Upload folder using huggingface_hub (#1)

- Upload folder using huggingface_hub (2b92e9863c406e077cc0b751fc6ad7514f78b865)

README.md

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----
-license: mit
----
+---
+license: mit
+library_name: pytorch-lightning
+pipeline_tag: tabular-regression
+tags:
+- biology
+- genomics
+datasets:
+- Genentech/decima-data
+---
+
+# Decima
+
+## Model Description
+Decima is a multi-task regression model designed to predict gene expression from genomic DNA sequences. This model was developed by fine-tuning the **Borzoi** architecture. It maps the genomic DNA sequence to quantitative expression levels across diverse cell types and conditions.
+
+For more details, please refer to the original paper: https://www.biorxiv.org/content/10.1101/2024.10.09.617507v3.
+
+- **Architecture:** Fine-tuned Borzoi
+- **Task:** Multi-task Regression
+- **Input:** Genomic sequences (hg38)
+- **Output:** Predicted expression values (log(CPM) + 1) for 8,856 pseudobulks.
+
+## Repository Content
+This repository contains four model replicates (`rep0` through `rep3`). Each replicate is provided in two formats:
+1. **`.ckpt`**: PyTorch Lightning checkpoints containing model weights, optimizer states, and hyperparameters.
+2. **`.safetensors`**: A lightweight, secure format for weights only.
+
+**Files:**
+* `rep0.ckpt`, `rep1.ckpt`, `rep2.ckpt`, `rep3.ckpt`
+* `rep0.safetensors`, `rep1.safetensors`, `rep2.safetensors`, `rep3.safetensors`
+
+## How to Use
+You can load any of the model replicates for inference or further fine-tuning using the `decima` package (https://github.com/Genentech/decima).
+
+### Loading via PyTorch Lightning Checkpoint
+```python
+from decima.model.lightning import LightningModel
+from huggingface_hub import hf_hub_download
+
+# Download a specific replicate (e.g., rep0)
+ckpt_path = hf_hub_download(
+    repo_id="Genentech/decima-model", 
+    filename="rep0.ckpt"
+)
+
+# Load the model
+model = LightningModel.load_from_checkpoint(ckpt_path)
+model.eval()
+
+# For a safetensor file, use LightningModel.load_safetensor(path)
+```

rep0.ckpt

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+size 2260600894

rep0.safetensors

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+size 755007760

rep1.ckpt

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+size 2260600894

rep1.safetensors

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+oid sha256:245bf6f4b4357f39ee15d8e38e32f79e6976ef64936a276d37bd03dbc266a7e3
+size 755007760

rep2.ckpt

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+oid sha256:da95328d7a7690edaba49943b26722064a0f4159141c792d1221dc8c9100a9b4
+size 2260600894

rep2.safetensors

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+size 755007760

rep3.ckpt

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+oid sha256:31127cc544b048db99bf84b3c859ef764b60be6f844d28195da26ace24cb69c5
+size 2260600894

rep3.safetensors

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