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Biomedical Applications of Prototype Based Classifiers and Relevance Learning

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Abstract

In this contribution, prototype-based systems and relevance learning are presented and discussed in the context of biomedical data analysis. Learning Vector Quantization and Matrix Relevance Learning serve as the main examples. After introducing basic concepts and related approaches, example applications of Generalized Matrix Relevance Learning are reviewed, including the classification of adrenal tumors based on steroid metabolomics data, the analysis of cytokine expression in the context of Rheumatoid Arthritis, and the prediction of recurrence risk in renal tumors based on gene expression.

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References

  1. Aggarwal, C.: Outlier Analysis. Springer, New York (2013)

    Book  MATH  Google Scholar 

  2. Aghaeepour, N., Finak, G., The FlowCAP Consortium, The DREAM Consortium\(^*\), Hoos, H., Mosmann, T., Brinkman, R., Gottardo, R., Scheuermann, R.: Critical assessment of automated flow cytometry data analysis techniques. Nat. Methods 10(3), 228–238 (2013)

    Google Scholar 

  3. Arlt, W., Biehl, M., Taylor, A., Hahner, S., Libe, R., Hughes, B., Schneider, P., Smith, D., Stiekema, H., Krone, N., Porfiri, E., Opocher, G., Bertherat, J., Mantero, F., Allolio, B., Terzolo, M., Nightingale, P., Shackleton, C., Bertagna, X., Fassnacht, M., Stewart, P.: Urine steroid metabolomics as a biomarker tool for detecting malignancy in adrenal tumors. J Clin. Endocrinol. Metab. 96, 3775–3784 (2011)

    Article  Google Scholar 

  4. Biehl, M., Breitling, R., Li, Y.: Analysis of tiling microarray data by Learning Vector Quantization and relevance learning. In: Yin, H., Tino, P., Corchado, E., Byrne, W., Yao, X. (eds.) IDEAL 2007. LNCS, vol. 4881, pp. 880–889. Springer, Heidelberg (2007). doi:10.1007/978-3-540-77226-2_88

    Chapter  Google Scholar 

  5. Biehl, M., Bunte, K., Schleif, F.M., Schneider, P., Villmann, T.: Large margin linear discriminative visualization by matrix relevance learning. In: The 2012 International Joint Conference on Neural Networks (IJCNN), pp. 1–8, June 2012

    Google Scholar 

  6. Biehl, M., Bunte, K., Schneider, P.: Analysis of flow cytometry data by matrix relevance Learning Vector Quantization. PLoS ONE 8(3), e59401 (2013). http://dx.doi.org/10.13712Fjournal.pone.0059401

    Article  Google Scholar 

  7. Biehl, M., Ghosh, A., Hammer, B.: Dynamics and generalization ability of LVQ algorithms. J. Mach. Learn. Res. 8, 323–360 (2007)

    MathSciNet  MATH  Google Scholar 

  8. Biehl, M., Hammer, B., Schleif, F.M., Schneider, P., Villmann, T.: Stationarity of matrix relevance LVQ. In: 2015 International Joint Conference on Neural Networks (IJCNN), pp. 1–8, July 2015

    Google Scholar 

  9. Biehl, M., Hammer, B., Schneider, P., Villmann, T.: Metric learning for prototype-based classification. In: Bianchini, M., Maggini, M., Scarselli, F., Jain, L. (eds.) Advances in Neural Information Paradigms. Springer Studies in Computational Intelligence, vol. 247, pp. 183–199. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  10. Biehl, M., Hammer, B., Verleysen, M., Villmann, T. (eds.): Similarity Based Clustering - Recent Developments and Biomedical Applications. LNAI, vol. 5400, 201 p. Springer, Heidelberg (2009)

    Google Scholar 

  11. Biehl, M., Hammer, B., Villmann, T.: Distance measures for prototype based classification. In: Grandinetti, L., Lippert, T., Petkov, N. (eds.) BrainComp 2013. LNCS, vol. 8603, pp. 100–116. Springer, Cham (2014). doi:10.1007/978-3-319-12084-3_9

    Google Scholar 

  12. Biehl, M., Sadowski, P., Bhanot, G., Bilal, E., Dayarian, A., Meyer, P., Norel, R., Rhrissorrakrai, K., Zeller, M., Hormoz, S.: Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. Bioinformatics 31(4), 453–461 (2015)

