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torchdrug

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.

90

1.18x
Quality

71%

Does it follow best practices?

Impact

94%

1.18x

Average score across 9 eval scenarios

SecuritybySnyk

Advisory

Suggest reviewing before use

Optimize this skill with Tessl

npx tessl skill review --optimize ./scientific-skills/torchdrug/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 its niche (PyTorch-native GNNs for molecular and protein tasks), provides explicit trigger guidance with natural domain terms, and proactively distinguishes itself from related skills (deepchem, pytdc). The description is concise yet comprehensive, covering what the skill does, when to use it, and when to prefer alternatives.

DimensionReasoningScore

Specificity

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

3 / 3

Completeness

Clearly answers both 'what' (PyTorch-native GNNs for molecules and proteins, custom model development, protein property prediction, retrosynthesis) and 'when' ('Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning'). Also includes explicit differentiation guidance for when NOT to use it.

3 / 3

Trigger Term Quality

Includes strong natural keywords users would say: 'graph neural networks', 'GNN', 'molecules', 'proteins', 'drug discovery', 'protein modeling', 'knowledge graph reasoning', 'retrosynthesis', 'PyTorch'. These are terms domain practitioners naturally use.

3 / 3

Distinctiveness Conflict Risk

Highly distinctive with clear niche (PyTorch-native GNNs) and explicitly differentiates from related skills (deepchem for pre-trained models, pytdc for benchmark datasets), which greatly reduces conflict risk.

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 excellent progressive disclosure and navigation structure, pointing clearly to reference files for detailed content. However, it is significantly over-verbose, repeating navigation information multiple times and including sections that explain concepts Claude already knows. The workflows lack executable code and validation checkpoints, reducing their actionability for complex multi-step processes.

Suggestions

Cut the 'When to Use This Skill' section entirely or reduce to 2-3 bullet points — Claude can infer appropriate use from the content itself.

Remove the duplicate navigation in 'Common Workflows' Navigation lines, 'Quick Reference Cheat Sheet', and 'Summary' — keep only one navigation section (the cheat sheet is the best candidate).

Add executable code to at least the most common workflows (e.g., Workflow 1: Molecular Property Prediction) instead of abstract step descriptions.

Add explicit validation checkpoints to workflows, especially retrosynthesis and generation (e.g., 'Validate generated SMILES with RDKit before proceeding').

DimensionReasoningScore

Conciseness

Extremely verbose with extensive repetition. The 'When to Use This Skill' section explains things Claude already knows, the 'Core Capabilities' section duplicates information from the workflows, and the 'Quick Reference Cheat Sheet' repeats navigation already provided in each capability section. The 'Common Workflows' section restates steps that are largely obvious given the code examples. Much of this could be cut by 60%+ without losing actionable information.

1 / 3

Actionability

The Quick Example and Integration Patterns sections provide executable code, but the five Common Workflows are described as abstract step lists without executable code. The workflows say things like 'Train center identification model (RGCN)' without showing how. The Quick Example is also missing an `import torch` statement, making it not fully copy-paste ready.

2 / 3

Workflow Clarity

Workflows are listed as numbered steps but lack validation checkpoints and error recovery loops. For tasks like retrosynthesis planning and molecular generation (which involve multi-step, potentially error-prone processes), there are no explicit validation steps within the workflow sequences. The troubleshooting section partially compensates but is disconnected from the workflows themselves.

2 / 3

Progressive Disclosure

The skill excels at progressive disclosure with a clear overview structure pointing to well-organized reference files one level deep. Each capability section has a concise summary followed by explicit 'Reference: See references/X.md for:' pointers with bullet points describing what each file contains. The Quick Reference Cheat Sheet provides excellent navigation.

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

metadata_version

'metadata.version' is missing

Warning

Total

10

/

11

Passed

Repository
K-Dense-AI/claude-scientific-skills
Reviewed

Table of Contents

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