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\subsection{Linear Regression}
\noindent{\bf Description}
Linear Regression scripts are used to model the relationship between one numerical
response variable and one or more explanatory (feature) variables.
The scripts are given a dataset $(X, Y) = (x_i, y_i)_{i=1}^n$ where $x_i$ is a
numerical vector of feature variables and $y_i$ is a numerical response value for
each training data record. The feature vectors are provided as a matrix $X$ of size
$n\,{\times}\,m$, where $n$ is the number of records and $m$ is the number of features.
The observed response values are provided as a 1-column matrix~$Y$, with a numerical
value $y_i$ for each~$x_i$ in the corresponding row of matrix~$X$.
In linear regression, we predict the distribution of the response~$y_i$ based on
a fixed linear combination of the features in~$x_i$. We assume that
there exist constant regression coefficients $\beta_0, \beta_1, \ldots, \beta_m$
and a constant residual variance~$\sigma^2$ such that
y_i \sim \Normal(\mu_i, \sigma^2) \,\,\,\,\textrm{where}\,\,\,\,
\mu_i \,=\, \beta_0 + \beta_1 x_{i,1} + \ldots + \beta_m x_{i,m}
Distribution $y_i \sim \Normal(\mu_i, \sigma^2)$ models the ``unexplained'' residual
noise and is assumed independent across different records.
The goal is to estimate the regression coefficients and the residual variance.
Once they are accurately estimated, we can make predictions about $y_i$ given~$x_i$
in new records. We can also use the $\beta_j$'s to analyze the influence of individual
features on the response value, and assess the quality of this model by comparing
residual variance in the response, left after prediction, with its total variance.
There are two scripts in our library, both doing the same estimation, but using different
computational methods. Depending on the size and the sparsity of the feature matrix~$X$,
one or the other script may be more efficient. The ``direct solve'' script
{\tt LinearRegDS} is more efficient when the number of features $m$ is relatively small
($m \sim 1000$ or less) and matrix~$X$ is either tall or fairly dense
(has~${\gg}\:m^2$ nonzeros); otherwise, the ``conjugate gradient'' script {\tt LinearRegCG}
is more efficient. If $m > 50000$, use only {\tt LinearRegCG}.
\noindent{\bf Usage}
{\tt{}-f }path/\/{\tt{}LinearRegDS.dml}
{\tt{} -nvargs}
{\tt{} X=}path/file
{\tt{} Y=}path/file
{\tt{} B=}path/file
{\tt{} O=}path/file
{\tt{} icpt=}int
{\tt{} reg=}double
{\tt{} fmt=}format
{\tt{}-f }path/\/{\tt{}LinearRegCG.dml}
{\tt{} -nvargs}
{\tt{} X=}path/file
{\tt{} Y=}path/file
{\tt{} B=}path/file
{\tt{} O=}path/file
{\tt{} Log=}path/file
{\tt{} icpt=}int
{\tt{} reg=}double
{\tt{} tol=}double
{\tt{} maxi=}int
{\tt{} fmt=}format
\noindent{\bf Arguments}
\item[{\tt X}:]
Location (on HDFS) to read the matrix of feature vectors, each row constitutes
one feature vector
\item[{\tt Y}:]
Location to read the 1-column matrix of response values
\item[{\tt B}:]
Location to store the estimated regression parameters (the $\beta_j$'s), with the
intercept parameter~$\beta_0$ at position {\tt B[}$m\,{+}\,1$, {\tt 1]} if available
\item[{\tt O}:] (default:\mbox{ }{\tt " "})
Location to store the CSV-file of summary statistics defined in
Table~\ref{table:linreg:stats}, the default is to print it to the standard output
\item[{\tt Log}:] (default:\mbox{ }{\tt " "}, {\tt LinearRegCG} only)
Location to store iteration-specific variables for monitoring and debugging purposes,
see Table~\ref{table:linreg:log} for details.
