Abstract
BackgroundSeveral prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.ResultsTo overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.ConclusionsparSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF.
Highlights
Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples
Genomic data are highly imbalanced toward the majority class because the single-nucleotide variants (SNVs) annotated as pathogenic represent a tiny minority of the overall genetic variation
In this article we present parSMURF, a high-performance computing tool for the prediction of pathogenic variants, designed to deal with the issues related to the inference of accurate predictions with highly unbalanced datasets
Summary
Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. In particular machine learning [3], wholegenome sequencing technologies [4,5], and large population genome sequencing projects [6, 7] play a central role for the detection of rare and common variants associated with genetic diseases and cancer [8, 9] In this context, while disease-associated variants falling in the protein-coding regions of the genome have been widely studied [10,11,12], this is not the case for disease-associated variants located in the non-coding regions of the genome, where our understanding of their impact on cis- and trans-regulation is largely incomplete. By combining different annotations into a single measure for each variant using first an ensemble of support vector machines and in the current version a fast and efficient logistic regression classifier, CADD likely represents the most used and well-known tool to predict deleterious variants [15]
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