Explanatory analysis of spectroscopic data using machine learning of simple, interpretable rules

Vibrational Spectroscopy

Volumn 32, Issue 1 SPEC., 2003, Pages 33-45

  Goodacre, Royston ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Artificial neural networks; FT IR; Genetic programming

Indexed keywords

IMAGE ANALYSIS; LEARNING SYSTEMS; LEAST SQUARES APPROXIMATIONS; NEURAL NETWORKS; PRINCIPAL COMPONENT ANALYSIS; REGRESSION ANALYSIS; TISSUE;

VIBRATIONAL SPECTROSCOPY;

FOURIER TRANSFORM INFRARED SPECTROSCOPY;

EID: 0041345720     PISSN: 09242031     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0924-2031(03)00045-6     Document Type: Conference Paper

References (78)

1. P.R. Griffiths, J.A. de Haseth, Fourier Transform Infrared Spectrometry, Wiley, New York, 1986.
2. N.B. Colthup, L.H. Daly, S.E. Wiberly, Introduction to Infrared and Raman Spectroscopy, Academic Press, New York, 1990.
3. J.T. Magee, in: M. Goodfellow, A.G. O'Donnell (Eds.), Handbook of New Bacterial Systematics, Academic Press, London, 1993, pp. 383-427.
4. Goodacre R., Timmins E.M., Burton R., Kaderbhai N., Woodward A.M., Kell D.B., Rooney P.J. Microbiology. 144:1998;1157-1170.
5. Lewis E.N., Treado P.J., Reeder R.C., Story G.M., Dowrey A.E., Marcott C., Levin I.W. Anal. Chem. 67:1995;3377-3781.
6. Colarusso P., Kidder L.H., Levin I.W., Fraser J.C., Arens J.F., Lewis E.N. Appl. Spectrosc. 52:1998;106A-120A.
7. Lasch P., Haensch W., Lewis E.N., Kidder L.H., Naumann D. Appl. Spectrosc. 56:2002;1-9.
8. Schmitt J., Flemming H.C. Int. Biodeterior. Biodegrad. 41:1998;1-11.
9. Mariey L., Signolle J.P., Amiel C., Travert J. Vib. Spectrosc. 26:2001;151-159.
10. Naumann D. Appl. Spectrosc. Rev. 36:2001;239-298.
11. Petrich W. Appl. Spectrosc. Rev. 36:2001;181-237.
12. Maquelin K., Kirschner C., Choo-Smith L.-P., van den Braak N., Endtz H.P., Naumann D., Puppels G.J. J. Microbiol. Methods. 51:2002;255-271.
13. H. Martens, T. Næs, Multivariate Calibration, Wiley, Chichester, 1989.
14. Goodacre R., Neal M.J., Kell D.B. Z. Bakteriol. 284:1996;516-539.
15. C. Chatfield, A.J. Collins, Introduction to Multivariate Analysis, Chapman & Hall, London, 1980.
16. J.W. Tukey, Exploratory Data Analysis, Addison-Wesley, Reading, MA, 1977.
17. R.O. Duda, P.E. Hart, D.E. Stork, Pattern Classification, 2nd edition, Wiley, London, 2001.
18. T. Hastie, R. Tibshirani, J. Friedman, The Elements of Statistical Learning: Data Mining, Inference and Prediction, Springer-Verlag, Berlin, 2001.
19. B.S. Everitt, Cluster Analysis, Edward Arnold, London, 1993.
20. I.T. Jolliffe, Principal Component Analysis, Springer-Verlag, New York, 1986.
21. B.F.J. Manly, Multivariate Statistical Methods: A Primer, Chapman & Hall, London, 1994.
22. H.L.C. Meuzelaar, J. Haverkamp, F.D. Hileman, Pyrolysis Mass Spectrometry of Recent and Fossil Biomaterials, Elsevier, Amsterdam, 1982.
