arXiv subjects

Tamal K. Dey

Publications and source records attributed to Tamal K. Dey.

At least 19 recordsLinked to original sources

arXiv2026

Computing Conley-Morse Persistence Barcode Efficiently by Updating Matrix Decompositions

Recent advances in combinatorial dynamical systems that generalize the classic discrete Morse theory have prompted algorithmic studies of combinatorial vector fields. In this regard, authors in [7] recently proposed the concept of Conley-Morse persistence barcode that summarizes the continuation of invariant sets in an evolving vector field through homological persistence. They proposed an algorithm to compute this barcode using a filtration of the so called \emph{index pairs} on a poset called \emph{transition diagram}. The algorithm becomes costly due to multiple runs of zigzag persistence it executes on filtrations of `unwieldy' structures of index pairs. We overcome this difficulty by replacing the index pairs with \emph{blocks}, which are structurally much simpler. These replacements need reversal of certain relations in the transition diagram resulting in a much simpler algorithm. The algorithm works by updating matrix decompositions akin to computing `vineyard' in standard persistence.

math.AT↗

arXiv2026

Linked Barcode for Persistence Induced by Filtrations

The well-known persistence algorithm summarizes the evolution of homological cycles into what is called a \emph{barcode} while scanning an input simplicial filtration. We show that this summarization process can be enriched by monitoring other algebraic structures that weave through different dimensions. In particular, we propose an algorithm to monitor the $(p+1)$-chains that make $p$-cycles to be $p$-boundaries and then morph into $(p+1)$-cycles. In effect, we get extra bars called \emph{links} connecting the bars in dimension $p$ with the bars in dimension $p+1$ in the persistence barcode. The links produce extra barcodes, which we call \emph{link barcodes} in addition to the usual ones obtained by standard persistence. The link barcodes, as such, are not stable. However, we can make them stable using a fixed ``reference'' filtration. We apply the link barcodes to the graph isomorphism problem and to the link prediction problem in temporal networks exhibiting its discriminating power through these experiments.

cs.CG↗

arXiv2026

Updating zigzag representatives efficiently

Computation of zigzag persistence has progressed in recent years, with results showing that complexities of many problems closely align with those in the non-zigzag setting. The major efficiency gap now lies in the updating of zigzag representatives. In this paper, we propose efficient algorithms for updating zigzag representatives based on a recent algorithm for extracting zigzag representatives from a $R=DV$ decomposition of a constructed non-zigzag. The main difficulty for designing our update algorithms lies in the adjacency change occurring in two operations that elongate or shorten a filtration. Despite the adjacency change, we find that the update can still be done efficiently in quadratic time.

cs.CG↗

arXiv2026

Computing Projective Implicit Representations from Poset Towers

A family of simplicial complexes connected by simplicial maps and indexed by a finite poset $P$ is called a poset tower. Poset towers subsume multi-parameter filtrations, zigzag filtrations, and one-parameter simplicial towers, while allowing arbitrary finite posets and simplicial maps. The homology of a poset tower is a $P$-persistence module. To compute it globally over $P$, we consider the chain complex segment of $P$-persistence modules $C_{\ell-1}\xleftarrow{\partial_{\ell}}C_\ell \xleftarrow{\partial_{\ell+1}}C_{\ell+1}$ induced by the simplices of the tower. Unlike in one-critical multi-filtrations, the chain modules $C_\ell$ need not be projective and may have a complicated structure. We address the problem of replacing this segment by projective modules and $P$-graded matrices while preserving homology. The resulting projective implicit representation (PiRep) plays the role of the graded boundary-matrix representation in the classical persistence algorithm: it converts simplicial data into algebraic input on which persistent homology can be computed globally over $P$. In particular, a PiRep can be used as input to algorithms for computing minimal presentations of persistent homology. We give an efficient algorithm to compute a PiRep from a poset tower. It constructs degreewise minimal presentations and asymptotically minimal second terms of projective resolutions of the chain modules $C_\ell$, lifts the boundary maps $\partial_\ell$ to these resolutions, and assembles the resulting data into a PiRep using an additional correction term. The method is tailored to chain complexes induced by poset towers and computes the required algebraic data combinatorially, exploiting their special structure and avoiding general-purpose algebraic reduction. In the context of poset towers, it is fully general and can serve as a foundation for efficient algorithms on specific posets.

math.AT↗

arXiv2026

Conley-Morse persistence barcode: a homological signature of combinatorial bifurcations

Bifurcation characterizes the qualitative changes in parameterized dynamical systems and is one of the major topics in the field. In this work, we study combinatorial bifurcations within the framework of combinatorial dynamical systems -- a young but already well-established theory. We introduce the Conley-Morse persistence barcode, a compact algebraic descriptor of combinatorial bifurcations. This barcode captures structural changes in a dynamical system at the level of Morse decompositions and provides a characterization of the nature of observed transitions in terms of the Conley index. The construction of Conley-Morse persistence barcode builds upon ideas from topological persistence. Specifically, we consider a persistence module obtained from the Conley index of invariant sets indexed over a poset. Using gentle algebras, we prove that this module decomposes into simple intervals (bars) and compute them by adapting the zigzag persistence algorithm to our purpose.

