Add pipeline #4317

vinx13 · 2018-05-30T14:49:22Z

No description provided.

vigsterkr

minor stuff

vigsterkr · 2018-05-30T14:59:45Z

src/shogun/machine/Pipeline.cpp

+		{
+			if (holds_alternative<CTransformer*>(stage))
+			{
+				CTransformer* transformer = shogun::get<CTransformer*>(stage);


oooootoooo, auto :)

vigsterkr · 2018-05-30T15:00:04Z

src/shogun/machine/Pipeline.cpp

+			if (holds_alternative<CTransformer*>(stage))
+			{
+				CTransformer* transformer = shogun::get<CTransformer*>(stage);
+				if (transformer->train_require_labels())


this could be a simple ternary expression:

transformer->train_require_labels() ? transformer->fit(data, m_labels) : transformer->fit(data);

vigsterkr · 2018-05-30T15:00:29Z

src/shogun/machine/Pipeline.cpp

+			}
+		}
+
+		return NULL; // unreachable


vigsterkr · 2018-05-30T15:00:39Z

src/shogun/machine/Pipeline.cpp

+		{
+			if (holds_alternative<CTransformer*>(stage))
+			{
+				CTransformer* transformer = shogun::get<CTransformer*>(stage);


vigsterkr · 2018-05-30T15:00:44Z

src/shogun/machine/Pipeline.cpp

+			}
+			else
+			{
+				CMachine* machine = shogun::get<CMachine*>(stage);


vigsterkr · 2018-05-30T15:01:30Z

src/shogun/machine/Pipeline.h

+	protected:
+		virtual bool train_machine(CFeatures* data = NULL) override;
+
+		std::vector<variant<CTransformer*, CMachine*>> m_stages;


sadly we wont be able to register this for a while :)
i.e. no serialization :D

vigsterkr · 2018-05-30T15:01:45Z

src/shogun/machine/Pipeline.cpp

+			}
+			else
+			{
+				CMachine* machine = shogun::get<CMachine*>(stage);


vigsterkr · 2018-05-31T21:07:29Z

@vinx13 would be great to add a simple xval cookbook where we use a CPruneVarSubMean transformer before doing PCA and applying k-means on a toy data :D

vigsterkr · 2018-05-31T21:07:41Z

adding unit test would be great

vigsterkr · 2018-05-31T21:09:15Z

aaaah and another thing: getter methods for the pipeline elements would be desirable. i.e. get the trained transformer etc.

vigsterkr · 2018-06-04T09:38:50Z

src/shogun/machine/Pipeline.cpp

+		return require_labels;
+	}
+
+	void CPipeline::list_stages() const


how about renaming this to

std::string to_string() const;

and basically return a string instead of directly writing SG_INFO.... that of course means that SGObject::to_string needs to be virtual

I like this more as well! users can then print the strings themselves

vigsterkr · 2018-06-04T09:50:58Z

src/shogun/machine/Pipeline.cpp

+		}
+	}
+
+	CTransformer* CPipeline::get_transformer(size_t index) const


maybe instead of accessing the pipeline elements like this it'd be good to have a way to access them by name? see for example http://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html#evaluation-of-the-performance-on-the-test-set
of course this would mean to be able to add elements as a tuple, say

Pipline().with(("customName", ZeroMean).with....

but that could be that we support both, meaning either having

Pipline().with(("customName", ZeroMean).with....

and

Pipline().with(ZeroMean).with....

and in the 2nd case we use the get_name() string...

vigsterkr · 2018-06-04T15:21:23Z

src/shogun/machine/Pipeline.cpp

+	void CPipeline::check_pipeline()
+	{
+		REQUIRE(!m_stages.empty(), "Pipeline is empty");
+		REQUIRE(


i wonder if we should start using typed exceptions, because for now EVERYTHING is ShogunException. things like MachineNotTrainedException etc....
@lisitsyn @karlnapf mm?

note, that for now the only way to infer the reason of exception is actually parsing the exception message... that's not really 'nice' from an automation/developer's perspective

Actually, this was part of the "user experience" GSoC project. So yes makes total sense imo

vigsterkr · 2018-06-04T15:29:13Z

src/shogun/machine/Pipeline.cpp

+				return shogun::get<CTransformer*>(stage.second);
+		}
+
+		SG_ERROR("Transformer with name %s not found.\n", name.c_str());


imo here std::invalid_argument be the more appropriate...
but in lot of the REQUIRE() case it's the same... namely a 'more specific type' of exception would be much more appropriate from a shogun user... if its getting integrated in a larger framework.

vigsterkr · 2018-06-04T15:32:44Z

tests/unit/machine/Pipeline_unittest.cc

+	pipeline->with(transformer1);
+
+	auto features = some<NiceMock<MockCFeatures>>();
+	EXPECT_THROW(pipeline->train(features), ShogunException);


the need for a more specific type of exception came up in my head here atm, because expecting there ShogunException is too broad.... it could actually come from a transformer or the machine in the pipeline... right? @karlnapf @lisitsyn @vinx13

vigsterkr · 2018-06-08T14:32:59Z

src/shogun/lib/ShogunException.h

+ * whenever an object in Shogun in invalid state is used. For example, a machine
+ * is used before training.
+ */
+class InvalidStateException : public ShogunException


i would define these in separate headers and cpp files :)

and in the case of "a machine is used before training" i would call that exception MachineNotTrainedException as invalid state could be a lot of things and the not trained case i believe should be explicitly spelled out for the user :)

vigsterkr · 2018-06-11T10:14:08Z

@lisitsyn @karlnapf so as trying to add pipeline to the swig interface it came out that with is a reserved keyword in python. see the design from 2017 ws: https://github.com/shogun-toolbox/shogun/wiki/Hackathon-2017-base-api#pipeline

how about changing Pipeline.with(Transformer) to Pipeline.over(Transformer), since add and as are kind of taken by SGObject, imo as could still fly but add would be matched. i'm wondering whether then would be a reserved keyword in any languages we support?

and another idea here: imo we should have a Pipeline that is inherited from CMachine, but the builder should be a separate base class, PipelineBuilder.

@vinx13 i would still like to have a builder that supports adding a list of elements. something like: add_stages([transf1, transf1, machine])

vigsterkr · 2018-06-12T07:10:18Z

@karlnapf we are getting travis problems here as well..... this branch is rebased over HEAD od develop, but octave is throwing this error

error: in method 'Evaluation_evaluate', argument 2 of type 'shogun::CLabels *' (SWIG_TypeError)

error: called from

    /opt/shogun/build/examples/meta/octave/multiclass/cartree.m at line 39 column 10

error: in method 'Evaluation_evaluate', argument 2 of type 'shogun::CLabels *' (SWIG_TypeError)

error: called from

    /opt/shogun/build/examples/meta/octave/binary/linear_support_vector_machine.m at line 42 column 10

vinx13 · 2018-06-12T07:15:01Z

the error also happens on python

  4/297 Test #238: generated_python-binary-linear_support_vector_machine ...................................***Failed    0.24 sec

Traceback (most recent call last):

  File "/opt/shogun/build/examples/meta/python/binary/linear_support_vector_machine.py", line 50, in <module>

    accuracy = eval.evaluate(labels_predict, labels_test)

TypeError: in method 'Evaluation_evaluate', argument 2 of type 'shogun::CLabels *'

swig/python detected a memory leak of type 'CBinaryLabels *', no destructor found.

Add initial pipeline implementation Add InvalidStateException and use it in pipeline Move exception to shogun/lib/exception Add MachineNotTrainedException

vigsterkr requested changes May 30, 2018

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vinx13 force-pushed the feature/pipeline branch from f71e7a3 to 62ab551 Compare May 31, 2018 02:56

vigsterkr approved these changes May 31, 2018

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vinx13 force-pushed the feature/pipeline branch 2 times, most recently from e260a20 to 860a9ed Compare June 2, 2018 05:30

vinx13 mentioned this pull request Jun 2, 2018

Add pipeline cookbook #4323

Merged

vigsterkr requested changes Jun 4, 2018

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vigsterkr force-pushed the feature/transformers branch from 45162b6 to 8ac8703 Compare June 4, 2018 15:09

vinx13 force-pushed the feature/pipeline branch from 23de4fd to 30fcfdd Compare June 4, 2018 15:13

vigsterkr reviewed Jun 4, 2018

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vigsterkr force-pushed the feature/transformers branch from b7d2ff9 to f211b65 Compare June 8, 2018 14:15

vinx13 force-pushed the feature/pipeline branch from 8e04386 to 394083d Compare June 8, 2018 14:28

vigsterkr requested changes Jun 8, 2018

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vigsterkr force-pushed the feature/transformers branch from f211b65 to 0fa4faa Compare June 11, 2018 18:30

vinx13 added 10 commits June 12, 2018 12:52

Add train_require_labels in machine and transformer

64ea3cf

Add initial pipeline implementation

ba90ff8

Add pipeline::get_trans/machine

512b534

Add pipeline unittests

5c278c2

Allow to specify transformer and machine name in pipeline

a9abca1

Add pipeline class doc

131a32f

Make error message in pipeline more verbose

83c8ec0

Use c_str when print string

8bd80a1

Add missing override

6718ac8

Check pipeline in get_machine

8cca995

vinx13 added 5 commits June 12, 2018 12:52

Add InvalidStateException and use it in pipeline

48e1692

Move exception to shogun/lib/exception

a8f5cfb

Add MachineNotTrainedException

08cfa5a

Add pipeline to swig

3add906

Rename pipeline::with to over, separate pipeline builder into a class

7d480f5

vinx13 force-pushed the feature/pipeline branch from a869313 to 7d480f5 Compare June 12, 2018 04:52

Fix swig include order

4ce59bc

vigsterkr merged commit ad75959 into shogun-toolbox:feature/transformers Jun 13, 2018

vigsterkr pushed a commit that referenced this pull request Jun 28, 2018

Add pipeline (#4317)

60197aa

Add initial pipeline implementation Add InvalidStateException and use it in pipeline Move exception to shogun/lib/exception Add MachineNotTrainedException

vigsterkr pushed a commit that referenced this pull request Jul 10, 2018

Add pipeline (#4317)

cbde1dd

Add initial pipeline implementation Add InvalidStateException and use it in pipeline Move exception to shogun/lib/exception Add MachineNotTrainedException

vigsterkr pushed a commit that referenced this pull request Jul 12, 2018

Add pipeline (#4317)

7e87f9d

Add initial pipeline implementation Add InvalidStateException and use it in pipeline Move exception to shogun/lib/exception Add MachineNotTrainedException

ktiefe pushed a commit to ktiefe/shogun that referenced this pull request Jul 30, 2019

Add pipeline (shogun-toolbox#4317)

ae0cb0d

Add initial pipeline implementation Add InvalidStateException and use it in pipeline Move exception to shogun/lib/exception Add MachineNotTrainedException

samdbrice added the Tag: GSoC label Sep 6, 2019

Add pipeline #4317

Add pipeline #4317

vinx13 commented May 30, 2018 •

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vigsterkr commented May 31, 2018

vigsterkr commented May 31, 2018

vigsterkr commented May 31, 2018

vigsterkr Jun 4, 2018

karlnapf Jun 4, 2018

vigsterkr Jun 4, 2018

vigsterkr Jun 4, 2018

vigsterkr Jun 4, 2018

karlnapf Jun 6, 2018

vigsterkr Jun 4, 2018 •

edited

vigsterkr Jun 4, 2018

vigsterkr Jun 8, 2018

vigsterkr Jun 8, 2018

vigsterkr commented Jun 11, 2018

vigsterkr commented Jun 12, 2018

vinx13 commented Jun 12, 2018

Add pipeline #4317

Add pipeline #4317

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vinx13 commented May 30, 2018 • edited

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vigsterkr commented May 31, 2018

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vigsterkr Jun 4, 2018 • edited

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vigsterkr commented Jun 11, 2018

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vinx13 commented Jun 12, 2018

vinx13 commented May 30, 2018 •

edited

vigsterkr Jun 4, 2018 •

edited