    Article  Google Scholar 

  13. Biehl, M., Schneider, P., Smith, D., Stiekema, H., Taylor, A., Hughes, B., Shackleton, C., Stewart, P., Arlt, W.: Matrix relevance LVQ in steroid metabolomics based classification of adrenal tumors. In: Verleysen, M. (ed.) 20th European Symposium on Artificial Neural Networks (ESANN 2012), pp. 423–428. d-side Publishing (2012)

    Google Scholar 

  14. Bishop, C.: Pattern Recognition and Machine Learning. Cambridge University Press, Cambridge (2007)

    MATH  Google Scholar 

  15. Boareto, M., Cesar, J., Leite, V., Caticha, N.: Supervised variational relevance learning, an analytic geometric feature selection with applications to omic data sets. IEEE/ACM Trans. Comput. Biol. Bioinform. 12(99), 705–711 (2015)

    Article  Google Scholar 

  16. Bojer, T., Hammer, B., Schunk, D., von Toschanowitz, K.T.: Relevance determination in Learning Vector Quantization. In: Verleysen, M. (ed.) European Symposium on Artificial Neural Networks, pp. 271–276 (2001)

    Google Scholar 

  17. Bottou, L.: Online algorithms and stochastic approximations. In: Saad, D. (ed.) Online Learning and Neural Networks, pp. 9–42. Cambridge University Press, Cambridge (1998)

    Google Scholar 

  18. Bunte, K., Schneider, P., Hammer, B., Schleif, F.M., Villmann, T., Biehl, M.: Limited rank matrix learning, discriminative dimension reduction, and visualization. Neural Netw. 26, 159–173 (2012)

    Article  Google Scholar 

  19. Chortis, V., Bancos, I., Sitch, A., Taylor, A., O’Neil, D., Lang, K., Quinkler, M., Terzolo, M., Manelli, M., Vassiliadi, D., Ambroziak, U., Conall Dennedy, M., Sherlock, M., Bertherat, J., Beuschlein, F., Fassnacht, M., Deeks, J., Biehl, M., Arlt, W.: Urine steroid metabolomics is a highly sensitive tool for post-operative recurrence detection in adrenocortical carcinoma. Endocrine Abstracts, vol. 41, OC1.4 (2016). doi:10.1530/endoabs.41.OC1.4

  20. Cichocki, A., Zdunek, R., Phan, A., Amari, S.I.: Nonnegative Matrix and Tensor Factorizations. Wiley, Chichester (2009)

    Book  Google Scholar 

  21. European Network for the Study of Adrenal Tumours: ENS@T (2002). http://www.ensat.org. Accessed 16 Mar 2017

  22. Fawcett, T.: An introduction to ROC analysis. Pattern Recogn. Lett. 27, 861–874 (2006)

    Article  Google Scholar 

  23. Frenay, B., Hofmann, D., Schulz, A., Biehl, M., Hammer, B.: Valid interpretation of feature relevance for linear data mappings. In: 2014 IEEE Symposium on Computational Intelligence and Data Mining (CIDM), pp. 149–156. IEEE (2014)

    Google Scholar 

  24. Ghosh, S., Baranowski, E., van Veen, R., de Vries, G., Biehl, M., Arlt, W., Tino, P., Bunte, K.: Comparison of strategies to learn from imbalanced classes for computer aided diagnosis of inborn steroidogenic disorders. In: Verleysen, M. (ed.) 25th European Symposium on Artificial Neural Networks (ESANN 2017). d-side Publishing (2017, in press)

    Google Scholar 

  25. Golubitsky, O., Watt, S.: Distance-based classification of handwritten symbols. Int. J. Doc. Anal. Recogn. (IJDAR) 13(2), 133–146 (2010)

    Article  Google Scholar 

  26. Hammer, B., Nebel, D., Riedel, M., Villmann, T.: Generative versus discriminative prototype based classification. In: Villmann, T., Schleif, F.-M., Kaden, M., Lange, M. (eds.) Advances in Self-organizing Maps and Learning Vector Quantization. AISC, vol. 295, pp. 123–132. Springer, Cham (2014). doi:10.1007/978-3-319-07695-9_12

