Scalable Peer-to-Peer Indexing with Constant State

We present a distributed indexing scheme for peer to peer networks. Past work on distributed indexing traded off fast search times with non-constant degree topologies or network-unfriendly behavior such as flooding. In contrast, the scheme we present optimizes all three of these performance measures. That is, we provide logarithmic round searches while maintaining connections to a fixed number of peers and avoiding network flooding. In comparison to the well known scheme Chord, we provide competitive constant factors. Finally, we observe that arbitrary linear speedups are possible and discuss both a general brute force approach and specific economical optimizations

Randomized Search of Graphs in Log Space and Probabilistic Computation

Reingold has shown that L = SL, that s-t connectivity in a poly-mixing digraph is complete for promise-RL, and that s-t connectivity for a poly-mixing out-regular digraph with known stationary distribution is in L. Several properties that bound the mixing times of random walks on digraphs have been identified, including the digraph conductance and the digraph spectral expansion. However, rapidly mixing digraphs can still have exponential cover time, thus it is important to specifically identify structural properties of digraphs that effect cover times. We examine the complexity of random walks on a basic parameterized family of unbalanced digraphs called Strong Chains (which model weakly symmetric logspace computations), and a special family of Strong Chains called Harps. We show that the worst case hitting times of Strong Chain families vary smoothly with the number of asymmetric vertices and identify the necessary condition for non-polynomial cover time. This analysis also yields bounds on the cover times of general digraphs. Next we relate random walks on graphs to the random walks that arise in Monte Carlo methods applied to optimization problems. We introduce the notion of the asymmetric states of Markov chains and use this definition to obtain some results about Markov chains. We also obtain some results on the mixing times for Markov Chain Monte Carlo Methods. Finally, we consider the question of whether a single long random walk or many short walks is a better strategy for exploration. These are walks which reset to the start after a fixed number of steps. We exhibit digraph families for which a few short walks are far superior to a single long walk. We introduce an iterative deepening random search. We use this strategy estimate the cover time for poly-mixing subgraphs. Finally we discuss complexity theoretic implications and future work

Metabolic Network Alignments and their Applications

The accumulation of high-throughput genomic and proteomic data allows for the reconstruction of the increasingly large and complex metabolic networks. In order to analyze the accumulated data and reconstructed networks, it is critical to identify network patterns and evolutionary relations between metabolic networks. But even finding similar networks becomes computationally challenging. The dissertation addresses these challenges with discrete optimization and the corresponding algorithmic techniques. Based on the property of the gene duplication and function sharing in biological network,we have formulated the network alignment problem which asks the optimal vertex-to-vertex mapping allowing path contraction, vertex deletion, and vertex insertions. We have proposed the first polynomial time algorithm for aligning an acyclic metabolic pattern pathway with an arbitrary metabolic network. We also have proposed a polynomial-time algorithm for patterns with small treewidth and implemented it for series-parallel patterns which are commonly found among metabolic networks. We have developed the metabolic network alignment tool for free public use. We have performed pairwise mapping of all pathways among five organisms and found a set of statistically significant pathway similarities. We also have applied the network alignment to identifying inconsistency, inferring missing enzymes, and finding potential candidates