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.
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Datasets and Benchmarks
Spatial representation learning (SRL) aims at learning general-purpose neural network representations from various types of spatial data (e.g., points, polylines, polygons, networks, images, etc.) in their native formats. Learning good spatial representations is a fundamental problem for various downstream applications such as species distribution modeling, weather forecasting, trajectory generation, geographic question answering, etc. Even though SRL has become the foundation of almost all geospatial artificial intelligence (GeoAI) research, we have not yet seen significant efforts to develop an extensive deep learning framework and benchmark to support SRL model development and evaluation. To fill this gap, we propose TorchSpatial, a learning framework and benchmark for location (point) encoding,which is one of the most fundamental data types of spatial representation learning. TorchSpatial contains three key components: 1) a unified location encoding framework that consolidates 15 commonly recognized location encoders, ensuring scalability and reproducibility of the implementations; 2) the LocBench benchmark tasks encompassing 7 geo-aware image classification and 10 geo-aware imageregression datasets; 3) a comprehensive suite of evaluation metrics to quantify geo-aware models’ overall performance as well as their geographic bias, with a novel Geo-Bias Score metric. Finally, we provide a detailed analysis and insights into the model performance and geographic bias of different location encoders. We believe TorchSpatial will foster future advancement of spatial representationlearning and spatial fairness in GeoAI research. The TorchSpatial model framework and LocBench benchmark are available at https://github.com/seai-lab/TorchSpatial, and the Geo-Bias Score evaluation framework is available at https://github.com/seai-lab/PyGBS.
Datasets and Benchmarks
Autonomous agents that control user interfaces to accomplish human tasks are emerging. Leveraging LLMs to power such agents has been of special interest, but unless fine-tuned on human-collected task demonstrations, performance is still relatively low. In this work we study whether fine-tuning alone is a viable approach for building real-world UI control agents. To this end we collect and release a new dataset, AndroidControl, consisting of 15,283 demonstrations of everyday tasks with Android apps. Compared to existing datasets, each AndroidControl task instance includes both high and low-level human-generated instructions, allowing us to explore the level of task complexity an agent can handle. Moreover, AndroidControl is the most diverse computer control dataset to date, including 14,548 unique tasks over 833 Android apps, thus allowing us to conduct in-depth analysis of the model performance in and out of the domain of the training data. Using the dataset, we find that when tested in domain fine-tuned models outperform zero and few-shot baselines and scale in such a way that robust performance might feasibly be obtained simply by collecting more data. Out of domain, performance scales significantly more slowly and suggests that in particular for high-level tasks, fine-tuning on more data alone may be insufficient for achieving robust out-of-domain performance.
Datasets and Benchmarks
Prior research in human-centric AI has primarily addressed single-modality tasks like pedestrian detection, action recognition, and pose estimation. However, the emergence of large multimodal models (LMMs) such as GPT-4V has redirected attention towards integrating language with visual content. Referring expression comprehension (REC) represents a prime example of this multimodal approach. Current human-centric REC benchmarks, typically sourced from general datasets, fall short in the LMM era due to their limitations, such as insufficient testing samples, overly concise referring expressions, and limited vocabulary, making them inadequate for evaluating the full capabilities of modern REC models. In response, we present HC-RefLoCo (Human-Centric Referring Expression Comprehension with Long Context), a benchmark that includes 13,452 images, 24,129 instances, and 44,738 detailed annotations, encompassing a vocabulary of 18,681 words. Each annotation, meticulously reviewed for accuracy, averages 93.2 words and includes topics such as appearance, human-object interaction, location, action, celebrity, and OCR. HC-RefLoCo provides a wider range of instance scales and diverse evaluation protocols, encompassing accuracy with various IoU criteria, scale-aware evaluation, and subject-specific assessments. Our experiments, which assess 24 models, highlight HC-RefLoCo’s potential to advance human-centric AI by challenging contemporary REC models with comprehensive and varied data. Our benchmark, along with the evaluation code, are available at https://github.com/ZhaoJingjing713/HC-RefLoCo.
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`.
