Redefining the Game: MVAE-DFDPnet's Low-Dimensional Embeddings for Superior Drug-Protein Interaction Predictions

Liang Yong Xia, Yu Wu, Longfei Zhao, Leying Chen, Shiyi Zhang, Mengdi Wang, Jie Luo

Research output: Contribution to journalArticlepeer-review


Precisely predicting drug-protein interactions (DPIs) is pivotal for drug discovery and advancing precision medicine. A significant challenge in this domain is the high-dimensional and heterogeneous data characterizing drug and protein attributes, along with their intricate interactions. In our study, we introduce a novel deep learning architecture: the <underline>M</underline>ulti-view <underline>V</underline>ariational <underline>A</underline>uto-<underline>E</underline>ncoder embedded within a cascade <underline>D</underline>eep <underline>F</underline>orest (MVAE-DFDPnet). This framework adeptly learns ultra-low-dimensional embedding for drugs and proteins. Notably, our t-SNE analysis reveals that two-dimensional embedding can clearly define clusters corresponding to diverse drug classes and protein families. These ultra-low-dimensional embedding likely contribute to the enhanced robustness and generalizability of our MVAE-DFDPnet. Impressively, our model surpasses current leading methods on benchmark datasets, functioning in significantly reduced dimensional spaces. The model&#x0027;s resilience is further evidenced by its sustained accuracy in predicting interactions involving novel drugs, proteins, and drug classes. Additionally, we have corroborated several newly identified DPIs with experimental evidence from the scientific literature. The code used to generate and analyze these results can be accessed from <uri></uri>.

Original languageEnglish (US)
Pages (from-to)1-10
Number of pages10
JournalIEEE Journal of Biomedical and Health Informatics
StateAccepted/In press - 2024
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Computer Science Applications
  • Health Informatics
  • Electrical and Electronic Engineering
  • Health Information Management


  • Biology
  • cascade deep forest
  • deep learning
  • Diseases
  • DPI
  • Drugs
  • ensemble learning
  • heterogeneous networks
  • multi-view
  • Protein engineering
  • Proteins
  • Random forests
  • Regression analysis


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