private static void FillValues(Float[] model, ref VBuffer <Float> src, ref VBuffer <Float> dst, int cdst)
{
int count = src.Count;
int length = src.Length;
var values = src.Values;
var indices = src.Indices;
Contracts.Assert(Utils.Size(values) >= count);
// Since the whitening process produces dense vector, always use dense representation of dst.
var a = Utils.Size(dst.Values) >= cdst ? dst.Values : new Float[cdst];
if (src.IsDense)
{
Mkl.Gemv(Mkl.Layout.RowMajor, Mkl.Transpose.NoTrans, cdst, length,
1, model, length, values, 1, 0, a, 1);
}
else
{
Contracts.Assert(Utils.Size(indices) >= count);
int offs = 0;
for (int i = 0; i < cdst; i++)
{
a[i] = DotProduct(model, offs, values, indices, count);
offs += length;
}
}
dst = new VBuffer <Float>(cdst, a, dst.Indices);
}
private static void FillValues(float[] model, ref VBuffer <float> src, ref VBuffer <float> dst, int cdst)
{
var values = src.GetValues();
int count = values.Length;
int length = src.Length;
// Since the whitening process produces dense vector, always use dense representation of dst.
var editor = VBufferEditor.Create(ref dst, cdst);
if (src.IsDense)
{
Mkl.Gemv(Mkl.Layout.RowMajor, Mkl.Transpose.NoTrans, cdst, length,
1, model, length, values, 1, 0, editor.Values, 1);
}
else
{
var indices = src.GetIndices();
int offs = 0;
for (int i = 0; i < cdst; i++)
{
// Returns a dot product of dense vector 'model' starting from offset 'offs' and sparse vector 'values'
// with first 'count' valid elements and their corresponding 'indices'.
editor.Values[i] = CpuMathUtils.DotProductSparse(model.AsSpan(offs), values, indices, count);
offs += length;
}
}
dst = editor.Commit();
}
private static void FillValues(float[] model, ref VBuffer <float> src, ref VBuffer <float> dst, int cdst)
{
int count = src.Count;
int length = src.Length;
var values = src.Values;
var indices = src.Indices;
Contracts.Assert(Utils.Size(values) >= count);
// Since the whitening process produces dense vector, always use dense representation of dst.
var a = Utils.Size(dst.Values) >= cdst ? dst.Values : new float[cdst];
if (src.IsDense)
{
Mkl.Gemv(Mkl.Layout.RowMajor, Mkl.Transpose.NoTrans, cdst, length,
1, model, length, values, 1, 0, a, 1);
}
else
{
Contracts.Assert(Utils.Size(indices) >= count);
int offs = 0;
for (int i = 0; i < cdst; i++)
{
// Returns a dot product of dense vector 'model' starting from offset 'offs' and sparse vector 'values'
// with first 'count' valid elements and their corresponding 'indices'.
a[i] = CpuMathUtils.DotProductSparse(model.AsSpan(offs), values, indices, count);
offs += length;
}
}
dst = new VBuffer <float>(cdst, a, dst.Indices);
}
public static void AssemblyInit()
{
System.Diagnostics.Debug.WriteLine("*** Setting test assertion handler");
var prev = Contracts.SetAssertHandler(AssertHandler);
Contracts.Check(prev == null, "Expected to replace null assertion handler!");
// HACK: ensure MklImports is loaded very early in the tests so it doesn't deadlock while loading it later.
// See https://github.com/dotnet/machinelearning/issues/1073
Mkl.PptrfInternal(Mkl.Layout.RowMajor, Mkl.UpLo.Up, 0, Array.Empty <double>());
}
public static void AssemblyInit()
{
System.Diagnostics.Debug.WriteLine("*** Setting test assertion handler");
var prev = Contracts.SetAssertHandler(AssertHandler);
Contracts.Check(prev == null, "Expected to replace null assertion handler!");
// Enable Conditional Numerical Reproducibility
// https://software.intel.com/en-us/articles/introduction-to-the-conditional-numerical-reproducibility-cnr
Environment.SetEnvironmentVariable("MKL_CBWR", "COMPATIBLE");
// HACK: ensure MklImports is loaded very early in the tests so it doesn't deadlock while loading it later.
