Related papers: The Largest Compatible Subset Problem for Phylogen…

Matchings and coverings are central topics in graph theory. The close relationship between these two has been key to many fundamental algorithmic and polyhedral results. For mixed graphs, the notion of matching forest was proposed as a…

Finding a minimum vertex cover in a network is a fundamental NP-complete graph problem. One way to deal with its computational hardness, is to trade the qualitative performance of an algorithm (allowing non-optimal outputs) for an improved…

Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…

We consider the challenges that arise when fitting complex ecological models to 'large' data sets. In particular, we focus on random effect models which are commonly used to describe individual heterogeneity, often present in ecological…

Near ubiquitous mobile computing has led to intense interest in dynamic graph theory. This provides a new and challenging setting for algorithmics and complexity theory. For any graph-based problem, the rapid evolution of a (possibly…

The densest $k$-subgraph problem is the problem of finding a $k$-vertex subgraph of a graph with the maximum number of edges. In order to solve large instances of the densest $k$-subgraph problem, we introduce two algorithms that are based…

A graph $H$ is {\em $p$-edge colorable} if there is a coloring $\psi: E(H) \rightarrow \{1,2,\dots,p\}$, such that for distinct $uv, vw \in E(H)$, we have $\psi(uv) \neq \psi(vw)$. The {\sc Maximum Edge-Colorable Subgraph} problem takes as…

Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…

An instance of the Connected Maximum Cut problem consists of an undirected graph G = (V, E) and the goal is to find a subset of vertices S $\subseteq$ V that maximizes the number of edges in the cut \delta(S) such that the induced graph…

We consider a natural generalization of the Partial Vertex Cover problem. Here an instance consists of a graph G = (V,E), a positive cost function c: V-> Z^{+}, a partition $P_1,..., P_r$ of the edge set $E$, and a parameter $k_i$ for each…

Problems in scientific computing, such as distributing large sparse matrix operations, have analogous formulations as hypergraph partitioning problems. A hypergraph is a generalization of a traditional graph wherein "hyperedges" may connect…

We consider numerical solution of elliptic problems with heterogeneous diffusion coefficients containing thin highly conductive structures. Such problems arise e.g. in fractured porous media, reinforced materials, and electric circuits. The…

We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…

Let $G=(V,E)$ and $H$ be two graphs. Packing problem is to find in $G$ the largest number of independent subgraphs each of which is isomorphic to $H$. Let $U\subset{V}$. If the graph $G-U$ has no subgraph isomorphic to $H$, $U$ is a cover…

In this paper, we introduce a new model for sublinear algorithms called \emph{dynamic sketching}. In this model, the underlying data is partitioned into a large \emph{static} part and a small \emph{dynamic} part and the goal is to compute a…

Let $G=(V, E)$ be a graph where $V(G)$ and $E(G)$ are the vertex and edge sets, respectively. In a graph $G$, two edges $e_1, e_2\in E(G)$ are said to have a \emph{common edge} $e\neq e_1, e_2$ if $e$ joins an endpoint of $e_1$ to an…

We give efficient distributed algorithms for the minimum vertex cover problem in bipartite graphs in the CONGEST model. From K\H{o}nig's theorem, it is well known that in bipartite graphs the size of a minimum vertex cover is equal to the…

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…

In this paper, we study a number of well-known combinatorial optimization problems that fit in the following paradigm: the input is a collection of (potentially inconsistent) local relationships between the elements of a ground set (e.g.,…

Large datasets represented by multidimensional data point clouds often possess non-trivial distributions with branching trajectories and excluded regions, with the recent single-cell transcriptomic studies of developing embryo being notable…