Discriminant Convex Non-negative Matrix Factorization for the classification of human brain tumours

The medical analysis of human brain tumours commonly relies on indirect measurements. Among these, magnetic resonance imaging (MRI) and spectroscopy (MRS) predominate in clinical settings as tools for diagnostic assistance. Pattern recognition (PR) methods have successfully been used in this task, usually interpreting diagnosis as a supervised classification problem. In MRS, the acquired spectral signal can be analyzed in an unsupervised manner to extract its constituent sources. Recently, this has been successfully accomplished using Non-negative Matrix Factorization (NMF) methods. In this paper, we present a method to introduce the available class information into the unsupervised source extraction process of a convex variant of NMF. Novel techniques to generate diagnostic predictions for new, unseen spectra using the proposed Discriminant Convex-NMF are also described and experimentally assessed.

[1]  Z. Wu,et al.  In vivo single-voxel proton MR spectroscopy in the differentiation of high-grade gliomas and solitary metastases. , 2004, Clinical radiology.

[2]  KlingenbergBradley,et al.  Non-negative matrix factorization , 2009 .

[3]  Joachim M. Buhmann,et al.  The Balanced Accuracy and Its Posterior Distribution , 2010, 2010 20th International Conference on Pattern Recognition.

[4]  H. Sebastian Seung,et al.  Algorithms for Non-negative Matrix Factorization , 2000, NIPS.

[5]  Yunde Jia,et al.  Non-negative matrix factorization framework for face recognition , 2005, Int. J. Pattern Recognit. Artif. Intell..

[6]  Seungjin Choi,et al.  Semi-Supervised Nonnegative Matrix Factorization , 2010, IEEE Signal Processing Letters.

[7]  Sabine Van Huffel,et al.  Multiproject–multicenter evaluation of automatic brain tumor classification by magnetic resonance spectroscopy , 2008, Magnetic Resonance Materials in Physics, Biology and Medicine.

[8]  Paulo J. G. Lisboa,et al.  Data Mining in Cancer Research [Application Notes] , 2010, IEEE Computational Intelligence Magazine.

[9]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[10]  Franklyn A. Howe,et al.  The clinical value of proton magnetic resonance spectroscopy in adult brain tumours. , 2007, Clinical radiology.

[11]  Paulo J. G. Lisboa,et al.  Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours , 2012, BMC Bioinformatics.

[12]  Nanning Zheng,et al.  Non-negative matrix factorization based methods for object recognition , 2004, Pattern Recognit. Lett..

[13]  Lucas C. Parra,et al.  Nonnegative matrix factorization for rapid recovery of constituent spectra in magnetic resonance chemical shift imaging of the brain , 2004, IEEE Transactions on Medical Imaging.

[14]  Paulo J. G. Lisboa,et al.  Convex Non-Negative Matrix Factorization for Brain Tumor Delimitation from MRSI Data , 2012, PloS one.

[15]  A. W. Simonetti,et al.  Development of a decision support system for diagnosis and grading of brain tumours using in vivo magnetic resonance single voxel spectra , 2006, NMR in biomedicine.

[16]  D. Louis WHO classification of tumours of the central nervous system , 2007 .

[17]  V. Govindaraju,et al.  Proton NMR chemical shifts and coupling constants for brain metabolites , 2000, NMR in biomedicine.

[18]  P J Lisboa,et al.  Assessment of statistical and neural networks methods in NMR spectral classification and metabolite selection , 1998, NMR in biomedicine.

[19]  C Arús,et al.  Robust discrimination of glioblastomas from metastatic brain tumors on the basis of single‐voxel 1H MRS , 2012, NMR in biomedicine.

[20]  Angle-Constrained Alternating Least Squares , 2011, Applied spectroscopy.

[21]  Chih-Jen Lin,et al.  Projected Gradient Methods for Nonnegative Matrix Factorization , 2007, Neural Computation.

[22]  Fei Wang,et al.  Semi-Supervised Clustering via Matrix Factorization , 2008, SDM.

[23]  Christophe Ladroue,et al.  Independent component analysis for automated decomposition of in vivo magnetic resonance spectra , 2003, Magnetic resonance in medicine.

[24]  Mark Gerstein,et al.  Tiling array data analysis: a multiscale approach using wavelets , 2011, BMC Bioinformatics.

[25]  Anastasios Tefas,et al.  Exploiting discriminant information in nonnegative matrix factorization with application to frontal face verification , 2006, IEEE Transactions on Neural Networks.

[26]  Stefan M. Wild,et al.  Improving non-negative matrix factorizations through structured initialization , 2004, Pattern Recognit..

[27]  M. Julià-Sapé,et al.  A Multi-Centre, Web-Accessible and Quality Control-Checked Database of in vivo MR Spectra of Brain Tumour Patients , 2006, Magnetic Resonance Materials in Physics, Biology and Medicine.

[28]  W. El-Deredy,et al.  Pattern recognition approaches in biomedical and clinical magnetic resonance spectroscopy: a review , 1997, NMR in biomedicine.

[29]  Paulo J. G. Lisboa,et al.  Application notes: data mining in cancer research , 2010 .

[30]  Enzo Mumolo,et al.  Spatial Map Building Using Fast Texture Analysis Of Rotating Sonar Sensor Data For Mobile Robots , 2005, Int. J. Pattern Recognit. Artif. Intell..

[31]  Chris H. Q. Ding,et al.  Convex and Semi-Nonnegative Matrix Factorizations , 2010, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[32]  Xiaoli Li,et al.  Multi-resolution independent component analysis for high-performance tumor classification and biomarker discovery , 2011, BMC Bioinformatics.

[33]  Anil K. Jain Data clustering: 50 years beyond K-means , 2010, Pattern Recognit. Lett..

[34]  Lluís A. Belanche Muñoz,et al.  Classifying malignant brain tumours from 1H-MRS data using Breadth Ensemble Learning , 2012, The 2012 International Joint Conference on Neural Networks (IJCNN).

[35]  R. Lenkinski,et al.  A systematic literature review of magnetic resonance spectroscopy for the characterization of brain tumors. , 2006, AJNR. American journal of neuroradiology.

[36]  Ioannis Pitas,et al.  A Novel Discriminant Non-Negative Matrix Factorization Algorithm With Applications to Facial Image Characterization Problems , 2007, IEEE Transactions on Information Forensics and Security.

[37]  W El-Deredy,et al.  Tumour grading from magnetic resonance spectroscopy: a comparison of feature extraction with variable selection , 2003, Statistics in medicine.

[38]  B. Scheithauer,et al.  The 2007 WHO classification of tumours of the central nervous system , 2007, Acta Neuropathologica.

[39]  Lluís A. Belanche Muñoz,et al.  Feature and model selection with discriminatory visualization for diagnostic classification of brain tumors , 2010, Neurocomputing.

[40]  Jong-Hwan Lee,et al.  A constrained alternating least squares nonnegative matrix factorization algorithm enhances task-related neuronal activity detection from single subject's fMRI data , 2011, 2011 International Conference on Machine Learning and Cybernetics.

[41]  H. Sebastian Seung,et al.  Learning the parts of objects by non-negative matrix factorization , 1999, Nature.