Treffer: FPGA-based hardware accelerator for the prediction of protein secondary class via fuzzy K-nearest neighbors with Lempel-Ziv complexity based distance measure
Title:
FPGA-based hardware accelerator for the prediction of protein secondary class via fuzzy K-nearest neighbors with Lempel-Ziv complexity based distance measure
Authors:
Source:
Neurocomputing (Amsterdam). 148:409-419
Publisher Information:
Amsterdam: Elsevier, 2015.
Publication Year:
2015
Physical Description:
print, 35 ref
Original Material:
INIST-CNRS
Subject Terms:
Cognition, Computer science, Informatique, Sciences exactes et technologie, Exact sciences and technology, Sciences appliquees, Applied sciences, Informatique; automatique theorique; systemes, Computer science; control theory; systems, Informatique théorique, Theoretical computing, Algorithmique. Calculabilité. Arithmétique ordinateur, Algorithmics. Computability. Computer arithmetics, Electronique, Electronics, Electronique des semiconducteurs. Microélectronique. Optoélectronique. Dispositifs à l'état solide, Semiconductor electronics. Microelectronics. Optoelectronics. Solid state devices, Circuits intégrés, Integrated circuits, Conception. Technologies. Analyse fonctionnement. Essais, Design. Technologies. Operation analysis. Testing, Circuits intégrés par fonction (dont mémoires et processeurs), Integrated circuits by function (including memories and processors), Sciences biologiques et medicales, Biological and medical sciences, Sciences biologiques fondamentales et appliquees. Psychologie, Fundamental and applied biological sciences. Psychology, Biophysique moleculaire, Molecular biophysics, Structure en biologie moléculaire, Structure in molecular biology, Structure tridimensionnelle, Tridimensional structure, Accélérateur, Accelerator, Acelerador, Algorithme flou, Fuzzy algorithm, Algoritmo borroso, Bioinformatique, Bioinformatics, Bioinformática, Biopolymère, Biopolymer, Biopolímero, Classification, Clasificación, Code longueur variable, Variable length code, Código longitud variable, Complexité algorithme, Algorithm complexity, Complejidad algoritmo, Conception circuit, Circuit design, Diseño circuito, Intervalle confiance, Confidence interval, Intervalo confianza, Logique floue, Fuzzy logic, Lógica difusa, Mesure complexité, Complexity measure, Medida complexidad, Mesure distance, Distance measurement, Plus proche voisin, Nearest neighbour, Vecino más cercano, Protéine, Protein, Proteína, Réseau neuronal, Neural network, Red neuronal, Réseau porte programmable, Field programmable gate array, Red puerta programable, Structure tertiaire, Tertiary structure, Estructura terciaria, Traitement incertitude, Uncertainty handling, Field programmable gate arrays, Fuzzy k-nearest-neighbor algorithm, K-NN classification algorithm, Lempel-Ziv algorithm, Protein secondary structure prediction, Protein structural class
Document Type:
Fachzeitschrift
Article
File Description:
text
Language:
English
Author Affiliations:
School of Electrical & Electronic Engineering, Universiti Sains Malaysia, Engineering Campus, 14300 Nibong Tebal, Penang, Malaysia
ISSN:
0925-2312
Rights:
Copyright 2015 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Computer science; theoretical automation; systems
Electronics
Molecular biophysics
Electronics
Molecular biophysics
Accession Number:
edscal.28844555
Database:
PASCAL Archive
Weitere Informationen
Correct prediction of protein secondary structural classes is vital for the prediction of tertiary structures and understanding of their function. Most of the prediction algorithms require lengthy computation time. Nearest neighbor ― complexity distance measure (NN-CDM) algorithm was one of the significant prediction algorithms using Lempel―Ziv (LZ) complexity-based distance measure, but it is slow and ineffective in handling uncertainties. To solve the problems, we propose fuzzy NN-CDM (FKNN-CDM) algorithm that incorporates the confidence level of prediction results and enhance the prediction process by designing hardware architecture that implements the proposed algorithm in an FPGA board. Highest average prediction accuracies for Z277 and 25PDB datasets using proposed algorithm are 84.12% and 47.81% respectively, with 15 times faster computation using an Altera DE2-115 FPGA board.