Other
* Bump version: 0.8.7 → 0.8.8. [Max Zwiessele]
* Bump version: 0.8.6 → 0.8.7. [Max Zwiessele]
* [py3] print statement. [Max Zwiessele]
* [pred_var] added predictive variable as property now. [Max Zwiessele]
* Bump version: 0.8.5 → 0.8.6. [Max Zwiessele]
* Merge branch 'master' of github.com:SheffieldML/GPy. [Max Zwiessele]
* Apply bug fix for set_XY. [Zhenwen Dai]
* Converting .md to .rst automatically now. [Max Zwiessele]
* Bump version: 0.8.4 → 0.8.5. [Max Zwiessele]
* Merge pull request 240 from SheffieldML/devel. [Max Zwiessele]
Devel
* Merge branch 'master' into devel. [Max Zwiessele]
* Merge branch 'master' into devel. [Max Zwiessele]
* Merge branch 'master' into devel. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Updated sampling and plots to be correct shape, and changed plotting of sampling to be posterior samples p(f*|f), like it used to be, and samples_y to plot samples of p(y*|y) [Alan Saul]
* Add ARD to MLP kernel. [Zhenwen Dai]
* Merge pull request 239 from mikecroucher/master. [mikecroucher]
Cython fix
* Cython fix. [Mike Croucher]
* [setup] check if darwin. [Max Zwiessele]
* Update README.md. [Max Zwiessele]
* [verbosity] option in tests. [Max Zwiessele]
* [plotting] no printing of warning unless you actually use plotting. [Max Zwiessele]
* [matplotlib] pylab -> pyplot. [Max Zwiessele]
* Bump version: 0.8.3 → 0.8.4. [Max Zwiessele]
* [merge] setup.py. [Max Zwiessele]
* Fixes for Python 3. [Mike Croucher]
* Fixed for Python3. [Mike Croucher]
* [README] updated. [Max Zwiessele]
* Bump version: 0.8.2 → 0.8.3. [Max Zwiessele]
* [requirements] added six as an requirement. [Max Zwiessele]
* Merge pull request 237 from SheffieldML/devel. [Max Zwiessele]
Merge pull request 236 from SheffieldML/master
* Merge pull request 236 from SheffieldML/master. [Max Zwiessele]
sync up master and devel
* Update setup.py. [Max Zwiessele]
* Merge branch 'master' of github.com:SheffieldML/GPy. [Max Zwiessele]
* Added universal wheels. [Mike Croucher]
* Changed author to generic email address. [Mike Croucher]
* Bump version: 0.8.1 → 0.8.2. [Max Zwiessele]
* [setup] another patch for source dist. [Max Zwiessele]
* Bump version: 0.8.0 → 0.8.1. [Max Zwiessele]
* Merge pull request 232 from SheffieldML/versionfile. [Max Zwiessele]
Versionfile
* [version] controlling the version from __version__.py using bumpversion and setup.cfg. [Max Zwiessele]
* [version] controlling the version from __version__.py using bumpversion and setup.cfg. [Max Zwiessele]
* [version] handling version in a file. [Max Zwiessele]
* Python 3 fixes. [Mike Croucher]
* Update README.md. [Max Zwiessele]
* [bumpversion] added bumpversion for release control. [Max Zwiessele]
* [linalg] testing suite update. [Max Zwiessele]
* Merge branch 'master' into devel. [Max Zwiessele]
* Update setup.py with new version number. [mikecroucher]
* Bug fix for the print function in samplers.py. [Zhenwen Dai]
* Bug fix for compilation on Mac. [Zhenwen Dai]
* Update README.md. [Neil Lawrence]
* Update AUTHORS.txt. [Neil Lawrence]
* Merge branch 'devel' [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Bug fix for compilation on Mac. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Removed annoying print. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Allowed gpyified var gauss. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Added full cov prediction. [Alan Saul]
* [merge] merge master into devel. [Max Zwiessele]
* [doc] build was pushed to github. [Max Zwiessele]
* Merge pull request 191 from mellorjc/master. [James Hensman]
adding an exponential prior
* Added Exponential prior. Made some minor (and not exhaustive) formatting changes based on pep8. [mellorjc]
* Merge pull request 1 from SheffieldML/master. [mellorjc]
merge updates from upstream
* Merge pull request 208 from strongh/tutorial-and-readme-updates. [James Hensman]
Tutorial and readme updates
* Remove docstring for missing tensor param from add/prod. [Homer Strong]
relevant to 162
* Update kernel tutorial. [Homer Strong]
* Fix links in readme. [Homer Strong]
the ! is for adding images, but these are just links
* Merge pull request 211 from PredictiveScienceLab/master. [Zhenwen Dai]
Fixes the PDF transformation bug by handpicking James Hensman's code from the devel branch
* Removed dir ib_tests. [Ilias Bilionis]
* PDF Transformation bug patched. [Ilias Bilionis]
* Handpicked James Hensman's code that ensures that fixes the PDF of transformed variables. Fixed minor plotting bug. [Ilias Bilionis]
* Fixed MCMC sampler. [Ilias Bilionis]
* Added compute of jacobian. [Ilias Bilionis]
* Beautification change. [Ilias Bilionis]
* Added proper comments to the test. [Ilias Bilionis]
* Fixed transformation plotting bug and added test that demonstrates the problem. [Ilias Bilionis]
* Merge pull request 184 from mikecroucher/master. [mikecroucher]
Bug fix for issue 161
* Bug fix for issue 161. [Mike Croucher]
* [misc test] if there was no overflow, dont fail the test. [Max Zwiessele]
* [readthedocs] forcing readthedocs into not failing. [Max Zwiessele]
* [readthedocs] forcing readthedocs into not failing. [Max Zwiessele]
* [test] adding some more tests for coverage. [Max Zwiessele]
* [readthedocs] forcing readthedocs into not failing. [Max Zwiessele]
* [readthedocs] forcing readthedocs into not failing. [Max Zwiessele]
* [readthedocs] forcing readthedocs into not failing. [Max Zwiessele]
* Git Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Update README.md. [Max Zwiessele]
updated installation instructions scipy 0.16
* [testing] [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Fixed for Python 3. [Mike Croucher]
* [doc] some changes to the doc, using mathjax some additions in math. [Max Zwiessele]
* Git pushMerge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Optimize util for mpi. [Zhenwen Dai]
* [licensing] replaced licensing with BSD, and erfcx. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Used scipy.log1p since it gives more consistent results cross-platform. [Mike Croucher]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Mike Croucher]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Changed gpu interface for mpi. [Zhenwen Dai]
* Switched to scipy.special.log1p [Mike Croucher]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Mike Croucher]
* Used scipy.log1p since it gives more consistent results cross-platform. [Mike Croucher]
* Fixed typos. [Mike Croucher]
* [more coverage] and predictive var fixes. [Max Zwiessele]
* Python 3 fixes. [Mike Croucher]
* Git pushMerge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Mike Croucher]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Speed tuning for mlp kernel and gauss qudrature for psi-statistics. [Zhenwen Dai]
* Python 3 fixes. [Mike Croucher]
* Fixes Cython compilation on Mac OS X. [Mike Croucher]
* Automatic fallback to Numpy if Cython modules not available. [Mike Croucher]
* [predict] using gp predict in sparse gp and predictive variable. [Max Zwiessele]
* [mean func] added in GPRegression. [Max Zwiessele]
* [coverage] tests for coverage increase. [Max Zwiessele]
* Fix linear kernel with NxMxM psi2. [Zhenwen Dai]
* New implementation for mlp kernel (speed improvemd) [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Merge pull request 227 from Dapid/clean_imports. [mikecroucher]
Clean some imports
* Cleanup unused imports. [David Menéndez Hurtado]
* Unify the interface of psicomp, but the psi2n of linear kernel and gaussian qradrature still needs to be done. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* [MRD] fixed mrd for new structure. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* [empty space] literally : ) [Max Zwiessele]
* [pickling] pickle error. [Max Zwiessele]
* Revert "[core] visited as propery" [Max Zwiessele]
This reverts commit a4ce1d473c13fa5cb577e4ff3dbdf76aa6a1a57f.
