https://github.com/GPflow/GPflow

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Revision Author Date Message Commit Date
47e788a Release 2.0.0 (#1396) 31 March 2020, 13:19 UTC
78238bd Prepare release 2.0.0-rc1 (#1153) 14 November 2019, 15:23 UTC
473e9bc Update contributors (#1152) 14 November 2019, 12:23 UTC
5ec3260 Update README (#1151) 14 November 2019, 12:22 UTC
624ed39 Gaussian process with neural network notebook (#1149) 14 November 2019, 11:54 UTC
32b76b7 Update CircleCI config (#1150) 14 November 2019, 11:05 UTC
a241dd3 Missing `full_output_cov` in VGP and GPLVM parameter prevents us from calling, `predict_f_samples` from the base class.. (#1147) 13 November 2019, 23:25 UTC
24b5733 Migrate MCMC notebook to gpflow2.0 (#1100) Migrate MCMC notebook to gpflow 2 using tensorflow probabilities. Changes required a few changes across the rest of the codebase, outside of the notebook. * small change to leaf printing function (fix bug, which was preventing printing of composite kernels) * parameters and trainable_parameters now return tuples, not generators, like tf implementation of variables, trainable_variables * tfp.distributions now work with different dtypes (by wrapping of parameters), so now play nicely with gpflow. 13 November 2019, 12:27 UTC
046b107 Create autodocumentation of API for GPFflow. (#1120) The script generate_rst.py creates a folder `gpflow` which contains all the rst for the autogeneration using sphinx. Also added is type checking to the documentation and css and logo for the docs. 13 November 2019, 10:36 UTC
1a38796 Updated contributors (#1128) 12 November 2019, 15:24 UTC
0cadb9e Remove persistent tape fixing #1142 (#1145) 12 November 2019, 14:24 UTC
f282e01 Minor fix in README.md (#1143) 12 November 2019, 13:06 UTC
ff339f8 Updated mixture_density_network notebook (#1141) 11 November 2019, 15:09 UTC
4cf768f Update notebook tests (#1140) 11 November 2019, 12:38 UTC
732f114 Deprecate neg_log_marginal_likelihood (#1139) 09 November 2019, 19:23 UTC
96940dd Computation of the gradient must be outside of the GradientTape 09 November 2019, 18:10 UTC
c13c49a Refactor config with a dataclass (#1135) 09 November 2019, 13:40 UTC
157aa4f Update custom mean function (#1134) 08 November 2019, 17:16 UTC
637534a Fix a bug for slice cov when tf.function(autograph=False) applied. (#1136) 08 November 2019, 14:05 UTC
d05f429 Use experimental_ref when using tf.Variable as key in Dicts (#1132) 08 November 2019, 13:41 UTC
015975e Fig importing bug in changepoints kernel (#1133) 07 November 2019, 14:01 UTC
bc68c52 Move positive and triangular to bijectors utilities (#1131) 07 November 2019, 11:47 UTC
76f6427 ChangePoints kernel (#1094) 06 November 2019, 23:21 UTC
1aa9d03 Resolve merge conflicts 06 November 2019, 23:03 UTC
95e4ca5 Move utility function to_default_* to utility module 06 November 2019, 22:59 UTC
ab054e0 Clear announcement about GPflow 2.0 (#1130) 06 November 2019, 11:10 UTC
1c80b70 Announcement 03 November 2019, 23:38 UTC
458a345 Announcement 03 November 2019, 23:36 UTC
f070a8b Unblacklist some notebooks so tests can run and delete the monitoring (#1121) 31 October 2019, 11:36 UTC
86b0ee6 Fix natural gradient notebook (#1126) 31 October 2019, 11:29 UTC
3dad746 Multiple assign (#1125) 30 October 2019, 16:55 UTC
7b59483 Fix set trainable method (#1124) 30 October 2019, 13:27 UTC
d2ad129 Fix training function, which refers to model in outside scope. (#1123) 30 October 2019, 11:04 UTC
b1e7b32 Removed warnings due to weird escape characters. (#1122) 29 October 2019, 11:25 UTC
a6f3043 Merge branch 'develop-2.0' of github.com:GPflow/GPflow into develop-2.0 27 October 2019, 17:21 UTC
