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pyhealth

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

66

Quality

83%

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SecuritybySnyk

Passed

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SKILL.md
Quality
Evals
Security

Quality

Content

75%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

A well-structured, highly actionable body with two complete executable workflows and a genuinely well-wired six-file reference bundle. Its weaknesses are redundancy (three statements of when-to-use, two overlapping pipeline examples, a word-count Resources recap) and inlining of long-form content that the reference architecture could absorb.

Suggestions

Collapse the Quick Start and the 90-line 'Example: Complete Workflow' into one canonical pipeline, or move the extended example into a reference file such as references/training_evaluation.md.

Delete the 'Resources' recap that re-lists the six reference files with word counts — the 'Detailed Documentation' sections already provide richer navigation to the same files.

Trim 'When to Use This Skill' and the per-reference 'Key Topics' lists, which restate the frontmatter description and duplicate the 'Read when' bullets respectively.

DimensionReasoningScore

Conciseness

The body has notable redundancy — "When to Use This Skill" restates the frontmatter description, the 90-line "Complete Workflow" largely re-covers the Quick Start, and "Resources" re-lists the six reference files already documented in "Detailed Documentation" with padding like "~28,000 words". It avoids explaining concepts Claude already knows, so it is mostly efficient but clearly could be tightened, rather than noticeably verbose with vacuous explanation.

3 / 5

Actionability

Two complete, executable pipelines (Quick Start and the numbered 10-step RETAIN mortality example including inference, attention analysis, and model saving), a concrete install command ("uv pip install pyhealth"), code snippets in Best Practices, and specific troubleshooting remedies. Copy-paste-ready code covers the common cases end to end.

5 / 5

Workflow Clarity

The 5-stage pipeline is clearly sequenced and both workflows use numbered steps with effective checkpoints — validation monitoring ("monitor='pr_auc_score'"), patient-level splitting to prevent leakage, and held-out test evaluation, plus Troubleshooting error-recovery guidance. It stops short of anchor 5 because no explicit "only proceed when validation passes" feedback loop is embedded in the workflow itself.

4 / 5

Progressive Disclosure

Scored against the actual bundle: all six cited references/*.md files exist, are one level deep, and each is clearly signaled with File / Read when / Key Topics navigation, with use cases routing to the correct file. The gap against anchor 5 is that the ~495-line body still inlines substantial detail (a second full pipeline example and six worked use cases) that could itself live in reference files.

4 / 5

Total

16

/

20

Passed

Description

86%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

A strong description with explicit, concrete trigger guidance and excellent natural keyword coverage spanning datasets, coding systems, and model names. Its main weakness is that the stated actions are generic verbs while the specificity rests on domain enumeration, and the broad ML phrasing slightly raises overlap risk with general ML skills.

DimensionReasoningScore

Specificity

The actions offered are generic verbs — "developing, testing, and deploying machine learning models with clinical data" — with the specificity coming almost entirely from domain enumeration (MIMIC-III/IV, ICD, EEG, RETAIN) rather than concrete verb-object operations. This matches the anchor for naming the domain with limited concrete actions; it does not reach the level of several specific actions like "extracts text, fills forms, converts pages to images".

3 / 5

Completeness

It explicitly answers both questions: the what ("comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data") and the when via an explicit trigger clause ("This skill should be used when working with electronic health records (EHR), clinical prediction tasks..."), matching the anchor that requires both with concrete trigger phrases.

5 / 5

Trigger Term Quality

Coverage includes exactly the natural terms users would say — "EHR", "mortality, readmission, drug recommendation", "ICD, NDC, ATC", "EEG, ECG", "MIMIC-III/IV, eICU, OMOP", "RETAIN, SafeDrug, Transformer, GNN" — with synonyms and both formal ("electronic health records") and shorthand forms present. This is comprehensive natural-term coverage rather than good-with-gaps.

5 / 5

Distinctiveness Conflict Risk

The healthcare niche (MIMIC, ICD, EEG, SafeDrug) is distinct and unlikely to trigger for the wrong skill, but phrases like "implementing deep learning models... (RETAIN, SafeDrug, Transformer, GNN)" and generic ML verbs carry minor overlap risk with a general machine-learning skill. Mostly distinct with minor overlap, not a fully clean niche.

4 / 5

Total

17

/

20

Passed

Validation

87%

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 14 / 16 Passed

Validation for skill structure

CriteriaDescriptionResult

metadata_version

'metadata.version' is missing

Warning

frontmatter_unknown_keys

Unknown frontmatter key(s) found; consider removing or moving to metadata

Warning

Total

14

/

16

Passed

Repository

synthetic-sciences/openscience

Path

backend/cli/skills/biology/pyhealth/SKILL.md

Reviewed

Table of Contents

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