Related papers: Computing the LCP Array of a Labeled Graph
The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
We present the analysis of the topological graph descriptor Local Degree Profile (LDP), which forms a widely used structural baseline for graph classification. Our study focuses on model evaluation in the context of the recently developed…
We consider how to assign labels to any undirected graph with n nodes such that, given the labels of two nodes and no other information regarding the graph, it is possible to determine the distance between the two nodes. The challenge in…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
In this study, we address the complex issue of graph clustering in signed graphs, which are characterized by positive and negative weighted edges representing attraction and repulsion among nodes, respectively. The primary objective is to…
Conformal prediction (CP) provides a distribution-free approach to uncertainty quantification with finite-sample guarantees. However, applying CP to graph neural networks (GNNs) remains challenging as the combinatorial nature of graphs…
We present novel graph kernels for graphs with node and edge labels that have ordered neighborhoods, i.e. when neighbor nodes follow an order. Graphs with ordered neighborhoods are a natural data representation for evolving graphs where…
Modern graph or network datasets often contain rich structure that goes beyond simple pairwise connections between nodes. This calls for complex representations that can capture, for instance, edges of different types as well as so-called…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…
In this paper, we consider the problem of counting and sampling structures in graphs. We define a class of "edge universal labeling problems"---which include proper $k$-colorings, independent sets, and downsets---and describe simple…
Automated ICD coding involves assigning standardized diagnostic codes to clinical narratives. The vast label space and extreme class imbalance continue to challenge precise prediction. To address these issues, LabGraph is introduced -- a…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we…
Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…
Solving classification with graph methods has gained huge popularity in recent years. This is due to the fact that the data can be intuitively modeled with graphs to utilize high level features to aid in solving the classification problem.…
We consider graph properties that can be checked from labels, i.e., bit sequences, of logarithmic length attached to vertices. We prove that there exists such a labeling for checking a first-order formula with free set variables in the…
We study the problem of matching a string in a labeled graph. Previous research has shown that unless the Orthogonal Vectors Hypothesis (OVH) is false, one cannot solve this problem in strongly sub-quadratic time, nor index the graph in…
In this paper, we present the first study of the computational complexity of converting an automata-based text index structure, called the Compact Directed Acyclic Word Graph (CDAWG), of size $e$ for a text $T$ of length $n$ into other text…