5d6336f GPflow 2.0 notebook update: SGPR upper bound (#1116) This PR updates the understanding/upper_bound.ipynb to work in gpflow2. It fixes the upper_bound code in gpflow/models/sgpr.py and restores the original (tighter) test tolerance that had both been changed by commit 45efebc The plots don't quite match up to what was in the GPflow1 version (nor does the tight bound in the 1-inducing-point example at the end), but otherwise this seems to work. 27 October 2019, 16:46 UTC
9b5bf76 GPflow 2.0 notebook update: SGPR upper bound (#1116) 27 October 2019, 16:41 UTC
f650c7b GPflow 2.0 notebook update: understanding/models.ipynb (#1118) 27 October 2019, 16:31 UTC
d048736 Change GPflow 2.0 scipy default method to L-BFGS-B (as in GPflow 1.0) (#1112) Explicitly sets the default optimization method for Scipy() to L-BFGS-B (as in gpflow1), instead of letting scipy.minimize() figure it out. This resulted in BFGS, which may be too aggressive when encountering complex optimization surfaces, so L-BFGS-B may be a more sensible default. 27 October 2019, 16:28 UTC
ca40b13 Natural Gradient for GPflow 2.0 (#1109) 25 October 2019, 09:34 UTC
b6cc953 Notebook fixed - broke in earlier PR (#1115) 23 October 2019, 15:21 UTC
cd3559f Set summary format is now fixed (#1114) * Some changes in convolutional notebook * Default summary format now loaded in `print_summary` instead of tabulate_module_summary * Default summary format now loaded in `print_summary` instead of tabulate_module_summary * Default summary format now loaded in `print_summary` instead of tabulate_module_summary 23 October 2019, 12:30 UTC
330074a GPflow 2.0 notebook update: FITC vs VFE (#1104) * WIP * make it run * rerun notebook * rerun notebook after merging in bugfix * Call step_callback through scipy.minimize's callback procedure (at the end of each step); previous behaviour was to call step_callback at each evaluation of objective function * adjust callback signature * changes to make it work under gpflow2: method=L-BFGS-B, tol=1e-11. increase callback frequency * rerun notebook * remove from notebook test blacklist * fix Scipy 23 October 2019, 10:16 UTC
6e43fec Change step_callback behaviour of Scipy optimizer in gpflow2 to behave as in gpflow1 (#1111) Changes behaviour of step_callback so that the callback only gets called once per optimisation step, not once per objective function evaluation. Makes gpflow2's Scipy() behave more like gpflow1's ScipyOptimizer()/monitoring. * Call step_callback through scipy.minimize's callback procedure (at the end of each step); previous behaviour was to call step_callback at each evaluation of objective function * split off from unpack_tensors (now stateless) the new assign_tensors (assigns to variables) * change callback_func to pass variables and their current values to step_callback, not assigning/computing loss/gradients * fix type signature * Improve docstring 22 October 2019, 16:54 UTC
a186ca5 Traverse function for DAG (tf.Module) structures (#1108) * Rewrite get_leaf_components and deepcopy_components with traverse Write/update tests for both * Tape should compute gradients outside context * Explanation of the test * Some changes in convolutional notebook * Update tests/test_deepcopy.py Co-Authored-By: st-- <st--@users.noreply.github.com> * Reorganising recursion on traverse * Update tests/test_deepcopy.py Co-Authored-By: st-- <st--@users.noreply.github.com> * Update tests/test_deepcopy.py Co-Authored-By: st-- <st--@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Update gpflow/utilities/utilities.py Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> * Separating deepcopy_components from clear_cache_bijectors * Remove ListWrapper and _DictWrapper Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> 22 October 2019, 16:38 UTC
51b2465 [GPflow2.0] notebook update: sanity_check.ipynb (#1078) 22 October 2019, 16:32 UTC
