An explainer for Chemprop based on LIME and PathExplain.
Project description
Chemexp
A Chemprop explainer based on LIME and PathExplain.
Installation
- Make sure your Python version is >= 3.8
conda
is required for ChemProp. If it is not installed on your machine, you can take a look at miniconda
- Install Chemprop
- Then simply run
pip install chemexp
- You're good to go!
Explanation
Using Python
import chemexp
from chemprop.utils import load_checkpoint
model = chemexp.ExplanationModel(load_checkpoint("models/fusion_db_1.pt"))
exp = model.explain_molecule("COC(=N)Cc1ccccc1")
chemexp.exp_to_png(exp, "mol.png")
A little more detail is available in test/test.py.
Web interface
Although you can use this Python module in your scripts, you can also experiment a user-friendly interface.
⚠️ Warning: this only works on Linux for the moment (this is due to the linux-specific paths used to save some files, but it can be adapted for Windows or Mac).
Use the following command to run the web server:
python -m chemexp <path>
where path
is a folder containing chemprop models / checkpoints (.pt files)
Authors
- BELLANGER Clément
- BERNIER Fabien
- MAIGRET Bernard
- NAPOLI Amedeo
To cite our work:
@mastersthesis{bernier:hal-03371070,
TITLE = {{A Study about Explainability and Fairness in Machine Learning and Knowledge Discovery}},
AUTHOR = {Bernier, Fabien},
URL = {https://hal.inria.fr/hal-03371070},
PAGES = {58},
SCHOOL = {{TELECOM Nancy}},
YEAR = {2021},
MONTH = Sep,
KEYWORDS = {machine learning ; explainability ; fairness ; antibiotic classification ; machine learning ; explicabilit{\'e} ; fairness ; classification antibiotique},
PDF = {https://hal.inria.fr/hal-03371070/file/M_moire_ing_nieur_Fabien.pdf#chapter.5},
HAL_ID = {hal-03371070},
HAL_VERSION = {v1},
}
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
chemexp-0.2.4.tar.gz
(66.8 kB
view hashes)
Built Distribution
chemexp-0.2.4-py3-none-any.whl
(69.9 kB
view hashes)