// See https://github.com/dotnet/machinelearning/issues/1073
Mkl.PptrfInternal(Mkl.Layout.RowMajor, Mkl.UpLo.Up, 0, Array.Empty <double>());
}
public void TestScikitAPI_MKL()
{
try
{
Mkl.PptrfInternal(Mkl.Layout.ColMajor, Mkl.UpLo.Lo, 2, new double[] { 0.1, 0.3 });
}
catch (DllNotFoundException e)
{
var os = Environment.OSVersion;
if (os.Platform == PlatformID.Unix)
{
Console.WriteLine("FAIL: TestScikitAPI_MKL due to {0}", e.ToString());
}
else
{
Console.WriteLine("FAIL: TestScikitAPI_MKL, OS={0}", os.ToString());
throw e;
}
}
}
private OlsLinearRegressionPredictor TrainCore(IChannel ch, FloatLabelCursor.Factory cursorFactory, int featureCount)
{
Host.AssertValue(ch);
ch.AssertValue(cursorFactory);
int m = featureCount + 1;
// Check for memory conditions first.
if ((long)m * (m + 1) / 2 > int.MaxValue)
{
throw ch.Except("Cannot hold covariance matrix in memory with {0} features", m - 1);
}
// Track the number of examples.
long n = 0;
// Since we are accumulating over many values, we use Double even for the single precision build.
var xty = new Double[m];
// The layout of this algorithm is a packed row-major lower triangular matrix.
var xtx = new Double[m * (m + 1) / 2];
// Build X'X (lower triangular) and X'y incrementally (X'X+=X'X_i; X'y+=X'y_i):
using (var cursor = cursorFactory.Create())
{
while (cursor.MoveNext())
{
var yi = cursor.Label;
// Increment first element of X'y
xty[0] += yi;
// Increment first element of lower triangular X'X
xtx[0] += 1;
var values = cursor.Features.GetValues();
if (cursor.Features.IsDense)
{
int ioff = 1;
ch.Assert(values.Length + 1 == m);
// Increment rest of first column of lower triangular X'X
for (int i = 1; i < m; i++)
{
ch.Assert(ioff == i * (i + 1) / 2);
var val = values[i - 1];
// Add the implicit first bias term to X'X
xtx[ioff++] += val;
// Add the remainder of X'X
for (int j = 0; j < i; j++)
{
xtx[ioff++] += val * values[j];
}
// X'y
xty[i] += val * yi;
}
ch.Assert(ioff == xtx.Length);
}
else
{
var fIndices = cursor.Features.GetIndices();
for (int ii = 0; ii < values.Length; ++ii)
{
int i = fIndices[ii] + 1;
int ioff = i * (i + 1) / 2;
var val = values[ii];
// Add the implicit first bias term to X'X
xtx[ioff++] += val;
// Add the remainder of X'X
for (int jj = 0; jj <= ii; jj++)
{
xtx[ioff + fIndices[jj]] += val * values[jj];
}
// X'y
xty[i] += val * yi;
}
}
n++;
}
ch.Check(n > 0, "No training examples in dataset.");
if (cursor.BadFeaturesRowCount > 0)
{
ch.Warning("Skipped {0} instances with missing features/label during training", cursor.SkippedRowCount);
}
if (_l2Weight > 0)
{
// Skip the bias term for regularization, in the ridge regression case.
// So start at [1,1] instead of [0,0].
// REVIEW: There are two ways to view this, firstly, it is more
// user friendly ot make this scaling factor behave similarly regardless
// of data size, so that if you have the same parameters, you get the same
// model if you feed in your data than if you duplicate your data 10 times.
