Multivariate Gaussian Process Classification (GPC) and Prediction

I’m trying to implement a binary classification problem with multi-dimensional inputs using something like the following code:

import pymc3 as pm
import scipy
import numpy as np
import theano.tensor as tt

n = 40 #number of observations
N = 10 #number of predictors

#make up some fake data
y = np.random.binomial(1, scipy.special.expit(np.random.normal(size=n)))
X = np.random.normal(size=(n+1,N))
X_new = X[-1,:] #data used for prediction
X = X[:-1,:]

#model setup
with pm.Model() as model:
    logl = pm.Uniform('log(l)', lower=np.log(1e-5), upper=np.log(1e5))

    cov =,active_dims=np.arange(N),ls=tt.exp(logl))
    gp =
    f = gp.prior('f', X=X)
    p = pm.Deterministic('p', pm.math.invlogit(f))
    y_ = pm.Bernoulli('y', p=p, observed=y)
    trace = pm.sample(draws=2000, chains=2, cores=2, random_seed=1)

I would now like to predict a new value of y, given the unseen data X_new, lets call it y_new. Hence I would expect the value of y_new to be either 0 or 1 in this case. As well as this, I would like to estimate the probability of this value of y_new (the same as the predict_proba functionality in sklearn.gaussian_process.GaussianProcessClassifier). Is this possible? I have read around a bit and I think I need to do something like:

with model:
    fcond = gp.conditional('fcond', X_new)
    ppc = pm.sample_posterior_predictive(trace=trace, vars=[fcond], samples=1000)

but I don’t really know how to interpret the output ppc['fcond'].

Many thanks.

sample_posterior_predictive will be generating simulated draws from the latent Gaussian process. We typically do this to characterize the fitted posterior GP (e.g. plotting them). If you want to sample from the likelihood, you will want to add the pred_noise=True argument to sample_posterior_predictive, which will then draw from the posterior predictive distribution.

To gain inferences on the underlying probabilities, you would draw without pred_noise and take the inverse logit of those values.


Thanks for your response. I have successfully managed to take the inverse logit of my ppc samples from the Latent conditional distribution, however sample_posterior_predictive does not have the option pred_noise? Neither does This is only a functionality of (and MarginalSparse, MarginalKron). Am I mis-understanding?