arXiv subjects

Anthea Monod

Publications and source records attributed to Anthea Monod.

At least 37 records · Page 2Linked to original sources

arXiv2025

Computing the Tropical Abel--Jacobi Transform and Tropical Distances for Metric Graphs

Metric graphs are important models for capturing the structure of complex data across various domains. While much effort has been devoted to extracting geometric and topological features from graph data, computational aspects of metric graphs as abstract tropical curves remains unexplored. In this paper, we present the first computational and machine learning-driven study of metric graphs from the perspective of tropical algebraic geometry. Specifically, we study the tropical Abel--Jacobi transform, a vectorization of points on a metric graph via the tropical Abel--Jacobi map into its associated flat torus, the tropical Jacobian. We develop algorithms to compute this transform and investigate how the resulting embeddings depend on different combinatorial models of the same metric graph. Once embedded, we compute pairwise distances between points in the tropical Jacobian under two natural metrics: the tropical polarization distance and the Foster--Zhang distance. Computing these distances are generally NP-hard as they turn out to be linked to classical lattice problems in computational complexity, however, we identify a class of metric graphs where fast and explicit computations are feasible. For the general case, we propose practical algorithms for both exact and approximate distance matrix computations using lattice basis reduction and mixed-integer programming solvers. Our work lays the groundwork for future applications of tropical geometry and the tropical Abel--Jacobi transform in machine learning and data analysis.

math.AG↗

arXiv2025

Tropical Gradient Descent

We propose a gradient descent method for solving optimization problems arising in settings of tropical geometry - a variant of algebraic geometry that has attracted growing interest in applications such as computational biology, economics, and computer science. Our approach takes advantage of the polyhedral and combinatorial structures arising in tropical geometry to propose a versatile method for approximating local minima in tropical statistical optimization problems - a rapidly growing body of work in recent years. Theoretical results establish global solvability for 1-sample problems and a convergence rate matching classical gradient descent. Numerical experiments demonstrate the method's superior performance compared to classical gradient descent for tropical optimization problems which exhibit tropical convexity but not classical convexity. We also demonstrate the seamless integration of tropical descent into advanced optimization methods, such as Adam, offering improved overall accuracy.

math.OC↗

arXiv2025

Generalized Persistent Laplacians and their Spectral Properties

Laplacian operators are classical objects that are fundamental in both pure and applied mathematics and are becoming increasingly prominent in modern computational and data science fields such as applied and computational topology and application areas such as machine learning and network science. In this paper, we introduce a unifying operator-theoretic framework of generalized Laplacians as invariants that encompasses and extends all existing constructions, from discrete combinatorial settings to de Rham complexes of smooth manifolds. Within this framework, we introduce and study a generalized notion of persistent Laplacians. While the classical persistent Laplacian fails to satisfy the desirable properties of monotonicity and stability -- both crucial for robustness and interpretability -- our framework allows us to isolate and analyze these properties systematically. We demonstrate that their component maps, the up- and down-persistent Laplacians, satisfy these properties individually. Moreover, we prove that the spectra of these separate components fully determine the spectra of the full Laplacians, making them not only preferable but sufficient for analysis. We study these questions comprehensively, in both the finite and infinite dimensional settings. Our work expands and strengthens the theoretical foundation of generalized Laplacian-based methods in pure, applied, and computational mathematics.

math.AT↗

arXiv2025

A Topological Gaussian Mixture Model for Bone Marrow Morphology in Leukaemia

Acute myeloid leukaemia (AML) is a type of blood and bone marrow cancer characterized by the proliferation of abnormal clonal haematopoietic cells in the bone marrow leading to bone marrow failure. Over the course of the disease, angiogenic factors released by leukaemic cells drastically alter the bone marrow vascular niches resulting in observable structural abnormalities. We use a technique from topological data analysis - persistent homology - to quantify the images and infer on the disease through the imaged morphological features. We find that persistent homology uncovers succinct dissimilarities between the control, early, and late stages of AML development. We then integrate persistent homology into stage-dependent Gaussian mixture models for the first time, proposing a new class of models which are applicable to persistent homology summaries and able to both infer patterns in morphological changes between different stages of progression as well as provide a basis for prediction.

