Computation of high-stability DC balancing scheme for ferroelectric liquid crystal on silicon holograms using graphics processing units.

Spatial light modulators based around liquid crystal on silicon have found use in a variety of telecommunications applications, including the optimization of multimode fibers, free-space communications, and wavelength selective switching. Ferroelectric liquid crystals are attractive in these areas due to their fast switching times and high phase stability, but the necessity for the liquid crystal to spend equal time in each of its two possible states is an issue of practical concern. Using the highly parallel nature of a graphics processing unit architecture, it is possible to calculate DC balancing schemes of exceptional quality and stability.

Investigation of acoustic units for LVCSR systems

One important issue in designing state-of-the-art LVCSR systems is the choice of acoustic units. Context dependent (CD) phones remain the dominant form of acoustic units. They can capture the co-articulatory effect in speech via explicit modelling. However, for other more complicated phonological processes, they rely on the implicit modelling ability of the underlying statistical models. Alternatively, it is possible to construct acoustic models based on higher level linguistic units, for example, syllables, to explicitly capture these complex patterns. When sufficient training data is available, this approach may show an advantage over implicit acoustic modelling. In this paper a wide range of acoustic units are investigated to improve LVCSR system performance. Significant error rate gains up to 7.1% relative (0.8% abs.) were obtained on a state-of-the-art Mandarin Chinese broadcast audio recognition task using word and syllable position dependent triphone and quinphone models. © 2011 IEEE.

BarraCUDA – a Fast Sequence Mapping Software using Graphics Processing Units

High-throughput DNA sequencing (HTS) instruments today are capable of generating millions of sequencing reads in a short period of time, and this represents a serious challenge to current bioinformatics pipeline in processing such an enormous amount of data in a fast and economical fashion. Modern graphics cards are powerful processing units that consist of hundreds of scalar processors in parallel in order to handle the rendering of high-definition graphics in real-time. It is this computational capability that we propose to harness in order to accelerate some of the time-consuming steps in analyzing data generated by the HTS instruments. We have developed BarraCUDA, a novel sequence mapping software that utilizes the parallelism of NVIDIA CUDA graphics cards to map sequencing reads to a particular location on a reference genome. While delivering a similar mapping fidelity as other mainstream programs , BarraCUDA is a magnitude faster in mapping throughput compared to its CPU counterparts. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the mapping throughput. BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the mapping of millions of sequencing reads generated by HTS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology. BarraCUDA is currently available at http://seqbarracuda.sf.net

BarraCUDA - a fast short read sequence aligner using graphics processing units.

BACKGROUND: With the maturation of next-generation DNA sequencing (NGS) technologies, the throughput of DNA sequencing reads has soared to over 600 gigabases from a single instrument run. General purpose computing on graphics processing units (GPGPU), extracts the computing power from hundreds of parallel stream processors within graphics processing cores and provides a cost-effective and energy efficient alternative to traditional high-performance computing (HPC) clusters. In this article, we describe the implementation of BarraCUDA, a GPGPU sequence alignment software that is based on BWA, to accelerate the alignment of sequencing reads generated by these instruments to a reference DNA sequence. FINDINGS: Using the NVIDIA Compute Unified Device Architecture (CUDA) software development environment, we ported the most computational-intensive alignment component of BWA to GPU to take advantage of the massive parallelism. As a result, BarraCUDA offers a magnitude of performance boost in alignment throughput when compared to a CPU core while delivering the same level of alignment fidelity. The software is also capable of supporting multiple CUDA devices in parallel to further accelerate the alignment throughput. CONCLUSIONS: BarraCUDA is designed to take advantage of the parallelism of GPU to accelerate the alignment of millions of sequencing reads generated by NGS instruments. By doing this, we could, at least in part streamline the current bioinformatics pipeline such that the wider scientific community could benefit from the sequencing technology.BarraCUDA is currently available from http://seqbarracuda.sf.net.