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.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Aggarwal, C.: Outlier Analysis. Springer, New York (2013)
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)
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)
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
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
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
Biehl, M., Ghosh, A., Hammer, B.: Dynamics and generalization ability of LVQ algorithms. J. Mach. Learn. Res. 8, 323–360 (2007)
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
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)
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)
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
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)
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)
Bishop, C.: Pattern Recognition and Machine Learning. Cambridge University Press, Cambridge (2007)
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)
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)
Bottou, L.: Online algorithms and stochastic approximations. In: Saad, D. (ed.) Online Learning and Neural Networks, pp. 9–42. Cambridge University Press, Cambridge (1998)
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)
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
Cichocki, A., Zdunek, R., Phan, A., Amari, S.I.: Nonnegative Matrix and Tensor Factorizations. Wiley, Chichester (2009)
European Network for the Study of Adrenal Tumours: ENS@T (2002). http://www.ensat.org. Accessed 16 Mar 2017
Fawcett, T.: An introduction to ROC analysis. Pattern Recogn. Lett. 27, 861–874 (2006)
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)
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)
Golubitsky, O., Watt, S.: Distance-based classification of handwritten symbols. Int. J. Doc. Anal. Recogn. (IJDAR) 13(2), 133–146 (2010)
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
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
Hammer, B., Villmann, T.: Generalized relevance learning vector quantization. Neural Netw. 15(8–9), 1059–1068 (2002)
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)
Hart, P.: The condensed nearest neighbor rule. IEEE Trans. Inf. Theory 14, 515–516 (1968)
Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd edn. Springer, New York (2009)
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
Kaplan, E., Meier, P.: Nonparametric estimation from incomplete observations. J. Am. Stat. Assoc. 53, 457–481 (1958)
Kingma, D.P., Ba, J.: Adam: a method for stochastic optimization. In: Proceedings of the 3rd International Conference on Learning Representations (ICLR) (2014)
Kohonen, T.: Learning Vector Quantization for pattern recognition. Technical report TKK-F-A601, Helsinki University of Technology, Espoo (1986)
Kohonen, T.: Improved versions of Learning Vector Quantization. In: International Joint Conference on Neural Networks, vol. 1, pp. 545–550 (1990)
Kohonen, T.: Self-organizing Maps. Springer, Heidelberg (1997)
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
Lange, M., Villmann, T.: Derivatives of lp-norms and their approximations. Machine Learning Reports MLR-03-2013 (2013)
Biehl, M.: GMLVQ demo code (2015). http://www.cs.rug.nl/~biehl. Accessed 16 Mar 2017
Biehl, M., Hammer, B., Villmann, T.: Prototype-based models in machine learning. Wileys Interdisicp. Rev. (Wires) Cogn. Sci. 7, 92–111 (2016)
Mahalanobis, P.: On the generalised distance in statistics. Proc. Natl. Inst. Sci. India 2(1), 49–55 (1936)
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
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
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
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)
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
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)
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
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)
National Cancer Institute and National Human Genome Research Institute: The Cancer Genome Atlas (TCGA) Portal. http://cancergenome.nih.gov. Accessed 16 Mar 2017
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
Nova, D., Estévez, P.: A review of Learning Vector Quantization classifiers. Neural Comput. Appl. 25(3–4), 511–524 (2014)
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)
Duda, R.O., Hart, P.E., Stork, D.G.: Pattern Classification. Wiley, Hoboken (2001)
Robbins, H., Monro, S.: A stochastic approximation method. Ann. Math. Stat. 22, 405 (1951)
Seo, S., Obermayer, K.: Soft learning vector. Neural Comput. 15, 1589–1604 (2003)
Seo, S., Obermayer, K.: Soft nearest prototype classification. IEEE Trans. Neural Netw. 14, 390–398 (2003)
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)
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
Schneider, P., Biehl, M., Hammer, B.: Adaptive relevance matrices in Learning Vector Quantization. Neural Comput. 21, 3532–3561 (2009)
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)
Schölkopf, B.: The kernel trick for distances. Adv. Neural Inf. Process. Syst. 13, 301–307 (2001)
Shawe-Taylor, J., Cristianini, N.: Kernel Methods for Pattern Analysis, 474 p. Cambridge University Press, Cambridge (2004)
Schaul, T., Zhang, S., LeCun, Y.: No more pesky learning rates. JMLR: W&CP 28, 342–351 (2013)
Cover, T.M., Hart, P.: Nearest neighbor pattern classification. IEEE Trans. Inf. Theory 13, 21–27 (1967)
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)
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
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)
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)
Weinberger, K., Saul, L.: Distance metric learning for large margin nearest neighbor classification. J. Mach. Learn. Res. 10, 207–244 (2009)
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)
Acknowledgments
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer International Publishing AG
About this paper
Cite this paper
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
Download citation
DOI: https://doi.org/10.1007/978-3-319-58163-7_1
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-58162-0
Online ISBN: 978-3-319-58163-7
eBook Packages: Computer ScienceComputer Science (R0)