CLIMATv2: Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data

This is the implementation of the paper CLIMATv2: https://arxiv.org/abs/2210.13889. Its previous version (CLIMATv1) can be found at https://arxiv.org/abs/2104.03642.

The concept of the framework is as follows

The differences of CLIMATv2 compared to CLIMATv1 are:

• General practitioner (GP) is allowed to utilize multimodalities to perform diagnosis prediction (i.e, y_0)
• The diagnosis predictions of Radiologist and GP is enforced to be consistent
• Cross-entropy loss is replaced by CLUB (Calibrated Loss based on Upper Bound), which takes into account both performance and calibration during optimization.

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Setup

Run commands:

git clone [email protected]:Oulu-IMEDS/CLIMATv2.git
cd ./CLIMATv2
conda create -n CLIMATv2 python=3.7
conda activate CLIMATv2
pip install -e .

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[ADNI] Alzheimer's Disease Status Prognosis Prediction

Input

Data preparation

You can use the ADNI metadata prepared in ./adni/Metadata/adni_fdgpet_prognosis.csv, or regenerated them using

# Modify input and output paths, then run
python ./common/adni/preprocess_adni.py
# Standard voxels if needed
python ./common/adni/standardize_voxels.py

Training

Command line:

# General setting using default values in configuration files in ./adni/configs/config_train.yaml
python train.py config=seq_multi_prog_climatv2

# Detailed setting
python train.py config=seq_multi_prog_climatv2 comment=mycomment \
    bs=${BATCH_SIZE} num_workers=${NUM_WORKERS} root.path=/path/to/ANDI meta_root=/path/to/meta_dir/ fold_index=1 \
    backbone_name=shufflenetv2 max_depth=4 num_cls_num=4 prognosis_coef=1 cons_coef=0.5 \ 
    loss_name=CLUB club.s=0.5

config can be

• seq_multi_prog_climatv1: CLIMATv1
• seq_multi_prog_climatv2: CLIMATv2

Processing:

• bs: batch size
• num_workers: the number of workers

Data setup:

• root.path: root directory of images
• meta_root: root directory of metadata (.csv or saved split configuration in .pkl)
• fold_index: fold index (starting from 1)

Model:

• backbone_name: backbone for imaging feature extraction
• max_depth: the number of CNN blocks in imaging feature extraction module
• n_meta_features: the length of metadata features
• num_cls_num: the number of [CLS] embebddings in transformer P

Coefficients in loss

• prognosis_coef: coefficient for prognosis prediction
• cons_coef: coefficient for consistency term

loss_name is either

• CLUB: Calibrated loss based on upper bound (ours). club.s: epsilon hyperparameter in CLUB.
• CE: cross-entropy loss
• FL: focal loss
• FLA: adaptive focal loss
• MTL: multi-task loss

Hyperparameters used in the paper:

Evaluation

python eval.py root.path=/path/to/imgs_dir/ meta_root=/path/to/metadata_dir/ \
    eval.root=/path/to/trained_models_dir/ eval.patterns=${PATTERN} eval.output=/path/to/output.json \
    use_only_baseline=True seed=${SEED} \
    save_predictions=${SAVE_PREDICTIONS} save_attn=${SAVE_ATTENTION_MAPS}

Input data for evaluation:

• root.path: root directory of images
• meta_root: root directory of metadata (.csv or saved split configuration in .pkl)
• eval.root: root directory containing sub-directories of trained settings
• eval.patterns: a common pattern of saved model files (e.g., pn_avg_ba for average balanced accuracies, or pn_avg_mauc for average mAUCs)
• eval.output: path to file storing evaluation results
• use_only_baseline: whether to use data at the baseline as input (always True)
• save_predictions: whether to save predictions for visualization
• save_attn: whether to save attention maps for visualization

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[OAI] Knee Osteoarthritis Structural Prognosis Prediction

Input

Data preparation

Run commands:

# Generate longitudinal data
python ./common/prepare_1img_seq_metadata.py

# Split data
python ./common/do_split.py

Training

# General setting using default values in configuration files in ./oai/configs/config_train.yaml
python train.py config=seq_multi_prog_climatv2

# Detailed setting
python train.py config=seq_multi_prog_climatv2 \
    bs=64 num_workers=8 root.path=/path/to/OAI/ meta_root=/path/to/meta_dir backbone_name=resnet18 site=C \ 
    prognosis_coef=1.0 cons_coef=0.5 loss_name=CLUB n_meta_features=128 \ 
    num_cls_num=8 club.s=0.5 grading=KL \
    fold_index=1 seed=12345 

Besides the arguments used for ADNI, we have the additional arguments for OAI:

Data:

• site: test acquisition site (C, with the most data, is chosen for testing, meaning that sites A, B, D, E are used for training and validation.)

grading can be:

• KL: Kellgren and Lawrence
• JSL: Lateral joint space
• JSM: Medial joint space
• OSFL: Lateral osteophyte in femur
• OSFM: Medial osteophyte in femur
• OSTL: Lateral osteophyte in tibia
• OSTM: Medial osteophyte in tibia

List of augmentations applied to knee images (Note: all right knee images are vertically flipped):

Evaluation

Same as above.

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Reference

If you find the manuscript or codes useful, please cite as follows

@article{nguyen2022clinically,
  title={Clinically-Inspired Multi-Agent Transformers for Disease Trajectory Forecasting from Multimodal Data},
  author={Nguyen, Huy Hoang and Blaschko, Matthew B and Saarakkala, Simo and Tiulpin, Aleksei},
  journal={arXiv preprint arXiv:2210.13889},
  year={2022}
}