# Introduction

We consider the setup of Lippert et al. (2011), where:

- $y\in\mathbb{R}^n$ is a response vector with values for $n$ samples,
- $X\in\mathbb{R}^{n\times d}$ is a matrix with data of $d$ covariates (fixed effects) in the same $n$ samples,
- $K\in\mathbb{R}^{n\times n}$ is a positive semi-definite sample similarity matrix, scaled such that $\mathrm{tr}(K)=n$,
- $\mu$ is an (unknown) overall mean parameter,
- $\beta\in\mathbb{R}^d$ is the (unknown) vector of fixed effect weights,
- $\sigma^2$ is the (unknown) variance explained by $K$,
- $\sigma_e^2$ is the (unknown) residual error variance,
- $\delta = \frac{\sigma_e^2}{\sigma^2}$ is the variance ratio,

and $y$ is distributed as

\[y \sim N\bigl(\mu + X\beta, \sigma^2 K + \sigma_e^2 I\bigr) = N\bigl( \mu + X\beta, \sigma^2 (K + \delta I)\bigr)\]

where $N$ denotes a multivariate normal distribution.

By adding a column of ones to $X$ we can absorb the parameter $\mu$ in the vector of fixed effect weights $\beta$. High-level functions in this package all accept a parameter `mean=true`

which will call this operation:

`FaSTLMMlight.create_covariate_matrix`

— Function`create_covariate_matrix(X; mean = true, n = 1)`

Create the covariate matrix from the provided covariates with an intercept column if `mean=true`

.

Low-level functions all work with the model where $\mu$ is not explicitly modelled and the unknown parameters are $(\beta,\sigma^2,\delta)$. If `mean=true`

then in the output the overall estimated mean corresponds to the first element $\beta[1]$.

The parameters $(\beta,\sigma^2,\delta)$ are estimated by maximum-likelihood (or restricted maximum-likelihood, see below), that is, by minimizing the negative log-likelihood function

\[\mathcal{L} = \log\det\bigl[ \sigma^2 (K + \delta I) \bigr] + \frac1{\sigma^2} \bigl\langle y-X\beta, (K + \delta I)^{-1} (y-X\beta)\bigr\rangle,\]

where $\langle u,v\rangle=u^Tv=\sum_{i=1}^n u_i v_i$ is the usual inner product on $\mathbb{R}^n$; note that for any matrix $A\in\mathbb{R}^{n\times n}$ and vectors $u,v \in \mathbb{R]^n$, $\langle u,Av\rangle=\mathrm{tr}(vu^TA)$.

Analytic expressions for the maximum-likelihood estimates $\hat{\beta}$ and $\hat{\sigma}^2$ as a function of $\delta$ are easy to obtain:

\[\begin{aligned} \hat\beta &= \bigl[ X^T(K+\delta I)^{-1}X\bigr]^{-1} X^T(K+\delta I)^{-1} y \\ \hat{\sigma}^2 &= \frac1n \bigl\langle y-X\hat\beta, (K+\delta I)^{-1} (y-X\hat\beta)\bigr\rangle, \end{aligned}\]

Plugging these expressions into the negative log-likelihood results in a (non-convex) function of the parameter $\delta$, which upto an additive constant is given by:

\[\mathcal{L}(\delta) = \log\det (K+\delta I) + n \log \hat{\sigma}^2\]

In Lippert et al. (2011), the eigenvalue decomposition of $K$ is used to increase the efficiency of evaluating $\mathcal{L}(\delta)$, and thereby speed up the process of finding the maximum-likelihood estimate $\hat\delta$. However, their method still expresses the evaluation of $\hat\beta(\delta)$ as the solution of a linear system (if the number of covariates $d>1$). This implies that the gradient of $\mathcal{L}(\delta)$ cannot be computed using automatic differentiation, which means that only gradient-free optimization algorithms can be used (Lippert et al. (2011) used a basic grid-based search).

Instead, FaST-LMM light first uses the singular value decomposition of the fixed effects matrix $X$ to express the negative log-likelihood on the space orthogonal to the columns of $X$ (in other words, uses restricted maximum likelihood). Then the spectral decomposition of $K$ on the restricted space is used in the same manner as in the original FaST-LMM method, which results in a restricted negative log-likelihood function $\mathcal{L}_R(\delta)$ whose gradient *can* be evaluated using automatic differentiation.