Deep learning is revolutionizing biomedical research by facilitating the integration of multi-omics data sets while bridging classical bioinformatics with existing knowledge. Building on this powerful potential, Zhang et al. proposed a semi-supervised learning framework called Autoencoder-Based Subtypes Detector for Cancer (ASD-cancer) to improve the multi-omics data analysis (H. Zhang, X. Xiong, M. Cheng, et al., 2024, mSystems 9:e01395-24, https://doi.org/10.1128/msystems.01395-24). By utilizing autoencoders pre-trained on The Cancer Genome Atlas data, the ASD-cancer framework outperforms the baseline model. This approach also makes the framework scalable, enabling it to process new data sets through transfer learning without retraining. This commentary explores the methodological innovations and scalability of ASD-cancer while suggesting future directions, such as the incorporation of additional data layers and the development of adaptive AI models through continuous learning. Notably, integrating large language models into ASD-cancer could enhance its interpretability, providing more profound insights into oncological research and increasing its influence in cancer subtyping and further analysis.