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

Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

We study the approximate string matching and regular expression matching problem for the case when the text to be searched is compressed with the Ziv-Lempel adaptive dictionary compression schemes. We present a time-space trade-off that leads to algorithms improving the previously known complexities for both problems. In particular, we significantly improve the space bounds, which in practical applications are likely to be a bottleneck

Communication channel analysis and real time compressed sensing for high density neural recording devices

Next generation neural recording and Brain- Machine Interface (BMI) devices call for high density or distributed systems with more than 1000 recording sites. As the recording site density grows, the device generates data on the scale of several hundred megabits per second (Mbps). Transmitting such large amounts of data induces significant power consumption and heat dissipation for the implanted electronics. Facing these constraints, efficient on-chip compression techniques become essential to the reduction of implanted systems power consumption. This paper analyzes the communication channel constraints for high density neural recording devices. This paper then quantifies the improvement on communication channel using efficient on-chip compression methods. Finally, This paper describes a Compressed Sensing (CS) based system that can reduce the data rate by > 10x times while using power on the order of a few hundred nW per recording channel

Compressed Sensing with Coherent and Redundant Dictionaries

This article presents novel results concerning the recovery of signals from undersampled data in the common situation where such signals are not sparse in an orthonormal basis or incoherent dictionary, but in a truly redundant dictionary. This work thus bridges a gap in the literature and shows not only that compressed sensing is viable in this context, but also that accurate recovery is possible via an L1-analysis optimization problem. We introduce a condition on the measurement/sensing matrix, which is a natural generalization of the now well-known restricted isometry property, and which guarantees accurate recovery of signals that are nearly sparse in (possibly) highly overcomplete and coherent dictionaries. This condition imposes no incoherence restriction on the dictionary and our results may be the first of this kind. We discuss practical examples and the implications of our results on those applications, and complement our study by demonstrating the potential of L1-analysis for such problems

A* Orthogonal Matching Pursuit: Best-First Search for Compressed Sensing Signal Recovery

Compressed sensing is a developing field aiming at reconstruction of sparse signals acquired in reduced dimensions, which make the recovery process under-determined. The required solution is the one with minimum $\ell_0$ norm due to sparsity, however it is not practical to solve the $\ell_0$ minimization problem. Commonly used techniques include $\ell_1$ minimization, such as Basis Pursuit (BP) and greedy pursuit algorithms such as Orthogonal Matching Pursuit (OMP) and Subspace Pursuit (SP). This manuscript proposes a novel semi-greedy recovery approach, namely A* Orthogonal Matching Pursuit (A*OMP). A*OMP performs A* search to look for the sparsest solution on a tree whose paths grow similar to the Orthogonal Matching Pursuit (OMP) algorithm. Paths on the tree are evaluated according to a cost function, which should compensate for different path lengths. For this purpose, three different auxiliary structures are defined, including novel dynamic ones. A*OMP also incorporates pruning techniques which enable practical applications of the algorithm. Moreover, the adjustable search parameters provide means for a complexity-accuracy trade-off. We demonstrate the reconstruction ability of the proposed scheme on both synthetically generated data and images using Gaussian and Bernoulli observation matrices, where A*OMP yields less reconstruction error and higher exact recovery frequency than BP, OMP and SP. Results also indicate that novel dynamic cost functions provide improved results as compared to a conventional choice.Comment: accepted for publication in Digital Signal Processin

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)

Distributed Representation of Geometrically Correlated Images with Compressed Linear Measurements

This paper addresses the problem of distributed coding of images whose correlation is driven by the motion of objects or positioning of the vision sensors. It concentrates on the problem where images are encoded with compressed linear measurements. We propose a geometry-based correlation model in order to describe the common information in pairs of images. We assume that the constitutive components of natural images can be captured by visual features that undergo local transformations (e.g., translation) in different images. We first identify prominent visual features by computing a sparse approximation of a reference image with a dictionary of geometric basis functions. We then pose a regularized optimization problem to estimate the corresponding features in correlated images given by quantized linear measurements. The estimated features have to comply with the compressed information and to represent consistent transformation between images. The correlation model is given by the relative geometric transformations between corresponding features. We then propose an efficient joint decoding algorithm that estimates the compressed images such that they stay consistent with both the quantized measurements and the correlation model. Experimental results show that the proposed algorithm effectively estimates the correlation between images in multi-view datasets. In addition, the proposed algorithm provides effective decoding performance that compares advantageously to independent coding solutions as well as state-of-the-art distributed coding schemes based on disparity learning

Mismatch and resolution in compressive imaging

Highly coherent sensing matrices arise in discretization of continuum problems such as radar and medical imaging when the grid spacing is below the Rayleigh threshold as well as in using highly coherent, redundant dictionaries as sparsifying operators. Algorithms (BOMP, BLOOMP) based on techniques of band exclusion and local optimization are proposed to enhance Orthogonal Matching Pursuit (OMP) and deal with such coherent sensing matrices. BOMP and BLOOMP have provably performance guarantee of reconstructing sparse, widely separated objects {\em independent} of the redundancy and have a sparsity constraint and computational cost similar to OMP's. Numerical study demonstrates the effectiveness of BLOOMP for compressed sensing with highly coherent, redundant sensing matrices.Comment: Figure 5 revise