oversaw data analysis and interpretation and edited the manuscript; J.J.N. conceived of the study, obtained funding, supervised data acquisition, supervised data analysis, interpreted data, and edited the manuscript.
UB designed the study, obtained funding, supervised and assisted with its execution, supervised analysis and interpretation of data, and critically reviewed the manuscript.
Encouraged by the good performance obtained with supervised SVMs, we have chosen to test a kernel-based semi-supervised approach known as the Transductive SVM, or TSVM [27], which has been applied with success, for example, in text recognition [27] and image processing [28].
Overall, the convergence of structures obtained using supervised assignments for the three target proteins, RTT, ms6282 and aLP, are better than or comparable to the convergence of structures obtained using 4D-CHAINS automated assignments, as expected (Table 1).
Compared to a previously identified 70-gene prognosis profile, obtained with supervised classification, the combination of signatures performs roughly equally well and might have additional value in the ER-negative subgroup.
A training set was obtained for supervised learning by manually selecting representative regions on the input image.
For instance, the accuracies for the negative classes are comparable to those obtained with supervised machine learning classifiers, such as support vector machines or decision trees, which operate exclusively on the BioGRID SL/SS categories [27] [29].
JM obtained funding, supervised data analysis, interpretation of the results and manuscript writing and approved the final manuscript.
(D ) Heatmap of TCGA sample co-occurrence between unsupervised consensus clusters and methylation subtypes obtained from (supervised) nearest centroid classification.
However, gene signatures obtained through supervised analysis were not superior to the molecular structure based prognostic predictions in validation (Additional file 1, Supplementary Figure S14).