// This is what I have now. The alternate point of view is to view this
// L2 regularization parameter as providing some sort of prior, in which
// case duplication 10 times should in fact be treated differently! (That
// is, we should not multiply by n below.) Both interpretations seem
// correct, in their way.
Double squared = _l2Weight * _l2Weight * n;
int ioff = 0;
for (int i = 1; i < m; ++i)
{
xtx[ioff += i + 1] += squared;
}
ch.Assert(ioff == xtx.Length - 1);
}
}
if (!(_l2Weight > 0) && n < m)
{
throw ch.Except("Ordinary least squares requires more examples than parameters. There are {0} parameters, but {1} examples. To enable training, use a positive L2 weight so this behaves as ridge regression.", m, n);
}
Double yMean = n == 0 ? 0 : xty[0] / n;
ch.Info("Trainer solving for {0} parameters across {1} examples", m, n);
// Cholesky Decomposition of X'X into LL'
try
{
Mkl.Pptrf(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, m, xtx);
}
catch (DllNotFoundException)
{
// REVIEW: Is there no better way?
throw ch.ExceptNotSupp("The MKL library (libMklImports) or one of its dependencies is missing.");
}
// Solve for beta in (LL')beta = X'y:
Mkl.Pptrs(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, m, 1, xtx, xty, 1);
// Note that the solver overwrote xty so it contains the solution. To be more clear,
// we effectively change its name (through reassignment) so we don't get confused that
// this is somehow xty in the remaining calculation.
var beta = xty;
xty = null;
// Check that the solution is valid.
for (int i = 0; i < beta.Length; ++i)
{
ch.Check(FloatUtils.IsFinite(beta[i]), "Non-finite values detected in OLS solution");
}
var weights = VBufferUtils.CreateDense <float>(beta.Length - 1);
for (int i = 1; i < beta.Length; ++i)
{
weights.Values[i - 1] = (float)beta[i];
}
var bias = (float)beta[0];
if (!(_l2Weight > 0) && m == n)
{
// We would expect the solution to the problem to be exact in this case.
ch.Info("Number of examples equals number of parameters, solution is exact but no statistics can be derived");
return(new OlsLinearRegressionPredictor(Host, in weights, bias, null, null, null, 1, float.NaN));
}
Double rss = 0; // residual sum of squares
Double tss = 0; // total sum of squares
using (var cursor = cursorFactory.Create())
{
var lrPredictor = new LinearRegressionPredictor(Host, in weights, bias);
var lrMap = lrPredictor.GetMapper <VBuffer <float>, float>();
float yh = default;
while (cursor.MoveNext())
{
var features = cursor.Features;
lrMap(in features, ref yh);
var e = cursor.Label - yh;
rss += e * e;
var ydm = cursor.Label - yMean;
tss += ydm * ydm;
}
}
var rSquared = ProbClamp(1 - (rss / tss));
// R^2 adjusted differs from the normal formula on account of the bias term, by Said's reckoning.
double rSquaredAdjusted;
if (n > m)
{
rSquaredAdjusted = ProbClamp(1 - (1 - rSquared) * (n - 1) / (n - m));
ch.Info("Coefficient of determination R2 = {0:g}, or {1:g} (adjusted)",
rSquared, rSquaredAdjusted);
}
else
{
rSquaredAdjusted = Double.NaN;
}
// The per parameter significance is compute intensive and may not be required for all practitioners.