    Chapter  Google Scholar 

  27. Hammer, B., Schleif, F.-M., Zhu, X.: Relational extensions of Learning Vector Quantization. In: Lu, B.-L., Zhang, L., Kwok, J. (eds.) ICONIP 2011. LNCS, vol. 7063, pp. 481–489. Springer, Heidelberg (2011). doi:10.1007/978-3-642-24958-7_56

    Chapter  Google Scholar 

  28. Hammer, B., Villmann, T.: Generalized relevance learning vector quantization. Neural Netw. 15(8–9), 1059–1068 (2002)

    Article  Google Scholar 

  29. Hammer, B., Villmann, T.: Classification using non-standard metrics. In: Verleysen, M. (ed.) European Symposium on Artificial Neural Networks, ESANN 2005, pp. 303–316. d-side publishing (2005)

    Google Scholar 

  30. Hart, P.: The condensed nearest neighbor rule. IEEE Trans. Inf. Theory 14, 515–516 (1968)

    Article  Google Scholar 

  31. Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd edn. Springer, New York (2009)

    Book  MATH  Google Scholar 

  32. Hocke, J., Martinetz, T.: Global metric learning by gradient descent. In: Wermter, S., Weber, C., Duch, W., Honkela, T., Koprinkova-Hristova, P., Magg, S., Palm, G., Villa, A.E.P. (eds.) ICANN 2014. LNCS, vol. 8681, pp. 129–135. Springer, Cham (2014). doi:10.1007/978-3-319-11179-7_17

    Google Scholar 

  33. Kaplan, E., Meier, P.: Nonparametric estimation from incomplete observations. J. Am. Stat. Assoc. 53, 457–481 (1958)

    Article  MathSciNet  MATH  Google Scholar 

  34. Kingma, D.P., Ba, J.: Adam: a method for stochastic optimization. In: Proceedings of the 3rd International Conference on Learning Representations (ICLR) (2014)

    Google Scholar 

  35. Kohonen, T.: Learning Vector Quantization for pattern recognition. Technical report TKK-F-A601, Helsinki University of Technology, Espoo (1986)

    Google Scholar 

  36. Kohonen, T.: Improved versions of Learning Vector Quantization. In: International Joint Conference on Neural Networks, vol. 1, pp. 545–550 (1990)

    Google Scholar 

  37. Kohonen, T.: Self-organizing Maps. Springer, Heidelberg (1997)

    Book  MATH  Google Scholar 

  38. Lang, K., Beuschlein, F., Biehl, M., Dietz, A., Riester, A., Hughes, B., O’Neil, D., Hahner, S., Quinkler, M., Lenders, J., Shackleton, C., Reincke, M., Arlt, W.: Urine steroid metabolomics as a diagnostic tool in primary aldosteronism. Endocrine Abstracts, vol. 38, OC1.6 (2015). doi:10.1530/endoabs.38.OC1.6

  39. Lange, M., Villmann, T.: Derivatives of lp-norms and their approximations. Machine Learning Reports MLR-03-2013 (2013)

    Google Scholar 

  40. Biehl, M.: GMLVQ demo code (2015). http://www.cs.rug.nl/~biehl. Accessed 16 Mar 2017

  41. Biehl, M., Hammer, B., Villmann, T.: Prototype-based models in machine learning. Wileys Interdisicp. Rev. (Wires) Cogn. Sci. 7, 92–111 (2016)

    Article  Google Scholar 

  42. Mahalanobis, P.: On the generalised distance in statistics. Proc. Natl. Inst. Sci. India 2(1), 49–55 (1936)

    MathSciNet  MATH  Google Scholar 

  43. Melchert, F., Seiffert, U., Biehl, M.: Functional representation of prototypes in LVQ and relevance learning. In: Merényi, E., Mendenhall, M.J., O’Driscoll, P. (eds.) Advances in Self-Organizing Maps and Learning Vector Quantization. AISC, vol. 428, pp. 317–327. Springer, Cham (2016). doi:10.1007/978-3-319-28518-4_28

    Chapter  Google Scholar 

  44. Moolla, A., Amin, A., Hughes, B., Arlt, W., Hassan-Smith, Z., Armstrong, M., Newsome, P., Shah, T., Gaal, L.V., Verrijken, A., Francque, S., Biehl, M., Tomlinson, J.: The urinary steroid metabolome as a non-invasive tool to stage nonalcoholic fatty liver disease. Endocrine Abstracts, vol. 44, OC1.4 (2016). doi:10.1530/endoabs.44.OC1.4

