When SMILES have Language: Drug Classification using Text Classification Methods on Drug SMILES Strings

Authors: Azmine Toushik Wasi, Šerbetar Karlo, Raima Islam, Taki Hasan Rafi, Dong-Kyu Chae
Accepted (invited to present) to the The Second Tiny Papers Track at ICLR 2024!
Read full paper in arXiv.

Abstract: Complex chemical structures, like drugs, are usually defined by SMILES strings as a sequence of molecules and bonds. These SMILES strings are used in different complex machine learning-based drug-related research and representation works. Escaping from complex representation, in this work, we pose a single question: What if we treat drug SMILES as conventional sentences and engage in text classification for drug classification? Our experiments affirm the possibility with very competitive scores. The study explores the notion of viewing each atom and bond as sentence components, employing basic NLP methods to categorize drug types, proving that complex problems can also be solved with simpler perspectives.

Setup and run

Data is available at ./Model/_DATA_
Dataloader is available at ./Model/data
To run the training script, place the dataset from DrugBank, go to ./Model/ folder and run: python train-ngram.py
To change parameters, you can check and edit 145-165 no lines of ./Model/train-ngram.py

Experimental Results

Model	Accuracy	Precision	Recall	F1 (Weighted)	F1 (Macro)	ROC-AUC
1-gram+MLP	0.622	0.610	0.622	0.604	0.406	0.760
2-gram+MLP	0.669	0.700	0.669	0.672	0.445	0.810
3-gram+MLP	0.737	0.764	0.737	0.744	0.553	0.848
4-gram+MLP	0.726	0.758	0.726	0.731	0.524	0.841
5-gram+MLP	0.728	0.740	0.728	0.730	0.563	0.838
AtomPair+MLP	0.799	0.804	0.800	0.799	0.702	0.876
MACCS+MLP	0.797	0.801	0.797	0.796	0.702	0.873
Morgan+MLP	0.800	0.804	0.800	0.799	0.703	0.876

Citation

@inproceedings{wasi2024drug_nlp,,
  author       = {Azmine Toushik Wasi and Šerbetar Karlo and Raima Islam and Taki Hasan Rafi and Dong-Kyu Chae},
  title        = {When SMILES have Language: Drug Classification using Text Classification Methods on Drug SMILES Strings},
  booktitle    = {The Second Tiny Papers Track at {ICLR} 2024, Tiny Papers @ {ICLR} 2024, Vienna Austria, May 11, 2024},
  publisher    = {OpenReview.net},
  year         = {2023},
  url          = {https://openreview.net/forum?id=VUYCyH8fCw}
}