a813515 GPflow2.0 notebook update: coregionalisation.ipynb (#1072) * explicitly set method="L-BFGS-B" and rerun 22 October 2019, 13:13 UTC
b0ddc6d Notebook for Variational Fourier Features (#1062) Adds a notebook that demonstrates how to add inter-domain inducing variables to GPflow without having to touch the core code base, at the example of variational Fourier features (Hensman, Durrande, Solin, JMLR 18 (2018)). 21 October 2019, 14:19 UTC
33ded03 Ensure all tf_probability distributions take the correct dtype parameters (#1103) 18 October 2019, 15:06 UTC
deb4508 Fix hidden bug in SGPR (#1106) 1. Fix hidden bug in SGPR 2. Add the sgpr.compute_qu method from gpflow1 1. [Bug]. SGPR likelihoods were previously using full rank matrices instead of diagonal ones in both upper bound and likelihood calculation. Ie `Kdiag` was not "diag". This error was being masked by the intentional deactivation of tests comparing to the SGPR to the GPR, and what appears to be a hack to make tests working on the upper bound case. 2. [Migration]. Fixing the above broke another test, originally used for sgpr.compute_qu. The method sgpr.compute_qu had not been migrated from gpflow1, and a test that was meant to check it had been patched up to pass, erroneously. After speaking to @markvdw, concluded this method is useful, in particular to compare to SVGP model. The test has been patched up and the method ported to gpflow2. 17 October 2019, 14:46 UTC
3b2a2ee Change gpflow.base.Module attributes `parameter` and `trainable parameter` to be wrapped in a tuple, not generators (#1102) This matches tf2 behaviour [here](https://github.com/tensorflow/tensorflow/blob/1cf0898dd4331baf93fe77205550f2c2e6c90ee5/tensorflow/python/module/module.py#L143) and prevents accidentally trying to reuse the same the generator once exhausted. 16 October 2019, 09:39 UTC
c62ad93 GPflow 2.0 notebook update: Multiclass classification (#1092) 15 October 2019, 10:08 UTC
b474291 GPflow2.0 notebook update: kernel design (#1087) 15 October 2019, 10:07 UTC
4aef40d fix bug in log_prior when a Parameter has a transform but no prior (#1099) Fixes a bug in the optimization objective for all `BayesianModel` subclasses when the model has parameters that have a `transform` (e.g. `positive()`, for kernel lengthscales and variances) but no `prior` (i.e. when doing Maximum Likelihood Estimation (MLE) inference). The objective should be independent of the parametrisation of the parameters, i.e. `log_prior()` of the parameters should be zero. 14 October 2019, 21:36 UTC
c5b91dd Merge pull request #1098 from GPflow/st/minor_cleanup Minor cleanup 11 October 2019, 14:56 UTC
f4688ba Apply suggestions from code review Fix types Co-Authored-By: Eric Hammy <6815729+condnsdmatters@users.noreply.github.com> 11 October 2019, 13:44 UTC
0ee881e Merge pull request #1097 from GPflow/st/quickfix_regression_notebook_test Quickfix: enable notebook test of regression.ipynb 11 October 2019, 11:12 UTC
a57569c Merge branch 'develop-2.0' of github.com:GPflow/GPflow into st/minor_cleanup 11 October 2019, 10:59 UTC
5cef76e regression.ipynb is ready for testing but had not been removed from blacklist 11 October 2019, 10:44 UTC
0b368ce Fix behaviour of likelihood quadrature tests (#1083) 11 October 2019, 10:37 UTC
7e6028c GPflow2.0 notebook update: varying_noise.ipynb (#1050) 11 October 2019, 09:21 UTC
ba28c56 GPflow2.0 notebook update: regression.ipynb (#1076) * regression notebook update to gpflow2 * now it has the correct text * restart&run all, and some minor text changes * minor updates * Update regression.ipynb 11 October 2019, 09:02 UTC
8e2e5cf Remove tf_graphs_and_sessions notebook (#1096) 10 October 2019, 18:40 UTC
