This repository is a part of the EU-funded RECeSS project (#101102016), and hosts the code for the open-source Python package JELI for the collaborative filtering approach.
Interpretability is a topical question in recommender systems, especially in healthcare applications. In drug repurposing, the goal is to identify novel therapeutic indications as drug-disease pairs. An interpretable drug repurposing algorithm quantifies the importance of each input feature for the predicted therapeutic drug-disease association in a non-ambiguous fashion, using post hoc methods. Unfortunately, different importance score-based approaches lead to different results, yielding unreliable interpretations.
We introduce the novel Joint Embedding Learning-classifier for improved Interpretability (JELI). It features a new structured recommender system and trains it jointly on a drug-disease-gene knowledge graph completion task. In particular, JELI simultaneously (a) learns the gene, drug, and disease embeddings; (b) predicts new drug-disease associations based on those embeddings; (c) provides importance scores for each gene. The drug and disease embeddings have a structure that depends on the gene embeddings. Therefore, JELI allows the introduction of graph-based priors on the connections between diseases, drugs, and genes in a generic fashion to recommend and argue for novel therapeutic drug-disease associations.
Contrary to prior works, the recommender system explicitly includes the importance scores, strengthening the link between the recommendations and the extracted scores while allowing the use of a generic embedding model. The recommendation strategy in JELI can also be readily applied beyond the task of drug repurposing for any sets of items, users, and features.
pip install jeli#Build Docker image
docker build -t jeli .
#Run Docker image built in previous step and drop into SSH
docker run -it --expose 3000 -p 3000:3000 jeliOS: developed and tested on Debian Linux.
The complete list of dependencies for JELI can be found at requirements.txt (pip).
from jeli.JELI import JELI
from stanscofi.utils import load_dataset
from stanscofi.training_testing import random_simple_split
import pandas as pd
## loads the Gottlieb drug repurposing data set
data_args = load_dataset("Gottlieb", "./")
dataset = Dataset(**data_args)
## splits in training and testing sets without leakage
(train_folds, test_folds), _ = random_simple_split(dataset, 0.2, random_state=1234)
train = dataset.subset(train_folds)
test = dataset.subset(test_folds)
classifier = JELI({"cuda_on": False, "n_dimensions": 10, "random_state": 1234, "epochs": 25})
## trains JELI on the training set
classifier.fit(train)
## predicts on the testing set
scores = classifier.predict_proba(test)
classifier.print_scores(scores)
predictions = classifier.predict(scores, threshold=0.5)
classifier.print_classification(predictions)
## computes an embedding i (item/drug)
item = pd.DataFrame(dataset.items.toarray()[:,0],index=dataset.item_features,columns=["0"])
i = model.transform(item, is_item=True)
## computes an embedding u (user/disease)
user = pd.DataFrame(dataset.users.toarray()[:,0],index=dataset.user_features,columns=["0"])
u = model.transform(user, is_item=False)
## computes the feature-wise importance scores from embeddings
embs = classifier.model["feature_embeddings"]
feature_scores = embs.sum(axis=1)This repository is under an OSI-approved MIT license.
If you use JELI in academic research, please cite it as follows
Clémence Réda, Jill-Jênn Vie, Olaf Wolkenhauer. Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering. 2024. hal-04625183.
Pull requests and issue flagging are welcome, and can be made through the GitHub interface. Support can be provided by reaching out to recess-project[at]proton.me. However, please note that contributors and users must abide by the Code of Conduct.