{"title":"Generalization of graph network inferences in higher-order graphical models","authors":"Yicheng Fei, Xaq Pitkow","doi":"10.1007/s41468-023-00147-4","DOIUrl":"https://doi.org/10.1007/s41468-023-00147-4","url":null,"abstract":"Abstract Probabilistic graphical models provide a powerful tool to describe complex statistical structure, with many real-world applications in science and engineering from controlling robotic arms to understanding neuronal computations. A major challenge for these graphical models is that inferences such as marginalization are intractable for general graphs. These inferences are often approximated by a distributed message-passing algorithm such as Belief Propagation, which does not always perform well on graphs with cycles, nor can it always be easily specified for complex continuous probability distributions. Such difficulties arise frequently in expressive graphical models that include intractable higher-order interactions. In this paper we define the Recurrent Factor Graph Neural Network (RF-GNN) to achieve fast approximate inference on graphical models that involve many-variable interactions. Experimental results on several families of graphical models demonstrate the out-of-distribution generalization capability of our method to different sized graphs, and indicate the domain in which our method outperforms Belief Propagation (BP). Moreover, we test the RF-GNN on a real-world Low-Density Parity-Check dataset as a benchmark along with other baseline models including BP variants and other GNN methods. Overall we find that RF-GNNs outperform other methods under high noise levels.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"61 16","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136283777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The topology of randomized symmetry-breaking distributed computing","authors":"Pierre Fraigniaud, Ran Gelles, Zvi Lotker","doi":"10.1007/s41468-023-00150-9","DOIUrl":"https://doi.org/10.1007/s41468-023-00150-9","url":null,"abstract":"Studying distributed computing through the lens of algebraic topology has been the source of many significant breakthroughs during the last 2 decades, especially in the design of lower bounds or impossibility results. Despite hundred of results considering deterministic algorithms, none apply to randomized algorithms. This paper aims at studying randomized synchronous distributed computing through the lens of algebraic topology. We do so by studying the wide class of (input-free) symmetry-breaking tasks, e.g., leader election, in synchronous fault-free anonymous systems. We design a topological framework, which allows analyzing such tasks and determining their solvability. The pivotal technical observation is that, unlike in deterministic algorithm, where solvability means that the topological complex describing the protocol can be globally mapped into an output protocol, in our framework the solvability is determined “locally”, i.e., for each simplex of the protocol complex individually, without requiring any global consistency. As an interesting application, we derive necessary and sufficient conditions for solving leader election in shared-memory and message-passing models in which there might be correlations between the randomness provided to the nodes. We find that solvability of leader election relates to the number of parties that possess correlated randomness, either directly or via their greatest common divisor, depending on the specific communication model.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"9 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134993015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Simplicial branching random walks","authors":"Ron Rosenthal","doi":"10.1007/s41468-023-00148-3","DOIUrl":"https://doi.org/10.1007/s41468-023-00148-3","url":null,"abstract":"","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"114 30","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135138044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Donald Woukeng, Damian Sadowski, Jakub Leśkiewicz, Michał Lipiński, Tomasz Kapela
{"title":"Rigorous computation in dynamics based on topological methods for multivector fields","authors":"Donald Woukeng, Damian Sadowski, Jakub Leśkiewicz, Michał Lipiński, Tomasz Kapela","doi":"10.1007/s41468-023-00149-2","DOIUrl":"https://doi.org/10.1007/s41468-023-00149-2","url":null,"abstract":"Abstract Motivated by the theoretical results of Mrozek et al. (Commun Nonlinear Sci Numer Simul 108:106–226, 2022) we present an algorithmic construction of a transversal cellular decomposition for a planar ODE. We then use the associated combinatorial multivector field to algorithmically detect the existence of an isolated invariant set with the Conley index of a periodic orbit and admitting a combinatorial Poincaré section. This construction combined with the theoretical results of Mrozek et al. (2022) leads to a method for automatized computer assisted proofs of the existence of periodic solutions in ODE’s.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"28 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135774489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bruno Benedetti, Crystal Lai, Davide Lofano, Frank H. Lutz
