Parameterized Complexity Dichotomy for Steiner Multicut

The Steiner Multicut problem asks, given an undirected graph G, terminals sets T1,...,Tt $\subseteq$ V(G) of size at most p, and an integer k, whether there is a set S of at most k edges or nodes s.t. of each set Ti at least one pair of terminals is in different connected components of G \ S. This problem generalizes several graph cut problems, in particular the Multicut problem (the case p = 2), which is fixed-parameter tractable for the parameter k [Marx and Razgon, Bousquet et al., STOC 2011]. We provide a dichotomy of the parameterized complexity of Steiner Multicut. That is, for any combination of k, t, p, and the treewidth tw(G) as constant, parameter, or unbounded, and for all versions of the problem (edge deletion and node deletion with and without deletable terminals), we prove either that the problem is fixed-parameter tractable or that the problem is hard (W[1]-hard or even (para-)NP-complete). We highlight that: - The edge deletion version of Steiner Multicut is fixed-parameter tractable for the parameter k+t on general graphs (but has no polynomial kernel, even on trees). We present two proofs: one using the randomized contractions technique of Chitnis et al, and one relying on new structural lemmas that decompose the Steiner cut into important separators and minimal s-t cuts. - In contrast, both node deletion versions of Steiner Multicut are W[1]-hard for the parameter k+t on general graphs. - All versions of Steiner Multicut are W[1]-hard for the parameter k, even when p=3 and the graph is a tree plus one node. Hence, the results of Marx and Razgon, and Bousquet et al. do not generalize to Steiner Multicut. Since we allow k, t, p, and tw(G) to be any constants, our characterization includes a dichotomy for Steiner Multicut on trees (for tw(G) = 1), and a polynomial time versus NP-hardness dichotomy (by restricting k,t,p,tw(G) to constant or unbounded).Comment: As submitted to journal. This version also adds a proof of fixed-parameter tractability for parameter k+t using the technique of randomized contraction

Cluster Before You Hallucinate: Approximating Node-Capacitated Network Design and Energy Efficient Routing

We consider circuit routing with an objective of minimizing energy, in a network of routers that are speed scalable and that may be shutdown when idle. We consider both multicast routing and unicast routing. It is known that this energy minimization problem can be reduced to a capacitated flow network design problem, where vertices have a common capacity but arbitrary costs, and the goal is to choose a minimum cost collection of vertices whose induced subgraph will support the specified flow requirements. For the multicast (single-sink) capacitated design problem we give a polynomial-time algorithm that is O(log^3n)-approximate with O(log^4 n) congestion. This translates back to a O(log ^(4{\alpha}+3) n)-approximation for the multicast energy-minimization routing problem, where {\alpha} is the polynomial exponent in the dynamic power used by a router. For the unicast (multicommodity) capacitated design problem we give a polynomial-time algorithm that is O(log^5 n)-approximate with O(log^12 n) congestion, which translates back to a O(log^(12{\alpha}+5) n)-approximation for the unicast energy-minimization routing problem.Comment: 22 pages (full version of STOC 2014 paper

Optimal competitiveness for the Rectilinear Steiner Arborescence problem

We present optimal online algorithms for two related known problems involving Steiner Arborescence, improving both the lower and the upper bounds. One of them is the well studied continuous problem of the {\em Rectilinear Steiner Arborescence} ($RSA$). We improve the lower bound and the upper bound on the competitive ratio for $RSA$ from $O(\log N)$ and $\Omega(\sqrt{\log N})$ to $\Theta(\frac{\log N}{\log \log N})$, where $N$ is the number of Steiner points. This separates the competitive ratios of $RSA$ and the Symetric-$RSA$, two problems for which the bounds of Berman and Coulston is STOC 1997 were identical. The second problem is one of the Multimedia Content Distribution problems presented by Papadimitriou et al. in several papers and Charikar et al. SODA 1998. It can be viewed as the discrete counterparts (or a network counterpart) of $RSA$. For this second problem we present tight bounds also in terms of the network size, in addition to presenting tight bounds in terms of the number of Steiner points (the latter are similar to those we derived for $RSA$)

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees

Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that “connect” the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian proteins/genes using literature-based protein-protein interaction networks. To avoid over-representation of hubs in the resultant Steiner Trees we assign a cost to Steiner Vertices based on their connectivity degree. We applied the algorithm to lists of genes commonly mutated in colorectal cancer to demonstrate the usefulness of this approach

Roots of bivariate polynomial systems via determinantal representations

We give two determinantal representations for a bivariate polynomial. They may be used to compute the zeros of a system of two of these polynomials via the eigenvalues of a two-parameter eigenvalue problem. The first determinantal representation is suitable for polynomials with scalar or matrix coefficients, and consists of matrices with asymptotic order $n^2/4$, where $n$ is the degree of the polynomial. The second representation is useful for scalar polynomials and has asymptotic order $n^2/6$. The resulting method to compute the roots of a system of two bivariate polynomials is competitive with some existing methods for polynomials up to degree 10, as well as for polynomials with a small number of terms.Comment: 22 pages, 9 figure

Compressing DNA sequence databases with coil

Background: Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results: We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion: coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work

The cavity approach for Steiner trees packing problems

The Belief Propagation approximation, or cavity method, has been recently applied to several combinatorial optimization problems in its zero-temperature implementation, the max-sum algorithm. In particular, recent developments to solve the edge-disjoint paths problem and the prize-collecting Steiner tree problem on graphs have shown remarkable results for several classes of graphs and for benchmark instances. Here we propose a generalization of these techniques for two variants of the Steiner trees packing problem where multiple "interacting" trees have to be sought within a given graph. Depending on the interaction among trees we distinguish the vertex-disjoint Steiner trees problem, where trees cannot share nodes, from the edge-disjoint Steiner trees problem, where edges cannot be shared by trees but nodes can be members of multiple trees. Several practical problems of huge interest in network design can be mapped into these two variants, for instance, the physical design of Very Large Scale Integration (VLSI) chips. The formalism described here relies on two components edge-variables that allows us to formulate a massage-passing algorithm for the V-DStP and two algorithms for the E-DStP differing in the scaling of the computational time with respect to some relevant parameters. We will show that one of the two formalisms used for the edge-disjoint variant allow us to map the max-sum update equations into a weighted maximum matching problem over proper bipartite graphs. We developed a heuristic procedure based on the max-sum equations that shows excellent performance in synthetic networks (in particular outperforming standard multi-step greedy procedures by large margins) and on large benchmark instances of VLSI for which the optimal solution is known, on which the algorithm found the optimum in two cases and the gap to optimality was never larger than 4 %