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Erschienen in: The Journal of Supercomputing 6/2020

03.04.2018

An artificial immune system-based algorithm for abnormal pattern in medical domain

verfasst von: L. Sharmila, U. Sakthi

Erschienen in: The Journal of Supercomputing | Ausgabe 6/2020

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Abstract

In general, medical pattern is a collection of characters formed using the characters such as ‘a’, ‘c’, ‘g’ and ‘t’. The length of the pattern varies from one disease to another disease, and the pattern also seems to be different for different patients. Identifying an unusual pattern from the information design is troublesome a decade ago. In this paper, with a specific end goal to enhance the precision of the anomalous distinguishing pattern, an Artificial Immune System (AIS) is framed. In the present study, AIS is used to obtain the abnormal pattern by learning the characteristics of the entire data set. Due to the powerful and adaptive nature of AIS, detecting and identifying abnormal pattern is more accurate. This proposed idea is implemented in MATLAB software and experimented on DNA/RNA dataset and the performance is verified.

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Literatur
1.
Zurück zum Zitat Hulshizer R, Blalock EM (2007) Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data. BMC Bioinform 8:240CrossRef Hulshizer R, Blalock EM (2007) Post hoc pattern matching: assigning significance to statistically defined expression patterns in single channel microarray data. BMC Bioinform 8:240CrossRef
2.
Zurück zum Zitat Perelman S, Mazzella MA, Muschietti J, Zhu T, Casal JJ (2003) Finding unexpected patterns in microarray data. Plant Physiol 133(4):1717–1725CrossRef Perelman S, Mazzella MA, Muschietti J, Zhu T, Casal JJ (2003) Finding unexpected patterns in microarray data. Plant Physiol 133(4):1717–1725CrossRef
3.
Zurück zum Zitat Valafar F (2002) Pattern recognition techniques in microarray data analysis: a survey. Ann NY Acad Sci 980:41–64CrossRef Valafar F (2002) Pattern recognition techniques in microarray data analysis: a survey. Ann NY Acad Sci 980:41–64CrossRef
4.
Zurück zum Zitat Stekel D (2006) Microarray bioinformatics. Cambridge University Press, Cambridge Stekel D (2006) Microarray bioinformatics. Cambridge University Press, Cambridge
5.
Zurück zum Zitat Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3–4):281–297CrossRef Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3–4):281–297CrossRef
6.
Zurück zum Zitat Eisen M, Spellman P, Brown P, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 95:863–868CrossRef Eisen M, Spellman P, Brown P, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci 95:863–868CrossRef
8.
Zurück zum Zitat Bohern BF, Hanley EN Jr (1995) Extracting knowledge from large medical databases: an automated approach. Comput Biomed Res 28:191–210CrossRef Bohern BF, Hanley EN Jr (1995) Extracting knowledge from large medical databases: an automated approach. Comput Biomed Res 28:191–210CrossRef
9.
Zurück zum Zitat Altschul SF, Miller W (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRef Altschul SF, Miller W (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRef
10.
Zurück zum Zitat Iyer VR (1999) The transcriptional program in the response of human fibroblasts to serum”. Science 283:83–87CrossRef Iyer VR (1999) The transcriptional program in the response of human fibroblasts to serum”. Science 283:83–87CrossRef
11.
Zurück zum Zitat Eisen MB et al (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863–14868CrossRef Eisen MB et al (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95(25):14863–14868CrossRef
12.
Zurück zum Zitat Tavazoie S (1999) Systematic determination of genetic network architecture. Nature Genet 22:281–285CrossRef Tavazoie S (1999) Systematic determination of genetic network architecture. Nature Genet 22:281–285CrossRef
13.
Zurück zum Zitat Tamayo P (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96(6):2907–2912CrossRef Tamayo P (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci USA 96(6):2907–2912CrossRef
14.
Zurück zum Zitat Alon U (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array. Proc Natl Acad Sci USA 96(12):6745–6750CrossRef Alon U (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide array. Proc Natl Acad Sci USA 96(12):6745–6750CrossRef
15.
Zurück zum Zitat Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3/4):281–297CrossRef Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 6(3/4):281–297CrossRef
16.
Zurück zum Zitat De Smet Frank (2002) Adaptive quality-based clustering of gene expression profiles. Bioinformatics 18:735–746CrossRef De Smet Frank (2002) Adaptive quality-based clustering of gene expression profiles. Bioinformatics 18:735–746CrossRef