math.DS↗

arXiv2026

A Fast Algorithm for Computing Zigzag Representatives

Zigzag filtrations of simplicial complexes generalize the usual filtrations by allowing simplex deletions in addition to simplex insertions. The barcodes computed from zigzag filtrations encode the evolution of homological features. Although one can locate a particular feature at any index in the filtration using existing algorithms, the resulting representatives may not be compatible with the zigzag: a representative cycle at one index may not map into a representative cycle at its neighbor. For this, one needs to compute compatible representative cycles along each bar in the barcode. It is known that the barcode for a zigzag filtration with $m$ insertions and deletions can be computed in $O(m^ω)$ time, where $ω< 2.373$ is the matrix multiplication exponent. However, it is not known how to compute the compatible representatives so efficiently. For a non-zigzag filtration, the classical matrix-based algorithm provides representatives in $O(m^3)$ time, which can be improved to $O(m^ω)$. However, no known algorithm for zigzag filtrations computes the representatives with the $O(m^3)$ time bound. We present an $O(m^2n)$ time algorithm for this problem, where $n\leq m$ is the size of the largest complex in the filtration.

cs.CG↗

arXiv2026

Fast free resolutions of bifiltered chain complexes

In a $k$-critical bifiltration, every simplex enters along a staircase with at most $k$ steps. Examples with $k>1$ include degree-Rips bifiltrations and models of the multicover bifiltration. We consider the problem of converting a $k$-critical bifiltration into a $1$-critical (i.e. free) chain complex with equivalent homology. This is known as computing a free resolution of the underlying chain complex and is a first step toward post-processing such bifiltrations. We present two algorithms. The first one computes free resolutions corresponding to path graphs and assembles them to a chain complex by computing additional maps. The simple combinatorial structure of path graphs leads to good performance in practice, as demonstrated by extensive experiments. However, its worst-case bound is quadratic in the input size because long paths might yield dense boundary matrices in the output. Our second algorithm replaces the simplex-wise path graphs with ones that maintain short paths which leads to almost linear runtime and output size. We demonstrate that pre-computing a free resolution speeds up the task of computing a minimal presentation of the homology of a $k$-critical bifiltration in a fixed dimension. Furthermore, our findings show that a chain complex that is minimal in terms of generators can be asymptotically larger than the non-minimal output complex of our second algorithm in terms of description size.

math.AT↗

arXiv2026

Limit Computation Over Posets via Minimal Initial Functors

It is well known that limits can be computed by restricting along an initial functor, and that this often simplifies limit computation. We systematically study the algorithmic implications of this idea for diagrams indexed by a finite poset. We say an initial functor $F\colon C\to D$ with $C$ small is \emph{minimal} if the sets of objects and morphisms of $C$ each have minimum cardinality, among the sources of all initial functors with target $D$. For $Q$ a finite poset or $Q\subseteq \mathbb N^d$ an interval (i.e., a convex, connected subposet), we describe all minimal initial functors $F\colon P\to Q$ and in particular, show that $F$ is always a subposet inclusion. We give efficient algorithms to compute a choice of minimal initial functor. In the case that $Q\subseteq \mathbb N^d$ is an interval, we give asymptotically optimal bounds on $|P|$, the number of relations in $P$ (including identities), in terms of the number $n$ of minima of $Q$: We show that $|P|=Θ(n)$ for $d\leq 3$, and $|P|=Θ(n^2)$ for $d>3$. We apply these results to give new bounds on the cost of computing $\lim G$ for a functor $G \colon Q\to \mathbf{Vec}$ valued in vector spaces. For $Q$ connected, we also give new bounds on the cost of computing the \emph{generalized rank} of $G$ (i.e., the rank of the induced map $\lim G\to \mathop{\mathrm{colim}} G$), which is of interest in topological data analysis.

math.AT↗

arXiv2026

Quasi Zigzag Persistence: A Topological Framework for Analyzing Time-Varying Data

In this paper, we propose Quasi Zigzag Persistent Homology (QZPH) as a framework for analyzing time-varying data by integrating multiparameter persistence and zigzag persistence. To this end, we introduce a stable topological invariant that captures both static and dynamic features at different scales. We present an algorithm to compute this invariant efficiently. We show that it enhances the machine learning models when applied to tasks such as sleep-stage detection, demonstrating its effectiveness in capturing the evolving patterns in time-varying datasets.

