Sparse Gaussian processes

README.md

@@ -4,46 +4,46 @@
 
 This repository is a collection of notebooks about *Bayesian Machine Learning*. The following links display 
 some of the notebooks via [nbviewer](https://nbviewer.jupyter.org/) to ensure a proper rendering of formulas.
+Dependencies are specified in `requirements.txt` files in subdirectories.
 
 - [Bayesian regression with linear basis function models](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-linear-regression/bayesian_linear_regression.ipynb). 
-  Introduction to Bayesian linear regression. Implementation from scratch with plain NumPy as well as usage of scikit-learn 
-  for comparison. See also 
-  [PyMC4 implementation](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-linear-regression/bayesian_linear_regression_pymc4.ipynb) and 
+  Introduction to Bayesian linear regression. Implementation with plain NumPy and scikit-learn. See also 
   [PyMC3 implementation](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-linear-regression/bayesian_linear_regression_pymc3.ipynb).
 
 - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes.ipynb)
   [Gaussian processes](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes.ipynb?flush_cache=true). 
-  Introduction to Gaussian processes for regression. Example implementations with plain NumPy/SciPy as well as with libraries 
-  scikit-learn and GPy ([requirements.txt](gaussian-processes/requirements.txt)). 
+  Introduction to Gaussian processes for regression. Implementation with plain NumPy/SciPy as well as with scikit-learn and GPy. 
 
 - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes_classification.ipynb)
   [Gaussian processes for classification](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes_classification.ipynb). 
-  Introduction to Gaussian processes for classification. Example implementations with plain NumPy/SciPy as well as with 
-  scikit-learn ([requirements.txt](gaussian-processes/requirements.txt)). 
+  Introduction to Gaussian processes for classification. Implementation with plain NumPy/SciPy as well as with scikit-learn. 
+
+- [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes_sparse.ipynb)
+  [Sparse Gaussian processes](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/gaussian-processes/gaussian_processes_sparse.ipynb). 
+  Introduction to sparse Gaussian processes using a variational approach. Example implementation with JAX. 
 
 - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-optimization/bayesian_optimization.ipynb)
   [Bayesian optimization](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-optimization/bayesian_optimization.ipynb). 
-  Introduction to Bayesian optimization. Example implementations with plain NumPy/SciPy as well as with libraries 
-  scikit-optimize and GPyOpt. Hyper-parameter tuning as application example.  
+  Introduction to Bayesian optimization. Implementation with plain NumPy/SciPy as well as with libraries scikit-optimize 
+  and GPyOpt. Hyper-parameter tuning as application example.  
 
 - [Variational inference in Bayesian neural networks](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-neural-networks/bayesian_neural_networks.ipynb). 
-  Demonstrates how to implement a Bayesian neural network and variational inference of network parameters. Example implementation 
-  with Keras ([requirements.txt](bayesian-neural-networks/requirements.txt)). See also 
-  [PyMC4 implementation](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/bayesian-neural-networks/bayesian_neural_networks_pymc4.ipynb).
+  Demonstrates how to implement a Bayesian neural network and variational inference of weights. Example implementation 
+  with Keras.
 
 - [Reliable uncertainty estimates for neural network predictions](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/noise-contrastive-priors/ncp.ipynb). 
-  Uses noise contrastive priors in Bayesian neural networks to get more reliable uncertainty estimates for OOD data.
-  Implemented with Tensorflow 2 and Tensorflow Probability ([requirements.txt](noise-contrastive-priors/requirements.txt)).
+  Uses noise contrastive priors for Bayesian neural networks to get more reliable uncertainty estimates for OOD data.
+  Implemented with Tensorflow 2 and Tensorflow Probability.
 
 - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/latent-variable-models/latent_variable_models_part_1.ipynb)
   [Latent variable models, part 1: Gaussian mixture models and the EM algorithm](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/latent-variable-models/latent_variable_models_part_1.ipynb).
-  Introduction to the expectation maximization (EM) algorithm and its application to Gaussian mixture models. Example
-  implementation with plain NumPy/SciPy and scikit-learn for comparison. See also 
+  Introduction to the expectation maximization (EM) algorithm and its application to Gaussian mixture models. 
+  Implementation with plain NumPy/SciPy and scikit-learn. See also 
   [PyMC3 implementation](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/latent-variable-models/latent_variable_models_part_1_pymc3.ipynb).
 
 - [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/krasserm/bayesian-machine-learning/blob/dev/latent-variable-models/latent_variable_models_part_2.ipynb)
   [Latent variable models, part 2: Stochastic variational inference and variational autoencoders](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/latent-variable-models/latent_variable_models_part_2.ipynb). 
-  Introduction to stochastic variational inference with variational autoencoder as application example. Implementation 
+  Introduction to stochastic variational inference with a variational autoencoder as application example. Implementation 
   with Tensorflow 2.x.
 
 - [Deep feature consistent variational autoencoder](https://nbviewer.jupyter.org/github/krasserm/bayesian-machine-learning/blob/dev/autoencoder-applications/variational_autoencoder_dfc.ipynb). 

gaussian-processes/gaussian_processes.ipynb

@@ -400,7 +400,8 @@
     }
    ],
    "source": [
-    "from numpy.linalg import cholesky, det, lstsq\n",
+    "from numpy.linalg import cholesky, det\n",
+    "from scipy.linalg import solve_triangular\n",
     "from scipy.optimize import minimize\n",
     "\n",
     "def nll_fn(X_train, Y_train, noise, naive=True):\n",
@@ -437,14 +438,15 @@
     "        # in http://www.gaussianprocess.org/gpml/chapters/RW2.pdf, Section\n",
     "        # 2.2, Algorithm 2.1.\n",
     "        \n",
-    "        def ls(a, b):\n",
-    "            return lstsq(a, b, rcond=-1)[0]\n",
-    "        \n",
     "        K = kernel(X_train, X_train, l=theta[0], sigma_f=theta[1]) + \\\n",
     "            noise**2 * np.eye(len(X_train))\n",
     "        L = cholesky(K)\n",
+    "        \n",
+    "        S1 = solve_triangular(L, Y_train, lower=True)\n",
+    "        S2 = solve_triangular(L.T, S1, lower=False)\n",
+    "        \n",
     "        return np.sum(np.log(np.diagonal(L))) + \\\n",
-    "               0.5 * Y_train.dot(ls(L.T, ls(L, Y_train))) + \\\n",
+    "               0.5 * Y_train.dot(S2) + \\\n",
     "               0.5 * len(X_train) * np.log(2*np.pi)\n",
     "\n",
     "    if naive:\n",