Tanay Nayak

Kevin Xu, Yeganeh Kordi, Tanay Nayak et al. · uw

Can advanced multi-modal models effectively tackle complex web-based tasks? Such tasks are often found on crowdsourcing platforms, where crowdworkers engage in challenging micro-tasks within web-based environments. Building on this idea, we present TurkingBench, a benchmark consisting of tasks presented as web pages with textual instructions and multi-modal contexts. Unlike previous approaches that rely on artificially synthesized web pages, our benchmark uses natural HTML pages originally designed for crowdsourcing workers to perform various annotation tasks. Each task's HTML instructions are instantiated with different values derived from crowdsourcing tasks, creating diverse instances. This benchmark includes 32.2K instances spread across 158 tasks. To support the evaluation of TurkingBench, we have developed a framework that links chatbot responses to actions on web pages (e.g., modifying a text box, selecting a radio button). We assess the performance of cutting-edge private and open-source models, including language-only and vision-language models (such as GPT4 and InternVL), on this benchmark. Our results show that while these models outperform random chance, there is still significant room for improvement. We hope that this benchmark will drive progress in the evaluation and development of web-based agents.

Mathew J. Koretsky, Maya Willey, Adi Asija et al.

Biomedical researchers increasingly rely on large-scale structured databases for complex analytical tasks. However, current text-to-SQL systems often struggle to map qualitative scientific questions into executable SQL, particularly when implicit domain reasoning is required. We introduce BiomedSQL, the first benchmark explicitly designed to evaluate scientific reasoning in text-to-SQL generation over a real-world biomedical knowledge base. BiomedSQL comprises 68,000 question/SQL query/answer triples generated from templates and grounded in a harmonized BigQuery knowledge base that integrates gene-disease associations, causal inference from omics data, and drug approval records. Each question requires models to infer domain-specific criteria, such as genome-wide significance thresholds, effect directionality, or trial phase filtering, rather than rely on syntactic translation alone. We evaluate a range of open- and closed-source LLMs across prompting strategies and interaction paradigms. Our results reveal a substantial performance gap: GPT-o3-mini achieves 59.0% execution accuracy, while our custom multi-step agent, BMSQL, reaches 62.6%, both well below the expert baseline of 90.0%. BiomedSQL provides a new foundation for advancing text-to-SQL systems capable of supporting scientific discovery through robust reasoning over structured biomedical knowledge bases. Our dataset is publicly available at https://huggingface.co/datasets/NIH-CARD/BiomedSQL, and our code is open-source at https://github.com/NIH-CARD/biomedsql.

Owen Bianchi, Mathew J. Koretsky, Maya Willey et al.

Large language models (LLMs) face significant challenges with needle-in-a-haystack tasks, where relevant information ("the needle") must be drawn from a large pool of irrelevant context ("the haystack"). Previous studies have highlighted positional bias and distractor quantity as critical factors affecting model performance, yet the influence of gold context size has received little attention. We address this gap by systematically studying how variations in gold context length impact LLM performance on long-context question answering tasks. Our experiments reveal that LLM performance drops sharply when the gold context is shorter, i.e., smaller gold contexts consistently degrade model performance and amplify positional sensitivity, posing a major challenge for agentic systems that must integrate scattered, fine-grained information of varying lengths. This pattern holds across three diverse domains (general knowledge, biomedical reasoning, and mathematical reasoning) and seven state-of-the-art LLMs of various sizes and architectures. Our work provides clear insights to guide the design of robust, context-aware LLM-driven systems.