Making test set prediction with BART

How to make test set prediction with BART. Below is the code used.

import theano
import pymc3 as pm
from sklearn.datasets import load_boston*
from sklearn.model_selection import train_test_split*
from sklearn.metrics import mean_squared_error*
import numpy as np *
import arviz as az*

data = load_boston()
X_train, X_test, y_train, y_test = train_test_split(data['data'], data['target'], test_size=0.2)
X_train_shared = theano.shared(X_train)
y_train_shared = theano.shared(y_train)
with pm.Model() as model:
    σ = pm.HalfNormal('σ', 1)
    μ = pm.BART('μ', X_train_shared.get_value(), y_train_shared.get_value(), m=65)
    y = pm.Normal('y', μ, σ, observed=y_train)
    trace = pm.sample(2000, return_inferencedata=False)
    ppc_train = pm.sample_posterior_predictive(trace, samples=500, progressbar=False) 
    pred_train = ppc_train['y'].mean(axis=0)
    std_train = ppc_train['y'].std(axis=0)

So far so good. But when I try to use the model to make prediction on the test data, the returned prediction vector has the same length as the train data.

with model:
    ppc_test = pm.sample_posterior_predictive(trace, samples=500, progressbar=False) 
    pred_test = ppc_test['y'].mean(axis=0)
    std_test = ppc_test['y'].std(axis=0)

Any help to solve this problem would be greatly appreciated.

Hi @Osman_Mamun, Unfortunately for the moment BART predictions does not work out of the box like with other models in PyMC3. You can do the following (no need to define shared variables).

with pm.Model() as model:
    σ = pm.HalfNormal('σ', 1)
    μ = pm.BART('μ', X_train, y_train, m=65)
    y = pm.Normal('y', μ, σ, observed=y_train)
    trace = pm.sample(2000, cores=1, return_inferencedata=False)

Then to get predictions you do


This has two caveats, first it will give predictions of the mean function (it does not take into account the values of σ, so you may need to add them “manually”), second you will need to run a single chain or run multiples chain with cores=1, i.e. not parallel chains.

Hopefully all this will become smoother in future releases.

Hi @aloctavodia, thank you for the reply. Hmm, because of the different implementation of the tree search, BART can’t use the usual interface of pm.sample and it takes y as an input to optimize the trees. I will follow your recipe to get the test set predictions. Best, Osman