Dimensional reduction based on peak fitting of Raman micro spectroscopy data improves detection of prostate cancer in tissue specimens

• Published in: Journal of biomedical optics Vol. 26; no. 11; p. 116501
• Main Authors: Plante, Arthur, Dallaire, Frédérick, Grosset, Andrée-Anne, Nguyen, Tien, Birlea, Mirela, Wong, Jahg, Daoust, François, Roy, Noémi, Kougioumoutzakis, André, Azzi, Feryel, Aubertin, Kelly, Kadoury, Samuel, Latour, Mathieu, Albadine, Roula, Prendeville, Susan, Boutros, Paul, Fraser, Michael, Bristow, Rob G, van der Kwast, Theodorus, Orain, Michèle, Brisson, Hervé, Benzerdjeb, Nazim, Hovington, Hélène, Bergeron, Alain, Fradet, Yves, Têtu, Bernard, Saad, Fred, Trudel, Dominique, Leblond, Frédéric
• Format: Journal Article
• Language: English
• Published: Bellingham Society of Photo-Optical Instrumentation Engineers 01.11.2021; S P I E - International Society for
• Subjects: Accuracy; Algorithms; Aluminum; Biomarkers; Classification; Cosmic rays; Datasets; Discriminant analysis; Feature selection; Health care networks; Kernel functions; Learning algorithms; Machine learning; Microscopy; Patients; Prostate cancer; Prostate carcinoma; Prostatic intraepithelial neoplasia; Radial basis function; Raman spectra; Raman spectroscopy; Reduction; Sensitivity analysis; Spectroscopy; Spectrum analysis; Support vector machines; Wavelengths; Raman micro-spectroscopy; prostate cancer; feature reduction; machine learning; feature selection
• ISSN: 1083-3668; 1560-2281; 1560-2281
• DOI: 10.1117/1.JBO.26.11.116501

Significance: Prostate cancer is the most common cancer among men. An accurate diagnosis of its severity at detection plays a major role in improving their survival. Recently, machine learning models using biomarkers identified from Raman micro-spectroscopy discriminated intraductal carcinoma of the prostate (IDC-P) from cancer tissue with a ≥85  %   detection accuracy and differentiated high-grade prostatic intraepithelial neoplasia (HGPIN) from IDC-P with a ≥97.8  %   accuracy. Aim: To improve the classification performance of machine learning models identifying different types of prostate cancer tissue using a new dimensional reduction technique. Approach: A radial basis function (RBF) kernel support vector machine (SVM) model was trained on Raman spectra of prostate tissue from a 272-patient cohort (Centre hospitalier de l’Université de Montréal, CHUM) and tested on two independent cohorts of 76 patients [University Health Network (UHN)] and 135 patients (Centre hospitalier universitaire de Québec-Université Laval, CHUQc-UL). Two types of engineered features were used. Individual intensity features, i.e., Raman signal intensity measured at particular wavelengths and novel Raman spectra fitted peak features consisting of peak heights and widths. Results: Combining engineered features improved classification performance for the three aforementioned classification tasks. The improvements for IDC-P/cancer classification for the UHN and CHUQc-UL testing sets in accuracy, sensitivity, specificity, and area under the curve (AUC) are (numbers in parenthesis are associated with the CHUQc-UL testing set): +4  %   (+8  %  ), +7  %   (+9  %  ), +2  %   (6%), +9 (+9) with respect to the current best models. Discrimination between HGPIN and IDC-P was also improved in both testing cohorts: +2.2  %   (+1.7  %  ), +4.5  %   (+3.6  %  ), +0  %   (+0  %  ), +2.3 (+0). While no global improvements were obtained for the normal versus cancer classification task [+0  %   (−2  %  ), +0  %   (−3  %  ), +2  %   (−2  %  ), +4 (+3)], the AUC was improved in both testing sets. Conclusions: Combining individual intensity features and novel Raman fitted peak features, improved the classification performance on two independent and multicenter testing sets in comparison to using only individual intensity features.