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Towards Automated Structure-Based NMR Resonance Assignment [chapter]

Richard Jang, Xin Gao, Ming Li
2010 Lecture Notes in Computer Science  
On a publicly available data set for Ubiquitin, where the type prediction accuracy is 83%, we achieved 91% assignment accuracy, compared to the 59% accuracy that was obtained without correcting for typing  ...  We propose a general framework for solving the structurebased NMR backbone resonance assignment problem.  ...  Acknowledgment We would like to thank Xiong, Pandurangan, Bailey-Kellogg for providing us with their program and the test data for 5 proteins.  ... 
doi:10.1007/978-3-642-12683-3_13 fatcat:yxn7pesorbgbpdj2nppny653nu

Towards Fully Automated Structure-Based NMR Resonance Assignment of 15N-Labeled Proteins From Automatically Picked Peaks

Richard Jang, Xin Gao, Ming Li
2011 Journal of Computational Biology  
The core consists of a pair of integer programming models: one for spin system forming and amino acid typing, and the other for backbone resonance assignment.  ...  On a publicly available data set for human ubiquitin, where the typing accuracy is 83%, we achieve 91% accuracy, compared to the 59% accuracy obtained without correcting for such errors.  ...  ACKNOWLEDGMENTS We would like to thank Xiong, Pandurangan, and Bailey-Kellogg for providing us with their program and the test data for five proteins.  ... 
doi:10.1089/cmb.2010.0251 pmid:21385039 fatcat:nryaflvjfzccdp354uvxyshqly

Automated diagnostics for resonance signature recognition on IMAGE/RPI plasmagrams

Ivan A. Galkin, Bodo W. Reinisch, Xueqin Huang, Robert F. Benson, Shing F. Fung
2004 Radio Science  
them in relation to model-based resonances.  ...  the accurate processing of the remote sensing information on the plasmagrams.  ...  A similar matching concept was used in the resonance interpretation algorithm by Trotignon et al. [2001] for the Whisper relaxation sounder aboard the Cluster-2 spacecraft.  ... 
doi:10.1029/2003rs002921 fatcat:wl735i75onay7pjp6jcz4uixnq

RESONATE: Reverberation environment simulation for improved classification of speech models

Robert F. Dickerson, Enamul Hoque, Philip Asare, Shahriar Nirjon, John A. Stankovic
2014 IPSN-14 Proceedings of the 13th International Symposium on Information Processing in Sensor Networks  
In this paper, we present a practical reverberation compensation method called RESONATE, which uses simulated room impulse responses to adapt a training corpus for use in multiple real reverberant rooms  ...  We demonstrate that the system creates robust classifiers that perform within 5 -10% of baseline accuracy of non-reverberant environments.  ...  Our results here show that our techniques to address reverberation significantly improve speaker identification accuracy compared to the non-matched scenario by roughly 30%, and in most cases closely approach  ... 
doi:10.1109/ipsn.2014.6846745 fatcat:4stourtt3rapbjbhpgi5ruvunq

Speaker normalization based on subglottal resonances

Shizhen Wang, Abeer Alwan, Steven M. Lulich
2008 Proceedings of the IEEE International Conference on Acoustics, Speech and Signal Processing  
Since the subglottal airways do not change for a specific speaker, the subglottal resonances are independent of the sound type (i.e., vowel, consonant, etc.) and remain constant for a given speaker.  ...  This paper presents a speaker normalization method based on estimating the second and third subglottal resonances.  ...  For the matched case, the HMM models were trained on the SI training portion of the database with 72 adult speakers, and tested on the SI testing set.  ... 
doi:10.1109/icassp.2008.4518600 dblp:conf/icassp/WangAL08 fatcat:2xcxpgutobfivknnk677ha5lka

Comprehensive Numerical Analysis of Finite Difference Time Domain Methods for Improving Optical Waveguide Sensor Accuracy

M. Samak, A. Bakar, Muhammad Kashif, Mohd Zan
2016 Sensors  
The alternating direction implicit technique can be considered a significant step forward for improving the efficiency of unconditionally stable FDTD schemes.  ...  This comparative study shows that the local one-dimensional method had minimum relative error ranges of less than 40% for analytical frequencies above 42.85 GHz, and the same accuracy was generated by  ...  All the authors are responsible for the numerical operations and arithmetic processes, and M. Mosleh E. Abu Samak wrote the paper, drew the figures and finalized the submitted manuscript.  ... 
doi:10.3390/s16040506 fatcat:suu4djuhyne7fl6kkgbfzglbdy

Extraction and Visualization of Ocular Blood Vessels in 3D Medical Images Based on Geometric Transformation Algorithm

Zhike Zhang, Shuixin Zhang, Hongyu Feng
2021 Journal of Healthcare Engineering  
The optimal stochastic resonance response of the nonlinear model of neurons in the global sense is obtained to detect the high-grade intensity signal; then, the input signal is defined as a local image  ...  The sensitivity of the multilevel segmentation method proposed in this paper is significantly improved compared with the global random resonance results, indicating that the method proposed in this paper  ...  For feature-based alignment algorithms, the alignment process involves the feature matching process of points, and good feature matching can lead to better experimental results for subsequent feature point-based  ... 
doi:10.1155/2021/5573381 doaj:badcf56707244c63bd8fe0b5fcf031a3 fatcat:f45wcy3uq5bg3dkavg7xsvme74

Pattern recognition approach to the detection of single-trial event-related functional magnetic resonance images

