arXiv subjects

Amir Nayyeri

Publications and source records attributed to Amir Nayyeri.

At least 19 recordsLinked to original sources

arXiv2026

Understanding Truncated Positional Encodings for Graph Neural Networks

Positional encodings (PEs) enhance the power of graph neural networks (GNNs), both theoretically and empirically. Two of the most popular families of PEs - spectral (e.g., Laplacian eigenspaces, effective resistance) and walk-based (polynomials of the adjacency matrix) - are theoretically equivalent in expressive power, with expressivity between the 1-WL and 3-WL tests. However, this equivalence assumes the GNN uses the "complete" version of these PEs, which requires $O(n^3)$ time and space complexity. Instead, practitioners commonly use truncated variants of these encodings, such as the first $k$ eigenspaces or powers of the adjacency matrix. However, the theoretical properties of these truncated PEs are unknown. In this work, we initiate the study of these truncated PEs. Theoretically, we show that, under truncation, several families of PEs are fundamentally different in expressive power. As a corollary, we show that truncated spectral PEs are no longer stronger than the 1-WL test. We also study a family of spectral PEs, the $k$-harmonic distances, to highlight the differences in expressive power of even closely related truncated PEs. Finally, we experimentally show that a mix of truncated PEs is preferable to any single family on real-world datasets.

cs.LG↗

arXiv2026

Reconstructing Bounded Treelength Graphs with Linearithmic Shortest Path Distance Queries

We consider the following graph reconstruction problem: given an unweighted connected graph $G = (V,E)$ with visible vertex set $V$ and an oracle which takes two vertices $u,v \in V$ and returns the shortest path distance between $u$ and $v$, how many queries are needed to reconstruct $E$? Specifically, we consider bounded degree $Δ$ and bounded treelength $\mathrm{tl}$ connected graphs and show that reconstruction can be done in $O_{Δ,\mathrm{tl}}(n \log n)$ queries with a deterministic algorithm. This result improves over the best known algorithm (deterministic or randomized) for this graph class by a $\log n$ factor and matches the known lower bound for the class of graphs with bounded chordality, which is a subclass of bounded treelength graphs.

cs.DS↗

arXiv2025

Graph Inference with Effective Resistance Queries

The goal of graph inference is to design algorithms for learning properties of a hidden graph using queries to an oracle that returns information about the graph. Graph reconstruction, verification, and property testing are all types of graph inference. In this work, we study graph inference using an oracle that returns the effective resistance (ER) between a pair of vertices. Effective resistance is a distance originating from the study of electrical circuits with many applications. However, ER has received little attention from a graph inference perspective. Indeed, although it is known that an $n$-vertex graph can be uniquely reconstructed from all $\binom{n}{2}$ possible ER queries, little else is known. We address this gap with several new results, including: 1. $O(n)$-query algorithms for testing whether a graph is a tree; deciding whether two graphs are equal assuming one is a subgraph of the other; and testing whether a given vertex (or edge) is a cut vertex (or cut edge). 2. Property testing algorithms, including for testing whether a graph is vertex- or edge-biconnected. We also give a reduction to adapt property testing results from the bounded-degree model to our ER query model. This yields ER-query-based algorithms for testing $k$-connectivity, bipartiteness, planarity, and containment of a fixed subgraph. 3. Graph reconstruction algorithms, including an algorithm for reconstructing a graph from a low-width tree decomposition; a $Θ(k^2)$-query, polynomial-time algorithm for recovering the adjacency matrix $A$ of a hidden graph, given $A$ with $k$ of its entries deleted; and a $k$-query, exponential-time algorithm for the same task. We also compare the power of ER queries and shortest path queries, which are closely related but better studied. Interestingly, we show that the two query models are incomparable in power.

cs.DS↗

arXiv2025

Biharmonic Distance of Graphs and its Higher-Order Variants: Theoretical Properties with Applications to Centrality and Clustering

