Partial least squares-discriminant analysis (PLS-DA) for classification of high-dimensional (HD) data: a review of contemporary practice strategies and knowledge gaps

Analyst, The - Tập 143 Số 15 - Trang 3526-3539
Loong Chuen Lee1,2, Choong-Yeun Liong2, Abdul Aziz Jemain2
1Forensic Science Programme, FSK, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, 50300 Kuala Lumpur, Malaysia
2Statistics Programme, FST, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia

Tóm tắt

This review highlights and discusses critically various knowledge gaps in classification modelling using PLS-DA for high dimensional data.

Từ khóa


Tài liệu tham khảo

Brereton, 2000, Analyst, 125, 2125, 10.1039/b003805i

Brereton, 2014, J. Chemom., 28, 213, 10.1002/cem.2609

M. L.Barker , Partial least squares for discrimination, statistical theory and implementation , LAP LAMBERT Academic Publishing , Germany , 2015

Ballabio, 2013, Anal. Methods, 5, 3790, 10.1039/c3ay40582f

Mehmood, 2016, J. Chemom., 30, 4, 10.1002/cem.2762

R. G.Brereton , Chemometrics for pattern recognition , John Wiley & Sons Ltd , Chichester, England , 2009

Kumar, 2014, Talanta, 123, 136, 10.1016/j.talanta.2014.02.003

Wu, 2017, TRAC, Trends Anal. Chem., 86, 25, 10.1016/j.trac.2016.10.013

Ahlinder, 2015, J. Chemom., 29, 267, 10.1002/cem.2699

Sattlecker, 2014, TRAC, Trends Anal. Chem., 59, 17, 10.1016/j.trac.2014.02.016

Trevisan, 2012, Analyst, 137, 2302, 10.1039/c2an16300d

Serrano-Cinca, 2013, Decis. Support Syst., 54, 1245, 10.1016/j.dss.2012.11.015

Soares, 2017, Microchem. J., 133, 258, 10.1016/j.microc.2017.03.028

Barker, 2003, J. Chemom., 17, 166, 10.1002/cem.785

L. C.Lee , C.-Y.Liong and A. A.Jemain , in Seminar Kebangsaan Institut Statistik Malaysia ke-11 (SKISM-XI) 2017 , UKM , 2017

Lee, 2016, AIP Conf. Proc., 1750, 060016, 10.1063/1.4954621

L. C.Lee , C.-Y.Liong and A. A.Jemain , in 2017 National Forensic Science Symposium (NFSS 2017) , Forensic Science Society of Malaysian , 2017

M.Grootveld , in Metabolic Profiling, Disease and Xenobiotics , Royal Society of Chemistry , England , 2012 , pp. 1–34

Gromski, 2015, Anal. Chim. Acta, 879, 10, 10.1016/j.aca.2015.02.012

Westerhuis, 2008, Metabolomics, 4, 81, 10.1007/s11306-007-0099-6

Szymanska, 2012, Metabolomics, 8, S3, 10.1007/s11306-011-0330-3

Amodio, 2017, Postharvest Biol. Technol., 125, 112, 10.1016/j.postharvbio.2016.11.013

Yang, 2017, Engineering, 9, 181, 10.4236/eng.2017.92009

Wu, 2017, PLoS One, e0175573, 10.1371/journal.pone.0175573

Vitova, 2017, BMC Nephrol., 18, 112, 10.1186/s12882-017-0519-4

Snowden, 2017, PLoS Med., 14, e1002266, 10.1371/journal.pmed.1002266

Sharma, 2017, Inflammation Res., 66, 97, 10.1007/s00011-016-0998-y

Peng, 2017, Innov. Food Sci. Emerg. Technol., 44, 212, 10.1016/j.ifset.2017.04.006

