Network propagation

Network propagation-based link prediction methods implemented in Python.

PRINCE and MINProp are available.

Requirements

Python 3.9

pip install -r requirements.txt

Network data

• Human protein-protein interaction network form HIPPIE (Human Integrated Protein-Protein Interaction rEference)
• Phenotypic disease similarity (zipped) from PRINCE Plugin
• OMIM disease-gene associations from PRINCE Plugin

Usage

Download and pickle the network data.

python download_pickle_data.py

PRINCE (PRIoritizatioN and Complex Elucidation)

Vanunu O, Magger O, Ruppin E, Shlomi T, Sharan R (2010) Associating Genes and Protein Complexes with Disease via Network Propagation. PLoS Comput Biol 6(1): e1000641. doi:10.1371/journal.pcbi.1000641

Usage

Protein-disease association prediction.

python run_prince.py --alpha 0.5

MINProp (Mutual Interaction-based Network Propagation)

Hwang TH, Kuang R (2010) A Heterogeneous Label Propagation Algorithm for Disease Gene Discovery. in Proceedings of the 2010 SIAM International Conference on Data Mining, 583-594. doi:10.1137/1.9781611972801.51

Usage

General

See example_minprop.py for the usage of the MINProp-related functions.

Example

Protein-disease association prediction using 2 homo subnetworks: the protein-protein interaction network and disease similarity network.

python run_minprop_PD.py --alphaP 0.15 --alphaD 0.05 --eps 0.01