Sora and Lumiere). Compared to existing benchmarks that focus on visual quality and text relevance of generated videos, *ChronoMagic-Bench* focuses on the models’ ability to generate time-lapse videos with significant metamorphic amplitude and temporal coherence. The benchmark probes T2V models for their physics, biology, and chemistry capabilities, in a free-form text control. For these purposes, *ChronoMagic-Bench* introduces **1,649** prompts and real-world videos as references, categorized into four major types of time-lapse videos: biological, human creation, meteorological, and physical phenomena, which are further divided into 75 subcategories. This categorization ensures a comprehensive evaluation of the models’ capacity to handle diverse and complex transformations. To accurately align human preference on the benchmark, we introduce two new automatic metrics, MTScore and CHScore, to evaluate the videos' metamorphic attributes and temporal coherence. MTScore measures the metamorphic amplitude, reflecting the degree of change over time, while CHScore assesses the temporal coherence, ensuring the generated videos maintain logical progression and continuity. Based on the *ChronoMagic-Bench*, we conduct comprehensive manual evaluations of eighteen representative T2V models, revealing their strengths and weaknesses across different categories of prompts, providing a thorough evaluation framework that addresses current gaps in video generation research. More encouragingly, we create a large-scale *ChronoMagic-Pro* dataset, containing **460k** high-quality pairs of 720p time-lapse videos and detailed captions. Each caption ensures high physical content and large metamorphic amplitude, which have a far-reaching impact on the video generation community. The source data and code are publicly available on [https://pku-yuangroup.github.io/ChronoMagic-Bench](https://pku-yuangroup.github.io/ChronoMagic-Bench).
Computer Vision · Segmentation
Visual recognition of materials and their states is essential for understanding the physical world, from identifying wet regions on surfaces or stains on fabrics to detecting infected areas or minerals in rocks. Collecting data that captures this vast variability is complex due to the scattered and gradual nature of material states. Manually annotating real-world images is constrained by cost and precision, while synthetic data, although accurate and inexpensive, lacks real-world diversity. This work aims to bridge this gap by infusing patterns automatically extracted from real-world images into synthetic data. Hence, patterns collected from natural images are used to generate and map materials into synthetic scenes. This unsupervised approach captures the complexity of the real world while maintaining the precision and scalability of synthetic data. We also present the first comprehensive benchmark for zero-shot material state segmentation, utilizing real-world images across a diverse range of domains, including food, soils, construction, plants, liquids, and more, each appears in various states such as wet, dry, infected, cooked, burned, and many others. The annotation includes partial similarity between regions with similar but not identical materials and hard segmentation of only identical material states. This benchmark eluded top foundation models, exposing the limitations of existing data collection methods. Meanwhile, nets trained on the infused data performed significantly better on this and related tasks. The dataset, code, and trained model are publicly available. We also share 300,000 extracted textures and SVBRDF/PBR materials to facilitate future datasets generation.
Datasets and Benchmarks
Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster preparedness and robust decision making amidst climate change. Yet, forecasting beyond the weather timescale is challenging because it deals with problems other than initial condition, including boundary interaction, butterfly effect, and our inherent lack of physical understanding. At present, existing benchmarks tend to have shorter forecasting range of up-to 15 days, do not include a wide range of operational baselines, and lack physics-based constraints for explainability. Thus, we propose ChaosBench, a challenging benchmark to extend the predictability range of data-driven weather emulators to S2S timescale. First, ChaosBench is comprised of variables beyond the typical surface-atmospheric ERA5 to also include ocean, ice, and land reanalysis products that span over 45 years to allow for full Earth system emulation that respects boundary conditions. We also propose physics-based, in addition to deterministic and probabilistic metrics, to ensure a physically-consistent ensemble that accounts for butterfly effect. Furthermore, we evaluate on a diverse set of physics-based forecasts from four national weather agencies as baselines to our data-driven counterpart such as ViT/ClimaX, PanguWeather, GraphCast, and FourCastNetV2. Overall, we find methods originally developed for weather-scale applications fail on S2S task: their performance simply collapse to an unskilled climatology. Nonetheless, we outline and demonstrate several strategies that can extend the predictability range of existing weather emulators, including the use of ensembles, robust control of error propagation, and the use of physics-informed models. Our benchmark, datasets, and instructions are available at https://leap-stc.github.io/ChaosBench.
Optimization
Optimization problems with continuous data appear in, e.g., robust machine learning, functional data analysis, and variational inference. Here, the target function is given as an integral over a family of (continuously) indexed target functions---integrated with respect to a probability measure. Such problems can often be solved by stochastic optimization methods: performing optimization steps with respect to the indexed target function with randomly switched indices. In this work, we study a continuous-time variant of the stochastic gradient descent algorithm for optimization problems with continuous data. This so-called stochastic gradient process consists in a gradient flow minimizing an indexed target function that is coupled with a continuous-time index process determining the index. Index processes are, e.g., reflected diffusions, pure jump processes, or other Lévy processes on compact spaces. Thus, we study multiple sampling patterns for the continuous data space and allow for data simulated or streamed at runtime of the algorithm. We analyze the approximation properties of the stochastic gradient process and study its longtime behavior and ergodicity under constant and decreasing learning rates. We end with illustrating the applicability of the stochastic gradient process in a polynomial regression problem with noisy functional data, as well as in a physics-informed neural network.
Datasets and Benchmarks
Since language models (LMs) now outperform average humans on many challenging tasks, it is becoming increasingly difficult to develop challenging, high-quality, and realistic evaluations. We address this by examining LM capabilities to generate code for solving real scientific research problems. Incorporating input from scientists and AI researchers in 16 diverse natural science sub-fields, including mathematics, physics, chemistry, biology, and materials science, we create a scientist-curated coding benchmark, SciCode. The problems naturally factorize into multiple subproblems, each involving knowledge recall, reasoning, and code synthesis. In total, SciCode contains 338 subproblems decomposed from 80 challenging main problems, and it offers optional descriptions specifying useful scientific background information and scientist-annotated gold-standard solutions and test cases for evaluation. OpenAI o1-preview, the best-performing model among those tested, can solve only 7.7\% of the problems in the most realistic setting. We believe that SciCode demonstrates both contemporary LMs' progress towards realizing helpful scientific assistants and sheds light on the building and evaluation of scientific AI in the future.