相关论文: Linear Time Construction of Indexable Founder Bloc…

Pattern matching on graphs has been widely studied lately due to its importance in genomics applications. Unfortunately, even the simplest problem of deciding if a string appears as a subpath of a graph admits a quadratic lower bound under…

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…

Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments…

Indexing labeled graphs for pattern matching is a central challenge of pangenomics. Equi et al. (Algorithmica, 2022) developed the Elastic Founder Graph ($\mathsf{EFG}$) representing an alignment of $m$ sequences of length $n$, drawn from…

The min-rank of a graph was introduced by Haemers (1978) to bound the Shannon capacity of a graph. This parameter of a graph has recently gained much more attention from the research community after the work of Bar-Yossef et al. (2006). In…

Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…

In this paper we consider the problem of computing an mRNA sequence of maximal similarity for a given mRNA of secondary structure constraints, introduced by Backofen et al. in [BNS02] denoted as the MRSO problem. The problem is known to be…

We consider the unrestricted, minimal, and bounded representation problems for unit interval (UIG) and unit circular-arc (UCA) graphs. In the unrestricted version, a proper circular-arc (PCA) model $\cal M$ is given and the goal is to…

The LCP array is an important tool in stringology, allowing to speed up pattern matching algorithms and enabling compact representations of the suffix tree. Recently, Conte et al. [DCC 2023] and Cotumaccio et al. [SPIRE 2023] extended the…

The independence number of a tree decomposition is the size of a largest independent set contained in a single bag. The tree-independence number of a graph $G$ is the minimum independence number of a tree decomposition of $G$. As shown…

For the first time we provide a succinct pattern matching index for arbitrary graphs that can be built in polynomial time, which requires less space and answers queries more efficiently than the one in [SODA 2021]. We show that, given an…

Simple graph algorithms such as PageRank have been the target of numerous hardware accelerators. Yet, there also exist much more complex graph mining algorithms for problems such as clustering or maximal clique listing. These algorithms are…

In this paper we consider sparse and identifiable linear latent variable (factor) and linear Bayesian network models for parsimonious analysis of multivariate data. We propose a computationally efficient method for joint parameter and model…

We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some…

In this paper we show how to combine two algorithmic techniques to obtain linear time algorithms for various optimization problems on graphs, and present a subroutine which will be useful in doing so. The first technique is iterative…

Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…

We present a data structure that can maintain a simple planar graph under edge contractions in linear total time. The data structure supports adjacency queries and provides access to neighbor lists in $O(1)$ time. Moreover, it can report…

Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…

Many approaches to transform classification problems from non-linear to linear by feature transformation have been recently presented in the literature. These notably include sparse coding methods and deep neural networks. However, many of…

Linear arrangements of graphs are a well-known type of graph labeling and are found in many important computational problems, such as the Minimum Linear Arrangement Problem ($\texttt{minLA}$). A linear arrangement is usually defined as a…