HP-GAS: prediction of Human Protein protein interactions based on automatic feature engineering and Genetic Algorithm driven Stacking method

HP-GAS is a software for prediction of human protein protein interactions based on graph, evolutionary and sequence features, and automatic feature engineering which utilizes genetic algorithm (GA) and automatic correlation based selection. HP-GAS uses the ensemble of models generated by machine learning (ML) algorithms as a method for PPI prediction, where automatic ensembling of ML algorithms was driven by supervized GA and unsupervized correlation filtering.

HP-GAS software was written in JAVA language and is available as standalone application, which can be executed on any operating system containing Java Virtual Machine. Minimum system requirements for HP-GAS are: RAM 1 GB; Disk space 1 GB.

In order to run the HP-GAS program it is necessary to install Java Runtime Environment 8 (JRE), which can be found for Windows, Linux, Mac OS and Solaris systems at: Java SE Runtime Environment 8 - Downloads

Please read the documentation for detailed information about the HP-GAS software and it's usage.

HP-GAS is a free software released under Apache License, Version 2.0.

HP-GAS application with required files and documentation is provided bellow.

Type	Filename	Size	Downloads	Link
Binaries	HP-GAS_Binaries.zip	697 MB	952
Documentation	HP-GAS_Manual.pdf	297 KB	14879
Sequences	HP-GAS_Sequences.zip	5.74 MB	907
Datasets	HP-GAS_Datasets.zip	76.75 MB	946
Supplementary data	HP-GAS_Supplements.zip	2.24 MB	859

The HP-GAS_Sequences.zip file contains 15,650 human sequences, with UniProt identifiers and entrynames in FASTA format, for which the predictions can be calculated.


If using HP-GAS, please cite:
Sumonja N, Gemovic B, Veljkovic N, Perovic V. (2019) Automated feature engineering improves prediction of protein-protein interactions. Amino Acids. DOI:10.1007/s00726-019-02756-9.