A practical index for approximate dictionary matching with few mismatches

Approximate dictionary matching is a classic string matching problem (checking if a query string occurs in a collection of strings) with applications in, e.g., spellchecking, online catalogs, geolocation, and web searchers. We present a surprisingly simple solution called a split index, which is based on the Dirichlet principle, for matching a keyword with few mismatches, and experimentally show that it offers competitive space-time tradeoffs. Our implementation in the C++ language is focused mostly on data compaction, which is beneficial for the search speed (e.g., by being cache friendly). We compare our solution with other algorithms and we show that it performs better for the Hamming distance. Query times in the order of 1 microsecond were reported for one mismatch for the dictionary size of a few megabytes on a medium-end PC. We also demonstrate that a basic compression technique consisting in $q$-gram substitution can significantly reduce the index size (up to 50% of the input text size for the DNA), while still keeping the query time relatively low

Bitwise Source Separation on Hashed Spectra: An Efficient Posterior Estimation Scheme Using Partial Rank Order Metrics

This paper proposes an efficient bitwise solution to the single-channel source separation task. Most dictionary-based source separation algorithms rely on iterative update rules during the run time, which becomes computationally costly especially when we employ an overcomplete dictionary and sparse encoding that tend to give better separation results. To avoid such cost we propose a bitwise scheme on hashed spectra that leads to an efficient posterior probability calculation. For each source, the algorithm uses a partial rank order metric to extract robust features that form a binarized dictionary of hashed spectra. Then, for a mixture spectrum, its hash code is compared with each source's hashed dictionary in one pass. This simple voting-based dictionary search allows a fast and iteration-free estimation of ratio masking at each bin of a signal spectrogram. We verify that the proposed BitWise Source Separation (BWSS) algorithm produces sensible source separation results for the single-channel speech denoising task, with 6-8 dB mean SDR. To our knowledge, this is the first dictionary based algorithm for this task that is completely iteration-free in both training and testing

On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)