Effective resistance is a distance between vertices of a graph that is both theoretically interesting and useful in applications. We study a variant of effective resistance called the biharmonic distance. While the effective resistance measures how well-connected two vertices are, we prove several theoretical results supporting the idea that the biharmonic distance measures how important an edge is to the global topology of the graph. Our theoretical results connect the biharmonic distance to well-known measures of connectivity of a graph like its total resistance and sparsity. Based on these results, we introduce two clustering algorithms using the biharmonic distance. Finally, we introduce a further generalization of the biharmonic distance that we call the $k$-harmonic distance. We empirically study the utility of biharmonic and $k$-harmonic distance for edge centrality and graph clustering.

cs.SI↗

arXiv2024

Comparing Graph Transformers via Positional Encodings

The distinguishing power of graph transformers is closely tied to the choice of positional encoding: features used to augment the base transformer with information about the graph. There are two primary types of positional encoding: absolute positional encodings (APEs) and relative positional encodings (RPEs). APEs assign features to each node and are given as input to the transformer. RPEs instead assign a feature to each pair of nodes, e.g., graph distance, and are used to augment the attention block. A priori, it is unclear which method is better for maximizing the power of the resulting graph transformer. In this paper, we aim to understand the relationship between these different types of positional encodings. Interestingly, we show that graph transformers using APEs and RPEs are equivalent in terms of distinguishing power. In particular, we demonstrate how to interchange APEs and RPEs while maintaining their distinguishing power in terms of graph transformers. Based on our theoretical results, we provide a study on several APEs and RPEs (including the resistance distance and the recently introduced stable and expressive positional encoding (SPE)) and compare their distinguishing power in terms of transformers. We believe our work will help navigate the huge number of choices of positional encoding and will provide guidance on the future design of positional encodings for graph transformers.

cs.LG↗

arXiv2024

Fréchet Edit Distance

We define and investigate the Fréchet edit distance problem. Given two polygonal curves $π$ and $σ$ and a threshhold value $δ>0$, we seek the minimum number of edits to $σ$ such that the Fréchet distance between the edited $σ$ and $π$ is at most $δ$. For the edit operations we consider three cases, namely, deletion of vertices, insertion of vertices, or both. For this basic problem we consider a number of variants. Specifically, we provide polynomial time algorithms for both discrete and continuous Fréchet edit distance variants, as well as hardness results for weak Fréchet edit distance variants.

cs.CG↗

arXiv2023

Topological $k$-metrics

Metric spaces $(X, d)$ are ubiquitous objects in mathematics and computer science that allow for capturing (pairwise) distance relationships $d(x, y)$ between points $x, y \in X$. Because of this, it is natural to ask what useful generalizations there are of metric spaces for capturing "$k$-wise distance relationships" $d(x_1, \ldots, x_k)$ among points $x_1, \ldots, x_k \in X$ for $k > 2$. To that end, Gähler (Math. Nachr., 1963) (and perhaps others even earlier) defined $k$-metric spaces, which generalize metric spaces, and most notably generalize the triangle inequality $d(x_1, x_2) \leq d(x_1, y) + d(y, x_2)$ to the "simplex inequality" $d(x_1, \ldots, x_k) \leq \sum_{i=1}^k d(x_1, \ldots, x_{i-1}, y, x_{i+1}, \ldots, x_k)$. (The definition holds for any fixed $k \geq 2$, and a $2$-metric space is just a (standard) metric space.) In this work, we introduce strong $k$-metric spaces, $k$-metric spaces that satisfy a topological condition stronger than the simplex inequality, which makes them "behave nicely." We also introduce coboundary $k$-metrics, which generalize $\ell_p$ metrics (and in fact all finite metric spaces induced by norms) and minimum bounding chain $k$-metrics, which generalize shortest path metrics (and capture all strong $k$-metrics). Using these definitions, we prove analogs of a number of fundamental results about embedding finite metric spaces including Fréchet embedding (isometric embedding into $\ell_{\infty}$) and isometric embedding of all tree metrics into $\ell_1$. We also study relationships between families of (strong) $k$-metrics, and show that natural quantities, like simplex volume, are strong $k$-metrics.

cs.CG↗

arXiv2023

An Incremental Span-Program-Based Algorithm and the Fine Print of Quantum Topological Data Analysis