// Also we can't estimate it, unless we can estimate the variance, which requires more examples than
// parameters.
if (!_perParameterSignificance || m >= n)
{
return(new OlsLinearRegressionPredictor(Host, in weights, bias, null, null, null, rSquared, rSquaredAdjusted));
}
ch.Assert(!Double.IsNaN(rSquaredAdjusted));
var standardErrors = new Double[m];
var tValues = new Double[m];
var pValues = new Double[m];
// Invert X'X:
Mkl.Pptri(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, m, xtx);
var s2 = rss / (n - m); // estimate of variance of y
for (int i = 0; i < m; i++)
{
// Initialize with inverse Hessian.
standardErrors[i] = (Single)xtx[i * (i + 1) / 2 + i];
}
if (_l2Weight > 0)
{
// Iterate through all entries of inverse Hessian to make adjustment to variance.
int ioffset = 1;
float reg = _l2Weight * _l2Weight * n;
for (int iRow = 1; iRow < m; iRow++)
{
for (int iCol = 0; iCol <= iRow; iCol++)
{
var entry = (Single)xtx[ioffset];
var adjustment = -reg * entry * entry;
standardErrors[iRow] -= adjustment;
if (0 < iCol && iCol < iRow)
{
standardErrors[iCol] -= adjustment;
}
ioffset++;
}
}
Contracts.Assert(ioffset == xtx.Length);
}
for (int i = 0; i < m; i++)
{
// sqrt of diagonal entries of s2 * inverse(X'X + reg * I) * X'X * inverse(X'X + reg * I).
standardErrors[i] = Math.Sqrt(s2 * standardErrors[i]);
ch.Check(FloatUtils.IsFinite(standardErrors[i]), "Non-finite standard error detected from OLS solution");
tValues[i] = beta[i] / standardErrors[i];
pValues[i] = (float)MathUtils.TStatisticToPValue(tValues[i], n - m);
ch.Check(0 <= pValues[i] && pValues[i] <= 1, "p-Value calculated outside expected [0,1] range");
}
return(new OlsLinearRegressionPredictor(Host, in weights, bias, standardErrors, tValues, pValues, rSquared, rSquaredAdjusted));
}
protected override void ComputeTrainingStatistics(IChannel ch, FloatLabelCursor.Factory cursorFactory, Float loss, int numParams)
{
Contracts.AssertValue(ch);
Contracts.AssertValue(cursorFactory);
Contracts.Assert(NumGoodRows > 0);
Contracts.Assert(WeightSum > 0);
Contracts.Assert(BiasCount == 1);
Contracts.Assert(loss >= 0);
Contracts.Assert(numParams >= BiasCount);
Contracts.Assert(CurrentWeights.IsDense);
ch.Info("Model trained with {0} training examples.", NumGoodRows);
// Compute deviance: start with loss function.
Float deviance = (Float)(2 * loss * WeightSum);
if (L2Weight > 0)
{
// Need to subtract L2 regularization loss.
// The bias term is not regularized.
var regLoss = VectorUtils.NormSquared(CurrentWeights.Values, 1, CurrentWeights.Length - 1) * L2Weight;
deviance -= regLoss;
}
if (L1Weight > 0)
{
// Need to subtract L1 regularization loss.
// The bias term is not regularized.
Double regLoss = 0;
VBufferUtils.ForEachDefined(ref CurrentWeights, (ind, value) => { if (ind >= BiasCount)
{
regLoss += Math.Abs(value);
}
});
deviance -= (Float)regLoss * L1Weight * 2;
}
ch.Info("Residual Deviance: \t{0} (on {1} degrees of freedom)", deviance, Math.Max(NumGoodRows - numParams, 0));
// Compute null deviance, i.e., the deviance of null hypothesis.
// Cap the prior positive rate at 1e-15.
Double priorPosRate = _posWeight / WeightSum;
Contracts.Assert(0 <= priorPosRate && priorPosRate <= 1);
Float nullDeviance = (priorPosRate <= 1e-15 || 1 - priorPosRate <= 1e-15) ?
