README.md

---
license: cc-by-nc-nd-4.0
language:
- en
dataset_info:
- config_name: 1Hr Per-breath Data
  features:
  - name: Case ID
    dtype: int64
  - name: Breath Number
    dtype: string
  - name: Dynamic Compliance (mL/cmH₂O)
    dtype: float64
  - name: Mean Airway Pressure (cmH₂O)
    dtype: float64
  - name: Peak Airway Pressure (cmH₂O)
    dtype: float64
  - name: Expiratory Volume (mL)
    dtype: float64
  splits:
  - name: train
    num_bytes: 7923
    num_examples: 150
- config_name: 2Hr Per-breath Data
  features:
  - name: Case ID
    dtype: int64
  - name: Breath Number
    dtype: string
  - name: Dynamic Compliance (mL/cmH₂O)
    dtype: float64
  - name: Mean Airway Pressure (cmH₂O)
    dtype: float64
  - name: Peak Airway Pressure (cmH₂O)
    dtype: float64
  - name: Expiratory Volume (mL)
    dtype: float64
  splits:
  - name: train
    num_bytes: 7923
    num_examples: 150
- config_name: 3Hr Per-breath Data
  features:
  - name: Case ID
    dtype: int64
  - name: Breath Number
    dtype: string
  - name: Dynamic Compliance (mL/cmH₂O)
    dtype: float64
  - name: Mean Airway Pressure (cmH₂O)
    dtype: float64
  - name: Peak Airway Pressure (cmH₂O)
    dtype: float64
  - name: Expiratory Volume (mL)
    dtype: float64
  splits:
  - name: train
    num_bytes: 7923
    num_examples: 150
- config_name: Lung Function Hourly Data
  features:
  - name: Case ID
    dtype: int64
  - name: Parameter
    dtype: string
  - name: 1st Hour
    dtype: float64
  - name: 2nd Hour
    dtype: float64
  - name: 3rd Hour
    dtype: float64
  splits:
  - name: train
    num_bytes: 3801
    num_examples: 63
- config_name: Lung X-ray Image Data
  features:
  - name: Case ID
    dtype: int64
  - name: Xray PC#
    dtype: string
  - name: 1st Hour
    dtype: float64
  - name: 3rd Hour
    dtype: float64
  splits:
  - name: train
    num_bytes: 1233
    num_examples: 30
- config_name: Protein Data
  features:
  - name: Case ID
    dtype: int64
  - name: Protein
    dtype: string
  - name: 1st Hour
    dtype: float64
  - name: 90 Minutes
    dtype: float64
  - name: 110 Minutes
    dtype: float64
  - name: 2nd Hour
    dtype: float64
  - name: 130 Minutes
    dtype: float64
  - name: 150 Minutes
    dtype: float64
  - name: 3rd Hour
    dtype: float64
  splits:
  - name: train
    num_bytes: 1077
    num_examples: 12
- config_name: Transcriptomics Data
  features:
  - name: Case ID
    dtype: int64
  - name: Pathway
    dtype: string
  - name: Baseline
    dtype: float64
  - name: Target
    dtype: float64
  splits:
  - name: train
    num_bytes: 8454
    num_examples: 156
configs:
- config_name: 1Hr Per-breath Data
  data_files:
  - split: train
    path: 1Hr Per-breath Data/*.csv
- config_name: 2Hr Per-breath Data
  data_files:
  - split: train
    path: 2Hr Per-breath Data/*.csv
- config_name: 3Hr Per-breath Data
  data_files:
  - split: train
    path: 3Hr Per-breath Data/*.csv
- config_name: Lung Function Hourly Data
  data_files:
  - split: train
    path: Lung Function Hourly Data/*.csv
- config_name: Lung X-ray Image Data
  data_files:
  - split: train
    path: Lung X-ray Image Data/*.csv
- config_name: Protein Data
  data_files:
  - split: train
    path: Protein Data/*.csv
- config_name: Transcriptomics Data
  data_files:
  - split: train
    path: Transcriptomics Data/*.csv
---

<h1 align="center">
  <span style="font-size:32px">
  Digital Twins of Ex Vivo Human Lungs Demo Dataset
  </span>
</h1>

