EXPORT

Overview

EXPlainable VAE for ORdinally perturbed Transcriptomics data (EXPORT) is an interpretable VAE model with a biological pathway informed architecture, to analyze ordinally perturbed transcriptomics data. Specifically, the low-dimensional latent representations in EXPORT are ordinally-guided by training an auxiliary deep ordinal regressor network and explicitly modeling the ordinality in the training loss function with an additional ordinal-based cumulative link loss term.

Citation

If you use this code, please cite our preprint paper:

Niyakan, S., Luo, X., Yoon, B. & Qian, X. (2024). Biologically Interpretable VAE with Supervision for Transcriptomics Data Under Ordinal Perturbations, bioRxiv. https://www.biorxiv.org/content/early/2024/03/29/2024.03.28.587231

Getting Started

EXPORT needs 3 main items to analyze your perturbed transcriptomics data:

1. Perturbed Gene Expression Data: The gene expression table of perturbed transcriptomics data under study.
2. Biological Pathway Data: A GMT file specifying the gene-pathway annotation data extracted from resources such as publicly available KEGG, Wikipathways and Reactome databases.
3. Ordinal Perturbation levels: The actual ordinal labels corresponding to perturbation ordinal dosages.

Tutorials

• Pre-processing Single cell-level TCDD data
• Analysis of Single cell-level TCDD data with EXPORT