* Revert "[caching] different error" [Max Zwiessele]
This reverts commit f7087ebc9003a6950b58533e0ce373c03c82a4a2.
* [caching] different error. [Max Zwiessele]
* [core] visited as propery. [Max Zwiessele]
* [setxy] always run the update after updating X and Y. [Max Zwiessele]
* Allow cache supporting boolean and integers. [Zhenwen Dai]
* [psi2n] Liner psi2 statistics now implemented for separate n. [James Hensman]
* Slightly improved computation for var_Gauss method. [James Hensman]
* [psi2n] added psi2n for static kernels. [Max Zwiessele]
* [spgp minibatch] linear calls the right psicomps and add kernel. [Max Zwiessele]
* [coverage] script to create coverage output html. [Max Zwiessele]
* [coverage] test predict sparse gp. [Max Zwiessele]
* [coverage] added normalizer tests. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* [psi2] NxMxM fixes for the add kernel. [Max Zwiessele]
* Fall back to the old psicomp interfacegit status! [Zhenwen Dai]
* Add psi-statistics test. [Zhenwen Dai]
* [mrd] fixes for updates on psi2. [Max Zwiessele]
* [spgp] minibatch testing. [Max Zwiessele]
* [merge] for spgp minibatch and psi NxMxM. [Max Zwiessele]
* [spgp minibatch] added new routine for psi NxMxM, much faster, little bigger mem footbprint. [Max Zwiessele]
* Small edits for linear kernel. [Alan Saul]
* Reindented, did some profiling which looks promising. [Alan Saul]
* Merge branch 'devel' into missing_opt. [Alan Saul]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Alan Saul]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Alan Saul]
* Corrected caching for psi derivatives. [Alan Saul]
* Try calculating dL_dpsi1*psi1 individually for each dimension as we go along. [Alan Saul]
* Passing psi statistics. [Alan Saul]
* Removed comment. [Alan Saul]
* Checking kerngrads full_value. [Alan Saul]
* Gradients for X seem to match. [Alan Saul]
* Made sparse gp work again. [Alan Saul]
* Tidied but broken. [Alan Saul]
* Optimizing missing data model, needs tidying but now much faster. [Alan Saul]
* Fixed array2string bug for N > 1000 default printing. [Alan Saul]
* Merge pull request 224 from Dapid/fix_print. [mikecroucher]
Fix print statement
* FIX: missing compatibility Py2/3. [David Menéndez Hurtado]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* [add] renamed>sum. [Max Zwiessele]
* [magnification] static corrections. [Max Zwiessele]
* [magnification] added static kernel support and faster derivative computations. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* [magnification] plot_magnification expanded. [Max Zwiessele]
* Add util.parallel into import. [Zhenwen Dai]
* Errorbars fixed. [Ricardo]
* Gperrors color as parameter. [Ricardo]
* Shape of heteroscedastic variance corrected. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
* Merge pull request 219 from Dapid/fix_209. [mikecroucher]
Now Scipy 0.16 is required, removing fixes for older versions.
* Fixing the blas arguments for DSYRK. [David Menéndez Hurtado]
* Fixing confussion between lapack and ctypes interfaces. [David Menéndez Hurtado]
* FIX: now Scipy 0.16 is required, removing fixes for older versions. Accessing blas through the scipy interface. [David Menéndez Hurtado]
* [magnification] mostly plotting and some model corrections for _predictive_variable. [Max Zwiessele]
* [hetnoise] import correction. [Max Zwiessele]
* [merge] [Max Zwiessele]
* Merge branch 'updates' into devel. [Max Zwiessele]
* [core] updating system, security branching. [Max Zwiessele]
* New function to plot just the errorbars of the training data. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
* Ensuring the shape of the mean vector at predict time fixes bug in EP prediction. [James Hensman]
* Note added to the docs. [Ricardo]
* Change in _diag_ufunc with mzwiessele. [Ricardo]
* New likelihood: HeteroscedasticGaussian. [Ricardo]
* Model uses the new HeteroscedasticGaussian likelihood. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Add MRD for regression benchmark. [Zhenwen Dai]
* Remove the old housing benchmark. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Fixed random seed for kronecker tests. [James Hensman]
* Adding a white kernel to a sparseGP test for stability. [James Hensman]
* Add the regression benchmark. [Zhenwen Dai]
* Add missing file. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Gradients w.r.t. kappa corrected. [Ricardo Andrade]
np.diag(dL_dK_small) needs to be copied
* Trying to make travis print warnings. [Alan Saul]
* Fixed laplace seed, added debugging for misc tests. [Alan Saul]
* Merge branch 'devel' of github.com:/sheffieldml/gpy into devel. [James Hensman]
* Removed installation conflict. [Alan Saul]
* Updated travis for 0.16 scipy. [Alan Saul]
* Sqrt(pi) term fix in Bernoulli. [James Hensman]
* Added variational expectation tests updates. [Alan Saul]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Alan Saul]
* Adding var_gauss.py. [James Hensman]
* Added fallback for non-identity link function for Gaussian variational expectations. [Alan Saul]
* Added testing of variational expectations, analytic vs numeric, and gradient checks. [Alan Saul]
* The Opper-Archambeau method is now implemented as an inference method in the GPy style. [James Hensman]
* Minor bugfixes in plotting: quantiles are now computed using predict_kw correctly. [James Hensman]
* Psi-statistics for any kernels via Gaussian quadrature. [Zhenwen Dai]
* Improve the stability of parallel inference code. [Zhenwen Dai]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Merge pull request 216 from Dapid/devel-cython_update. [James Hensman]
* ENH: various Cython enhancements, mostly releasing the GIL when not needed. [David Menéndez Hurtado]
* Tidied link_fn tests. [James Hensman]
* Tidied setup.py. [James Hensman]
* Merge branch 'Dapid-devel-cythonchol' into devel. [James Hensman]
* Running cython. [James Hensman]
* Reenabling gil. [James Hensman]
* Minor corrections :) [James Hensman]
* Merge branch 'devel' into Dapid-devel-cythonchol. [James Hensman]
* Adding new test for cholesky backprop. [James Hensman]
* Merge branch 'devel-cythonchol' of git://github.com/Dapid/GPy into Dapid-devel-cythonchol. [James Hensman]
* FIX: ensuring contiguity of the buffers for BLAS call and returning a Numpy array. [David Menéndez Hurtado]
* FIX: transforming the indexing to 2D. [David Menéndez Hurtado]
* ENH: implementing the Cholesky backpropagation through Scipy's BLAS. [David Menéndez Hurtado]
* ENH: fixed up BCGPLVM to work with new framework. [James Hensman]
* Another relative import (py3) bug. [James Hensman]
* Merge pull request 183 from AlexGrig/std_periodic_kernel. [James Hensman]
* TEST: Making test for the Standard Periodic Kernel similar to other kernel tests. [Alexander Grigorievskiy]
* TEST: Adding test for periodic kernel. [Alexander Grigorievskiy]
* ENH: Adding standard periodic kernel. [Alexander Grigorievskiy]
The standard periodic kernel is the one which is mentioned
in the Rasmussen and Williams book about Gaussian Processes.
* Fixing qualtile code for some likelhoods. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Change the default name of sparse_gp_mpi class. [Zhenwen Dai]
* Fixed a plotting bug. [James Hensman]
* Tidied model_tests. [James Hensman]
* Removed randomness from inference tests by setting np.seed. [James Hensman]
* Caught warnings in misc_tests. [James Hensman]
* Fixed relative import in spline. [James Hensman]
* Fixed conflict in plotting. [James Hensman]
* Merge branch 'tjhgit-devel' into devel. [James Hensman]
* Merging. conflict in relative import styles. [James Hensman]
* Merge remote-tracking branch 'upstream/devel' into devel. [tjhgit]
Conflicts:
GPy/kern/__init__.py
* Added spline kernel (from P. Hennig) to GPy. [tjhgit]
Had to modify the base_plots and model_plots.py, since I had troubles
installing GPy in anaconda on debian linux due to the dependency on
Tango. Why is Tango needed to represent colors that can also be typed in
Hex format thus eliminating further dependencies.