0f : (Float)(2 * WeightSum * MathUtils.Entropy(priorPosRate, true));
ch.Info("Null Deviance: \t{0} (on {1} degrees of freedom)", nullDeviance, NumGoodRows - 1);
// Compute AIC.
ch.Info("AIC: \t{0}", 2 * numParams + deviance);
// Show the coefficients statistics table.
var featureColIdx = cursorFactory.Data.Schema.Feature.Index;
var schema = cursorFactory.Data.Data.Schema;
var featureLength = CurrentWeights.Length - BiasCount;
var namesSpans = VBufferUtils.CreateEmpty <DvText>(featureLength);
if (schema.HasSlotNames(featureColIdx, featureLength))
{
schema.GetMetadata(MetadataUtils.Kinds.SlotNames, featureColIdx, ref namesSpans);
}
Host.Assert(namesSpans.Length == featureLength);
// Inverse mapping of non-zero weight slots.
Dictionary <int, int> weightIndicesInvMap = null;
// Indices of bias and non-zero weight slots.
int[] weightIndices = null;
// Whether all weights are non-zero.
bool denseWeight = numParams == CurrentWeights.Length;
// Extract non-zero indices of weight.
if (!denseWeight)
{
weightIndices = new int[numParams];
weightIndicesInvMap = new Dictionary <int, int>(numParams);
weightIndices[0] = 0;
weightIndicesInvMap[0] = 0;
int j = 1;
for (int i = 1; i < CurrentWeights.Length; i++)
{
if (CurrentWeights.Values[i] != 0)
{
weightIndices[j] = i;
weightIndicesInvMap[i] = j++;
}
}
Contracts.Assert(j == numParams);
}
// Compute the standard error of coefficients.
long hessianDimension = (long)numParams * (numParams + 1) / 2;
if (hessianDimension > int.MaxValue)
{
ch.Warning("The number of parameter is too large. Cannot hold the variance-covariance matrix in memory. " +
"Skipping computation of standard errors and z-statistics of coefficients. Consider choosing a larger L1 regularizer" +
"to reduce the number of parameters.");
_stats = new LinearModelStatistics(Host, NumGoodRows, numParams, deviance, nullDeviance);
return;
}
// Building the variance-covariance matrix for parameters.
// The layout of this algorithm is a packed row-major lower triangular matrix.
// E.g., layout of indices for 4-by-4:
// 0
// 1 2
// 3 4 5
// 6 7 8 9
var hessian = new Double[hessianDimension];
// Initialize diagonal elements with L2 regularizers except for the first entry (index 0)
// Since bias is not regularized.
if (L2Weight > 0)
{
// i is the array index of the diagonal entry at iRow-th row and iRow-th column.
// iRow is one-based.
int i = 0;
for (int iRow = 2; iRow <= numParams; iRow++)
{
i += iRow;
hessian[i] = L2Weight;
}
Contracts.Assert(i == hessian.Length - 1);
}
// Initialize the remaining entries.
var bias = CurrentWeights.Values[0];
using (var cursor = cursorFactory.Create())
{
while (cursor.MoveNext())
{
var label = cursor.Label;
var weight = cursor.Weight;
var score = bias + VectorUtils.DotProductWithOffset(ref CurrentWeights, 1, ref cursor.Features);
// Compute Bernoulli variance n_i * p_i * (1 - p_i) for the i-th training example.
var variance = weight / (2 + 2 * Math.Cosh(score));
// Increment the first entry of hessian.
hessian[0] += variance;
var values = cursor.Features.Values;
if (cursor.Features.IsDense)
{
int ioff = 1;
// Increment remaining entries of hessian.