\item[{\tt icpt}:] (default:\mbox{ }{\tt 0})
Intercept presence and shifting/rescaling the features in~$X$:\\
{\tt 0} = no intercept (hence no~$\beta_0$), no shifting or rescaling of the features;\\
{\tt 1} = add intercept, but do not shift/rescale the features in~$X$;\\
{\tt 2} = add intercept, shift/rescale the features in~$X$ to mean~0, variance~1
\item[{\tt reg}:] (default:\mbox{ }{\tt 0.000001})
L2-regularization parameter~\mbox{$\lambda\geq 0$}; set to nonzero for highly dependent,
sparse, or numerous ($m \gtrsim n/10$) features
\item[{\tt tol}:] (default:\mbox{ }{\tt 0.000001}, {\tt LinearRegCG} only)
Tolerance \mbox{$\eps\geq 0$} used in the convergence criterion: we terminate conjugate
gradient iterations when the $\beta$-residual reduces in L2-norm by this factor
\item[{\tt maxi}:] (default:\mbox{ }{\tt 0}, {\tt LinearRegCG} only)
Maximum number of conjugate gradient iterations, or~0 if no maximum
limit provided
\item[{\tt fmt}:] (default:\mbox{ }{\tt "text"})
Matrix file output format, such as {\tt text}, {\tt mm}, or {\tt csv};
see read/write functions in SystemML Language Reference for details.
Name & Meaning \\
{\tt AVG\_TOT\_Y} & Average of the response value $Y$ \\
{\tt STDEV\_TOT\_Y} & Standard Deviation of the response value $Y$ \\
{\tt AVG\_RES\_Y} & Average of the residual $Y - \mathop{\mathrm{pred}}(Y|X)$, i.e.\ residual bias \\
{\tt STDEV\_RES\_Y} & Standard Deviation of the residual $Y - \mathop{\mathrm{pred}}(Y|X)$ \\
{\tt DISPERSION} & GLM-style dispersion, i.e.\ residual sum of squares / \#deg.\ fr. \\
{\tt PLAIN\_R2} & Plain $R^2$ of residual with bias included vs.\ total average \\
{\tt ADJUSTED\_R2} & Adjusted $R^2$ of residual with bias included vs.\ total average \\
{\tt PLAIN\_R2\_NOBIAS} & Plain $R^2$ of residual with bias subtracted vs.\ total average \\
{\tt ADJUSTED\_R2\_NOBIAS} & Adjusted $R^2$ of residual with bias subtracted vs.\ total average \\
{\tt PLAIN\_R2\_VS\_0} & ${}^*$Plain $R^2$ of residual with bias included vs.\ zero constant \\
{\tt ADJUSTED\_R2\_VS\_0} & ${}^*$Adjusted $R^2$ of residual with bias included vs.\ zero constant \\
\multicolumn{2}{r}{${}^{*\mathstrut}$ The last two statistics are only printed if there is no intercept ({\tt icpt=0})} \\
\caption{Besides~$\beta$, linear regression scripts compute a few summary statistics
listed above. The statistics are provided in CSV format, one comma-separated name-value
pair per each line.}
Name & Meaning \\
{\tt CG\_RESIDUAL\_NORM} & L2-norm of conjug.\ grad.\ residual, which is $A \pxp \beta - t(X) \pxp y$ \\
& where $A = t(X) \pxp X + \diag (\lambda)$, or a similar quantity \\
{\tt CG\_RESIDUAL\_RATIO} & Ratio of current L2-norm of conjug.\ grad.\ residual over the initial \\
The {\tt Log} file for {\tt{}LinearRegCG} script contains the above \mbox{per-}iteration
variables in CSV format, each line containing triple (Name, Iteration\#, Value) with
Iteration\# being~0 for initial values.}
\noindent{\bf Details}
To solve a linear regression problem over feature matrix~$X$ and response vector~$Y$,
we can find coefficients $\beta_0, \beta_1, \ldots, \beta_m$ and $\sigma^2$ that maximize
the joint likelihood of all $y_i$ for $i=1\ldots n$, defined by the assumed statistical
model~(\ref{eqn:linregdef}). Since the joint likelihood of the independent
$y_i \sim \Normal(\mu_i, \sigma^2)$ is proportional to the product of
$\exp\big({-}\,(y_i - \mu_i)^2 / (2\sigma^2)\big)$, we can take the logarithm of this
product, then multiply by $-2\sigma^2 < 0$ to obtain a least squares problem:
\sum_{i=1}^n \, (y_i - \mu_i)^2 \,\,=\,\,
\sum_{i=1}^n \Big(y_i - \beta_0 - \sum_{j=1}^m \beta_j x_{i,j}\Big)^2
This may not be enough, however. The minimum may sometimes be attained over infinitely many
$\beta$-vectors, for example if $X$ has an all-0 column, or has linearly dependent columns,
or has fewer rows than columns~\mbox{($n < m$)}. Even if~(\ref{eqn:linregls}) has a unique
solution, other $\beta$-vectors may be just a little suboptimal\footnote{Smaller likelihood
difference between two models suggests less statistical evidence to pick one model over the
other.}, yet give significantly different predictions for new feature vectors. This results
in \emph{overfitting}: prediction error for the training data ($X$ and~$Y$) is much smaller
than for the test data (new records).
