论文检索

Datasets and Benchmarks

Bingqiao Luo, Zhen Zhang, Qian Wang, Bingsheng He

Machine learning applied to blockchain graphs offers significant opportunities for enhanced data analysis and applications. However, the potential of this field is constrained by the lack of a large-scale, cross-chain dataset that includes hierarchical graph-level data. To address this issue, we present novel datasets that provide detailed label information at the token level and integrate interactions between tokens across multiple blockchain platforms. We model transactions within each token as local graphs and the relationships between tokens as global graphs, collectively forming a "Graphs of Graphs" (GoG) approach. This innovative approach facilitates a deeper understanding of systemic structures and hierarchical interactions, which are essential for applications such as link prediction, anomaly detection, and token classification. We conduct a series of experiments demonstrating that this dataset delivers new insights and challenges for exploring GoG within the blockchain domain. Our work promotes advancements and opens new avenues for research in both the blockchain and graph communities. Source code and datasets are available at https://github.com/Xtra-Computing/Cryptocurrency-Graphs-of-graphs.

Fairness

Mariia Vladimirova, Federico Pavone, Eustache Diemert

We introduce a fairness-aware dataset for job recommendation in advertising, designed to foster research in algorithmic fairness within real-world scenarios. It was collected and prepared to comply with privacy standards and business confidentiality. An additional challenge is the lack of access to protected user attributes such as gender, for which we propose a pragmatic solution to obtain a proxy estimate. Despite being anonymized and including a proxy for a sensitive attribute, our dataset preserves predictive power and maintains a realistic and challenging benchmark. This dataset addresses a significant gap in the availability of fairness-focused resources for high-impact domains like advertising -- the actual impact being having access or not to precious employment opportunities, where balancing fairness and utility is a common industrial challenge. We also explore various stages in the advertising process where unfairness can occur and introduce a method to compute a fair utility metric for the job recommendations in online systems case from a biased dataset. Experimental evaluations of bias mitigation techniques on the released dataset demonstrate potential improvements in fairness and the associated trade-offs with utility.The dataset is hosted at https://huggingface.co/datasets/criteo/FairJob. Source code for the experiments is hosted at https://github.com/criteo-research/FairJob-dataset/.

Graph Neural Networks

Yuankai Luo, Lei Shi, Xiao-Ming Wu

Graph Transformers (GTs) have recently emerged as popular alternatives to traditional message-passing Graph Neural Networks (GNNs), due to their theoretically superior expressiveness and impressive performance reported on standard node classification benchmarks, often significantly outperforming GNNs. In this paper, we conduct a thorough empirical analysis to reevaluate the performance of three classic GNN models (GCN, GAT, and GraphSAGE) against GTs. Our findings suggest that the previously reported superiority of GTs may have been overstated due to suboptimal hyperparameter configurations in GNNs. Remarkably, with slight hyperparameter tuning, these classic GNN models achieve state-of-the-art performance, matching or even exceeding that of recent GTs across 17 out of the 18 diverse datasets examined. Additionally, we conduct detailed ablation studies to investigate the influence of various GNN configurations—such as normalization, dropout, residual connections, and network depth—on node classification performance. Our study aims to promote a higher standard of empirical rigor in the field of graph machine learning, encouraging more accurate comparisons and evaluations of model capabilities. Our implementation is available at https://github.com/LUOyk1999/tunedGNN.

Datasets and Benchmarks

Yury Kuratov, Aydar Bulatov, Petr Anokhin, Ivan Rodkin, Dmitry Sorokin, Artyom Sorokin, Mikhail Burtsev

In recent years, the input context sizes of large language models (LLMs) have increased dramatically. However, existing evaluation methods have not kept pace, failing to comprehensively assess the efficiency of models in handling long contexts. To bridge this gap, we introduce the BABILong benchmark, designed to test language models' ability to reason across facts distributed in extremely long documents. BABILong includes a diverse set of 20 reasoning tasks, including fact chaining, simple induction, deduction, counting, and handling lists/sets. These tasks are challenging on their own, and even more demanding when the required facts are scattered across long natural text. Our evaluations show that popular LLMs effectively utilize only 10-20% of the context and their performance declines sharply with increased reasoning complexity. Among alternatives to in-context reasoning, Retrieval-Augmented Generation methods achieve a modest 60% accuracy on single-fact question answering, independent of context length. Among context extension methods, the highest performance is demonstrated by recurrent memory transformers after fine-tuning, enabling the processing of lengths up to 50 million tokens. The BABILong benchmark is extendable to any length to support the evaluation of new upcoming models with increased capabilities, and we provide splits up to 10 million token lengths.