{"title":"Random simple-homotopy theory","authors":"Bruno Benedetti, Crystal Lai, Davide Lofano, Frank H. Lutz","doi":"10.1007/s41468-023-00139-4","DOIUrl":"https://doi.org/10.1007/s41468-023-00139-4","url":null,"abstract":"Abstract We implement an algorithm RSHT (random simple-homotopy) to study the simple-homotopy types of simplicial complexes, with a particular focus on contractible spaces and on finding substructures in higher-dimensional complexes. The algorithm combines elementary simplicial collapses with pure elementary expansions . For triangulated d -manifolds with $$dle 6$$ <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <mml:mrow> <mml:mi>d</mml:mi> <mml:mo>≤</mml:mo> <mml:mn>6</mml:mn> </mml:mrow> </mml:math> , we show that RSHT reduces to (random) bistellar flips. Among the many examples on which we test RSHT, we describe an explicit 15-vertex triangulation of the Abalone, and more generally, $$(14k+1)$$ <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <mml:mrow> <mml:mo>(</mml:mo> <mml:mn>14</mml:mn> <mml:mi>k</mml:mi> <mml:mo>+</mml:mo> <mml:mn>1</mml:mn> <mml:mo>)</mml:mo> </mml:mrow> </mml:math> -vertex triangulations of a new series of Bing’s houses with k rooms, $$kge 3$$ <mml:math xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"> <mml:mrow> <mml:mi>k</mml:mi> <mml:mo>≥</mml:mo> <mml:mn>3</mml:mn> </mml:mrow> </mml:math> , which all can be deformed to a point using only six pure elementary expansions.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136157610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Yarn ball knots and faster computations","authors":"Dror Bar-Natan, Itai Bar-Natan, Iva Halacheva, Nancy Scherich","doi":"10.1007/s41468-023-00144-7","DOIUrl":"https://doi.org/10.1007/s41468-023-00144-7","url":null,"abstract":"Abstract We make use of the 3D nature of knots and links to find savings in computational complexity when computing knot invariants such as the linking number and, in general, most finite type invariants. These savings are achieved in comparison with the 2D approach to knots using knot diagrams.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"19 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136157611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Multivariate central limit theorems for random clique complexes","authors":"Tadas Temčinas, Vidit Nanda, Gesine Reinert","doi":"10.1007/s41468-023-00146-5","DOIUrl":"https://doi.org/10.1007/s41468-023-00146-5","url":null,"abstract":"Abstract Motivated by open problems in applied and computational algebraic topology, we establish multivariate normal approximation theorems for three random vectors which arise organically in the study of random clique complexes. These are: the vector of critical simplex counts attained by a lexicographical Morse matching, the vector of simplex counts in the link of a fixed simplex, and the vector of total simplex counts. The first of these random vectors forms a cornerstone of modern homology algorithms, while the second one provides a natural generalisation for the notion of vertex degree, and the third one may be viewed from the perspective of U -statistics. To obtain distributional approximations for these random vectors, we extend the notion of dissociated sums to a multivariate setting and prove a new central limit theorem for such sums using Stein’s method.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"7 4","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135510925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spherical coordinates from persistent cohomology","authors":"Nikolas C. Schonsheck, Stefan C. Schonsheck","doi":"10.1007/s41468-023-00141-w","DOIUrl":"https://doi.org/10.1007/s41468-023-00141-w","url":null,"abstract":"","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135511557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Finding the homology of manifolds using ellipsoids","authors":"Sara Kališnik, Davorin Lešnik","doi":"10.1007/s41468-023-00145-6","DOIUrl":"https://doi.org/10.1007/s41468-023-00145-6","url":null,"abstract":"Abstract A standard problem in applied topology is how to discover topological invariants of data from a noisy point cloud that approximates it. We consider the case where a sample is drawn from a properly embedded \"Equation missing\"<!-- image only, no MathML or LaTex -->-submanifold without boundary in a Euclidean space. We show that we can deformation retract the union of ellipsoids, centered at sample points and stretching in the tangent directions, to the manifold. Hence the homotopy type, and therefore also the homology type, of the manifold is the same as that of the nerve complex of the cover by ellipsoids. By thickening sample points to ellipsoids rather than balls, our results require a smaller sample density than comparable results in the literature. They also advocate using elongated shapes in the construction of barcodes in persistent homology.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"18 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136354168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"On the nodal structures of random fields: a decade of results","authors":"Igor Wigman","doi":"10.1007/s41468-023-00140-x","DOIUrl":"https://doi.org/10.1007/s41468-023-00140-x","url":null,"abstract":"Abstract We survey a decade worth of work pertaining to the nodal structures of random fields, with emphasis on the transformative techniques that shaped the field.","PeriodicalId":73600,"journal":{"name":"Journal of applied and computational topology","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136279525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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