arXiv subjects

Xuanlyu Zhu

Publications and source records attributed to Xuanlyu Zhu.

2 recordsLinked to original sources

arXiv2026

Overview of CHIP 2026 Shared Task 1: Patient-Specific Phenotype Concept Recognition in Full-Text Biomedical Literature

Automatic phenotype information extraction plays an important role in rare disease diagnosis, genotype-phenotype analysis, and precision medicine. However, accurately identifying phenotype concepts and determining their associations with specific patients remain challenging, particularly in full-text biomedical articles involving multiple patients and complex clinical descriptions. This paper presents an overview of CHIP 2026 Shared Task 1, which aims to promote the development of methods for patient-specific phenotype concept recognition from full-text biomedical literature. The task consists of two subtasks: full-text phenotype concept recognition and patient-specific phenotype association. For this evaluation, we used 200 annotated full-text biomedical articles from the PatientPheX dataset, containing 506 patients, 15,193 phenotype mentions, and 5,656 patient-phenotype associations. A total of 455 teams registered for the competition, with 189 and 103 valid submissions received on the Phase A and Phase B leaderboards, respectively. The best-performing system achieved an overall score of 0.7389 on the final test set, outperforming the baseline by 8.37 percentage points. The top-performing teams explored diverse approaches combining biomedical language models, large language models (LLMs), and ensemble strategies. The evaluation results highlight both the potential of these approaches and the remaining challenges in patient attribution and phenotype normalization from full-text biomedical literature. The post-evaluation phase remains open at https://tianchi.aliyun.com/competition/entrance/532512.

cs.CL↗

arXiv2026

Tool-Augmented Large Language Models for Reliable Medical Calculation from Patient Notes

Medical calculators translate raw patient observations into clinically actionable values and scores. However, applying these calculators directly to free-form patient notes requires precise variable extraction combined with the exact execution of complex formulas, scoring rules, and output conventions. Relying solely on direct large language model (LLM) prompting is unreliable in this context, as rule recall, parameter extraction, arithmetic reasoning, and formatting become entangled within a single generative step. To address these limitations, we propose a tool-augmented LLM framework for reliable medical calculation from patient notes. The framework retrieves and structures calculator specifications, generates reusable executable tools, and uses a constrained extractor to map each patient note to calculator-ready inputs. The tools then perform deterministic calculation, separating clinical language understanding from rule execution and arithmetic. Evaluated on the MedCalc-Bench dataset, our method achieves 86.73% final-answer accuracy, outperforming the one-shot prompting and supervised fine tuning-only baselines by 24.0 and 17.27 percentage points. Ablation and error analyses show that these performance gains are primarily driven by rule-grounded tool synthesis and schema-constrained extraction, whereas remaining failures are concentrated in clinical-semantic extraction and benchmark-specific output contracts. By grounding calculator logic in executable tools, the proposed approach alleviates arithmetic hallucinations and improves the computational reliability of the final clinical outputs.

cs.AI↗