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Add to EdgeMycorrhiza: Genotype Assignment usingPhylogenetic Networks
Oct 14, 2020
Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.
Generative Adversarial Networks Applied to Observational Health Data
May 28, 2020
Having been collected for its primary purpose in patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics. However, the potential for secondary usage of OHD continues to be hampered by the fiercely private nature of patient-related data. Generative Adversarial Networks (GAN) have Generative Adversarial Networks (GAN) have recently emerged as a groundbreaking approach to efficiently learn generative models that produce realistic Synthetic Data (SD). However, the application of GAN to OHD seems to have been lagging in comparison to other fields. We conducted a review of GAN algorithms for OHD in the published literature, and report our findings here.