D. Burke, K. Murphy, H. Garavan, R. Reilly
2004 Medical and Biological Engineering and Computing  
A novel application of parametric modelling yielded an accuracy of 69.8 AE 6.3%, and a matched filtering approach yielded an accuracy of 71.9 AE 5.4%.  ...  Functional magnetic resonance imaging (FMRI) is an imaging technique for determining which regions of the brain are activated in response to a stimulus or event.  ...  To improve accuracy, information regarding the underlying haemodynamic response is included by way of matched filtering and a novel application of an autoregressive with exogenous input (ARX) model for  ... 
doi:10.1007/bf02347541 pmid:15503960 fatcat:rjxwj6ttdre7jb7sahh7pbozrm

Robust retrospective frequency and phase correction for single-voxel MR spectroscopy

Martin Wilson
2018 Magnetic Resonance in Medicine  
ACKNOWLEDGMENTS The support of Philips Healthcare Clinical Science for the provision of the MEGA-PRESS implementation.  ...  Results: RATS offers improved accuracy and stability for large frequency shifts and unstable baselines.  ...  The observation of an elevated GSH resonance in the processing variants with visible misalignment artifacts suggests improved alignment with the RATS method results in more accurate subtraction, and therefore  ... 
doi:10.1002/mrm.27605 pmid:30417937 fatcat:hvi4rgbsqfazbjxxrp7q6rerjy

Scalar production and decay to top quarks including interference effects at NLO in QCD in an EFT approach

Diogo Buarque Franzosi, Eleni Vryonidou, Cen Zhang
2017 Journal of High Energy Physics  
Scalar and pseudo-scalar resonances decaying to top quarks are common predictions in several scenarios beyond the standard model (SM) and are extensively searched for by LHC experiments.  ...  We also discuss how our computation can be used to improve the predictions for physics scenarios where the gluon-scalar loop is resolved and the effective approach is less applicable.  ...  Acknowledgments We would like to thank Rikkert Frederix and Stefano Frixione for discussions regarding the parton shower treatment of resonances.  ... 
doi:10.1007/jhep10(2017)096 fatcat:xtxld2aznrdnpkw4io6pntzaj4

Scalar production and decay to top quarks including interference effects at NLO in QCD in an EFT approach [article]

Diogo Buarque Franzosi, Eleni Vryonidou, Cen Zhang
2017 arXiv   pre-print
Scalar and pseudo-scalar resonances decaying to top quarks are common predictions in several scenarios beyond the standard model (SM) and are extensively searched for by LHC experiments.  ...  We also discuss how our computation can be used to improve the predictions for physics scenarios where the gluon-scalar loop is resolved and the effective approach is less applicable.  ...  Acknowledgements We would like to thank Rikkert Frederix and Stefano Frixione for discussions regarding the parton shower treatment of resonances.  ... 
arXiv:1707.06760v2 fatcat:6x5m2a422nhg5jxa3uotbh55c4

A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments

Christopher James Langmead, Anthony Yan, Ryan Lilien, Lincong Wang, Bruce Randall Donald
2004 Journal of Computational Biology  
accuracy), matched to a variety of 3D structural models.  ...  We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of a homologous structure.  ...  Werner-Reiss, and all members of Donald Lab for helpful discussions and comments on drafts.  ... 
doi:10.1089/1066527041410436 pmid:15285893 fatcat:cdfib2ztkbbxtl4anuukjp3lba

An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments

Christopher James Langmead, Bruce Randall Donald
2004 Journal of Biomolecular NMR  
accuracy), matched to a variety of 3D structural models.  ...  We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of a homologous structure.  ...  Werner-Reiss, and all members of Donald Lab for helpful discussions and comments on drafts.  ... 
doi:10.1023/b:jnmr.0000019247.89110.e6 pmid:15014227 fatcat:oqeinlngjfa2ncoki6rktsuul4

Large a polynomial-time nuclear vector replacement algorithm for automated NMR resonance assignments

Christopher James Langmead, Anthony Yan, Ryan Lilien, Lincong Wang, Bruce Randall Donald
2003 Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03  
accuracy), matched to a variety of 3D structural models.  ...  We report an automated procedure for high-throughput NMR resonance assignment for a protein of known structure, or of a homologous structure.  ...  Werner-Reiss, and all members of Donald Lab for helpful discussions and comments on drafts.  ... 
doi:10.1145/640075.640098 dblp:conf/recomb/LangmeadYLWD03 fatcat:c2vxx46nn5ah3nshhhhnu354z4

Based on Soft Competition ART Neural Network Ensemble and Its Application to the Fault Diagnosis of Bearing

Dan Yang, Hailin Mu, Zengbing Xu, Zhigang Wang, Cancan Yi, Changming Liu
2017 Mathematical Problems in Engineering  
This paper presents a novel method for fault diagnosis based on an improved adaptive resonance theory (ART) neural network and ensemble technique. The method consists of three stages.  ...  Firstly, the improved ART neural network is comprised of the soft competition technique based on fuzzy competitive learning (FCL) and ART based on Yu's norm, the neural nodes in the competition layer are  ...  Section 2 reviews the adaptive resonance theory and Yu's norm ART. An improved method for fault diagnosis-Yu's norm ART based on soft competition is proposed in Section 3.  ... 
doi:10.1155/2017/2641546 fatcat:6pfsqnjud5ezzeltkxlpektzii
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