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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.

76

Quality

71%

Does it follow best practices?

Impact

Pending

No eval scenarios have been run

SecuritybySnyk

Passed

No known issues

Optimize this skill with Tessl

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

Quality

Discovery

100%

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

This is an excellent skill description that clearly defines the tool's capabilities, domain, and use cases with specific trigger terms. It excels at distinctiveness by explicitly differentiating itself from related skills (deepchem, pytdc), helping Claude make the right selection. The only minor note is that it lacks a formal 'Use when...' clause, but the 'Best for...' and 'Suitable for...' phrasing effectively serves the same purpose.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions and use cases: 'building custom GNN architectures', 'drug discovery', 'protein modeling', 'knowledge graph reasoning', 'custom model development', 'protein property prediction', and 'retrosynthesis'.

3 / 3

Completeness

Clearly answers 'what' (PyTorch-native GNN framework for molecules and proteins, building custom GNN architectures) and 'when' ('Best for custom model development, protein property prediction, and retrosynthesis'). It also provides explicit negative triggers distinguishing from deepchem and pytdc, which serves as 'when not to use' guidance.

3 / 3

Trigger Term Quality

Includes strong natural keywords users would say: 'PyTorch', 'Graph Neural Network', 'GNN', 'molecules', 'proteins', 'drug discovery', 'protein modeling', 'knowledge graph', 'retrosynthesis', 'protein property prediction'. These cover a wide range of natural terms a user in this domain would use.

3 / 3

Distinctiveness Conflict Risk

Highly distinctive with explicit differentiation from related skills (deepchem for pretrained models, pytdc for benchmark datasets). The niche of PyTorch-native GNN for molecular/protein modeling is very specific and unlikely to conflict with other skills.

3 / 3

Total

12

/

12

Passed

Implementation

42%

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

The skill has good structural organization with clear progressive disclosure to reference files, and provides a reasonable executable quick-start example. However, it is severely bloated by redundant boilerplate sections (duplicate 'When to Use', generic 'Key Features', templated 'Implementation Details') that waste tokens without adding value. The workflows lack validation checkpoints and executable code, reducing their practical utility.

Suggestions

Remove the entire boilerplate top section (first 'When to Use', 'Key Features', 'Dependencies', 'Example Usage', 'Implementation Details') which is generic template filler that adds no TorchDrug-specific value.

Add executable code snippets to the Common Workflows section instead of descriptive bullet points — e.g., show actual scaffold splitting, evaluation calls, and knowledge graph querying code.

Add validation checkpoints to workflows: verify dataset loading succeeded (print dataset size), check training loss is decreasing, validate model predictions on test set with explicit metric thresholds.

Fix the Quick Example to use torchdrug's proper data utilities (e.g., `torchdrug.data.DataLoader`) instead of PyTorch's generic DataLoader, which won't properly collate graph batches.

DimensionReasoningScore

Conciseness

The skill is extremely verbose with significant redundancy. The 'When to Use' section appears twice with overlapping content, 'Key Features' restates the description, 'Implementation Details' is generic boilerplate, and there's extensive padding with generic meta-instructions ('validate the request, choose the packaged workflow') that add no value. The top half of the file is templated filler that Claude doesn't need.

1 / 3

Actionability

The Quick Example provides executable Python code for molecular property prediction, and installation commands are concrete. However, the Common Workflows sections are descriptive rather than executable (listing steps as bullet points without code), and the training loop in the quick example may not be fully functional without proper collation handling for graph batches (should use torchdrug's DataLoader or a collate function).

2 / 3

Workflow Clarity

The Common Workflows section provides clear step sequences for three scenarios, but lacks validation checkpoints entirely. There's no guidance on verifying model convergence, checking data loading success, or validating outputs. For scientific model training workflows, missing validation/verification steps (e.g., checking loss convergence, validating predictions) is a notable gap.

2 / 3

Progressive Disclosure

The skill effectively uses progressive disclosure by providing concise overviews of each capability area and pointing to specific reference files (molecular_property_prediction.md, protein_modeling.md, knowledge_graphs.md, etc.) for detailed guidance. References are one level deep and clearly signaled with 'Reference: See X.md' patterns.

3 / 3

Total

8

/

12

Passed

Validation

90%

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

Validation10 / 11 Passed

Validation for skill structure

CriteriaDescriptionResult

frontmatter_unknown_keys

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

Warning

Total

10

/

11

Passed

Repository
aipoch/medical-research-skills
Reviewed

Table of Contents

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