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license: cc-by-nc-2.0
library_name: diffusers
tags:
- transcriptomics
- bioinformatics
- gene-expression
- genomics
datasets:
- silicobio/hoike_normal_expression_GTEx_Analysis_v10_log2tpmplus1
- silicobio/hoike_condition_expression_TCGA_various_log2tpmplus1
---
# Hōʻike: A Joint-Embedding Predictive Architecture for Transcriptome Data Generation with Diffusion Models
<h3 align="right">Silico Biosciences</h3>
Visit the GitHub repository for the full framework code: https://github.com/silicobio/hoike
## Usage
```py
## 1. Look up the condition samples for a tissue that exists in the normal reference set.
user_target_tissue = "Skin"
condition_subset = dataset.condition_df[dataset.condition_df["tissue_type"] == user_target_tissue].reset_index(drop=True)
normal_baseline_array = dataset.normal_profiles[user_target_tissue]
## 2. Generate with sampling-time normalization consistent with diffusion training.
generated_df = generate_synthetic_condition_data_consistent(
normal_profile=normal_baseline_array,
jepa=jepa_model,
diffusion=diff_model,
scheduler=scheduler,
gene_cols=dataset.gene_cols,
num_samples=2500,
value_cap=condition_value_cap,
sampling_noise_scale=1.1,
)
``` |