  45. Mudali, D., Biehl, M., Leenders, K.L., Roerdink, J.B.T.M.: LVQ and SVM classification of FDG-PET brain data. In: Merényi, E., Mendenhall, M.J., O’Driscoll, P. (eds.) Advances in Self-Organizing Maps and Learning Vector Quantization. AISC, vol. 428, pp. 205–215. Springer, Cham (2016). doi:10.1007/978-3-319-28518-4_18

    Chapter  Google Scholar 

  46. Mudali, D., Biehl, M., Meles, S., Renken, R., Garcia-Garcia, D., Clavero, P., Arbizu, J., Obeso, J., Rodriguez-Oroz, M., Leenders, K., Roerdink, J.: Differentiating early and late stage Parkinson’s disease patients from healthy controls. J. Biomed. Eng. Med. Imaging 3, 33–43 (2016)

    Google Scholar 

  47. Mukherjee, G., Bhanot, G., Raines, K., Sastry, S., Doniach, S., Biehl, M.: Predicting recurrence in clear cell Renal Cell Carcinoma: analysis of TCGA data using outlier analysis and generalized matrix LVQ. In: 2016 IEEE Congress on Evolutionary Computation (CEC), pp. 656–661, July 2016

    Google Scholar 

  48. Mwebaze, E., Bearda, G., Biehl, M., Zühlke, D.: Combining dissimilarity measures for prototype-based classification. In: Verleysen, M. (ed.) 23rd European Symposium on Artificial Neural Networks (ESANN 2015), pp. 31–36. d-side Publishing (2015)

    Google Scholar 

  49. Mwebaze, E., Biehl, M.: Prototype-based classification for image analysis and its application to crop disease diagnosis. In: Merényi, E., Mendenhall, M.J., O’Driscoll, P. (eds.) Advances in Self-Organizing Maps and Learning Vector Quantization. AISC, vol. 428, pp. 329–339. Springer, Cham (2016). doi:10.1007/978-3-319-28518-4_29

    Chapter  Google Scholar 

  50. Mwebaze, E., Schneider, P., Schleif, F.M., Aduwo, J., Quinn, J., Haase, S., Villmann, T., Biehl, M.: Divergence based classification in Learning Vector Quantization. Neural Comput. 74(9), 1429–1435 (2011)

    Google Scholar 

  51. National Cancer Institute and National Human Genome Research Institute: The Cancer Genome Atlas (TCGA) Portal. http://cancergenome.nih.gov. Accessed 16 Mar 2017

  52. Nebel, D., Hammer, B., Villmann, T.: A median variant of generalized Learning Vector Quantization. In: Lee, M., Hirose, A., Hou, Z.-G., Kil, R.M. (eds.) ICONIP 2013. LNCS, vol. 8227, pp. 19–26. Springer, Heidelberg (2013). doi:10.1007/978-3-642-42042-9_3

    Chapter  Google Scholar 

  53. Nova, D., Estévez, P.: A review of Learning Vector Quantization classifiers. Neural Comput. Appl. 25(3–4), 511–524 (2014)

    Article  Google Scholar 

  54. Papari, G., Bunte, K., Biehl, M.: Waypoint averaging and step size control in learning by gradient descent (Technical report). In: Schleif, F.M., Villmann, T. (eds.) Mittweida Workshop on Computational Intelligence. MIWOCI 2011, Machine Learning Reports, volaa. MLR-2011-06, pp. 16–26. University of Bielefeld (2011)

    Google Scholar 

  55. Duda, R.O., Hart, P.E., Stork, D.G.: Pattern Classification. Wiley, Hoboken (2001)

    MATH  Google Scholar 

  56. Robbins, H., Monro, S.: A stochastic approximation method. Ann. Math. Stat. 22, 405 (1951)

    Article  MathSciNet  MATH  Google Scholar 

  57. Seo, S., Obermayer, K.: Soft learning vector. Neural Comput. 15, 1589–1604 (2003)

    Article  MATH  Google Scholar 

  58. Seo, S., Obermayer, K.: Soft nearest prototype classification. IEEE Trans. Neural Netw. 14, 390–398 (2003)

    Article  Google Scholar 

  59. Sato, A.S., Yamada, K.: Generalized Learning Vector Quantization. In: Touretzky, D.S., Mozer, M.C., Hasselmo, M.E. (eds.) Proceedings of the Neural Information Processing Systems (NIPS), vol. 8, pp. 423–429. MIT Press, Cambridge (1996)