* Fixed strange bug. In python 3, numbers startin 0 are octal. [James Hensman]
* Merge pull request 212 from mikecroucher/devel. [mikecroucher]
Python 3 fixes
* Python 3 fixes. [Mike Croucher]
* Fixed SVGP tests. [James Hensman]
* Rbf psi-statistics speed improvement. [Zhenwen Dai]
* Bug fix: the name of parameterable object is not removed when unlinking. [Zhenwen Dai]
* Allow Y to be uncertain. [Zhenwen Dai]
* The bug fix for the cblas.h problem in Mac os x. [Zhenwen Dai]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* Merge the changes. [Fariba]
* Fix DGPLVM prior. [Zhenwen Dai]
* Improve the documentation of infer_newX. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Change crescent data to optimize with .optimize() [Neil Lawrence]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
* Commit to pull. [Neil Lawrence]
* Fixed model test. [Alan Saul]
* Changed quantile computation via sampling and added fallback for predictive mean and variance if conditional mean and variance are not implemented yet. [Alan Saul]
* Passing metadata. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Generalized the variatinoal Gaussian approximatino revisited code for any likelihood. [James Hensman]
* Cache some values. [Alan Saul]
* Changes. [Fariba]
* [bgplvm] technical new stuff. [mzwiessele]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* Some correction for ibp ssgplvm. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Python 3 fixes. [Mike Croucher]
* Passing on y_metadata. [Alan Saul]
* Allowing set initial noise variance for GPRegression. [javiergonzalezh]
* Sqrt pi term was missing in variational expectations. [James Hensman]
* Lots of work on cython choleskies. [James Hensman]
* Fiddling with cholesky backprop. [James Hensman]
* Parallelizing backprop of cholesky. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Jacobians should not be computed only for transforms. [James Hensman]
* Jacobians should not be computed only for transforms. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Updated plotting. [Alan Saul]
* [inference] minibatch inference needed polishing. [mzwiessele]
* [plotting] parameterized.values. [mzwiessele]
* [parameterized] merge in jacobian for priors? [mzwiessele]
* [verbose opt] verbose needed clear after finish push through. [mzwiessele]
* Merge branch 'devel' of github.com:/sheffieldml/gpy into devel. [James Hensman]
* Allow to set color for the skeleton visualization. [Zhenwen Dai]
* [ssgplvm] change the default gamma interval. [Zhenwen Dai]
* Jacobian bugfix. [James Hensman]
* Added log jacobian transofms for Exponent, Logexp. [James Hensman]
* Minor bugfix in raw_predict with full_cov for sparseGP. [James Hensman]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Alan Saul]
* [ssmrd] implement with IBP prior. [Zhenwen Dai]
* Reshaped log predictive density to have D outputs. [Alan Saul]
* Added option for plotting with SVGP. [Alan Saul]
* [ssgplvm] implement IBP prior. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* [param] added multilevel indexing note to doc. [Max Zwiessele]
* Merge branch 'devel' of github.com:/sheffieldml/gpy into devel. [James Hensman]
* Some cython improvments for stationary kerns. [James Hensman]
* Minor bugfix in mlp kernel. [James Hensman]
* Svgp bugfix. [James Hensman]
* [ssgplvm] group spike. [Zhenwen Dai]
* Start implement ICP for ssgplvm. [Zhenwen Dai]
* Prevent the predicted variance to be negative. [Zhenwen Dai]
* Small bug in cython tests. [James Hensman]
* Merge branch 'reorder_choleskies' into devel. [James Hensman]
* Svgp working with reordered chols. [James Hensman]
* Interim svgp commit. [James Hensman]
* Merge branch 'devel' into reorder_choleskies. [James Hensman]
* Svgp, more c-ordering. [James Hensman]
* Svgp tests are passing with re-ordered chols. [James Hensman]
* Preliminary reconfiguring or choleskies ordering. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* Change the behavior the optimize_restarts to keep the original model parameters for the firt run. [Zhenwen Dai]
* Omp for gradients_X. [James Hensman]
* [heteroscedastic gauss] Implemented Heteroscedastic Guassian Lik with ric70x7. [Max Zwiessele]
* [heteroscedastic gauss] Implemented Heteroscedastic Guassian Lik with ric70x7. [Max Zwiessele]
* [opt messages] show DDdHHhMMmSSsMS. [Max Zwiessele]
* [opt messages] show dd/hh:mm:ss.ms. [Max Zwiessele]
* [cython import] error notices where it happens. [Max Zwiessele]
* [predict] documentation. [Max Zwiessele]
* [predict] documentation. [Max Zwiessele]
* Again with gradients. [Alan Saul]
* Fixing constant mapping gradients. [Alan Saul]
* Small name change. [Alan Saul]
* Addint constant mapping. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele]
* [changepoint] cp is array. [mzwiessele]
* Fixed linalg for general matricies. [Alan Saul]
* Added another einsum operation. [Alan Saul]
* Added a constant mappiung. [James Hensman]
* Removing silly einsum. [James Hensman]
* Better cython compiler directives for choleskies. [James Hensman]
* Bugfix: confused output dim and num_latents in svgp. [James Hensman]
* Added faster einsums to linalg, with a couple of tests. [Alan Saul]
* Faster einsums in svgp. [James Hensman]
* Adding limited support for svg to have differnet number of latent functions to columns of Y. [James Hensman]
* Update .travis.yml. [James Hensman]
* Added cholesy backprop test. [James Hensman]
* Merge by running cython. [James Hensman]
* Added backprop of cholesky grads. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Update .travis.yml. [James Hensman]
* Update MANIFEST.in. [James Hensman]
* Merge branch 'cython2' into devel. [James Hensman]
* Changes to comments in compiled cython file. [James Hensman]
* Merge branch 'cython2' into devel. [James Hensman]
* All tests passing. [James Hensman]
* Fixed coregionalize cython. [James Hensman]
* Tests passing (cython) [James Hensman]
* Tidien up coregionlize w AS. [James Hensman]
* More edits to stationary to clean up for cython. [James Hensman]
* Modifiying stationary.py. [James Hensman]
* Some eidts to choleskies.pyx. [James Hensman]
* Help choleskies along a little. [James Hensman]
* Adding choleskies cythonized. [James Hensman]
* Start of cythoning coregionalize. [James Hensman]
* Added cython code for lengthscale gradients. [James Hensman]
* Initial cython commit. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* [basis funcs] memory efficient posterior inference. [mzwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele]
* [plotting] added predict_kw to plot function. [mzwiessele]
* [inference] exact Gaussian some constant jitter. [mzwiessele]
* [paramnonparam] adding cdf like. [mzwiessele]
* Fixed deg free gradient. [Alan Saul]
* Added log predictive density, student t degrees of freedom gradients and plotting functionality. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* [basisfunckern] gradients for non ard adjusted. [mzwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [mzwiessele]
* Merge with commit of dgplvm. [frb-yousefi]
* Prior with Lambda. [frb-yousefi]
* Descrimative BGPLVM prior with lambda added. [frb-yousefi]
* [basisfuncs] updated kernel to better reflect linear trends and added ARD support. [mzwiessele]
* [basis funcs] linear slope identifiability higher, symmetry plus true linear effect. [mzwiessele]
* [sparse gp] memory overflow with big data, iterating over dimensions now. [mzwiessele]
* Quadrature appeared to be out by a factor of 1/sqrt(pi) [Alan Saul]
* Reverted back. [Alan Saul]
* Updated svgp kernel gradients. [Alan Saul]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* Manual merging with AS. [James Hensman]
* Fixed log predictive density, added option for LOO to provide some intemediate variables. [Alan Saul]
