Survival Models Survival models, also known as time-to-event models, are specialized statistical methods designed to analyze the time until the occurrence of an event of interest. In this notebook, a review of survival analysis (using non-parametric and parametric methods) and censored data is provided, followed by a survival model implementation in Bambi. This blog post is a copy of the survival models documentation I wrote for Bambi. The original post can be found here. ...

Predict New Groups In Bambi, it is possible to perform predictions on new, unseen, groups of data that were not in the observed data used to fit the model with the argument sample_new_groups in the model.predict() method. This is useful in the context of hierarchical modeling, where groups are assumed to be a sample from a larger group. This blog post is a copy of the zero inflated models documentation I wrote for Bambi. The original post can be found here. ...

#| code-fold: true import arviz as az import matplotlib.pyplot as plt from matplotlib.lines import Line2D import numpy as np import pandas as pd import warnings import bambi as bmb warnings.filterwarnings("ignore", category=FutureWarning) WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions. Ordinal Regression This blog post is a copy of the ordinal models documentation I wrote for Bambi. The original post can be found here. In some scenarios, the response variable is discrete, like a count, and ordered. Common examples of such data come from questionnaires where the respondent is asked to rate a product, service, or experience on a scale. This scale is often referred to as a Likert scale. For example, a five-level Likert scale could be: ...

#| code-fold: true import arviz as az import matplotlib.pyplot as plt from matplotlib.lines import Line2D import numpy as np import pandas as pd import scipy.stats as stats import seaborn as sns import warnings import bambi as bmb warnings.simplefilter(action='ignore', category=FutureWarning) WARNING (pytensor.tensor.blas): Using NumPy C-API based implementation for BLAS functions. Zero inflated models This blog post is a copy of the zero inflated models documentation I wrote for Bambi. The original post can be found here. ...

My project “Better tools to interpret complex Bambi regression models” was completed under the organization of NumFOCUS, and mentors Tomás Capretto and Osvaldo Martin. Before I describe the project, objectives, and work completed, I would like to thank my mentors Tomás and Osvaldo for their precious time and support throughout the summer. They were always available and timely in communicating over Slack and GitHub, and provided valuable feedback during code reviews. Additionally, I would like to thank NumFOCUS and the Google Summer of Code (GSoC) program for providing the opportunity to work on such an open source project over the summer. It has been an invaluable experience, and I look forward to contributing to open source projects in the future. ...

It is currently the beginning of week ten of Google Summer of Code 2023. According to the original deliverables table outlined in my proposal, the goal was to have opened a draft PR for the basic functionality of the plot_slopes. Subsequently, week 11 was reserved to further develop the plot_slopes function, and to write tests and a notebook for the documentation, respectively. However, at the beginning of week ten, I have a PR open with the majority of the functionality that marginaleffects has for slopes. In addition, I also exposed the slopes function, added tests, and have a PR open for the documentation. ...

It is currently the end of week five of Google Summer of Code 2023. According to the original deliverables table outlined in my proposal, the goal was to have opened a draft PR for the core functionality of the plot_comparisons. Subsequently, week six and seven were to be spent further developing the plot_comparisons function, and writing tests and a demo notebook for the documentation, respectively. However, at the end of week five, I have a PR open with the majority of the functionality that marginaleffects has. In addition, I also exposed the comparisons function, added tests (which can and will be improved), and have started on documentation. ...

A variant of the Metropolis-Hastings (MH) algorithm that uses clever proposals and is therefore more efficient (you can get a good approximate of the posterior with far fewer samples) is Gibbs sampling. A problem with MH is the need to choose the proposal distribution, and the fact that the acceptance rate may be low. The improvement arises from adaptive proposals in which the distribution of proposed parameter values adjusts itself intelligently, depending upon the parameter values at the moment. This dependence upon the parameters at that moment is an exploitation of conditional independence properties of a graphical model to automatically create a good proposal, with acceptance probability equal to one. ...

Main Idea Metropolis-Hastings (MH) is one of the simplest kinds of MCMC algorithms. The idea with MH is that at each step, we propose to move from the current state $x$ to a new state $x’$ with probability $q(x’|x)$, where $q$ is the proposal distribution. The user is free to choose the proposal distribution and the choice of the proposal is dependent on the form of the target distribution. Once a proposal has been made to move to $x’$, we then decide whether to accept or reject the proposal according to some rule. If the proposal is accepted, the new state is $x’$, else the new state is the same as the current state $x$. ...

Inference In the probabilistic approach to machine learning, all unknown quantities—predictions about the future, hidden states of a system, or parameters of a model—are treated as random variables, and endowed with probability distributions. The process of inference corresponds to computing the posterior distribution over these quantities, conditioning on whatever data is available. Given that the posterior is a probability distribution, we can draw samples from it. The samples in this case are parameter values. The Bayesian formalism treats parameter distributions as the degrees of relative plausibility, i.e., if this parameter is chosen, how likely is the data to have arisen? We use Bayes’ rule for this process of inference. Let $h$ represent the uknown variables and $D$ the known variables, i.e., the data. Given a likelihood $p(D|h)$ and a prior $p(h)$, we can compute the posterior $p(h|D)$ using Bayes’ rule: ...