Clinical reasoning agents based on large language models (LLMs) aim to automate tasks such as intensive care unit (ICU) monitoring and patient state tracking from electronic health records (EHRs). Existing systems typically rely on manually curated clinical tools or skills for concepts such as sepsis detection and organ failure assessment. However, maintaining these tool libraries requires substantial expert effort, while zero-shot querying or code generation often produces inefficient and unreliable reasoning chains, especially under institution-specific clinical policies. We introduce CodeClinic, a benchmark built on MIMIC-IV for evaluating whether LLM agents can synthesize and compose reusable clinical skills instead of relying on fixed toolboxes. The benchmark contains two complementary tasks: longitudinal ICU surveillance and compositional information seeking. The longitudinal setting simulates monitoring patient trajectories with structured decisions every four hours across 25 findings and eight clinical families, while the compositional setting spans 63k instances across 259 tasks in nine domains and is stratified by compositional dependency depth to evaluate increasingly complex multi-step reasoning. We further propose an offline autoformalization pipeline that converts natural-language clinical guidelines into reusable and verified Python skill libraries through iterative LLM refinement. Compared with zero-shot code generation, the resulting libraries improve consistency while reducing per-query token usage by up to 40%.
Clinical practice guidelines (CPGs) encode diagnostic criteria, but LLM systems typically retrieve guideline text or absorb it through training rather than execute its rules. We introduce GuideSkill, an external reasoning layer that compiles disease-specific criteria into executable functions returning ordinal diagnostic-support scores. GuideSkill-Zero is initialized from guidelines, while GuideSkill-Evo uses case--diagnosis pairs to refine covered skills and add missing diagnoses. At inference, an LLM proposes a differential diagnosis, grounds the features required by each matched skill, and fuses its ranking with the executed skill scores. Across four benchmarks and four backbones, GuideSkill-Zero improves macro-average accuracy over guideline RAG by 13.45% on average. GuideSkill-Evo achieves the highest macro-average for every backbone, improves over direct inference by 18.49% relatively, and increases gold-label skill coverage from 56.5% to 99.5%. On Qwen3.5-9B, it also exceeds the strongest parameter-update baseline by 11.16% without updating the backbone. Expert evaluation further indicates that GuideSkill produces clinically sound and broadly acceptable skills, suggesting that its initialized and evolved rules are reliable and practically meaningful. These results support executable skills as a model-agnostic mechanism for combining guideline-derived procedures with case-derived diagnostic patterns.
Clinical data-science agents must transform heterogeneous longitudinal records into auditable analyses, yet existing benchmarks largely isolate medical question answering, structured-table reasoning, or generic scientific repositories. We introduce CLINLENS, a benchmark of 200 executable tasks over five linked MIMIC resources spanning structured electronic health records, notes, electrocardiograms, chest radiographs, and echocardiograms. A 4 x 5 taxonomy crosses four patient-time scopes with five analysis capabilities. Program-first reverse synthesis pairs each bounded semi-raw package with an evaluator-private reference workflow and checks required artifacts, cohort and temporal semantics, and the final answer. On a fixed 126-task suite, the strongest of 24 standardized model-scaffold configurations achieves 56.3% scope-macro STRICTPASS despite 100% EXECSUCCESS. For reference, a separately configured coding agent solves 83 of 126 tasks, while five biomedical systems adapted to GPT-4o-mini reach at most 2.9% scope-macro STRICTPASS. These results expose a substantial gap between runnable submissions and correct clinical analyses.
As LLM agents are increasingly built around reusable skills, a central challenge is no longer only whether agents can use provided skills, but whether they can generate correct, reusable, and executable skills from repositories and documents. Existing benchmarks primarily evaluate the efficacy of given skills or the ability of agents to solve downstream tasks from raw context, but they do not isolate skill generation itself as the object of study. We introduce SkillGenBench, a benchmark for evaluating skill generation pipelines under a unified and controlled protocol. In SkillGenBench, a generator receives raw corpora and produces standardized skill artifacts, which are then executed under fixed harnesses and assessed with unified evaluation procedures. The benchmark covers two generation regimes: task-conditioned generation, where a task-specific skill is synthesized after the task is revealed, and task-agnostic generation, where a reusable skill library must be distilled before downstream tasks are known. It also spans two complementary procedural sources: repository-grounded instances, where procedures are distributed across code, configuration, and scripts, and document-grounded instances, where procedures and constraints must be distilled from long-form text. We provide standardized task specifications, pinned environments, and evaluation protocols centered on deterministic execution-based checks, supplemented by auxiliary signals for diagnosis. Experiments across a range of skill-generation methods and backbones show substantial performance variation, highlight the difficulty of reusable skill distillation, and reveal distinct failure modes in skill generation from software repositories versus long-form documents. SkillGenBench establishes a reproducible testbed for studying skill generation as an independent research problem in agent systems.