stat.AP↗

arXiv2025

Confidence Bands for Multiparameter Persistence Landscapes

Multiparameter persistent homology is a generalization of classical persistent homology, a central and widely-used methodology from topological data analysis, which takes into account density estimation and is an effective tool for data analysis in the presence of noise. Similar to its classical single-parameter counterpart, however, it is challenging to compute and use in practice due to its complex algebraic construction. In this paper, we study a popular and tractable invariant for multiparameter persistent homology in a statistical setting: the multiparameter persistence landscape. We derive a functional central limit theorem for multiparameter persistence landscapes, from which we compute confidence bands, giving rise to one of the first statistical inference methodologies for multiparameter persistence landscapes. We provide an implementation of confidence bands and demonstrate their application in a machine learning task on synthetic data.

math.ST↗

arXiv2025

A Geometric Condition for Uniqueness of Fréchet Means of Persistence Diagrams

The Fréchet mean is an important statistical summary and measure of centrality of data; it has been defined and studied for persistent homology captured by persistence diagrams. However, the complicated geometry of the space of persistence diagrams implies that the Fréchet mean for a given set of persistence diagrams is not necessarily unique, which prohibits theoretical guarantees for empirical means with respect to population means. In this paper, we derive a variance expression for a set of persistence diagrams exhibiting a multi-matching between the persistence points known as a grouping. Moreover, we propose a condition for groupings, which we refer to as flatness; we prove that sets of persistence diagrams that exhibit flat groupings give rise to unique Fréchet means. We derive a finite sample convergence result for general groupings, which results in convergence for Fréchet means if the groupings are flat. We then interpret flat groupings in a recently-proposed general framework of Fréchet means in Alexandrov geometry. Finally, we show that for manifold-valued data, the persistence diagrams can be truncated to construct flat groupings.

math.MG↗

arXiv2024

On the Limitations of Fractal Dimension as a Measure of Generalization

Bounding and predicting the generalization gap of overparameterized neural networks remains a central open problem in theoretical machine learning. There is a recent and growing body of literature that proposes the framework of fractals to model optimization trajectories of neural networks, motivating generalization bounds and measures based on the fractal dimension of the trajectory. Notably, the persistent homology dimension has been proposed to correlate with the generalization gap. This paper performs an empirical evaluation of these persistent homology-based generalization measures, with an in-depth statistical analysis. Our study reveals confounding effects in the observed correlation between generalization and topological measures due to the variation of hyperparameters. We also observe that fractal dimension fails to predict generalization of models trained from poor initializations. We lastly reveal the intriguing manifestation of model-wise double descent in these topological generalization measures. Our work forms a basis for a deeper investigation of the causal relationships between fractal geometry, topological data analysis, and neural network optimization.

cs.LG↗

arXiv2024

Probability Metrics for Tropical Spaces of Different Dimensions

The problem of comparing probability distributions is at the heart of many tasks in statistics and machine learning. Established comparison methods treat the standard setting that the distributions are supported in the same space. Recently, a new geometric solution has been proposed to address the more challenging problem of comparing measures in Euclidean spaces of differing dimensions. Here, we study the same problem of comparing probability distributions of different dimensions in the tropical setting, which is becoming increasingly relevant in applications involving complex data structures such as phylogenetic trees. Specifically, we construct a Wasserstein distance between measures on different tropical projective tori -- the focal metric spaces in both theory and applications of tropical geometry -- via tropical mappings between probability measures. We prove equivalence of the directionality of the maps, whether mapping from a low dimensional space to a high dimensional space or vice versa. As an important practical implication, our work provides a framework for comparing probability distributions on the spaces of phylogenetic trees with different leaf sets. We demonstrate the computational feasibility of our approach using existing optimisation techniques on both simulated and real data.

