A Python toolkit and dataset registry for machine-learning research on medicines and treatments. PyTDC helps discover approved therapeutic datasets, load them, split them for different testing situations, and measure model results.

It helps find datasets, use scaffold, cold-start, temporal, or combination splits, evaluate predictions, work with benchmark groups, and run limited molecular-oracle experiments.

It reduces confusion about which datasets and evaluation methods fit a therapeutic prediction task. It also records environment constraints needed for reproducible runs.

pytdc — Skill for Claude Code by K-Dense-AI

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add K-Dense-AI/drug-discovery-agent-skills --skill pytdc

Clone the repo

git clone --depth 1 https://github.com/K-Dense-AI/drug-discovery-agent-skills

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/k-dense-ai/drug-discovery-agent-skills/pytdc/github.svg)](https://agentmods.dev/skills/k-dense-ai/drug-discovery-agent-skills/pytdc)

Your own site

<a href="https://agentmods.dev/skills/k-dense-ai/drug-discovery-agent-skills/pytdc"><img src="https://agentmods.dev/badge/skills/k-dense-ai/drug-discovery-agent-skills/pytdc/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/k-dense-ai/drug-discovery-agent-skills/pytdc"><img src="https://agentmods.dev/badge/skills/k-dense-ai/drug-discovery-agent-skills/pytdc.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 150 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,485 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector pass 7 Sept 2026

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00150	$0.03485
Opus 5	$0.00075	$0.01742
Sonnet 5	$0.00030	$0.00697
Haiku 4.5	$0.00015	$0.00348

Measured 12d ago against content hash 38a388d83d60, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

pytdc scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 12d ago.

The scan reads SKILL.md. This mod also ships 6 executable files (scripts/_common.py, scripts/benchmark_evaluation.py, scripts/cache_audit.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/pytdc/SKILL.md · 315 lines

How it starts

The opening of the file, as written. The whole thing — 315 lines — stays where its author put it; the contents beside it link to each section on GitHub.

PyTDC (Therapeutics Data Commons)

Use the official PyTDC distribution (import tdc) to discover therapeutic ML tasks, load approved datasets, apply task-appropriate splits, evaluate predictions, and work with curated benchmark groups. Prefer package metadata over copied dataset lists, and plan network/storage effects before constructing any loader.

Verified snapshot

Research date: 2026-07-23
PyPI stable: PyTDC 1.1.15, released 2025-03-31
Package/source repository: mims-harvard/TDC
Code license: MIT
PyPI supplies only a source distribution and declares no Requires-Python
The dependency graph makes CPython 3.11 the reproducible target used here: cellxgene-census==1.15.0 excludes Python 3.12, and PyTDC's constrained RDKit release has no CPython 3.13 wheel
PyTDC imports deprecated pkg_resources at runtime. Setuptools 82 removed that module; pin the verified compatibility release setuptools 80.9.0.
tdc.readthedocs.io still identifies itself as TDC 0.4.1; use it as API cross-reference, not as release-version evidence
Upstream publishes no GitHub tags/releases or maintained changelog. Treat undocumented migration claims as uncertainty and verify against the installed 1.1.15 source/metadata.

See references/sources.md for dated evidence and known documentation conflicts.

Installation

Use an isolated CPython 3.11 environment and pin the reviewed snapshot:

uv venv --python 3.11 .venv-pytdc
uv pip install --dry-run --python .venv-pytdc/bin/python \
  "setuptools==80.9.0" "PyTDC==1.1.15"
uv pip install --python .venv-pytdc/bin/python \
  "setuptools==80.9.0" "PyTDC==1.1.15"

The tested macOS ARM64 resolution installed 123 packages, including large scientific/ML dependencies, so the environment itself can transfer and occupy hundreds of megabytes before any dataset is downloaded. Review the dry run and available disk first. The direct pins identify the reviewed API snapshot; generate a platform-specific uv.lock in the user's project when every transitive version must also be frozen.

Read the full file on GitHub · 315 lines

Files

What ships with it

10 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

12d ago First seen · 315 lines · 150 tokens per session scan A 38a388d83d60

Subscribe to this mod's changes

pytdc is a skill published in the GitHub repository K-Dense-AI/drug-discovery-agent-skills (28 stars, last pushed 5d ago), licensed MIT. It adds 150 tokens to every session and 3,485 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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