Related papers: Variations on the Problem of Identifying Spectrum-…

Using quantum annealing to solve an optimization problem requires minor embeddings of a logic graph into a known hardware graph. In an effort to reduce the complexity of the minor embedding problem, we introduce the minor set cover (MSC) of…

Aligning sequencing reads on graph representations of genomes is an important ingredient of pan-genomics. Such approaches typically find a set of local anchors that indicate plausible matches between substrings of a read to subpaths of the…

Neighborhood graphs are a critical but often fragile step in spectral clustering of text embeddings. On realistic text datasets, standard $k$-NN graphs can contain many disconnected components at practical sparsity levels (small $k$),…

Spectral-based subspace clustering methods have proved successful in many challenging applications such as gene sequencing, image recognition, and motion segmentation. In this work, we first propose a novel spectral-based subspace…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

We show variants of spectral sparsification routines can preserve the total spanning tree counts of graphs, which by Kirchhoff's matrix-tree theorem, is equivalent to determinant of a graph Laplacian minor, or equivalently, of any SDDM…

In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…

In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…

The Column Subset Selection Problem (CSSP) and the Nystr\"om method are among the leading tools for constructing small low-rank approximations of large datasets in machine learning and scientific computing. A fundamental question in this…

Most of the recent studies tackling routing problems like the Traveling Salesman Problem (TSP) with machine learning use a transformer or Graph Neural Network (GNN) based encoder architecture. However, many of them apply these encoders…

Word-representable graphs, which are the same as semi-transitively orientable graphs, generalize several fundamental classes of graphs. In this paper we propose a novel approach to study word-representability of graphs using a technique of…

Graph representation learning has emerged as a cornerstone for tasks like node classification and link prediction, yet prevailing self-supervised learning (SSL) methods face challenges such as computational inefficiency, reliance on…

Many complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into…

A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…

RNA-Seq technology offers new high-throughput ways for transcript identification and quantification based on short reads, and has recently attracted great interest. The problem is usually modeled by a weighted splicing graph whose nodes…

We propose a simple, powerful, and flexible machine learning framework for (i) reducing the search space of computationally difficult enumeration variants of subset problems and (ii) augmenting existing state-of-the-art solvers with…

Spectral clustering is a fundamental method for graph partitioning, but its reliance on eigenvector computation limits scalability to massive graphs. Classical sparsification methods preserve spectral properties by sampling edges…

The inference of minimum spanning arborescences within a set of objects is a general problem which translates into numerous application-specific unsupervised learning tasks. We introduce a unified and generic structure called edit…

Let G be a simple connected graph with vertex set V(G) and edge set E(G. Each vertex of V(G) is colored by a color from the set of colors {c_1, c_2,\dots, c_{\alpha}}. We take a subset S of V(G), such that for every vertex v in V(G)\S, at…

Clustering is a well-known and studied problem, one of its variants, called contiguity-constrained clustering, accepts as a second input a graph used to encode prior information about cluster structure by means of contiguity constraints…