for (int i = 1; i < numParams; i++)
{
ch.Assert(ioff == i * (i + 1) / 2);
int wi = weightIndices == null ? i - 1 : weightIndices[i] - 1;
Contracts.Assert(0 <= wi && wi < cursor.Features.Length);
var val = values[wi] * variance;
// Add the implicit first bias term to X'X
hessian[ioff++] += val;
// Add the remainder of X'X
for (int j = 0; j < i; j++)
{
int wj = weightIndices == null ? j : weightIndices[j + 1] - 1;
Contracts.Assert(0 <= wj && wj < cursor.Features.Length);
hessian[ioff++] += val * values[wj];
}
}
ch.Assert(ioff == hessian.Length);
}
else
{
var indices = cursor.Features.Indices;
for (int ii = 0; ii < cursor.Features.Count; ++ii)
{
int i = indices[ii];
int wi = i + 1;
if (weightIndicesInvMap != null && !weightIndicesInvMap.TryGetValue(i + 1, out wi))
{
continue;
}
Contracts.Assert(0 < wi && wi <= cursor.Features.Length);
int ioff = wi * (wi + 1) / 2;
var val = values[ii] * variance;
// Add the implicit first bias term to X'X
hessian[ioff] += val;
// Add the remainder of X'X
for (int jj = 0; jj <= ii; jj++)
{
int j = indices[jj];
int wj = j + 1;
if (weightIndicesInvMap != null && !weightIndicesInvMap.TryGetValue(j + 1, out wj))
{
continue;
}
Contracts.Assert(0 < wj && wj <= cursor.Features.Length);
hessian[ioff + wj] += val * values[jj];
}
}
}
}
}
// Apply Cholesky Decomposition to find the inverse of the Hessian.
Double[] invHessian = null;
try
{
// First, find the Cholesky decomposition LL' of the Hessian.
Mkl.Pptrf(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, numParams, hessian);
// Note that hessian is already modified at this point. It is no longer the original Hessian,
// but instead represents the Cholesky decomposition L.
// Also note that the following routine is supposed to consume the Cholesky decomposition L instead
// of the original information matrix.
Mkl.Pptri(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, numParams, hessian);
// At this point, hessian should contain the inverse of the original Hessian matrix.
// Swap hessian with invHessian to avoid confusion in the following context.
Utils.Swap(ref hessian, ref invHessian);
Contracts.Assert(hessian == null);
}
catch (DllNotFoundException)
{
throw ch.ExceptNotSupp("The MKL library (Microsoft.ML.MklImports.dll) or one of its dependencies is missing.");
}
Float[] stdErrorValues = new Float[numParams];
stdErrorValues[0] = (Float)Math.Sqrt(invHessian[0]);
for (int i = 1; i < numParams; i++)
{
// Initialize with inverse Hessian.
stdErrorValues[i] = (Single)invHessian[i * (i + 1) / 2 + i];
}
if (L2Weight > 0)
{
// Iterate through all entries of inverse Hessian to make adjustment to variance.
// A discussion on ridge regularized LR coefficient covariance matrix can be found here:
// http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3228544/
// http://www.inf.unibz.it/dis/teaching/DWDM/project2010/LogisticRegression.pdf
int ioffset = 1;
for (int iRow = 1; iRow < numParams; iRow++)
{
for (int iCol = 0; iCol <= iRow; iCol++)
{
var entry = (Single)invHessian[ioffset];
var adjustment = -L2Weight * entry * entry;
stdErrorValues[iRow] -= adjustment;
if (0 < iCol && iCol < iRow)
{
stdErrorValues[iCol] -= adjustment;
}
ioffset++;
}
}
Contracts.Assert(ioffset == invHessian.Length);
}
for (int i = 1; i < numParams; i++)
{
stdErrorValues[i] = (Float)Math.Sqrt(stdErrorValues[i]);
}
VBuffer <Float> stdErrors = new VBuffer <Float>(CurrentWeights.Length, numParams, stdErrorValues, weightIndices);
_stats = new LinearModelStatistics(Host, NumGoodRows, numParams, deviance, nullDeviance, ref stdErrors);
}
// Performs whitening training for each column separately. Notice that for both PCA and ZCA, _models and _invModels
// will have dimension input_vec_size x input_vec_size. In the getter, the matrix will be truncated to only keep
// PcaNum columns, and thus produce the desired output size.
