Systematic mapping of chemical perturbation responses is revolutionizing polypharmacological drug discovery, yet remains constrained by experimental scalability. Here, we introduce XPert, a biologically informed Dual-Branch Transformer model that predicts gene-specific drug responses across dose-time conditions, outperforming VAE-based methods. It generalizes to unseen cells, transfers knowledge to clinical settings, and reveals mechanistic insights, offering a scalable solution for precision medicine and perturbation-based drug discovery.

The repository is organised as follows:

- `processed_data/` contains processed data files;

- `HG_data/` contains the data for training the knowledge heterogeneous graph and the pre-trained embeddings;

- `dataset/` contains the necessary files for creating the dataset;

- `models/` contains different modules of XPert;

- `configs/` contains all the config files adapted for different datasets and scenarios;

- `experiment/` contains log files and output files;

- `scripts/` contains the scripts for training, inference, and testing the model;

- `saved_model/` contains the trained and pretrained weights;

- `evaluation_metrics/` contains all the evaluation metrics mentioned in the paper;

- `reproducing/` contains the code for reproducing the analysis results and figures from the paper;

 

HG_data.zip: Located under the 'XPert/' directory, this package includes the datasets used for constructing the knowledge-informed heterogeneous graph, together with the corresponding pre-trained node embeddings.

saved_model.zip: Located under the 'XPert/' directory, this package contains the trained model weights and associated pre-trained parameters.

reproducing.zip: Located under the 'XPert/' directory, this package provides the code for reproducing the main analysis and figures reported in the paper.

processed_data.zip: Located under the XPert/ directory, this package contains all processed datasets and meta used in this study.

All other files not included in the compressed archives above are provided under the XPert/processed_data/ directory. Users may retrieve these resources as needed and should place them in the designated file paths to ensure full reproducibility of the analyses.