Genomic data analysis using grid-based computing

Microarray experiments generate a plethora of genomic data; therefore we need techniques and architectures to analyze this data more quickly. This thesis presents a solution for reducing the computation time of a highly computationally intensive data analysis part of a genomic application. The application used is the Stanford Microarray Database (SMD). SMD\u27s implementation, working, and analysis features are described. The reasons for choosing the computationally intensive problems of the SMD, and the background importance of these problems are presented. This thesis presents an effective parallel solution to the computational problem, including the difficulties faced with the parallelization of the problem and the results achieved. Finally, future research directions for achieving even greater speedups are presented

Parallel progressive multiple sequence alignment on reconfigurable meshes

<p>Abstract</p> <p>Background</p> <p>One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing extensive task. In addition, the advancement in DNA/RNA and Protein sequencing techniques has created a vast amount of sequences to be analyzed that exceeding the capability of traditional computing models. Therefore, an effective parallel multiple sequence alignment model capable of resolving these issues is in a great demand.</p> <p>Results</p> <p>We design <it>O</it>(1) run-time solutions for both local and global dynamic programming pair-wise alignment algorithms on reconfigurable mesh computing model. To align <it>m </it>sequences with max length <it>n</it>, we combining the parallel pair-wise dynamic programming solutions with newly designed parallel components. We successfully reduce the progressive multiple sequence alignment algorithm's run-time complexity from <it>O</it>(<it>m </it>× <it>n</it>⁴) to <it>O</it>(<it>m</it>) using <it>O</it>(<it>m </it>× <it>n</it>³) processing units for scoring schemes that use three distinct values for match/mismatch/gap-extension. The general solution to multiple sequence alignment algorithm takes <it>O</it>(<it>m </it>× <it>n</it>⁴) processing units and completes in <it>O</it>(<it>m</it>) time.</p> <p>Conclusions</p> <p>To our knowledge, this is the first time the progressive multiple sequence alignment algorithm is completely parallelized with <it>O</it>(<it>m</it>) run-time. We also provide a new parallel algorithm for the Longest Common Subsequence (LCS) with <it>O</it>(1) run-time using <it>O</it>(<it>n</it>³) processing units. This is a big improvement over the current best constant-time algorithm that uses <it>O</it>(<it>n</it>⁴) processing units.</p

Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations

Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences\u27 structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes. In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity. In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm

Efficient Hardware Architectures for Accelerating Deep Neural Networks: Survey

In the modern-day era of technology, a paradigm shift has been witnessed in the areas involving applications of Artificial Intelligence (AI), Machine Learning (ML), and Deep Learning (DL). Specifically, Deep Neural Networks (DNNs) have emerged as a popular field of interest in most AI applications such as computer vision, image and video processing, robotics, etc. In the context of developed digital technologies and the availability of authentic data and data handling infrastructure, DNNs have been a credible choice for solving more complex real-life problems. The performance and accuracy of a DNN is a way better than human intelligence in certain situations. However, it is noteworthy that the DNN is computationally too cumbersome in terms of the resources and time to handle these computations. Furthermore, general-purpose architectures like CPUs have issues in handling such computationally intensive algorithms. Therefore, a lot of interest and efforts have been invested by the research fraternity in specialized hardware architectures such as Graphics Processing Unit (GPU), Field Programmable Gate Array (FPGA), Application Specific Integrated Circuit (ASIC), and Coarse Grained Reconfigurable Array (CGRA) in the context of effective implementation of computationally intensive algorithms. This paper brings forward the various research works carried out on the development and deployment of DNNs using the aforementioned specialized hardware architectures and embedded AI accelerators. The review discusses the detailed description of the specialized hardware-based accelerators used in the training and/or inference of DNN. A comparative study based on factors like power, area, and throughput, is also made on the various accelerators discussed. Finally, future research and development directions are discussed, such as future trends in DNN implementation on specialized hardware accelerators. This review article is intended to serve as a guide for hardware architectures for accelerating and improving the effectiveness of deep learning research.publishedVersio