otiliastr/brain_task_effect

Official repository for the paper "Modeling Task Effects on Meaning Representation in the Brain via Zero-Shot MEG Prediction"

Modeling Task Effects on Meaning Representation in the Brain via Zero-Shot MEG Prediction

This is the official code repository for

Modeling Task Effects on Meaning Representation in the Brain via Zero-Shot MEG Prediction.
Mariya Toneva*, Otilia Stretcu*, Barnabás Póczos, Leila Wehbe, and Tom Mitchell.
In Proceedings of the Thirty-fourth Conference on Neural Information Processing Systems 2020.

In this work, we study the effect of a task on the representation of meaning in the brain.

We include the implementation of the 4 hypotheses discussed in our paper on how the task and stimulus may combine together to give rise to the recorded neural activity.

For more information about the methods in this repository, please check out our:

• NeurIPS 2020 paper
• slides
• 3 min video
• 13 min video

If using this code, please cite:

@inproceedings{taskeffects2020,
  title={Modeling Task Effects on Meaning Representation in the Brain via Zero-Shot MEG Prediction},
  author={Toneva*, Mariya and Stretcu*, Otilia and Póczos, Barnabás and Wehbe, Leila and Mitchell, Tom M.},
  booktitle={Proceedings of the Thirty-fourth Conference on Neural Information Processing Systems},
  year={2020}
}

Code structure

The code is organized into the following folders:

• data: contains classes and methods for loading and preprocessing data.
• experiments: contains the running script for running experiments for the 20-Questions dataset discussed in our paper.
• methods: contains implementation of various models, and code for training them.
• utils: other utility functions, not specific to this project.

Requirements

Our code was implemented in Python 3.7 with Tensorflow 1.15 using eager execution. It also requires the following Python packages:

• csv
• json
• keras==2.3.1
• matplotlib
• numpy
• pandas
• scipy
• seaborn
• sklearn
• tabulate
• tqdm
• urllib
• yaml

Data

We thank Gustavo Sudre for collecting and sharing the MEG dataset, and Dean Pomerleau for the human-judgment Mechanical Turk dataset! With their permission we provide the Mechanical Turk data. Additionally, we provide the BERT and word2vec representations for the stimuli and questions used in our experiments. Further details below.

Mechanical Turk responses and semantic features The Mechanical Turk responses for all combinations of 1000 words and 218 questions can be found at data/MTurk_semantic_features.npz. We provide further information on the structure of this file and how to load it at data/README.md.

BERT semantic features We provide the BERT representations used in our experiments presented in Appendix D. We provide further information on the structure of these files and how to load them at data/README.md.

Word2vec semantic features We provide the word2vec vector representations for the stimuli used in our experiment. These can be found at data/word2vec_dict.npz. We provide further information on the structure of this file and how to load it at data/README.md.

MEG data Due to the IRB when the data was first collected, the brain data is unfortunately not available to share beyond the Mitchell laboratory. However, the existing code framework can be extended to other datasets by implementing necessary data loading pipelines.

How to run

The entry point of our experiments is at src/experiments/run.py.

To specify the intended hypothesis to test or other data preprocessing or training configurations, make the desired choices in the experiment configuration file at src/experiments/config.py.

To execute the code, from the main folder, run:

python3.7 -m src.experiments.run

When running the RidgeWithLearnedAttention model corresponding to hypothesis 4.2 in our paper, we recommend running using a GPU. With CUDA, this can be done using the command:

CUDA_VISIBLE_DEVICES=your-gpu-number python3.7 -m src.experiments.run