Analyzing large-scale DNA Sequences on Multi-core Architectures

Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA forensics. However, real-world DNA sequences may comprise several Gigabytes and the process of DNA analysis demands adequate computational resources to be completed within a reasonable time. In this paper we present a scalable approach for parallel DNA analysis that is based on Finite Automata, and which is suitable for analyzing very large DNA segments. We evaluate our approach for real-world DNA segments of mouse (2.7GB), cat (2.4GB), dog (2.4GB), chicken (1GB), human (3.2GB) and turkey (0.2GB). Experimental results on a dual-socket shared-memory system with 24 physical cores show speed-ups of up to 17.6x. Our approach is up to 3x faster than a pattern-based parallel approach that uses the RE2 library.Comment: The 18th IEEE International Conference on Computational Science and Engineering (CSE 2015), Porto, Portugal, 20 - 23 October 201

MatchPy: A Pattern Matching Library

Pattern matching is a powerful tool for symbolic computations, based on the well-defined theory of term rewriting systems. Application domains include algebraic expressions, abstract syntax trees, and XML and JSON data. Unfortunately, no lightweight implementation of pattern matching as general and flexible as Mathematica exists for Python Mathics,MacroPy,patterns,PyPatt. Therefore, we created the open source module MatchPy which offers similar pattern matching functionality in Python using a novel algorithm which finds matches for large pattern sets more efficiently by exploiting similarities between patterns.Comment: arXiv admin note: substantial text overlap with arXiv:1710.0007

Fast multi-image matching via density-based clustering

We consider the problem of finding consistent matches across multiple images. Previous state-of-the-art solutions use constraints on cycles of matches together with convex optimization, leading to computationally intensive iterative algorithms. In this paper, we propose a clustering-based formulation. We first rigorously show its equivalence with the previous one, and then propose QuickMatch, a novel algorithm that identifies multi-image matches from a density function in feature space. We use the density to order the points in a tree, and then extract the matches by breaking this tree using feature distances and measures of distinctiveness. Our algorithm outperforms previous state-of-the-art methods (such as MatchALS) in accuracy, and it is significantly faster (up to 62 times faster on some bechmarks), and can scale to large datasets (with more than twenty thousands features).Accepted manuscriptSupporting documentatio

A Binary Neural Shape Matcher using Johnson Counters and Chain Codes

In this paper, we introduce a neural network-based shape matching algorithm that uses Johnson Counter codes coupled with chain codes. Shape matching is a fundamental requirement in content-based image retrieval systems. Chain codes describe shapes using sequences of numbers. They are simple and flexible. We couple this power with the efficiency and flexibility of a binary associative-memory neural network. We focus on the implementation details of the algorithm when it is constructed using the neural network. We demonstrate how the binary associative-memory neural network can index and match chain codes where the chain code elements are represented by Johnson codes

Cluster-Wise Ratio Tests for Fast Camera Localization

Feature point matching for camera localization suffers from scalability problems. Even when feature descriptors associated with 3D scene points are locally unique, as coverage grows, similar or repeated features become increasingly common. As a result, the standard distance ratio-test used to identify reliable image feature points is overly restrictive and rejects many good candidate matches. We propose a simple coarse-to-fine strategy that uses conservative approximations to robust local ratio-tests that can be computed efficiently using global approximate k-nearest neighbor search. We treat these forward matches as votes in camera pose space and use them to prioritize back-matching within candidate camera pose clusters, exploiting feature co-visibility captured by clustering the 3D model camera pose graph. This approach achieves state-of-the-art camera localization results on a variety of popular benchmarks, outperforming several methods that use more complicated data structures and that make more restrictive assumptions on camera pose. We also carry out diagnostic analyses on a difficult test dataset containing globally repetitive structure that suggest our approach successfully adapts to the challenges of large-scale image localization

Large-scale Binary Quadratic Optimization Using Semidefinite Relaxation and Applications

In computer vision, many problems such as image segmentation, pixel labelling, and scene parsing can be formulated as binary quadratic programs (BQPs). For submodular problems, cuts based methods can be employed to efficiently solve large-scale problems. However, general nonsubmodular problems are significantly more challenging to solve. Finding a solution when the problem is of large size to be of practical interest, however, typically requires relaxation. Two standard relaxation methods are widely used for solving general BQPs--spectral methods and semidefinite programming (SDP), each with their own advantages and disadvantages. Spectral relaxation is simple and easy to implement, but its bound is loose. Semidefinite relaxation has a tighter bound, but its computational complexity is high, especially for large scale problems. In this work, we present a new SDP formulation for BQPs, with two desirable properties. First, it has a similar relaxation bound to conventional SDP formulations. Second, compared with conventional SDP methods, the new SDP formulation leads to a significantly more efficient and scalable dual optimization approach, which has the same degree of complexity as spectral methods. We then propose two solvers, namely, quasi-Newton and smoothing Newton methods, for the dual problem. Both of them are significantly more efficiently than standard interior-point methods. In practice, the smoothing Newton solver is faster than the quasi-Newton solver for dense or medium-sized problems, while the quasi-Newton solver is preferable for large sparse/structured problems. Our experiments on a few computer vision applications including clustering, image segmentation, co-segmentation and registration show the potential of our SDP formulation for solving large-scale BQPs.Comment: Fixed some typos. 18 pages. Accepted to IEEE Transactions on Pattern Analysis and Machine Intelligenc