diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000000000000000000000000000000000000..3ac7d16c6d65254515d766fe9344fbeda3444afb --- /dev/null +++ b/.gitignore @@ -0,0 +1,3 @@ +.idea/ +.DS_Store +node_modules/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1c89dc9322ed93fae5c500a058efb6ac7373fb78 --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,71 @@ +default_language_version: + python: python3 +repos: + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: check-added-large-files + args: ["--maxkb=30000"] + - id: check-ast + - id: check-byte-order-marker + - id: check-builtin-literals + - id: check-case-conflict + - id: check-docstring-first + - id: check-merge-conflict + - id: check-symlinks + - id: check-toml + - id: check-yaml + - id: debug-statements + - id: destroyed-symlinks + - id: end-of-file-fixer + - id: fix-byte-order-marker + - id: mixed-line-ending + - id: file-contents-sorter + files: "envs/requirements*.txt" + - id: trailing-whitespace + - repo: https://github.com/astral-sh/ruff-pre-commit + rev: v0.11.8 + hooks: + # run the linter + - id: ruff + args: [--fix] + # run the formatter + - id: ruff-format + - repo: https://github.com/pre-commit/mirrors-mypy + rev: v1.15.0 + hooks: # https://github.com/python/mypy/issues/4008#issuecomment-582458665 + - id: mypy + name: mypy + pass_filenames: false + args: + [ + --strict-equality, + --disallow-untyped-calls, + --disallow-untyped-defs, + --disallow-incomplete-defs, + --disallow-any-generics, + --check-untyped-defs, + --disallow-untyped-decorators, + --warn-redundant-casts, + --warn-unused-ignores, + --no-warn-no-return, + --warn-unreachable, + ] + additional_dependencies: ["types-requests"] + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v4.0.0-alpha.8 + hooks: + - id: prettier + args: + - --print-width=120 + - --prose-wrap=always + - --tab-width=2 + - repo: https://github.com/codespell-project/codespell + rev: v2.4.1 + hooks: + - id: codespell + name: codespell + description: Checks for common misspellings in text files. + entry: codespell + language: python + types: [text] diff --git a/README.md b/README.md index 7be5fc7f47d5db027d120b8024982df93db95b74..411c402c37e4829b6ee5a1e10ccc4d3ecb096b67 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,92 @@ ---- -license: mit ---- +--- +license: mit +language: + - en +--- + +# CineMA - A Foundation Model for Cine Cardiac Magnetic Resonance Images 🎥🫀 + +This repository contains the weights for **CineMA**, a foundation model for **Cine** cardiac magnetic resonance (CMR) +imaging based on **M**asked-**A**utoencoder. The model was pre-trained on over 74,000 pairs of short-axis and long-axis +cine CMR images from the UK Biobank. + +CineMA was evaluated across a diverse range of clinically relevant downstream tasks, including + +- Ventricle and myocardium segmentation +- Cardiovascular disease (CVD) detection and classification +- Patient sex classification +- CMR machine vendor classification +- Ejection fraction (EF) regression +- Patient body mass index (BMI) regression +- Patient age regression +- Mid-ventricular and apical landmark localization + +These tasks were studied across multiple datasets: + +- [ACDC](https://www.creatis.insa-lyon.fr/Challenge/acdc/) +- [M&Ms](https://www.ub.edu/mnms/) +- [M&Ms2](https://www.ub.edu/mnms-2/) +- [Kaggle](https://www.kaggle.com/c/second-annual-data-science-bowl/data) +- [Rescan](https://www.ahajournals.org/doi/full/10.1161/CIRCIMAGING.119.009214) +- [Landmark](https://pubs.rsna.org/doi/10.1148/ryai.2021200197) + +Compared to convolutional neural network baselines such as UNet and ResNet, CineMA demonstrated superior or comparable +performance, especially in sample efficiency and generalization to out-of-distribution data not seen during pretraining +or fine-tuning. + +By releasing the model weights and code for pretraining, fine-tuning, and inference, CineMA aims to lower the barrier to +entry for cardiac imaging research, foster reproducibility, and encourage broader adoption across institutions. + +➡️ **Manuscript:** [TBD](https://arxiv.org/) + +➡️ **Code:** [mathpluscode/CineMA](https://github.com/mathpluscode/CineMA) + +## Fine-tuned CineMA Models + +The filenames of fine-tuned model weights follow the convention of `finetuned//__.safetensors` +where number 0, 1, and 2 correspond to the different training seeds. + +Check the "Inference Example" column to see example inference scripts using these trained models. + +| Training Task | Training Data | Input View | Input Timeframes | Model Weights and Configurations | Inference Example | +| ----------------------------------------------- | ------------- | ---------- | ---------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | +| Ventricle and myocardium segmentation | ACDC | SAX | 1 | [finetuned/segmentation/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_0.safetensors)
[finetuned/segmentation/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_1.safetensors)
[finetuned/segmentation/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/acdc_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms | SAX | 1 | [finetuned/segmentation/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_0.safetensors)
[finetuned/segmentation/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_1.safetensors)
[finetuned/segmentation/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms2 | SAX | 1 | [finetuned/segmentation/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_0.safetensors)
[finetuned/segmentation/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_1.safetensors)
[finetuned/segmentation/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_sax_2.safetensors)
