HSSM 0.1.0

HSSM - Hierarchical Sequential Sampling Modeling

Overview

HSSM is a Python toolbox that provides a seamless combination of state-of-the-art likelihood approximation methods with the wider ecosystem of probabilistic programming languages. It facilitates flexible hierarchical model building and inference via modern MCMC samplers. HSSM is user-friendly and provides the ability to rigorously estimate the impact of neural and other trial-by-trial covariates through parameter-wise mixed-effects models for a large variety of cognitive process models.

• Allows approximate hierarchical Bayesian inference via various likelihood approximators.
• Estimate impact of neural and other trial-by-trial covariates via native hierarchical mixed-regression support.
• Extensible for users to add novel models with corresponding likelihoods.
• Built on PyMC with support from the Python Bayesian ecosystem at large.
• Incorporates Bambi's intuitive lmer-like regression parameter specification for within- and between-subject effects.
• Native ArviZ support for plotting and other convenience functions to aid the Bayesian workflow.
• Utilizes the ONNX format for translation of differentiable likelihood approximators across backends.

Installation

hssm is available through PyPI. You can install it with Pip via:

pip install hssm

You can also install the bleeding edge version of hssm directly from this repo:

pip install git+https://github.com/lnccbrown/hssm.git

Example

Here is a simple example of how to use HSSM:

import hssm
from hssm import load_data

# Load a package-supplied dataset
cav_data = load_data('cavanagh_theta')

# Define a basic hierarchical model with trial-level covariates
model = hssm.HSSM(
    model="ddm",
    data=cav_data,
    include=[
        {
            "name": "v",
            "prior": {
                "Intercept": {"name": "Uniform", "lower": -3.0, "upper": 3.0},
                "theta": {"name": "Uniform", "lower": -1.0, "upper": 1.0},
            },
            "formula": "v ~ (1|subj_idx) + theta",
            "link": "identity",
        },
    ],
)

# Sample from the posterior for this model
model.sample()

Example

HSSM is licensed under Copyright 2023, Brown University, Providence, RI

Support

For questions, bug reports, or other unexpected issues, please open an issue on the GitHub repository.

Contribution

If you want to contribute to this project, please familiarize yourself with our contribution guidelines.

Acknowledgements

We would like to extend our gratitude to the following individuals for their valuable contributions to the development of the HSSM package:

• Bambi - A special thanks to the Bambi project for providing inspiration, guidance, and support throughout the development process. Tomás Capretto, a key contributor to Bambi, provided invaluable assistance in the development of the HSSM package.

Those contributions have greatly enhanced the functionality and quality of the HSSM.