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Innovations and challenges in detecting long read overlaps: an evaluation of the state-of-the-art

Justin Chu, Hamid Mohamadi, René L. Warren, Chen Yang, Inanç Birol
2016 Bioinformatics  
Here, we review the current state-of-the-art read-to-read overlap tools for error-prone long reads, including BLASR, DALIGNER, MHAP, GraphMap and Minimap.  ...  Though akin to the read-to-reference alignment problem, read-to-read overlap detection is a distinct problem that can benefit from specialized algorithms that perform efficiently and robustly on high error  ...  The content of this work is solely the responsibility of the authors, and does not necessarily represent the official views of the National Institutes of Health or other funding organizations.  ... 
doi:10.1093/bioinformatics/btw811 pmid:28003261 pmcid:PMC5408847 fatcat:veduiqhzorbxjkbcit6fegfcwy

Merging real and virtual worlds: An analysis of the state of the art and practical evaluation of Microsoft Hololens [article]

Adrien Coppens
2017 arXiv   pre-print
After investigating those technical aspects, I carry out an objective comparison of the existing state-of-the-art and state-of-the-practice in those domains, and I discuss present and potential applications  ...  Achieving a symbiotic blending between reality and virtuality is a dream that has been lying in the minds of many people for a long time.  ...  Finally, based on the experience acquired and the state of the art, chapter 7 will dicuss current limitations as well as future prospects and research in those areas.  ... 
arXiv:1706.08096v1 fatcat:rl4p3bcfonfqdczruiwek37xbu

Overlapping long sequence reads: Current innovations and challenges in developing sensitive, specific and scalable algorithms [article]

Justin Chu, Hamid Mohamadi, Rene Warren, Chen Yang, Inanc Birol
2016 bioRxiv   pre-print
Here, we review the current state-of-the-art read-to-read overlap tools for error-prone long reads, including BLASR, DALIGNER, MHAP, GraphMap, and Minimap.  ...  Though akin to the read-to-reference alignment problem, read-to-read overlap detection is a distinct problem that can benefit from specialized algorithms that perform efficiently and robustly on high error  ...  Acknowledgements The authors would like to thank Sergey Koren, Ivan Sović for their help and suggestions when running MHAP and GraphMap, respectively, as well as their insights into the behaviour and results  ... 
doi:10.1101/081596 fatcat:bft5rd5svrhh5mgnaozkh35nue

Disentangling Overlapping Beliefs by Structured Matrix Factorization [article]

Chaoqi Yang, Jinyang Li, Ruijie Wang, Shuochao Yao, Huajie Shao, Dongxin Liu, Shengzhong Liu, Tianshi Wang, Tarek F. Abdelzaher
2020 arXiv   pre-print
The case when individuals with different beliefs agree on some subset of points was less explored. We observe that social beliefs overlap even in polarized scenarios.  ...  In the space of unsupervised belief separation algorithms, the emphasis was mostly given to the problem of identifying disjoint (e.g., conflicting) beliefs.  ...  The results of this comparison show that our algorithm significantly outperforms the state of the art.  ... 
arXiv:2002.05797v1 fatcat:lidriksqsfe5faiw2snrpklbey

Interventions at the end of life – a taxonomy for 'overlapping consensus'

David Clark, Hamilton Inbadas, Ben Colburn, Catriona Forrest, Naomi Richards, Sandy Whitelaw, Shahaduz Zaman
2017 Wellcome Open Research  
Following the inspiration of political philosopher John Rawls, we seek to foster an 'overlapping consensus' on how interventions at the end of life can be construed, understood and assessed.  ...  What interventions are emerging in the face of these challenges? We conceptualize a comprehensive taxonomy of interventions, Methods: defined as 'organized responses to end of life issues'.  ...  Author contributions All authors made substantial contributions to the conception of the work, in particular the underlying notion of a taxonomy of end of life interventions and its constituent parts,  ... 
doi:10.12688/wellcomeopenres.10722.1 pmid:28261674 pmcid:PMC5336190 fatcat:jei7n345brfytcjyscdxxoq4rq

Empirical Evaluation on the Impact of Class Overlap for EEG-based Early Epileptic Seizure Detection

Yubin Qu, Xiang Chen, Fang Li, Fan Yang, Junxia Ji, Long Li
2020 IEEE Access  
MODELING METHODS In our experiments, three preprocessing strategies were evaluated and compared with four state-of-art classification algorithms.  ...  RQ1 and RQ2 aim to compare the performance of the existing state-of-the-art learning models by removing overlapping instances in the epilepsy seizure datasets.  ... 
doi:10.1109/access.2020.3028139 fatcat:ew7zn7onqrgd5jljsomj36bvta

Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era

Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni
2019 Quantitative Biology  
Conclusions: We complete our analysis with a discussion on the algorithmic issues of assembling from long reads (e.g., PacBio and Oxford Nanopore).  ...  De novo genome assembly relies on two kinds of graphs: de Bruijn graphs and overlap graphs.  ...  An evaluation pipeline is the main focus of [9] , which presents and compares ten long read assemblers (thirdgeneration reads) in terms of contiguity, completeness and accuracy.  ... 
doi:10.1007/s40484-019-0181-x fatcat:diii4vjqijf4hglbg2neuvcm44

A Relation-Oriented Model With Global Context Information for Joint Extraction of Overlapping Relations and Entities

