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Features/340 gaussian nb#474

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coquelin77 merged 232 commits intomasterhelmholtz-analytics/heat:masterfrom features/340-GaussianNBhelmholtz-analytics/heat:features/340-GaussianNBCopy head branch name to clipboardMar 3, 2020

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Commits on Dec 4, 2019

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Commits on Dec 6, 2019

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Commits on Dec 10, 2019

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Commits on Dec 12, 2019

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Commits on Dec 19, 2019

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Commits on Jan 9, 2020

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Commits on Jan 16, 2020

• GaussianNB first pass, replaced numpy with heat calls, added input sanitation

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Commits on Jan 23, 2020

• Merge branch 'master' into features/340-GaussianNB

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• Moved relevant _BaseNB methods to GaussianNB class, removed _BaseNB for now.

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• Integrate heat.core.naive_bayes in set up.

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• Replacing np.in1d call with ht.eq, equivalent in this context.

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• _partial_fit(), temporary (hacky) replacement for np.searchsorted.

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Commits on Jan 26, 2020

• Improved temporary searchsorted, debugging

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• Adapted joint_log_likelihood to absence of append() for torch/heat tensors

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• Adapted predict() to ht.argmax returning a heat tensor

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• Implemented GaussianNB.logsumexp() (hacky early version)

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• Merge branch 'master' into features/340-GaussianNB

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• Modified _joint_log_likelihood to not rely on append(). No need to transpose jll as correct shape is defined from the start

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• Fixed mistake in shape of joint_log_likelihood tensor

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• Implementing test_gaussiannb(). First pass, test locally.

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• Implemented testing of distributed GaussianNB (fails).

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• Merge branch 'master' into features/340-GaussianNB

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• Distributed __getitem__ now returns tensor of values at LIST of indices (as long as the indices are present on node)

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• Testing gnb predictions vs. test labels

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• Added docs for __joint_log_likelihood

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Commits on Feb 8, 2020

• Move naive_bayes one level up

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• Removed heat/core/naive_bayes

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• Fixing flake8 "E402 module level import not at top of file" complaint

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Commits on Feb 10, 2020

• Removed -quiet option from pip install.

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• Rewrote test_gaussiannb to compare to sklearn gnb() without importing sklearn module

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• Bypassing test with 7 procs for now as test dataset is too small

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• Setting pip install back to -quiet

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• Increasing test coverage. Testing exceptions

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• Switching pip install out of quiet mode again

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• Added checks for sample_weight = 0 locally

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• Added test case for sample_weight not None (split=None)

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Commits on Feb 11, 2020

• __getitem__ call on sample_weight

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• testing GaussianNB when sample_weight is not None, sample_weight not distributed

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Commits on Feb 17, 2020

• nonzero now returns 1-D tensor if input is 1-D

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Commits on Feb 19, 2020

• Modified __getitem__ for case in which the only input (key) is a list of indices

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• ht.average(), improved weighted average when weights are 1-D and input tensor is not.

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• Adapted test_average() to changes in statistics.average

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• Small change to __getitem__ call

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• Added test for GaussianNB with weights, both local and distributed

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• Updated test_average()

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• Skipping test on 7 nodes for now. Cf. #490

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Commits on Feb 20, 2020

• Extending test coverage: weighted average with 3d weights.

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• ht.average(), NotImplementedError if weights.split != x.split until #425 resolution.

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• test_average(), test NotImplementedError when weights.split != x.split

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• Extending test coverage: testing exceptions.

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• Increasing test coverage.

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• Tests fail on 7 nodes, #490

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Commits on Feb 28, 2020

• Added tests for gnb.predict_proba()

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• Shape of log_prob_x must match __joint_log_likelihood(X) output

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• scikit-learn predict_proba output for testing/comparison

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• Resolving conflicts with master

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Commits on Mar 1, 2020

• Updated documentation and example of GaussianNB

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Commits on Mar 2, 2020

• Adapted documentation from scikit-learn to HeAT.

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• ht.var() now returns same dtype as input tensor in distributed mode as well

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• Extending test coverage to gnb attributes

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• turn gnb.priors into ht.DNDarray only if it isn't already

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• Test coverage gnb.partial_fit(), gnb.priors

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• Removed dtype mismatch embuggerance between priors.sum() and 1.0

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• More tests

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• Merge branch 'master' into features/340-GaussianNB

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Commits on Mar 3, 2020

• Improving tests

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• Merge branch 'features/340-GaussianNB' of https://github.com/helmholtz-analytics/heat into features/340-GaussianNB

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• 7-node test

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• Removing 7-node testing again

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• Extending test coverage

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• Improved conditional statement as per review

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• Added references section to documentation

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• Added References section to __update_mean_variance documentation

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• Test coverage

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• More test coverage

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• Removed dead code

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• added extra dtype calls

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