We introduce a new quantum algorithm for computing the Betti numbers of a simplicial complex. In contrast to previous quantum algorithms that work by estimating the eigenvalues of the combinatorial Laplacian, our algorithm is an instance of the generic Incremental Algorithm for computing Betti numbers that incrementally adds simplices to the simplicial complex and tests whether or not they create a cycle. In contrast to existing quantum algorithms for computing Betti numbers that work best when the complex has close to the maximal number of simplices, our algorithm works best for sparse complexes. To test whether a simplex creates a cycle, we introduce a quantum span-program algorithm. We show that the query complexity of our span program is parameterized by quantities called the effective resistance and effective capacitance of the boundary of the simplex. Unfortunately, we also prove upper and lower bounds on the effective resistance and capacitance, showing both quantities can be exponentially large with respect to the size of the complex, implying that our algorithm would have to run for exponential time to exactly compute Betti numbers. However, as a corollary to these bounds, we show that the spectral gap of the combinatorial Laplacian can be exponentially small. As the runtime of all previous quantum algorithms for computing Betti numbers are parameterized by the inverse of the spectral gap, our bounds show that all quantum algorithms for computing Betti numbers must run for exponentially long to exactly compute Betti numbers. Finally, we prove some novel formulas for effective resistance and effective capacitance to give intuition for these quantities.

quant-ph↗

arXiv2023

Understanding Oversquashing in GNNs through the Lens of Effective Resistance

Message passing graph neural networks (GNNs) are a popular learning architectures for graph-structured data. However, one problem GNNs experience is oversquashing, where a GNN has difficulty sending information between distant nodes. Understanding and mitigating oversquashing has recently received significant attention from the research community. In this paper, we continue this line of work by analyzing oversquashing through the lens of the effective resistance between nodes in the input graph. Effective resistance intuitively captures the ``strength'' of connection between two nodes by paths in the graph, and has a rich literature spanning many areas of graph theory. We propose to use total effective resistance as a bound of the total amount of oversquashing in a graph and provide theoretical justification for its use. We further develop an algorithm to identify edges to be added to an input graph to minimize the total effective resistance, thereby alleviating oversquashing. We provide empirical evidence of the effectiveness of our total effective resistance based rewiring strategies for improving the performance of GNNs.

cs.LG↗

arXiv2022

Hodge Decomposition and General Laplacian Solvers for Embedded Simplicial Complexes

We describe a nearly-linear time algorithm to solve the linear system $L_1x = b$ parameterized by the first Betti number of the complex, where $L_1$ is the 1-Laplacian of a simplicial complex $K$ that is a subcomplex of a collapsible complex $X$ linearly embedded in $\mathbb{R}^{3}$. Our algorithm generalizes the work of Black et al.~[SODA2022] that solved the same problem but required that $K$ have trivial first homology. Our algorithm works for complexes $K$ with arbitrary first homology with running time that is nearly-linear with respect to the size of the complex and polynomial with respect to the first Betti number. The key to our solver is a new algorithm for computing the Hodge decomposition of 1-chains of $K$ in nearly-linear time. Additionally, our algorithm implies a nearly quadratic solver and nearly quadratic Hodge decomposition for the 1-Laplacian of any simplicial complex $K$ embedded in $\mathbb{R}^{3}$, as $K$ can always be expanded to a collapsible embedded complex of quadratic complexity.

math.NA↗

arXiv2022

Finding minimum bounded and homologous chains in simplicial complexes with bounded-treewidth 1-skeleton

We consider two problems on simplicial complexes: the Optimal Bounded Chain Problem and the Optimal Homologous Chain Problem. The Optimal Bounded Chain Problem asks to find the minimum weight $d$-chain in a simplicial complex $K$ bounded by a given $(d{-}1)$-chain, if such a $d$-chain exists. The Optimal Homologous Chain problem asks to find the minimum weight $(d{-}1)$-chain in $K$ homologous to a given $(d{-}1)$-chain. Both of these problems are NP-hard and hard to approximate within any constant factor assuming the Unique Games Conjecture. We prove that these problems are fixed-parameter tractable with respect to the treewidth of the 1-skeleton of $K$.

