Algebraic and Combinatorial Methods in Computational Complexity

Computational Complexity is concerned with the resources that are required for algorithms to detect properties of combinatorial objects and structures. It has often proven true that the best way to argue about these combinatorial objects is by establishing a connection (perhaps approximate) to a more well-behaved algebraic setting. Indeed, many of the deepest and most powerful results in Computational Complexity rely on algebraic proof techniques. The Razborov-Smolensky polynomial-approximation method for proving constant-depth circuit lower bounds, the PCP characterization of NP, and the Agrawal-Kayal-Saxena polynomial-time primality test are some of the most prominent examples. The algebraic theme continues in some of the most exciting recent progress in computational complexity. There have been significant recent advances in algebraic circuit lower bounds, and the so-called chasm at depth 4 suggests that the restricted models now being considered are not so far from ones that would lead to a general result. There have been similar successes concerning the related problems of polynomial identity testing and circuit reconstruction in the algebraic model (and these are tied to central questions regarding the power of randomness in computation). Another surprising connection is that the algebraic techniques invented to show lower bounds now prove useful to develop efficient algorithms. For example, Williams showed how to use the polynomial method to obtain faster all-pair-shortest-path algorithms. This emphases once again the central role of algebra in computer science. The seminar aims to capitalize on recent progress and bring together researchers who are using a diverse array of algebraic methods in a variety of settings. Researchers in these areas are relying on ever more sophisticated and specialized mathematics and this seminar can play an important role in educating a diverse community about the latest new techniques, spurring further progress

Fingerprints in Compressed Strings

The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string S of size N compressed by a context-free grammar of size n that answers fingerprint queries. That is, given indices i and j, the answer to a query is the fingerprint of the substring S[i,j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(logN) query time, and for Linear SLPs (an SLP derivative that captures LZ78 compression and its variations) we get O(log log N) query time. Hence, our data structures has the same time and space complexity as for random access in SLPs. We utilize the fingerprint data structures to solve the longest common extension problem in query time O(log N log l) and O(log l log log l + log log N) for SLPs and Linear SLPs, respectively. Here, l denotes the length of the LCE

Optimal Assembly for High Throughput Shotgun Sequencing

We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in terms of the repeat statistics of the genome. Building on earlier works, we design a de Brujin graph based assembly algorithm which can achieve very close to the lower bound for repeat statistics of a wide range of sequenced genomes, including the GAGE datasets. The results are based on a set of necessary and sufficient conditions on the DNA sequence and the reads for reconstruction. The conditions can be viewed as the shotgun sequencing analogue of Ukkonen-Pevzner's necessary and sufficient conditions for Sequencing by Hybridization.Comment: 26 pages, 18 figure

Fingerprints in compressed strings

Abstract. The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string S of size N compressed by a context-free grammar of size n that answers fingerprint queries. That is, given indices i and j, the answer to a query is the fingerprint of the substring S[i, j]. We present the first O(n) space data structures that answer fingerprint queries without decompressing any characters. For Straight Line Programs (SLP) we get O(logN) query time, and for Linear SLPs (an SLP derivative that captures LZ78 compression and its variations) we get O(log logN) query time. Hence, our data structures has the same time and space complexity as for random access in SLPs. We utilize the fingerprint data structures to solve the longest common extension problem in query time O(logN log `) and O(log ` log log `+ log logN) for SLPs and Linear SLPs, respectively. Here, ` denotes the length of the LCE.