* Removed jitter printing. [Alan Saul]
* Changed LOO implementation for Eq 30 instead of 37. [Alan Saul]
* Added LOO for laplace and exact inference on training data, Gaussian logpdf appeared to be wrong, now fixed. [Alan Saul]
* Added to init. [Alan Saul]
* Added option to plot the transformed link function (posterior once the link function has been applied) [Alan Saul]
* Added hessian and skew gradient checkers, some block functions. [Alan Saul]
* Fix for model gradients. [Alan Saul]
* Added some numerical stability to link functions with tests for link functions. [Alan Saul]
* Fix typo. [Alan Saul]
* Minor commenting changes. [Alan Saul]
* Added numerical clipping. [Alan Saul]
* Manual merging. [James Hensman]
* Merge pull request 189 from mikecroucher/devel. [James Hensman]
Python 3 Compatibility
* Merge remote-tracking branch 'upstream/devel' into devel. [Mike Croucher]
* Fix printing error. [Mike Croucher]
* Added (SLOW) Pure Python implementations of flat_to_triang and triang_to_flat. [Mike Croucher]
* Working in Py2 but broken in Py3. [Mike Croucher]
* Fix merge conflicts. [Mike Croucher]
* Resolve merge conflicts. [Mike Croucher]
* Used 'six' to support Py3 and Py2 simultaneously. [Mike Croucher]
* Merge from upstream. [Mike Croucher]
* Fix README.md formatting. [Mike Croucher]
* Fix README.md formatting. [Mike Croucher]
* Xrange fixes for Python 3. [Mike Croucher]
* Updated README.md for recent Py3 work. [Mike Croucher]
* Kern fix. All tests now pass. [Mike Croucher]
* 2to3 itertools fixer. [Mike Croucher]
* Fixed leaky comprehension behaviour for Py3. [Mike Croucher]
* Various Py3 fixes. [Mike Croucher]
* Python 3 metaclass fix. [Mike Croucher]
* Various Python 3 fixes. [Mike Croucher]
* Types.TupleType -> tuple fix for python 3. [Mike Croucher]
* Im_self->__self__ fix for python 3. [Mike Croucher]
* Iterkeys fix for Python 3. [Mike Croucher]
* Removed debugger set up command. [Mike Croucher]
* Map fix for Python 3. [Mike Croucher]
* Changed refereences to iteritems() to items() for Py3 compat. [Mike Croucher]
* Updated README now that dict issues are fixed. [Mike Croucher]
* Fixed 'dict changed size' errors. [Mike Croucher]
* Import fixes for Py3. [Mike Croucher]
* Various Py3 related import fixes. [Mike Croucher]
* Changed refereences to iteritems() to items() for Py3 compat. [Mike Croucher]
* CPickle fix for Py3. [Mike Croucher]
* Changed refereences to iteritems() to items() for Py3 compat. [Mike Croucher]
* Updated README.m to refelect recent Py3 work. [Mike Croucher]
* Commented out weave functions for Py3 support. [Mike Croucher]
* Commented out weave functions for Py3 support. [Mike Croucher]
* Itertools fixes from 2to3. [Mike Croucher]
* Need to explicitly turn a range object to a list in for these tests. [Mike Croucher]
* Has_key has been removed from Python 3. [Mike Croucher]
* From functools import reduce for Py3 compat. [Mike Croucher]
* Ensure that object.__new__ never gets called with arguments. [Mike Croucher]
* Import reduce from functools for Py3 compat. [Mike Croucher]
* Ensure that object.__new__ never gets called with arguments. [Mike Croucher]
* Ensure that object.__new__ never gets called with arguments. [Mike Croucher]
* Fixed integer division for Python 3 compat. [Mike Croucher]
* Fixed string encoding for Python 3. [Mike Croucher]
* Reduce fix for Python 3. [Mike Croucher]
* Changed metaclass syntax to be Py3 compatible. This breaks Py2 compatibility. [Mike Croucher]
* Import reduce from functools for py3 compatibility. [Mike Croucher]
* Python3 compatbility fixes. [Mike Croucher]
* Print fixes for Python 3. [Mike Croucher]
* Print fixes for Python 3. [Mike Croucher]
* Fixed tab/space indentation issue. [Mike Croucher]
* Fix weave import for Py3. [Mike Croucher]
* More import fixes for Py3. [Mike Croucher]
* Import fixes for Py3. [Mike Croucher]
* Fixed inconsistent tab error. [Mike Croucher]
* Fixed inconsistent tab error. [Mike Croucher]
* More input fixes. [Mike Croucher]
* More input fixes. [Mike Croucher]
* Import fixes for Py3. [Mike Croucher]
* Import fix for Py3. [Mike Croucher]
* Changed <> to != for Py3 compatibility. [Mike Croucher]
* Updated Py3 work. [Mike Croucher]
* Removed import urllib2 since it wasn't being used. [Mike Croucher]
* Urllib2 fixes for Py3 compatibility. [Mike Croucher]
* Fixed cPickle import for Python 3. [Mike Croucher]
* Exception raising fix for Python 3. [Mike Croucher]
* Put weave import in a try block so it fails gracefullt in Py3. [Mike Croucher]
* Merge remote-tracking branch 'upstream/devel' into devel. [Mike Croucher]
* Fixed ConfigParser for Python 3 compat. [Mike Croucher]
* Commented out cholupdate since it uses weave and appears not to be used. [Mike Croucher]
* Added Python 3 progress to README.md. [Mike Croucher]
* Resolved merge conflict. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Exception fixes for Python 3 compat. [Mike Croucher]
* Typo. [Mike Croucher]
* Fixed Python 2 compatibility. [Mike Croucher]
* Convert print to function for Python 3 compatibility. [Mike Croucher]
* Convert print to function for Python 3 compatibility. [Mike Croucher]
* Convert print to function for Python 3 compatibility. This breaks compatibility for versions of Python < 2.6. [Mike Croucher]
* Convert print to function for Python 3 compatibility. [Mike Croucher]
* Convert print to function for Python 3 compatibility. This breaks compatibility for versions of Python < 2.6. [Mike Croucher]
* Convert print to function for Python 3 compatibility. [Mike Croucher]
* Merge remote-tracking branch 'upstream/devel' into devel. [Mike Croucher]
* Added details of Python 3 work. [Mike Croucher]
* Convert print to function for Python 3 compatibility. This breaks compatibility for versions of Python < 2.6. [Mike Croucher]
* More relative import fixes for Python 3 compatibility. [Mike Croucher]
* Relative import fixes for Python 3 compatibility. [Mike Croucher]
* Updated README.md to refer to GPy/testing for running the tests. [Mike Croucher]
* Speed ups for normal cdf. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Added Y_metadata to log_predictive_density. [Alan Saul]
* [minor edits] [mzwiessele]
* [basis func kernels] added support for simple basis function kernels, can be easily extended by implementing phi function in BasisFuncKern. [mzwiessele]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* Small bugfix in white kernel. [James Hensman]
* Tests to probe the mean-function functionality. [James Hensman]
* Merge branch 'mean_functions' into devel. [James Hensman]
* Merges. [James Hensman]
* Whitespace. [James Hensman]
* Mean functions now working for svgp. with tests. [James Hensman]
* Fixed up product kernel tests. [James Hensman]
* Mappings, including tests. [James Hensman]
* Working mean function examples. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into mean_functions. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into mean_functions. [James Hensman]
* Merged. ish. [James Hensman]
* Merge pull request 174 from beckdaniel/kernel_prod_bugfix. [James Hensman]
Kernel product bugfix
* Test + code change in gradients_X. [Daniel Beck]
* A cleaner test. [Daniel Beck]
* Changed operator.mul to np.multiply for consistency. [Daniel Beck]
* Added decorator that changes numpy invalid op warning to exception. [Daniel Beck]
* First attempt. [Daniel Beck]
* Merge pull request 177 from mellorjc/master. [James Hensman]
matplotlib interactive mode only in IPython
* Catch only a specific error. [mellorjc]
catch only NameError, rather than everything.
* Matplotlib interactive mode only in IPython. [mellorjc]
have interactive mode only in IPython so that running scripts that plot from python behave like normal.
