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This work presents a framework for studying temporal networks using zigzag persistence, a tool from the field of Topological Data Analysis (TDA). The resulting approach is general and applicable to a wide variety of time-varying graphs. For example, these graphs may correspond to a system modeled as a network with edges whose weights are functions of time, or they may represent a time series of a complex dynamical system. We use simplicial complexes to represent snapshots of the temporal networks that can then be analyzed using zigzag persistence. We show two applications of our method to dynamic networks: an analysis of commuting trends on multiple temporal scales, e.g., daily and weekly, in the Great Britain transportation network, and the detection of periodic/chaotic transitions due to intermittency in dynamical systems represented by temporal ordinal partition networks. Our findings show that the resulting zero- and one-dimensional zigzag persistence diagrams can detect changes in the networks’ shapes that are missed by traditional connectivity and centrality graph statistics. 

Graphs drawn in the plane are ubiquitous, arising from data sets through a variety of methods ranging from GIS analysis to image classification to shape analysis. A fundamental problem in this type of data is comparison: given a set of such graphs, can we rank how similar they are in such a way that we capture their geometric “shape” in the plane? We explore a method to compare two such embedded graphs, via a simplified combinatorial representation called a tail-less merge tree which encodes the structure based on a fixed direction. First, we examine the properties of a distance designed to compare merge trees called the branching distance, and show that the distance as defined in previous work fails to satisfy some of the requirements of a metric. We incorporate this into a new distance function called average branching distance to compare graphs by looking at the branching distance for merge trees defined over many directions. Despite the theoretical issues, we show that the definition is still quite useful in practice by using our open-source code to cluster data sets of embedded graphs. 

Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.

 

Graphs in metric spaces appear in a wide range of data sets, and there is a large body of work focused on comparing, matching, or analyzing collections of graphs in different ambient spaces. In this survey, we provide an overview of a diverse collection of distance measures that can be defined on the set of finite graphs immersed (and in some cases, embedded) in a metric space. For each of the distance measures, we recall their definitions and investigate which of the properties of a metric they satisfy. Furthermore we compare the distance measures based on these properties and discuss their computational complexity.

 

Persian walnuts (Juglans regiaL.) are the second most produced and consumed tree nut, with over 2.6 million metric tons produced in the 2022–2023 harvest cycle alone. The United States is the second largest producer, accounting for 25% of the total global supply. Nonetheless, producers face an ever‐growing demand in a more uncertain climate landscape, which requires effective and efficient walnut selection and breeding of new cultivars with increased kernel content and easy‐to‐open shells. Past and current efforts select for these traits using hand‐held calipers and eye‐based evaluations. Yet there is plenty of morphology that meets the eye but goes unmeasured, such as the volume of inner air or the convexity of the kernel. Here, we study the shape of walnut fruits based on X‐ray computed tomography three‐dimensional reconstructions. We compute 49 different morphological phenotypes for 1264 individual nuts comprising 149 accessions. These phenotypes are complemented by traits of breeding interest such as ease of kernel removal and kernel‐to‐nut weight ratio. Through allometric relationships, relative growth of one tissue to another, we identify possible biophysical constraints at play during development. We explore multiple correlations between all morphological and commercial traits and identify which morphological traits can explain the most variability of commercial traits. We show that using only volume‐ and thickness‐based traits, especially inner air content, we can successfully encode several of the commercial traits.

 

Abstract Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare and analyse this information embedded in a robust and concise way, we turn to topological data analysis (TDA), specifically the Euler characteristic transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray computed tomography (CT) technology at 127 μm resolution. The Euler characteristic transform measures shape by analysing topological features of an object at thresholds across a number of directional axes. A Kruskal–Wallis analysis of the information encoded by the topological signature reveals that the Euler characteristic transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of ‘hidden’ shape nuances which are otherwise not detected. 

In this paper, we introduce an extension of smoothing on Reeb graphs, which we call truncated smoothing; this in turn allows us to define a new family of metrics which generalize the interleaving distance for Reeb graphs. Intuitively, we "chop off" parts near local minima and maxima during the course of smoothing, where the amount cut is controlled by a parameter τ. After formalizing truncation as a functor, we show that when applied after the smoothing functor, this prevents extensive expansion of the range of the function, and yields particularly nice properties (such as maintaining connectivity) when combined with smoothing for 0 ≤ τ ≤ 2ε, where ε is the smoothing parameter. Then, for the restriction of τ ∈ [0,ε], we have additional structure which we can take advantage of to construct a categorical flow for any choice of slope m ∈ [0,1]. Using the infrastructure built for a category with a flow, this then gives an interleaving distance for every m ∈ [0,1], which is a generalization of the original interleaving distance, which is the case m = 0. While the resulting metrics are not stable, we show that any pair of these for m, m' ∈ [0,1) are strongly equivalent metrics, which in turn gives stability of each metric up to a multiplicative constant. We conclude by discussing implications of this metric within the broader family of metrics for Reeb graphs. 

Abstract We study the probabilistic convergence between the mapper graph and the Reeb graph of a topological space $${\mathbb {X}}$$ X equipped with a continuous function $$f: {\mathbb {X}}\rightarrow \mathbb {R}$$ f : X → R . We first give a categorification of the mapper graph and the Reeb graph by interpreting them in terms of cosheaves and stratified covers of the real line $$\mathbb {R}$$ R . We then introduce a variant of the classic mapper graph of Singh et al. (in: Eurographics symposium on point-based graphics, 2007), referred to as the enhanced mapper graph, and demonstrate that such a construction approximates the Reeb graph of $$({\mathbb {X}}, f)$$ ( X , f ) when it is applied to points randomly sampled from a probability density function concentrated on $$({\mathbb {X}}, f)$$ ( X , f ) . Our techniques are based on the interleaving distance of constructible cosheaves and topological estimation via kernel density estimates. Following Munch and Wang (In: 32nd international symposium on computational geometry, volume 51 of Leibniz international proceedings in informatics (LIPIcs), Dagstuhl, Germany, pp 53:1–53:16, 2016), we first show that the mapper graph of $$({\mathbb {X}}, f)$$ ( X , f ) , a constructible $$\mathbb {R}$$ R -space (with a fixed open cover), approximates the Reeb graph of the same space. We then construct an isomorphism between the mapper of $$({\mathbb {X}},f)$$ ( X , f ) to the mapper of a super-level set of a probability density function concentrated on $$({\mathbb {X}}, f)$$ ( X , f ) . Finally, building on the approach of Bobrowski et al. (Bernoulli 23 (1):288–328, 2017b), we show that, with high probability, we can recover the mapper of the super-level set given a sufficiently large sample. Our work is the first to consider the mapper construction using the theory of cosheaves in a probabilistic setting. It is part of an ongoing effort to combine sheaf theory, probability, and statistics, to support topological data analysis with random data.