Nieuwoudt, 2017, Appl. Spectrosc., 71, 308, 10.1177/0003702816653130

Martins, 2017, Food Chem., 229, 142, 10.1016/j.foodchem.2017.02.024

Mabood, 2017, J. Adv. Dairy Res., 5, 1000167, 10.4172/2329-888X.1000167

Mabood, 2017, Food Chem., 221, 746, 10.1016/j.foodchem.2016.11.109

Li, 2017, PLoS One, 12, 0169430

Khoshmanesh, 2017, Anal. Chem., 89, 5285, 10.1021/acs.analchem.6b04827

Milanez, 2017, Microchem. J., 133, 669, 10.1016/j.microc.2017.03.004

Jorgensen, 2017, Fertil. Steril., 107, 1191, 10.1016/j.fertnstert.2017.03.013

Azcarate, 2017, Microchem. J., 130, 1, 10.1016/j.microc.2016.07.016

Garriga, 2017, Front. Plant Sci., 8, 280, 10.3389/fpls.2017.00280

DeFilippis, 2017, PLoS One, 12, e0175591, 10.1371/journal.pone.0175591

Boccio, 2017, Adv. Radiat. Oncol., 2, 118, 10.1016/j.adro.2016.12.005

Manfredi, 2017, Appl. Phys. A, 123, 35, 10.1007/s00339-016-0663-x

Georgouli, 2017, Food Chem., 217, 735, 10.1016/j.foodchem.2016.09.011

Kharbach, 2017, Chemom. Intell. Lab. Syst., 162, 182, 10.1016/j.chemolab.2017.02.003

Santos, 2017, Chemom. Intell. Lab. Syst., 161, 70, 10.1016/j.chemolab.2016.12.004

Peng, 2017, Sci. Rep., 7, 44551, 10.1038/srep44551

Bogdanovska, 2017, Saudi Pharm. J., 25, 1022, 10.1016/j.jsps.2017.03.006

Cuevas, 2017, Food Chem., 221, 1930, 10.1016/j.foodchem.2016.11.156

Reed, 2017, Neoplasia, 19, 165, 10.1016/j.neo.2016.11.003

Rios-Reina, 2017, Food Chem., 230, 108, 10.1016/j.foodchem.2017.02.118

Soares, 2017, Food Chem., 219, 1, 10.1016/j.foodchem.2016.09.127

Vermathen, 2017, Food Chem., 233, 391, 10.1016/j.foodchem.2017.04.089

Manheim, 2016, Appl. Spectrosc., 70, 1109, 10.1177/0003702816652321

Alewijn, 2016, J. Food Compos. Anal., 51, 15, 10.1016/j.jfca.2016.06.003

Valderrama, 2016, Chemom. Intell. Lab. Syst., 156, 188, 10.1016/j.chemolab.2016.06.009

Santana, 2016, Food Chem., 209, 228, 10.1016/j.foodchem.2016.04.051

Melucci, 2016, Food Chem., 204, 263, 10.1016/j.foodchem.2016.02.131

Diniz, 2016, Food Chem., 192, 374, 10.1016/j.foodchem.2015.07.022

Hou, 2016, J. Chemom., 30, 663, 10.1002/cem.2830

de Carvalho, 2016, Anal Methods, 28, 5658, 10.1039/C6AY01325B

Zotti, 2016, Food Chem., 196, 601, 10.1016/j.foodchem.2015.09.087

Rodrigues Jr., 2016, Food Chem., 196, 584, 10.1016/j.foodchem.2015.09.055

Hirri, 2016, Basic Res. J., 5, 103

Liu, 2016, J. Spectrosc., 1603609

Li, 2016, PLoS One, 11, e0168998, 10.1371/journal.pone.0168998

Borras, 2016, Food Chem., 203, 314, 10.1016/j.foodchem.2016.02.038

Shrestha, 2016, Sens. Actuators, B, 237, 1027, 10.1016/j.snb.2016.08.170

Racz, 2016, Chemom. Intell. Lab. Syst., 151, 34, 10.1016/j.chemolab.2015.11.009

Lenhardt, 2015, Food Chem., 175, 284, 10.1016/j.foodchem.2014.11.162

Ho, 2015, Forensic Sci. Int., 251, 61, 10.1016/j.forsciint.2015.03.002

Wang, 2015, Sci. Rep., 5, 18926

Mazivila, 2015, J. Braz. Chem. Soc., 26, 642

Shao, 2015, Sensor, 15, 26726, 10.3390/s151026726

Hirri, 2015, Int. J. Chem. Mater. Environ. Res., 2, 30

Moncayo, 2015, Chemom. Intell. Lab. Syst., 146, 354, 10.1016/j.chemolab.2015.06.004

Calvini, 2015, Chemom. Intell. Lab. Syst., 146, 503, 10.1016/j.chemolab.2015.07.010

