This SHREC 2025 track dedicated to protein surface shape retrieval involved 9 participating teams. We evaluated the performance in retrieval of 15 proposed methods on a large dataset of 11,555 protein surfaces with calculated electrostatic potential (a key molecular surface descriptor). The performance in retrieval of the proposed methods was evaluated through different metrics (Accuracy, Balanced accuracy, F1 score, Precision and Recall). The best retrieval performance was achieved by the proposed methods that used the electrostatic potential complementary to molecular surface shape. This observation was also valid for classes with limited data which highlights the importance of taking into account additional molecular surface descriptors.

Given a 3D point cloud, we propose a method for suitably resampling the cloud while reconstructing and preserving the feature curves to which some points are identified to belong. The first phase of our strategy enriches the cloud by approximating the curvilinear profiles outlined by the feature points with piece-wise polynomial parametric space curves through the use of the Hough transform. The second phase describes how the removal of a point or its insertion can be performed without affecting the approximated profiles and preserving the enriched structure of the cloud. The combination of the two steps provides multiple possibilities for processing a point cloud by varying its size or improving its density homogeneity without affecting the retrieved feature curves. The various capabilities of our approach are investigated to produce simplification, refinement, and resampling techniques whose effectiveness is evaluated through experiments and comparisons.

Voltage-gated sodium (Nav) channels constitute a prime target for drug design and discovery, given their implication in various diseases such as epilepsy, migraine and ataxia to name a few. In this regard, performing morphological analysis is a crucial step in comprehensively understanding their biological function and mechanism, as well as in uncovering subtle details of their mechanism that may be elusive to experimental observations. Despite their tremendous therapeutic potential, drug design resources are deficient, particularly in terms of accurate and comprehensive geometric information. This paper presents a geometric dataset of molecular surfaces that are representative of Nav channels in mammals. For each structure we provide three representations and a number of geometric measures, including length, volume and straightness of the recognized channels. To demonstrate the effective use of GEO-Nav, we have tested it on two methods belonging to two different categories of approaches: a sphere-based and a tessellation-based method.

Compression aims to reduce the size of an input, while maintaining its relevant properties. For multi-parameter persistent homology, compression is a necessary step in any computational pipeline, since standard constructions lead to large inputs, and computational tasks in this area tend to be expensive. We propose two compression methods for chain complexes of free 2-parameter persistence modules. The first method extends the multi-chunk algorithm for one-parameter persistent homology, returning the smallest chain complex among all the ones quasi-isomorphic to the input. The second method produces minimal presentations of the homology of the input; it is based on an algorithm of Lesnick and Wright, but incorporates several improvements that lead to substantial performance gains. The two methods are complementary, and can be combined to compute minimal presentations for complexes with millions of generators in a few seconds. The methods have been implemented, and the software is publicly available. We report on experimental evaluations, which demonstrate substantial improvements in performance compared to previously available compression strategies.

We give necessary and sufficient criteria for elementary operations in a two-dimensional terrain to preserve the persistent homology induced by the height function. These operations are edge flips and removals of interior vertices, re-triangulating the link of the removed vertex. This problem is motivated by topological terrain simplification, which means removing as many critical vertices of a terrain as possible while maintaining geometric closeness to the original surface. Existing methods manage to reduce the maximal possible number of critical vertices, but increase thereby the number of regular vertices. Our method can be used to post-process a simplified terrain, drastically reducing its size and preserving its favorable properties.

Abstract Simplicial complexes are widely used to discretize shapes. In low dimensions, a 3D shape is represented by discretizing its boundary surface, encoded as a triangle mesh, or by discretizing the enclosed volume, encoded as a tetrahedral mesh. High‐dimensional simplicial complexes have recently found their application in topological data analysis. Topological data analysis aims at studying a point cloud P, possibly embedded in a high‐dimensional metric space, by investigating the topological characteristics of the simplicial complexes built on P. Analysing such complexes is not feasible due to their size and dimensions. To this aim, the idea of simplifying a complex while preserving its topological features has been proposed in the literature. Here, we consider the problem of efficiently simplifying simplicial complexes in arbitrary dimensions. We provide a new definition for the edge contraction operator, based on a top‐based data structure, with the objective of preserving structural aspects of a simplicial shape (i.e., its homology), and a new algorithm for verifying the link condition on a top‐based representation. We implement the simplification algorithm obtained by coupling the new edge contraction and the link condition on a specific top‐based data structure, that we use to demonstrate the scalability of our approach.

The extension of persistent homology to multi-parameter setups is an algorithmic challenge. Since most computation tasks scale badly with the size of the input complex, an important pre-processing step consists of simplifying the input while maintaining the homological information. We present an algorithm that drastically reduces the size of an input. Our approach is an extension of the chunk algorithm for persistent homology (Bauer et al., Topological Methods in Data Analysis and Visualization III, 2014). We show that our construction produces the smallest multi-filtered chain complex among all the complexes quasi-isomorphic to the input, improving on the guarantees of previous work in the context of discrete Morse theory. Our algorithm also offers an immediate parallelization scheme in shared memory. Already its sequential version compares favorably with existing simplification schemes, as we show by experimental evaluation.

We consider the problem of efficiently computing a discrete Morse complex on simplicial complexes of arbitrary dimension and very large size. Based on a common graph-based formalism, we analyze existing data structures for simplicial complexes, and we define an efficient encoding for the discrete Morse gradient on the most compact of such representations. We theoretically compare methods based on reductions and coreductions for computing a discrete Morse gradient, proving that the combination of reductions and coreductions produces new mutually equivalent approaches. We design and implement a new algorithm for computing a discrete Morse complex on simplicial complexes. We show that our approach scales very well with the size and the dimension of the simplicial complex also through comparisons with the only existing public-domain algorithm for discrete Morse complex computation. We discuss applications to the computation of multi-parameter persistent homology and of extremum graphs for visualization of time-varying 3D scalar fields.

Complex networks require effective tools and visualizations for their analysis and comparison. Clique communities have been recognized as a powerful concept for describing cohesive structures in networks. We propose an approach that extends the computation of clique communities by considering persistent homology, a topological paradigm originally introduced to characterize and compare the global structure of shapes. Our persistence-based algorithm is able to detect clique communities and to keep track of their evolution according to different edge weight thresholds. We use this information to define comparison metrics and a new centrality measure, both reflecting the relevance of the clique communities inherent to the network. Moreover, we propose an interactive visualization tool based on nested graphs that is capable of compactly representing the evolving relationships between communities for different thresholds and clique degrees. We demonstrate the effectiveness of our approach on various network types.

Abstract Morse theory offers a natural and mathematically‐sound tool for shape analysis and understanding. It allows studying the behavior of a scalar function defined on a manifold. Starting from a Morse function, we can decompose the domain of the function into meaningful regions associated with the critical points of the function. Such decompositions, called Morse complexes, provide a segmentation of a shape and are extensively used in terrain modeling and in scientific visualization. Discrete Morse theory, a combinatorial counterpart of smooth Morse theory defined over cell complexes, provides an excellent basis for computing Morse complexes in a robust and efficient way. Moreover, since a discrete Morse complex computed over a given complex has the same homology as the original one, but fewer cells, discrete Morse theory is a fundamental tool for efficiently detecting holes in shapes through homology and persistent homology. In this survey, we review, classify and analyze algorithms for computing and simplifying Morse complexes in the context of such applications with an emphasis on discrete Morse theory and on algorithms based on it.