* A temporal fix for the problem of sometimes the model not being updated. [Zhenwen Dai]
* Add mcmc into inference import. [Zhenwen Dai]
* Bug in linalg jitchol!!! [Alan Saul]
* Merge branch 'master' of github.com:SheffieldML/GPy. [Nicolo Fusi]
* Merge branch 'devel' [Max Zwiessele]
* Implement update_gradients_diag for MLP kernel. [Zhenwen Dai]
* Re-implemented warpedGP for new release of GPy. [Nicolo Fusi]
* Fixed minor bug in sparse gp minibatch. [Nicolo Fusi]
* Minimual edits to exact_inference. [James Hensman]
* Added mean function into the prediction. [James Hensman]
* Added parseing of mean func to gp.py. [James Hensman]
* Mean functions in place. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Optimize sslinear kernel. [Zhenwen Dai]
* Fallback the implementation of spike and slab prior. [Zhenwen Dai]
* Change the name of kernel DiffGenomeKern to DEtime. [Zhenwen Dai]
* More samples for predictive quantile. [Alan Saul]
* Merge branch 'saul_merge' into devel. [Alan Saul]
* Added safe_exp and tests. [Alan Saul]
* Small tidying up. [Alan Saul]
* Merge branch 'devel' into saul_merge. [Alan Saul]
* Merging with private repo, mostly fixed. [Alan Saul]
* Added block matrix dot product. [Alan Saul]
* Adding likelihoods and block matrices. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Relaxed inference test requirement. [Alan Saul]
* Adding a comment to clarify predictive_gradeints (Thanks AT) [James Hensman]
* Extra kernel stressing in benchmarks, bugfix in svgp. [James Hensman]
* Adding the beginnings of some benchmarks. [James Hensman]
* Shape changes for gradeitns of likelihood parameters in variational_expectations. [James Hensman]
* Added some clarifying comments with NDL. [James Hensman]
* Some tests for the svgp, and some changes to the likelihoods. [James Hensman]
* Derivatives of likelihood things now working for svgp. [James Hensman]
* Stupid bug. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Lots of changes to mappings. [James Hensman]
* [var plots] wrong return values. [mzwiessele]
* [variational] plot needed kwargs. [mzwiessele]
* [verbose opt] ipython notebook new version widget changes. [mzwiessele]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* A little work on mappings. [James Hensman]
* [verbose opt] ipython notebook new version widget changes. [mzwiessele]
* [optimization] html widget api changes in ipython notebook? [mzwiessele]
* [sparse gp] doc changes for missing data. [mzwiessele]
* [ploting init] minor. [mzwiessele]
* [optimization] model prints how many parameters there are to optimize. [mzwiessele]
* Remove printing. [Zhenwen Dai]
* Fix the param renaming problem. [Zhenwen Dai]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Zhenwen Dai]
* [optimize] max_f_eval -> max_iters. [mzwiessele]
* [optimize] added clear functionality for ipython notebook and kern input sensitivity error handling. [mzwiessele]
* Add trigger update to set_{X,Y,Z} [Zhenwen Dai]
* Add set_Z function. [Zhenwen Dai]
* Updated other likelihoods to give back logpdf and gradients for each link_f rather than summing on the inside. [Alan Saul]
* Added binomial likelihood. [James Hensman]
Also some changes to pass through Y_metadata, where it had previously
been (errorneously) omitted.
* Messy merge. [James Hensman]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [frb-yousefi]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mzwiessele]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Reconfigured svgp inference a little. [James Hensman]
* Added more stable expectations for Bernoulli. [James Hensman]
* [pickling errors] due to too little constant jitter, the gradient checks in pickle tests did not pass. [mzwiessele]
* [verbose optimization] added automatic detection of ipython notebook support, this is experimental. [mzwiessele]
* [sparse gp] prediction without missing data and uncertain inputs was bugged. [mzwiessele]
* [optimization] experimental auto detect of ipython notebook. [mzwiessele]
* [updateable] update field in observable. [mzwiessele]
* [var_dtc] constant jitter 1e-10. [mzwiessele]
* Add save param_array. [Zhenwen Dai]
* Minor error in corregionalization corrected. [javiergonzalezh]
* [sparse gp] prediction with uncertain inputs. [mzwiessele]
* Force set_XY to update the model. [Zhenwen Dai]
* DGPLVM. [frb-yousefi]
* Removed climin dependency unless actually needed. [James Hensman]
* Minor weave/numpy bug in coregionalize. [James Hensman]
* Merge branch 'devel' of github.com:sheffieldml/GPy into devel. [James Hensman]
* Added logging for jitter so we know how much has been added and how many tries have been taken. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* [var dtc] added code for additional covariates, not affecting normal procedures. [Max Zwiessele]
* Bug in linalg jitchol!!! [Alan Saul]
* Fixed a plotting bug for sliced plots. [James Hensman]
* Update __init__.py. [Neil Lawrence]
Add inference to __init__.py
* Update hmc.py. [Neil Lawrence]
* Update __init__.py. [Cristian Guarnizo]
Added EQ_ODE2.
* Create eq_ode2.py. [Cristian Guarnizo]
Added ODE2 kernel for latent force models.
* [opt] unified printing of status of optimization. [Max Zwiessele]
* [transformations] bugfix for pickling. [Max Zwiessele]
* [opt] bugfix. [Max Zwiessele]
* [verbose opt] messages would be overwritten when using ipython_notebooks, fixed. [Max Zwiessele]
* [kern] added Fixed kern to import list in GPY.kern. [Max Zwiessele]
* [objective grads] undid the change, as this would lead to dramatic problems in reloading old models using the pickle module. [Max Zwiessele]
* [objective grads] undid the change, as this would lead to dramatic problems in reloading old models using the pickle module. [Max Zwiessele]
* [progress] show progress of optimization using optimize(itpython_notebook=True) [Max Zwiessele]
* [progress] show progress of optimization using optimize(itpython_notebook=True) [Max Zwiessele]
* [updates] now handled in observable, should have from the begining :/ [Max Zwiessele]
* [optimization prints] unified printouts for optimizers, added ipython_notebook flag for use in ipython notebooks. [Max Zwiessele]
* [parent notification] is now priority -1000, instead of -inf. [Max Zwiessele]
* [model print] updates now shown in print out. [Max Zwiessele]
* [natural gradients] added natural gradients, usable but not analysed. [Max Zwiessele]
* Renamed opimizer methods to unobscure gradients and objective. [Max Zwiessele]
* [parameterized] print outs for ipython notebook. [Max Zwiessele]
* SVI now working with minibatches. [Alan Saul]
* SVI now implemented without natural natural gradients or batches. [Alan Saul]
* Multi-outputted the svgp inference (buggy, probably) [James Hensman]
* Added svgp in partially broken state ready for multiouputs. [Alan Saul]
* Fixed quadrature for bernoulli likelihood, started adding Gaussian likelihood derivatives for quadrature. [Alan Saul]
* Svgp inference added -- not working yet. [James Hensman]
* [html print] more table based corrections for html printing. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Implement update_gradients_diag for MLP kernel. [Zhenwen Dai]
* [html repr] included css styling for html print outs. [Max Zwiessele]
* [vardtc] sparse gplvm in bayesian gplvm minibatch. [Max Zwiessele]
* [vardtc] predict with uncertain inputs, the non principled way. [Max Zwiessele]
* [natgrad] taking the gradient in the old direction, without adjustment. [Max Zwiessele]
* [model] update messages a little nicer. [Max Zwiessele]
* [stationary] lengthscales will be scaled by variance now. [Max Zwiessele]
* [Updateable] deprecated updates. [Max Zwiessele]
* [setup] new version number, to avoid confusion. This will be the next minor update, including changes to README and bugfixes. [Max Zwiessele]
* Update README.md. [James Hensman]
* Update README.md. [James Hensman]
* Update README.md. [James Hensman]
* Huge merge correcting upstream master. [Alan Saul]
* Merge branch 'devel' [Max Zwiessele]
* Merge branch 'devel' of github.com:/sheffieldml/GPy into devel. [James Hensman]
* Another attempt by installing a mini version of anaconda, should be easier to maintain. [Alan Saul]
* Attempting to fix travis build. [Alan Saul]
* Removed more sgd. [James Hensman]
* [huge merge] the second. [Max Zwiessele]
* [huge merge] trying to merge old master and master. [Max Zwiessele]
* Merge pull request 148 from martinsch/normalization_fix. [James Hensman]
* Normalization: avoid division by zero for constant feature dimensions. [mschiegg]
* Merge pull request 160 from slinderman/master. [James Hensman]
Removing set of numpy random seed
Great spot! We're just about to relase the next iteratino of GPy, we'll make sure it happens there too.