Datasets and Benchmarks

Ruisheng Cao, Fangyu Lei, Haoyuan Wu, Jixuan Chen, Yeqiao Fu, Hongcheng Gao, Xinzhuang Xiong, Hanchong Zhang, Wenjing Hu, Yuchen Mao 等

Data science and engineering workflows often span multiple stages, from warehousing to orchestration, using tools like BigQuery, dbt, and Airbyte. As vision language models (VLMs) advance in multimodal understanding and code generation, VLM-based agents could potentially automate these workflows by generating SQL queries, Python code, and GUI operations. This automation can improve the productivity of experts while democratizing access to large-scale data analysis. In this paper, we introduce Spider2-V, the first multimodal agent benchmark focusing on professional data science and engineering workflows, featuring 494 real-world tasks in authentic computer environments and incorporating 20 enterprise-level professional applications. These tasks, derived from real-world use cases, evaluate the ability of a multimodal agent to perform data-related tasks by writing code and managing the GUI in enterprise data software systems. To balance realistic simulation with evaluation simplicity, we devote significant effort to developing automatic configurations for task setup and carefully crafting evaluation metrics for each task. Furthermore, we supplement multimodal agents with comprehensive documents of these enterprise data software systems. Our empirical evaluation reveals that existing state-of-the-art LLM/VLM-based agents do not reliably automate full data workflows (14.0% success). Even with step-by-step guidance, these agents still underperform in tasks that require fine-grained, knowledge-intensive GUI actions (16.2%) and involve remote cloud-hosted workspaces (10.6%). We hope that Spider2-V paves the way for autonomous multimodal agents to transform the automation of data science and engineering workflow. Our code and data are available at https://spider2-v.github.io.

Datasets and Benchmarks

Junho Myung, Nayeon Lee, Yi Zhou, Jiho Jin, Rifki Putri, Dimosthenis Antypas, Hsuvas Borkakoty, Eunsu Kim, Carla Perez-Almendros, Abinew Ali Ayele 等

Large language models (LLMs) often lack culture-specific everyday knowledge, especially across diverse regions and non-English languages. Existing benchmarks for evaluating LLMs' cultural sensitivities are usually limited to a single language or online sources like Wikipedia, which may not reflect the daily habits, customs, and lifestyles of different regions. That is, information about the food people eat for their birthday celebrations, spices they typically use, musical instruments youngsters play or the sports they practice in school is not always explicitly written online. To address this issue, we introduce BLEnD, a hand-crafted benchmark designed to evaluate LLMs' everyday knowledge across diverse cultures and languages. The benchmark comprises 52.6k question-answer pairs from 16 countries/regions, in 13 different languages, including low-resource ones such as Amharic, Assamese, Azerbaijani, Hausa, and Sundanese. We evaluate LLMs in two formats: short-answer questions, and multiple-choice questions. We show that LLMs perform better in cultures that are more present online, with a maximum 57.34% difference in GPT-4, the best-performing model, in the short-answer format.Furthermore, we find that LLMs perform better in their local languages for mid-to-high-resource languages. Interestingly, for languages deemed to be low-resource, LLMs provide better answers in English. We make our dataset publicly available at: https://github.com/nlee0212/BLEnD.

Datasets and Benchmarks

David Castillo-Bolado, Joseph Davidson, Finlay Gray, Marek Rosa

We introduce a dynamic benchmarking system for conversational agents that evaluates their performance through a single, simulated, and lengthy user$\leftrightarrow$agent interaction. The interaction is a conversation between the user and agent, where multiple tasks are introduced and then undertaken concurrently. We context switch regularly to interleave the tasks, which constructs a realistic testing scenario in which we assess the Long-Term Memory, Continual Learning, and Information Integration capabilities of the agents. Results from both proprietary and open-source Large-Language Models show that LLMs in general perform well on single-task interactions, but they struggle on the same tasks when they are interleaved. Notably, short-context LLMs supplemented with an LTM system perform as well as or better than those with larger contexts. Our benchmark suggests that there are other challenges for LLMs responding to more natural interactions that contemporary benchmarks have heretofore not been able to capture.