99e8988 Sync notebooks with develop (includes moving files from notebooks2 back to doc/source/notebooks) (#1073) 09 October 2019, 20:19 UTC
3a21b65 adjust import for py3.8 09 October 2019, 13:42 UTC
d8bbeb7 make docstrings r"" 09 October 2019, 13:42 UTC
a8f9348 minor changes 09 October 2019, 13:32 UTC
760bf04 add noise_variance argument to GPR and SGPR 09 October 2019, 13:30 UTC
4dba79d Clean up dependencies and setup instructions (#1074) 08 October 2019, 10:24 UTC
5a5c34e Merge pull request #1085 from GPflow/sergio_pasc/gpflow-2.0/updated-print-summary-tests Test on print_summary now checks string output straight 07 October 2019, 14:59 UTC
5654336 merging 07 October 2019, 14:50 UTC
ecd0b82 Updated method names and signatures 07 October 2019, 14:47 UTC
ab73c4b Update gpflow/utilities/utilities.py Co-Authored-By: st-- <st--@users.noreply.github.com> 07 October 2019, 14:31 UTC
74cf61b Test on print_summary now checks string output straight 07 October 2019, 14:10 UTC
cba9732 Remove default argument of the set_trainable (was False) (#1060) 07 October 2019, 14:09 UTC
e3c3f96 Fix bug in print_summary for composition kernels (#1071) Closes #1066 07 October 2019, 13:17 UTC
2974b94 Improve gpflow2 code coverage by adding tests (#1079) * add tests of gpflow.config * make config tests pass * use raise NotImplementedError in abstractmethod so codecov does not count it * swap order of tests so that it ends up in the original state * pca_reduce: turn assert into ValueError * add tests for gplvm constructor checks * add pragma no cover to scipy optimizer type check * more NotImplementedErrors * update codecov.yml * add missing logdensities tests * Change code coverage threshold to 95% so that the build status reports actually mean something again * improve test_dtype_errorcheck * pragma: no cover for ValueError check * . 07 October 2019, 12:47 UTC
48933ab minor cleanup of RobustMax (#1075) 04 October 2019, 15:12 UTC
81ae0be Remove Natural Gradient to increase code coverage 02 October 2019, 20:22 UTC
36c4736 Fix test coregion (#1067) 02 October 2019, 09:50 UTC
57f176c Merge branch 'awav/gpflow-2.0' of github.com:GPflow/GPflow into awav/gpflow-2.0 02 October 2019, 09:31 UTC
8dfba0c Remove hmc.py optimizer 02 October 2019, 09:31 UTC
6e57626 GPflow 2.0 notebook update: GPs for big data (#1048) 01 October 2019, 19:13 UTC
705380d Rename inducing_variables -> inducing_variable as model attribute (#1063) 01 October 2019, 15:39 UTC
a39317b GPflow 2.0 notebook update: classification (#1044) 01 October 2019, 15:36 UTC
f9c3052 Improved convolutional GP notebook. (#1061) 25 September 2019, 16:31 UTC
13dd839 Added convolutional code (#1034) 25 September 2019, 12:17 UTC
1aff010 Mark/gpflow 2.0/kl dispatch (#1035) * Multiple dispatch for KL divergences. * prevent overwriting dispatcher * fix SVGP 24 September 2019, 09:53 UTC
f359d17 Added more elaborate documentation to multioutput notebook. (#1054) 24 September 2019, 08:13 UTC
102bf48 Remove tf.function(autograph=True) in gplvm notebook 22 September 2019, 15:43 UTC
292e446 Wrap gplvm training in tf.function 22 September 2019, 15:16 UTC
db6d2fb Add ci_utils.py module to the notebooks 22 September 2019, 14:57 UTC
8c54b52 Import tensorflow in gplvm.ipynb 22 September 2019, 14:00 UTC
f35fd17 Update README.md 22 September 2019, 13:58 UTC
f63857b Temporary change in README.md file 21 September 2019, 21:08 UTC
41dce7d GPflow 2.0 notebook update: GPLVM 16 September 2019, 15:43 UTC
e1cb9e7 GPflow 2.0 notebook update: Ordinal Regression (#1049) 16 September 2019, 10:40 UTC
aaee8b1 GPflow2.0 notebook update: multioutput (#1047) 16 September 2019, 10:33 UTC
da5c727 GPflow 2.0 notebook update: kernels (#1046) 16 September 2019, 10:31 UTC
9a278ac Update notebook test 16 September 2019, 10:18 UTC
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