[finetuned/segmentation/sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/sax.yaml) | [segmentation_sax.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_sax.py) | +| Ventricle and myocardium segmentation | M&Ms2 | LAX 4C | 1 | [finetuned/segmentation/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_0.safetensors)
[finetuned/segmentation/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_1.safetensors)
[finetuned/segmentation/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/mnms2_lax_4c_2.safetensors)
[finetuned/segmentation/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/segmentation/lax_4c.yaml) | [segmentation_lax_4c.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/segmentation_lax_4c.py) | +| CVD classification | ACDC | SAX | 2 (ED and ES) | [finetuned/classification_cvd/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_0.safetensors)
[finetuned/classification_cvd/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_1.safetensors)
[finetuned/classification_cvd/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax_2.safetensors)
[finetuned/classification_cvd/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/acdc_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_0.safetensors)
[finetuned/classification_cvd/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_1.safetensors)
[finetuned/classification_cvd/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax_2.safetensors)
[finetuned/classification_cvd/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_0.safetensors)
[finetuned/classification_cvd/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_1.safetensors)
[finetuned/classification_cvd/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax_2.safetensors)
[finetuned/classification_cvd/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_sax.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| CVD classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_cvd/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_0.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_1.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c_2.safetensors)
[finetuned/classification_cvd/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_cvd/mnms2_lax_4c.yaml) | [classification_cvd.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_cvd.py) | +| Patient sex classification | M&Ms | SAX | 2 (ED and ES) | [finetuned/classification_sex/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_0.safetensors)
[finetuned/classification_sex/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_1.safetensors)
[finetuned/classification_sex/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax_2.safetensors)
[finetuned/classification_sex/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_sex/mnms_sax.yaml) | [classification_sex.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_sex.py) | +| CMR machine vendor classification | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_0.safetensors)
[finetuned/classification_vendor/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_1.safetensors)
[finetuned/classification_vendor/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax_2.safetensors)
[finetuned/classification_vendor/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_sax.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | +| CMR machine vendor classification | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/classification_vendor/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_0.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_1.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c_2.safetensors)
[finetuned/classification_vendor/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/classification_vendor/mnms2_lax_4c.yaml) | [classification_vendor.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/classification_vendor.py) | +| EF regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_ef/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_0.safetensors)
[finetuned/regression_ef/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_1.safetensors)
[finetuned/regression_ef/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax_2.safetensors)
[finetuned/regression_ef/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/acdc_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| EF regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_0.safetensors)
[finetuned/regression_ef/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_1.safetensors)
[finetuned/regression_ef/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax_2.safetensors)
[finetuned/regression_ef/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| EF regression | M&Ms2 | SAX | 2 (ED and ES) | [finetuned/regression_ef/mnms2_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_0.safetensors)
[finetuned/regression_ef/mnms2_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_1.safetensors)
[finetuned/regression_ef/mnms2_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax_2.safetensors)
[finetuned/regression_ef/mnms2_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_sax.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| EF regression | M&Ms2 | LAX 4C | 2 (ED and ES) | [finetuned/regression_ef/mnms2_lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_0.safetensors)
[finetuned/regression_ef/mnms2_lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_1.safetensors)
[finetuned/regression_ef/mnms2_lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c_2.safetensors)
[finetuned/regression_ef/mnms2_lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_ef/mnms2_lax_4c.yaml) | [regression_ef.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_ef.py) | +| Patient BMI regression | ACDC | SAX | 2 (ED and ES) | [finetuned/regression_bmi/acdc_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_0.safetensors)