Datasets and Benchmarks

Jehan Yang, Maxwell Soh, Vivianna Lieu, Douglas Weber, Zackory Erickson

This paper introduces the first generalization and adaptation benchmark using machine learning for evaluating out-of-distribution performance of electromyography (EMG) classification algorithms. The ability of an EMG classifier to handle inputs drawn from a different distribution than the training distribution is critical for real-world deployment as a control interface. By predicting the user’s intended gesture using EMG signals, we can create a wearable solution to control assistive technologies, such as computers, prosthetics, and mobile manipulator robots. This new out-of-distribution benchmark consists of two major tasks that have utility for building robust and adaptable control interfaces: 1) intersubject classification, and 2) adaptation using train-test splits for time-series. This benchmark spans nine datasets, the largest collection of EMG datasets in a benchmark. Among these, a new dataset is introduced, featuring a novel, easy-to-wear high-density EMG wearable for data collection. The lack of open-source benchmarks has made comparing accuracy results between papers challenging for the EMG research community. This new benchmark provides researchers with a valuable resource for analyzing practical measures of out-of-distribution performance for EMG datasets. Our code and data from our new dataset can be found at emgbench.github.io.

Datasets and Benchmarks

Pavan Kalyan Tankala, Piyush Pasi, Sahil Dharod, Azeem Motiwala, Preethi Jyothi, Aditi Chaudhary, Krishna Srinivasan

Cross-modal (image-to-text and text-to-image) retrieval is an established task used in evaluation benchmarks to test the performance of vision-language models (VLMs). Several state-of-the-art VLMs (e.g. CLIP, BLIP-2) have achieved near-perfect performance on widely-used image-text retrieval benchmarks such as MSCOCO-Test-5K and Flickr30K-Test-1K. As a measure of out-of-distribution (OOD) generalization, prior works rely on zero-shot performance evaluated on one dataset (Flickr) using a VLM finetuned on another one (MSCOCO). We argue that such comparisons are insufficient to assess the OOD generalization capability of models due to high visual and linguistic similarity between the evaluation and finetuning datasets. To address this gap, we introduce WikiDO (drawn from Wikipedia Diversity Observatory), a novel cross-modal retrieval benchmark to assess the OOD generalization capabilities of pretrained VLMs. This consists of newly scraped 380K image-text pairs from Wikipedia with domain labels, a carefully curated, human-verified a)in-distribution (ID) test set (3K) and b) OOD test set (3K). The image-text pairs are very diverse in topics and geographical locations. We evaluate different VLMs of varying capacity on the \wikido benchmark; BLIP-2 achieves zero-shot performance of $R@1\approx66\%$ on the OOD test set, compared to $\approx$ $81\%$ on COCO and $\approx95\%$ on Flickr. When fine-tuned on WikiDO, the $R@1$ improvement is at most $\approx5\%$ on OOD instances compared to $\approx12\%$ on ID instances. We probe the VLMs with varying finetuning objectives and datasets of varying sizes to identify what aids OOD generalization the most. Our results confirm that WikiDO offers a strong cross-modal benchmark for current VLMs in specifically evaluating for OOD generalization. Our benchmark is hosted as a competition at https://kaggle.com/competitions/wikido24 with public access to dataset and code.

Robotics

Cherie Ho, Jiaye Zou, Omar Alama, Sai Mitheran Jagadesh Kumar, Cheng-Yu Chiang, Taneesh Gupta, Chen Wang, Nikhil Keetha, Katia Sycara, Sebastian Scherer