Computational Biology
Nanopore sequencing is the third-generation sequencing technology with capabilities of generating long-read sequences and directly measuring modifications on DNA/RNA molecules, which makes it ideal for biological applications such as human Telomere-to-Telomere (T2T) genome assembly, Ebola virus surveillance and COVID-19 mRNA vaccine development. However, accuracies of computational methods in various tasks of Nanopore sequencing data analysis are far from satisfactory. For instance, the base calling accuracy of Nanopore RNA sequencing is $\sim$90\%, while the aim is $\sim$99.9\%. This highlights an urgent need of contributions from the machine learning community. A bottleneck that prevents machine learning researchers from entering this field is the lack of a large integrated benchmark dataset. To this end, we present NanoBaseLib, a comprehensive multi-task benchmark dataset. It integrates 16 public datasets with over 30 million reads for four critical tasks in Nanopore data analysis. To facilitate method development, we have preprocessed all the raw data using a uniform workflow, stored all the intermediate results in uniform formats, analysed test datasets with various baseline methods for four benchmark tasks, and developed a software package to easily access these results. NanoBaseLib is available at https://nanobaselib.github.io.
Datasets and Benchmarks
Underwater Object Tracking (UOT) is essential for identifying and tracking submerged objects in underwater videos, but existing datasets are limited in scale, diversity of target categories and scenarios covered, impeding the development of advanced tracking algorithms. To bridge this gap, we take the first step and introduce WebUOT-1M, \ie, the largest public UOT benchmark to date, sourced from complex and realistic underwater environments. It comprises 1.1 million frames across 1,500 video clips filtered from 408 target categories, largely surpassing previous UOT datasets, \eg, UVOT400. Through meticulous manual annotation and verification, we provide high-quality bounding boxes for underwater targets. Additionally, WebUOT-1M includes language prompts for video sequences, expanding its application areas, \eg, underwater vision-language tracking. Given that most existing trackers are designed for open-air conditions and perform poorly in underwater environments due to domain gaps, we propose a novel framework that uses omni-knowledge distillation to train a student Transformer model effectively. To the best of our knowledge, this framework is the first to effectively transfer open-air domain knowledge to the UOT model through knowledge distillation, as demonstrated by results on both existing UOT datasets and the newly proposed WebUOT-1M. We have thoroughly tested WebUOT-1M with 30 deep trackers, showcasing its potential as a benchmark for future UOT research. The complete dataset, along with codes and tracking results, are publicly accessible at \href{https://github.com/983632847/Awesome-Multimodal-Object-Tracking}{\color{magenta}{here}}.
Applications
Large language models (LLMs) have achieved impressive performance across various natural language benchmarks, prompting a continual need to curate more difficult datasets for larger LLMs, which is costly and time-consuming. In this paper, we propose to automate dataset updating and provide systematical analysis regarding its effectiveness in dealing with benchmark leakage issue, difficulty control, and stability. Thus, once current benchmark has been mastered or leaked, we can update it for timely and reliable evaluation. There are two updating strategies: 1) mimicking strategy to generate similar samples based on original data, preserving stylistic and contextual essence, and 2) extending strategy that further expands existing samples at varying cognitive levels by adapting Bloom’s taxonomy of educational objectives. Extensive experiments on updated MMLU and BIG-Bench demonstrate the stability of the proposed strategies and find that the mimicking strategy can effectively alleviate issues of overestimation from benchmark leakage. In cases where the efficient mimicking strategy fails, our extending strategy still shows promising results. Additionally, by controlling the difficulty, we can better discern the models’ performance and enable fine-grained analysis — neither too difficult nor too easy an exam can fairly judge students’ learning status. To the best of our knowledge, we are the first to automate updating benchmarks for reliable and timely evaluation. Our demo leaderboard can be found at https://yingjiahao14.github.io/Automating-DatasetUpdates/.
