mirror of
https://github.com/SheffieldML/GPy.git
synced 2026-05-24 14:15:14 +02:00
Merge branch 'devel'
This commit is contained in:
Nicolo Fusi
commit
ebd2752d5b
194 changed files with 15884 additions and 11008 deletions
|
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@ -9,6 +9,46 @@ core Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`domains` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.core.domains
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`fitc` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.core.fitc
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp` Module
|
||||
----------------
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||||
|
||||
.. automodule:: GPy.core.gp
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_base` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.core.gp_base
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapping` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.core.mapping
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`model` Module
|
||||
-------------------
|
||||
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||||
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@ -17,10 +57,10 @@ core Package
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|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`parameterised` Module
|
||||
:mod:`parameterized` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.core.parameterised
|
||||
.. automodule:: GPy.core.parameterized
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
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@ -33,3 +73,35 @@ core Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.core.sparse_gp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`svigp` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.core.svigp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`transformations` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.core.transformations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`variational` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.core.variational
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
|
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|||
|
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@ -25,10 +25,10 @@ examples Package
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|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`non_gaussian` Module
|
||||
--------------------------
|
||||
:mod:`laplace_approximations` Module
|
||||
------------------------------------
|
||||
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||||
.. automodule:: GPy.examples.non_gaussian
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||||
.. automodule:: GPy.examples.laplace_approximations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
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@ -41,6 +41,14 @@ examples Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`stochastic` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: GPy.examples.stochastic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`tutorials` Module
|
||||
-----------------------
|
||||
|
||||
|
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@ -1,10 +1,18 @@
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|||
inference Package
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||||
=================
|
||||
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||||
:mod:`SGD` Module
|
||||
-----------------
|
||||
:mod:`conjugate_gradient_descent` Module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: GPy.inference.SGD
|
||||
.. automodule:: GPy.inference.conjugate_gradient_descent
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gradient_descent_update_rules` Module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: GPy.inference.gradient_descent_update_rules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
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@ -25,3 +33,19 @@ inference Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`scg` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.inference.scg
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sgd` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.inference.sgd
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
|
|
|||
275
doc/GPy.kern.parts.rst
Normal file
275
doc/GPy.kern.parts.rst
Normal file
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@ -0,0 +1,275 @@
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|||
parts Package
|
||||
=============
|
||||
|
||||
:mod:`parts` Package
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Brownian` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.Brownian
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Matern32` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.Matern32
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Matern52` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.Matern52
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ODE_1` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.ODE_1
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ODE_UY` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.ODE_UY
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bias` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.bias
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`coregionalize` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.coregionalize
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`eq_ode1` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.eq_ode1
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`exponential` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.exponential
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`finite_dimensional` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.finite_dimensional
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`fixed` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.fixed
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gibbs` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.gibbs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hetero` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.hetero
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`hierarchical` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.hierarchical
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`independent_outputs` Module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.independent_outputs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`kernpart` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.kernpart
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`linear` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.linear
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mlp` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.mlp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_Matern32` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.periodic_Matern32
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_Matern52` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.periodic_Matern52
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_exponential` Module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.periodic_exponential
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`poly` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.poly
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`prod` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.prod
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`prod_orthogonal` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.prod_orthogonal
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rational_quadratic` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.rational_quadratic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rbf` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.rbf
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rbf_inv` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.rbf_inv
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rbfcos` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.rbfcos
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`spline` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.spline
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`symmetric` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.symmetric
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sympy_helpers` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.sympy_helpers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sympykern` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.sympykern
