Balanced Families of Perfect Hash Functions and Their Applications

The construction of perfect hash functions is a well-studied topic. In this paper, this concept is generalized with the following definition. We say that a family of functions from $[n]$ to $[k]$ is a $\delta$-balanced $(n,k)$-family of perfect hash functions if for every $S \subseteq [n]$, $|S|=k$, the number of functions that are 1-1 on $S$ is between $T/\delta$ and $\delta T$ for some constant $T>0$. The standard definition of a family of perfect hash functions requires that there will be at least one function that is 1-1 on $S$, for each $S$ of size $k$. In the new notion of balanced families, we require the number of 1-1 functions to be almost the same (taking $\delta$ to be close to 1) for every such $S$. Our main result is that for any constant $\delta > 1$, a $\delta$-balanced $(n,k)$-family of perfect hash functions of size $2^{O(k \log \log k)} \log n$ can be constructed in time $2^{O(k \log \log k)} n \log n$. Using the technique of color-coding we can apply our explicit constructions to devise approximation algorithms for various counting problems in graphs. In particular, we exhibit a deterministic polynomial time algorithm for approximating both the number of simple paths of length $k$ and the number of simple cycles of size $k$ for any $k \leq O(\frac{\log n}{\log \log \log n})$ in a graph with $n$ vertices. The approximation is up to any fixed desirable relative error

Parameterized algorithms and hardness results for some graph motif problems

Abstract. We study the NP-complete Graph Motif problem: given a vertex-colored graph G = (V, E) and a multiset M of colors, does there exist an S ⊆ V such that G[S] is connected and carries exactly (also with respect to multiplicity) the colors in M ? We present an improved randomized algorithm for Graph Motif with running time O(4.32 . We extend our algorithm to list-colored graph vertices and the case where the motif G[S] needs not be connected. By way of contrast, we show that extending the request for motif connectedness to the somewhat "more robust" motif demands of biconnectedness or bridgeconnectedness leads to W[1]-complete problems. Actually, we show that the even simpler problems of finding biconnected or bridge-connected subgraphs are W[1]-complete with respect to the subgraph size. Answering an open question from the literature, we further show that the parameter number of connected motif components leads to W[1]-hardness even when restricted to the very special case of graphs that are paths

Fixed-parameter algorithms for some combinatorial problems in bioinformatics

Fixed-parameterized algorithmics has been developed in 1990s as an approach to solve NP-hard problem optimally in a guaranteed running time. It offers a new opportunity to solve NP-hard problems exactly even on large problem instances. In this thesis, we apply fixed-parameter algorithms to cope with three NP-hard problems in bioinformatics: Flip Consensus Tree Problem is a combinatorial problem arising in computational phylogenetics. Using the formulation of the Flip Consensus Tree Problem as a graph-modification problem, we present a set of data reduction rules and two fixed-parameter algorithms with respect to the number of modifications. Additionally, we discuss several heuristic improvements to accelerate the running time of our algorithms in practice. We also report computational results on phylogenetic data. Weighted Cluster Editing Problem is a graph-modification problem, that arises in computational biology when clustering objects with respect to a given similarity or distance measure. We present one of our fixed-parameter algorithms with respect to the minimum modification cost and describe the idea of our fastest algorithm for this problem and its unweighted counterpart. Bond Order Assignment Problem asks for a bond order assignment of a molecule graph that minimizes a penalty function. We prove several complexity results on this problem and give two exact fixed-parameter algorithms for the problem. Our algorithms base on the dynamic programming approach on a tree decomposition of the molecule graph. Our algorithms are fixed-parameter with respect to the treewidth of the molecule graph and the maximum atom valence. We implemented one of our algorithms with several heuristic improvements and evaluate our algorithm on a set of real molecule graphs. It turns out that our algorithm is very fast on this dataset and even outperforms a heuristic algorithm that is usually used in practice