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abPOA: an SIMD-based C library for fast partial order alignment using adaptive band [article]

Yan Gao, Yongzhuang Liu, Yanmei Ma, Bo Liu, Yadong Wang, Yi Xing
2020 bioRxiv   pre-print
We present abPOA (adaptive banded Partial Order Alignment), a Single Instruction Multiple Data (SIMD) based C library for fast partial order alignment using adaptive banded dynamic programming.  ...  Compared to a state-of-the-art tool (SPOA), abPOA is up to 15 times faster with a comparable alignment accuracy.Availability and implementationabPOA is implemented in C.  ...  Yuan Gao and Yadong Liu for assistance with testing abPOA and providing comments on the manuscript. Conflict of Interest: Y.X. is a scientific cofounder of Panorama Medicine.  ... 
doi:10.1101/2020.05.07.083196 fatcat:vbh57rwxc5ddhdjrytz23enjdm

Developing a platoon-wide Eco-Cooperative Adaptive Cruise Control (CACC) system

Ziran Wang, Guoyuan Wu, Peng Hao, Kanok Boriboonsomsin, Matthew Barth
2017 2017 IEEE Intelligent Vehicles Symposium (IV)  
As an example, Cooperative Adaptive Cruise Control (CACC) systems are of high interest, allowing CAVs to communicate and cooperate with each other to form platoons, where one vehicle follows another with  ...  A full spectrum of environmentally-friendly CACC maneuvers are explored and the associated protocols are developed, including sequence determination, gap closing and opening, platoon cruising with gap  ...  [9] found that emissions could be reduced by up to almost 20% through three different strategies: congestion mitigation strategies that allow traffic to flow at better speeds, speed management techniques  ... 
doi:10.1109/ivs.2017.7995884 dblp:conf/ivs/WangWHBB17 fatcat:yo4mmpzb4jgunbeex65v7okp7y

Which Distributed Averaging Algorithm Should I Choose for my Sensor Network?

P. Denantes, F. Benezit, P. Thiran, M. Vetterli
2008 2008 Proceedings IEEE INFOCOM - The 27th Conference on Computer Communications  
Finally, we use these tools to make some experimental observations illustrating the behavior of the convergence speed with respect to network topology and reliability in both average consensus and gossip  ...  Confronted with the diversity of these algorithms, the engineer may be puzzled in his choice for one of them.  ...  There are three main average consensus strategies for the choice of the weights.  ... 
doi:10.1109/infocom.2007.152 fatcat:ftgzb4mod5hfbcndt3l2eiro6m

Which Distributed Averaging Algorithm Should I Choose for my Sensor Network?

P. Denantes, F. Benezit, P. Thiran, M. Vetterli
2008 IEEE INFOCOM 2008 - The 27th Conference on Computer Communications  
Finally, we use these tools to make some experimental observations illustrating the behavior of the convergence speed with respect to network topology and reliability in both average consensus and gossip  ...  Confronted with the diversity of these algorithms, the engineer may be puzzled in his choice for one of them.  ...  There are three main average consensus strategies for the choice of the weights.  ... 
doi:10.1109/infocom.2008.152 dblp:conf/infocom/DenantesBTV08 fatcat:3v5we46ix5bttiml6ru7jem6fe

Fast filtering for RNA homology search

D. L. Kolbe, S. R. Eddy
2011 Bioinformatics  
A vector-parallel implementation of this method gives up to 100-fold speed-up; vector-parallel implementations of standard gapped alignment at two levels of precision give 3-and 6-fold speed-ups.  ...  Typical acceleration strategies rely on at least one filtering stage using sequence-only search.  ...  The empirical speed-up of this stage depends both on the parallelization and on the MSCYK heuristic; we compare MSCYK to its closest equivalent, a CYK algorithm adapted for scanning long sequences.  ... 
doi:10.1093/bioinformatics/btr545 pmid:21965818 pmcid:PMC3208395 fatcat:xvs4dkrzunfchjwwpwoaah2h3i

