Expanding P-NET, a multi-purpose biologically informed deep learning framework

We present expanded P-NET, a versatile frame-work for deep learning in computational biology based on P-NET, leveraging biological pathways for interpretable predictions. Our framework achieves competitive performance in genomic & transcriptomic prediction tasks. We demonstrate its stability and interpretability compared to traditional machine learning models. P-NET 2.0 incorporates gene and pathway information, providing valuable insights into complex biological processes. The framework is publicly available, enabling its application to various computational biology tasks.