An efficient algorithm for the blocked pattern matching problem

Motivation: Tandem mass spectrometry (MS) has become the method of choice for protein identification and quantification. In the era of big data biology, tandem mass spectra are often searched against huge protein databases generated from genomes or RNA-Seq data for peptide identification. However, most existing tools for MS-based peptide identification compare a tandem mass spectrum against all peptides in a database whose molecular masses are similar to the precursor mass of the spectrum, making mass spectral data analysis slow for huge databases. Tag-based methods extract peptide sequence tags from a tandem mass spectrum and use them as a filter to reduce the number of candidate peptides, thus speeding up the database search. Recently, gapped tags have been introduced into mass spectral data analysis because they improve the sensitivity of peptide identification compared with sequence tags. However, the blocked pattern matching (BPM) problem, which is an essential step in gapped tag-based peptide identification, has not been fully solved. Results: In this article, we propose a fast and memory-efficient algorithm for the BPM problem. Experiments on both simulated and real datasets showed that the proposed algorithm achieved high speed and high sensitivity for peptide filtration in peptide identification by database search

A New Computational Framework for Efficient Parallelization and Optimization of Large Scale Graph Matching

There are so many applications in data fusion, comparison, and recognition that require a robust and efficient algorithm to match features of multiple images. To improve accuracy and get a more stable result is important to take into consideration both local appearance and the pairwise relationship of features. Graphs are a powerful and flexible data structure, allowing for the description of complex relationships between data elements, whose nodes correspond to salient features and edges correspond to relational aspects between features. Therefore, the problem of graph matching is to find a mapping between the two sets of nodes that preserves the relationships between them as much as possible. This graph-matching problem is mathematically formulated as an IQP problem which solving it is NP-hard, and obtaining exact Optima only plausible for very small data. Therefore, handling large-scale scientific visual data is quite limited, necessitating both efficient serial algorithms, as well as scalable parallel formulations. In this thesis, we first focused on exploring techniques to reduce the computation cost as well as memory usage of Pairwise graph matching by adopting a heuristic pruning strategy together with a redundancy pattern suppression scheme. We also modified the structure of the affinity matrix for minimizing memory requirement and parallelizing our algorithm by employing CPU’s and GPU’s accelerated libraries. Any pair of features with similar distance from first image results in same sub-matrices, therefore instead of constructing the whole affinity matrix, we only built the sub-blocked affinity for those distinct feature distances. By employing this scheme not only saved large memory and reduced computation time tremendously but also, the matrix-vector multiplication of gradient computation performed in parallel, where each block-vector calculation computed independently without synchronization. The accelerated libraries such as MKL, cuSparse, cuBlas and thrust applied to solving the GM problem, following the scheme of the spectral matching algorithm. We also extended our work for Multi-graph imaging, since many tasks require finding correspondences across multiple images. Also, considering more graph improves the matching accuracy. Most algorithms obtain approximate solutions for solving the GM NP-hard problem, result in a weak optimal solution. Therefore, we proposed a new solver, which iteratively modified the affinity matrix and binarized the solution by optimizing the original problem with its integer constraints

Parsing Expression Grammars Made Practical

Parsing Expression Grammars (PEGs) define languages by specifying recursive-descent parser that recognises them. The PEG formalism exhibits desirable properties, such as closure under composition, built-in disambiguation, unification of syntactic and lexical concerns, and closely matching programmer intuition. Unfortunately, state of the art PEG parsers struggle with left-recursive grammar rules, which are not supported by the original definition of the formalism and can lead to infinite recursion under naive implementations. Likewise, support for associativity and explicit precedence is spotty. To remedy these issues, we introduce Autumn, a general purpose PEG library that supports left-recursion, left and right associativity and precedence rules, and does so efficiently. Furthermore, we identify infix and postfix operators as a major source of inefficiency in left-recursive PEG parsers and show how to tackle this problem. We also explore the extensibility of the PEG paradigm by showing how one can easily introduce new parsing operators and how our parser accommodates custom memoization and error handling strategies. We compare our parser to both state of the art and battle-tested PEG and CFG parsers, such as Rats!, Parboiled and ANTLR.Comment: "Proceedings of the International Conference on Software Language Engineering (SLE 2015)" - 167-172 (ISBN : 978-1-4503-3686-4