Gene PointNet for Tumor Classification

Abstract The rising incidence of cancer underscores the imperative for innovative diagnostic and prognostic methodologies. This study delves into the potential of RNA-Seq gene expression data to enhance cancer classification accuracy. Introducing a pioneering approach, we model gene expression data as point clouds, capitalizing on the data’s intrinsic properties to bolster classification performance. Utilizing PointNet, a typical technique for processing point cloud data, as our framework’s cornerstone, we incorporate inductive biases pertinent to gene expression and pathways. This integration markedly elevates model efficacy, culminating in developing an end-to-end deep learning classifier with an accuracy rate surpassing 99%. Our findings not only illuminate the capabilities of AI-driven models in the realm of oncology but also highlight the criticality of acknowledging biological dataset nuances in model design. This research provides insights into application of deep learning in medical science, setting the stage for further innovation in cancer classification through sophisticated biological data analysis. The source code for our study is accessible at: https://github.com/cialab/GPNet .