Related papers: Pairwise Rearrangement is Fixed-Parameter Tractabl…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
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…
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:…
Redistricting is the problem of dividing a state into a number $k$ of regions, called districts. Voters in each district elect a representative. The primary criteria are: each district is connected, district populations are equal (or nearly…
Our work is motivated by the challenges presented in preparing arrays of atoms for use in quantum simulation. The recently-developed process of loading atoms into traps results in approximately half of the traps being filled. To consolidate…
What is the minimal information that a robot must retain to achieve its task? To design economical robots, the literature dealing with reduction of combinatorial filters approaches this problem algorithmically. As lossless state compression…
We study the perfect matching reconfiguration problem: Given two perfect matchings of a graph, is there a sequence of flip operations that transforms one into the other? Here, a flip operation exchanges the edges in an alternating cycle of…
This paper studies the unification problem with associative, commutative, and associative-commutative functions mainly from a viewpoint of the parameterized complexity on the number of variables. It is shown that both associative and…
In this work, we explore heuristics for the Adjacency Graph Packing problem, which can be applied to the Double Cut and Join (DCJ) Distance Problem. The DCJ is a rearrangement operation and the distance problem considering it is a well…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…
Probabilistic Circuits (PCs) are a promising avenue for probabilistic modeling. They combine advantages of probabilistic graphical models (PGMs) with those of neural networks (NNs). Crucially, however, they are tractable probabilistic…
The graph parameter of pathwidth can be seen as a measure of the topological resemblance of a graph to a path. A popular definition of pathwidth is given in terms of node search where we are given a system of tunnels that is contaminated by…
A matching is a set of edges in a graph with no common endpoint. A matching M is called acyclic if the induced subgraph on the endpoints of the edges in M is acyclic. Given a graph G and an integer k, Acyclic Matching Problem seeks for an…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Given a graph G, a matching is a subset of edges of G that do not share an endpoint. A matching M is uniquely restricted if the subgraph induced by the endpoints of the edges of M has exactly one perfect matching. Given a graph G and a…
Autonomous reconfiguration of agent-based systems is a key challenge in the study of programmable matter, distributed robotics, and molecular self-assembly. While substantial prior work has focused on size-preserving transformations, much…
Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…
In this article, we study parameterized complexity theory from the perspective of logic, or more specifically, descriptive complexity theory. We propose to consider parameterized model-checking problems for various fragments of first-order…
We study the fixed-parameter tractability of the following fundamental problem: given two directed graphs $\vec H$ and $\vec G$, count the number of copies of $\vec H$ in $\vec G$. The standard setting, where the tractability is well…