Sub-fingerprint masking for a robust audio fingerprinting system in a real-noise environment for portable consumer devices

The file attached is author's final draft.The robustness of audio fingerprinting system in a noisy environment is a principal challenge in the area of content-based audio retrieval, especially for use in portable consumer devices. Our new audio fingerprint method using sub-fingerprint masking based on the predominant pitch extraction increases the accuracy of the audio fingerprinting system in a noisy environment dramatically, while requiring much less computing power compared to the expanded hash table lookup method, where the searching complexity increases by the factor of 33 times the degree of expansion.Supported by Seoul R&BD Program # 10581

RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison

Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns. Herein, we show that the overlap complexity of a pattern set that was introduced by Ilie and Ilie is closely related to the variance of the number of matches between two evolutionarily related sequences with respect to this pattern set. We propose a modified hill-climbing algorithm to optimize pattern sets for database searching, read mapping and alignment-free sequence comparison of nucleic-acid sequences; our implementation of this algorithm is called rasbhari. Depending on the application at hand, rasbhari can either minimize the overlap complexity of pattern sets, maximize their sensitivity in database searching or minimize the variance of the number of pattern-based matches in alignment-free sequence comparison. We show that, for database searching, rasbhari generates pattern sets with slightly higher sensitivity than existing approaches. In our Spaced Words approach to alignment-free sequence comparison, pattern sets calculated with rasbhari led to more accurate estimates of phylogenetic distances than the randomly generated pattern sets that we previously used. Finally, we used rasbhari to generate patterns for short read classification with CLARK-S. Here too, the sensitivity of the results could be improved, compared to the default patterns of the program. We integrated rasbhari into Spaced Words; the source code of rasbhari is freely available at http://rasbhari.gobics.de

Using Program Synthesis for Program Analysis

In this paper, we identify a fragment of second-order logic with restricted quantification that is expressive enough to capture numerous static analysis problems (e.g. safety proving, bug finding, termination and non-termination proving, superoptimisation). We call this fragment the {\it synthesis fragment}. Satisfiability of a formula in the synthesis fragment is decidable over finite domains; specifically the decision problem is NEXPTIME-complete. If a formula in this fragment is satisfiable, a solution consists of a satisfying assignment from the second order variables to \emph{functions over finite domains}. To concretely find these solutions, we synthesise \emph{programs} that compute the functions. Our program synthesis algorithm is complete for finite state programs, i.e. every \emph{function} over finite domains is computed by some \emph{program} that we can synthesise. We can therefore use our synthesiser as a decision procedure for the synthesis fragment of second-order logic, which in turn allows us to use it as a powerful backend for many program analysis tasks. To show the tractability of our approach, we evaluate the program synthesiser on several static analysis problems.Comment: 19 pages, to appear in LPAR 2015. arXiv admin note: text overlap with arXiv:1409.492

Regular Expression Search on Compressed Text

We present an algorithm for searching regular expression matches in compressed text. The algorithm reports the number of matching lines in the uncompressed text in time linear in the size of its compressed version. We define efficient data structures that yield nearly optimal complexity bounds and provide a sequential implementation --zearch-- that requires up to 25% less time than the state of the art.Comment: 10 pages, published in Data Compression Conference (DCC'19