arXiv subjects

Anthea Monod

Publications and source records attributed to Anthea Monod.

43 records · Page 3Linked to original sources

arXiv2022

Tropical Geometry of Phylogenetic Tree Space: A Statistical Perspective

Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry. Although they are important data structures, they face the significant challenge that sets of trees form a non-Euclidean phylogenetic tree space, which means that standard computational and statistical methods cannot be directly applied. In this work, we explore the statistical feasibility of a pure mathematical representation of the set of all phylogenetic trees based on tropical geometry for both descriptive and inferential statistics, and unsupervised and supervised machine learning. Our exploration is both theoretical and practical. We show that the tropical geometric phylogenetic tree space endowed with a generalized Hilbert projective metric exhibits analytic, geometric, and topological properties that are desirable for theoretical studies in probability and statistics and allow for well-defined questions to be posed. We illustrate the statistical feasibility of the tropical geometric perspective for phylogenetic trees with an example of both a descriptive and inferential statistical task. Moreover, this approach exhibits increased computational efficiency and statistical performance over the current state-of-the-art, which we illustrate with a real data example on seasonal influenza. Our results demonstrate the viability of the tropical geometric setting for parametric statistical and probabilistic studies of sets of phylogenetic trees.

math.MG↗

arXiv2022

Tropical Geometric Variation of Phylogenetic Tree Shapes

We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is given by the tree's branching configuration and leaf labeling. We use the tropical line segment as a framework to define notions of variance as well as invariance of tree topologies: we provide a combinatorial search theorem that describes all tree topologies occurring along a tropical line segment, as well as a setting under which tree topologies do not change along a tropical line segment. Our study is motivated by comparison to the moduli space endowed with a geodesic metric proposed by Billera, Holmes, and Vogtmann (referred to as BHV space); we consider the tropical geometric setting as an alternative framework to BHV space for sets of phylogenetic trees. We give an algorithm to compute tropical line segments which is lower in computational complexity than the fastest method currently available for BHV geodesics and show that its trajectory behaves more subtly: while the BHV geodesic traverses the origin for vastly different tree topologies, the tropical line segment bypasses it.

math.CO↗

arXiv2021

Curved Markov Chain Monte Carlo for Network Learning

We present a geometrically enhanced Markov chain Monte Carlo sampler for networks based on a discrete curvature measure defined on graphs. Specifically, we incorporate the concept of graph Forman curvature into sampling procedures on both the nodes and edges of a network explicitly, via the transition probability of the Markov chain, as well as implicitly, via the target stationary distribution, which gives a novel, curved Markov chain Monte Carlo approach to learning networks. We show that integrating curvature into the sampler results in faster convergence to a wide range of network statistics demonstrated on deterministic networks drawn from real-world data.

stat.ML↗

arXiv2021

Tropical Optimal Transport and Wasserstein Distances

We study the problem of optimal transport in tropical geometry and define the Wasserstein-$p$ distances in the continuous metric measure space setting of the tropical projective torus. We specify the tropical metric -- a combinatorial metric that has been used to study of the tropical geometric space of phylogenetic trees -- as the ground metric and study the cases of $p=1,2$ in detail. The case of $p=1$ gives an efficient computation of the infinitely-many geodesics on the tropical projective torus, while the case of $p=2$ gives a form for Fréchet means and a general inner product structure. Our results also provide theoretical foundations for geometric insight a statistical framework in a tropical geometric setting. We construct explicit algorithms for the computation of the tropical Wasserstein-1 and 2 distances and prove their convergence. Our results provide the first study of the Wasserstein distances and optimal transport in tropical geometry. Several numerical examples are provided.

math.OC↗

arXiv2019

Predicting Clinical Outcomes in Glioblastoma: An Application of Topological and Functional Data Analysis

Glioblastoma multiforme (GBM) is an aggressive form of human brain cancer that is under active study in the field of cancer biology. Its rapid progression and the relative time cost of obtaining molecular data make other readily-available forms of data, such as images, an important resource for actionable measures in patients. Our goal is to utilize information given by medical images taken from GBM patients in statistical settings. To do this, we design a novel statistic---the smooth Euler characteristic transform (SECT)---that quantifies magnetic resonance images (MRIs) of tumors. Due to its well-defined inner product structure, the SECT can be used in a wider range of functional and nonparametric modeling approaches than other previously proposed topological summary statistics. When applied to a cohort of GBM patients, we find that the SECT is a better predictor of clinical outcomes than both existing tumor shape quantifications and common molecular assays. Specifically, we demonstrate that SECT features alone explain more of the variance in GBM patient survival than gene expression, volumetric features, and morphometric features. The main takeaways from our findings are thus twofold. First, they suggest that images contain valuable information that can play an important role in clinical prognosis and other medical decisions. Second, they show that the SECT is a viable tool for the broader study of medical imaging informatics.

stat.AP↗

arXiv2019

Tropical Sufficient Statistics for Persistent Homology

We show that an embedding in Euclidean space based on tropical geometry generates stable sufficient statistics for barcodes. In topological data analysis, barcodes are multiscale summaries of algebraic topological characteristics that capture the `shape' of data; however, in practice, they have complex structures that make them difficult to use in statistical settings. The sufficiency result presented in this work allows for classical probability distributions to be assumed on the tropical geometric representation of barcodes. This makes a variety of parametric statistical inference methods amenable to barcodes, all while maintaining their initial interpretations. More specifically, we show that exponential family distributions may be assumed, and that likelihood functions for persistent homology may be constructed. We conceptually demonstrate sufficiency and illustrate its utility in persistent homology dimensions 0 and 1 with concrete parametric applications to human immunodeficiency virus and avian influenza data.

math.ST↗

arXiv2017

Estimating thresholding levels for random fields via Euler characteristics

We introduce Lipschitz-Killing curvature (LKC) regression, a new method to produce $(1-α)$ thresholds for signal detection in random fields that does not require knowledge of the spatial correlation structure. The idea is to fit observed empirical Euler characteristics to the Gaussian kinematic formula via generalized least squares, which quickly and easily provides statistical estimates of the LKCs --- complex topological quantities that can be extremely challenging to compute, both theoretically and numerically. With these estimates, we can then make use of a powerful parametric approximation via Euler characteristics for Gaussian random fields to generate accurate $(1-α)$ thresholds and $p$-values. The main features of our proposed LKC regression method are easy implementation, conceptual simplicity, and facilitated diagnostics, which we demonstrate in a variety of simulations and applications.

math.ST↗