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`white` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.kern.parts.white
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
161
doc/GPy.kern.rst
161
doc/GPy.kern.rst
|
|
@ -9,38 +9,6 @@ kern Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Brownian` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.Brownian
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Matern32` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.Matern32
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Matern52` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.kern.Matern52
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bias` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.kern.bias
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`constructors` Module
|
||||
--------------------------
|
||||
|
||||
|
|
@ -49,30 +17,6 @@ kern Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`coregionalise` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.kern.coregionalise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`exponential` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.kern.exponential
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`finite_dimensional` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.finite_dimensional
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`kern` Module
|
||||
------------------
|
||||
|
||||
|
|
@ -81,107 +25,10 @@ kern Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`kernpart` Module
|
||||
----------------------
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. automodule:: GPy.kern.kernpart
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
.. toctree::
|
||||
|
||||
:mod:`linear` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.linear
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_Matern32` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.periodic_Matern32
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_Matern52` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.periodic_Matern52
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`periodic_exponential` Module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.periodic_exponential
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`prod` Module
|
||||
------------------
|
||||
|
||||
.. automodule:: GPy.kern.prod
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`prod_orthogonal` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.kern.prod_orthogonal
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rational_quadratic` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: GPy.kern.rational_quadratic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`rbf` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.kern.rbf
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`spline` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.kern.spline
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`symmetric` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.kern.symmetric
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sympykern` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.kern.sympykern
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`white` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.kern.white
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
GPy.kern.parts
|
||||
|
||||
|
|
|
|||
75
doc/GPy.likelihoods.noise_models.rst
Normal file
75
doc/GPy.likelihoods.noise_models.rst
Normal file
|
|
@ -0,0 +1,75 @@
|
|||
noise_models Package
|
||||
====================
|
||||
|
||||
:mod:`noise_models` Package
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bernoulli_noise` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.bernoulli_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`exponential_noise` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.exponential_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gamma_noise` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.gamma_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gaussian_noise` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.gaussian_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_transformations` Module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.gp_transformations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`noise_distributions` Module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.noise_distributions
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`poisson_noise` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.poisson_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`student_t_noise` Module
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.noise_models.student_t_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
|
@ -9,7 +9,7 @@ likelihoods Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`EP` Module
|
||||
:mod:`ep` Module
|
||||
----------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.ep
|
||||
|
|
@ -17,7 +17,15 @@ likelihoods Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Gaussian` Module
|
||||
:mod:`ep_mixed_noise` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.ep_mixed_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gaussian` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.gaussian
|
||||
|
|
@ -25,6 +33,22 @@ likelihoods Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gaussian_mixed_noise` Module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.gaussian_mixed_noise
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`laplace` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.laplace
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`likelihood` Module
|
||||
------------------------
|
||||
|
||||
|
|
@ -33,11 +57,18 @@ likelihoods Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`likelihood_functions` Module
|
||||
----------------------------------
|
||||
:mod:`noise_model_constructors` Module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: GPy.likelihoods.likelihood_functions
|
||||
.. automodule:: GPy.likelihoods.noise_model_constructors
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
GPy.likelihoods.noise_models
|
||||
|
||||
|
|
|
|||
35
doc/GPy.mappings.rst
Normal file
35
doc/GPy.mappings.rst
Normal file
|
|
@ -0,0 +1,35 @@
|
|||
mappings Package
|
||||
================
|
||||
|
||||
:mod:`mappings` Package
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.mappings
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`kernel` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.mappings.kernel
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`linear` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.mappings.linear
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mlp` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.mappings.mlp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
|
|
@ -1,83 +0,0 @@
|
|||
models Package
|
||||
==============
|
||||
|
||||
:mod:`models` Package
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.models
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`Bayesian_GPLVM` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.models.bayesian_gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp` Module
|
||||
----------------
|
||||
|
||||
.. automodule:: GPy.models.gp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gplvm` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.models.gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_regression` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.models.gp_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.models.sparse_gp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`SparseGPLVM` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: GPy.models.sparse_gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp_regression` Module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: GPy.models.sparse_gp_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
.. :mod:`uncollapsed_sparse_GP` Module
|
||||
.. -----------------------------------
|
||||
|
||||
.. .. automodule:: GPy.models.uncollapsed_sparse_GP
|
||||
.. :members:
|
||||
.. :undoc-members:
|
||||
.. :show-inheritance:
|
||||
|
||||
:mod:`warped_gp` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.models.warped_gp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
131
doc/GPy.models_modules.rst
Normal file
131
doc/GPy.models_modules.rst
Normal file
|
|
@ -0,0 +1,131 @@
|
|||
models_modules Package
|
||||
======================
|
||||
|
||||
:mod:`models_modules` Package
|
||||
