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+ + Digital Twins of Ex Vivo Human Lungs + +

+ +

+ + Project Page + + + GitHub Code + + + Colab: DT Lung Demo + + + Streamlit Web App + + + Hugging Face Model + + + Hugging Face Dataset + +

+ +## Purpose + +This is the official model repository that accompanies [Digital Twin of Ex Vivo Human Lungs Project](https://github.com/Sage-Lab-ai/DT_Lung). This repository contains *a full collection of multi-modal models for creating digital twins of ex vivo human lungs*. + +**Authors** +
+ +Xuanzi Zhou MHSc¹⁻³, Bo Wang PhD⁴⁻⁷, Yiyang Wei BCS¹⁻³, Serena Hacker MScAC1,2,4, Sumin Kim MSc1,2,4, +Thomas Borrillo MHSc1,2, Abby McCaig BSc¹⁻³, Haaniya Ahmed1,2, Youxue Ren MSc1,2, +Olivia Hough PhD1,2, Luca Orsini MD1,2,8, Bonnie T. Chao PhD1,2, Micheal McInnis MD⁹, +Marcelo Cypel MD1-3,10, Mingyao Liu MD1-3,10, Jonathan C. Yeung MD1-3,10, +Lorenzo Del Sorbo MD1,2,8, Shaf Keshavjee* MD1-3,10, and Andrew T. Sage* PhD1-3,10 + +
+ +
+ +1. Latner Thoracic Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
+2. Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
+3. Institute of Medical Science, University of Toronto, Toronto, ON, Canada
+4. Department of Computer Science, University of Toronto, Toronto, ON, Canada
+5. Peter Munk Cardiac Centre, University Health Network, Toronto, ON, Canada
+6. Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
+7. Vector Institute, Toronto, ON, Canada
+8. Interdepartmental Division of Critical Care Medicine, Medical and Surgical Intensive Care Unit, University Health Network, Toronto, ON, Canada
+9. Department of Medical Imaging, Temerty Faculty of Medicine, University of Toronto, University Health Network, Toronto, ON, Canada
+10. Department of Surgery, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
+
+
+ +
+*Co-Senior authors +
+ + +--- + +## Highlights +- ✅ Trained on the world's largest ex vivo lung function dataset +- ⚡ Fast inference: Creating a digital lung within minutes +- 📊 Predicts over 75 multi-modal lung functional parameters including lung physiology, biochemistry, images, protein and transcriptomic markers. +- 🔄 Supports both static (single‑timepoint) and dynamic (continuous recalibration) forecasting + +--- + +## Available Models +The DT model is built using two machine learning model architectures: gated recurrent unit (GRU) and XGBoost (XGB). + +1. **GRU‑based Time‑Series Models** + + - `DT_Lung/GRU` + - `A1F50_A2F50` – Collection of GRU models for static digital lung forecasting (Forecast 2nd hour lung function using 1st hour baseline data) + - `A1F50_A3F50` – Collection of GRU models for static digital lung forecasting (Forecast 3rd hour lung function using 1st hour baseline data) + - `A1F50A2F50_A3F50` – Collection of GRU models for dynamic digital lung forecasting (Forecast 3rd hour lung function using 1st and 2nd hour observed data) + + Legend: `A = assessment period`, `F = first breaths`, `numbers = the number of breaths included`
+ *Note: everything before _ is included as input to the model, and everything after _ is forecasted by the model.*
+ Each folder contains the best-performing GRU models resulting from our hyperparameter tuning for the specified digital lung setup. + +2. **XGBoost Tabular Regressors** + + Each folder below contains the best-performing XGBoost models resulting from our hyperparameter tuning for the specified lung function parameters for each digital lung setup. + + - `DT_Lung/XGB` – Collection of XGBoost models for multiple data modalities + - `Hourly` – XGBoost models for predicting hourly lung functional parameters (e.g., oxygenation level, compliance, pH, etc.) + - `H1_to_H2`: Models for static digital lung forecasting (Forecast 2nd hour lung function using 1st hour baseline data) + - `H1_to_H3`: Models for static