cs.LG↗

arXiv2026

HalluZig: Hallucination Detection using Zigzag Persistence

The factual reliability of Large Language Models (LLMs) remains a critical barrier to their adoption in high-stakes domains due to their propensity to hallucinate. Current detection methods often rely on surface-level signals from the model's output, overlooking the failures that occur within the model's internal reasoning process. In this paper, we introduce a new paradigm for hallucination detection by analyzing the dynamic topology of the evolution of model's layer-wise attention. We model the sequence of attention matrices as a zigzag graph filtration and use zigzag persistence, a tool from Topological Data Analysis, to extract a topological signature. Our core hypothesis is that factual and hallucinated generations exhibit distinct topological signatures. We validate our framework, HalluZig, on multiple benchmarks, demonstrating that it outperforms strong baselines. Furthermore, our analysis reveals that these topological signatures are generalizable across different models and hallucination detection is possible only using structural signatures from partial network depth.

cs.CL↗

arXiv2025

Decomposing Multiparameter Persistence Modules

Dey and Xin (J.Appl.Comput.Top., 2022, arXiv:1904.03766) describe an algorithm to decompose finitely presented multiparameter persistence modules using a matrix reduction algorithm. Their algorithm only works for modules whose generators and relations are distinctly graded. We extend their approach to work on \emph{all} finitely presented modules and introduce several improvements that lead to significant speed-ups in practice. Our algorithm is fixed parameter tractable with respect to the maximal number of relations with the same degree and with further optimisation we obtain an $O(n^3)$ algorithm for interval-decomposable modules. In particular, we can decide interval-decomposability in this time. As a by-product to the proofs of correctness we develop a theory of parameter restriction for persistence modules. Our algorithm is implemented as a software library \textsc{aida} which is the first to enable the decomposition of large inputs. We show its capabilities via extensive experimental evaluation.

math.RT↗

arXiv2025

Computing Generalized Ranks of Persistence Modules via Unfolding to Zigzag Modules

For a $P$-indexed persistence module ${\sf M}$, the (generalized) rank of ${\sf M}$ is defined as the rank of the limit-to-colimit map for the diagram of vector spaces of ${\sf M}$ over the poset $P$. For $2$-parameter persistence modules, recently a zigzag persistence based algorithm has been proposed that takes advantage of the fact that generalized rank for $2$-parameter modules is equal to the number of full intervals in a zigzag module defined on the boundary of the poset. Analogous definition of boundary for $d$-parameter persistence modules or general $P$-indexed persistence modules does not seem plausible. To overcome this difficulty, we first unfold a given $P$-indexed module ${\sf M}$ into a zigzag module ${\sf M}_{ZZ}$ and then check how many full interval modules in a decomposition of ${\sf M}_{ZZ}$ can be folded back to remain full in a decomposition of ${\sf M}$. This number determines the generalized rank of ${\sf M}$. For special cases of degree-$d$ homology for $d$-complexes, we obtain a more efficient algorithm including a linear time algorithm for degree-$1$ homology in graphs.

math.AT↗

arXiv2025

Computing a Connection Matrix and Persistence Efficiently from a Morse Decomposition

Morse decompositions partition the flows in a vector field into equivalent structures. Given such a decomposition, one can define a further summary of its flow structure by what is called a connection matrix.These matrices, a generalization of Morse boundary operators from classical Morse theory, capture the connections made by the flows among the critical structures - such as attractors, repellers, and orbits - in a vector field. Recently, in the context of combinatorial dynamics, an efficient persistence-like algorithm to compute connection matrices has been proposed in~\cite{DLMS24}. We show that, actually, the classical persistence algorithm with exhaustive reduction retrieves connection matrices, both simplifying the algorithm of~\cite{DLMS24} and bringing the theory of persistence closer to combinatorial dynamical systems. We supplement this main result with an observation: the concept of persistence as defined for scalar fields naturally adapts to Morse decompositions whose Morse sets are filtered with a Lyapunov function. We conclude by presenting preliminary experimental results.

math.DS↗

arXiv2025

Approximating 1-Wasserstein Distance between Persistence Diagrams by Graph Sparsification

Persistence diagrams (PD)s play a central role in topological data analysis. This analysis requires computing distances among such diagrams such as the $1$-Wasserstein distance. Accurate computation of these PD distances for large data sets that render large diagrams may not scale appropriately with the existing methods. The main source of difficulty ensues from the size of the bipartite graph on which a matching needs to be computed for determining these PD distances. We address this problem by making several algorithmic and computational observations in order to obtain, in theory, a near-linear fully polynomial-time approximation scheme. This is theoretically optimal assuming the $(1+ε)$-approximate EMD conjecture in constant dimension, which is that the EMD problem on the plane cannot be approximated by a PTAS in time $O(\frac{1}{ε^2}n)$ up to polylog factors. In our implementation, first, taking advantage of the distribution of PD points, we \emph{condense} them thereby decreasing the number of nodes in the graph for computation. The increase in point multiplicities is addressed by reducing the matching problem to a min-cost flow problem on a transshipment network. Second, we use Well Separated Pair Decomposition to sparsify the graph to a size that is linear in the number of points. Both node and arc sparsifications contribute to the approximation factor where we leverage a lower bound given by the Relaxed Word Mover's distance. Third, we eliminate bottlenecks during the sparsification procedure by introducing parallelism. Fourth, we develop an open source software called PDoptFlow based on our algorithm, exploiting parallelism by GPU and multicore. We perform extensive experiments and show that the actual empirical error is very low. We also show that we can achieve high performance at low guaranteed relative errors, improving upon the state of the arts.

