Greedy Algorithms for Steiner Forest

In the Steiner Forest problem, we are given terminal pairs $\{s_i, t_i\}$, and need to find the cheapest subgraph which connects each of the terminal pairs together. In 1991, Agrawal, Klein, and Ravi, and Goemans and Williamson gave primal-dual constant-factor approximation algorithms for this problem; until now, the only constant-factor approximations we know are via linear programming relaxations. We consider the following greedy algorithm: Given terminal pairs in a metric space, call a terminal "active" if its distance to its partner is non-zero. Pick the two closest active terminals (say $s_i, t_j$), set the distance between them to zero, and buy a path connecting them. Recompute the metric, and repeat. Our main result is that this algorithm is a constant-factor approximation. We also use this algorithm to give new, simpler constructions of cost-sharing schemes for Steiner forest. In particular, the first "group-strict" cost-shares for this problem implies a very simple combinatorial sampling-based algorithm for stochastic Steiner forest

Generalized Buneman pruning for inferring the most parsimonious multi-state phylogeny

Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from optimal. Practical exact methods, which yield exponential worst-case running times but generally much better times in practice, provide an important alternative. We report progress in this direction by introducing a provably optimal method for the weighted multi-state maximum parsimony phylogeny problem. The method is based on generalizing the notion of the Buneman graph, a construction key to efficient exact methods for binary sequences, so as to apply to sequences with arbitrary finite numbers of states with arbitrary state transition weights. We implement an integer linear programming (ILP) method for the multi-state problem using this generalized Buneman graph and demonstrate that the resulting method is able to solve data sets that are intractable by prior exact methods in run times comparable with popular heuristics. Our work provides the first method for provably optimal maximum parsimony phylogeny inference that is practical for multi-state data sets of more than a few characters.Comment: 15 page

Routing for analog chip designs at NXP Semiconductors

During the study week 2011 we worked on the question of how to automate certain aspects of the design of analog chips. Here we focused on the task of connecting different blocks with electrical wiring, which is particularly tedious to do by hand. For digital chips there is a wealth of research available for this, as in this situation the amount of blocks makes it hopeless to do the design by hand. Hence, we set our task to finding solutions that are based on the previous research, as well as being tailored to the specific setting given by NXP. This resulted in an heuristic approach, which we presented at the end of the week in the form of a protoype tool. In this report we give a detailed account of the ideas we used, and describe possibilities to extend the approach

On the utility of network coding in dynamic environments

Many wireless applications, such as ad-hoc networks and sensor networks, require decentralized operation in dynamically varying environments. We consider a distributed randomized network coding approach that enables efficient decentralized operation of multi-source multicast networks. We show that this approach provides substantial benefits over traditional routing methods in dynamically varying environments. We present a set of empirical trials measuring the performance of network coding versus an approximate online Steiner tree routing approach when connections vary dynamically. The results show that network coding achieves superior performance in a significant fraction of our randomly generated network examples. Such dynamic settings represent a substantially broader class of networking problems than previously recognized for which network coding shows promise of significant practical benefits compared to routing