Fast training on large genomics data using distributed Support Vector Machines

Abstract

The field of genomics has seen a glorious explosion of high-quality data, with tremendous strides having been made in genomic sequencing instruments and computational genomics applications meant to make sense of the data. A common use case for genomics data is to answer the question if a specific genetic signature is correlated with some disease manifestations. Support Vector Machine (SVM) is a widely used classifier in computational literature. Previous studies have shown success in using these SVMs for the above use case of genomics data. However, SVMs suffer from a widely-recognized scalability problem in both memory use and computational time. It is as yet an unanswered question if training such classifiers can scale to the massive sizes that characterize many of the genomics data sets. We answer that question here for a specific dataset, in order to decipher whether some regulatory module of a particular combinatorial epigenetic “pattern” will regulate the expression of a gene. However, the specifics of the dataset is likely of less relevance to the claims of our work. We take a proposed theoretical technique for efficient training of SVM, namely Cascade SVM, create our classifier called EP-SVM, and empirically evaluate how it scales to the large genomics dataset. We implement Cascade SVM on the Apache Spark platform and open source this implementation1. Through our evaluation, we bring out the computational cost on each application process, the way of distributing the overall workload among multiple processes, which can potentially execute on different cores or different machines, and the cost of data transfer to different cores or different machines. We believe we are the first to shed light on the computational and network costs of training an SVM on a multi-dimensional genomics dataset. We also evaluate the accuracy of the classifier result as a function of the parameters of the SVM model.