Trustworthy Machine Learning
Although Large Language Models (LLMs) have demonstrated significant capabilities in executing complex tasks in a zero-shot manner, they are susceptible to jailbreak attacks and can be manipulated to produce harmful outputs. Recently, a growing body of research has categorized jailbreak attacks into token-level and prompt-level attacks. However, previous work primarily overlooks the diverse key factors of jailbreak attacks, with most studies concentrating on LLM vulnerabilities and lacking exploration of defense-enhanced LLMs. To address these issues, we introduced JailTrickBench to evaluate the impact of various attack settings on LLM performance and provide a baseline for jailbreak attacks, encouraging the adoption of a standardized evaluation framework. Specifically, we evaluate the eight key factors of implementing jailbreak attacks on LLMs from both target-level and attack-level perspectives. We further conduct seven representative jailbreak attacks on six defense methods across two widely used datasets, encompassing approximately 354 experiments with about 55,000 GPU hours on A800-80G. Our experimental results highlight the need for standardized benchmarking to evaluate these attacks on defense-enhanced LLMs. Our code is available at https://github.com/usail-hkust/JailTrickBench.
Datasets and Benchmarks
Most existing out-of-distribution (OOD) detection benchmarks classify samples with novel labels as the OOD data. However, some marginal OOD samples actually have close semantic contents to the in-distribution (ID) sample, which makes determining the OOD sample a Sorites Paradox. In this paper, we construct a benchmark named Incremental Shift OOD (IS-OOD) to address the issue, in which we divide the test samples into subsets with different semantic and covariate shift degrees relative to the ID dataset. The data division is achieved through a shift measuring method based on our proposed Language Aligned Image feature Decomposition (LAID). Moreover, we construct a Synthetic Incremental Shift (Syn-IS) dataset that contains high-quality generated images with more diverse covariate contents to complement the IS-OOD benchmark. We evaluate current OOD detection methods on our benchmark and find several important insights: (1) The performance of most OOD detection methods significantly improves as the semantic shift increases; (2) Some methods like GradNorm may have different OOD detection mechanisms as they rely less on semantic shifts to make decisions; (3) Excessive covariate shifts in the image are also likely to be considered as OOD for some methods. Our code and data are released in https://github.com/qqwsad5/IS-OOD.
PEACE: A Dataset of Pharmaceutical Care for Cancer Pain Analgesia Evaluation and Medication Decision
Datasets and Benchmarks
Over half of cancer patients experience long-term pain management challenges. Recently, interest has grown in systems for cancer pain treatment effectiveness assessment (TEA) and medication recommendation (MR) to optimize pharmacological care. These systems aim to improve treatment effectiveness by recommending personalized medication plans based on comprehensive patient information. Despite progress, current systems lack multidisciplinary treatment (MDT) team assessments of treatment and the patient's perception of medication, crucial for effective cancer pain management. Moreover, managing cancer pain medication requires multiple adjustments to the treatment plan based on the patient's evolving condition, a detail often missing in existing datasets. To tackle these issues, we designed the PEACE dataset specifically for cancer pain medication research. It includes detailed pharmacological care records for over 38,000 patients, covering demographics, clinical examination, treatment outcomes, medication plans, and patient self-perceptions. Unlike existing datasets, PEACE records not only long-term and multiple follow-ups both inside and outside hospitals but also includes patients' self-assessments of medication effects and the impact on their lives. We conducted a proof-of-concept study with 13 machine learning algorithms on the PEACE dataset for the TEA (classification task) and MR (regression task). These experiments provide valuable insights into the potential of the PEACE dataset for advancing personalized cancer pain management. The dataset is accessible at: [https://github.com/YTYTYD/PEACE].
Datasets and Benchmarks
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--50m), 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) 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.
Graph Neural Networks
Given a relational database (RDB), how can we predict missing column values in some target table of interest? Although RDBs store vast amounts of rich, informative data spread across interconnected tables, the progress of predictive machine learning models as applied to such tasks arguably falls well behind advances in other domains such as computer vision or natural language processing. This deficit stems, at least in part, from the lack of established/public RDB benchmarks as needed for training and evaluation purposes. As a result, related model development thus far often defaults to tabular approaches trained on ubiquitous single-table benchmarks, or on the relational side, graph-based alternatives such as GNNs applied to a completely different set of graph datasets devoid of tabular characteristics. To more precisely target RDBs lying at the nexus of these two complementary regimes, we explore a broad class of baseline models predicated on: (i) converting multi-table datasets into graphs using various strategies equipped with efficient subsampling, while preserving tabular characteristics; and (ii) trainable models with well-matched inductive biases that output predictions based on these input subgraphs. Then, to address the dearth of suitable public benchmarks and reduce siloed comparisons, we assemble a diverse collection of (i) large-scale RDB datasets and (ii) coincident predictive tasks. From a delivery standpoint, we operationalize the above four dimensions (4D) of exploration within a unified, scalable open-source toolbox called 4DBInfer; please see https://github.com/awslabs/multi-table-benchmark .