Thanks.
* Removing set of numpy random seed. [Scott Linderman]
* Removed unnecessary spaces from citation. [Nicolo Fusi]
* Added a way to cite. [Nicolo Fusi]
* Modified logexp transformation to prevent it returning zero when argument is under -36. [Neil Lawrence]
* Version change. [Max Zwiessele]
* Dim reduction examples clearer and init not as much black magic anymore. [Max Zwiessele]
* Plot_latent now shows selected inputs, even after switching dimensions. [Max Zwiessele]
* Added hapmap3 as dataset. [Max Zwiessele]
* Sparse gp stability improved. [Max Zwiessele]
* HapMap3 dataset added. [Max Zwiessele]
* Added hapmap download, need to put in data preprocessing for actual usability. [Max Zwiessele]
* Dim reduction examples. [mzwiessele]
* Dim reduction examples. [mzwiessele]
* Bgplvm steepest gradient map update. [mzwiessele]
* Bgplvm steepest gradient map update. [mzwiessele]
* Merge branch 'master' of github.com:SheffieldML/GPy. [mzwiessele]
* Update README.md with funding acknowledgements. [Neil Lawrence]
* Plotting bug for bgplvm fixed. [mzwiessele]
* Scg optimizer scale bounds back to 1e-15. [mzwiessele]
* Parameterized: added warning switch. [mzwiessele]
* Mrd corrections. [mzwiessele]
* Version change (early beta, do not change until everythin works. [Max Zwiessele]
* Fixed the SCG optimizer, thanks to Yarin Gal. [James Hensman]
* Version now 48. [Max Zwiessele]
* Version update. [Max Zwiessele]
* Merge branch 'master' of github.com:SheffieldML/GPy. [Max Zwiessele]
* Pickling now allways binary as well as protocol -1. [Max Zwiessele]
* Pickling now allways binary as well as protocol -1. [Max Zwiessele]
* Using lbfgs algorithm from scipy.minimize, starting to convert all optimizers to minimize format. [Max Zwiessele]
* Windows -.- [Max Zwiessele]
* Versions update. [Max Zwiessele]
* Image is a PIL requirement and should only be imported when actually using it. [Max Zwiessele]
* Plot handling greatly improved for latent space visualizations. [Max Zwiessele]
* Version file added. [Max Zwiessele]
* Fixed Ctrl-C behaviour on Windows. [Nicolo Fusi]
* Merge branch 'master' of github.com:SheffieldML/GPy. [Nicolo Fusi]
* Fixed come path issues in sympykern. [James Hensman]
* Rename and redoc. [Alan Saul]
* Moving imports, attempting to update RTD. [Alan Saul]
* Changed initalise_latent to take lower of init=PCA and corrected import. [Alan Saul]
* Change order of imports for RTD. [Alan Saul]
* Merge branch 'devel' [Alan Saul]
* Merge branch 'master' into devel. [Alan Saul]
* Removed variational.py. [Alan Saul]
* Fixed plot_latent failure. [Alan Saul]
* Ignore example tests. [Alan Saul]
* Removed yes pipe for travis. [Alan Saul]
* Seems to handle without answering now. [Alan Saul]
* Reverse travis to see what it asks for. [Alan Saul]
* Fixed some tests. [Alan Saul]
* Merged and fixed conflict in ODE_UY.py. [Alan Saul]
* Merge completed. [Max Zwiessele]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mu]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Andreas]
* Small changes in svigp. [Andreas]
* ODE UY dkdtheta. [mu]
* UY dkdtheta. [mu]
* UY dkdtheta. [mu]
* BGPLVM with missing data. [Max Zwiessele]
* Pca adjustements to lvm models. [Max Zwiessele]
* Ppca added, ppca missing data not working yet. [Max Zwiessele]
* Diagonal operations. [Max Zwiessele]
* Subarray indexing. [Max Zwiessele]
* Documenting. [Max Zwiessele]
* Bug in ODE_UY fix. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Fixed the numerical quadrature, won't work with large f unless normalized. [Alan Saul]
* Fixed lots of breaking tests, reduced step size for checkgrad to 1e-4 in tests (perhaps this should be global), added some missing attributes to data_resources.json. [Alan Saul]
* Set warnings for truncated hessian, it has been noted that that by truncating we can have incorrect posteriors, though at convergence this should not be a problem, could be fixed by not using Cholsky as the decomposition as it cannot handle non-positive definite mats. [Alan Saul]
* Merge pull request 90 from jamesmcm/master. [Alan Saul]
Fixing ReadTheDocs reading docstrings, adding data_resources.json
* Adding data_resources.json to setup data files. [James McMurray]
* Testing modification for ReadTheDocs to stop docstring errors. [James McMurray]
* Ensure_defaiult constraints in svigp. [James Hensman]
* Fixed Ctrl-C behaviour on Windows. [Nicolo Fusi]
* Removed print statements from config parser, commented out ODE kerns. [Nicolo Fusi]
* Merge branch 'devel' [Nicolo Fusi]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mu]
* Ode UY. [mu]
* Dk dparameter. [mu]
* ODE_UY. [mu]
* Merge branch 'devel' [Nicolo Fusi]
* Added some more error checking for downloading datasets. [Neil Lawrence]
* Fixed some bugs in mocap.py where errors weren't being raised when file format was incorrect and made datasets.py check for 404 errors which previously were occuring silently ... shhhhh. [Neil Lawrence]
* Fixed bugs in cmu_mocap loader where cmu_url was missing and loading in mocap data twice in same session led to incorrect url through copy error. [Neil Lawrence]
* Fixed examples tests, started changing datasets code which has a few bugs. [Alan Saul]
* Minor changes to naming of signitures. [Alan Saul]
* Changed more examples to accept optimize and plot. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Added comments for models module and adjusted setup. [Max Zwiessele]
* Merge branch 'naniny' into devel. [Max Zwiessele]
* Rename _models to models_modules to include in doc. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Some tidying in the regression examples. [James Hensman]
* Added optimize and plot for classification, non_gaussian and stochastic examples. [Alan Saul]
* Fixed gp_base and svigp for sampling (doesn't use it but needs the arguments) [Alan Saul]
* Added constant to Z_tilde, now log likelihoods are equal! [Alan Saul]
* Changed some parameters of the laplace, tidied up examples. [Alan Saul]
* Dimensionality reduction examples updated with optimize, plot and verbose. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Changing the seed seems to fix Alan's bug. [James Hensman]
* Fixed symmetry in checkgrad issue. [James Hensman]
* Reverted the brent optimisation in laplace. [James Hensman]
(For the 1D linesearch using Brent)
* Improved detectino of sympy. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Fixed exception handling bug in GPy/util/linalg.py:29. [Teo de Campos]
* Argghdfklg. [James Hensman]
* Better warings for cathcing of blaslib detection. [James Hensman]
* Changeing models to _models in setup.py. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Fixed step size for likelihood tests and allowed randomizing of laplace. [Alan Saul]
* Fixed student_t approximation demo and changed convergence critera to difference of f. [Alan Saul]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Alan Saul]
* Added cfg file to manfiest and package_data. [Alan Saul]
* Dimensionality reduction example (oil) updated. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Removed ipdb statement from kern, cleaned up some nasty whitespace. [James Hensman]
* More readme. [James Hensman]
* More readme stuff. [James Hensman]
* More readme edits. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Minor edits to the README. [James Hensman]
* Gradient checker comments and import updates. [Max Zwiessele]
* Gradientchecker added as a model. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Push minor fix to eq_sympy kernel test. [Neil Lawrence]
* Added some tips to the readme. [James Hensman]
* Fixed import errors in tests. [Max Zwiessele]
* Sympykern kern_tests now passing, code is inefficient but should be numerically stable. [Neil Lawrence]
* Modified to improve part of stability, gradient checks still passing. [Neil Lawrence]
* Added gradient of sympy kernel, seems to pass tests, but know it's not numerically stable. Checking in before making numerically stable. [Neil Lawrence]
