Package: lungs
3D Neural Network for Lung Cancer Risk Prediction on CT VolumesOverviewThis repository contains my implementation of the "full-volume" model from the paper:End-to-end lung cancer screening with three-dimensional deep learning on low-dose chest computed tomography.Ardila, D., Kiraly, A.P., Bharadwaj, S. et al. Nat Med 25, 954–961 (2019).The model uses a three-dimensional (3D) CNN to perform end-to-end analysis of whole-CT volumes, using LDCT
volumes with pathology-confirmed cancer as training data.
The CNN architecture is an Inflated 3D ConvNet (I3D) (Carreira and
Zisserman).DataWe use the NLST dataset which contains chest LDCT volumes with pathology-confirmed cancer evaluations. For description and access to the dataset refer to theNCI website.SetuppipinstalllungsRunning the codeInferenceimportlungslungs.predict('path/to/data')From command line (with preprocessed data):pythonmain.py--preprocessed--inputpath/to/preprocessed/dataTrainingThe inputs to the training procedure are training and validation.listfiles containing coupled data - a volume path and its label in each row.
These.listfiles need to be generated beforehand usingpreprocess.py, as described in the next section.importlungs# train with default hyperparameterslungs.train(train='path/to/train.list',val='path/to/val.list')Themain.pymodule contains training (fine-tuning) and inference procedures.
The inputs are preprocessed CT volumes, as produced bypreprocess.py.
For usage example, refer to the arguments' description and default values in the bottom ofmain.py.Data PreprocessingPreprocess volumesEach CT volume in NLST is adirectoryof DICOM files (each.dcmfile is one slice of the CT).
Thepreprocess.pymodule accepts a directorypath/to/datacontainingmultiplesuch directories (volumes).
It performs several preprocessing steps, and writes each preprocessed volume as an.npzfile inpath/to/data_preprocssed.
These steps are based onthistutorial, and include:Resampling to a 1.5mm voxel size (slow)Coarse lung segmentation – used to compute lung center for alignment and reduction of problem spaceTo save storage space, the following preprocessing steps are performed online (during training/inference):Windowing – clip pixel values to focus on lung volumeRGB normalizationExample usage:fromlungsimportpreprocess# Step 1: Preprocess all volumes, will save them to '/path/to/dataset_preprocessed'preprocess.preprocess_all('/path/to/dataset')Create train/val.listfilesOnce the preprocessed data is ready, the next step is to split it randomly into train/val sets,
and save each set as a.listfile of paths/labels, required for the training procedure.Example usage:fromlungsimportpreprocess# Step 2: Split preprocessed data into train/val coupled `.list` filespreprocess.split(positives='/path/to/dataset_preprocessed/positives',negatives='/path/to/dataset_preprocessed/negatives',lists_dir='/path/to/write/lists',split_ratio=0.7)Provided checkpointBy default, if theckptargument is not given, the model is initialized using our best fine-tuned checkpoint.
Due to limited storage and compute time, our checkpoint was trained on a small subset of NLST containing 1,045 volumes (34% positive).Note that in order to obtain a general purpose prediction model, one would have to train on the full NLST dataset. Steps include:Gainng access to theNLST datasetDownloading ~6TB of positive and negative volumes (requires storage and a few days for downloading)Preprocessing (see Data Preprocessing section above)Training (requires a capable GPU)Even though we used a samll subset of NLST, we still achieved a state-of-the-art AUC score of 0.892 on a validation set of 448 volumes.
This is comparable to the original paper's AUC for the full-volume model (see the paper's supplemtary material), trained on 47,974 volumes (1.34% positive).To train this model we first initialized by bootstrapping the filters from theImageNet pre-trained 2D Inception-v1 modelinto 3D, as described in the I3D paper.
It was then fine-tuned on the preprocessed CT volumes to predict cancer within 1 year (binary classification). Each of these volumes was a large region cropped around the center of the bounding box, as determined by lung segmentation in the preprocessing step.For the training setup, we set the dropout keep_prob to 0.7, and trained in mini-batches of size of 2 (due to limited GPU memory). We usedtf.train.AdamOptimizerwith a small learning rate of 5e-5, (due to the small batch size) and stopped the training before overfitting started around epoch 37.
The focal loss function from the paper is provided in the code, but we did not experience improved results using it, compared to cross-entropy loss which was used instead. The likely reason is that our dataset was more balanced than the original paper's.The follwoing plots show loss, AUC, and accuracy progression during training, along with ROC curves for selected epochs:AcknowledgmentsThe author thanks the National Cancer Institute for access to NCI's data collected by the National Screening Trial (NLST).
The statements contained herein are solely those of the author and do not represent or imply concurrence or endorsement by NCI.