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intermediate split of GP out of LogLinear models
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144 changes: 144 additions & 0 deletions
144
src/dr/evomodel/treedatalikelihood/discrete/LogCtmcRateGradient.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,144 @@ | ||
| /* | ||
| * LogCtmcRateGradient.java | ||
| * | ||
| * Copyright (c) 2002-2023 Alexei Drummond, Andrew Rambaut and Marc Suchard | ||
| * | ||
| * This file is part of BEAST. | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership and licensing. | ||
| * | ||
| * BEAST is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU Lesser General Public License as | ||
| * published by the Free Software Foundation; either version 2 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * BEAST is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public | ||
| * License along with BEAST; if not, write to the | ||
| * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, | ||
| * Boston, MA 02110-1301 USA | ||
| */ | ||
|
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| package dr.evomodel.treedatalikelihood.discrete; | ||
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| import dr.evomodel.substmodel.GlmSubstitutionModel; | ||
| import dr.evomodel.substmodel.LogAdditiveCtmcRateProvider; | ||
| import dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate; | ||
| import dr.evomodel.treedatalikelihood.TreeDataLikelihood; | ||
| import dr.inference.loggers.LogColumn; | ||
| import dr.inference.model.Parameter; | ||
| import dr.util.Citation; | ||
| import dr.util.CommonCitations; | ||
|
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| import java.util.Collections; | ||
| import java.util.List; | ||
|
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| /** | ||
| * @author Filippo Monti | ||
| * @author Marc A. Suchard | ||
| */ | ||
|
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| public class LogCtmcRateGradient extends AbstractLogAdditiveSubstitutionModelGradient { | ||
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| private final LogAdditiveCtmcRateProvider.DataAugmented rateProvider; | ||
| private final int[][] mapEffectToIndices; | ||
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| public LogCtmcRateGradient(String traitName, | ||
| TreeDataLikelihood treeDataLikelihood, | ||
| BeagleDataLikelihoodDelegate likelihoodDelegate, | ||
| GlmSubstitutionModel substitutionModel) { | ||
| super(traitName, treeDataLikelihood, likelihoodDelegate, substitutionModel, | ||
| ApproximationMode.FIRST_ORDER); | ||
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| if (substitutionModel.getRateProvider() instanceof LogAdditiveCtmcRateProvider.DataAugmented) | ||
| this.rateProvider = (LogAdditiveCtmcRateProvider.DataAugmented) | ||
| substitutionModel.getRateProvider(); | ||
| else { | ||
| throw new IllegalArgumentException("Invalid substitution model"); | ||
| } | ||
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| this.mapEffectToIndices = makeAsymmetricMap(); | ||
| } | ||
|
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| @Override | ||
| protected double preProcessNormalization(double[] differentials, double[] generator, | ||
| boolean normalize) { | ||
| double total = 0.0; | ||
| if (normalize) { | ||
| for (int i = 0; i < stateCount; ++i) { | ||
| for (int j = 0; j < stateCount; ++j) { | ||
| final int ij = i * stateCount + j; | ||
| total += differentials[ij] * generator[ij]; | ||
| } | ||
| } | ||
| } | ||
| return total; | ||
| } | ||
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| private int[][] makeAsymmetricMap() { | ||
| int[][] map = new int[stateCount * (stateCount - 1)][]; | ||
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| int k = 0; | ||
| for (int i = 0; i < stateCount; ++i) { | ||
| for (int j = i + 1; j < stateCount; ++j) { | ||
| map[k++] = new int[]{i, j}; | ||
| } | ||
| } | ||
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| for (int j = 0; j < stateCount; ++j) { | ||
| for (int i = j + 1; i < stateCount; ++i) { | ||
| map[k++] = new int[]{i, j}; | ||
| } | ||
| } | ||
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| return map; | ||
| } | ||
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| @Override | ||
| double processSingleGradientDimension(int k, double[] differentials, double[] generator, double[] pi, | ||
| boolean normalize, double normalizationConstant) { | ||
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| final int i = mapEffectToIndices[k][0], j = mapEffectToIndices[k][1]; | ||
| final int ii = i * stateCount + i; | ||
| final int ij = i * stateCount + j; | ||
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| double element = generator[ij]; | ||
| double total = (differentials[ij] - differentials[ii]) * element; | ||
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| if (normalize) { | ||
| total -= element * pi[i] * normalizationConstant; | ||
| } | ||
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| return total; | ||
| } | ||
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| @Override | ||