digital lung forecasting (Forecast 3rd hour lung function using 1st hour baseline data) + - `H1_H2_to_H3`: Models for dynamic digital lung forecasting (Forecast 3rd hour lung function using 1st and 2nd hour observed data) + - `Protein` – XGBoost models for predicting protein markers (e.g., interleukin-8, interleukin-6, etc.) + - `H1_to_H2`: Models for static digital lung forecasting (Forecast 2nd hour lung function using 1st hour baseline data) + - `H1_to_H3`: Models for static digital lung forecasting (Forecast 3rd hour lung function using 1st hour baseline data) + - `H1_predH2_to_H3`: Models for static digital lung forecasting (Forecast 3rd hour lung function using 1st hour baseline data and predicted 2nd hour data) + - `H1_H2_to_H3`: Models for dynamic digital lung forecasting (Forecast 3rd hour lung function using 1st and 2nd hour obsereved data) + - `Transcriptomics` – XGBoost models for predicting transcriptomic pathways (e.g., TGF-β, apoptosis, etc.) + - `static_forecasting`: Models for static digital lung forecasting of gene enrichment scores (Forecast post-perfusion gene enrichment scores using baseline data) + - `dynamic_forecasting`: Models for dynamic digital lung forecasting of gene enrichment scores (Forecast post-perfusion gene enrichment scores using hourly observed data) + + + - `DT_Lung/XGB_PC` – Collection of XGBoost models for lung x-ray images + - `models_static` – XGBoost models to create static digital lung image features (Forecast 3rd hour lung X-ray derived features using 1st hour baseline data) + - `models_dynamic` – XGBoost models to create dynamic digital lung image features (Forecast 3rd hour lung X-ray derived features using 1st and 2nd hour observed data) + +3. Folders with the `.tar.gz` extension are provided to make model download and distribution easier. Their contents are identical to those in the corresponding folders without the `.tar.gz` extension. + +--- + +## Downloading Models + +### Option 1: Download individual models + +``` +from huggingface_hub import hf_hub_download + +gru_model_dir = hf_hub_download( + repo_id="SageLabUHN/DT_Lung", + filename="GRU/A1F50_A2F50/Dy_comp.pt", # example path, please modify accordingly + local_dir="DT_Lung/models" # example path, specify your local directory +) + +print(f"Model downloaded to: {gru_model_dir}") +``` + +### Option 2: Download all models to a specific folder + +``` +from huggingface_hub import snapshot_download + +model_dir = snapshot_download( + repo_id="SageLabUHN/DT_Lung", + local_dir="DT_Lung/Model", # make sure the Model folder is in the project root dir +) + +print(f"Models downloaded to: {model_dir}") +``` + +Alternatively, you can manually download the models from the [Hugging Face repository page](https://huggingface.co/SageLabUHN/DT_Lung/tree/main). + +## Intended Use + +**Intended for** +- Research and education use + +**Not for** +- Clinical decisions without further validation +- Commercial deployment (non‑commercial only) + +--- + +## License + +This repository and all model weights are released under the **Creative Commons Attribution‑NonCommercial‑ShareAlike 4.0 International (CC BY‑NC‑SA 4.0)** license. +Commercial use is **prohibited**. \ No newline at end of file diff --git a/XGB.tar.gz b/XGB.tar.gz new file mode 100644 index 0000000000000000000000000000000000000000..20f8e8c8a4a30fe911e42b1c43758eb288aaf9b2 --- /dev/null +++ b/XGB.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a85f4060d9bed511fc91e64b02cce8fc767533a484cb2b76b96f8d563662df75 +size 5626781 diff --git a/XGB/Hourly/H1_H2_to_H3/90_Calc Delta PCO2.pkl b/XGB/Hourly/H1_H2_to_H3/90_Calc Delta PCO2.pkl new file mode 100644 index 0000000000000000000000000000000000000000..a549590d0d1fea92bc4e4fd9220a112e0e478d1f --- /dev/null +++ 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