Huihui Han, Jian Wang, Xiaowen Wang
2022 Frontiers in Neurorobotics  
Comprehensive experiments conducted on two public datasets, NYT and WebNLG, show that our model can effectively extract overlapping relation triples and outperforms the current state-of-the-art methods  ...  The decoder part consists of a multi-relation classifier for the relation classification task, and an improved long short-term memory for the entity recognition task.  ...  ACKNOWLEDGMENTS The work described in this study was conducted at the Computer Integrated Manufacturing System Research Center, College of Electronics and Information Engineering, and Tongji University  ... 
doi:10.3389/fnbot.2022.914705 pmid:35859657 pmcid:PMC9290867 fatcat:djurofdwanb4jovmmk44jae5gu

Collaborative Filtering with Attribution Alignment for Review-based Non-overlapped Cross Domain Recommendation [article]

Weiming Liu, Xiaolin Zheng, Mengling Hu, Chaochao Chen
2022 arXiv   pre-print
Our empirical study on Douban and Amazon datasets demonstrates that CFAA significantly outperforms the state-of-the-art models under the RNCDR setting.  ...  In this paper, we focus on the Review-based Non-overlapped Recommendation (RNCDR) problem.  ...  . (3) Extensive empirical studies on Douban and Amazon datasets demonstrate that CFAA significantly improves the state-of-the-art models under the RNCDR setting.  ... 
arXiv:2202.04920v1 fatcat:lqnltllc4ngvjmp47iqww3kg5i

Infrared Small Target Detection Based on Non-Overlapping Patch Model via l0-l1 Norm

Jiaqi Yang, Yi Cui, Fei Song, Tao Lei
2020 Electronics  
with respect to state-of-the-art methods.  ...  The proposed method ultimately yielded favorable detection results.Adequate experiment results demonstrate that the proposed method is competitive in terms ofbackground suppression and true target detection  ...  Acknowledgments: The authors would thank the published code of Gao's model and Zhang's model for comparison. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/electronics9091426 fatcat:fppipwz3fndipjwvcj2hwkd22i

FPGA-Based Inter-layer Pipelined Accelerators for Filter-Wise Weight-Balanced Sparse Fully Convolutional Networks with Overlapped Tiling

Masayuki Shimoda, Youki Sada, Hiroki Nakahara
2021 Journal of Signal Processing Systems  
AbstractConvolutional neural networks (CNNs) exhibit state-of-the-art performance while performing computer-vision tasks.  ...  We also propose an overlapped tiling algorithm, where tiles are extracted with overlap to prevent both accuracy degradation and high utilization of BRAMs storing high-resolution images.  ...  Acknowledgements This research is supported in part by the Grants in Aid for Scientistic Research of JSPS, Industry-academia collaborative R&D programs centre of innovation (COI) program, Core Research  ... 
doi:10.1007/s11265-021-01642-6 fatcat:vfcfmfjvyfahphf6xiuy5zagqu

Market positioning: the shifting effects of niche overlap

J. Bruggeman, D. Grunow, M. A. A. M. Leenders, I. Vermeulen, J. G. Kuilman
2012 Industrial and Corporate Change  
Data on consumers' impressions of Dutch music festivals and on the growth and decline of early Internet search engines were used to test the proposition that niche overlap may, in fact, be non-monotonically  ...  The results confirm that both the appeal that organizations generate as well as their growth rates are non-monotonically related to niche overlap, and that positive effects of niche overlap decrease with  ...  Acknowledgements We are grateful to Arjen van Witteloostuijn for his comments, as well as discussants at a seminar at the University of Amsterdam and at the second European organizational ecology workshop  ... 
doi:10.1093/icc/dts009 fatcat:rdtgd4ouerfa7ii4pbqu33qgnq

The impact of stress on pain

David Finn
2017 Physiology News  
Note the attainment of a steady state in moderate exercise, the delayed attainment of a steady state in heavy exercise and the absence of a steady state and the achievement of maximal oxygen uptake (4.20  ...  a relatively young age due to an inability to detect and respond appropriately to critical illness, injury, or accumulation of injuries.  ... 
doi:10.36866/pn.108.25 fatcat:shs64xwqsnh5pdoxytgstadtce

A Text Recognition and Retrieval System for e-Business Image Management [chapter]

Jiang Zhou, Kevin McGuinness, Noel E. O'Connor
2018 Lecture Notes in Computer Science  
In this paper, we explore the power of text recognition for e-business image management and propose an innovative system based on photo OCR.  ...  We compared our system with two other approaches for scene text recognition, and the results show our system outperforms other state-ofthe-art on the new challenging dataset.  ...  Acknowledgements This research has been supported by Science Foundation Ireland under grant number SFI/12/RC/2289 which is co-funded by the European Regional Development Fund.  ... 
doi:10.1007/978-3-319-73600-6_3 fatcat:v4wgmgalvbgtdjx27jbgur6ugy

Estimation of Blood Alcohol Concentration from Smartphone Gait Data using Neural Networks

Ruojun Li, Ganesh Prasanna Balakrishnan, Jiaming Nie, Yu Li, Emmanuel Agu, Kristin Grimone, Debra Herman, Ana M Abrantes, Michael D. Stein
2021 IEEE Access  
Our Bi-LSTM architecture achieves an RMSE of 0.0167 and the CNN architecture achieves an RMSE of 0.0168, outperforming state-of-the-art intoxication detection models using Bayesian Regularized Multilayer  ...  Passive methods of proactively detecting drivers who are too drunk to drive in order to notify them and prevent accidents, have recently been proposed.  ...  This reduces variability and improve model robustness to perturbing user movements. • Evaluation and comparison with state-of-the-art models: We rigorously evaluated our proposed models and found that  ... 
doi:10.1109/access.2021.3054515 pmid:34527505 pmcid:PMC8439437 fatcat:wvcm3rgehze7xmekzlhasgfn4q
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