A Comparative Analysis of RANSAC Techniques Leading to Adaptive Real-Time Random Sample Consensus [chapter]

Rahul Raguram, Jan-Michael Frahm, Marc Pollefeys
2008 Lecture Notes in Computer Science  
The Random Sample Consensus (RANSAC) algorithm is a popular tool for robust estimation problems in computer vision, primarily due to its ability to tolerate a tremendous fraction of outliers.  ...  The technique we develop is capable of efficiently adapting to the constraints presented by a fixed time budget, while at the same time providing accurate estimation over a wide range of inlier ratios.  ...  Adaptive Real-Time Random Sample Consensus In this section, we describe a novel framework for Adaptive Real-Time Random Sample Consensus (ARRSAC), which is capable of providing accurate real-time estimation  ... 
doi:10.1007/978-3-540-88688-4_37 fatcat:gzdc3v6aezd6lghhyaolow47ui

Fast ADMM Algorithm for Distributed Optimization with Adaptive Penalty [article]

Changkyu Song and Sejong Yoon and Vladimir Pavlovic
2015 arXiv   pre-print
The proposed method accelerates the speed of convergence by automatically deciding the constraint penalty needed for parameter consensus in each iteration.  ...  We propose new methods to speed up convergence of the Alternating Direction Method of Multipliers (ADMM), a common optimization tool in the context of large scale and distributed learning.  ...  Next, we propose the novel penalty parameter update strategy for ADMM speed up that does not require manual tuning of τ t .  ... 
arXiv:1506.08928v1 fatcat:vpz3qvnyc5hc3myzc2ah3lhlbi

A flexible and efficient template format for circular consensus sequencing and SNP detection

K. J. Travers, C.-S. Chin, D. R. Rank, J. S. Eid, S. W. Turner
2010 Nucleic Acids Research  
Furthermore, this consensus sequence is obtained from both the sense and antisense strands of the insert region.  ...  We demonstrate the generation of high-quality consensus accuracy from single molecules, as well as the use of SMRTbell templates in the identification of rare sequence variants.  ...  sequencing experiments.  ... 
doi:10.1093/nar/gkq543 pmid:20571086 pmcid:PMC2926623 fatcat:ac7m6q76uzd6hf4mbwi43mfga4

A Review on Cooperative Adaptive Cruise Control (CACC) Systems: Architectures, Controls, and Applications [article]

Ziran Wang, Guoyuan Wu, Matthew Barth
2018 arXiv   pre-print
Cooperative adaptive cruise control (CACC), for example, is one promising technology to allow CAVs to be driven in a cooperative manner and introduces system-wide benefits.  ...  Applications of CACC technology are demonstrated with detailed literature, which draw an overall landscape of CACC, point out current opportunities and challenges, and anticipate its development in the  ...  Cooperative adaptive cruise control (CACC) is one of the most promising technologies for CAVs, which extends adaptive cruise control (ACC) with cooperative maneuvers by CAVs.  ... 
arXiv:1809.02867v1 fatcat:ciutcyhsd5dancwu7ue446so2q

Atria: an ultra-fast and accurate trimmer for adapter and quality trimming

Jiacheng Chuan, Aiguo Zhou, Lawrence Richard Hale, Miao He, Xiang Li
2021 Gigabyte  
There is a need for a fast trimming algorithm to remove adapters precisely, especially in read tails with relatively low quality.  ...  With advances in next-generation sequencing, adapters attached to reads and low-quality bases directly and implicitly hinder downstream analysis.  ...  ACKNOWLEDGEMENTS The technical assistance of Jingbai Nie is greatly acknowledged. The advice on algorithm optimization, encouragement, and support of Drs.  ... 
doi:10.46471/gigabyte.31 fatcat:pppq5xpxhbbcjbk3as7gpjvdda

Social Choice-based Explanations: An Approach to Enhancing Fairness and Consensus Aspects