-----------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bayesian_gplvm` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.bayesian_gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bcgplvm` Module
|
||||
---------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.bcgplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`fitc_classification` Module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.fitc_classification
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_classification` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.gp_classification
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_multioutput_regression` Module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.gp_multioutput_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_regression` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.gp_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gplvm` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gradient_checker` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.gradient_checker
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mrd` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.models_modules.mrd
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp_classification` Module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.sparse_gp_classification
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp_multioutput_regression` Module
|
||||
----------------------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.sparse_gp_multioutput_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gp_regression` Module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.sparse_gp_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gplvm` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.sparse_gplvm
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`svigp_regression` Module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.svigp_regression
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`warped_gp` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.models_modules.warped_gp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
11
doc/GPy.rst
11
doc/GPy.rst
|
|
@ -9,6 +9,14 @@ GPy Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`models` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.models
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
|
|
@ -19,7 +27,8 @@ Subpackages
|
|||
GPy.inference
|
||||
GPy.kern
|
||||
GPy.likelihoods
|
||||
GPy.models
|
||||
GPy.mappings
|
||||
GPy.models_modules
|
||||
GPy.testing
|
||||
GPy.util
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,22 @@
|
|||
testing Package
|
||||
===============
|
||||
|
||||
:mod:`testing` Package
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.testing
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bcgplvm_tests` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.testing.bcgplvm_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`bgplvm_tests` Module
|
||||
--------------------------
|
||||
|
||||
|
|
@ -9,6 +25,14 @@ testing Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`cgd_tests` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.testing.cgd_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`examples_tests` Module
|
||||
----------------------------
|
||||
|
||||
|
|
@ -17,6 +41,14 @@ testing Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gp_transformation_tests` Module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: GPy.testing.gp_transformation_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`gplvm_tests` Module
|
||||
-------------------------
|
||||
|
||||
|
|
@ -33,6 +65,30 @@ testing Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`likelihoods_tests` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.testing.likelihoods_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mapping_tests` Module
|
||||
---------------------------
|
||||
|
||||
.. automodule:: GPy.testing.mapping_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mrd_tests` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.testing.mrd_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`prior_tests` Module
|
||||
-------------------------
|
||||
|
||||
|
|
@ -41,6 +97,22 @@ testing Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`psi_stat_expectation_tests` Module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: GPy.testing.psi_stat_expectation_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`psi_stat_gradient_tests` Module
|
||||
-------------------------------------
|
||||
|
||||
.. automodule:: GPy.testing.psi_stat_gradient_tests
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`sparse_gplvm_tests` Module
|
||||
--------------------------------
|
||||
|
||||
|
|
|
|||
27
doc/GPy.util.latent_space_visualizations.controllers.rst
Normal file
27
doc/GPy.util.latent_space_visualizations.controllers.rst
Normal file
|
|
@ -0,0 +1,27 @@
|
|||
controllers Package
|
||||
===================
|
||||
|
||||
:mod:`controllers` Package
|
||||
--------------------------
|
||||
|
||||
.. automodule:: GPy.util.latent_space_visualizations.controllers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`axis_event_controller` Module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: GPy.util.latent_space_visualizations.controllers.axis_event_controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`imshow_controller` Module
|
||||
-------------------------------
|
||||
|
||||
.. automodule:: GPy.util.latent_space_visualizations.controllers.imshow_controller
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
19
doc/GPy.util.latent_space_visualizations.rst
Normal file
19
doc/GPy.util.latent_space_visualizations.rst
Normal file
|
|
@ -0,0 +1,19 @@
|
|||
latent_space_visualizations Package
|
||||
===================================
|
||||
|
||||
:mod:`latent_space_visualizations` Package
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: GPy.util.latent_space_visualizations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
GPy.util.latent_space_visualizations.controllers
|
||||
GPy.util.latent_space_visualizations.views
|
||||
|
||||
119
doc/GPy.util.rst
119
doc/GPy.util.rst
|
|
@ -17,6 +17,30 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`block_matrices` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.util.block_matrices
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`classification` Module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: GPy.util.classification
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`config` Module
|
||||
--------------------
|
||||
|
||||
.. automodule:: GPy.util.config
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`datasets` Module
|
||||
----------------------
|
||||
|
||||
|
|
@ -25,6 +49,22 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`decorators` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: GPy.util.decorators
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`erfcx` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.util.erfcx
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`linalg` Module
|
||||
--------------------
|
||||
|
||||
|
|
@ -33,6 +73,14 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`ln_diff_erfs` Module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: GPy.util.ln_diff_erfs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`misc` Module
|
||||
------------------
|
||||
|
||||
|
|
@ -41,6 +89,38 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`mocap` Module
|
||||
-------------------
|
||||
|
||||
.. automodule:: GPy.util.mocap
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`multioutput` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.util.multioutput
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`netpbmfile` Module
|
||||
------------------------
|
||||
|
||||
.. automodule:: GPy.util.netpbmfile
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`pca` Module
|
||||
-----------------
|
||||
|
||||
.. automodule:: GPy.util.pca
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plot` Module
|
||||
------------------
|
||||
|
||||
|
|
@ -49,6 +129,14 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`plot_latent` Module
|
||||
-------------------------
|
||||
|
||||
.. automodule:: GPy.util.plot_latent
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`squashers` Module
|
||||
-----------------------
|
||||
|
||||
|
|
@ -57,6 +145,30 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`symbolic` Module
|
||||
----------------------
|
||||
|
||||
.. automodule:: GPy.util.symbolic
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`univariate_Gaussian` Module
