Related papers: Combinatorial Parameterized Algorithms for Chemica…
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…
Dynamic programming on path and tree decompositions of graphs is a technique that is ubiquitous in the field of parameterized and exponential-time algorithms. However, one of its drawbacks is that the space usage is exponential in the…
There has been intensive work on the parameterized complexity of the typically NP-hard task to edit undirected graphs into graphs fulfilling certain given vertex degree constraints. In this work, we lift the investigations to the case of…
We study the Induced $H$ Partition problem from the parameterized complexity point of view. In the Induced $H$ Partition problem the task is to partition vertices of a graph $G$ into sets $V_1,V_2,\dots,V_n$ such that the graph $H$ is…
A range of quantum algorithms, especially those leveraging variational parameterization and circuit-based optimization, are being studied as alternatives for solving classically intractable combinatorial optimization problems (COPs).…
Mass spectrometry (MS) is an important technique for chemical profiling which calculates for a sample a high dimensional histogram-like spectrum. A crucial step of MS data processing is the peak picking which selects peaks containing…
We initiate a systematic study of utilizing predictions to improve over approximation guarantees of classic algorithms, without increasing the running time. We propose a systematic method for a wide class of optimization problems that ask…
Many practical problems in almost all scientific and technological disciplines have been classified as computationally hard (NP-hard or even NP-complete). In life sciences, combinatorial optimization problems frequently arise in molecular…
The contributions of model complexity, data volume, and feature modalities to knowledge graph-based drug repurposing remain poorly quantified under rigorous temporal validation. We constructed a pharmacology knowledge graph from ChEMBL 36…
In this paper we compare and illustrate the algorithmic use of graphs of bounded tree-width and graphs of bounded clique-width. For this purpose we give polynomial time algorithms for computing the four basic graph parameters independence…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Graph-structured data arise ubiquitously in many application domains. A fundamental problem is to quantify their similarities. Graph kernels are often used for this purpose, which decompose graphs into substructures and compare these…
In this study, we present a method of pattern mining based on network theory that enables the identification of protein structures or complexes from synthetic volume densities, without the knowledge of predefined templates or human biases…
Query evaluation over probabilistic databases is notoriously intractable -- not only in combined complexity, but often in data complexity as well. This motivates the study of approximation algorithms, and particularly of combined FPRASes,…
It is known that problems like Vertex Cover, Feedback Vertex Set and Odd Cycle Transversal are polynomial time solvable in the class of chordal graphs. We consider these problems in a graph that has at most $k$ vertices whose deletion…
The theoretical notions of graph classes with bounded expansion and that are nowhere dense are meant to capture structural sparsity of real world networks that can be used to design efficient algorithms. In the area of sparse graphs, the…
In a recent breakthrough, Kelley and Meka (FOCS 2023) obtained a strong upper bound on the density of sets of integers without nontrivial three-term arithmetic progressions. In this work, we extend their result, establishing similar bounds…
We study the classical problem of computing geometric thickness, i.e., finding a straight-line drawing of an input graph and a partition of its edges into as few parts as possible so that each part is crossing-free. Since the problem is…
A set S of vertices of a graph is a defensive alliance if, for each element of S, the majority of its neighbors is in S. The problem of finding a defensive alliance of minimum size in a given graph is NP-hard and there are polynomial-time…