Datasets and Benchmarks
Situation awareness is essential for understanding and reasoning about 3D scenes in embodied AI agents. However, existing datasets and benchmarks for situated understanding suffer from severe limitations in data modality, scope, diversity, and scale. To address these limitations, we propose Multi-modal Situated Question Answering (MSQA), a large-scale multi-modal situated reasoning dataset, scalably collected leveraging 3D scene graphs and vision-language models (VLMs) across a diverse range of real-world 3D scenes. MSQA includes 251K situated questionanswering pairs across 9 distinct question categories, covering complex scenarios and object modalities within 3D scenes. We introduce a novel interleaved multimodal input setting in our benchmark to provide both texts, images, and point clouds for situation and question description, aiming to resolve ambiguity in describing situations with single-modality inputs (e.g., texts). Additionally, we devise the Multi-modal Next-step Navigation (MSNN) benchmark to evaluate models’ grounding of actions and transitions between situations. Comprehensive evaluations on reasoning and navigation tasks highlight the limitations of existing vision-language models and underscore the importance of handling multi-modal interleaved inputs and situation modeling. Experiments on data scaling and crossdomain transfer further demonstrate the effectiveness of leveraging MSQA as a pre-training dataset for developing more powerful situated reasoning models, contributing to advancements in 3D scene understanding for embodied AI.
Datasets and Benchmarks
A major obstacle to the advancements of machine learning models in marine science, particularly in sonar imagery analysis, is the scarcity of AI-ready datasets. While there have been efforts to make AI-ready sonar image dataset publicly available, they suffer from limitations in terms of environment setting and scale. To bridge this gap, we introduce $\texttt{SeafloorAI}$, the first extensive AI-ready datasets for seafloor mapping across 5 geological layers that is curated in collaboration with marine scientists. We further extend the dataset to $\texttt{SeafloorGenAI}$ by incorporating the language component in order to facilitate the development of both $\textit{vision}$- and $\textit{language}$-capable machine learning models for sonar imagery. The dataset consists of 62 geo-distributed data surveys spanning 17,300 square kilometers, with 696K sonar images, 827K annotated segmentation masks, 696K detailed language descriptions and approximately 7M question-answer pairs. By making our data processing source code publicly available, we aim to engage the marine science community to enrich the data pool and inspire the machine learning community to develop more robust models. This collaborative approach will enhance the capabilities and applications of our datasets within both fields.
Datasets and Benchmarks
Reconstructing accurate 3D surfaces for street-view scenarios is crucial for applications such as digital entertainment and autonomous driving simulation. However, existing street-view datasets, including KITTI, Waymo, and nuScenes, only offer noisy LiDAR points as ground-truth data for geometric evaluation of reconstructed surfaces. These geometric ground-truths often lack the necessary precision to evaluate surface positions and do not provide data for assessing surface normals. To overcome these challenges, we introduce the SS3DM dataset, comprising precise \textbf{S}ynthetic \textbf{S}treet-view \textbf{3D} \textbf{M}esh models exported from the CARLA simulator. These mesh models facilitate accurate position evaluation and include normal vectors for evaluating surface normal. To simulate the input data in realistic driving scenarios for 3D reconstruction, we virtually drive a vehicle equipped with six RGB cameras and five LiDAR sensors in diverse outdoor scenes. Leveraging this dataset, we establish a benchmark for state-of-the-art surface reconstruction methods, providing a comprehensive evaluation of the associated challenges. For more information, visit our homepage at https://ss3dm.top.
