The g3mclass is a practical software for multiclass classification on biomarkers

The analytes qualified as biomarkers are potent tools to diagnose various diseases, monitor therapy responses, and design therapeutic interventions. The early assessment of the diverseness of human disease is essential for the speedy and cost-efficient implementation of personalized medicine. We developed g3mclass, the Gaussian mixture modeling software for molecular assay data classification. This software automates the validated multiclass classifier applicable to single analyte tests and multiplexing assays. The g3mclass achieves automation using the original semi-constrained expectation-maximization (EM) algorithm that allows inference from the test, control, and query data that human experts cannot interpret. In this study, we used real-world clinical data and gene expression datasets (ERBB2, ESR1, PGR) to provide examples of how g3mclass may help overcome the problems of over-/underdiagnosis and equivocal results in diagnostic tests for breast cancer. We showed the g3mclass output’s accuracy, robustness, scalability, and interpretability. The user-friendly interface and free dissemination of this multi-platform software aim to ease its use by research laboratories, biomedical pharma, companion diagnostic developers, and healthcare regulators. Furthermore, the g3mclass automatic extracting information through probabilistic modeling is adaptable for blending with machine learning and artificial intelligence. We collected tissue lysates from the formalin-fixed paraffin-embedded sections from the human breast tissue (noncancerous, carcinoma in situ, invasive carcinoma) and analyzed the expression of several genes in samples by Affymetrix QuantiGene Plex 2.0 assay. Test tissue sample lysates were obtained from five tissue curls of 10-micron each. Please note that each *txt (series supplementary) file contains raw data for multiple sasmples, as indicated in the corresponding sample title and description field (3 raw data txt files for all 251 samples).