Bicriteria Network Design Problems

We study a general class of bicriteria network design problems. A generic problem in this class is as follows: Given an undirected graph and two minimization objectives (under different cost functions), with a budget specified on the first, find a <subgraph \from a given subgraph-class that minimizes the second objective subject to the budget on the first. We consider three different criteria - the total edge cost, the diameter and the maximum degree of the network. Here, we present the first polynomial-time approximation algorithms for a large class of bicriteria network design problems for the above mentioned criteria. The following general types of results are presented. First, we develop a framework for bicriteria problems and their approximations. Second, when the two criteria are the same %(note that the cost functions continue to be different) we present a ``black box'' parametric search technique. This black box takes in as input an (approximation) algorithm for the unicriterion situation and generates an approximation algorithm for the bicriteria case with only a constant factor loss in the performance guarantee. Third, when the two criteria are the diameter and the total edge costs we use a cluster-based approach to devise a approximation algorithms --- the solutions output violate both the criteria by a logarithmic factor. Finally, for the class of treewidth-bounded graphs, we provide pseudopolynomial-time algorithms for a number of bicriteria problems using dynamic programming. We show how these pseudopolynomial-time algorithms can be converted to fully polynomial-time approximation schemes using a scaling technique.Comment: 24 pages 1 figur

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 &#x201c;connect&#x201d; 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

The Minimum Wiener Connector

The Wiener index of a graph is the sum of all pairwise shortest-path distances between its vertices. In this paper we study the novel problem of finding a minimum Wiener connector: given a connected graph $G=(V,E)$ and a set $Q\subseteq V$ of query vertices, find a subgraph of $G$ that connects all query vertices and has minimum Wiener index. We show that The Minimum Wiener Connector admits a polynomial-time (albeit impractical) exact algorithm for the special case where the number of query vertices is bounded. We show that in general the problem is NP-hard, and has no PTAS unless $\mathbf{P} = \mathbf{NP}$. Our main contribution is a constant-factor approximation algorithm running in time $\widetilde{O}(|Q||E|)$. A thorough experimentation on a large variety of real-world graphs confirms that our method returns smaller and denser solutions than other methods, and does so by adding to the query set $Q$ a small number of important vertices (i.e., vertices with high centrality).Comment: Published in Proceedings of the 2015 ACM SIGMOD International Conference on Management of Dat

The Power of Dynamic Distance Oracles: Efficient Dynamic Algorithms for the Steiner Tree

In this paper we study the Steiner tree problem over a dynamic set of terminals. We consider the model where we are given an $n$-vertex graph $G=(V,E,w)$ with positive real edge weights, and our goal is to maintain a tree which is a good approximation of the minimum Steiner tree spanning a terminal set $S \subseteq V$, which changes over time. The changes applied to the terminal set are either terminal additions (incremental scenario), terminal removals (decremental scenario), or both (fully dynamic scenario). Our task here is twofold. We want to support updates in sublinear $o(n)$ time, and keep the approximation factor of the algorithm as small as possible. We show that we can maintain a $(6+\varepsilon)$-approximate Steiner tree of a general graph in $\tilde{O}(\sqrt{n} \log D)$ time per terminal addition or removal. Here, $D$ denotes the stretch of the metric induced by $G$. For planar graphs we achieve the same running time and the approximation ratio of $(2+\varepsilon)$. Moreover, we show faster algorithms for incremental and decremental scenarios. Finally, we show that if we allow higher approximation ratio, even more efficient algorithms are possible. In particular we show a polylogarithmic time $(4+\varepsilon)$-approximate algorithm for planar graphs. One of the main building blocks of our algorithms are dynamic distance oracles for vertex-labeled graphs, which are of independent interest. We also improve and use the online algorithms for the Steiner tree problem.Comment: Full version of the paper accepted to STOC'1

Network Design with Coverage Costs

We study network design with a cost structure motivated by redundancy in data traffic. We are given a graph, g groups of terminals, and a universe of data packets. Each group of terminals desires a subset of the packets from its respective source. The cost of routing traffic on any edge in the network is proportional to the total size of the distinct packets that the edge carries. Our goal is to find a minimum cost routing. We focus on two settings. In the first, the collection of packet sets desired by source-sink pairs is laminar. For this setting, we present a primal-dual based 2-approximation, improving upon a logarithmic approximation due to Barman and Chawla (2012). In the second setting, packet sets can have non-trivial intersection. We focus on the case where each packet is desired by either a single terminal group or by all of the groups, and the graph is unweighted. For this setting we present an O(log g)-approximation. Our approximation for the second setting is based on a novel spanner-type construction in unweighted graphs that, given a collection of g vertex subsets, finds a subgraph of cost only a constant factor more than the minimum spanning tree of the graph, such that every subset in the collection has a Steiner tree in the subgraph of cost at most O(log g) that of its minimum Steiner tree in the original graph. We call such a subgraph a group spanner.Comment: Updated version with additional result

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 %