|
||||
---------------------------------
|
||||
|
||||
.. automodule:: GPy.util.univariate_Gaussian
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`visualize` Module
|
||||
-----------------------
|
||||
|
||||
.. automodule:: GPy.util.visualize
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
:mod:`warping_functions` Module
|
||||
-------------------------------
|
||||
|
||||
|
|
@ -65,3 +177,10 @@ util Package
|
|||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
|
||||
GPy.util.latent_space_visualizations
|
||||
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
#
|
||||
|
||||
# You can set these variables from the command line.
|
||||
SPHINXOPTS =
|
||||
SPHINXOPTS = -a -w log.txt -E
|
||||
SPHINXBUILD = sphinx-build
|
||||
PAPER =
|
||||
BUILDDIR = _build
|
||||
|
|
|
|||
|
|
@ -83,6 +83,7 @@ print "finished importing"
|
|||
#############################################################################
|
||||
|
||||
class Mock(object):
|
||||
__all__ = []
|
||||
def __init__(self, *args, **kwargs):
|
||||
pass
|
||||
|
||||
|
|
@ -103,8 +104,10 @@ class Mock(object):
|
|||
#import mock
|
||||
|
||||
print "Mocking"
|
||||
MOCK_MODULES = ['pylab', 'sympy', 'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache', 'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser', 'matplotlib']
|
||||
#'matplotlib', 'matplotlib.color', 'matplotlib.pyplot', 'pylab' ]
|
||||
MOCK_MODULES = ['sympy',
|
||||
'sympy.utilities', 'sympy.utilities.codegen', 'sympy.core.cache',
|
||||
'sympy.core', 'sympy.parsing', 'sympy.parsing.sympy_parser', 'Tango', 'numdifftools'
|
||||
]
|
||||
for mod_name in MOCK_MODULES:
|
||||
sys.modules[mod_name] = Mock()
|
||||
|
||||
|
|
@ -288,7 +291,7 @@ latex_elements = {
|
|||
#'pointsize': '10pt',
|
||||
|
||||
# Additional stuff for the LaTeX preamble.
|
||||
#'preamble': '',
|
||||
'preamble': '\\usepackage{MnSymbol}',
|
||||
}
|
||||
|
||||
# Grouping the document tree into LaTeX files. List of tuples
|
||||
|
|
|
|||
|
|
@ -11,9 +11,13 @@ For a quick start, you can have a look at one of the tutorials:
|
|||
* `Interacting with models <tuto_interacting_with_models.html>`_
|
||||
* `A kernel overview <tuto_kernel_overview.html>`_
|
||||
* `Writing new kernels <tuto_creating_new_kernels.html>`_
|
||||
* `Writing new models <tuto_creating_new_models.html>`_
|
||||
|
||||
You may also be interested by some examples in the GPy/examples folder.
|
||||
|
||||
The detailed Developers Documentation is listed below
|
||||
=====================================================
|
||||
|
||||
Contents:
|
||||
|
||||
.. toctree::
|
||||
|
|
|
|||
64
doc/tuto_creating_new_models.rst
Normal file
64
doc/tuto_creating_new_models.rst
Normal file
|
|
@ -0,0 +1,64 @@
|
|||
.. _creating_new_models:
|
||||
|
||||
*******************
|
||||
Creating new Models
|
||||
*******************
|
||||
|
||||
In GPy all models inherit from the base class :py:class:`~GPy.core.parameterized.Parameterized`. :py:class:`~GPy.core.parameterized.Parameterized` is a class which allows for parameterization of objects. All it holds is functionality for tying, bounding and fixing of parameters. It also provides the functionality of searching and manipulating parameters by regular expression syntax. See :py:class:`~GPy.core.parameterized.Parameterized` for more information.
|
||||
|
||||
The :py:class:`~GPy.core.model.Model` class provides parameter introspection, objective function and optimization.
|
||||
|
||||
In order to fully use all functionality of :py:class:`~GPy.core.model.Model` some methods need to be implemented / overridden. In order to explain the functionality of those methods we will use a wrapper to the numpy ``rosen`` function, which holds input parameters :math:`\mathbf{X}`. Where :math:`\mathbf{X}\in\mathbb{R}^{N\times 1}`.