Thi Ngoc Trang Tran, Muesluem Atas, Man Le, Ralph Samer, Martin Stettinger
2020 Journal of universal computer science (Online)  
In the context of repeated decisions, group members' satisfaction from previous decisions are helpful to improve the fairness perception of users concerning group recommendations and speed up the group  ...  In this paper, we proposed different types of explanations and found the most effective ones in terms of increasing the fairness perception, consensus perception and satisfaction of group members with  ...  consensus perception, as well as speed up the group decision-making process.  ... 
doi:10.3897/jucs.2020.021 fatcat:pbqefy3exnhvre2vttnyo4ppdq

ViralFlow: A Versatile Automated Workflow for SARS-CoV-2 Genome Assembly, Lineage Assignment, Mutations and Intrahost Variant Detection

Filipe Zimmer Dezordi, Antonio Marinho da Silva Neto, Túlio de Lima Campos, Pedro Miguel Carneiro Jeronimo, Cleber Furtado Aksenen, Suzana Porto Almeida, Gabriel Luz Wallau, on behalf of the Fiocruz COVID-19 Genomic Surveillance Network
2022 Viruses  
The current deluge of SARS-CoV-2 genomic data generated worldwide has put additional pressure on the urgent need for streamlined bioinformatics workflows.  ...  Here, we describe a workflow developed by our group to process and analyze large-scale SARS-CoV-2 Illumina amplicon sequencing data.  ...  Surveillance Network for testing and sources of information to compare the results.  ... 
doi:10.3390/v14020217 pmid:35215811 pmcid:PMC8877152 fatcat:wqarqcakxvav5mbqguusekpfty

Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution

Martin Lehmann, Markus Wyss
2001 Current Opinion in Biotechnology  
Serrano L, Day AG, Fersht AR: Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability.  ...  Pantoliano MW, Whitlow M, Wood JF, Dodd SW, Hardman KD, Rollence ML, Bryan PN: Large increases in general stability for subtilisin BPN′ ′ through incremental changes in the free energy of unfolding.  ...  This reduces speed and throughput and thereby limits the sequence space amenable to testing.  ... 
doi:10.1016/s0958-1669(00)00229-9 pmid:11551465 fatcat:luatffjjmre3vo7gyrvxeajo3m

A Game Theory Based Ramp Merging Strategy for Connected and Automated Vehicles in the Mixed Traffic: A Unity-SUMO Integrated Platform [article]

Xishun Liao and Xuanpeng Zhao and Guoyuan Wu and Matthew Barth and Ziran Wang and Kyungtae Han and Prashant Tiwari
2021 arXiv   pre-print
In this paper, a game theory-based ramp merging strategy has been developed for the optimal merging coordination of CAVs in the mixed traffic, which determines dynamic merging sequence and corresponding  ...  The results show that the average speed of traffic flow can be increased up to 110%, and the fuel consumption can be reduced up to 77%, respectively.  ...  The contents of this paper only reflect the views of the authors, who are responsible for the facts and the accuracy of the data presented herein.  ... 
arXiv:2101.11237v1 fatcat:rlsiuikdzrhbpcus2mhqpnlak4

Atria: An Ultra-fast and Accurate Trimmer for Adapter and Quality Trimming [article]

Jiacheng Chuan, Aiguo Zhou, Lawrence Richard Hale, Miao He, Xiang Li
2021 bioRxiv   pre-print
As Next Generation Sequencing takes a dominant role in terms of output capacity and sequence length, adapters attached to the reads and low-quality bases hinder the performance of downstream analysis directly  ...  The algorithm can be used in a broad range of short-sequence matching applications, such as primer search and seed scanning before alignment.  ...  Acknowledgments The technical assistance of Jingbai Nie is greatly acknowledged. The financial support of CFIA to JC is greatly appreciated.  ... 
doi:10.1101/2021.09.07.459340 fatcat:ik552vwobbha3kpvqplkgtpf2u
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