Shouji: A Fast and Efficient Pre-Alignment Filter for Sequence Alignment

Motivation: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly-parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern FPGA (Field-Programmable Gate Array) architectures to further boost the performance of our algorithm. Results: Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8x. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step. Availability: https://github.com/CMU-SAFARI/ShoujiComment: https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btz234/5421509, Bioinformatics Journal 201

Feature Trajectory Dynamic Time Warping for Clustering of Speech Segments

Dynamic time warping (DTW) can be used to compute the similarity between two sequences of generally differing length. We propose a modification to DTW that performs individual and independent pairwise alignment of feature trajectories. The modified technique, termed feature trajectory dynamic time warping (FTDTW), is applied as a similarity measure in the agglomerative hierarchical clustering of speech segments. Experiments using MFCC and PLP parametrisations extracted from TIMIT and from the Spoken Arabic Digit Dataset (SADD) show consistent and statistically significant improvements in the quality of the resulting clusters in terms of F-measure and normalised mutual information (NMI).Comment: 10 page

Aligning Community-Engaged Research to Context.

Community-engaged research is understood as existing on a continuum from less to more community engagement, defined by participation and decision-making authority. It has been widely assumed that more is better than less engagement. However, we argue that what makes for good community engagement is not simply the extent but the fit or alignment between the intended approach and the various contexts shaping the research projects. This article draws on case studies from three Community Engagement Cores (CECs) of NIEHS-funded Environmental Health Science Core Centers (Harvard University, UC Davis and University of Arizona,) to illustrate the ways in which community engagement approaches have been fit to different contexts and the successes and challenges experienced in each case. We analyze the processes through which the CECs work with researchers and community leaders to develop place-based community engagement approaches and find that different strategies are called for to fit distinct contexts. We find that alignment of the scale and scope of the environmental health issue and related research project, the capacities and resources of the researchers and community leaders, and the influences of the sociopolitical environment are critical for understanding and designing effective and equitable engagement approaches. These cases demonstrate that the types and degrees of alignment in community-engaged research projects are dynamic and evolve over time. Based on this analysis, we recommend that CBPR scholars and practitioners select a range of project planning and management techniques for designing and implementing their collaborative research approaches and both expect and allow for the dynamic and changing nature of alignment

Online and Offline Character Recognition Using Alignment to Prototypes

Nearest neighbor classifiers are simple to implement, yet they can model complex non-parametric distributions, and provide state-of-the-art recognition accuracy in OCR databases. At the same time, they may be too slow for practical character recognition, especially when they rely on similarity measures that require computationally expensive pairwise alignments between characters. This paper proposes an efficient method for computing an approximate similarity score between two characters based on their exact alignment to a small number of prototypes. The proposed method is applied to both online and offline character recognition, where similarity is based on widely used and computationally expensive alignment methods, i.e., Dynamic Time Warping and the Hungarian method respectively. In both cases significant recognition speedup is obtained at the expense of only a minor increase in recognition error.Office of Naval Research (N00014-03-1-0108); National Science Foundation (IIS-0308213, EIA-0202067