    Google Scholar 

  60. Schleif, F.-M., Villmann, T., Hammer, B., Schneider, P., Biehl, M.: Generalized derivative based kernelized Learning Vector Quantization. In: Fyfe, C., Tino, P., Charles, D., Garcia-Osorio, C., Yin, H. (eds.) IDEAL 2010. LNCS, vol. 6283, pp. 21–28. Springer, Heidelberg (2010). doi:10.1007/978-3-642-15381-5_3

    Chapter  Google Scholar 

  61. Schneider, P., Biehl, M., Hammer, B.: Adaptive relevance matrices in Learning Vector Quantization. Neural Comput. 21, 3532–3561 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  62. Schneider, P., Bunte, K., Stiekema, H., Hammer, B., Villmann, T., Biehl, M.: Regularization in matrix relevance learning. IEEE Trans. Neural Netw. 21, 831–840 (2010)

    Article  Google Scholar 

  63. Schölkopf, B.: The kernel trick for distances. Adv. Neural Inf. Process. Syst. 13, 301–307 (2001)

    Google Scholar 

  64. Shawe-Taylor, J., Cristianini, N.: Kernel Methods for Pattern Analysis, 474 p. Cambridge University Press, Cambridge (2004)

    Google Scholar 

  65. Schaul, T., Zhang, S., LeCun, Y.: No more pesky learning rates. JMLR: W&CP 28, 342–351 (2013)

    Google Scholar 

  66. Cover, T.M., Hart, P.: Nearest neighbor pattern classification. IEEE Trans. Inf. Theory 13, 21–27 (1967)

    Article  MATH  Google Scholar 

  67. Villmann, T., Bohnsack, A., Kaden, M.: Can Learning Vector Quantization be an alternative to SVM and Deep Learning? - Recent trends and advanced variants of Learning Vector Quantization for classification learning. J. Artif. Intell. Soft Comput. Res. 7, 65–81 (2017)

    Article  Google Scholar 

  68. Villmann, T., Kaden, M., Hermann, W., Biehl, M.: Learning vector quantization classifiers for ROC-optimization. Comput. Stat., 1–22 (2016). doi:10.1007/s00180-016-0678-y

  69. Villmann, T., Kästner, M., Nebel, D., Riedel, M.: ICMLA face recognition challenge - results of the team ‘Computational Intelligence Mittweida’. In: Proceedings of the International Conference on Machine Learning Applications (ICMLA 2012), pp. 7–10. IEEE Computer Society Press (2012)

    Google Scholar 

  70. Weinberger, K., Blitzer, J., Saul, L.: Distance metric learning for large margin nearest neighbor classification. In: Weiss, Y., Schölkopf, B., Platt, J. (eds.) Advances in Neural Information Processing Systems, vol. 18, pp. 1473–1480. MIT Press, Cambridge (2006)

    Google Scholar 

  71. Weinberger, K., Saul, L.: Distance metric learning for large margin nearest neighbor classification. J. Mach. Learn. Res. 10, 207–244 (2009)

    MATH  Google Scholar 

  72. Yeo, L., Adlard, N., Biehl, M., Juarez, M., Smallie, T., Snow, M., Buckley, C., Raza, K., Filer, A., Scheel-Toellner, D.: Expression of chemokines CXCL4 and CXCL7 by synovial macrophages defines an early stage of rheumatoid athritis. Ann. Rheum. Dis. 75, 763–771 (2015)

    Article  Google Scholar 

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The author would like to thank the collaboration partners and co-authors of the publications which are reviewed in this contribution or could be mentioned only briefly.

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Biehl, M. (2017). Biomedical Applications of Prototype Based Classifiers and Relevance Learning. In: Figueiredo, D., Martín-Vide, C., Pratas, D., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2017. Lecture Notes in Computer Science(), vol 10252. Springer, Cham. https://doi.org/10.1007/978-3-319-58163-7_1

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