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PU Learning Toolbox

Positive-Unlabeled learning in Python -- sklearn-compatible API, 17 research paper methods, SCAR & SAR support.

Features

• 17 algorithms from recent PU learning research, all native clean-room implementations (method cards)
• sklearn-compatible API -- fit(X, y) / predict(X) / decision_function(X), works with pipelines and cross-validation
• SCAR & SAR -- constant and instance-dependent labeling mechanisms, with a data simulator
• Data profiling + recommender -- automatic quality checks, SCAR/SAR evidence, and a 7-dimension scoring recommender that picks the method for your data
• Auditable pipeline -- one-call PUPipeline (profile -> prior -> train -> PU-stratified CV -> evaluate) plus structured diagnostic reports and prior/propensity sensitivity analysis
• CLI -- pu-toolbox turns the whole pipeline into terminal commands

Quick Start

pip install pu-toolbox                # core dependencies (Python >= 3.10)
pip install "pu-toolbox[torch]"       # + PyTorch-based methods (nnPU, Dist-PU, Self-PU, ...)

Installation environments

Any Python interpreter >= 3.10 works: the package is a pure-Python universal wheel with no compiled extensions, so the interpreter source does not matter. Notes per environment:

• venv / uv (recommended): standard isolated environments, nothing special.
• System Python (python.org / Ubuntu / Homebrew): must be >= 3.10. Ubuntu 22.04+ and Debian 12+ block pip install into the system environment (PEP 668) -- create a venv instead.
• Anaconda / Miniconda: pip install pu-toolbox inside a conda env (the package is PyPI-only; conda install will not find it). If you already installed torch via conda, a plain pip install pu-toolbox (without the [torch] extra) still enables the PyTorch-based methods -- torch is an optional dependency loaded lazily.

Hello World

import numpy as np
from pu_toolbox.preprocessing import make_sar_dataset
from pu_toolbox import PUPipeline

# Synthetic PU data: some positives are labeled (1), rest are unlabeled (0)
X, y_pu, y_true, _ = make_sar_dataset(
    n_samples=1000, n_features=8, class_prior=0.3, random_state=42,
)

# One call: profile -> class prior -> train -> PU-stratified CV -> evaluate
report = PUPipeline().fit_evaluate(X, y_pu, y_true=y_true)
print(report.summary())

Full docs (Chinese): docs/README.md. More runnable examples: examples/minimal/.

Command Line

The pu-toolbox console command wraps the full pipeline. Full guide: docs/user/howto/cli.md.

# 1. Generate SCAR demo data (X.csv / y_pu.csv / y_true.csv)
pu-toolbox make-demo-data --out-dir demo/ --n 200 --seed 42

# 2. One-shot full pipeline run (auto mode picks the algorithm)
pu-toolbox run --data demo/X.csv --labels demo/y_pu.csv --out-dir results/

# 3. Inspect results
#    results/report.md     full Markdown report
#    results/report.json   strict JSON (no NaN), machine-readable

Documentation

Docs are split by audience; the full index is docs/README.md.

AI workflow skill

pu-workflow (Agent Skills open standard) drives the full PU analysis workflow — profiling, assumption diagnosis, method recommendation, training, and result interpretation — from natural language. Loaded natively by Claude Code / Cursor (.claude/skills/) and Codex / Gemini CLI / Windsurf (.agents/skills/).

Development

git clone https://github.com/shuidisjtu/pu-learning-toolbox.git
cd pu-learning-toolbox
pip install -e ".[dev,torch]"   # development install
uv run pytest tests/ -v -m "not slow and not e2e"   # fast tests (e2e runs nightly)
uv run ruff check pu_toolbox/               # lint
uv run ruff format --check pu_toolbox/      # format check

# Quality gates
uv run python scripts/check_test_quality.py
uv run python scripts/check_doc_links.py
uv run python scripts/check_project_metadata.py
uv run python scripts/check_math_rendering.py
uv run python scripts/check_skill_sync.py
uv run python scripts/check_format.py        # ruff check + format --check (full scope)

See CONTRIBUTING.md for contribution guidelines.

License

MIT