benchnirs 1.7.1

Benchmarking framework for machine learning with fNIRS

BenchNIRS

Benchmarking framework for machine learning with fNIRS

Quick links
→ Journal article
→ BenchNIRS source code
→ Install BenchNIRS
→ Documentation
→ Examples
→ Issue tracker

Features

• loading of open access datasets
• signal processing and feature extraction on fNIRS data
• training, hyperparameter tuning and evaluation of machine learning models (including deep learning)
• production of training graphs, metrics and other useful figures for evaluation
• benchmarking and comparison of machine learning models
• much more!

Documentation

The documentation of the framework with examples can be found here.

Recommendation checklist

A checklist of recommendations towards best practices for machine learning with fNIRS can be found here. We welcome contributions from the community in order to improve it, please see below for more information on how to contribute.

Setting up BenchNIRS

1. Download and install Python 3.9 or greater, for example with Miniconda.

2. To install the package with pip (cf. PyPI), open a terminal (eg. Anaconda Prompt) and type:

pip install benchnirs

3. Download the datasets (see below).

Alternatively to install from source in development mode, download and unzip the repository (or clone it with Git), and run devinstall.py.

Downloading datasets

• Herff et al. 2014 (n-back task): you can download the dataset by making a request here.
• Shin et al. 2018 (n-back and word generation tasks): you can download the dataset here.
• Shin et al. 2016 (mental arithmetic task): you can download the dataset by filling out the form here. Then click on NIRS_01-29 to download the fNIRS data.
• Bak et al. 2019 (motor execution task): you can download the dataset here.

Keeping BenchNIRS up to date

To update BenchNIRS to the latest version with pip, open a terminal (eg. Anaconda Prompt) and type:

pip install --upgrade benchnirs

Examples

A set of example scripts showing how to use the framework can be found here.

Simple use case

Define a model with PyTorch:

import torch.nn as nn
import torch.nn.functional as F


class MyModel(nn.Module):

    def __init__(self, n_classes):
        super().__init__()
        self.fc1 = nn.Linear(400, 250)
        self.fc2 = nn.Linear(250, 150)
        self.fc3 = nn.Linear(150, 60)
        self.fc4 = nn.Linear(60, n_classes)

    def forward(self, x):
        batch_size = x.size(0)
        x = x.view(batch_size, -1)  # flatten
        x = F.relu(self.fc1(x))
        x = F.relu(self.fc2(x))
        x = F.relu(self.fc3(x))
        x = self.fc4(x)
        return x

Evaluate the model on one of the datasets:

import benchnirs as bn

# Download dataset: https://figshare.com/ndownloader/files/18069143

# Load and process data:
epochs = bn.load_dataset('bak_2019_me', roi_sides=True, path='./bak_2019')
data = bn.process_epochs(epochs['right', 'left', 'foot'])

# Benchmark model:
results = bn.deep_learn(MyModel, *data)
print(results)

Contributing

Contributions to this repository are very welcome under the form of issues (for reporting bugs or requesting new features) and merge requests (for fixing bugs and implementing new features). Please refer to this tutorial for creating merge requests from a fork of the repository.

Contributors

Johann Benerradi • Jeremie Clos • Aleksandra Landowska • Michel F. Valstar • Max L. Wilson • Yujie Yao

Acknowledgements

If you are using BenchNIRS, please cite this article:

@article{benerradi2023benchmarking,
  title={Benchmarking framework for machine learning classification from fNIRS data},
  author={Benerradi, Johann and Clos, Jeremie and Landowska, Aleksandra and Valstar, Michel F and Wilson, Max L},
  journal={Frontiers in Neuroergonomics},
  volume={4},
  year={2023},
  publisher={Frontiers Media},
  url={https://www.frontiersin.org/articles/10.3389/fnrgo.2023.994969},
  doi={10.3389/fnrgo.2023.994969},
  issn={2673-6195}
}

If you are using the datasets of the framework, please also cite those related works:

• Herff et al. 2014
• Shin et al. 2018
• Shin et al. 2016
• Bak et al. 2019