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Given a graph and a root, the Maximum Bounded Rooted-Tree Packing (MBRTP) problem aims at finding K rooted-trees that span the largest subset of vertices, when each vertex has a limited outdegree. This problem is motivated by peer-to-peer…
We consider the max-cut and max-$k$-cut problems under graph-based constraints. Our approach can handle any constraint specified using monadic second-order (MSO) logic on graphs of constant treewidth. We give a $\frac{1}{2}$-approximation…
In this paper we study a scheduling problem arising from executing numerical simulations on HPC architectures. With a constant number of parallel machines, the objective is to minimize the makespan under memory constraints for the machines.…
We present a general technique, based on parametric search with some twist, for solving a variety of optimization problems on a set of semi-algebraic geometric objects of constant complexity. The common feature of these problems is that…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Considering the worst-case scenario, junction tree algorithm remains the most general solution for exact MAP inference with polynomial run-time guarantees. Unfortunately, its main tractability assumption requires the treewidth of a…
We consider the problem of minimizing the makespan on batch processing identical machines, subject to compatibility constraints, where two jobs are compatible if they can be processed simultaneously in a same batch. These constraints are…
Graph alignment aims at finding the vertex correspondence between two correlated graphs, a task that frequently occurs in graph mining applications such as social network analysis. Attributed graph alignment is a variant of graph alignment,…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
We consider drawings of graphs in the plane in which vertices are assigned distinct points in the plane and edges are drawn as simple curves connecting the vertices and such that the edges intersect only at their common endpoints. There is…
This paper introduces the Simultaneous assignment problem. Let us given a graph with a weight and a capacity function on its edges, and a set of its subgraphs along with a degree upper bound function for each of them. We are also given a…
We introduce and study the problem of optimizing arbitrary functions over degree sequences of hypergraphs and multihypergraphs. We show that over multihypergraphs the problem can be solved in polynomial time. For hypergraphs, we show that…
Many complex questions in biology, physics, and mathematics can be mapped to the graph isomorphism problem and the closely related graph automorphism problem. In particular, these problems appear in the context of network visualization,…
We study two variants of \textsc{Maximum Cut}, which we call \textsc{Connected Maximum Cut} and \textsc{Maximum Minimal Cut}, in this paper. In these problems, given an unweighted graph, the goal is to compute a maximum cut satisfying some…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
(Induced) Subgraph Isomorphism and Maximum Common (Induced) Subgraph are fundamental problems in graph pattern matching and similarity computation. In graphs derived from time-series data or protein structures, a natural total ordering of…
A common approach for designing scalable algorithms for massive data sets is to distribute the computation across, say $k$, machines and process the data using limited communication between them. A particularly appealing framework here is…
The graphical realization of a given degree sequence and given partition adjacency matrix simultaneously is a relevant problem in data driven modeling of networks. Here we formulate common generalizations of this problem and the Exact…
This paper presents a new anytime algorithm for the marginal MAP problem in graphical models. The algorithm is described in detail, its complexity and convergence rate are studied, and relations to previous theoretical results for the…
We consider the massively parallel computation (MPC) model, which is a theoretical abstraction of large-scale parallel processing models such as MapReduce. In this model, assuming the widely believed 1-vs-2-cycles conjecture, solving many…