Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

A Proximity-Aware Hierarchical Clustering of Faces

In this paper, we propose an unsupervised face clustering algorithm called "Proximity-Aware Hierarchical Clustering" (PAHC) that exploits the local structure of deep representations. In the proposed method, a similarity measure between deep features is computed by evaluating linear SVM margins. SVMs are trained using nearest neighbors of sample data, and thus do not require any external training data. Clusters are then formed by thresholding the similarity scores. We evaluate the clustering performance using three challenging unconstrained face datasets, including Celebrity in Frontal-Profile (CFP), IARPA JANUS Benchmark A (IJB-A), and JANUS Challenge Set 3 (JANUS CS3) datasets. Experimental results demonstrate that the proposed approach can achieve significant improvements over state-of-the-art methods. Moreover, we also show that the proposed clustering algorithm can be applied to curate a set of large-scale and noisy training dataset while maintaining sufficient amount of images and their variations due to nuisance factors. The face verification performance on JANUS CS3 improves significantly by finetuning a DCNN model with the curated MS-Celeb-1M dataset which contains over three million face images

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing