Skip to content

Commit

Permalink
Fixes onnx exports for binary classification trainers (#4463)
Browse files Browse the repository at this point in the history 
* Squashed commit of the following:

commit a5e274ef8869576190bbb794360a5f56d998b470
Merge: b7db4fa d7f9996
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Thu Nov 14 14:51:21 2019 -0800

    Merge branch 'onnx_bin_classifiers' of https://github.com/Lynx1820/machinelearning into onnx_bin_classifiers

commit b7db4fa
Author: Harish Kulkarni <harishsk@users.noreply.github.com>
Date:   Thu Nov 14 17:41:12 2019 +0000

    Added onnx export support for KeyToValueMappingTransformer (#4455)

commit f3e0f6b
Author: Eric Erhardt <eric.erhardt@microsoft.com>
Date:   Thu Nov 14 07:22:12 2019 -0600

    Fix a flaky Extensions.ML test. (#4458)

    * Fix a flaky Extensions.ML test.

    Make the reload model tests more resistant to timing changes.

    * PR feedback.

commit c1e190a
Author: Harish Kulkarni <harishsk@users.noreply.github.com>
Date:   Thu Nov 14 05:24:14 2019 +0000

    Added onnx export support for OptionalColumnTransform  (#4454)

    * Initial work for adding onnx export support for OptionalColumnTransform

    * Implemented support for optional initializers in OnnxTranformer to support OptionalColumnTransform

    * Fixed handling of double values and non-long numeric types

    * Removed redundant line

    * Updated review comment

commit f96761b
Author: Harish Kulkarni <harishsk@users.noreply.github.com>
Date:   Thu Nov 14 03:17:12 2019 +0000

    Fixed model saving and loading of OneVersusAllTrainer to include SoftMax (#4472)

    * Fixed model saving and loading of OneVersusAllTrainer to include SoftMax

    * Modified existing test to include SoftMax option

    * Modified test to verify both cases: when UseSoftmax is true and false

commit d45cc8a
Author: Jake <31937616+JakeRadMSFT@users.noreply.github.com>
Date:   Wed Nov 13 17:26:49 2019 -0800

    Add InternalsVisibleTo in AutoML and CodeGenerator for the assembly Microsoft.ML.ModelBuilder.AutoMLService.Gpu (#4474)

commit 5e83e23
Author: Eric Erhardt <eric.erhardt@microsoft.com>
Date:   Wed Nov 13 16:09:05 2019 -0600

    CpuMathNative assembly is not getting copied when using packages.config. (#4465)

    When we refactored CpuMath to support netcoreapp3.0, we broke the packages.config support to copy the native assembly. This fixes it again by copying the file from the correct location.

    Fix #93

commit 693250b
Author: Harish Kulkarni <harishsk@users.noreply.github.com>
Date:   Wed Nov 13 21:58:07 2019 +0000

    Added onnx export support for WordTokenizingTransformer and NgramExtractingTransformer (#4451)

    * Added onnx export support for string related transforms

    * Updated baseline test files

    A large portion of this commit is upgrading the baseline test files. The rest of the fixes deal with build breaks resulting from the upgrade of ORT version.

    * Fixed bugs in ValueToKeyMappingTransformer and added additional tests

commit 5910910
Author: Antonio Velázquez <38739674+antoniovs1029@users.noreply.github.com>
Date:   Mon Nov 11 17:19:39 2019 -0800

    Fixes #4292 about using PFI with BPT and CMPB (#4306)

    *Changes in PredictionTransformer.cs and Calibrator.cs to fix the problem of the create methods not being called, to make CMP load its internal calibrator and predictor first so to assign the correct paramaters types and runtimes, and added a PredictionTransformerLoadTypeAttribute so that the binary prediction transformer knows what type to assign when loading a CMP as its internal model.
    *Added a working sample for using PFI with BPT and CMPB while loading a model from disk. This is based entirely in the original sample.
    *Added file CalibratedModelParametersTests.cs with tests that the CMPs modified in this PR are now being correctly loaded from disk.
    *Changed a couple of tests in LbfgsTests.cs that failed because they used casts that now return 'null'.

commit bcdac55
Author: Brian Stark <54910472+bpstark@users.noreply.github.com>
Date:   Mon Nov 11 13:42:42 2019 -0800

    Stabilize the LR test (#4446)

    * Stabilize the LR test

    Found issue with how we were using random for our
    ImageClassificationTrainer. This caused instability in our unit test, as
    we were not able to control the random seed. Modified the code to now
    use the same random object throughout, the trainer, thus allowing us to
    control the seed and therefor have predictable output.

commit d7f9996
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Mon Nov 11 11:33:17 2019 -0800

    workaround Scores

commit 7fba31c
Merge: 93388b6 c96d690
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Mon Nov 11 11:25:28 2019 -0800

    merging changes

commit 93388b6
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Mon Nov 11 11:19:59 2019 -0800

    Added extraction of score column before node creation

commit ea71828
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Fri Nov 8 15:53:11 2019 -0800

    fix for binary classification trainers export to onnx

commit 6fad293
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Thu Oct 31 15:26:43 2019 -0700

    Revert "draft regression test"

    This reverts commit 1ad45c995516b9d39fc05aca855ce2abe96c407b.

commit 83c1c80
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Thu Oct 31 15:24:23 2019 -0700

    draft regression test

commit 8884161
Author: frank-dong-ms <55860649+frank-dong-ms@users.noreply.github.com>
Date:   Fri Nov 8 20:20:53 2019 -0800

    nightly build pipeline (#4444)

    * nightly build pipeline

commit c96d690
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Fri Nov 8 15:53:11 2019 -0800

    fix for binary classification trainers export to onnx

commit 8100364
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Thu Oct 31 15:26:43 2019 -0700

    Revert "draft regression test"

    This reverts commit 1ad45c995516b9d39fc05aca855ce2abe96c407b.

commit 81381e2
Author: Keren Fuentes <dkeren@seas.upenn.edu>
Date:   Thu Oct 31 15:24:23 2019 -0700

    draft regression test

* update name and remove some dependency code

* baseline file changes

* Refactored function
  • Loading branch information
@Lynx1820
Lynx1820 authored Dec 2, 2019
1 parent e63fa8f commit d9584cf
Show file tree
Hide file tree
Showing 7 changed files with 147 additions and 16 deletions.
26 changes: 20 additions & 6 deletions src/Microsoft.ML.Data/Scorers/BinaryClassifierScorer.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -184,6 +184,7 @@ private protected override void SaveAsOnnxCore(OnnxContext ctx)
{
Host.CheckValue(ctx, nameof(ctx));
Host.Assert(Bindable is IBindableCanSaveOnnx);
Host.Assert(Bindings.InfoCount >= 2);

if (!ctx.ContainsColumn(DefaultColumnNames.Features))
return;
Expand All @@ -197,15 +198,28 @@ private protected override void SaveAsOnnxCore(OnnxContext ctx)
for (int iinfo = 0; iinfo < Bindings.InfoCount; ++iinfo)
outColumnNames[iinfo] = Bindings.GetColumnName(Bindings.MapIinfoToCol(iinfo));

//Check if "Probability" column was generated by the base class, only then
//label can be predicted.
if (Bindings.InfoCount >= 3 && ctx.ContainsColumn(outColumnNames[2]))
/* If the probability column was generated, then the classification threshold is set to 0.5. Otherwise,
the predicted label is based on the sign of the score.
*/
string opType = "Binarizer";
OnnxNode node;
var binarizerOutput = ctx.AddIntermediateVariable(null, "BinarizerOutput", true);

if (Bindings.InfoCount >= 3)
{
string opType = "Binarizer";
var node = ctx.CreateNode(opType, new[] { ctx.GetVariableName(outColumnNames[2]) },
new[] { ctx.GetVariableName(outColumnNames[0]) }, ctx.GetNodeName(opType));
Host.Assert(ctx.ContainsColumn(outColumnNames[2]));
node = ctx.CreateNode(opType, ctx.GetVariableName(outColumnNames[2]), binarizerOutput, ctx.GetNodeName(opType));
node.AddAttribute("threshold", 0.5);
}
else
{
node = ctx.CreateNode(opType, ctx.GetVariableName(outColumnNames[1]), binarizerOutput, ctx.GetNodeName(opType));
node.AddAttribute("threshold", 0.0);
}
opType = "Cast";
node = ctx.CreateNode(opType, binarizerOutput, ctx.GetVariableName(outColumnNames[0]), ctx.GetNodeName(opType), "");
var t = InternalDataKindExtensions.ToInternalDataKind(DataKind.Boolean).ToType();
node.AddAttribute("to", t);
}

private protected override IDataTransform ApplyToDataCore(IHostEnvironment env, IDataView newSource)
Expand Down
4 changes: 3 additions & 1 deletion src/Microsoft.ML.FastTree/FastTree.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3049,6 +3049,7 @@ private enum AggregateFunction
private protected virtual bool SaveAsOnnx(OnnxContext ctx, string[] outputNames, string featureColumn)
{
Host.CheckValue(ctx, nameof(ctx));
Host.Check(Utils.Size(outputNames) >= 1);

//Nodes.
var nodesTreeids = new List<long>();
Expand Down Expand Up @@ -3111,7 +3112,8 @@ private protected virtual bool SaveAsOnnx(OnnxContext ctx, string[] outputNames,
}

string opType = "TreeEnsembleRegressor";
var node = ctx.CreateNode(opType, new[] { featureColumn }, outputNames, ctx.GetNodeName(opType));
string scoreVarName = (Utils.Size(outputNames) == 2) ? outputNames[1] : outputNames[0]; // Get Score from PredictedLabel and/or Score columns
var node = ctx.CreateNode(opType, new[] { featureColumn }, new[] { scoreVarName }, ctx.GetNodeName(opType));

node.AddAttribute("post_transform", PostTransform.None.GetDescription());
node.AddAttribute("n_targets", 1);
Expand Down
5 changes: 3 additions & 2 deletions src/Microsoft.ML.StandardTrainers/Standard/LinearModelParameters.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -136,9 +136,10 @@ internal LinearModelParameters(IHostEnvironment env, string name, in VBuffer<flo
private protected virtual bool SaveAsOnnx(OnnxContext ctx, string[] outputs, string featureColumn)
{
Host.CheckValue(ctx, nameof(ctx));
Host.Check(Utils.Size(outputs) == 1);
Host.Check(Utils.Size(outputs) >= 1);
string opType = "LinearRegressor";
var node = ctx.CreateNode(opType, new[] { featureColumn }, outputs, ctx.GetNodeName(opType));
string scoreVarName = (Utils.Size(outputs) == 2) ? outputs[1] : outputs[0]; // Get Score from PredictedLabel and/or Score columns
var node = ctx.CreateNode(opType, new[] { featureColumn }, new[] { scoreVarName }, ctx.GetNodeName(opType));
// Selection of logit or probit output transform. enum {'NONE', 'LOGIT', 'PROBIT}
node.AddAttribute("post_transform", "NONE");
node.AddAttribute("targets", 1);
Expand Down
19 changes: 18 additions & 1 deletion ...Output/Common/Onnx/BinaryClassification/BreastCancer/ExcludeVariablesInOnnxConversion.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -416,7 +416,7 @@
"Probability"
],
"output": [
"PredictedLabel"
"BinarizerOutput"
],
"name": "Binarizer",
"opType": "Binarizer",
Expand All @@ -429,6 +429,23 @@
],
"domain": "ai.onnx.ml"
},
{
"input": [
"BinarizerOutput"
],
"output": [
"PredictedLabel"
],
"name": "Cast1",
"opType": "Cast",
"attribute": [
{
"name": "to",
"i": "9",
"type": "INT"
}
]
},
{
"input": [
"PredictedLabel"
Expand Down
19 changes: 18 additions & 1 deletion test/BaselineOutput/Common/Onnx/BinaryClassification/BreastCancer/ModelWithLessIO.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -742,7 +742,7 @@
"Probability"
],
"output": [
"PredictedLabel"
"BinarizerOutput"
],
"name": "Binarizer",
"opType": "Binarizer",
Expand All @@ -755,6 +755,23 @@
],
"domain": "ai.onnx.ml"
},
{
"input": [
"BinarizerOutput"
],
"output": [
"PredictedLabel"
],
"name": "Cast1",
"opType": "Cast",
"attribute": [
{
"name": "to",
"i": "9",
"type": "INT"
}
]
},
{
"input": [
"PredictedLabel"
Expand Down
19 changes: 18 additions & 1 deletion test/BaselineOutput/Common/Onnx/BinaryClassification/BreastCancer/OneHotBagPipeline.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -369,7 +369,7 @@
"Probability"
],
"output": [
"PredictedLabel"
"BinarizerOutput"
],
"name": "Binarizer",
"opType": "Binarizer",
Expand All @@ -382,6 +382,23 @@
],
"domain": "ai.onnx.ml"
},
{
"input": [
"BinarizerOutput"
],
"output": [
"PredictedLabel"
],
"name": "Cast1",
"opType": "Cast",
"attribute": [
{
"name": "to",
"i": "9",
"type": "INT"
}
]
},
{
"input": [
"Label"
Expand Down
71 changes: 67 additions & 4 deletions test/Microsoft.ML.Tests/OnnxConversionTest.cs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,15 @@ private class BreastCancerMulticlassExample
public float[] Features;
}

private class BreastCancerBinaryClassification
{
[LoadColumn(0)]
public bool Label;

[LoadColumn(2, 9), VectorType(8)]
public float[] Features;
}

[LessThanNetCore30OrNotNetCoreFact("netcoreapp3.0 output differs from Baseline. Tracked by https://github.com/dotnet/machinelearning/issues/2087")]
public void KmeansOnnxConversionTest()
{
Expand Down Expand Up @@ -202,14 +211,15 @@ public void RegressionTrainersOnnxConversionTest()
List<IEstimator<ITransformer>> estimators = new List<IEstimator<ITransformer>>()
{
mlContext.Regression.Trainers.Sdca("Target","FeatureVector"),
mlContext.Regression.Trainers.Ols("Target","FeatureVector"),
mlContext.Regression.Trainers.Ols("Target","FeatureVector"),
mlContext.Regression.Trainers.OnlineGradientDescent("Target","FeatureVector"),
mlContext.Regression.Trainers.FastForest("Target", "FeatureVector"),
mlContext.Regression.Trainers.FastTree("Target", "FeatureVector"),
mlContext.Regression.Trainers.FastTreeTweedie("Target", "FeatureVector"),
mlContext.Regression.Trainers.LbfgsPoissonRegression("Target", "FeatureVector"),
};
if (Environment.Is64BitProcess) {
if (Environment.Is64BitProcess)
{
estimators.Add(mlContext.Regression.Trainers.LightGbm("Target", "FeatureVector"));
}
foreach (var estimator in estimators)
Expand All @@ -232,7 +242,7 @@ public void RegressionTrainersOnnxConversionTest()
CompareSelectedR4ScalarColumns(transformedData.Schema[2].Name, outputNames[2], transformedData, onnxResult, 3); // compare score results
}
// Compare the Onnx graph to a baseline if OnnxRuntime is not supported
else
else
{
var onnxFileName = $"{estimator.ToString()}.txt";
var subDir = Path.Combine("..", "..", "BaselineOutput", "Common", "Onnx", "Regression", "Adult");
Expand All @@ -244,6 +254,58 @@ public void RegressionTrainersOnnxConversionTest()
Done();
}

[Fact]
public void BinaryClassificationTrainersOnnxConversionTest()
{
var mlContext = new MLContext(seed: 1);
string dataPath = GetDataPath("breast-cancer.txt");
// Now read the file (remember though, readers are lazy, so the actual reading will happen when the data is accessed).
var dataView = mlContext.Data.LoadFromTextFile<BreastCancerBinaryClassification>(dataPath, separatorChar: '\t', hasHeader: true);
List<IEstimator<ITransformer>> estimators = new List<IEstimator<ITransformer>>()
{
mlContext.BinaryClassification.Trainers.AveragedPerceptron(),
mlContext.BinaryClassification.Trainers.FastForest(),
mlContext.BinaryClassification.Trainers.FastTree(),
mlContext.BinaryClassification.Trainers.LbfgsLogisticRegression(),
mlContext.BinaryClassification.Trainers.LinearSvm(),
mlContext.BinaryClassification.Trainers.SdcaLogisticRegression(),
mlContext.BinaryClassification.Trainers.SdcaNonCalibrated(),
mlContext.BinaryClassification.Trainers.SgdCalibrated(),
mlContext.BinaryClassification.Trainers.SgdNonCalibrated(),
mlContext.BinaryClassification.Trainers.SymbolicSgdLogisticRegression(),
};
if (Environment.Is64BitProcess)
{
estimators.Add(mlContext.BinaryClassification.Trainers.LightGbm());
}

var initialPipeline = mlContext.Transforms.ReplaceMissingValues("Features").
Append(mlContext.Transforms.NormalizeMinMax("Features"));
foreach (var estimator in estimators)
{
var pipeline = initialPipeline.Append(estimator);
var model = pipeline.Fit(dataView);
var transformedData = model.Transform(dataView);
var onnxModel = mlContext.Model.ConvertToOnnxProtobuf(model, dataView);
// Compare model scores produced by ML.NET and ONNX's runtime.
if (IsOnnxRuntimeSupported())
{
var onnxFileName = $"{estimator.ToString()}.onnx";
var onnxModelPath = GetOutputPath(onnxFileName);
SaveOnnxModel(onnxModel, onnxModelPath, null);
// Evaluate the saved ONNX model using the data used to train the ML.NET pipeline.
string[] inputNames = onnxModel.Graph.Input.Select(valueInfoProto => valueInfoProto.Name).ToArray();
string[] outputNames = onnxModel.Graph.Output.Select(valueInfoProto => valueInfoProto.Name).ToArray();
var onnxEstimator = mlContext.Transforms.ApplyOnnxModel(outputNames, inputNames, onnxModelPath);
var onnxTransformer = onnxEstimator.Fit(dataView);
var onnxResult = onnxTransformer.Transform(dataView);
CompareSelectedR4ScalarColumns(transformedData.Schema[5].Name, outputNames[3], transformedData, onnxResult, 3);
CompareSelectedScalarColumns<Boolean>(transformedData.Schema[4].Name, outputNames[2], transformedData, onnxResult);
}
}
Done();
}

private class DataPoint
{
[VectorType(3)]
Expand Down Expand Up @@ -1225,7 +1287,8 @@ private void CreateDummyExamplesToMakeComplierHappy()
var dummyExample = new BreastCancerFeatureVector() { Features = null };
var dummyExample1 = new BreastCancerCatFeatureExample() { Label = false, F1 = 0, F2 = "Amy" };
var dummyExample2 = new BreastCancerMulticlassExample() { Label = "Amy", Features = null };
var dummyExample3 = new SmallSentimentExample() { Tokens = null };
var dummyExample3 = new BreastCancerBinaryClassification() { Label = false, Features = null };
var dummyExample4 = new SmallSentimentExample() { Tokens = null };
}

private void CompareResults(string leftColumnName, string rightColumnName, IDataView left, IDataView right)
Expand Down

0 comments on commit d9584cf

Please sign in to comment.