cs.CG↗

arXiv2022

ETH-tight algorithms for finding surfaces in simplicial complexes of bounded treewidth

Given a simplicial complex with $n$ simplices, we consider the Connected Subsurface Recognition (c-SR) problem of finding a subcomplex that is homeomorphic to a given connected surface with a fixed boundary. We also study the related Sum-of-Genus Subsurface Recognition (SoG) problem, where we instead search for a surface whose boundary, number of connected components, and total genus are given. For both of these problems, we give parameterized algorithms with respect to the treewidth $k$ of the Hasse diagram that run in $2^{O(k \log k)}n^{O(1)}$ time. For the SoG problem, we also prove that our algorithm is optimal assuming the exponential-time hypothesis. In fact, we prove the stronger result that our algorithm is ETH-tight even without restriction on the total genus.

cs.CG↗

arXiv2022

On Cyclic Solutions to the Min-Max Latency Multi-Robot Patrolling Problem

We consider the following surveillance problem: Given a set $P$ of $n$ sites in a metric space and a set of $k$ robots with the same maximum speed, compute a patrol schedule of minimum latency for the robots. Here a patrol schedule specifies for each robot an infinite sequence of sites to visit (in the given order) and the latency $L$ of a schedule is the maximum latency of any site, where the latency of a site $s$ is the supremum of the lengths of the time intervals between consecutive visits to $s$. When $k=1$ the problem is equivalent to the travelling salesman problem (TSP) and thus it is NP-hard. We have two main results. We consider cyclic solutions in which the set of sites must be partitioned into $\ell$ groups, for some~$\ell \leq k$, and each group is assigned a subset of the robots that move along the travelling salesman tour of the group at equal distance from each other. Our first main result is that approximating the optimal latency of the class of cyclic solutions can be reduced to approximating the optimal travelling salesman tour on some input, with only a $1+\varepsilon$ factor loss in the approximation factor and an $O\left(\left( k/\varepsilon \right)^k\right)$ factor loss in the runtime, for any $\varepsilon >0$. Our second main result shows that an optimal cyclic solution is a $2(1-1/k)$-approximation of the overall optimal solution. Note that for $k=2$ this implies that an optimal cyclic solution is optimal overall. The results have a number of consequences. For the Euclidean version of the problem, for instance, combining our results with known results on Euclidean TSP, yields a PTAS for approximating an optimal cyclic solution, and it yields a $(2(1-1/k)+\varepsilon)$-approximation of the optimal unrestricted solution. If the conjecture mentioned above is true, then our algorithm is actually a PTAS for the general problem in the Euclidean setting.

cs.CG↗

arXiv2021

Generalized max-flows and min-cuts in simplicial complexes

We consider high dimensional variants of the maximum flow and minimum cut problems in the setting of simplicial complexes and provide both algorithmic and hardness results. By viewing flows and cuts topologically in terms of the simplicial (co)boundary operator we can state these problems as linear programs and show that they are dual to one another. Unlike graphs, complexes with integral capacity constraints may have fractional max-flows. We show that computing a maximum integral flow is NP-hard. Moreover, we give a combinatorial definition of a simplicial cut that seems more natural in the context of optimization problems and show that computing such a cut is NP-hard. However, we provide conditions on the simplicial complex for when the cut found by the linear program is a combinatorial cut. For $d$-dimensional simplicial complexes embedded into $\mathbb{R}^{d+1}$ we provide algorithms operating on the dual graph: computing a maximum flow is dual to computing a shortest path and computing a minimum cut is dual to computing a minimum cost circulation. Finally, we investigate the Ford-Fulkerson algorithm on simplicial complexes, prove its correctness, and provide a heuristic which guarantees it to halt.