math.MG↗

arXiv2024

Stability for Inference with Persistent Homology Rank Functions

Persistent homology barcodes and diagrams are a cornerstone of topological data analysis that capture the "shape" of a wide range of complex data structures, such as point clouds, networks, and functions. However, their use in statistical settings is challenging due to their complex geometric structure. In this paper, we revisit the persistent homology rank function, which is mathematically equivalent to a barcode and persistence diagram, as a tool for statistics and machine learning. Rank functions, being functions, enable the direct application of the statistical theory of functional data analysis (FDA)-a domain of statistics adapted for data in the form of functions. A key challenge they present over barcodes in practice, however, is their lack of stability-a property that is crucial to validate their use as a faithful representation of the data and therefore a viable summary statistic. In this paper, we fill this gap by deriving two stability results for persistent homology rank functions under a suitable metric for FDA integration. We then study the performance of rank functions in functional inferential statistics and machine learning on real data applications, in both single and multiparameter persistent homology. We find that the use of persistent homology captured by rank functions offers a clear improvement over existing non-persistence-based approaches.

math.AT↗

arXiv2024

Fast Topological Signal Identification and Persistent Cohomological Cycle Matching

Within the context of topological data analysis, the problems of identifying topological significance and matching signals across datasets are important and useful inferential tasks in many applications. The limitation of existing solutions to these problems, however, is computational speed. In this paper, we harness the state-of-the-art for persistent homology computation by studying the problem of determining topological prevalence and cycle matching using a cohomological approach, which increases their feasibility and applicability to a wider variety of applications and contexts. We demonstrate this on a wide range of real-life, large-scale, and complex datasets. We extend existing notions of topological prevalence and cycle matching to include general non-Morse filtrations. This provides the most general and flexible state-of-the-art adaptation of topological signal identification and persistent cycle matching, which performs comparisons of orders of ten for thousands of sampled points in a matter of minutes on standard institutional HPC CPU facilities.

math.AT↗

arXiv2024

Wavelet-Based Density Estimation for Persistent Homology

Persistent homology is a central methodology in topological data analysis that has been successfully implemented in many fields and is becoming increasingly popular and relevant. The output of persistent homology is a persistence diagram -- a multiset of points supported on the upper half plane -- that is often used as a statistical summary of the topological features of data. In this paper, we study the random nature of persistent homology and estimate the density of expected persistence diagrams from observations using wavelets; we show that our wavelet-based estimator is optimal. Furthermore, we propose an estimator that offers a sparse representation of the expected persistence diagram that achieves near-optimality. We demonstrate the utility of our contributions in a machine learning task in the context of dynamical systems.

math.ST↗

arXiv2023

$k$-Means Clustering for Persistent Homology

Persistent homology is a methodology central to topological data analysis that extracts and summarizes the topological features within a dataset as a persistence diagram; it has recently gained much popularity from its myriad successful applications to many domains. However, its algebraic construction induces a metric space of persistence diagrams with a highly complex geometry. In this paper, we prove convergence of the $k$-means clustering algorithm on persistence diagram space and establish theoretical properties of the solution to the optimization problem in the Karush--Kuhn--Tucker framework. Additionally, we perform numerical experiments on various representations of persistent homology, including embeddings of persistence diagrams as well as diagrams themselves and their generalizations as persistence measures; we find that $k$-means clustering performance directly on persistence diagrams and measures outperform their vectorized representations.

stat.AP↗

arXiv2023

Topological Community Detection: A Sheaf-Theoretic Approach

We propose a model for network community detection using topological data analysis, a branch of modern data science that leverages theory from algebraic topology to statistical analysis and machine learning. Specifically, we use cellular sheaves, which relate local to global properties of various algebraic topological constructions, to propose three new algorithms for vertex clustering over networks to detect communities. We apply our algorithms to real social network data in numerical experiments and obtain near optimal results in terms of modularity. Our work is the first implementation of sheaves on real social network data and provides a solid proof-of-concept for future work using sheaves as tools to study complex systems captured by networks and simplicial complexes.

cs.SI↗

arXiv2023

Generalized Morse Theory of Distance Functions to Surfaces for Persistent Homology

