Image Feature Extraction
timm
Safetensors
English
university-of-kentucky
medical
radiology
chest-ct
vision
lejepa
Instructions to use Kentucky-Open-Science/DALE-CT-1S with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- timm
How to use Kentucky-Open-Science/DALE-CT-1S with timm:
import timm model = timm.create_model("hf-hub:Kentucky-Open-Science/DALE-CT-1S", pretrained=True) - Notebooks
- Google Colab
- Kaggle
Update README.md
Browse files
README.md
CHANGED
|
@@ -40,15 +40,16 @@ This model is intended for research purposes in the field of medical imaging and
|
|
| 40 |
* Foundational backbone for downstream models predicting organ anomalies, segmentation, or volume-level analysis via MIL.
|
| 41 |
|
| 42 |
## Training Data
|
| 43 |
-
* **Dataset(s):** The model was trained exclusively on the train split of the [CT-RATE](https://huggingface.co/datasets/ibrahimhamamci/CT-RATE) dataset, leveraging annotations for
|
|
|
|
| 44 |
* **Preprocessing:** Hounsfield Units (HU) were strictly clipped between `[-997.0, 888.0]`. These values correspond to the 0.5% and 99.5% pixel intensities of the foreground voxels calculated on a subset of the CT-RATE dataset. The clipped values were mapped to a `[0, 1]` range, followed by Z-score normalization utilizing a dataset mean of `-142.39` and standard deviation of `360.97`.
|
| 45 |
|
| 46 |
## Training Procedure
|
| 47 |
-
* **Training System/Framework:** LeJEPA with a
|
| 48 |
* **Hardware & Scale:** The model was trained across 8x NVIDIA H200 GPUs for a total of 50,000 steps (executed in two 25,000-step runs) with a global batch size of 512.
|
| 49 |
* **Training Strategy:** Unlike standard 2D slice-by-slice SSL training, this model was trained with spatial and anatomical awareness. Global and local crops were sampled from within a 12mm physical slab (using dynamic Z-spacing calculations) rather than a single 2D plane.
|
| 50 |
* **Base Model:** Initialized from scratch using the `vit_large_patch14_dinov2` architecture defined in the `timm` library. No pre-trained weights were used.
|
| 51 |
-
* **Training Objective(s):** Self-supervised LeJEPA loss combined with an auxiliary multi-hot supervised loss predicting the presence of 118 [TotalSegmentator](https://github.com/wasserth/TotalSegmentator) classes within the cropped regions.
|
| 52 |
|
| 53 |
### Training Convergence
|
| 54 |
|
|
@@ -58,10 +59,10 @@ This model is intended for research purposes in the field of medical imaging and
|
|
| 58 |
### Data Augmentation Pipeline
|
| 59 |
During training, a specialized, GPU-accelerated augmentation pipeline was applied to generate the multi-crop views required for the LeJEPA architecture.
|
| 60 |
|
| 61 |
-
**1. Spatial &
|
| 62 |
* **Global Crops:** 2 global crops were generated per volume, sized at 224x224 pixels, with a random scale between 60% and 100% of the original image dimensions.
|
| 63 |
* **Local Crops:** 8 local crops were generated per volume, sized at 140x140 pixels, with a random scale between 30% and 60% of the original image dimensions.
|
| 64 |
-
* **Anatomy & Label Guidance:** Local crops had an 80% probability of being explicitly centered on physical anatomy (probabilistically
|
| 65 |
* **Flip & Resize:** All crops were resized using nearest-neighbor interpolation to prevent the artificial averaging of Hounsfield Units, followed by a random horizontal flip applied with a 50% probability.
|
| 66 |
|
| 67 |
**2. Intensity & Noise Augmentations**
|
|
|
|
| 40 |
* Foundational backbone for downstream models predicting organ anomalies, segmentation, or volume-level analysis via MIL.
|
| 41 |
|
| 42 |
## Training Data
|
| 43 |
+
* **Dataset(s):** The model was trained exclusively on the train split of the [CT-RATE](https://huggingface.co/datasets/ibrahimhamamci/CT-RATE) dataset, leveraging annotations for targeted
|
| 44 |
+
* cropping from [ReXGroundingCT](https://huggingface.co/datasets/rajpurkarlab/ReXGroundingCT).
|
| 45 |
* **Preprocessing:** Hounsfield Units (HU) were strictly clipped between `[-997.0, 888.0]`. These values correspond to the 0.5% and 99.5% pixel intensities of the foreground voxels calculated on a subset of the CT-RATE dataset. The clipped values were mapped to a `[0, 1]` range, followed by Z-score normalization utilizing a dataset mean of `-142.39` and standard deviation of `360.97`.
|
| 46 |
|
| 47 |
## Training Procedure
|
| 48 |
+
* **Training System/Framework:** LeJEPA with a targeted semi-3D cropping strategy, along with an auxiliary supervised loss. Distributed Data Parallel (DDP) was utilized for scaling.
|
| 49 |
* **Hardware & Scale:** The model was trained across 8x NVIDIA H200 GPUs for a total of 50,000 steps (executed in two 25,000-step runs) with a global batch size of 512.
|
| 50 |
* **Training Strategy:** Unlike standard 2D slice-by-slice SSL training, this model was trained with spatial and anatomical awareness. Global and local crops were sampled from within a 12mm physical slab (using dynamic Z-spacing calculations) rather than a single 2D plane.
|
| 51 |
* **Base Model:** Initialized from scratch using the `vit_large_patch14_dinov2` architecture defined in the `timm` library. No pre-trained weights were used.
|
| 52 |
+
* **Training Objective(s):** Self-supervised LeJEPA loss combined with an auxiliary multi-hot supervised loss to "guide" representations, predicting the presence of 118 [TotalSegmentator](https://github.com/wasserth/TotalSegmentator) classes within the cropped regions.
|
| 53 |
|
| 54 |
### Training Convergence
|
| 55 |
|
|
|
|
| 59 |
### Data Augmentation Pipeline
|
| 60 |
During training, a specialized, GPU-accelerated augmentation pipeline was applied to generate the multi-crop views required for the LeJEPA architecture.
|
| 61 |
|
| 62 |
+
**1. Spatial & Targeted Cropping**
|
| 63 |
* **Global Crops:** 2 global crops were generated per volume, sized at 224x224 pixels, with a random scale between 60% and 100% of the original image dimensions.
|
| 64 |
* **Local Crops:** 8 local crops were generated per volume, sized at 140x140 pixels, with a random scale between 30% and 60% of the original image dimensions.
|
| 65 |
+
* **Anatomy & Label Guidance:** Local crops had an 80% probability of being explicitly centered on physical anatomy (probabilistically targeted by TotalSegmentator or ReXGroundingCT masks) to ensure the model learns from tissue rather than background air.
|
| 66 |
* **Flip & Resize:** All crops were resized using nearest-neighbor interpolation to prevent the artificial averaging of Hounsfield Units, followed by a random horizontal flip applied with a 50% probability.
|
| 67 |
|
| 68 |
**2. Intensity & Noise Augmentations**
|