23. Altshuler D., Daly M., Kruglyak L. Nat. Genet. 26:2000;135-137.
24. Oliver S.G. Nature. 403:2000;601-603.
25. T.M. Mitchell, Machine Learning, McGraw-Hill, New York, 1997.
26. R.C. Beavis, S.M. Colby, R. Goodacre, P.B. Harrington, J.P. Reilly, S. Sokolow, C.W. Wilkerson, in: R.A. Meyers (Eds.), Encyclopaedia of Analytical Chemistry, Wiley, Chichester, 2000, pp. 11558-11597.
27. Alsberg B.K., Kell D.B., Goodacre R. Anal. Chem. 70:1998;4126-4133.
28. D.E. Rumelhart, J.L. McClelland, The PDP Research Group Parallel Distributed Processing, Experiments in the Microstructure of Cognition, vols. I and II, MIT Press, Cambridge, MA, 1986.
29. P.J. Werbos, The Roots of Back-Propagation: From Ordered Derivatives to Neural Networks and Political Forecasting, Wiley, Chichester, 1994.
30. Broomhead D.S., Lowe D. Complex Syst. 2:1988;321-355.
31. A. Saha, J.D. Keller, in: D. Touretzky (Eds.), Advances in Neural Information Processing Systems, Morgan Kaufmann, San Mateo, CA, 1990, pp. 482-489.
32. C.M. Bishop, Neural Networks for Pattern Recognition, Clarendon Press, Oxford, 1995.
33. Wold S., Antti H., Lindgren F., Ohman J. Chemom. Intell. Lab. Syst. 44:1998;175-185.
34. Hoskuldsson A. Chemom. Intell. Lab. Syst. 55:2001;23-38.
35. Seasholtz M.B., Kowalski B. Anal. Chim. Acta. 277:1993;165-177.
36. Kell D.B., Sonnleitner B. Tibtech. 13:1995;481-492.
37. L. Breiman, J.H. Friedman, R.A. Olshen, C.J. Stone, Classification and Regression Trees, Wadsworth, Pacific Grove, CA, 1984.
38. J.R. Quinlan, C4.5: Programs for Machine Learning, Morgan Kaufmann, San Mateo, CA, 1993.
39. King R.D., Muggleton S., Lewis R.A., Sternberg M.J.E. Proc. Natl. Acad. Sci. 89:1992;11322-11326.
40. N. Lavrac, S. Dzeroski, Inductive Logic Programming: Techniques and Applications, Ellis Horwood, Chichester, 1994.
41. J.H. Holland, Adaption in Natural and Artificial Systems, MIT Press, Cambridge, MA, 1992.
42. J.R. Koza, Genetic Programming: On the Programming of computers by Means of Natural Selection, MIT Press, Cambridge, MA, 1992.
43. T. Bäck, D.B. Fogel, Z. Michalewicz, Handbook of Evolutionary Computation, IOP Publishing/Oxford University Press, Oxford, 1997.
44. D. Corne, M. Dorigo, F. Glover (Eds.), New Ideas in Optimization. McGraw-Hill, London, 1999.
45. Z. Michalewicz, D.B. Fogel, How to Solve it: Modern Heuristics, Springer-Verlag, Heidelberg, 2000.
46. D.E. Goldberg, Genetic Algorithms in Search, Optimization and Machine Learning, Addison-Wesley, Reading, MA, 1989.
47. M. Mitchell, An Introduction to Genetic Algorithms, MIT Press, Boston, 1995.
48. H.-G. Beyer, The Theory of Evolution Strategies, Springer-Verlag, Berlin, 2001.
49. D.B. Fogel, Evolutionary Computation: Towards a New Philosophy of Machine Intelligence, IEEE Press, Piscataway, 2000.
50. W. Banzhaf, P. Nordin, R.E. Keller, F.D. Francone, Genetic Programming: An Introduction, Morgan Kaufmann, San Francisco, CA, 1998.