This paper brings together three distinct theories with the goal of quantifying shape textures with complex morphologies. Distance fields are central objects in shape representation, while topological data analysis uses algebraic topology to characterize geometric and topological patterns in shapes. The most well-known and widely applied tool from this approach is persistent homology, which tracks the evolution of topological features in a dynamic manner as a barcode. Morse theory is a framework from differential topology that studies critical points of functions on manifolds; it has been used to characterize the birth and death of persistent homology features. However, a significant limitation to Morse theory is that it cannot be readily applied to distance functions because distance functions lack smoothness, which is required in Morse theory. Our contributions to addressing this issue is two fold. First, we generalize Morse theory to Euclidean distance functions of bounded sets with smooth boundaries. We focus in particular on distance fields for shape representation and we study the persistent homology of shape textures using a sublevel set filtration induced by the signed distance function. We use transversality theory to prove that for generic embeddings of a smooth compact surface in $\mathbb{R}^3$, signed distance functions admit finitely many non-degenerate critical points. This gives rise to our second contribution, which is that shapes and textures can both now be quantified and rigorously characterized in the language of persistent homology: signed distance persistence modules of generic shapes admit a finite barcode decomposition whose birth and death points can be classified and described geometrically. We use this approach to quantify shape textures on both simulated data and real vascular data from biology.

math.AT↗

arXiv2023

An Invitation to Tropical Alexandrov Curvature

We study Alexandrov curvature in the tropical projective torus with respect to the tropical metric, which has been useful in various statistical analyses, particularly in phylogenomics. Alexandrov curvature is a generalization of classical Riemannian sectional curvature to more general metric spaces; it is determined by a comparison of triangles in an arbitrary metric space to corresponding triangles in Euclidean space. In the polyhedral setting of tropical geometry, triangles are a combinatorial object, which adds a combinatorial dimension to our analysis. We study the effect that the triangle types have on curvature, and what can be revealed about these types from the curvature. We find that positive, negative, zero, and undefined Alexandrov curvature can exist concurrently in tropical settings and that there is a tight connection between triangle combinatorial type and curvature. Our results are established both by proof and computational experiments, and shed light on the intricate geometry of the tropical projective torus. In this context, we discuss implications for statistical methodologies which admit inherent geometric interpretations. This paper is dedicated to Bernd Sturmfels on the occasion of his 60th birthday.

math.MG↗

arXiv2022

Learning Linear Non-Gaussian Polytree Models

In the context of graphical causal discovery, we adapt the versatile framework of linear non-Gaussian acyclic models (LiNGAMs) to propose new algorithms to efficiently learn graphs that are polytrees. Our approach combines the Chow--Liu algorithm, which first learns the undirected tree structure, with novel schemes to orient the edges. The orientation schemes assess algebraic relations among moments of the data-generating distribution and are computationally inexpensive. We establish high-dimensional consistency results for our approach and compare different algorithmic versions in numerical experiments.

stat.ML↗

arXiv2022

Rewiring Networks for Graph Neural Network Training Using Discrete Geometry

Information over-squashing is a phenomenon of inefficient information propagation between distant nodes on networks. It is an important problem that is known to significantly impact the training of graph neural networks (GNNs), as the receptive field of a node grows exponentially. To mitigate this problem, a preprocessing procedure known as rewiring is often applied to the input network. In this paper, we investigate the use of discrete analogues of classical geometric notions of curvature to model information flow on networks and rewire them. We show that these classical notions achieve state-of-the-art performance in GNN training accuracy on a variety of real-world network datasets. Moreover, compared to the current state-of-the-art, these classical notions exhibit a clear advantage in computational runtime by several orders of magnitude.

stat.ML↗

arXiv2022

Topological Information Retrieval with Dilation-Invariant Bottleneck Comparative Measures

Appropriately representing elements in a database so that queries may be accurately matched is a central task in information retrieval; recently, this has been achieved by embedding the graphical structure of the database into a manifold in a hierarchy-preserving manner using a variety of metrics. Persistent homology is a tool commonly used in topological data analysis that is able to rigorously characterize a database in terms of both its hierarchy and connectivity structure. Computing persistent homology on a variety of embedded datasets reveals that some commonly used embeddings fail to preserve the connectivity. We show that those embeddings which successfully retain the database topology coincide in persistent homology by introducing two dilation-invariant comparative measures to capture this effect: in particular, they address the issue of metric distortion on manifolds. We provide an algorithm for their computation that exhibits greatly reduced time complexity over existing methods. We use these measures to perform the first instance of topology-based information retrieval and demonstrate its increased performance over the standard bottleneck distance for persistent homology. We showcase our approach on databases of different data varieties including text, videos, and medical images.

stat.ML↗