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torchdrug-english

PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, and retrosynthesis. If you need pretrained models and diverse feature extractors, use deepchem; if you need benchmark datasets, use pytdc.

59

Quality

74%

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tessl review fix ./scientific-skills/Data Analysis/TorchDrug-English/SKILL.md
SKILL.md
Quality
Evals
Security

Quality

Content

60%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.

The substantive core (Overview, Getting Started, Core Capabilities, Common Workflows) is well structured with an executable quick example, concrete API guidance, and well-signaled one-level-deep references. It is dragged down by roughly 55 lines of auto-generated template boilerplate at the top — filler "When to Use" bullets, a vacuous "Key Features" section, a packaging-noise "Example Usage" block, and a broken "See `## Overview` above" forward reference.

Suggestions

Delete the template filler sections (the boilerplate "When to Use" bullets, "Key Features", "Dependencies", "Example Usage" block, and "Implementation Details") — they carry no TorchDrug-specific information and consume a third of the body.

Remove or fix the dangling "See `## Overview` above for related details" line, which points forward to a section defined below it.

Link core_concepts.md from the body (e.g., in Core Capabilities) and use full paths like `references/molecular_property_prediction.md` in the "Reference:" lines so navigation is unambiguous.

DimensionReasoningScore

Conciseness

Roughly the first third of the body is template boilerplate: generic filler bullets ("Use this skill when a data analytics task needs a packaged method instead of ad-hoc freeform output", "Structured execution path designed to keep outputs consistent and reviewable"), an auto-generated "Example Usage" block ("Skill directory: 20260316/... No packaged executable script was detected"), and a "Dependencies" section that adds no information. "See `## Overview` above for related details" even references a section defined below it. The substantive half (Overview through Common Workflows) is efficient, so this is not a 1.

2 / 5

Actionability

The Quick Example is complete, executable training code (datasets.BBBP, models.GIN, tasks.PropertyPrediction, full optimization loop) and the workflows name concrete API calls (KnowledgeGraphCompletion, negative sampling, scaffold split). Not a 5 because the three workflows remain step-level descriptions rather than copy-paste-ready code.

4 / 5

Workflow Clarity

Each workflow has a clear ordered sequence (load dataset, choose model, define task, train, evaluate) with an evaluation endpoint as the checkpoint, plus navigation lines into reference files. Not a 5: no expected metric values, convergence checks, or error-recovery loops; no destructive/batch validation cap applies.

4 / 5

Progressive Disclosure

The body acts as an overview with seven named reference files, all verified to exist one level deep in references/ and substantive. Not a 5: the "Reference: See X.md" lines omit the references/ path and are not links, and core_concepts.md exists in the bundle but is never referenced from the body.

4 / 5

Total

14

/

20

Passed

Description

78%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: it names the domain, lists several concrete capabilities, provides task-based when-guidance, and explicitly disambiguates against deepchem and pytdc. The main gaps are a missing explicit "Use when..." clause and some natural synonym terms.

Suggestions

Add an explicit "Use when..." clause with concrete trigger phrases (e.g., "Use when training GNNs on molecular or protein data, predicting molecular properties, or planning retrosynthesis routes") to strengthen the when-guidance.

Include common user-facing synonyms such as "molecules", "SMILES", and "molecular property prediction" so the description triggers on natural phrasing users actually type.

DimensionReasoningScore

Specificity

Names the domain and several concrete capabilities ("building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning", "protein property prediction, and retrosynthesis"), but coverage has minor gaps — molecular generation, dataset tooling, and binding prediction only appear in the body.

4 / 5

Completeness

The "what" is explicit ("PyTorch-native Graph Neural Network framework for molecules and proteins") and a "when" is present via "Best for custom model development, protein property prediction, and retrosynthesis". The when-guidance is concrete but lacks the explicit "Use when..." phrasing of a top score.

4 / 5

Trigger Term Quality

Contains natural terms users would say: "GNN", "graph neural network", "drug discovery", "protein modeling", "knowledge graph reasoning", "retrosynthesis", "pretrained models", "benchmark datasets". Missing common synonyms and variations such as "molecules", "SMILES", or "molecular property prediction".

4 / 5

Distinctiveness Conflict Risk

Explicitly differentiates from adjacent skills — "If you need pretrained models and diverse feature extractors, use deepchem; if you need benchmark datasets, use pytdc" — carving out a clear niche with minimal conflict risk.

5 / 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

frontmatter_unknown_keys

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

Warning

referenced_paths_exist

Referenced path issues: 2 missing

Warning

Total

14

/

16

Passed

Repository
aipoch/medical-research-skills
Reviewed

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