Related papers: Algorithms for the Constrained Perfect Phylogeny w…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Set covering problem is an important class of combinatorial optimization problems, which has been widely applied and studied in many fields. In this paper, we propose an improved column generation algorithm with neural prediction (CG-P) for…
The Consecutive-Ones Property (C1P) is a classical concept in discrete mathematics that has been used in several genomics applications, from physical mapping of contemporary genomes to the assembly of ancient genomes. A common issue in…
We study the problem of maximizing a monotone submodular function with viability constraints. This problem originates from computational biology, where we are given a phylogenetic tree over a set of species and a directed graph, the…
Recent advances in text-to-image generation models have unlocked vast potential for visual creativity. However, the users that use these models struggle with the generation of consistent characters, a crucial aspect for numerous real-world…
Linear Genetic Programming (LGP) is a powerful technique that allows for a variety of problems to be solved using a linear representation of programs. However, there still exists some limitations to the technique, such as the need for…
We introduce a problem class we call Polynomial Constraint Satisfaction Problems, or PCSP. Where the usual CSPs from computer science and optimization have real-valued score functions, and partition functions from physics have monomials,…
Traditional Linear Genetic Programming (LGP) algorithms are based only on the selection mechanism to guide the search. Genetic operators combine or mutate random portions of the individuals, without knowing if the result will lead to a…
Contemporary genetic programming (GP) systems for general program synthesis have been primarily concerned with evolving programs that can manipulate values from a standard set of primitive data types and simple indexed data structures. In…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…
Given an indeterminate string pattern $p$ and an indeterminate string text $t$, the problem of order-preserving pattern matching with character uncertainties ($\mu$OPPM) is to find all substrings of $t$ that satisfy one of the possible…
This work aims to introduce the framework of polynomial optimization theory to solve fractional polynomial problems (FPPs). Unlike other widely used optimization frameworks, the proposed one applies to a larger class of FPPs, not…
In phylogenetic analysis, for non-molecular data, particularly morphology, parsimony optimization is the most commonly employed approach. In the past and present application of the parsimony principle, extra step numbers have been added…
We investigate the parameterized complexity of finding subgraphs with hereditary properties on graphs belonging to a hereditary graph class. Given a graph $G$, a non-trivial hereditary property $\Pi$ and an integer parameter $k$, the…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
The closest pair problem (CPP) is one of the well studied and fundamental problems in computing. Given a set of points in a metric space, the problem is to identify the pair of closest points. Another closely related problem is the fixed…
Perfect Matching-Cut is the problem of deciding whether a graph has a perfect matching that contains an edge-cut. We show that this problem is NP-complete for planar graphs with maximum degree four, for planar graphs with girth five, for…
We study the graphs formed from instances of the stable matching problem by connecting pairs of elements with an edge when there exists a stable matching in which they are matched. Our results include the NP-completeness of recognizing…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…