Skip to content

Commit

Permalink
Update README.rst
Browse files Browse the repository at this point in the history
  • Loading branch information
Dong555 authored Nov 6, 2023
1 parent b18dc6d commit fbdb625
Showing 1 changed file with 5 additions and 5 deletions.
10 changes: 5 additions & 5 deletions README.rst
Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,8 @@ SuSiE-PCA
SuSiE PCA is the abbreviation for the Sum of Single Effects model [1]_ for principal component analysis. We develop SuSiE PCA
for an efficient variable selection in PCA when dealing with high dimensional data with sparsity, and for quantifying
uncertainty of contributing features for each latent component through posterior inclusion probabilities (PIPs). We
implement the model with the `JAX <https://github.com/google/jax>`_ library developed by Google which enable the fast
training on CPU, GPU or TPU.
implement the model with the `JAX <https://github.com/google/jax>`_ library developed by Google which enables fast
training on CPU, GPU, or TPU. The paper has been published in iScience: https://www.sciencedirect.com/science/article/pii/S2589004223022587

|Documentation|_ | |Installation|_ | |Example|_ | |Notes|_ | |References|_ | |Support|_

Expand All @@ -66,9 +66,9 @@ $$w_{kl} \\sim \\mathcal{N}(0,\\sigma^2_{0kl})$$
$$\\gamma_{kl} | \\pi \\sim \\text{Multi}(1,\\pi) $$

Notice that each row vector $\\mathbf{w}_k$ is a sum of single effect vector $\\mathbf{w}_{kl}$, which is length $P$ vector
contains only one non-zero effect $w_{kl}$ and zero elsewhere. And the coordinate of the non-zero effect is determined by
contains only one non-zero effect $w_{kl}$ and zero elsewhere. The coordinate of the non-zero effect is determined by
$\\gamma_{kl}$ that follows a multinomial distribution with parameter $\\pi$. By construction, each factor inferred from the
SuSiE PCA will have at most $L$ number of associated features from the original data. Moreover, we can quantify the probability
SuSiE PCA will have at most $L$ associated features from the original data. Moreover, we can quantify the probability
of the strength of association through the posterior inclusion probabilities (PIPs). Suppose the posterior distribution of
$\\gamma_{kl} \\sim \\text{Multi}(1,\\mathbf{\\alpha}_{kl})$, then the probability the feature $i$ contributing to the factor
$\\mathbf{w}_k$ is given by:
Expand All @@ -82,7 +82,7 @@ Install SuSiE PCA
=================
The source code for SuSiE PCA is written fully in Python 3.8 with JAX (see
`JAX installation guide <https://github.com/google/jax#installation>`_ for JAX). Follow the code provided below to quickly
get started using SuSiE PCA. Users can clone this github repository and install the SuSiE PCA. (Pypi installation will
get started using SuSiE PCA. Users can clone this GitHub repository and install the SuSiE PCA. (Pypi installation will
be supported soon).

.. code:: bash
Expand Down

0 comments on commit fbdb625

Please sign in to comment.