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A mixed dominating set is a collection of vertices and edges that dominates all vertices and edges of a graph. We study the complexity of exact and parameterized algorithms for \textsc{Mixed Dominating Set}, resolving some open questions.…
Many proposals have already been made for realizing programmable matter, ranging from shape-changing molecules, DNA tiles, and synthetic cells to reconfigurable modular robotics. Envisioning systems of nano-sensors devices, we are…
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…
Packing optimization is a prevalent problem that necessitates robust and efficient algorithms that are also simple to implement. One group of approaches is the raster methods, which rely on approximating the objects with pixelated…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
We consider the Minimum Convex Partition problem: Given a set P of n points in the plane, draw a plane graph G on P, with positive minimum degree, such that G partitions the convex hull of P into a minimum number of convex faces. We show…
The \emph{Steiner tree} problem is one of the fundamental and classical problems in combinatorial optimization. In this paper, we study this problem in the $\mathcal{CONGESTED}$ $\mathcal{CLIQUE}$ model of distributed computing and present…
Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled…
One of the major applications of generative models for drug Discovery targets the lead-optimization phase. During the optimization of a lead series, it is common to have scaffold constraints imposed on the structure of the molecules…
A number of intriguing decision scenarios revolve around partitioning a collection of objects to optimize some application specific objective function. This problem is generally referred to as the Object Partitioning Problem (OPP) and is…
It has recently been shown that starting with a classical query algorithm (decision tree) and a guessing algorithm that tries to predict the query answers, we can design a quantum algorithm with query complexity $O(\sqrt{GT})$ where $T$ is…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Recently, convex nested stochastic composite optimization (NSCO) has received considerable attention for its applications in reinforcement learning and risk-averse optimization. The current NSCO algorithms have worse stochastic oracle…
Many recent studies on first-order methods (FOMs) focus on \emph{composite non-convex non-smooth} optimization with linear and/or nonlinear function constraints. Upper (or worst-case) complexity bounds have been established for these…
We investigate the Optimal Obstacle Placement (OOP) problem under uncertainty, framed as the dual of the Optimal Traversal Path problem in the Stochastic Obstacle Scene paradigm. We consider both continuous domains, discretized for…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the…
Many graph problems were first shown to be fixed-parameter tractable using the results of Robertson and Seymour on graph minors. We show that the combination of finite, computable, obstruction sets and efficient order tests is not just one…
We consider the ideal orientation problem in planar graphs. In this problem, we are given an undirected graph $G$ with positive edge lengths and $k$ pairs of distinct vertices $(s_1, t_1), \dots, (s_k, t_k)$ called terminals, and we want to…