Top-down Bird's Eye View (BEV) maps are a popular perception representation for ground robot navigation due to their richness and flexibility for downstream tasks. While recent methods have shown promise for predicting BEV maps from First-Person View (FPV) images, their generalizability is limited to small regions captured by current autonomous vehicle-based datasets. In this context, we show that a more scalable approach towards generalizable map prediction can be enabled by using two large-scale crowd-sourced mapping platforms, Mapillary for FPV images and OpenStreetMap for BEV semantic maps.We introduce Map It Anywhere (MIA), a data engine that enables seamless curation and modeling of labeled map prediction data from existing open-source map platforms. Using our MIA data engine, we display the ease of automatically collecting a 1.2 million FPV & BEV pair dataset encompassing diverse geographies, landscapes, environmental factors, camera models & capture scenarios. We further train a simple camera model-agnostic model on this data for BEV map prediction.Extensive evaluations using established benchmarks and our dataset show that the data curated by MIA enables effective pretraining for generalizable BEV map prediction, with zero-shot performance far exceeding baselines trained on existing datasets by 35%. Our analysis highlights the promise of using large-scale public maps for developing & testing generalizable BEV perception, paving the way for more robust autonomous navigation.Website: mapitanywhere.github.io

Datasets and Benchmarks

Dapeng Hu, Romy Luo, Jian Liang, Chuan Sheng Foo

Selecting appropriate hyperparameters is crucial for unlocking the full potential of advanced unsupervised domain adaptation (UDA) methods in unlabeled target domains. Although this challenge remains under-explored, it has recently garnered increasing attention with the proposals of various model selection methods. Reliable model selection should maintain performance across diverse UDA methods and scenarios, especially avoiding highly risky worst-case selections—selecting the model or hyperparameter with the worst performance in the pool.\textit{Are existing model selection methods reliable and versatile enough for different UDA tasks?} In this paper, we provide a comprehensive empirical study involving 8 existing model selection approaches to answer this question. Our evaluation spans 12 UDA methods across 5 diverse UDA benchmarks and 5 popular UDA scenarios.Surprisingly, we find that none of these approaches can effectively avoid the worst-case selection. In contrast, a simple but overlooked ensemble-based selection approach, which we call EnsV, is both theoretically and empirically certified to avoid the worst-case selection, ensuring high reliability. Additionally, EnsV is versatile for various practical but challenging UDA scenarios, including validation of open-partial-set UDA and source-free UDA.Finally, we call for more attention to the reliability of model selection in UDA: avoiding the worst-case is as significant as achieving peak selection performance and should not be overlooked when developing new model selection methods. Code is available at https://github.com/LHXXHB/EnsV.

Language · Speech

Junyi AO, Yuancheng Wang, Xiaohai Tian, Dekun Chen, Jun Zhang, Lu Lu, Yuxuan Wang, Haizhou Li, Zhizheng Wu

Speech encompasses a wealth of information, including but not limited to content, paralinguistic, and environmental information.This comprehensive nature of speech significantly impacts communication and is crucial for human-computer interaction.Chat-Oriented Large Language Models (LLMs), known for their general-purpose assistance capabilities, have evolved to handle multi-modal inputs, including speech.Although these models can be adept at recognizing and analyzing speech, they often fall short of generating appropriate responses.We argue that this is due to the lack of principles on task definition and model development, which requires open-source datasets and metrics suitable for model evaluation.To bridge the gap, we present SD-Eval, a benchmark dataset aimed at multidimensional evaluation of spoken dialogue understanding and generation.SD-Eval focuses on paralinguistic and environmental information and includes 7,303 utterances, amounting to 8.76 hours of speech data. The data is aggregated from eight public datasets, representing four perspectives: emotion, accent, age, and background sound.To assess the SD-Eval benchmark dataset, we implement three different models and construct a training set following a process similar to that of SD-Eval. The training set contains 1,052.72 hours of speech data and 724.4k utterances. We also conduct a comprehensive evaluation using objective evaluation methods (e.g. BLEU and ROUGE), subjective evaluations and LLM-based metrics for the generated responses.Models conditioned with paralinguistic and environmental information outperform their counterparts in both objective and subjective measures.Moreover, experiments demonstrate that LLM-based metrics show a higher correlation with human evaluation compared to traditional metrics.We open-source SD-Eval at https://github.com/amphionspace/SD-Eval.