Borba, 2015, Forensic Sci. Int., 249, 73, 10.1016/j.forsciint.2015.01.027

Chen, 2015, Spectrochim. Acta, Part A, 135, 185, 10.1016/j.saa.2014.07.005

Botelho, 2015, Food Chem., 181, 31, 10.1016/j.foodchem.2015.02.077

Gromski, 2014, Anal. Bioanal. Chem., 406, 7581, 10.1007/s00216-014-8216-7

Silva, 2014, Microchem. J., 116, 235, 10.1016/j.microc.2014.05.013

Paulo, 2014, Energy Fuels, 28, 4355, 10.1021/ef5003827

Tang, 2014, Spectrochim. Acta, Part A, 121, 678, 10.1016/j.saa.2013.11.104

Devos, 2014, Food Chem., 148, 124, 10.1016/j.foodchem.2013.10.020

Borras, 2014, Food Chem., 153, 15, 10.1016/j.foodchem.2013.12.032

Capuano, 2014, Food Chem., 164, 234, 10.1016/j.foodchem.2014.05.011

Gan, 2014, Food Chem., 146, 149, 10.1016/j.foodchem.2013.09.024

Drivelos, 2014, Food Chem., 165, 316, 10.1016/j.foodchem.2014.03.083

Silvestri, 2014, Chemom. Intell. Lab. Syst., 137, 181, 10.1016/j.chemolab.2014.06.012

Almeida, 2013, Microchem. J., 109, 170, 10.1016/j.microc.2012.03.006

Encyclopedia of Spectroscopy and spectrometry , ed. J. C. Lindom , G. E. Tranter and D. W. Koppennaal , Elsevier , Amsterdam , 3rd edn, 2017

Muro, 2015, Anal. Chem., 87, 306, 10.1021/ac504068a

Yang, 2003, Pattern Recognit., 36, 563, 10.1016/S0031-3203(02)00048-1

Nocairi, 2005, Comput. Stat. Data Anal., 48, 139, 10.1016/j.csda.2003.09.008

Nguyen, 2002, Bioinformatics, 18, 39, 10.1093/bioinformatics/18.1.39

Brereton, 2015, Chemom. Intell. Lab. Syst., 149, 90, 10.1016/j.chemolab.2015.06.012

Kemsley, 1996, Chemom. Intell. Lab. Syst., 33, 47, 10.1016/0169-7439(95)00090-9

Defernez, 1997, TRAC, Trends Anal. Chem., 16, 216, 10.1016/S0165-9936(97)00015-0

Marigheto, 1998, J. Am. Oil Chem. Soc., 75, 987, 10.1007/s11746-998-0276-4

Tang, 2014, PLoS One, 9, e96944, 10.1371/journal.pone.0096944

Nguyen, 2002, Bioinformatics, 18, 1216, 10.1093/bioinformatics/18.9.1216

Ciosek, 2005, Talanta, 67, 590, 10.1016/j.talanta.2005.03.006

Kjedahl, 2010, J. Chemom., 24, 558, 10.1002/cem.1346

Filzmoser, 2012, J. Chemom., 26, 42, 10.1002/cem.1418

Brereton, 2006, TRAC, Trends Anal. Chem., 25, 1103, 10.1016/j.trac.2006.10.005

Perez, 2009, Chemom. Intell. Lab. Syst., 95, 122, 10.1016/j.chemolab.2008.09.005

Botella, 2009, Talanta, 80, 321, 10.1016/j.talanta.2009.06.072

Galtier, 2011, Vib. Spectrosc., 55, 132, 10.1016/j.vibspec.2010.09.012

Serrano-Lourido, 2012, Food Chem., 135, 1425, 10.1016/j.foodchem.2012.06.010

Engel, 2013, TRAC, Trends Anal. Chem., 50, 96, 10.1016/j.trac.2013.04.015

Lasch, 2012, Chemom. Intell. Lab. Syst., 117, 100, 10.1016/j.chemolab.2012.03.011

Lee, 2017, AIP Conf. Proc., 1830, 080008, 10.1063/1.4980992

Rinnan, 2009, TRAC, Trends Anal. Chem., 28, 1201, 10.1016/j.trac.2009.07.007

Bocklitz, 2011, Anal. Chim. Acta, 704, 47, 10.1016/j.aca.2011.06.043

A. R.Webb and K. D.Copsey , Statistical Pattern Recognition , Wiley , Chichester , 3rd edn, 2011

Guyon, 2003, J. Mach. Learn. Res., 3, 1157

Xie, 2015, Sci. Rep., 5, 10930, 10.1038/srep10930

Yin, 2016, Anal. Methods, 13, 2794, 10.1039/C6AY00259E

Cheng, 2016, Food Chem., 197, 855, 10.1016/j.foodchem.2015.11.019

Aliakbarzadeh, 2016, Chemom. Intell. Lab. Syst., 158, 165, 10.1016/j.chemolab.2016.09.002

Mehmood, 2012, Chemom. Intell. Lab. Syst., 118, 62, 10.1016/j.chemolab.2012.07.010