Overfitting and degeneracy in the data is commonly mitigated by adding a regularization penalty
term to the least squares function:
\sum_{i=1}^n \Big(y_i - \beta_0 - \sum_{j=1}^m \beta_j x_{i,j}\Big)^2
\,+\,\, \lambda \sum_{j=1}^m \beta_j^2
The choice of $\lambda>0$, the regularization constant, typically involves cross-validation
where the dataset is repeatedly split into a training part (to estimate the~$\beta_j$'s) and
a test part (to evaluate prediction accuracy), with the goal of maximizing the test accuracy.
In our scripts, $\lambda$~is provided as input parameter~{\tt reg}.
The solution to least squares problem~(\ref{eqn:linreglsreg}), through taking the derivative
and setting it to~0, has the matrix linear equation form
A\left[\textstyle\beta_{1:m}\atop\textstyle\beta_0\right] \,=\, \big[X,\,1\big]^T Y,\,\,\,
A \,=\, \big[X,\,1\big]^T \big[X,\,1\big]\,+\,\hspace{0.5pt} \diag(\hspace{0.5pt}
\underbrace{\raisebox{0pt}[0pt][0.5pt]{$\lambda,\ldots, \lambda$}}_{\raisebox{2pt}{$\scriptstyle m$}}
\hspace{0.5pt}, 0)
where $[X,\,1]$ is $X$~with an extra column of~1s appended on the right, and the
diagonal matrix of $\lambda$'s has a zero to keep the intercept~$\beta_0$ unregularized.
If the intercept is disabled by setting {\tt icpt=0}, the equation is simply
\mbox{$X^T X \beta = X^T Y$}.
We implemented two scripts for solving equation~(\ref{eqn:linregeq}): one is a ``direct solver''
that computes $A$ and then solves $A\beta = [X,\,1]^T Y$ by calling an external package,
the other performs linear conjugate gradient~(CG) iterations without ever materializing~$A$.
The CG~algorithm closely follows Algorithm~5.2 in Chapter~5 of~\cite{Nocedal2006:Optimization}.
Each step in the CG~algorithm computes a matrix-vector multiplication $q = Ap$ by first computing
$[X,\,1]\, p$ and then $[X,\,1]^T [X,\,1]\, p$. Usually the number of such multiplications,
one per CG iteration, is much smaller than~$m$. The user can put a hard bound on it with input
parameter~{\tt maxi}, or use the default maximum of~$m+1$ (or~$m$ if no intercept) by
having {\tt maxi=0}. The CG~iterations terminate when the L2-norm of vector
$r = A\beta - [X,\,1]^T Y$ decreases from its initial value (for~$\beta=0$) by the tolerance
factor specified in input parameter~{\tt tol}.
The CG algorithm is more efficient if computing
$[X,\,1]^T \big([X,\,1]\, p\big)$ is much faster than materializing $A$,
an $(m\,{+}\,1)\times(m\,{+}\,1)$ matrix. The Direct Solver~(DS) is more efficient if
$X$ takes up a lot more memory than $A$ (i.e.\ $X$~has a lot more nonzeros than~$m^2$)
and if $m^2$ is small enough for the external solver ($m \lesssim 50000$). A more precise
determination between CG and~DS is subject to further research.