private static void TrainModels(IHostEnvironment env, IChannel ch, float[][] columnData, int[] rowCounts,
ref float[][] models, ref float[][] invModels, ColumnType[] srcTypes, params ColumnInfo[] columns)
{
ch.Assert(columnData.Length == rowCounts.Length);
for (int iinfo = 0; iinfo < columns.Length; iinfo++)
{
var ex = columns[iinfo];
var data = columnData[iinfo];
int crow = rowCounts[iinfo];
int ccol = srcTypes[iinfo].ValueCount;
// If there is no training data, simply initialize the model matrices to identity matrices.
if (crow == 0)
{
var matrixSize = ccol * ccol;
models[iinfo] = new float[matrixSize];
invModels[iinfo] = new float[matrixSize];
for (int i = 0; i < ccol; i++)
{
models[iinfo][i * ccol + i] = 1;
invModels[iinfo][i * ccol + i] = 1;
}
continue;
}
// Compute covariance matrix.
var u = new float[ccol * ccol];
ch.Info("Computing covariance matrix...");
Mkl.Gemm(Layout, Mkl.Transpose.Trans, Mkl.Transpose.NoTrans,
ccol, ccol, crow, 1 / (float)crow, data, ccol, data, ccol, 0, u, ccol);
ch.Info("Computing SVD...");
var eigValues = new float[ccol]; // Eigenvalues.
var unconv = new float[ccol]; // Superdiagonal unconverged values (if any). Not used but seems to be required by MKL.
// After the next call, values in U will be ovewritten by left eigenvectors.
// Each column in U will be an eigenvector.
int r = Mkl.Svd(Layout, Mkl.SvdJob.MinOvr, Mkl.SvdJob.None,
ccol, ccol, u, ccol, eigValues, null, ccol, null, ccol, unconv);
ch.Assert(r == 0);
if (r > 0)
{
throw ch.Except("SVD did not converge.");
}
if (r < 0)
{
throw ch.Except("Invalid arguments to LAPACK gesvd, error: {0}", r);
}
ch.Info("Scaling eigenvectors...");
// Scale eigenvalues first so we don't have to compute sqrt for every matrix element.
// Scaled eigenvalues are used to compute inverse transformation matrix
// while reciprocal (eigValuesRcp) values are used to compute whitening matrix.
for (int i = 0; i < eigValues.Length; i++)
{
eigValues[i] = MathUtils.Sqrt(Math.Max(0, eigValues[i]) + ex.Epsilon);
}
var eigValuesRcp = new float[eigValues.Length];
for (int i = 0; i < eigValuesRcp.Length; i++)
{
eigValuesRcp[i] = 1 / eigValues[i];
}
// Scale eigenvectors. Note that resulting matrix is transposed, so the scaled
// eigenvectors are stored row-wise.
var uScaled = new float[u.Length];
var uInvScaled = new float[u.Length];
int isrc = 0;
for (int irowSrc = 0; irowSrc < ccol; irowSrc++)
{
int idst = irowSrc;
for (int icolSrc = 0; icolSrc < ccol; icolSrc++)
{
uScaled[idst] = u[isrc] * eigValuesRcp[icolSrc];
uInvScaled[idst] = u[isrc] * eigValues[icolSrc];
isrc++;
idst += ccol;
}
}
// For ZCA need to do additional multiply by U.
if (ex.Kind == WhiteningKind.Pca)
{
// Save all components for PCA. Retained components will be selected during evaluation.
models[iinfo] = uScaled;
if (ex.SaveInv)
{
invModels[iinfo] = uInvScaled;
}
}
else if (ex.Kind == WhiteningKind.Zca)
{
models[iinfo] = new float[u.Length];
Mkl.Gemm(Layout, Mkl.Transpose.NoTrans, Mkl.Transpose.NoTrans,
ccol, ccol, ccol, 1, u, ccol, uScaled, ccol, 0, models[iinfo], ccol);
if (ex.SaveInv)
{
invModels[iinfo] = new float[u.Length];
Mkl.Gemm(Layout, Mkl.Transpose.NoTrans, Mkl.Transpose.NoTrans,
ccol, ccol, ccol, 1, u, ccol, uInvScaled, ccol, 0, invModels[iinfo], ccol);
}
}
else
{
ch.Assert(false);
}
}
}
public void TestScikitAPI_MKL()
{
Mkl.PptrfInternal(Mkl.Layout.ColMajor, Mkl.UpLo.Lo, 2, new double[] { 0.1, 0.3 });
}
/// <summary>
/// Computes the standart deviation matrix of each of the non-zero training weights, needed to calculate further the standart deviation,
/// p-value and z-Score.
