Zhixuan Chu
Publications
EHR-Complex: Benchmarking Medical Agents for Complex Clinical Reasoning
Clinical agents promise to democratize access to electronic health records (EHRs), yet existing benchmarks fail to reflect the complexity of practical EHR analysis, e.g., often operating on idealized, clean EHRs via static SQL generation rather than interactive execution. In this work, we introduce EHR-Complex, a large-scale benchmark designed for interactive clinical database reasoning. Built on the large MIMIC-IV substrate (365K patients, 31 tables, 500M+ records), EHR-Complex comprises about 52K tasks spanning six clinical intents, supporting both patient-level and population-level queries, where each task requires an agent to interact with a sandboxed environment by executing SQL queries or Python code. Notably, EHR-Complex considers the real-world SQL task complexity for longitudinal multi-table aggregation and compositional reasoning, resulting in 31.93 SQL structural components per query on average. Evaluation results on EHR-Complex reveal the clinical difficulty of these EHR reasoning scenarios, with the top-performing model achieving only 62.3% exact-match accuracy. Pass^k consistency drops below 50% for nearly all evaluated models at k=4, exposing broad stochastic fragility. A fine-grained analysis of more than 3,800 failed trajectories for representative LLMs reveals three dominant failure modes: SQL logic errors, medical-code lookup failures, and semantic misunderstandings. EHR-Complex provides a rigorous testbed for clinical agents and highlights remaining gaps in robust reasoning for large-scale EHR analysis.
Explainable Token-level Noise Filtering for LLM Fine-tuning Datasets
Large Language Models (LLMs) have seen remarkable advancements, achieving state-of-the-art results in diverse applications. Fine-tuning, an important step for adapting LLMs to specific downstream tasks, typically involves further training on corresponding datasets. However, a fundamental discrepancy exists between current fine-tuning datasets and the token-level optimization mechanism of LLMs: most datasets are designed at the sentence-level, which introduces token-level noise, causing negative influence to final performance. In this paper, we propose XTF, an explainable token-level noise filtering framework. XTF decomposes the complex and subtle contributions of token-level data to the fine-tuning process into three distinct and explicit attributes (reasoning importance, knowledge novelty, and task relevance), which can be assessed using scoring methods, and then masks the gradients of selected noisy tokens accordingly to optimize the performance of fine-tuned LLMs. We conduct extensive experiments on three representative downstream tasks (math, code and medicine) across 7 mainstream LLMs. The results demonstrate that XTF can significantly improve downstream performance by up to 13.7% compared to regular fine-tuning. Our work highlights the importance of token-level dataset optimization, and demonstrates the potential of strategies based on attribute decomposition for explaining complex training mechanisms.