zabir-nabil / fibro-cosanet

Idiopathic pulmonary fibrosis (IPF) is a restrictive interstitial lung disease that causes lung function decline by lung tissue scarring. Although lung function decline is assessed by the forced vital capacity (FVC), determining the accurate progression of IPF remains a challenge. To address this challenge, we proposed Fibro-CoSANet, a novel end-to-end multi-modal learning-based approach, to predict the FVC decline. Fibro-CoSANet utilized CT images and demographic information in convolutional neural network frameworks with a stacked attention layer. Extensive experiments on the OSIC Pulmonary Fibrosis Progression Dataset demonstrated the superiority of our proposed Fibro-CoSANet by achieving the new state-of-the-art modified Laplace Log-Likelihood score of -6.68. This network may benefit research areas concerned with designing networks to improve the prognostic accuracy of IPF.

Fibro-CoSANet: Pulmonary Fibrosis Prognosis Prediction using a Convolutional Self Attention Network

Installation

1. git clone https://github.com/zabir-nabil/osic-pulmonary-fibrosis-progression.git
2. cd osic-pulmonary-fibrosis-progression
3. Install Anaconda Anaconda
4. conda create -n pulmo python==3.7.5
5. conda activate pulmo
6. conda install -c intel mkl_fft (opt.)
7. conda install -c intel mkl_random (opt.)
8. conda install -c anaconda mkl-service (opt.)
9. pip install -r requirements.txt

Download Dataset

1. Download the kaggle.json from Kaggle account. Kaggle authentication
2. Keep the kaggle.json file inside data_download folder.
3. sudo mkdir /root/.kaggle
4. sudo cp kaggle.json /root/.kaggle/
5. sudo apt install unzip if not installed already

• cd data_download; python dataset_download.py; mv osic-pulmonary-fibrosis-progression.zip ../../; unzip ../../osic-pulmonary-fibrosis-progression.zip -d ../../; cd ../; python train_slopes.py

Training

1. Set the training hyperparameters in config.py
2. Slope Prediction
   • To train slopes model run python train_slopes.py
   • trained model weights and results will be saved inside hyp.results_dir
3. Quantile Regression
   • To train qreg model run python train_qreg.py
   • trained model weights and results will be saved inside hyp.results_dir

• Volume calculation: https://www.kaggle.com/furcifer/q-regression-with-ct-tabular-features-pytorch

Arxiv pre-print

https://arxiv.org/abs/2104.05889

fibro-cosanet's Issues

Why the score function use 'percent' as sigma?

def score_avg(p, a): # patient id, predicted a
percent_true = train.Percent.values[train.Patient == p]
fvc_true = train.FVC.values[train.Patient == p]
weeks_true = train.Weeks.values[train.Patient == p]
fvc = a * (weeks_true - weeks_true[0]) + fvc_true[0]
percent = percent_true[0] - a * abs(weeks_true - weeks_true[0])
return score(fvc_true, fvc, percent)

The last sentence use 'percent' as confidence, i dont understand. Who can teach me?