Diagnosis of Malignancy Using Developmental Relationships and Machine Learning

A computer-implemented method and system uses a map which maps from gene expression data for a plurality of training tumors in a tumor atlas to gene expression data representing single cells derived from mammal samples in developmental stages in a single-cell atlas. The method and system: (A) use the map to extract, from the plurality of training tumors, a plurality of biological components, thereby generating, for each training tumor-biological component pair, a corresponding biological component score; and (B) construct, based on the two atlases and the map, a machine learning perceptron classifier that outputs a tumor type of an input tumor based on its gene expression data. The method and system may generate the map before using it. The method and system may apply the machine learning perceptron classifier to the input tumor's gene expression data to generate the tumor type of the input tumor.