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GaitForeMer: Self-Supervised Pre-Training of Transformers via Human Motion Forecasting for Few-Shot Gait Impairment Severity Estimation

GaitForeMer (Gait Forecasting and impairment estimation transforMer) predicts MDS-UPDRS gait impairment severity scores using learned motion features from the pre-training task of human motion forecasting. This work will be presented in MICCAI 2022 later this year!

Requirements

• Pytorch>=1.7.
• Numpy.
• Tensorboard for pytorch.

Pretext Task

The pre-trained weights are available for download here.

If you would like, you can perform your own pre-training. In order to run your own pre-training, you will have to download the NTURGB+D dataset. Place nturgbd_skeletons_s001_to_s017.zip into the data/nturgb+d_data directory and unzip the file. You will then have to process the data by running python data/NTURGDDataset.py. This will create all the needed files for pre-training the model. Once these steps have been completed, use the following script to do your own pre-training.

python training/transformer_model_fn.py \
  --task=pretext \
  --model_prefix=nturgb+d_out \
  --batch_size=16 \
  --data_path=data/nturgb+d_data \
  --learning_rate=0.0001 \
  --max_epochs=200 \
  --steps_per_epoch=200 \
  --loss_fn=l1 \
  --model_dim=128 \
  --num_encoder_layers=4 \
  --num_decoder_layers=4 \
  --num_heads=4 \
  --dim_ffn=2048 \
  --dropout=0.3 \
  --lr_step_size=400 \
  --learning_rate_fn=step \
  --warmup_epochs=100 \
  --pose_format=None \
  --pose_embedding_type=gcn_enc \
  --dataset=ntu_rgbd \
  --pre_normalization \
  --pad_decoder_inputs \
  --non_autoregressive \
  --pos_enc_alpha=10 \
  --pos_enc_beta=500 \
  --predict_activity \
  --action=all \
  --source_seq_len=40 \
  --target_seq_len=20

Downstream Task

Once you have pre-trained weights, you can run the downstream task of gait impairment severity estimation.

Data

The PD dataset used in the paper is not publically available, but the CASIA Gait Database is available upon request. This repo has the steps for extracting poses and preprocessing the data. We follow this setup in our work.

Training and Evaluating

To train and evaluate GaitForeMer, run this command:

python3 training/transformer_model_fn.py \
  --downstream_strategy=both_then_class \
  --model_prefix=output_models/finetune_both_branches_then_class_branch \
  --batch_size=16 \
  --data_path=<PATH_TO_PD_DATA> \
  --learning_rate=0.0001 \
  --max_epochs=100 \
  --steps_per_epoch=200 \
  --loss_fn=l1 \
  --model_dim=128 \
  --num_encoder_layers=4 \
  --num_decoder_layers=4 \
  --num_heads=4 \
  --dim_ffn=2048 \
  --dropout=0.3 \
  --lr_step_size=400 \
  --learning_rate_fn=step \
  --warmup_epochs=10 \
  --pose_format=None \
  --pose_embedding_type=gcn_enc \
  --dataset=pd_gait \
  --pad_decoder_inputs \
  --non_autoregressive \
  --pos_enc_alpha=10 \
  --pos_enc_beta=500 \
  --predict_activity \
  --action=all \
  --source_seq_len=40 \
  --target_seq_len=20 \
  --finetuning_ckpt=<PATH_TO_PRETRAINED_MODEL_CHECKPOINT e.g. pre-trained_ntu_ckpt_epoch_0099>

You can change the fine-tuning strategy by alterning the downstream_strategy parameter.