[BIBM 2025] GeneQuery: Generalized Gene Expression Prediction from Histology Images via Image-Gene QA

dataset

We have processed the data into h5ad data, which includes:

AnnData object with n_obs × n_vars = spots_num × gene_num
    obs: 'x', 'y', 'new_x', 'new_y', 'pixel_x', 'pixel_y', 'selected', 'barcode'
    var: 'hugo symbol', 'uid'

GSE_chatgpt_definition.txt, HBD_chatgpt_definition.txt and her2_chatgpt_definition.txt have some gene definition from ChatGPT.

wsi-aware code

wsi-aware/

run code, take GSE dataset for example

bash scripts/run_gse.sh

gene-aware code

gene-aware

run code, take GSE dataset for example

bash scripts/run_gse.sh

Acknowledgements

https://github.com/bowang-lab/BLEEP

https://github.com/maxpmx/HisToGene