|
||||
|
||||
Obligatory methods
|
||||
==================
|
||||
|
||||
:py:meth:`~GPy.core.model.Model.__init__` :
|
||||
Initialize the model with the given parameters. In our example we have to store shape information of :math:`\mathbf X` and the parameters themselves::
|
||||
|
||||
self.X = X
|
||||
self.num_inputs = self.X.shape[0]
|
||||
assert self.X.ndim == 1, only vector inputs allowed
|
||||
|
||||
:py:meth:`~GPy.core.model.Model._get_params` :
|
||||
Return parameters of the model as a flattened numpy array-like. So, in our example we have to return the input parameters::
|
||||
|
||||
return self.X.flatten()
|
||||
|
||||
:py:meth:`~GPy.core.model.Model._set_params` :
|
||||
Set parameters, which have been fetched through :py:meth:`~GPy.core.model.Model._get_params`. In other words, "invert" the functionality of :py:meth:`~GPy.core.model.Model._get_params`::
|
||||
|
||||
self.X = params[:self.num_inputs*self.input_dim].reshape(self.num_inputs)
|
||||
|
||||
:py:meth:`~GPy.core.model.Model.log_likelihood` :
|
||||
Returns the log-likelihood of the new model. For our example this is just the call to ``rosen``::
|
||||
|
||||
return scipy.optimize.rosen(self.X)
|
||||
|
||||
:py:meth:`~GPy.core.model.Model._log_likelihood_gradients` :
|
||||
Returns the gradients with respect to all parameters::
|
||||
|
||||
return scipy.optimize.rosen_der(self.X)
|
||||
|
||||
|
||||
Optional methods
|
||||
================
|
||||
|
||||
If you want some special functionality please provide the following methods:
|
||||
|
||||
Using the pickle functionality
|
||||
------------------------------
|
||||
|
||||
To be able to use the pickle functionality ``m.pickle(<path>)`` the methods ``getstate(self)`` and ``setstate(self, state)`` have to be provided. The convention for a ``state`` in ``GPy`` is a list of all parameters, which are needed to restore the model. All classes provided in ``GPy`` follow this convention, thus you can just append to the state of the inherited class and call the inherited class' ``setstate`` with the appropriate state.
|
||||
|
||||
:py:meth:`~GPy.core.model.Model.getstate` :
|
||||
This method returns a state of the model, following the memento pattern. As we are inheriting from :py:class:`~GPy.core.model.Model`, we have to return the state of Model as well. In out example we have `X` and `num_inputs` as state::
|
||||
|
||||
return Model.getstate(self) + [self.X, self.num_inputs]
|
||||
|
||||
:py:meth:`~GPy.core.model.Model.setstate` :
|
||||
This method restores this model with the given ``state``::
|
||||
|
||||
self.num_inputs = state.pop()
|
||||
self.X = state.pop()
|
||||
return Model.setstate(self, state)
|
||||
|
|
@ -1,3 +1,5 @@
|
|||
.. _interacting_with_models:
|
||||
|
||||
*************************************
|
||||
Interacting with models
|
||||
*************************************
|
||||
|
|
@ -18,7 +20,7 @@ All of the examples included in GPy return an instance
|
|||
of a model class, and therefore they can be called in
|
||||
the following way: ::
|
||||
|
||||
import numpy as np
|
||||
import numpy as np
|
||||
import pylab as pb
|
||||
pb.ion()
|
||||
import GPy
|
||||
|
|
@ -105,7 +107,7 @@ inputs: ::
|
|||
m['iip'] = np.arange(-5,0)
|
||||
|
||||
Getting the model's likelihood and gradients
|
||||
===========================================
|
||||
=============================================
|
||||
Appart form the printing the model, the marginal
|
||||
log-likelihood can be obtained by using the function
|
||||
``log_likelihood()``. Also, the log-likelihood gradients
|
||||
|
|
@ -210,6 +212,6 @@ white_variance and noise_variance are tied together.::
|
|||
|
||||
Further Reading
|
||||
===============
|
||||
All of the mechansiams for dealing with parameters are baked right into GPy.core.model, from which all of the classes in GPy.models inherrit. To learn how to construct your own model, you might want to read ??link?? creating_new_models.
|
||||
All of the mechansiams for dealing with parameters are baked right into GPy.core.model, from which all of the classes in GPy.models inherrit. To learn how to construct your own model, you might want to read :ref:`creating_new_models`.
|
||||
|
||||
By deafult, GPy uses the tnc optimizer (from scipy.optimize.tnc). To use other optimisers, and to control the setting of those optimisers, as well as other funky features like automated restarts and diagnostics, you can read the optimization tutorial ??link??.
|
||||
By deafult, GPy uses the scg optimizer. To use other optimisers, and to control the setting of those optimisers, as well as other funky features like automated restarts and diagnostics, you can read the optimization tutorial ??link??.
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue