Biologically inspired intelligent decision making: a commentary on the use of artificial neural networks in bioinformatics

Bioengineered
Timmy ManningPaul Walsh

Abstract

Artificial neural networks (ANNs) are a class of powerful machine learning models for classification and function approximation which have analogs in nature. An ANN learns to map stimuli to responses through repeated evaluation of exemplars of the mapping. This learning approach results in networks which are recognized for their noise tolerance and ability to generalize meaningful responses for novel stimuli. It is these properties of ANNs which make them appealing for applications to bioinformatics problems where interpretation of data may not always be obvious, and where the domain knowledge required for deductive techniques is incomplete or can cause a combinatorial explosion of rules. In this paper, we provide an introduction to artificial neural network theory and review some interesting recent applications to bioinformatics problems.

References

Dec 25, 1992·Nucleic Acids Research·J W Fickett, C S Tung
Dec 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·E C Uberbacher, R J Mural
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Apr 25, 1990·Nucleic Acids Research·K WadaT Ikemura
Aug 20, 1988·Journal of Molecular Biology·N Qian, T J Sejnowski
Sep 11, 1982·Nucleic Acids Research·J W Fickett
Jul 20, 1993·Journal of Molecular Biology·B Rost, C Sander
Jun 15, 1996·Genomics·M Burset, R Guigó
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 6, 1998·Annual Review of Biochemistry·R Y Tsien
May 20, 1999·Cytometry·P J SjöströmL U Wahlberg
Jun 27, 2000·Bioinformatics·L J McGuffinD T Jones
Feb 24, 2001·Proceedings of the National Academy of Sciences of the United States of America·R J Roberts
Mar 22, 2001·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·C M Dobson
Jul 10, 2001·Liver Transplantation : Official Publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society·V F HughesA K Trull
Feb 15, 2002·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Bob DjavanMichael Marberger
Aug 16, 2002·Evolutionary Computation·Kenneth O Stanley, Risto Miikkulainen
Sep 7, 2002·IEEE Transactions on Bio-medical Engineering·Kwokleung ChanTerrence J Sejnowski
Feb 14, 2003·Academic Radiology·Ruey-Feng ChangDar-Ren Chen
Feb 28, 2004·Bioinformatics·Thorsteinn Rögnvaldsson, Liwen You
Dec 31, 2005·International Journal of Neural Systems·Xiaoming ChenToshimi Okada
Apr 6, 2006·Proceedings of the National Academy of Sciences of the United States of America·Liat Ein-DorEytan Domany
Jun 13, 2006·Neural Computation·Geoffrey E HintonYee-Whye Teh
Jul 28, 2006·Bioinformatics·Conrad PlakeUlf Leser
Apr 7, 2007·Annals of the New York Academy of Sciences·J IllesE Racine
Oct 18, 2007·Molecular Systems Biology·Han-Yu ChuangTrey Ideker
Nov 20, 2008·Current Treatment Options in Oncology·Peter H Wiernik
Jun 17, 2009·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jeff HawkinsJamie Niemasik
Nov 10, 2009·Behavior Research Methods·Kevin DurdaRichard Caron
Nov 9, 2010·Orthopedics·Jonathan D LesterChristopher S Ahmad
Mar 10, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Salim A ChowdhuryMehmet Koyutürk
Jun 4, 2011·Bioengineered Bugs·Marine HenryRoy D Sleator
Aug 24, 2011·IEEE Transactions on Neural Networks·Saman Razavi, Bryan A Tolson
Nov 19, 2011·Bioengineered Bugs·Roy D Sleator
Dec 2, 2011·Methods in Molecular Biology·Roy D Sleator
Mar 20, 2012·Journal of Neural Engineering·David SussilloKrishna Shenoy
May 9, 2012·Nucleic Acids Research·João P G L M RodriguesGaurav Chopra
Aug 22, 2012·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ozan IrsoyEthem Alpaydin
Oct 12, 2012·Journal of Neurophysiology·Jordan A TaylorRichard B Ivry
Oct 27, 2012·Bioengineered·Roy D Sleator

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Citations

Feb 10, 2016·Saudi Journal of Biological Sciences·Fanxin MengLirong Teng
Sep 5, 2015·Bioengineered·Roy D Sleator
Jan 27, 2015·European Journal of Trauma and Emergency Surgery : Official Publication of the European Trauma Society·K SøreideJ A Søreide
Apr 26, 2017·Stroke; a Journal of Cerebral Circulation·Vida AbediRamin Zand
Aug 24, 2021·Journal of Medical Internet Research·Xueping WangLing Liu

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Methods Mentioned

BETA
X-ray
protein folding

Software Mentioned

ATHENA ( Analysis Tool for Heritable and Environmental Network...
quick
Github
NeuroEvolution of Augmenting ( NEAT
PSI
Sourceforge
Google Code
GRAIL
WEKA
genomeSIMLA

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