<p align="center">
  
  <a href="https://sage-lab-ai.github.io/DT_Lung/">
    <img alt="Project Page"
         src="https://img.shields.io/badge/Project-Page-green" />
  </a>
  <a href="https://github.com/Sage-Lab-ai/DT_Lung">
    <img alt="GitHub Code"
         src="https://img.shields.io/badge/GitHub-Code-black?logo=github" />
  </a>
  <a href="https://huggingface.co/SageLabUHN/DT_Lung">
    <img alt="Hugging Face Model"
         src="https://img.shields.io/badge/HuggingFace-Model-yellow?logo=huggingface" />
  </a>
  <a href="https://huggingface.co/datasets/SageLabUHN/DT_Lung_Demo_Data">
    <img alt="Hugging Face Dataset"
         src="https://img.shields.io/badge/HuggingFace-Dataset-yellow?logo=huggingface" />
  </a>

</p>

<p align="center">
  <a href="https://colab.research.google.com/drive/1IrzccQ09mP5amxQTZy07n4LgLSC2r1uj?usp=sharing">
    <img alt="Colab: DT Lung Demo"
         src="https://img.shields.io/badge/Colab-DT%20Lung%20Demo-orange?logo=google-colab" />
  </a>
  
  <a href="https://dt-lung.streamlit.app/">
    <img alt="Streamlit Web App"
         src="https://img.shields.io/badge/Streamlit-Web%20App-red?logo=streamlit" />
  </a>
  
  <a href="https://hub.docker.com/u/sagelabuhn">
  <img alt="Docker Hub"
       src="https://img.shields.io/badge/Docker-Hub-blue?logo=docker&logoColor=white" />
  </a>
</p>


**Model Repository:** [Published Models](https://huggingface.co/SageLabUHN/DT_Lung)  
**Project Repository:** [Digital Twin of Ex Vivo Human Lungs Project](https://github.com/Sage-Lab-ai/DT_Lung)<br>
**Updated:** 2025-July  

---

## Dataset Summary

This demo dataset accompanies the [Digital Twin of Ex Vivo Human Lungs Project](https://github.com/Sage-Lab-ai/DT_Lung). It provides demo data to test and demonstrate inference workflows with our [published models](https://huggingface.co/SageLabUHN/DT_Lung).

The dataset includes:
- Demo data on three clinical ex vivo human lung cases
- Multi-modal data including lung physiology, biochemistry, X-ray image-derived features, protein markers, transcriptomic markers, and per-breath time-series data.

---

## Dataset Structure

```
DT_Lung_Demo_Data/
├── DT Lung Demo Case 1.xlsx
├── DT Lung Demo Case 2.xlsx
├── DT Lung Demo Case 3.xlsx
```

Each Excel file in this directory represents an independent clinical ex vivo human lung case. Each tab in the Excel file contains data for each data modality. 

## Downloading Dataset

Option 1: Recommended 

```
from huggingface_hub import snapshot_download

dataset_dir = snapshot_download(
    repo_id="SageLabUHN/DT_Lung_Demo_Data",
    repo_type="dataset",
    local_dir="DT_Lung/Data"
)

print(f"Dataset downloaded to: {dataset_dir}")
```

Option 2: Manual download from browser
1. Click on the Excel file you want to download, click "Download".
2. Place downloaded files under the correct directory: "work_dir/DT_Lung/Data"

## Intended Use

This dataset is intended for:
- Testing inference pipelines in research and demos  
- Demonstrating data structure for digital twin modeling  
- Reproducing examples from our [Google Colab Demo](https://colab.research.google.com/drive/1EsiyQ0c0HK2p3X3w2nd8E0J7ag9dyV9T?authuser=1#scrollTo=-qFeBnInM4a0) and [Web App Demo](https://dt-lung.streamlit.app/)

**Not intended** for model training or clinical decision-making.

## License

This dataset is released under the **Creative Commons Attribution‑NonCommercial‑ShareAlike 4.0 International (CC BY‑NC‑SA 4.0)** license.
Commercial use is **prohibited**.