[finetuned/regression_bmi/acdc_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_1.safetensors)
[finetuned/regression_bmi/acdc_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax_2.safetensors)
[finetuned/regression_bmi/acdc_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_bmi/acdc_sax.yaml) | [regression_bmi.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_bmi.py) | +| Patient age regression | M&Ms | SAX | 2 (ED and ES) | [finetuned/regression_age/mnms_sax_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_0.safetensors)
[finetuned/regression_age/mnms_sax_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_1.safetensors)
[finetuned/regression_age/mnms_sax_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax_2.safetensors)
[finetuned/regression_age/mnms_sax.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/regression_age/mnms_sax.yaml) | [regression_age.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/regression_age.py) | +| Landmark localization by heatmap regression | Landmark | LAX 2C | 1 | [finetuned/landmark_heatmap/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_0.safetensors)
[finetuned/landmark_heatmap/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_1.safetensors)
[finetuned/landmark_heatmap/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c_2.safetensors)
[finetuned/landmark_heatmap/lax_2c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_2c.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | +| Landmark localization by heatmap regression | Landmark | LAX 4C | 1 | [finetuned/landmark_heatmap/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_0.safetensors)
[finetuned/landmark_heatmap/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_1.safetensors)
[finetuned/landmark_heatmap/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c_2.safetensors)
[finetuned/landmark_heatmap/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_heatmap/lax_4c.yaml) | [landmark_heatmap.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_heatmap.py) | +| Landmark localization by coordinates regression | Landmark | LAX 2C | 1 | [finetuned/landmark_coordinate/lax_2c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_0.safetensors)
[finetuned/landmark_coordinate/lax_2c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_1.safetensors)
[finetuned/landmark_coordinate/lax_2c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c_2.safetensors)
[finetuned/landmark_coordinate/lax_2c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_2c.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | +| Landmark localization by coordinates regression | Landmark | LAX 4C | 1 | [finetuned/landmark_coordinate/lax_4c_0.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_0.safetensors)
[finetuned/landmark_coordinate/lax_4c_1.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_1.safetensors)
[finetuned/landmark_coordinate/lax_4c_2.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c_2.safetensors)
[finetuned/landmark_coordinate/lax_4c.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/finetuned/landmark_coordinate/lax_4c.yaml) | [landmark_coordinate.py](https://github.com/mathpluscode/CineMA/blob/main/examples/inference/landmark_coordinate.py) | + +## Pre-trained CineMA Model + +The pre-trained CineMA model backbone is available at +[pretrained/cinema.safetensors](https://huggingface.co/mathpluscode/CineMA/blob/main/pretrained/cinema.safetensors) with +configuration [pretrained/cinema.yaml](https://huggingface.co/mathpluscode/CineMA/blob/main/pretrained/cinema.yaml). + +Following scripts demonstrated how to fine-tune this backbone using +[a preprocessed version of ACDC dataset](https://huggingface.co/datasets/mathpluscode/ACDC): + +- [Ventricle and myocardium segmentation](https://github.com/mathpluscode/CineMA/blob/main/examples/train/segmentation.py) +- [Cardiovascular disease classification](https://github.com/mathpluscode/CineMA/blob/main/examples/train/classification.py) +- [Ejection fraction regression](https://github.com/mathpluscode/CineMA/blob/main/examples/train/regression.py) + +## Citation + +## Contact + +For questions or collaborations, please contact Yunguan Fu (yunguan.fu.18@ucl.ac.uk). diff --git a/finetuned/classification_cvd/acdc_sax.yaml b/finetuned/classification_cvd/acdc_sax.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f8226fed5b32992860f35dc8cd268e812d555257 --- /dev/null +++ b/finetuned/classification_cvd/acdc_sax.yaml @@ -0,0 +1,21 @@ +grad_ckpt: True +data: + sax: + spacing: [1.0, 1.0, 10.0] + patch_size: [192, 192, 16] + in_chans: 1 + class_column: "pathology" + pathology: ["DCM", "HCM", "MINF", "NOR", "RV"] +model: + name: convvit + views: sax + n_frames: 2 + out_chans: null + convvit: + size: base + enc_patch_size: [4, 4, 1] + enc_scale_factor: [2, 2, 1] + enc_conv_chans: [64, 128] + enc_conv_n_blocks: 2 + dropout: 0.1 + drop_path: 0.1 diff --git a/finetuned/classification_cvd/acdc_sax_0.safetensors b/finetuned/classification_cvd/acdc_sax_0.safetensors new file mode 100644 index 0000000000000000000000000000000000000000..a525061e34376aabc1e0d12199e98fcc8a79eea3 --- /dev/null +++ b/finetuned/classification_cvd/acdc_sax_0.safetensors @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:96fe4d1d53d62db0b4aa05ed7c67ff0de8c866d6969f07e14019ecfd3aaa3ce8 +size 358021664 diff --git a/finetuned/classification_cvd/acdc_sax_1.safetensors b/finetuned/classification_cvd/acdc_sax_1.safetensors new file mode 100644 index 0000000000000000000000000000000000000000..3ade9789885593ebb8f012bba822487413d58fe3 --- /dev/null +++ b/finetuned/classification_cvd/acdc_sax_1.safetensors @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2bf42e0792ee184a8b984c88783bdf64155def9d3329ce904f933f636dd2a400 +size 358021664 diff --git 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