Metadata-Version: 2.4
Name: EDKG-DL
Version: 1.0.1
Summary: Deep Learning framework with causality-integrated Endocrine Disruption Knowledge Graph
Author-email: haoyuejudy <njutanhaoyue@nju.edu.cn>
License-Expression: LicenseRef-Custom-Academic-Research
Project-URL: Homepage, https://edkgdl.com/
Project-URL: Repository, https://github.com/haoyuejudy/EDKG-DL
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: huggingface-hub>=0.32
Requires-Dist: joblib>=1.5.1
Requires-Dist: networkx>=3.1
Requires-Dist: numpy<3,>=1.26
Requires-Dist: padelpy>=0.1.16
Requires-Dist: pandas>=2.0
Requires-Dist: platformdirs>=4.3
Requires-Dist: requests>=2.31
Requires-Dist: scikit-learn>=1.6.1
Requires-Dist: torch>=2.0.0
Requires-Dist: torch-geometric>=2.4
Requires-Dist: xgboost>=3.0.2
Requires-Dist: xlsxwriter>=3.1
Provides-Extra: api
Requires-Dist: fastapi[standard]>=0.115; extra == "api"
Provides-Extra: plots
Requires-Dist: matplotlib>=3.8; extra == "plots"
Dynamic: license-file

# EDKG-DL

English | [简体中文](https://github.com/haoyuejudy/EDKG-DL/blob/main/README_zh.md)

**D**eep **L**earning framework with causality-integrated **E**ndocrine **D**isruption **K**nowledge **G**raph. Predicts endocrine-disrupting effects (EDC), applicability domain (AD), and sensitive event pathways from compound SMILES using machine learning and an AOP network.

Pipeline: PaDEL 2D descriptors/fingerprints → qualitative/quantitative event-endpoint models → dual-track EDC classification (tabular model + graph neural network, GCN) → sensitive event and AOP pathway inference, producing JSON / Excel reports. Results are for research support only and must not replace experimental or regulatory conclusions.

## Installation

Install from PyPI (Python ≥ 3.10):

```bash
pip install edkg-dl
# or
uv add edkg-dl
```

Optional extras: `pip install "edkg-dl[api]"` (HTTP service) and `pip install "edkg-dl[plots]"` (applicability-domain plots). See [installation docs](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/installation.md) for details, including the automatic Temurin JRE download for PaDEL.

Model assets (~930 MB) are fetched automatically from [Hugging Face](https://huggingface.co/HaoyueTan/edkg-dl-models) on first use — no manual setup required.

## Quick start

CLI:

```bash
edkg-dl-predict "CCO"                                   # JSON to stdout
edkg-dl-predict "CCO" -o runs/example --ad-plots        # reports + PCA plots
edkg-dl-predict batch molecules.txt -o runs/batch       # batch from a text file
```

Python:

```python
from edkg_dl import Predictor

predictor = Predictor.from_assets("./models")
result = predictor.predict("CCO")
```

## Documentation

| Topic | Link |
| --- | --- |
| Installation | [installation.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/installation.md) |
| Model assets | [assets.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/assets.md) |
| CLI usage | [cli.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/cli.md) |
| Python API | [python-api.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/python-api.md) |
| HTTP API | [http-api.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/http-api.md) |
| Output formats | [output.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/output.md) |
| Development | [development.md](https://github.com/haoyuejudy/EDKG-DL/blob/main/docs/en/development.md) |
