Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis

Project Overview:

This repository contains supplementary file, codebase and data generated for our paper titled "Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis" which is currently under peer-review in a bioinformatics conference.

Supplementary File: The supplementary file to our paper can be found here.

Code: The notebooks folder contains the following jupyter notebooks:

1. clinical_data_analysis.ipynb: Notebook for analyzing clinical data and suitable patient profile selection.
2. data_preperation.ipynb: Notebook for preprocessing data to make it suitable for Mondrian Map Visualization.
3. pathway_embeddings.ipynb: Here, we've experimented with different embedding techniques with different prompting strategies.
4. visualize_mondrian_map.ipynb: In this notebook, we've generated the Mondrian Maps in our Gliblastoma case study.

Data: All the datasets used and processed are stored in the data folder.

Flow Chart

Mondrian Map Generation

Results

Cite Us

If you find out tool useful, cite our latest preprint.

@article {AlAbir_MondrianMap,
	author = {Al Abir, Fuad and Chen, Jake Y.},
	title = {Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis},
	elocation-id = {2024.04.11.589093},
	year = {2024},
	doi = {10.1101/2024.04.11.589093},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/08/19/2024.04.11.589093},
	eprint = {https://www.biorxiv.org/content/early/2024/08/19/2024.04.11.589093.full.pdf},
	journal = {bioRxiv}
}

Contact

Reach us at jakechen@uab.edu or fuad021@uab.edu.

License

Mondrian Map codebase is under MIT license.