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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.

58

Quality

67%

Does it follow best practices?

Impact

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, target use cases, and explicitly differentiates itself from related skills (deepchem, pytdc). It uses domain-appropriate terminology that users would naturally employ, and provides both positive and negative selection criteria. The only minor note is it lacks a formal 'Use when...' clause, but the 'Best for...' and 'If you need...' constructions serve the same purpose effectively.

DimensionReasoningScore

Specificity

Lists multiple specific concrete actions and use cases: 'building custom GNN architectures', 'drug discovery', 'protein modeling', 'knowledge graph reasoning', 'protein property prediction', and 'retrosynthesis'. These are concrete, domain-specific capabilities.

3 / 3

Completeness

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

3 / 3

Trigger Term Quality

Includes strong natural keywords users would say: 'Graph Neural Network', 'GNN', 'molecules', 'proteins', 'drug discovery', 'protein modeling', 'knowledge graph reasoning', 'retrosynthesis', 'PyTorch'. These cover the domain well and match how practitioners would phrase requests.

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

35%

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

The skill contains useful domain-specific content about TorchDrug's capabilities, datasets, and models, but is severely undermined by extensive generic boilerplate in the first half that adds no value. The actionable code is limited to one quick example, while the workflow sections remain descriptive rather than executable. Significant redundancy (repeated descriptions, two 'When to Use' sections) wastes token budget.

Suggestions

Remove the entire generic boilerplate section (When to Use with generic bullets, Key Features, Dependencies, Example Usage with 'no packaged script' text, Implementation Details) — these add no TorchDrug-specific value and waste ~40% of the token budget.

Add executable code examples for each Common Workflow instead of descriptive bullet points — e.g., show actual code for protein function prediction and knowledge graph reasoning, not just component names.

Add validation checkpoints to workflows: e.g., 'Verify dataset loaded correctly: print(len(train_set))', 'Check model output shape before training', 'Validate AUROC > 0.5 baseline before proceeding'.

Consolidate the two 'When to Use' sections into a single concise section that focuses on decision criteria (when TorchDrug vs DeepChem vs PyTDC).

DimensionReasoningScore

Conciseness

The skill is extremely verbose with significant redundancy. The 'When to Use' section repeats the description nearly verbatim, 'Key Features' restates the description again, and there are two separate 'When to Use' sections. The 'Implementation Details' and 'Example Usage' sections contain generic boilerplate that adds no TorchDrug-specific value. Much of the content explains concepts Claude already knows.

1 / 3

Actionability

The Quick Example provides executable Python code for molecular property prediction, which is good. However, the Common Workflows sections are descriptive bullet points rather than executable code, and the training loop in the quick example may not be fully correct (the task(batch) call pattern depends on TorchDrug's actual API). Most capability sections just list components without showing how to use them.

2 / 3

Workflow Clarity

The Common Workflows section provides sequenced steps for three scenarios, but they lack validation checkpoints, error handling, and feedback loops. There's no guidance on what to do if training fails, how to verify model quality, or how to validate inputs. For a framework involving model training and molecular data processing, missing validation steps are a significant gap.

2 / 3

Progressive Disclosure

The skill references multiple files in references/ (molecular_property_prediction.md, protein_modeling.md, knowledge_graphs.md, etc.) which is good structure, but no bundle files are provided to verify these exist. The main SKILL.md itself is too long with inline content that could be in reference files, and the first half is generic boilerplate that obscures the useful content in the second half.

2 / 3

Total

7

/

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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