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Poisson Generalized Additive Model (PGAM)

A PGAM for the efficient estimation of neural tuning functions. Responses are represented in terms of B-splines regularized by a smoothing enforcing penalization. B-spline coefficients and regularization hyperparameters are jointly learned from the data by numerical optimization of a cross-validation score. The model infers marginal confidence bounds for the contribution of each feature to the neural response and uses such bounds to identify the minimal subset of features each neuron responds to. This implies that the model selects a subset of variables based on statistical testing, as opposed to time costly forward-backward selection, that may be unfeasible when the number of regressors is large. See [1] for a more technical details as well as benchmarking vs traditional regularized GLMs.

PGAM-GLM-compare

The repository includes two tutorials. The first (PGAM_tutorial) is intended to familiarize users with B-splines and the regularization used in the code. It is meant to showcase how the model/code works, conceptually. The second tutorial (Standardized_PGAM_Fit_with_examples) is more practical, meant to show how to work the code. It details standard inputs and outputs from the model, and how to run it.

Table of Contents

Setup

The package was implemented on macOS (Monterey version 12.5.1) and tested on Linux (RHEL version 8.4) and Windows 10. It requires python (>=3.6), and R (>= 3.6).

Below we provide two recommended ways of setting up the package:

  1. Download and run a Docker image.
  2. Install all software requirements and create a dedicated conda environment

Docker image

Downloading a Docker image and running it in a Docker container is very simple and makes the setup of the package trivial. However, working with docker containers requires some familiarity with the concept of docker container itself and the docker syntax (starting, stopping, and removing containers, mounting volumes, etc.); I would recommend checking out one of the many tutorials available online before starting to work with docker, for example https://www.youtube.com/watch?v=3c-iBn73dDE&t=2755s.

Download and run the PGAM Docker image

Download and install Docker.

Start Docker.

Download the PGAM Docker image with the terminal/command prompt command

docker pull  edoardobalzani87/pgam:1.0

You can check the list of all the downloaded images with the command,

docker images

You can run the image in a Docker container and inspect the contents with the command,

docker run -ti  edoardobalzani87/pgam:1.0 /bin/bash

The command will run a Linux bash shell that allows you to inspect the image content. python, R, and all the required packages are already installed and the environment variables are set up. Type exit, to exit the bash shell and stop the container.

The run command creates a new container each time, however, if you haven't removed an old container, it can be restarted with the command docker start CONTAINER-ID. Inspect the inactive containers with docker ps -a. You can stop a container with docker stop CONTAINER-ID

You can delete a stopped container with the command docker rm CONTAINER-ID . The container ID can be found with the command docker ps -a, which will list all available containers, their IDs, the image that they run, and the command that they execute.

Working with jupyter

To run the PGAM image in a container and launch jupyter notebook use the following command,

	docker run   -v your-notebook-folder:/notebooks -ti -p 8888:8888 edoardobalzani87/pgam:1.0

The -v option mounts the folder your-notebook-folder on your computer as a volume in the Docker container virtual file system linking it to the virtual folder /notebook .

Files saved by the container in the /notebook virtual folder will be automatically copied in your-notebook-folder, and files already present in your-notebook-folder will be automatically copied in /notebook when the container is started.

Files that the container saves in other directories of the virtual file system will be lost once the container is stopped or removed (the container as a temporary file system).

The -p local-port:container-port option connects port 8888 of the container with that of the host operating system, allowing the container and the operating system to interact.

Open a browser, and browse to

localhost:8888/

to connect to jupyter. You can test the library by working with the "PGAM Tutorial.ipynb" (see section below) or you can create your own notebook. Files will be stored in the your-notebook-folder.

Running a script

If you want to run yourscript.py enter the code,

docker run -v your-script-folder/:/scripts -ti -p 8888:8888 edoardobalzani87/pgam:1.0 /bin/bash -c "python scripts/yourscript.py"

The -v option mounts your-script-folder as a volume in the container, and links it to the virtual folder /scripts, while the -c option executes a shell command, in this case, python yourscript.py.

Note that eventual the inputs loaded by yourscript.py needs to be saved in your-script-folder to be available within the container. Similarly, all the outputs that yourscript.py saves, must be saved in the virtual folder scripts/ to be copied in the host file system.

Conda environment

Instruction on how to set up a conda environment with the specified packages are provided below.

  1. Download and install R and Anaconda . Make sure that the path to R is in the system PATH environment variable after the installation, add it otherwise.

  2. Open the terminal/command prompt and create a conda environment with

    conda create -n pgam python=3.9

  3. Activate the environment and install the required python packages

    conda activate pgam
conda install jupyter
conda install numpy pandas dill scikit-learn matplotlib -y
conda install seaborn pyyaml h5py numba -y
pip install rpy2 opt_einsum statsmodels

  4. Install the R package survey. The recommended option is to install the package directly through rpy2 with the following steps:

    1. Run python, import r utils and install the package survey 
    python
from rpy2.robjects.packages import importr
utils = importr('utils')
utils.chooseCRANmirror(ind=1) # any CRAN mirror id
utils.install_packages('survey')
exit()

Test the installation by cd to the src/PGAM directory and run,

	python
	from GAM_library import *
	exit()

Inspect and edit the PATH environment variable

On windows:

Inspect the PATH variable by entering the command prompt,

	echo %PATH:;=&echo.%

The R home folder should be listed (usually C:\R\R-version\).

If not, edit the PATH variable (Windows 10):

  1. open the "Control Panel"

  2. search for "environment"

  3. click on "Edit the system environment variables"->"Edit variables..."

  4. scroll on "System variables" and click on "Path"

  5. click on "Edit..." -> "New", type the path to the R home folder and click "Ok".

  6. close the pop-up by clicking on "Ok"

  7. click "Apply" and then "Ok".

  8. restart the command prompt.



On mac OS X and Linux,

Inspect the PATH variable by entering in the terminal,

	echo $PATH | tr : '\n'

If the R home folder is not listed,

On mac OS X:

  1. Open the .bash_profile file in your home directory (for example, /Users/your-user-name/.bash_profile) in a text editor.

  2. Add
    export PATH="your-dir:$PATH"
    to the last line of the file, where your-dir is the R home directory.

  3. Save the .bash_profile file.

  4. Restart your terminal.

On Linux:

  1. Open the .bashrc file in your home directory (for example, /home/your-user-name/.bashrc) in a text editor.

  2. Add
    export PATH="your-dir:$PATH"
    to the last line of the file, where your-dir is the R home directory.

  3. Save the .bashrc file.

  4. Restart your terminal.

Tutorials and Usage

With the PGAM library, we provide two notebooks:

  1. PGAM_Tutorial.ipynb
  2. Standardized_PGAM_Fit_with_examples.ipynb

The first notebook aims to introduce the user to some concepts of GAM theory and showcase how the PGAM library implements those concepts with the aim of estimating tuning functions from spike count vectors. The main functionality of the library will be detailed as well as the parameters and inputs that the PGAM needs to set up the model and learn the model parameters.

With the second notebook we provide a standardized pipeline for fitting experimental data. We aim for it to be general, to require few programming skills, and to be easily parellelizable on High Performance Computing (HPC). We will detail how the user can run the pipeline through Docker (for local usage) and singularity (for HPC usage). The singularity image can be downloaded here.

References

[1] Balzani, Edoardo , et al., "Efficient estimation of neural tuning during naturalistic behavior." Advances in Neural Information Processing Systems 33 (2020): 12604-12614.