Benchmark Datasets
Published benchmark datasets for each task, ready to download and train on.
Upload a file to the matching model builder and map its columns there. The label column is spelled
lable in these files; 1 means interaction and 0 means no interaction.
PPI
Protein-Protein Interaction
Columns: ProteinA, ProteinB, lable
Human PPI Benchmark
Human protein pairs labeled as interacting or non-interacting.
File: PPI-processed.csv
Paper: Large-Scale Prediction of Human Protein-Protein Interactions from Amino Acid Sequence Based on Latent Topic Features
Pan, Zhang, and Shen, Journal of Proteome Research, 2010.
DTPI
Drug-Target Protein Interaction
Columns: SMILES, Protein, lable
NASNet-DTI Benchmark
Drug SMILES and protein sequences labeled for interaction prediction.
File: DTPI-processed.csv
Paper: NASNet-DTI: accurate drug-target interaction prediction using heterogeneous graphs and node adaptation
Zhong and Du, Briefings in Bioinformatics, 2025.
RPI
RNA-Protein Interaction
Columns: RNA, Protein, lable
RNA-Protein Benchmark
RNA and protein sequence pairs labeled as interacting or non-interacting.
File: RPI-processed.csv
Paper: RNA-protein interaction prediction using network-guided deep learning
Liu, Jian, Zeng, and Zhao, Communications Biology, 2025.