MetaPhenotype: A Transferable Meta-Learning Model for Single-Cell Mass Spectrometry-Based Cell Phenotype Prediction Using Limited Number of Cells

Single-cell mass spectrometry (SCMS) is an emerging tool for studying cell heterogeneity according to variation of molecular species in single cells. Although it has become increasingly common to employ machine learning models in SCMS data analysis, such as the classification of cell phenotypes, the existing machine learning models often suffer from low adaptability and transferability. In addition, SCMS studies of rare cells can be restricted by limited number of cell samples. To overcome these limitations, we performed SCMS analyses of melanoma cancer cell lines with two phenotypes (i.e., primary and metastatic cells). We then developed a meta-learning-based model, MetaPhenotype, that can be trained using a small amount of SCMS data to accurately classify cells into primary or metastatic phenotypes. Our results show that compared with standard transfer learning models, MetaPhenotype can rapidly predict and achieve a high accuracy of over 90% with fewer new training samples. Overall, our work opens the possibility of accurate cell phenotype classification based on fewer SCMS samples, thus lowering the demand for sample acquisition.