Phenotype Prediction from Metagenomic Data Using Clustering and Assembly with Multiple Instance Learning (CAMIL)

• Published in: IEEE/ACM transactions on computational biology and bioinformatics 2020-05, Vol.17 (3), p.828-840
• Main Authors: Rahman, Mohammad Arifur, LaPierre, Nathan, Rangwala, Huzefa
• Format: Article
• Language: English
• Subjects: Algorithms; Assembly; Canopies; canopy; Classifiers; Cluster Analysis; Clustering; Computer applications; Diabetes mellitus; Diseases; Feature extraction; Genomics; Genotype & phenotype; Humans; Labels; Learning; LSH; Machine Learning; Metagenome; Metagenome - genetics; Metagenomics; Metagenomics - methods; Microorganisms; multiple instance learning; Phenotype; Phenotypes; Pipelines; Sequential analysis; Support vector machines
• ISSN: 1545-5963; 1557-9964
• DOI: 10.1109/TCBB.2017.2758782

The recent advent of Metagenome Wide Association Studies (MGWAS) provides insight into the role of microbes on human health and disease. However, the studies present several computational challenges. In this paper, we demonstrate a novel, efficient, and effective Multiple Instance Learning (MIL) based computational pipeline to predict patient phenotype from metagenomic data. MIL methods have the advantage that besides predicting the clinical phenotype, we can infer the instance level label or role of microbial sequence reads in the specific disease. Specifically, we use a Bag of Words method, which has been shown to be one of the most effective and efficient MIL methods. This involves assembly of the metagenomic sequence data, clustering of the assembled contigs, extracting features from the contigs, and using an SVM classifier to predict patient labels and identify the most relevant sequence clusters. With the exception of the given labels for the patients, this entire process is de novo (unsupervised). We call our pipeline "CAMIL", which stands for Clustering and Assembly with Multiple Instance Learning. We use multiple state-of-the-art clustering methods for feature extraction, evaluation, and comparison of the performance of our proposed approach for each of these clustering methods. We also present a fast and scalable pre-clustering algorithm as a preprocessing step for our proposed pipeline. Our approach achieves efficiency by partitioning the large number of sequence reads into groups (called canopies) using locality sensitive hashing (LSH). These canopies are then refined by using state-of-the-art sequence clustering algorithms. We use data from a well-known MGWAS study of patients with Type-2 Diabetes and show that our pipeline significantly outperforms the classifier used in that paper, as well as other common MIL methods.