0. If you just want the Mean MLP model source code

Go to src/models/mlp.py. MeanMLP and default_HPs is what you need.

1. Requirements

conda create -n mlp_nn python=3.9
conda activate mlp_nn
conda install pytorch torchvision torchaudio pytorch-cuda=11.3 -c pytorch -c nvidia
pip install -r requirements.txt

Optional

• prefix: custom prefix for the project
  • default prefix is UTC time
  • appears in the name of logs directory and the name of WandB project
  • exp mode runs with custom prefix will use HPs from tune mode runs with the same prefix
    • unless model.default_HP is set to True
• permute: whether TS models should be trained on time-reshuffled data
  • set to permute=Multiple to permute
• HP_path: path to custom hyperparams to load
• follow_splits: path to an experiment which splist you want to replicate

scripts/run_experiments.py options:

Required:

• mode:

  • tune - tune mode: run multiple experiments with different hyperparams
  • exp - experiment mode: run experiments with the best hyperparams found in the tune mode, or with default hyperparams default_HPs is set to True

• model: model for the experiment. Models' config files can be found at src/conf/model, and their sourse code is located at src/models

  • mlp - our hero, TS model

  • lstm - classic LSTM model for classification, TS model (not used in the paper)

  • mean_lstm - lstm with LSTM output embeddings averaging, TS model

  • pe_transformer - BERT-inspired model, uses transformer endocder, TS model (not used in the paper)

  • mean_pe_transformer - pe_transformer with encoder output averaging, TS model

  • dice - TS model, https://www.sciencedirect.com/science/article/pii/S1053811922008588?via%3Dihub

  • milc - TS model, https://arxiv.org/abs/2007.16041

  • bnt - FNC model, https://arxiv.org/abs/2210.06681

  • fbnetgen - TS+FNC model, https://arxiv.org/abs/2205.12465

  • brainnetcnn - FNC model, https://www.sciencedirect.com/science/article/pii/S1053811916305237

  • lr - Logistic Regression, FNC model

• dataset: dataset for the experiments. Datasets' config files can be found at src/conf/dataset, and their loading scripts are located at src/datasets.

  • fbirn - ICA FBIRN dataset

  • fbirn_sex - ICA FBIRN dataset wtih sex labels

  • cobre - ICA COBRE dataset

  • bsnip - ICA BSNIP dataset

  • abide - ICA ABIDE dataset (not used in the paper)

  • abide_869 - ICA ABIDE extended dataset

  • oasis - ICA OASIS dataset

  • adni - ICA ADNI dataset

  • hcp - ICA HCP dataset

  • ukb - ICA UKB dataset with sex labels

  • ukb_age_bins - ICA UKB dataset with sex X age bins labels

  • fbirn_roi - Schaefer 200 ROIs FBIRN dataset

  • abide_roi - Schaefer 200 ROIs ABIDE dataset

  • hcp_roi_752 - Schaefer 200 ROIs HCP dataset

  • hcp_non_mni_2 - Deskian/Killiany ROIs HCP dataset in ORIG space

  • hcp_mni_3 - Deskian/Killiany ROIs HCP dataset in MNI space

  • hcp_schaefer - Noisy Schaefer 200 ROIs HCP dataset

  • hcp_time - ICA HCP dataset with normal/inversed time direcion