17.
Zurück zum Zitat Cavallaro S, D’Agata V, Manickam P, Dufour F, Alkon DL (2002) Memory specific temporal profiles of gene expression in the hippocampus. Proc Natl Acad Sci USA 99(25):16279–16284CrossRef Cavallaro S, D’Agata V, Manickam P, Dufour F, Alkon DL (2002) Memory specific temporal profiles of gene expression in the hippocampus. Proc Natl Acad Sci USA 99(25):16279–16284CrossRef
18.
Zurück zum Zitat Pavlidis P, Noble WS (2001) Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2(10)CrossRef Pavlidis P, Noble WS (2001) Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2(10)CrossRef
19.
Zurück zum Zitat Reid R, Dix DJ, Miller D, Krawetz SA (2001) Recovering filter-based microarray data for pathways analysis using a multipoint alignment strategy. Biotechniques 30(4):762–766CrossRef Reid R, Dix DJ, Miller D, Krawetz SA (2001) Recovering filter-based microarray data for pathways analysis using a multipoint alignment strategy. Biotechniques 30(4):762–766CrossRef
20.
Zurück zum Zitat Genter MB, Van Veldhoven PP, Jegga AG, Sakthivel B, Kong S, Stanley K, Witte DP, Ebert CL, Aronow BJ (2003) Microarray-based discovery of highly expressed olfactory mucosal genes: potential roles in the various functions of the olfactory system. Physiol Genomics 16(1):67–81CrossRef Genter MB, Van Veldhoven PP, Jegga AG, Sakthivel B, Kong S, Stanley K, Witte DP, Ebert CL, Aronow BJ (2003) Microarray-based discovery of highly expressed olfactory mucosal genes: potential roles in the various functions of the olfactory system. Physiol Genomics 16(1):67–81CrossRef
21.
Zurück zum Zitat Hutton JJ, Jegga AG, Kong S, Gupta A, Ebert C, Williams S, Katz JD, Aronow BJ (2004) Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genom 5(1):82CrossRef Hutton JJ, Jegga AG, Kong S, Gupta A, Ebert C, Williams S, Katz JD, Aronow BJ (2004) Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system. BMC Genom 5(1):82CrossRef
22.
Zurück zum Zitat Li H, Wood CL, Liu Y, Getchell TV, Getchell ML, Stromberg AJ (2006) Identification of gene expression patterns using planned linear contrasts. BMC Bioinform 7:245CrossRef Li H, Wood CL, Liu Y, Getchell TV, Getchell ML, Stromberg AJ (2006) Identification of gene expression patterns using planned linear contrasts. BMC Bioinform 7:245CrossRef
23.
Zurück zum Zitat Liu H, Tarima S, Borders AS, Getchell TV, Getchell ML, Stromberg AJ (2005) Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. BMC Bioinform 6:106CrossRef Liu H, Tarima S, Borders AS, Getchell TV, Getchell ML, Stromberg AJ (2005) Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments. BMC Bioinform 6:106CrossRef
24.
Zurück zum Zitat Balasubramaniyan R, Hullermeier E, Weskamp N, Kamper J (2005) Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics 21(7):1069–1077CrossRef Balasubramaniyan R, Hullermeier E, Weskamp N, Kamper J (2005) Clustering of gene expression data using a local shape-based similarity measure. Bioinformatics 21(7):1069–1077CrossRef
25.
Zurück zum Zitat Conesa A, Nueda MJ, Ferrer A, Talon M (2006) maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22(9):1096–1102CrossRef Conesa A, Nueda MJ, Ferrer A, Talon M (2006) maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments. Bioinformatics 22(9):1096–1102CrossRef
26.
Zurück zum Zitat Eckel JE, Gennings C, Chinchilli VM, Burgoon LD, Zacharewski TR (2004) Empirical bayes gene screening tool for time-course or dose–response microarray data. J Biopharm Stat 14(3):647–670MathSciNetCrossRef Eckel JE, Gennings C, Chinchilli VM, Burgoon LD, Zacharewski TR (2004) Empirical bayes gene screening tool for time-course or dose–response microarray data. J Biopharm Stat 14(3):647–670MathSciNetCrossRef
27.
Zurück zum Zitat de Castro LN, Timmis J (2002) Artificial immune systems: a novel paradigm to pattern recognition, SOCO-2002, University of Paisley, UK, pp 67-84 de Castro LN, Timmis J (2002) Artificial immune systems: a novel paradigm to pattern recognition, SOCO-2002, University of Paisley, UK, pp 67-84
28.
Zurück zum Zitat Sharmila L, Sakthi U, Sagadevan Suresh (2017) A support vector machine based dynamic clustering and classification on gene expression data. Int J of Chemtech Res 10(4):442–447 Sharmila L, Sakthi U, Sagadevan Suresh (2017) A support vector machine based dynamic clustering and classification on gene expression data. Int J of Chemtech Res 10(4):442–447
29.
Zurück zum Zitat Somogyi R, Wen X, Ma W, Barker JL (1995) Developmental Kinetics of GAD family mRNAs parallel neurogenesis in the rat spinal cord. J Neuro Sci 15(4):2575, 2591 Somogyi R, Wen X, Ma W, Barker JL (1995) Developmental Kinetics of GAD family mRNAs parallel neurogenesis in the rat spinal cord. J Neuro Sci 15(4):2575, 2591