Datasets and Benchmarks

Hien Vu, Omkar Chandrakant Prabhune, Unmesh Raskar, Dimuth Panditharatne, Hanwook Chung, Christopher Choi, Younghyun Kim

Precision livestock farming (PLF) has been transformed by machine learning (ML), enabling more precise and timely interventions that enhance overall farm productivity, animal welfare, and environmental sustainability. However, despite the availability of various sensing technologies, few datasets leverage multiple modalities, which are crucial for developing more accurate and efficient monitoring devices and ML models. To address this gap, we present MmCows, a multimodal dataset for dairy cattle monitoring. This dataset comprises a large amount of synchronized, high-quality measurement data on behavioral, physiological, and environmental factors. It includes two weeks of data collected using wearable and implantable sensors deployed on ten milking Holstein cows, such as ultra-wideband (UWB) sensors, inertial sensors, and body temperature sensors. In addition, it features 4.8 million frames of high-resolution image sequences from four isometric view cameras, as well as temperature and humidity data from environmental sensors. We also gathered milk yield data and outdoor weather conditions. One full day’s worth of image data is annotated as ground truth, totaling 20,000 frames with 213,000 bounding boxes of 16 cows, along with their 3D locations and behavior labels. An extensive analysis of MmCows is provided to evaluate the modalities individually and their complementary benefits. The release of MmCows and its benchmarks will facilitate research on multimodal monitoring of dairy cattle, thereby promoting sustainable dairy farming. The dataset and the code for benchmarks are available at https://github.com/neis-lab/mmcows.

Datasets and Benchmarks

Alejandro Lozano, Jeffrey Nirschl, James Burgess, Sanket Rajan Gupte, Yuhui Zhang, Alyssa Unell, Serena Yeung

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers’ efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs’ perception and cognition capabilities in biological image understanding. To address this gap, we introduce Micro-Bench, an expert-curated benchmark encompassing 24 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on Micro-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release Micro-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Datasets and Benchmarks

Anushrut Nirmal Jignasu, Kelly Marshall, Ankush Kumar Mishra, Lucas Nerone Rillo, Baskar Ganapathysubramanian, Aditya Balu, Chinmay Hegde, Adarsh Krishnamurthy

G-code (Geometric code) or RS-274 is the most widely used computer numerical control (CNC) and 3D printing programming language. G-code provides machine instructions for the movement of the 3D printer, especially for the nozzle, stage, and extrusion of material for extrusion-based additive manufacturing. Currently, there does not exist a large repository of curated CAD models along with their corresponding G-code files for additive manufacturing. To address this issue, we present Slice-100K, a first-of-its-kind dataset of over 100,000 G-code files, along with their tessellated CAD model, LVIS (Large Vocabulary Instance Segmentation) categories, geometric properties, and renderings. We build our dataset from triangulated meshes derived from Objaverse-XL and Thingi10K datasets. We demonstrate the utility of this dataset by finetuning GPT-2 on a subset of the dataset for G-code translation from a legacy G-code format (Sailfish) to a more modern, widely used format (Marlin). Our dataset can be found here. Slice-100K will be the first step in developing a multimodal foundation model for digital manufacturing.

Graph Neural Networks

Zhonghao Wang, Danyu Sun, Sheng Zhou, Haobo Wang, Jiapei Fan, Longtao Huang, Jiajun Bu

Graph Neural Networks (GNNs) exhibit strong potential in node classification task through a message-passing mechanism. However, their performance often hinges on high-quality node labels, which are challenging to obtain in real-world scenarios due to unreliable sources or adversarial attacks. Consequently, label noise is common in real-world graph data, negatively impacting GNNs by propagating incorrect information during training. To address this issue, the study of Graph Neural Networks under Label Noise (GLN) has recently gained traction. However, due to variations in dataset selection, data splitting, and preprocessing techniques, the community currently lacks a comprehensive benchmark, which impedes deeper understanding and further development of GLN. To fill this gap, we introduce NoisyGL in this paper, the first comprehensive benchmark for graph neural networks under label noise. NoisyGL enables fair comparisons and detailed analyses of GLN methods on noisy labeled graph data across various datasets, with unified experimental settings and interface. Our benchmark has uncovered several important insights that were missed in previous research, and we believe these findings will be highly beneficial for future studies. We hope our open-source benchmark library will foster further advancements in this field. The code of the benchmark can be found in https://github.com/eaglelab-zju/NoisyGL.