* Fixed test in kern.py to request correct output dim for multioutput covariances. [Neil Lawrence]
* ODE_UY. [mu]
* Fixing up the blas detectino in linalg. [James Hensman]
* Removing ipdb statements. [James Hensman]
* Lots of medding with the likelihoods to get the tests working. the tests still don;t work. [James Hensman]
* Formatting docstring. [James Hensman]
* Changed nasty whitespace. [James Hensman]
* Eq_ode1 working but test failing? [Neil Lawrence]
* Added eq_ode1 to constructors.py. [Neil Lawrence]
* Fixed bug in sympy kernel and added sympolic.py back into utils __init__.py. [Neil Lawrence]
* Merge with James's changes. [Neil Lawrence]
* Merge. [James Hensman]
* Removed some sympy stuff. [James Hensman]
* Merge with James's changes. [Neil Lawrence]
* Committing change for master check out. [Neil Lawrence]
* Skipping crossterm tests instead of expected failure. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Added a path for the data resources. not all users will be working in the GPy directory. [James Hensman]
* Moved data resource information to a json file. [Neil Lawrence]
* Bug fix for single output sympy kernel. [Neil Lawrence]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [mu]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Nicolo Fusi]
* Fixed problem in warping. [Nicolo Fusi]
* Constructor and init for ODE_UY. [mu]
* Working eq_ode1 in sympy now. [Neil Lawrence]
* Dim reduction imports. [Max Zwiessele]
* Testing imports update and expected failure for crossterms. [Max Zwiessele]
* Rename models to _models and import models in models.py. [Max Zwiessele]
* Psistattests update. [Max Zwiessele]
* Updated crossterms, rbf x any not working yet (derivatives) [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Weird merge. [James Hensman]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
* Part implementation of ode_eq functionality. Not yet numerically stable or efficient (some horrible use of cut and paste to get things working ...) [Neil Lawrence]
* A trial namespace renaming. [James Hensman]
* Better handling of missing config files. [James Hensman]
* Debugging the config paths. [James Hensman]
* Allowing the passing of 1D X to a GP. with warning of course. [James Hensman]
* More fiddling with the windows path for config. [James Hensman]
Where is the windows guru? out playing beach volley?
* Changed how we search for config files on windows. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Fixed up symmetric kern. [James Hensman]
* Half way through crossterm objective. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Added block matrix utility. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Added **likelihood_params to predictive_values. [Ricardo]
* Changes in plot function: sampling vs numerical approximation. [Ricardo]
* Adding docstring for symmetric kern. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [James Hensman]
* Bug fixed in numerical approx. to the predictive variance. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
* Numerical predictions fixed, sampling predictions are not working. [Ricardo]
* Predictive_mean and predictive_variance now use gp_var as a parameter, rather than gp_std. [Ricardo]
* Fixed product kern get and set state. [James Hensman]
* Added getstate/setstate for product kernel. [James Hensman]
* In the middle of crossterms. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* 2D plots fixed. [Ricardo]
* Passing **noise_args into predictive_values. [Ricardo]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Ricardo]
* Missing term in the likelihood. [Ricardo]
* Reverted broken kern. [Max Zwiessele]
* Added variational distribution for latent space. [Max Zwiessele]
* BGPLVM test for crossterms. [Max Zwiessele]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Even more data plotting. [James Hensman]
* Fixed plotting isue with plot_f. [James Hensman]
* Fixed the dpotrs use.. [Alan Saul]
* Added dpotrs instead of cho_solve. [Alan Saul]
* Removed ipython dependency from kern. [Alan Saul]
* Sped up sampling a lot for student t, bernoulli and poisson, added sampling for gaussian and exponential (untested) [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' [Alan Saul]
* Ignoring examples tests again. [Alan Saul]
* Added sampling to student_t noise distribution, very slow and is possible to speed up. predictive mean analytical and variance need checking. [Alan Saul]
* Tidying up and fixed objective being vector. [Alan Saul]
* Added sampling for predictive quantiles and also mean and variance where necessary. [Alan Saul]
* Rederived gamma distribution. [Alan Saul]
* Added derivatives for poisson and a couple of examples, need to fix for EP. [Alan Saul]
* Merged with devel. [Alan Saul]
* Reimplemented gradients for exponential, seems to work for laplace now, needs a visual test though. [Alan Saul]
* Was a bug in the examples_tests.py, fixed and added brendan faces to ignore list. [Alan Saul]
* Minor clean up. [Alan Saul]
* Removed unnecessary laplace examples. [Alan Saul]
* Updated laplace example to use predictive density aswell as RMSE. [Alan Saul]
* Added log predictive density, ln p(y*|D) [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' [Alan Saul]
* Updated boston tests (more folds, allow a bias as the datasets are not normalized once split) and more folds. Tweaked some laplace line search parameters, added basis tests for ep. [Alan Saul]
* Fixed bug in gradient checker where it worked differently given a integer parameter to a float. [Alan Saul]
* Removed derivatives of variance wrt gp and derivatives of means with respect to gp from noise models. [Alan Saul]
* Tore out code no longer used from noise_distributions due to rewriting using quadrature. [Alan Saul]
* Added numerical mean and variance with quadrature, about to clean up. [Alan Saul]
* Merge branch 'master' into merge_branch. [Alan Saul]
* Changed the gradients (perhaps for the worse) [Alan Saul]
* A few typos. [Alan Saul]
* Gaussian likelihood errors, still not working. [Alan Saul]
* Added gaussian checker and gaussian likelihood, not checkgrading yet. [Alan Saul]
* Started adding gaussian sanity checker. [Alan Saul]
* Got rid of some overdoing the approximation. [Alan Saul]
* Started adding gaussian likelihood, changed round preloading old_a. [Alan Saul]
* Trying to debug kernel parameters learning (fails even when noise fixed) may be some instablility, seems like it can get it if it starts close. [Alan Saul]
* Fixed 2*variance plotting instead of 2*std plotting, tidied up. [Alan Saul]
* Changed incorrect naming. [Alan Saul]
* Reparameratised in terms of sigma2. [Alan Saul]
* Playing trying to find what makes it want to go so low. [Alan Saul]
* Fixed bug where B wasn't refering to current f location. [Alan Saul]
* Everything seems to be gradchecking again. [Alan Saul]
* Added minimizer for finding f, doesn't help. [Alan Saul]
* Now checkgrads a lot more of the time, but still fails in optimisation, seems also odd that when parameter is fixed kernel parameters go to infinity. [Alan Saul]
* Added another optimisation which doesn't use gradients. Seems like F is almost always found, but Y can be off, suggesting that Wi__Ki_W is wrong, maybe W? [Alan Saul]
* Trying to fix optimisation problem, fixed a few bugs but still fails at very low noise. [Alan Saul]
* Starting to fiddle with mode finding code. [Alan Saul]
* Fixed a sign wrong, now gradchecks weirdly only above certain points. [Alan Saul]
* Now gradchecks everytime but student_t fit is bad, noise is underestimated by a long way. [Alan Saul]
* Checkgrads with explicit and implicit components half the time. [Alan Saul]
* About to input new derivations for Z's... [Alan Saul]
* Took out all the asserts and using pure broadcasting method of diagonal now. [Alan Saul]
* Made it use the fact that W is diagonal and put assertions in to ensure that the results are the same. [Alan Saul]
