Accurate grading of brain gliomas by soft independent modeling of class analogy based on non-negative matrix factorization of proton magnetic resonance spectra

• Published in: Magnetic resonance in chemistry Vol. 54; no. 2; pp. 119 - 125
• Main Authors: Ghasemi, K., Khanmohammadi, M., Saligheh Rad, H.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.02.2016; Wiley Subscription Services, Inc
• Subjects: 1H-magnetic resonance spectroscopy; Algorithms; Analogies; Aspartic Acid - analogs & derivatives; Aspartic Acid - analysis; Brain; Brain Neoplasms - diagnosis; Brain Neoplasms - pathology; brain tumors; Choline - analysis; Classification; Creatine - analysis; Factorization; glioma; Glioma - diagnosis; Glioma - pathology; Glycine - analysis; Humans; Magnetic resonance; Metabolites; Modelling; Neoplasm Grading; NMF; PCA; Principal Component Analysis; Proton Magnetic Resonance Spectroscopy - methods; Quality; SIMCA; glioma; brain tumors; NMF; SIMCA; 1H-magnetic resonance spectroscopy; PCA
• ISSN: 0749-1581; 1097-458X; 1097-458X
• DOI: 10.1002/mrc.4326

Hydrogen magnetic resonance spectroscopy (1H‐MRS) is a non‐invasive technique which provides a ‘frequency‐signal intensity’ spectrum of biochemical compounds of tissues in the body. Although this method is currently used in human brain studies, accurate classification of in‐vivo 1H‐MRS is a challenging task in the diagnosis of brain tumors. Problems such as overlapping metabolite peaks, incomplete information on background component and low signal‐to‐noise ratio disturb classification results of this spectroscopic method. This study presents an alternative approach to the soft independent modeling of class analogy (SIMCA) technique, using non‐negative matrix factorization (NMF) for dimensionality reduction. In the adopted strategy, the performance of SIMCA was improved by application of a robust algorithm for classification in the presence of noisy measurements. Total of 219 spectra from two databases were taken by water‐suppressed short echo‐time 1H‐MRS, acquired from different subjects with different stages of glial brain tumors (Grade II (26 cases), grade III (24 cases), grade IV (41 cases), as well as 25 healthy cases). The SIMCA was performed using two approaches: (i) principal component analysis (PCA) and (ii) non‐negative matrix factorization (NMF), as a modified approach. Square prediction error was considered to assess the class membership of the external validation set. Finally, several figures of merit such as the correct classification rate (CCR), sensitivity and specificity were calculated. Results of SIMCA based on NMF showed significant improvement in percentage of correctly classified samples, 91.4% versus 83.5% for PCA‐based model in an independent test set. Copyright © 2015 John Wiley & Sons, Ltd. 1H‐MRS is a non‐invasive technique in assessment of brain's metabolites. The performance of Soft Modeling Class Analogy (SIMCA) classifier was improved by application of non‐negative matrix factorization for accurate grading of brain glioma.