README

This page reproduces the package README in full. Raw README.

hobbs (High dimensiOnal Bayesian omniBus Sampler)

R package for high dimensional Bayesian data analysis

• Enables high dimensional statistical modeling using Bayesian inference.

• Probabilistic programming language for high dimensional problems.

See more on the website: https://hobbs.github.io

Visit the community forum: https://groups.google.com/g/hobbs-users

Installation

hobbs requires a C compiler and Rust with Cargo.

Install Rust: https://rustup.rs/

Windows users also need Rtools: https://cran.r-project.org/bin/windows/Rtools/

macOS users also need the Xcode Command Line Tools. Install them by running the following command in Terminal:

xcode-select --install

Linux users need a C compiler and standard build tools. For example, on Ubuntu or Debian:

sudo apt install build-essential

Install the development version from GitHub:

install.packages("pak")
pak::install_github("hobbs-dev/hobbs")

Once the package is installed, check your compiler toolchain, build the sampler, and check the sampler:

library(hobbs)
hobbs_check_toolchain()
hobbs_build_sampler()
hobbs_check_sampler()

A first block example: Gaussian linear regression

This example simulates a regression problem with an x matrix, estimates the regression coefficients, and estimates the residual standard deviation through logsigma.

library(hobbs)

set.seed(1)

n <- 1000L
p <- 5L

x <- matrix(rnorm(n * p), nrow = n, ncol = p)
x <- cbind(1, x)        # first column is the intercept
p <- ncol(x)

beta_true <- c(0.5, 1.0, -0.75, 0.5, 0.0, -0.25)
sigma_true <- 0.75

y <- as.numeric(x %*% beta_true + rnorm(n, 0, sigma_true))

data <- list(
  n = n,
  p = p,
  x = x,
  y = y
)

The model below declares two parameter blocks:

• beta(p) for the intercept and regression coefficients;
• logsigma(1) for the log residual standard deviation.

The block beta(j) updates one coefficient at a time. The block logsigma(1) updates the residual scale.

The update rule for each block is to evaluate the prior contribution for the parameter being updated and then evaluate all direct children of that parameter. In this example, the full likelihood is the only direct child of every parameter.

model_src <- '
param beta(p);
param logsigma(1);

func y_lpdf() {
  double sigma = exp(logsigma(1));

  for (i = 1:n) {
    double mu = 0.0;
    for (j = 1:p) {
      mu += beta(j) * x(i,j);
    }
    y(i) ~ dnorm(mu,sigma);
  }
}

block beta(j) {
  beta(j) ~ dnorm(0,10);
  y_lpdf();
}

block logsigma(1) {
  logsigma(1) ~ dnorm(0,2);
  y_lpdf();
}
'

fit <- hobbs(
  model = model_src,
  data = data,
  samples = 2000,
  burnin = 1000,
  out = "chain_regression.bin"
)

draws <- read_hobbs("chain_regression.bin")
head(draws)

Posterior means can be compared with the simulated truth:

beta_cols <- paste0("beta[", seq_len(p), "]")

colMeans(draws[, beta_cols])
beta_true

exp(mean(draws[, "logsigma[1]"]))
sigma_true

Choosing RWMH or slice sampling by parameter

Continuous parameters use the adaptive scalar random-walk Metropolis sampler by default. The sampler can be selected independently for each parameter declaration:

param beta(p) save=mean sampler=rwmh;
param u(n, p) sampler=slice;

sampler=slice uses scalar stepping-out/shrinkage slice sampling. Its width is adapted during burn-in and then frozen for retained sampling. RWMH and slice declarations can be mixed in the same model, and both use the same parameter-local block target and exact transactional cache/update machinery. Bounded dparam declarations continue to use exact finite-state Gibbs updates.

The save=mean and sampler= modifiers are independent and may be written in either order, for example param u(n, p) sampler=slice save=mean;.

Optimizing the regression with a deterministic cache

In the plain model, every update to one coefficient rebuilds the whole linear predictor:

mu_i = beta(1) * x(i,1) + ... + beta(p) * x(i,p)

That costs roughly O(n * p) per scalar coefficient proposal. For large p, this is wasteful because changing beta(j) only changes mu_i by one rank-one update:

mu_i <- mu_i + (new beta_j - old beta_j) * x(i,j)

hobbs supports attached deterministic caches for this pattern. The next model declares a persistent cached vector mu(n), initializes it once, and then updates it whenever beta(j) changes.

model_src_cached <- '
param beta(p) save=mean;
param logsigma(1);

func y_lpdf() {
  double sigma = exp(logsigma(1));

  for (i = 1:n) {
    y(i) ~ dnorm(mu(i),sigma);
  }
}

block beta(j) {
  beta(j) ~ dnorm(0,10);
  y_lpdf();
} cache mu(n) {
  for (i = 1:n) {
    for (k = 1:p) {
      mu(i) += beta(k) * x(i,k);
    }
  }
} update mu(n) {
  for (i = 1:n) {
    mu(i) += (proposal(beta(j)) - current(beta(j))) * x(i,j);
  }
}

block logsigma(1) {
  logsigma(1) ~ dnorm(0,2);
  y_lpdf();
}
'

fit_cached <- hobbs(
  model = model_src_cached,
  data = data,
  samples = 2000,
  burnin = 1000,
  out = "chain_regression_cached.bin"
)

draws <- read_hobbs("chain_regression_cached.bin")
draws_mean <- read_hobbs("chain_regression_cached.mean.bin")

The cached model is mathematically the same model as the plain version. The difference is computational: mu(n) is maintained incrementally instead of being rebuilt from all p predictors after every scalar coefficient proposal.

The important cache rules are:

• cache mu(n) { ... } declares and initializes the persistent cached vector;
• update mu(n) { ... } tells hobbs how to update that cache for the attached block;
• proposal(beta(j)) is the proposed scalar value being evaluated;
• current(beta(j)) is the currently accepted scalar value;
• if a proposal is rejected, hobbs restores the cache automatically.

This optimization is most useful when p is large and parameters are updated one at a time. For small regressions, the plain model may already be fast enough.

Next steps

The same block syntax can be used for discrete parameters, sparse variable-selection models, random effects, and other models where only part of the likelihood changes for each parameter update. See https://hobbs.github.io for more examples and reference material.