title: Convex non-negative matrix factorization for brain tumor delimitation from MRSI data.
abstract: BACKGROUND
  Pattern Recognition techniques can provide invaluable insights in the field of neuro-oncology. This is because the clinical analysis of brain tumors requires the use of non-invasive methods that generate complex data in electronic format. Magnetic Resonance (MR), in the modalities of spectroscopy (MRS) and spectroscopic imaging (MRSI), has been widely applied to this purpose. The heterogeneity of the tissue in the brain volumes analyzed by MR remains a challenge in terms of pathological area delimitation.
  
  
  RESULTS
  A pre-clinical study was carried out using seven brain tumor-bearing mice. Imaging and spectroscopy information was acquired from the brain tissue. A methodology is proposed to extract tissue type-specific sources from these signals by applying Convex Non-negative Matrix Factorization (Convex-NMF). Its suitability for the delimitation of pathological brain area from MRSI is experimentally confirmed by comparing the images obtained with its application to selected target regions, and to the gold standard of registered histopathology data. The former showed good accuracy for the solid tumor region (proliferation index (PI)>30%). The latter yielded (i) high sensitivity and specificity in most cases, (ii) acquisition conditions for safe thresholds in tumor and non-tumor regions (PI>30% for solid tumoral region; ≤5% for non-tumor), and (iii) fairly good results when borderline pixels were considered.
  
  
  CONCLUSIONS
  The unsupervised nature of Convex-NMF, which does not use prior information regarding the tumor area for its delimitation, places this approach one step ahead of classical label-requiring supervised methods for discrimination between tissue types, minimizing the negative effect of using mislabeled voxels. Convex-NMF also relaxes the non-negativity constraints on the observed data, which allows for a natural representation of the MRSI signal. This should help radiologists to accurately tackle one of the main sources of uncertainty in the clinical management of brain tumors, which is the difficulty of appropriately delimiting the pathological area.
authors.affiliation: Departament de Bioquímica i Biología Molecular, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
authors.forename: Sandra
authors.initials: S
authors.lastname: Ortega-Martorell
authors.forename: Paulo J G
authors.initials: PJ
authors.lastname: Lisboa
authors.forename: Alfredo
authors.initials: A
authors.lastname: Vellido
authors.forename: Rui V
authors.initials: RV
authors.lastname: Simões
authors.forename: Martí
authors.initials: M
authors.lastname: Pumarola
authors.forename: Margarida
authors.initials: M
authors.lastname: Julià-Sapé
authors.forename: Carles
authors.initials: C
authors.lastname: Arús
mesh_terms: D000818:Animals; D001932:Brain Neoplasms / Q000473:pathology*; D005909:Glioblastoma / Q000473:pathology*; D008279:Magnetic Resonance Imaging / Q000379:methods*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D051379:Mice; D008954:Models, Biological; D010363:Pattern Recognition, Automated / Q000379:methods*; D012680:Sensitivity and Specificity