Nicole Kuznetsov

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 $\textit{gold context size}$, the length of the answer-containing document, has received little attention. We present a 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., $\textbf{smaller gold contexts consistently degrade model performance and amplify positional sensitivity}$, posing a major challenge for agentic systems that must integrate scattered, fine-grained information of $\textit{varying lengths}$. 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.

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 $\textit{BiomedSQL}$, 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.