Related papers: A Compact DAG for Storing and Searching Maximal Co…
The construction of complementary sets (CSs) of sequences with different set size and sequence length become important due to its practical application for OFDM systems. Most of the constructions of CSs, based on generalized Boolean…
Finding maximal exact matches (MEMs) between strings is an important task in bioinformatics, but it is becoming increasingly challenging as geneticists switch to pangenomic references. Fortunately, we are usually interested only in the…
The problem of finding the longest common subsequence (LCS) for a set of sequences is a very interesting and challenging problem in computer science. This problem is NP-complete, but because of its importance, many heuristic algorithms have…
A DAG compression of a (typically dense) graph is a simple data structure that stores how vertex clusters are connected, where the clusters are described indirectly as sets of reachable sinks in a directed acyclic graph (DAG). They…
This paper studies the completeness of conjunctive queries over a partially complete database and the approximation of incomplete queries. Given a query and a set of completeness rules (a special kind of tuple generating dependencies) that…
In the Minimum Consistent Subset (MCS) problem, we are presented with a connected simple undirected graph $G=(V,E)$, consisting of a vertex set $V$ of size $n$ and an edge set $E$. Each vertex in $V$ is assigned a color from the set…
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…
Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches…
Minimal Strong Digraphs (MSDs) can be regarded as a generalization of the concept of tree to directed graphs. Their cyclic structure and some spectral properties have been studied in several articles. In this work, we further study some…
We present practical linear and almost linear-time algorithms to compute a chain decomposition of a directed acyclic graph (DAG), $G=(V,E)$. The number of vertex-disjoint chains computed is very close to the minimum. The time complexity of…
This paper reformulates the problem of finding a longest common increasing subsequence of the two given input sequences in a very succinct way. An extremely simple linear space algorithm based on the new formula can find a longest common…
In the problem of the longest common substring with $k$ mismatches we are given two strings $X, Y$ and must find the maximal length $\ell$ such that there is a length-$\ell$ substring of $X$ and a length-$\ell$ substring of $Y$ that differ…
At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…
A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once. Let R denote the length of a repetition free LCS of two sequences of n symbols each one chosen…
We describe computationally efficient methods for learning mixtures in which each component is a directed acyclic graphical model (mixtures of DAGs or MDAGs). We argue that simple search-and-score algorithms are infeasible for a variety of…
Maximal Clique Enumeration (MCE) is a fundamental graph mining problem, and is useful as a primitive in identifying dense structures in a graph. Due to the high computational cost of MCE, parallel methods are imperative for dealing with…
Directed Acyclic Graphs (DAGs) are a standard tool in causal modeling, but their suitability for capturing the complexity of large-scale multimodal data is questionable. In practice, real-world multimodal datasets are often collected from…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
A recent approach to building consensus protocols on top of Directed Acyclic Graphs (DAGs) shows much promise due to its simplicity and stable throughput. However, as each node in the DAG typically includes a linear number of references to…
Causal discovery from observational data is pivotal for deciphering complex relationships. Causal Structure Learning (CSL), which focuses on deriving causal Directed Acyclic Graphs (DAGs) from data, faces challenges due to vast DAG spaces…