American Institute of Mathematical Sciences

Advanced
2003, 2003(Special): 898-904. doi: 10.3934/proc.2003.2003.898

Learning theory applied to Sigmoid network classification of protein biological function using primary protein structure

D. Warren 1, and  K Najarian 1,

1. 

College of Information Technology The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, United States

Received  September 2002 Revised  March 2003 Published  April 2003

Recently, Valiant’s Probably Approximately Correct (PAC) learning theory has been extended to learning m-dependent data. With this extension, training data set size for sigmoid neural networks have been bounded without underlying assumptions for the distribution of the training data. These extensions allow learning theory to be applied to training sets which are definitely not independent samples of a complete input space. In our work, we are developing length independent measures as training data for protein classification. This paper applies these learning theory methods to the problem of training a sigmoid neural network to recognize protein biological activity classes as a function of protein primary structure. Specifically, we explore the theoretical training set sizes for classifiers using the full amino acid sequence of the protein as the training data and using length independent measures as the training data. Results show bounds for training set sizes given protein size limits for the full sequence input compared to bounds for input that is sequence length independent.
Keywords: Neural Networks, Protein Function Prediction, DNA Sequencing, Learning Theory, Protein Sequencing, Gene Function Prediction.
Mathematics Subject Classification: Primary: 58F15, 58F17, 58F11; Secondary: 53C3.
Citation: D. Warren, K Najarian. Learning theory applied to Sigmoid network classification of protein biological function using primary protein structure. Conference Publications, 2003, 2003 (Special) : 898-904. doi: 10.3934/proc.2003.2003.898
[1]

Manisha Pujari, Rushed Kanawati. Link prediction in multiplex networks. Networks and Heterogeneous Media, 2015, 10 (1) : 17-35. doi: 10.3934/nhm.2015.10.17
[2]

Serap Ergün, Osman Palanci, Sirma Zeynep Alparslan Gök, Şule Nizamoğlu, Gerhard Wilhelm Weber. Sequencing grey games. Journal of Dynamics and Games, 2020, 7 (1) : 21-35. doi: 10.3934/jdg.2020002
[3]

David Hales, Stefano Arteconi. Motifs in evolving cooperative networks look like protein structure networks. Networks and Heterogeneous Media, 2008, 3 (2) : 239-249. doi: 10.3934/nhm.2008.3.239
[4]

Chen Li, Fajie Wei, Shenghan Zhou. Prediction method based on optimization theory and its application. Discrete and Continuous Dynamical Systems - S, 2015, 8 (6) : 1213-1221. doi: 10.3934/dcdss.2015.8.1213
[5]

Pavol Bokes. Exact and WKB-approximate distributions in a gene expression model with feedback in burst frequency, burst size, and protein stability. Discrete and Continuous Dynamical Systems - B, 2022, 27 (4) : 2129-2145. doi: 10.3934/dcdsb.2021126
[6]

Leonor Cruzeiro. The VES hypothesis and protein misfolding. Discrete and Continuous Dynamical Systems - S, 2011, 4 (5) : 1033-1046. doi: 10.3934/dcdss.2011.4.1033
[7]

H. N. Mhaskar, T. Poggio. Function approximation by deep networks. Communications on Pure and Applied Analysis, 2020, 19 (8) : 4085-4095. doi: 10.3934/cpaa.2020181
[8]

Shui-Nee Chow, Xiaojing Ye, Hongyuan Zha, Haomin Zhou. Influence prediction for continuous-time information propagation on networks. Networks and Heterogeneous Media, 2018, 13 (4) : 567-583. doi: 10.3934/nhm.2018026
[9]

Lambertus A. Peletier. Modeling drug-protein dynamics. Discrete and Continuous Dynamical Systems - S, 2012, 5 (1) : 191-207. doi: 10.3934/dcdss.2012.5.191
[10]

Mirosław Lachowicz, Martin Parisot, Zuzanna Szymańska. Intracellular protein dynamics as a mathematical problem. Discrete and Continuous Dynamical Systems - B, 2016, 21 (8) : 2551-2566. doi: 10.3934/dcdsb.2016060
[11]

Xilin Fu, Zhang Chen. New discrete analogue of neural networks with nonlinear amplification function and its periodic dynamic analysis. Conference Publications, 2007, 2007 (Special) : 391-398. doi: 10.3934/proc.2007.2007.391
[12]

Laltu Sardar, Sushmita Ruj. The secure link prediction problem. Advances in Mathematics of Communications, 2019, 13 (4) : 733-757. doi: 10.3934/amc.2019043
[13]

Wenjun Xia, Jinzhi Lei. Formulation of the protein synthesis rate with sequence information. Mathematical Biosciences & Engineering, 2018, 15 (2) : 507-522. doi: 10.3934/mbe.2018023
[14]

Xiaoshuang Xing, Gaofei Sun, Yong Jin, Wenyi Tang, Xiuzhen Cheng. Relay selection based on social relationship prediction and information leakage reduction for mobile social networks. Mathematical Foundations of Computing, 2018, 1 (4) : 369-382. doi: 10.3934/mfc.2018018
[15]

Fok Ricky, Lasek Agnieszka, Li Jiye, An Aijun. Modeling daily guest count prediction. Big Data & Information Analytics, 2016, 1 (4) : 299-308. doi: 10.3934/bdia.2016012
[16]

Armin Eftekhari, Michael B. Wakin, Ping Li, Paul G. Constantine. Randomized learning of the second-moment matrix of a smooth function. Foundations of Data Science, 2019, 1 (3) : 329-387. doi: 10.3934/fods.2019015
[17]

Yao Kuang, Raphael Douady. Crisis risk prediction with concavity from Polymodel. Journal of Dynamics and Games, 2022, 9 (1) : 97-115. doi: 10.3934/jdg.2021027
[18]

Yuantian Xia, Juxiang Zhou, Tianwei Xu, Wei Gao. An improved deep convolutional neural network model with kernel loss function in image classification. Mathematical Foundations of Computing, 2020, 3 (1) : 51-64. doi: 10.3934/mfc.2020005
[19]

Gerasimos G. Rigatos, Efthymia G. Rigatou, Jean Daniel Djida. Change detection in the dynamics of an intracellular protein synthesis model using nonlinear Kalman filtering. Mathematical Biosciences & Engineering, 2015, 12 (5) : 1017-1035. doi: 10.3934/mbe.2015.12.1017
[20]

Sunmoo Yoon, Maria Patrao, Debbie Schauer, Jose Gutierrez. Prediction models for burden of caregivers applying data mining techniques. Big Data & Information Analytics, 2017  doi: 10.3934/bdia.2017014

 Impact Factor: 

Tools

Metrics

  • PDF downloads (32)
  • HTML views (0)
  • Cited by (0)

Other articles
by authors

[Back to Top]

Copyright © 2022 American Institute of Mathematical Sciences | Privacy Policy