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Mathew J. Koretsky

Publications and source records attributed to Mathew J. Koretsky.

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Hidden in the Haystack: Smaller Needles are More Difficult for LLMs to Find

Large language models (LLMs) face significant challenges with needle-in-ahaystack 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, the length of the answer-containing document, has received little attention. We present the first systematic study of gold context size in long-context question answering, spanning three diverse benchmarks (general knowledge, biomedical reasoning, and mathematical reasoning), eleven state-of-the-art LLMs (including recent reasoning models), and more than 150K controlled runs. 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 effect persists under rigorous confounder analysis: even after controlling for gold context position, answer token repetition, gold-to-distractor ratio, distractor volume, and domain specificity, gold context size remains a decisive, independent predictor of success. Our work provides clear insights to guide the design of robust, context-aware LLM-driven systems.

cs.CL

BiomedSQL: Text-to-SQL for Scientific Reasoning on Biomedical Knowledge Bases

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 database 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: Gemini-3-Pro achieves 58.1% execution accuracy under baseline prompting, 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 that support scientific discovery through robust reasoning over structured biomedical knowledge bases. The BiomedSQL benchmark and codebase are publicly available at https://datatecnica.github.io/biomedbench-suite/biomedsql.

cs.CL