cs.DS↗

arXiv2020

Approximation Algorithms for Multi-Robot Patrol-Scheduling with Min-Max Latency

We consider the problem of finding patrol schedules for $k$ robots to visit a given set of $n$ sites in a metric space. Each robot has the same maximum speed and the goal is to minimize the weighted maximum latency of any site, where the latency of a site is defined as the maximum time duration between consecutive visits of that site. The problem is NP-hard, as it has the traveling salesman problem as a special case (when $k=1$ and all sites have the same weight). We present a polynomial-time algorithm with an approximation factor of $O(k^2 \log \frac{w_{\max}}{w_{\min}})$ to the optimal solution, where $w_{\max}$ and $w_{\min}$ are the maximum and minimum weight of the sites respectively. Further, we consider the special case where the sites are in 1D. When all sites have the same weight, we present a polynomial-time algorithm to solve the problem exactly. If the sites may have different weights, we present a $12$-approximate solution, which runs in polynomial time when the number of robots, $k$, is a constant.

cs.DS↗

arXiv2020

Low-stretch spanning trees of graphs with bounded width

We study the problem of low-stretch spanning trees in graphs of bounded width: bandwidth, cutwidth, and treewidth. We show that any simple connected graph $G$ with a linear arrangement of bandwidth $b$ can be embedded into a distribution $\mathcal T$ of spanning trees such that the expected stretch of each edge of $G$ is $O(b^2)$. Our proof implies a linear time algorithm for sampling from $\mathcal T$. Therefore, we have a linear time algorithm that finds a spanning tree of $G$ with average stretch $O(b^2)$ with high probability. We also describe a deterministic linear-time algorithm for computing a spanning tree of $G$ with average stretch $O(b^3)$. For graphs of cutwidth $c$, we construct a spanning tree with stretch $O(c^2)$ in linear time. Finally, when $G$ has treewidth $k$ we provide a dynamic programming algorithm computing a minimum stretch spanning tree of $G$ that runs in polynomial time with respect to the number of vertices of $G$.

cs.DS↗

arXiv2020

Minimum bounded chains and minimum homologous chains in embedded simplicial complexes

We study two optimization problems on simplicial complexes with homology over $\mathbb{Z}_2$, the minimum bounded chain problem: given a $d$-dimensional complex $\mathcal{K}$ embedded in $\mathbb{R}^{d+1}$ and a null-homologous $(d-1)$-cycle $C$ in $\mathcal{K}$, find the minimum $d$-chain with boundary $C$, and the minimum homologous chain problem: given a $(d+1)$-manifold $\mathcal{M}$ and a $d$-chain $D$ in $\mathcal{M}$, find the minimum $d$-chain homologous to $D$. We show strong hardness results for both problems even for small values of $d$; $d = 2$ for the former problem, and $d=1$ for the latter problem. We show that both problems are APX-hard, and hard to approximate within any constant factor assuming the unique games conjecture. On the positive side, we show that both problems are fixed parameter tractable with respect to the size of the optimal solution. Moreover, we provide an $O(\sqrt{\log β_d})$-approximation algorithm for the minimum bounded chain problem where $β_d$ is the $d$th Betti number of $\mathcal{K}$. Finally, we provide an $O(\sqrt{\log n_{d+1}})$-approximation algorithm for the minimum homologous chain problem where $n_{d+1}$ is the number of $d$-simplices in $\mathcal{M}$.

cs.CG↗

arXiv2019

Minimum Cuts in Surface Graphs

We describe algorithms to efficiently compute minimum $(s,t)$-cuts and global minimum cuts of undirected surface-embedded graphs. Given an edge-weighted undirected graph $G$ with $n$ vertices embedded on an orientable surface of genus $g$, our algorithms can solve either problem in $g^{O(g)} n \log \log n$ or $2^{O(g)} n \log n$ time, whichever is better. When $g$ is a constant, our $g^{O(g)} n \log \log n$ time algorithms match the best running times known for computing minimum cuts in planar graphs. Our algorithms for minimum cuts rely on reductions to the problem of finding a minimum-weight subgraph in a given $\mathbb{Z}_2$-homology class, and we give efficient algorithms for this latter problem as well. If $G$ is embedded on a surface with $b$ boundary components, these algorithms run in $(g + b)^{O(g + b)} n \log \log n$ and $2^{O(g + b)} n \log n$ time. We also prove that finding a minimum-weight subgraph homologous to a single input cycle is NP-hard, showing it is likely impossible to improve upon the exponential dependencies on $g$ for this latter problem.

cs.DS↗