RRRR

Python implementation of Reduced Rank Ridge Regression introduced in the work:

Mukherjee, A., & Zhu, J. (2011). Reduced rank ridge regression and its kernel extensions. Statistical analysis and data mining: the ASA data science journal, 4(6), 612-622.

And used in the paper:

Transfer learning of deep neural network representations for fMRI decoding
Svanera, M., Savardi, M., Benini, S., Signoroni, A., Raz, G., Hendler, T., ... & Valente, G. (2019). Journal of neuroscience methods, 328, 108319.

Description

The code import fMRI data and CNN data, applies a pre-processing, and runs an optimisation process to obtain the best values, for rank (number of hidden components) and reg (regularisation term), to reconstruct fc7 from brain data. The search space for these parameters is defined by the variable:

	space = [Integer(1, 50),
			  Real(1, 1e+12, "log-uniform")]

A log file is saved with any useful information.

Requirements

Not particular requirement are needed, except common python packages (Numpy, Scipy, sklearn, skopt). It works with Python2 and Python3.

Training and testing

To train (and test) the method:

python ./training.py \
		--n_calls=500 \
		--correlation_measure=pearsonr \
		--selected_layer='fc7_R' \
		--n_random_starts=100 \
		--log_name='./results_RRRR/my_log.log' 

Demo

Please look at demo.py to see an example on how to use the code.

Authors

Michele Svanera

Mattia Savardi

Citation

If you find this code useful in your research, please consider citing our paper:

@article {SSB19,
	author = {Svanera, Michele and Savardi, Mattia and Benini, Sergio and Signoroni, Alberto and Raz, Gal and Hendler, Talma and Muckli, Lars and Goebel, Rainer and Valente, Giancarlo},
	title = {Transfer learning of deep neural network representations for fMRI decoding},
	elocation-id = {535377},
	year = {2019},
	doi = {10.1101/535377},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2019/02/04/535377},
	eprint = {https://www.biorxiv.org/content/early/2019/02/04/535377.full.pdf},
	journal = {bioRxiv}
}

And cite the original work:

@article{MZ11,
	title={Reduced rank ridge regression and its kernel extensions},
	author={Mukherjee, Ashin and Zhu, Ji},
	journal={Statistical analysis and data mining: the ASA data science journal},
	volume={4},
	number={6},
	pages={612--622},
	year={2011},
	publisher={Wiley Online Library}
}