Datasets and Benchmarks

Jiasheng Zhang, Jialin Chen, Menglin Yang, Aosong Feng, Shuang Liang, Jie Shao, Rex Ying

Dynamic text-attributed graphs (DyTAGs) are prevalent in various real-world scenarios, where each node and edge are associated with text descriptions, and both the graph structure and text descriptions evolve over time. Despite their broad applicability, there is a notable scarcity of benchmark datasets tailored to DyTAGs, which hinders the potential advancement in many research fields. To address this gap, we introduce Dynamic Text-attributed Graph Benchmark (DTGB), a collection of large-scale, time-evolving graphs from diverse domains, with nodes and edges enriched by dynamically changing text attributes and categories. To facilitate the use of DTGB, we design standardized evaluation procedures based on four real-world use cases: future link prediction, destination node retrieval, edge classification, and textual relation generation. These tasks require models to understand both dynamic graph structures and natural language, highlighting the unique challenges posed by DyTAGs. Moreover, we conduct extensive benchmark experiments on DTGB, evaluating 7 popular dynamic graph learning algorithms and their variants of adapting to text attributes with LLM embeddings, along with 6 powerful large language models (LLMs). Our results show the limitations of existing models in handling DyTAGs. Our analysis also demonstrates the utility of DTGB in investigating the incorporation of structural and textual dynamics. The proposed DTGB fosters research on DyTAGs and their broad applications. It offers a comprehensive benchmark for evaluating and advancing models to handle the interplay between dynamic graph structures and natural language. The dataset and source code are available at https://github.com/zjs123/DTGB.

Datasets and Benchmarks

Alvin Tan, Chunhua Yu, Bria Long, Wanjing Ma, Tonya Murray, Rebecca Silverman, Jason Yeatman, Michael C Frank

How (dis)similar are the learning trajectories of vision–language models and children? Recent modeling work has attempted to understand the gap between models’ and humans’ data efficiency by constructing models trained on less data, especially multimodal naturalistic data. However, such models are often evaluated on adult-level benchmarks, with limited breadth in language abilities tested, and without direct comparison to behavioral data. We introduce DevBench, a multimodal benchmark comprising seven language evaluation tasks spanning the domains of lexical, syntactic, and semantic ability, with behavioral data from both children and adults. We evaluate a set of vision–language models on these tasks, comparing models and humans on their response patterns, not their absolute performance. Across tasks, models exhibit variation in their closeness to human response patterns, and models that perform better on a task also more closely resemble human behavioral responses. We also examine the developmental trajectory of OpenCLIP over training, finding that greater training results in closer approximations to adult response patterns. DevBench thus provides a benchmark for comparing models to human language development. These comparisons highlight ways in which model and human language learning processes diverge, providing insight into entry points for improving language models.

Computational Biology

Artur Szałata, Andrew Benz, Robrecht Cannoodt, Mauricio Cortes, Jason Fong, Sunil Kuppasani, Richard Lieberman, Tianyu Liu, Javier Mas-Rosario, Rico Meinl 等

Single-cell transcriptomics has revolutionized our understanding of cellular heterogeneity and drug perturbation effects. However, its high cost and the vast chemical space of potential drugs present barriers to experimentally characterizing the effect of chemical perturbations in all the myriad cell types of the human body. To overcome these limitations, several groups have proposed using machine learning methods to directly predict the effect of chemical perturbations either across cell contexts or chemical space. However, advances in this field have been hindered by a lack of well-designed evaluation datasets and benchmarks. To drive innovation in perturbation modeling, the Open Problems Perturbation Prediction (OP3) benchmark introduces a framework for predicting the effects of small molecule perturbations on cell type-specific gene expression. OP3 leverages the Open Problems in Single-cell Analysis benchmarking infrastructure and is enabled by a new single-cell perturbation dataset, encompassing 146 compounds tested on human blood cells. The benchmark includes diverse data representations, evaluation metrics, and winning methods from our "Single-cell perturbation prediction: generalizing experimental interventions to unseen contexts" competition at NeurIPS 2023. We envision that the OP3 benchmark and competition will drive innovation in single-cell perturbation prediction by improving the accessibility, visibility, and feasibility of this challenge, thereby promoting the impact of machine learning in drug discovery.

Datasets and Benchmarks

Nikhil Khandekar, Qiao Jin, Guangzhi Xiong, Soren Dunn, Serina Applebaum, Zain Anwar, Maame Sarfo-Gyamfi, Conrad Safranek, Abid Anwar, Andrew Zhang 等

Current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks. MedCalc-Bench is publicly available at: https://github.com/ncbi-nlp/MedCalc-Bench.