cs.CG↗

arXiv2025

Computing Optimal Persistent Cycles for Levelset Zigzag on Manifold-like Complexes

In standard persistent homology, a persistent cycle born and dying with a persistence interval (bar) associates the bar with a concrete topological representative, which provides means to effectively navigate back from the barcode to the topological space. Among the possibly many, optimal persistent cycles bring forth further information due to having guaranteed quality. However, topological features usually go through variations in the lifecycle of a bar which a single persistent cycle may not capture. Hence, for persistent homology induced from PL functions, we propose levelset persistent cycles consisting of a sequence of cycles that depict the evolution of homological features from birth to death. Our definition is based on levelset zigzag persistence which involves four types of persistence intervals as opposed to the two types in standard persistence. For each of the four types, we present a polynomial-time algorithm computing an optimal sequence of levelset persistent $p$-cycles for the so-called weak $(p+1)$-pseudomanifolds. Given that optimal cycle problems for homology are NP-hard in general, our results are useful in practice because weak pseudomanifolds do appear in applications. Our algorithms draw upon an idea of relating optimal cycles to min-cuts in a graph that was exploited earlier for standard persistent cycles. Notice that levelset zigzag poses non-trivial challenges for the approach because a sequence of optimal cycles instead of a single one needs to be computed in this case. We show some empirical evidence that optimal cycles produced by our implemented software have nice quality.

cs.CG↗

arXiv2025

Apex Representatives

Given a zigzag filtration, we want to find its barcode representatives, i.e., a compatible choice of bases for the homology groups that diagonalize the linear maps in the zigzag. To achieve this, we convert the input zigzag to a levelset zigzag of a real-valued function. This function generates a Mayer-Vietoris pyramid of spaces, which generates an infinite strip of homology groups. We call the origins of indecomposable (diamond) summands of this strip their apexes and give an algorithm to find representative cycles in these apexes from ordinary persistence computation. The resulting representatives map back to the levelset zigzag and thus yield barcode representatives for the input zigzag. Our algorithm for lifting a $p$-dimensional cycle from ordinary persistence to an apex representative takes $O(p \cdot m \log m)$ time. From this we can recover zigzag representatives in time $O(\log m + C)$, where $C$ is the size of the output.

cs.CG↗

arXiv2025

D-GRIL: End-to-End Topological Learning with 2-parameter Persistence

End-to-end topological learning using 1-parameter persistence is well-known. We show that the framework can be enhanced using 2-parameter persistence by adopting a recently introduced 2-parameter persistence based vectorization technique called GRIL. We establish a theoretical foundation of differentiating GRIL producing D-GRIL. We show that D-GRIL can be used to learn a bifiltration function on standard benchmark graph datasets. Further, we exhibit that this framework can be applied in the context of bio-activity prediction in drug discovery.

cs.LG↗

arXiv2024

Expressive Higher-Order Link Prediction through Hypergraph Symmetry Breaking

A hypergraph consists of a set of nodes along with a collection of subsets of the nodes called hyperedges. Higher-order link prediction is the task of predicting the existence of a missing hyperedge in a hypergraph. A hyperedge representation learned for higher order link prediction is fully expressive when it does not lose distinguishing power up to an isomorphism. Many existing hypergraph representation learners, are bounded in expressive power by the Generalized Weisfeiler Lehman-1 (GWL-1) algorithm, a generalization of the Weisfeiler Lehman-1 algorithm. However, GWL-1 has limited expressive power. In fact, induced subhypergraphs with identical GWL-1 valued nodes are indistinguishable. Furthermore, message passing on hypergraphs can already be computationally expensive, especially on GPU memory. To address these limitations, we devise a preprocessing algorithm that can identify certain regular subhypergraphs exhibiting symmetry. Our preprocessing algorithm runs once with complexity the size of the input hypergraph. During training, we randomly replace subhypergraphs identified by the algorithm with covering hyperedges to break symmetry. We show that our method improves the expressivity of GWL-1. Our extensive experiments also demonstrate the effectiveness of our approach for higher-order link prediction on both graph and hypergraph datasets with negligible change in computation.

cs.LG↗