30.
Zurück zum Zitat Wen X, Fuhrman S, Michales GS, Sarr DB, Smith S (1999) Large-scale temporal gene expression mapping of central nervous system development. PNAS 95(1):334, 339 Wen X, Fuhrman S, Michales GS, Sarr DB, Smith S (1999) Large-scale temporal gene expression mapping of central nervous system development. PNAS 95(1):334, 339
31.
Zurück zum Zitat Eisen MB, Spellman PT, Prown PO (1999) Cluster analysis and display of genome-wide expression pattern. PNAS 95:14863, 14868 Eisen MB, Spellman PT, Prown PO (1999) Cluster analysis and display of genome-wide expression pattern. PNAS 95:14863, 14868
32.
Zurück zum Zitat Spellman PT, Sherlock G et al (1998) Comprehensive identification of cell cycle-regulated genes of he yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273, 3297CrossRef Spellman PT, Sherlock G et al (1998) Comprehensive identification of cell cycle-regulated genes of he yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9:3273, 3297CrossRef
33.
Zurück zum Zitat Tmaayo P, Slonim D, Medirov J (1999) Interpreting patterns of gene expression with SOM: Methods Appl Hematopoietic Differ. PNAS 96:2907, 2912 Tmaayo P, Slonim D, Medirov J (1999) Interpreting patterns of gene expression with SOM: Methods Appl Hematopoietic Differ. PNAS 96:2907, 2912
34.
Zurück zum Zitat Alon U, Barkai N, Notterman DA et al (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS 96:6745–6750CrossRef Alon U, Barkai N, Notterman DA et al (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS 96:6745–6750CrossRef
35.
Zurück zum Zitat Gordon AD (1999) Classification, 2nd edn. Chapman and Hall/CRC, Boca RatonMATH Gordon AD (1999) Classification, 2nd edn. Chapman and Hall/CRC, Boca RatonMATH
36.
Zurück zum Zitat Bock H (1996) Probabilistic models in cluster analysis. Comput Stat Data An. 23:5–28MATHCrossRef Bock H (1996) Probabilistic models in cluster analysis. Comput Stat Data An. 23:5–28MATHCrossRef
37.
Zurück zum Zitat Golub TR, Slonim DK, Tamayo P et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439):531–537CrossRef Golub TR, Slonim DK, Tamayo P et al (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439):531–537CrossRef
38.
Zurück zum Zitat Alizadeh AA, Eisen MB, Davis RE et al (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769):503–511CrossRef Alizadeh AA, Eisen MB, Davis RE et al (2000) Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769):503–511CrossRef
39.
Zurück zum Zitat Bittner M, Meltzer P, Chen Y et al (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406(6795):536–540CrossRef Bittner M, Meltzer P, Chen Y et al (2000) Molecular classification of cutaneous malignant melanoma by gene expression profiling. Nature 406(6795):536–540CrossRef
40.
Zurück zum Zitat Nielsen TO, West RB, Linn SC et al (2002) Molecular characterization of soft tissue tumours: a gene expression study. Lancet 359(9314):1301–1307CrossRef Nielsen TO, West RB, Linn SC et al (2002) Molecular characterization of soft tissue tumours: a gene expression study. Lancet 359(9314):1301–1307CrossRef
41.
Zurück zum Zitat Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99(10):6567–6572CrossRef Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99(10):6567–6572CrossRef
42.
Zurück zum Zitat Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E (2002) A statistical framework for expression-based molecular classification in cancer. J Roy Statist SocSer B. 64(4):717–736MathSciNetMATHCrossRef Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E (2002) A statistical framework for expression-based molecular classification in cancer. J Roy Statist SocSer B. 64(4):717–736MathSciNetMATHCrossRef
43.
Zurück zum Zitat Sharmila L, Sakthi U (2016) Analysis on various search algorithms. Global J Pure Appl Math 12(2):1397–1402 Sharmila L, Sakthi U (2016) Analysis on various search algorithms. Global J Pure Appl Math 12(2):1397–1402
44.
Zurück zum Zitat Sharmila L, Sakthi U (2018) Chronological pattern exploration algorithm for gene expression data clustering and classification. Wirel Pers Commun 98(1). ISSN 0929-6212 Sharmila L, Sakthi U (2018) Chronological pattern exploration algorithm for gene expression data clustering and classification. Wirel Pers Commun 98(1). ISSN 0929-6212
Metadaten
Titel
An artificial immune system-based algorithm for abnormal pattern in medical domain
verfasst von
L. Sharmila
U. Sakthi
Publikationsdatum
03.04.2018
Verlag
Springer US
Erschienen in
The Journal of Supercomputing / Ausgabe 6/2020
Print ISSN: 0920-8542
Elektronische ISSN: 1573-0484
DOI
https://doi.org/10.1007/s11227-018-2340-7

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