In addition to the $\beta$-vector, the scripts estimate the residual standard
deviation~$\sigma$ and the~$R^2$, the ratio of ``explained'' variance to the total
variance of the response variable. These statistics only make sense if the number
of degrees of freedom $n\,{-}\,m\,{-}\,1$ is positive and the regularization constant
$\lambda$ is negligible or zero. The formulas for $\sigma$ and $R^2$~are:
R^2_{\textrm{plain}} = 1 - \frac{\mathrm{RSS}}{\mathrm{TSS}},\quad
\sigma \,=\, \sqrt{\frac{\mathrm{RSS}}{n - m - 1}},\quad
R^2_{\textrm{adj.}} = 1 - \frac{\sigma^2 (n-1)}{\mathrm{TSS}}
\mathrm{RSS} \,=\, \sum_{i=1}^n \Big(y_i - \hat{\mu}_i -
\frac{1}{n} \sum_{i'=1}^n \,(y_{i'} - \hat{\mu}_{i'})\Big)^2; \quad
\mathrm{TSS} \,=\, \sum_{i=1}^n \Big(y_i - \frac{1}{n} \sum_{i'=1}^n y_{i'}\Big)^2
Here $\hat{\mu}_i$ are the predicted means for $y_i$ based on the estimated
regression coefficients and the feature vectors. They may be biased when no
intercept is present, hence the RSS formula subtracts the bias.
Lastly, note that by choosing the input option {\tt icpt=2} the user can shift
and rescale the columns of~$X$ to have zero average and the variance of~1.
This is particularly important when using regularization over highly disbalanced
features, because regularization tends to penalize small-variance columns (which
need large~$\beta_j$'s) more than large-variance columns (with small~$\beta_j$'s).
At the end, the estimated regression coefficients are shifted and rescaled to
apply to the original features.
\noindent{\bf Returns}
The estimated regression coefficients (the $\hat{\beta}_j$'s) are populated into
a matrix and written to an HDFS file whose path/name was provided as the ``{\tt B}''
input argument. What this matrix contains, and its size, depends on the input
argument {\tt icpt}, which specifies the user's intercept and rescaling choice:
\item[{\tt icpt=0}:] No intercept, matrix~$B$ has size $m\,{\times}\,1$, with
$B[j, 1] = \hat{\beta}_j$ for each $j$ from 1 to~$m = {}$ncol$(X)$.
\item[{\tt icpt=1}:] There is intercept, but no shifting/rescaling of~$X$; matrix~$B$
has size $(m\,{+}\,1) \times 1$, with $B[j, 1] = \hat{\beta}_j$ for $j$ from 1 to~$m$,
and $B[m\,{+}\,1, 1] = \hat{\beta}_0$, the estimated intercept coefficient.
\item[{\tt icpt=2}:] There is intercept, and the features in~$X$ are shifted to
mean${} = 0$ and rescaled to variance${} = 1$; then there are two versions of
the~$\hat{\beta}_j$'s, one for the original features and another for the
shifted/rescaled features. Now matrix~$B$ has size $(m\,{+}\,1) \times 2$, with
$B[\cdot, 1]$ for the original features and $B[\cdot, 2]$ for the shifted/rescaled
features, in the above format. Note that $B[\cdot, 2]$ are iteratively estimated
and $B[\cdot, 1]$ are obtained from $B[\cdot, 2]$ by complementary shifting and
The estimated summary statistics, including residual standard deviation~$\sigma$ and
the~$R^2$, are printed out or sent into a file (if specified) in CSV format as
defined in Table~\ref{table:linreg:stats}. For conjugate gradient iterations,
a log file with monitoring variables can also be made available, see
\noindent{\bf Examples}
\hml -f LinearRegCG.dml -nvargs X=/user/biadmin/X.mtx Y=/user/biadmin/Y.mtx
B=/user/biadmin/B.mtx fmt=csv O=/user/biadmin/stats.csv
icpt=2 reg=1.0 tol=0.00000001 maxi=100 Log=/user/biadmin/log.csv
\hml -f LinearRegDS.dml -nvargs X=/user/biadmin/X.mtx Y=/user/biadmin/Y.mtx
B=/user/biadmin/B.mtx fmt=csv O=/user/biadmin/stats.csv
icpt=2 reg=1.0
% \smallskip
% \noindent{\bf See Also}
% \smallskip
% In case of binary classification problems, please consider using L2-SVM or
% binary logistic regression; for multiclass classification, use multiclass~SVM
% or multinomial logistic regression. For more complex distributions of the
% response variable use the Generalized Linear Models script.