Devos, 2011, Chemom. Intell. Lab. Syst., 107, 50, 10.1016/j.chemolab.2011.01.008

Andersen, 2010, J. Chemom., 24, 728, 10.1002/cem.1360

Issakson, 2008, Pattern Recognit. Lett., 29, 1960, 10.1016/j.patrec.2008.06.018

Martens, 1998, Chemom. Intell. Lab. Syst., 44, 99, 10.1016/S0169-7439(98)00167-1

Esbensen, 2010, J. Chemom., 24, 168, 10.1002/cem.1310

Arlot, 2010, Stat. Surveys, 4, 40, 10.1214/09-SS054

Breiman, 1992, Int. Stat. Rev., 60, 291, 10.2307/1403680

T.Hastie , R.Tibshirani and J. H.Friedman , in The Elements of Statistical Learning, Data Mining, Inference and Prediction , Springer , New York , 2009 , ch. 7.10, pp. 214–217

Galvao, 2005, Talanta, 67, 736, 10.1016/j.talanta.2005.03.025

Daszykowski, 2002, Anal. Chim. Acta, 468, 91, 10.1016/S0003-2670(02)00651-7

Goot, 1999, Anal. Chim. Acta, 392, 67, 10.1016/S0003-2670(99)00193-2

T.Borovicka , M.Jirina Jr. , P.Kordik and M.Jirina , in Advances in Data Mining Knowledge discovery and applications , InTech , Croatia , 2012

Wehrens, 2000, Chemom. Intell. Lab. Syst., 54, 35, 10.1016/S0169-7439(00)00102-7

P.Golland , F.Liang , S.Mukherjee and D.Panchenko , in Learning Theory , Springer , Berlin/Heidelberg , 2005 , pp. 501–515

http://wiki.eigenvector.com/index.php?title=Using_Cross-Validation

Kennard, 1969, Technometrics, 11, 137, 10.1080/00401706.1969.10490666

Quintas, 2012, Metabolomics, 8, 86, 10.1007/s11306-011-0292-5

Rojas, 2017, Front. Chem., 5, 53, 10.3389/fchem.2017.00053

Hawkins, 2010, J. Chemom., 24, 188, 10.1002/cem.1311

Molinaro, 2005, Bioinformatics, 21, 3301, 10.1093/bioinformatics/bti499

Filzmoser, 2009, J. Chemom., 23, 160, 10.1002/cem.1225

T.Hastie , R.Tibshirani and J.Friedman , The wrong and right way to do cross-validation , in Elements of Statistical Learning, Data Mining, Inference, Prediction , Springer , NY , 2009 , pp. 245–247

Chevallier, 2006, J. Chemom., 20, 221, 10.1002/cem.994

Bylesjo, 2006, J. Chemom., 20, 341, 10.1002/cem.1006

G.James , D.Witten , T.Hastie and R.Tibshiranim , Assessing Model Accuracy , in An introduction to statistical learning , Springer , New York , 2013 , pp. 29–36

Brown, 2006, Chemom. Intell. Lab. Syst., 80, 24, 10.1016/j.chemolab.2005.05.004

Reid, 2005, Food Res. Int., 38, 1109, 10.1016/j.foodres.2005.03.005

Dixon, 2009, Chemom. Intell. Lab. Syst., 99, 111, 10.1016/j.chemolab.2009.07.016

Smit, 2007, Anal. Chim. Acta, 592, 210, 10.1016/j.aca.2007.04.043

Efron, 1983, J. Am. Stat. Assoc., 78, 316, 10.1080/01621459.1983.10477973

P.Refaeilzadeh , L.Tang and H.Liu , in Encyclopedia of Database systems , Springer , New York , 2009 , pp. 532–538

Xu, 2004, J. Chemom., 19, 112, 10.1002/cem.858

Xu, 2001, Chemom. Intell. Lab. Syst., 56, 1, 10.1016/S0169-7439(00)00122-2

Krakowska, 2015, Analyst, 141, 1060, 10.1039/C5AN01656H

A. J.Izenman , in Modern Multivariate Statistical Techniques , Springer , England , 2013 , pp. 237–280

Brereton, 2011, J. Chemom., 25, 225, 10.1002/cem.1397

Lorena, 2011, Expert Syst. Appl., 38, 5268, 10.1016/j.eswa.2010.10.031

Noord, 1994, Chemom. Intell. Lab. Syst., 23, 65, 10.1016/0169-7439(93)E0065-C

Hawkins, 2004, J. Chem. Inf. Comput. Sci., 44, 1, 10.1021/ci0342472