Vighnesh Subramaniam, Colin Conwell, Christopher Wang, Gabriel Kreiman, Boris Katz, Ignacio Cases, Andrei Barbu
This is the main code base of the paper "Revealing Vision-Language Integration of the Brain Using Multimodal Networks", accepted in ICML 2024.
- pytorch >= 1.12.1
pip install -r requirements.txt
- Install the SLIP Models by cloning the repo to the
vil_embedsdirectory.
The data is based on the Brain Treebank. In order to streamline this process, we zip the data with all the necessary preprocessing. This is available here(This is coming soon!).
The directory should be named data-by-subject. In this directory, there are several subdirectories named according to a subject ID. Each directory contains a parquet file which contains the averaged neural response from each electrode across 161 time bins. We also include the stimuli in CSVs. The language-aligned CSV contains the words and paths to the corresponding frame. The vision-aligned CSVs contains paths to the scenes and the closest sentence.
To run a regression, select a subject, model, dataset alignment and layer. You can use the subdirectories to choose a subject. The dataset alignment can either be language-aligned or vision-aligned. More details on these design choices are in the paper.
To find an available model, check out model_layer_dict.py. This has a dictionary with all models and the corresponding layers. If you just want the best performing layer (usually the final layer), choose the the layer subset with best in the string. If you want to give a list of layers, add the layer names to the python file, run python model_layer_dict.py to get the model layer dictionary, and run the regression with this sublist. If you want to use a randomly initialized model, use the -r flag.
First run
python model_layer_dict.py
Then, run the following:
python run_regression -s [SUBJECT] -t trial000 -a [ALIGNMENT] -w 200 -mn [MODEL_NAME] -mo [MODEL_EXTRACTION_OUTPUT] [-r]
The results are saved to a parquet file which can be opened in pandas.
To run a boostrapping analysis, you can run
python bootstrap_test.py -s [SUBJECT] -t trial000 -a [ALIGNMENT] -w 200 -mn [MODEL_NAME] -mo [MODEL_EXTRACTION_OUTPUT] [-r]
If you want to run the analysis correctly, you should save your bootstrap indices so that the same resampled inputs are used across subjects and models. The bootstrap_test.py file does use using the resample_indices_caller function. Uncomment that line and re-run the analysis on your own data.
We include the a python notebook, comparison_analysis.ipynb, to walk through our methodology to compare network scores against each other per electrode. We will also include a raw results from our analysis to give the final output structure needed to perform the analysis if you want to do so on your own data.