arXiv subjects

Matthew W. Hahn

Publications and source records attributed to Matthew W. Hahn.

3 recordsLinked to original sources

arXiv2025

On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks

Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by Bayesian and maximum likelihood search procedures based on complex models of molecular evolution. In this work we describe minimal neural network architectures that can approximate classic phylogenetic distance functions and the properties required to learn distances under a variety of molecular evolutionary models. In contrast to model-based inference (and recently proposed model-free convolutional and transformer networks), these architectures have a small computational footprint and are scalable to large numbers of taxa and molecular characters. The learned distance functions generalize well and, given an appropriate training dataset, achieve results comparable to state-of-the art inference methods.

cs.LG↗

arXiv2018

The sequencing and interpretation of the genome obtained from a Serbian individual

Recent genetic studies and whole-genome sequencing projects have greatly improved our understanding of human variation and clinically actionable genetic information. Smaller ethnic populations, however, remain underrepresented in both individual and large-scale sequencing efforts and hence present an opportunity to discover new variants of biomedical and demographic significance. This report describes the sequencing and analysis of a genome obtained from an individual of Serbian origin, introducing tens of thousands of previously unknown variants to the currently available pool. Ancestry analysis places this individual in close proximity of the Central and Eastern European populations; i.e., closest to Croatian, Bulgarian and Hungarian individuals and, in terms of other Europeans, furthest from Ashkenazi Jewish, Spanish, Sicilian, and Baltic individuals. Our analysis confirmed gene flow between Neanderthal and ancestral pan-European populations, with similar contributions to the Serbian genome as those observed in other European groups. Finally, to assess the burden of potentially disease-causing/clinically relevant variation in the sequenced genome, we utilized manually curated genotype-phenotype association databases and variant-effect predictors. We identified several variants that have previously been associated with severe early-onset disease that is not evident in the proband, as well as variants that could yet prove to be clinically relevant to the proband over the next decades. The presence of numerous private and low-frequency variants along with the observed and predicted disease-causing mutations in this genome exemplify some of the global challenges of genome interpretation, especially in the context of understudied ethnic groups.

q-bio.GN↗

arXiv2018

A new class of metrics for learning on real-valued and structured data

We propose a new class of metrics on sets, vectors, and functions that can be used in various stages of data mining, including exploratory data analysis, learning, and result interpretation. These new distance functions unify and generalize some of the popular metrics, such as the Jaccard and bag distances on sets, Manhattan distance on vector spaces, and Marczewski-Steinhaus distance on integrable functions. We prove that the new metrics are complete and show useful relationships with $f$-divergences for probability distributions. To further extend our approach to structured objects such as concept hierarchies and ontologies, we introduce information-theoretic metrics on directed acyclic graphs drawn according to a fixed probability distribution. We conduct empirical investigation to demonstrate intuitive interpretation of the new metrics and their effectiveness on real-valued, high-dimensional, and structured data. Extensive comparative evaluation demonstrates that the new metrics outperformed multiple similarity and dissimilarity functions traditionally used in data mining, including the Minkowski family, the fractional $L^p$ family, two $f$-divergences, cosine distance, and two correlation coefficients. Finally, we argue that the new class of metrics is particularly appropriate for rapid processing of high-dimensional and structured data in distance-based learning.

stat.ML↗