* Broken it by getting rid of squeeze, but now working on making it faster using proper vector multiplciation for diagonals. [Alan Saul]
* Made more numerically stable in a hope that it will work and I will find a bug... [Alan Saul]
* Lots of name changing and went through all likelihood gradients again. [Alan Saul]
* Ripped out all things Laplace parameter estimation, starting again with new tactic. [Alan Saul]
* About to rip out old chain rule method of learning gradients. [Alan Saul]
* Trying to fix dL_dytil gradient. [Alan Saul]
* Changed name. [Alan Saul]
* FIXED DYTIL_DFHAT. [Alan Saul]
* Workong on doing explicit gradients. [Alan Saul]
* Gradients almost there for dytil_dfhat, diagonal terms are right. [Alan Saul]
* Merged with devel. [Alan Saul]
* Still getting closer to grads for likelihood. [Alan Saul]
* Almost have likelihood gradients working but kernels still way off. [Alan Saul]
* Working on putting callback to update laplace in callback. [Alan Saul]
* Seem to have gradients much closer now. [Alan Saul]
* Scale and switch KW+I. [Alan Saul]
* Merged with upstream. [Alan Saul]
* Added a debug examples. [Alan Saul]
* Merging. [Alan Saul]
* Merged with master. [Alan Saul]
* Plotting problematic kernel. [Alan Saul]
* Adding gradients, shapes starting to make sense. [Alan Saul]
* Attempted to introduce gradient methods, won't work yet I doubt. [Alan Saul]
* Merge remote-tracking branch 'upstream/devel' [Alan Saul]
* Merged likelihood functions. [Alan Saul]
* Should be working now, needed to change relative path names. [Alan Saul]
* Merge branch 'merge_trial' [Alan Saul]
* Merge branch 'old_repo' into merge_trial. [Alan Saul]
* Make directory structure match that of GPy. [Alan Saul]
* Tidy up comments. [Alan Saul]
* Merged in the GPy upstream. [Alan Saul]
* Merged in branch which had old_repo merged in. [Alan Saul]
* Adding weibull likelihood, requires 'extra_data' to be passed to likelihood, i.e. the censoring information. [Alan Saul]
* Fixed the z scalings. [Alan Saul]
* Fixed laplace approximation and made more numerically stable with cholesky decompositions, and commented. [Alan Saul]
* Stabalised most of the algorithm (apart from the end inversion which is impossible) [Alan Saul]
* Added timing and realised mdot can be faster as its almost always a diagonal matrix its multiplying with. [Alan Saul]
* Got the mode finding without computing Ki. [Alan Saul]
* Fixed broadcasting bug, rasm now appears to work. [Alan Saul]
* Still working on rasmussen, link function needs vectorizing I think. [Alan Saul]
* Tidying up. [Alan Saul]
* Added predicted values for student t, works well. [Alan Saul]
* Working laplace, just needs predictive values. [Alan Saul]
* Seemed to be working, now its not. [Alan Saul]
* Changing definitions again... [Alan Saul]
* Worked out in terms of W, needs gradients implementing. [Alan Saul]
* Just breaking some things... [Alan Saul]
* Following naming convention better, lots of inverses which should be able to get rid of one or two, unsure if it works. [Alan Saul]
* Got an idea of how to implement! written in docs. [Alan Saul]
* Trying to 'debug' [Alan Saul]
* Got most of laplace approximation working. [Alan Saul]
* Added some comments. [Alan Saul]
* Initial commit, setting up the laplace approximation for a student t. [Alan Saul]
* Initial commit. [James Hensman]
* Use bfgs for laplace instead. [Alan Saul]
* Moved transf_data to make data -1 or 1 from 0 or 1 for bernoulli with probit into the analytical moment match (but it 10% slower), needs removing from epmixednoise. [Alan Saul]
* Changed naming from old derivatives of likelihoods to new ones in noise distributions. [Alan Saul]
* Fixed breakage of dvar, tidied up to make more efficient. [Alan Saul]
* Doc stringing. [Alan Saul]
* Added quadrature numerical moment matching (but not predictive yet) [Alan Saul]
* Fixed a few laplace bits. [Alan Saul]
* Refactored gradients wrt parameters slightly, need to future proof against _get_param_names() disappearing. [Alan Saul]
* Added more options to generic tests (constraining link function values as bernoulli requies R^{0,1}) and implemented new gradients for bernoulli. [Alan Saul]
* Rename Binomial to Bernoulli (maybe generalise it with the constant later, but tilted distribution may change) [Alan Saul]
* Added pdf_link's for gaussian and student t, added third derivatives for transformations and tests for them. [Alan Saul]
* Renamed laplace_tests to likelihoods_tests. [Alan Saul]
* Tidying up laplace_tests.py. [Alan Saul]
* Fixed some bugs, added third derivative for log transformation, and did some doccing. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Still tidying up, laplace now working again, gaussian and student_t likelihoods now done. [Alan Saul]
* Started on chaining, must remember to chain _laplace_gradients aswell! [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Finished tearing gaussian noise down, time for student t. [Alan Saul]
* Beginning to merge lik_functions and derivatives with richardos. [Alan Saul]
* Docs. [Alan Saul]
* Removed fit as it is unused. [Alan Saul]
* More doc strings. [Alan Saul]
* Doccing and testing for D dimensional input (not multiple dimensional Y yet) [Alan Saul]
* Tidying up a lot, works for 1D, need to check for more dimensions. [Alan Saul]
* Tidied up laplace. [Alan Saul]
* Integrated Laplace and merged Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
Conflicts:
GPy/core/gp.py
GPy/likelihoods/__init__.py
GPy/likelihoods/likelihood_functions.py
GPy/likelihoods/link_functions.py
* Fixed white variance. [Alan Saul]
* Boston housing works (apart from variance of student t is not valid below 2) [Alan Saul]
* Tests setup but not fitting properly yet. [Alan Saul]
* Changed the examples (started boston data) and increased tolerance of finding fhat. [Alan Saul]
* Added some stability and tidied up. [Alan Saul]
* Tidying up. [Alan Saul]
* Student t likelihood function checkgrads (summed gradients wrt to sigma2), maybe some numerical instability in laplace. [Alan Saul]
* Now checkgrads for gaussian, and ALMOST for student t. [Alan Saul]
* All gradients now gradcheck. [Alan Saul]
* Merge remote-tracking branch 'gpy_real/devel' into merge_branch. [Alan Saul]
* Refactored tests. [Alan Saul]
* Tidied up grad checking. [Alan Saul]
* Added tests and fixed some naming. [Alan Saul]
* Modified gradient_checker to allow for variable 'f' [Alan Saul]
* Renamed some things, made some small (incorrect) gradient changes, generalised the gp regression for any likelihood, and added a place holder link function waiting for Richardos changes. [Alan Saul]
* Removed unneeded dependency. [Alan Saul]
* Merged GP models. [Alan Saul]
* Dragged likelihood_function changes in. [Alan Saul]
* Checked out relavent files. [Alan Saul]
* Merged in real gpy. [Alan Saul]
* Empty branch. [Alan Saul]
* SPELLAFSDIUN. [Max Zwiessele]
* Fixed up plotting in sparse_gp also. [James Hensman]
* Fixed up the plotting. [James Hensman]
* Fixed up plot in GP_base. [James Hensman]
* Started changing the plotting in examples to remove plot_single_output. [James Hensman]
* General tidying in models. [James Hensman]
* Improved docstrings in svigp. [James Hensman]
* Some tidying in gp.py. [James Hensman]
* Docstrings and removal of duplicated plotting code in gp_base. [James Hensman]
* Turned omp off by default as discussed. [James Hensman]
* Merge branch 'devel' of github.com:SheffieldML/GPy into devel. [Max Zwiessele]
* Added configuration file. [Nicolò Fusi]
this was done to solve the OpenMP problem on Windows/mac, but I think it
is useful in general. All unit tests pass except the sympy kern ones.
* Added xw_pen data. [Neil Lawrence]
* Added xw_pen data. [Neil Lawrence]
* Merge branch 'devel' of https://github.com/SheffieldML/GPy into devel. [Neil Lawrence]
* Basic sim code functional. [Neil Lawrence]
* Minor change in tutorial. [mu]
* Added link to user mailing list. [James Hensman]