| public Parameter getParameter() { | ||
| return rateProvider.getLogRateParameter(); | ||
| } | ||
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| @Override | ||
| public LogColumn[] getColumns() { | ||
| throw new RuntimeException("Not yet implemented"); | ||
| } | ||
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| @Override | ||
| public Citation.Category getCategory() { | ||
| return Citation.Category.SUBSTITUTION_MODELS; | ||
| } | ||
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| @Override | ||
| public String getDescription() { | ||
| return null; // TODO | ||
| } | ||
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| @Override | ||
| public List<Citation> getCitations() { | ||
| // TODO Update | ||
| return Collections.singletonList(CommonCitations.LEMEY_2014_UNIFYING); | ||
| } | ||
| } |
87 changes: 87 additions & 0 deletions
87
src/dr/evomodelxml/continuous/hmc/ApproximateLogCtmcRateGradientParser.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| /* | ||
| * GamGpSubstitutionModelGradientParser.java | ||
| * | ||
| * Copyright (c) 2002-2023 Alexei Drummond, Andrew Rambaut and Marc Suchard | ||
| * | ||
| * This file is part of BEAST. | ||
| * See the NOTICE file distributed with this work for additional | ||
| * information regarding copyright ownership and licensing. | ||
| * | ||
| * BEAST is free software; you can redistribute it and/or modify | ||
| * it under the terms of the GNU Lesser General Public License as | ||
| * published by the Free Software Foundation; either version 2 | ||
| * of the License, or (at your option) any later version. | ||
| * | ||
| * BEAST is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU Lesser General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU Lesser General Public | ||
| * License along with BEAST; if not, write to the | ||
| * Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, | ||
| * Boston, MA 02110-1301 USA | ||
| */ | ||
|
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| package dr.evomodelxml.continuous.hmc; | ||
|
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| import dr.evomodel.substmodel.GlmSubstitutionModel; | ||
| import dr.evomodel.treedatalikelihood.BeagleDataLikelihoodDelegate; | ||
| import dr.evomodel.treedatalikelihood.DataLikelihoodDelegate; | ||
| import dr.evomodel.treedatalikelihood.TreeDataLikelihood; | ||
| import dr.evomodel.treedatalikelihood.discrete.AbstractGlmSubstitutionModelGradient; | ||
| import dr.evomodel.treedatalikelihood.discrete.LogCtmcRateGradient; | ||
| import dr.evomodelxml.treelikelihood.TreeTraitParserUtilities; | ||
| import dr.xml.*; | ||
|
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| import static dr.evomodelxml.treelikelihood.TreeTraitParserUtilities.DEFAULT_TRAIT_NAME; | ||
|
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| /** | ||
| * @author Filippo Monti | ||
| * @author Marc A. Suchard | ||
| */ | ||
|
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| public class ApproximateLogCtmcRateGradientParser extends AbstractXMLObjectParser { | ||
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| private static final String PARSER_NAME = "approximateLogCtmcRateGradient"; | ||
| private static final String TRAIT_NAME = TreeTraitParserUtilities.TRAIT_NAME; | ||
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| public String getParserName(){ return PARSER_NAME; } | ||
|
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| public Object parseXMLObject(XMLObject xo) throws XMLParseException { | ||
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| String traitName = xo.getAttribute(TRAIT_NAME, DEFAULT_TRAIT_NAME); | ||
| final TreeDataLikelihood treeDataLikelihood = (TreeDataLikelihood) xo.getChild(TreeDataLikelihood.class); | ||
| GlmSubstitutionModel substitutionModel = (GlmSubstitutionModel) xo.getChild(GlmSubstitutionModel.class); | ||
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| DataLikelihoodDelegate delegate = treeDataLikelihood.getDataLikelihoodDelegate(); | ||
| if (!(delegate instanceof BeagleDataLikelihoodDelegate)) { | ||
| throw new XMLParseException("Unknown likelihood delegate type"); | ||
| } | ||
|
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| return new LogCtmcRateGradient(traitName, treeDataLikelihood, | ||
| (BeagleDataLikelihoodDelegate) delegate, substitutionModel); | ||
| } | ||
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| @Override | ||
| public XMLSyntaxRule[] getSyntaxRules() { | ||
| return rules; | ||
| } | ||
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| private final XMLSyntaxRule[] rules = { | ||
| AttributeRule.newStringRule(TRAIT_NAME, true), | ||
| new ElementRule(TreeDataLikelihood.class), | ||
| new ElementRule(GlmSubstitutionModel.class), | ||
| }; | ||
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| @Override | ||
| public String getParserDescription() { | ||
| return null; | ||
| } | ||
|
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| @Override | ||
| public Class getReturnType() { | ||
| return AbstractGlmSubstitutionModelGradient.class; | ||
| } | ||
| } | ||
|
|
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