SWAPHI: Smith-Waterman Protein Database Search on Xeon Phi Coprocessors

The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm computationally demanding for big databases. In this paper, we present SWAPHI, the first parallelized algorithm employing Xeon Phi coprocessors to accelerate SW protein database search. SWAPHI is designed based on the scale-and-vectorize approach, i.e. it boosts alignment speed by effectively utilizing both the coarse-grained parallelism from the many co-processing cores (scale) and the fine-grained parallelism from the 512-bit wide single instruction, multiple data (SIMD) vectors within each core (vectorize). By searching against the large UniProtKB/TrEMBL protein database, SWAPHI achieves a performance of up to 58.8 billion cell updates per second (GCUPS) on one coprocessor and up to 228.4 GCUPS on four coprocessors. Furthermore, it demonstrates good parallel scalability on varying number of coprocessors, and is also superior to both SWIPE on 16 high-end CPU cores and BLAST+ on 8 cores when using four coprocessors, with the maximum speedup of 1.52 and 1.86, respectively. SWAPHI is written in C++ language (with a set of SIMD intrinsics), and is freely available at http://swaphi.sourceforge.net.Comment: A short version of this paper has been accepted by the IEEE ASAP 2014 conferenc

Regrasp Planning using 10,000s of Grasps

This paper develops intelligent algorithms for robots to reorient objects. Given the initial and goal poses of an object, the proposed algorithms plan a sequence of robot poses and grasp configurations that reorient the object from its initial pose to the goal. While the topic has been studied extensively in previous work, this paper makes important improvements in grasp planning by using over-segmented meshes, in data storage by using relational database, and in regrasp planning by mixing real-world roadmaps. The improvements enable robots to do robust regrasp planning using 10,000s of grasps and their relationships in interactive time. The proposed algorithms are validated using various objects and robots

Focussed palmtop information access combining starfield displays and profile-based recommendations

This paper presents two palmtop applications: Taeneb CityGuide and Taeneb ConferenceGuide. Both applications are centred around Starfield displays on palmtop computers - this provides fast, dynamic access to information on a small platform. The paper describes the applications focussing on this novel palmtop information access method and on the user-profiling aspect of the CityGuide, where restaurants are recommended to users based on both the match of restaurant type to the users' observed previous interactions and the rating given by reviewers with similar observed preferences

Sources of radiation from neutron stars

I give a brief introduction to the problem of detecting gravitational radiation from neutron stars. After a review of the mechanisms by which such stars may produce radiation, I consider the different search strategies appropriate to the different kinds of sources: isolated known pulsars, neutron stars in binaries, and unseen neutron stars. The problem of an all-sky survey for unseen stars is the most taxing one that we face in analysing data from interferometers. I describe the kinds of hierarchical methods that are now being investigated to reach the maximal sensitivity, and I suggest a replacement for standard Fourier-transform search methods that requires fewer floating-point operations for Fourier-based searches over large parameter spaces, and in addition is highly parallelizable, working just as well on a loosely coupled network of workstations as on a tightly coupled parallel computer.Comment: 11 pages, no figure