51. Kell D.B., Darby R.M., Draper J. Plant Physiol. 126:2001;943-951.
52. Kell D.B. Trends Genet. 18:2002;555-559.
53. J.R. Koza, Genetic Programming II: Automatic Discovery of Reusable Programs, MIT Press, Cambridge, MA, 1994.
54. Gilbert R.J., Goodacre R., Woodward A.M., Kell D.B. Anal. Chem. 69:1997;4381-4389.
55. W.B. Langdon, Genetic Programming and Data Structures: Genetic Programming + Data Structures = Automatic Programming!, Kluwer Academic Publishers, Boston, 1998.
56. J.R. Koza, F.H. Bennett, M.A. Keane, D. Andre, Genetic Programming III: Darwinian Invention and Problem Solving, Morgan Kaufmann, San Francisco, CA, 1999.
57. W.B. Langdon, R. Poli, Foundations of Genetic Programming, Springer-Verlag, Berlin, 2002.
58. W.B. Langdon, R. Poli, in: W. Banzhaf, R. Poli, M. Schoenauer, T.C. Fogarty (Eds.), Proceedings of the First European Workshop on Genetic Programming, Springer-Verlag, Berlin, 1998, pp. 37-48.
59. Podgorelec V., Kokol P. Genet. Program. Proc. 1802:2000;326-337.
60. G. Rudolph, Convergence Properties of Evolutionary Algorithms, Verlag Dr Kovac, Hamburg, 1997.
61. Goodacre R., Shann B., Gilbert R.J., Timmins E.M., McGovern A.C., Alsberg B.K., Kell D.B., Logan N.A. Anal. Chem. 72:2000;119-127.
62. M. Dando, Biological Warfare in the 21st Century, Brassey's Ltd., London, 1994.
63. W. Barnaby, The Plague Makers: The Secret World of Biolgoical Warfare, Vision Paperbacks, London, 1997.
64. McGovern A.C., Broadhurst D., Taylor J., Kaderbhai N., Winson M.K., Small D.A., Rowland J.J., Kell D.B., Goodacre R. Biotechnol. Bioeng. 78:2002;527-538.
65. McGovern A.C., Ernill R., Kara B.V., Kell D.B., Goodacre R. J. Biotechnol. 72:1999;157-167.
66. Shaw A.D., Kaderbhai N., Jones A., Woodward A.M., Goodacre R., Rowland J.J., Kell D.B. Appl. Spectrosc. 53:1999;1419-1428.
67. Vaidyanathan S., Macaloney G., McNeill B. Analyst. 124:1999;157-162.
68. Ellis D.I., Broadhurst D., Kell D.B., Rowland J.J., Goodacre R. Appl. Environ. Microbiol. 68:2002;2822-2828.
69. Dainty R.H. J. Food Microbiol. 33:1996;19-33.
70. Nychas G.J.E., Tassou C.C. J. Food Microbiol. 74:1997;199-208.
71. Ellis D.I., Goodacre R. Trends Food Sci. Technol. 12:2002;413-423.
72. T. Maniatis, F. Fritsch, J. Shambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbour Laboratory, New York, 1982.
73. de la Cruz F., Grinsted J. J. Bacteriol. 151:1982;222-228.
74. Timmins E.M., Goodacre R. J. Appl. Microbiol. 83:1997;208-218.
75. Lasch P., Naumann D. Cell. Mol. Biol. 44:1998;189-202.
76. Jackson M., Mantsch H.H. Crit. Rev. Biochem. Mol. Biol. 30:1995;95-120.
77. R. Goodacre, D.B. Kell, in: G.G. Harrigan, R. Goodacre (Eds.), Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, Kluwer Academic Publishers, Dordrecht, 2003.
78. D. Oldroyd, The Arch of Knowledge: An Introduction to the History of the Philosophy and Methodology of Science, Methuen, New York, 1986.