Datasets and Benchmarks
Healthcare applications pose significant challenges to existing reinforcement learning (RL) methods due to implementation risks, low data availability, short treatment episodes, sparse rewards, partial observations, and heterogeneous treatment effects. Despite significant interest in using RL to generate dynamic treatment regimes for longitudinal patient care scenarios, no standardized benchmark has yet been developed.To fill this need we introduce *Episodes of Care* (*EpiCare*), a benchmark designed to mimic the challenges associated with applying RL to longitudinal healthcare settings. We leverage this benchmark to test five state-of-the-art offline RL models as well as five common off-policy evaluation (OPE) techniques.Our results suggest that while offline RL may be capable of improving upon existing standards of care given large data availability, its applicability does not appear to extend to the moderate to low data regimes typical of healthcare settings. Additionally, we demonstrate that several OPE techniques which have become standard in the the medical RL literature fail to perform adequately on our benchmark. These results suggest that the performance of RL models in dynamic treatment regimes may be difficult to meaningfully evaluate using current OPE methods, indicating that RL for this application may still be in its early stages. We hope that these results along with the benchmark itself will facilitate the comparison of existing methods and inspire further research into techniques that increase the practical applicability of medical RL.
Datasets and Benchmarks
Large multimodal models (LMMs) have proven flexible and generalisable across many tasks and fields. Although they have strong potential to aid scientific research, their capabilities in this domain are not well characterised. A key aspect of scientific research is the ability to understand and interpret figures, which serve as a rich, compressed source of complex information. In this work, we present SciFIBench, a scientific figure interpretation benchmark consisting of 2000 questions split between two tasks across 8 categories. The questions are curated from arXiv paper figures and captions, using adversarial filtering to find hard negatives and human verification forquality control. We evaluate 28 LMMs on SciFIBench, finding it to be a challenging benchmark. Finally, we investigate the alignment and reasoning faithfulness of the LMMs on augmented question sets from our benchmark. We release SciFIBench to encourage progress in this domain.
Datasets and Benchmarks
The rapid progress in Large Language Models (LLMs) poses potential risks such as generating unethical content. Assessing the values embedded in LLMs' generated responses can help expose their misalignment, but this relies on reference-free value evaluators, e.g. fine-tuned LLMs or closed-source models like GPT-4. Nevertheless, two key challenges emerge in open-ended value evaluation: the evaluator should adapt to changing human value definitions with minimal annotation, against their own bias (adaptability); and remain robust across varying value expressions and scenarios (generalizability). To handle these challenges, we introduce CLAVE, a novel framework that integrates two complementary LLMs: a large model to extract high-level value concepts from diverse responses, leveraging its extensive knowledge and generalizability, and a small model fine-tuned on these concepts to adapt to human value annotations. This dual-model framework enables adaptation to any value system using <100 human-labeled samples per value type. We also present ValEval, a comprehensive dataset comprising 13k+ (text,value,label) tuples across diverse domains, covering three major value systems. We benchmark the performance of 15+ popular LLM evaluators and fully analyze their strengths and weaknesses. Our findings reveal that CLAVE combining a large prompt-based model and a small fine-tuned one serves as an optimal balance in value evaluation.
Datasets and Benchmarks
Formal verification (FV) has witnessed growing significance with current emerging program synthesis by the evolving large language models (LLMs). However, current formal verification mainly resorts to symbolic verifiers or hand-craft rules, resulting in limitations for extensive and flexible verification. On the other hand, formal languages for automated theorem proving, such as Isabelle, as another line of rigorous verification, are maintained with comprehensive rules and theorems. In this paper, we propose FVEL, an interactive Formal Verification Environment with LLMs. Specifically, FVEL transforms a given code to be verified into Isabelle, and then conducts verification via neural automated theorem proving with an LLM. The joined paradigm leverages the rigorous yet abundant formulated and organized rules in Isabelle and is also convenient for introducing and adjusting cutting-edge LLMs. To achieve this goal, we extract a large-scale FVELER. The FVELER dataset includes code dependencies and verification processes that are formulated in Isabelle, containing 758 theories, 29,304 lemmas, and 201,498 proof steps in total with in-depth dependencies. We benchmark FVELER in the FVEL environment by first fine-tuning LLMs with FVELER and then evaluating them on Code2Inv and SV-COMP. The results show that FVEL with FVELER fine-tuned Llama3-8B solves 17.39% (69→81) more problems, and Mistral-7B 12% (75→84) more problems in SV-COMP. And the proportion of proof errors is reduced. Project page: https://fveler.github.io/.