/// If you need faster calculations, use the ComputeStd method from the Microsoft.ML.HALLearners package, which makes use of hardware acceleration.
/// Due to the existence of regularization, an approximation is used to compute the variances of the trained linear coefficients.
/// </summary>
/// <param name="hessian"></param>
/// <param name="weightIndices"></param>
/// <param name="numSelectedParams"></param>
/// <param name="currentWeightsCount"></param>
/// <param name="ch">The <see cref="IChannel"/> used for messaging.</param>
/// <param name="l2Weight">The L2Weight used for training. (Supply the same one that got used during training.)</param>
public override VBuffer <float> ComputeStd(double[] hessian, int[] weightIndices, int numSelectedParams, int currentWeightsCount, IChannel ch, float l2Weight)
{
Contracts.AssertValue(ch);
Contracts.AssertValue(hessian, nameof(hessian));
Contracts.Assert(numSelectedParams > 0);
Contracts.Assert(currentWeightsCount > 0);
Contracts.Assert(l2Weight > 0);
// Apply Cholesky Decomposition to find the inverse of the Hessian.
Double[] invHessian = null;
try
{
// First, find the Cholesky decomposition LL' of the Hessian.
Mkl.Pptrf(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, numSelectedParams, hessian);
// Note that hessian is already modified at this point. It is no longer the original Hessian,
// but instead represents the Cholesky decomposition L.
// Also note that the following routine is supposed to consume the Cholesky decomposition L instead
// of the original information matrix.
Mkl.Pptri(Mkl.Layout.RowMajor, Mkl.UpLo.Lo, numSelectedParams, hessian);
// At this point, hessian should contain the inverse of the original Hessian matrix.
// Swap hessian with invHessian to avoid confusion in the following context.
Utils.Swap(ref hessian, ref invHessian);
Contracts.Assert(hessian == null);
}
catch (DllNotFoundException)
{
throw ch.ExceptNotSupp("The MKL library (MklImports.dll) or one of its dependencies is missing.");
}
float[] stdErrorValues = new float[numSelectedParams];
stdErrorValues[0] = (float)Math.Sqrt(invHessian[0]);
for (int i = 1; i < numSelectedParams; i++)
{
// Initialize with inverse Hessian.
stdErrorValues[i] = (float)invHessian[i * (i + 1) / 2 + i];
}
if (l2Weight > 0)
{
// Iterate through all entries of inverse Hessian to make adjustment to variance.
// A discussion on ridge regularized LR coefficient covariance matrix can be found here:
// http://www.aloki.hu/pdf/0402_171179.pdf (Equations 11 and 25)
// http://www.inf.unibz.it/dis/teaching/DWDM/project2010/LogisticRegression.pdf (Section "Significance testing in ridge logistic regression")
int ioffset = 1;
for (int iRow = 1; iRow < numSelectedParams; iRow++)
{
for (int iCol = 0; iCol <= iRow; iCol++)
{
var entry = (float)invHessian[ioffset++];
AdjustVariance(entry, iRow, iCol, l2Weight, stdErrorValues);
}
}
Contracts.Assert(ioffset == invHessian.Length);
}
for (int i = 1; i < numSelectedParams; i++)
{
stdErrorValues[i] = (float)Math.Sqrt(stdErrorValues[i]);
}
// currentWeights vector size is Weights2 + the bias
return(new VBuffer <float>(currentWeightsCount, numSelectedParams, stdErrorValues, weightIndices));
}
