Related papers: The Binary Perfect Phylogeny with Persistent chara…
This paper discusses scalability of standard genetic programming (GP) and the probabilistic incremental program evolution (PIPE). To investigate the need for both effective mixing and linkage learning, two test problems are considered:…
We introduce a binary embedding framework, called Proximity Preserving Code (PPC), which learns similarity and dissimilarity between data points to create a compact and affinity-preserving binary code. This code can be used to apply fast…
Binary (0-1) integer programming (BIP) is pivotal in scientific domains requiring discrete decision-making. As the advance of AI computing, recent works explore neural network-based solvers for integer linear programming (ILP) problems.…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
Recently, the perfect phylogeny model with persistent characters has attracted great attention in the literature. It is based on the assumption that complex traits or characters can only be gained once and lost once in the course of…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
We describe two BQP-complete problems concerning properties of sparse graphs having a certain symmetry. The graphs are specified by efficiently computable functions which output the adjacent vertices for each vertex. Let i and j be two…
A pattern p (i.e., a string of variables and terminals) matches a word w, if w can be obtained by uniformly replacing the variables of p by terminal words. The respective matching problem, i.e., deciding whether or not a given pattern…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Completion problems, of recovering a point from a set of observed coordinates, are abundant in applications to image reconstruction, phylogenetics, and data science. We consider a completion problem coming from algebraic statistics: to…
The graph coloring problem (GCP) is one of the most studied NP-HARD problems in computer science. Given a graph , the task is to assign a color to all vertices such that no vertices sharing an edge receive the same color and that the number…
Given an integer $k$ and a graph where every edge is colored either red or blue, the goal of the exact matching problem is to find a perfect matching with the property that exactly $k$ of its edges are red. Soon after Papadimitriou and…
We show that the problem of counting perfect matchings remains #P-complete even if we restrict the input to very dense graphs, proving the conjecture in [5]. Here "dense graphs" refer to bipartite graphs of bipartite independence number…
NP complete problem is one of the most challenging issues. The question of whether all problems in NP are also in P is generally considered one of the most important open questions in mathematics and theoretical computer science as it has…
We present a quantum algorithm in bioinformatics for solving the Binary Near-Perfect Phylogeny Problem (BNPP) with a complexity bound of $O(8.926^q + 8^q nm2)$, where n is the number of input taxa and m is the sequence length for each taxon…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…