---
title: "Bayesian Boolean Network Inference with BBNI"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Bayesian Boolean Network Inference with BBNI}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---



## Overview

The `BBNI` (Bayesian Boolean Network Inference) package implements the Bayesian Boolean network inference algorithm of [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806) on binary gene-expression data. The package computes both the directed network topology (including root and non-root nodes) and the Boolean transition functions corresponding to each defined node.

This approach deliberately attempts to compensate for biological noise and model uncertainty, two central priorities stated in [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806). Employing a Metropolis-within-Gibbs Markov chain Monte Carlo (MCMC) process, the `BBNI` sampler is able to estimate the posterior distribution of valid directed acyclic graph (DAG) topologies and their corresponding Boolean logic functions.

This vignette presents an example simulated workflow utilizing the package: simulating a noisy dataset from an initial topology and transition functions, running the implemented MCMC sampler, and evaluating how well the algorithm recovered the original topology and Boolean functions. The method assumes binary data, a directed acyclic graph, and a maximum in-degree of two; noise is modeled as independent Bernoulli bit flips.

## Setup and simulation

First, we load the package:


``` r
library(BBNI)
```

After setup, we will use the package's simulation functions `GenerateNetwork` and `GenerateSample` (both exported). These will initialize a random, known network topology and the associated transition functions, and subsequently take a simulated sample from it (either time-series or independent). Keeping a stored reference point allows for assessment of final recovery of both the edge structure and the Boolean transition functions.


``` r
set.seed(303)
num_nodes <- 20
sample_size <- 110

# 1. Generate random DAG topology (T) and associated Boolean transition functions (F)
true_network <- GenerateNetwork(num.node = num_nodes)
# visualize "true" synthetic topology before inference
true_layout <- igraph::layout_with_fr(igraph::graph_from_adjacency_matrix(t((true_network > 0) * 1), mode = "directed")) # for graph reproducibility
plot_network(true_network, layout = true_layout)
```

![plot of chunk simulate-data](figures/simulate-data-1.png)

``` r

# 2. Set Beta prior hyperparameters. Root nodes use Beta(3, 3), defining a prior
#    mean of 0.5 while also permitting node-specific variation. Final row specifies
#    hyperparameters for the global noise parameter and satisfies beta1 < beta2.
prior_para <- matrix(3, nrow = num_nodes + 1, ncol = 2)
prior_para[num_nodes + 1, 1] <- 2
prior_para[num_nodes + 1, 2] <- 100

# Sample independent root node expression probabilities from Beta priors
para <- numeric(num_nodes + 1)
for (i in 1:(num_nodes + 1)) {
  para[i] <- rbeta(1, prior_para[i, 1], prior_para[i, 2])
}
# For simulation, fix the noise rate at 20% instead of the raw
# Beta(2, 100) draw so we have clear benchmark for validation.
para[num_nodes + 1] <- 0.20

# 3. Generate noise matrix and simulate observational dataset (G)
error_matrix <- matrix(rbinom(num_nodes * sample_size, 1, para[num_nodes + 1]),
  nrow = num_nodes, ncol = sample_size
)
simulated_data <- GenerateSample(
  trans_matrix = true_network,
  num.node = num_nodes,
  SampleSize = sample_size,
  para = para,
  error = error_matrix
)
# BBNI also supports independent data. By toggling timeseries = FALSE, the algorithm
# resolves parent and child states at the same time within the exact same sample
# rather than assuming time lag
# NOTE: We won't execute a separate simulated chain for this, as the real-world
# application section will already demonstrate independent data functionality
simulated_data_indep <- GenerateSample(
  trans_matrix = true_network,
  num.node = num_nodes,
  SampleSize = sample_size,
  para = para,
  error = error_matrix,
  timeseries = FALSE
)
```

`true_network` is a `num_nodes` x `num_nodes` matrix encoding both the DAG topology generated by `GenerateNetwork`:

- An entry of `0` at position `[i, j]` signifies that node `j` is not a parent of node `i`.
- A nonzero entry at `[i, j]` signifies that node `j` is a parent of node `i`; the integer value corresponds to the Boolean transition function defining that parent relation.

`simulated_data` is the simulated observed data matrix ($G$): a `num_nodes` x `sample_size` binary matrix in which each row represents a gene/node and each column represents an observation. The matrix is simulated from the Boolean logic defined in `true_network` and then distorted using the simulated noise matrix (`error_matrix`).

For real-world usage, `GeneData` must use the same format: an `n` x `m` binary matrix with rows corresponding to nodes, like genes, and columns corresponding to observations or sequenced time points. All entries must be recorded as binary (0/1) expression states.

## Running the MCMC sampler

We next execute `run_bbni()` on the simulated data. The main arguments are:

- `num_update` - total number of MCMC outer iterations.
- `penalty` - structural-prior hyperparameter in $(0, 1]$. Values below `1` apply an edge-count penalty that favors sparser networks. Setting `penalty = 1` disables the sparsity prior and instead uses a uniform prior over valid topologies, matching [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806)'s original model. The default value is `0.1` (used throughout this vignette)
- `prop.ratio` - final probability of selecting the empirical proposal after the first 10% of outer iterations. During the first 10% of outer iterations, the empirical proposal is used with probability 0.9.
- `prior_para` - hyperparameter matrix in which the first `n` rows define Beta prior parameters for root-node Bernoulli activation probabilities; row `n+1` sets the prior parameters for the global noise rate $e$, with the required constraint $\beta_1 < \beta_2$.
- `burn_in` - numeric value between 0 and 1 representing the proportion of initial MCMC samples to discard as burn-in. The leftover samples are used to calculate posterior edge probabilities.


``` r
# Define MCMC and prior hyperparameters
num_update <- 5000 # Total MCMC iterations
penalty <- 0.1 # Structural prior penalty for network complexity
prop_ratio <- 0.1 # Initial proposal mixture coefficient

run_start <- Sys.time()
mcmc_results <- run_bbni(
  GeneData = simulated_data,
  num.node = num_nodes,
  SampleSize = sample_size,
  prior_para = prior_para,
  num_update = num_update,
  penalty = penalty,
  prop.ratio = prop_ratio,
  timeseries = TRUE,
  burn_in = 0.75
)

run_end <- Sys.time()
```

`run_bbni()` accepts a `verbose` argument (default `FALSE`) that displays a text progress bar during sampling; it's left default here to keep the vignette clean.


``` r
cat(
  "Sampler completed", num_update, "iterations (",
  num_nodes * num_update, "node updates) in",
  round(as.numeric(difftime(run_end, run_start, units = "mins")), 2), "minutes\n"
)
#> Sampler completed 5000 iterations ( 1e+05 node updates) in 2.04 minutes
```

As of v0.2.2, the MCMC sampler has been substantially optimized relative to the original CRAN release (v0.1.1). Controlled benchmarks show roughly a 10-fold speedup for 20-node networks; exact runtimes depend on hardware and system load.

## Analyzing the output

`run_bbni()` returns a list containing the sampled path of the Markov chain:

- `log_posterior` - numeric vector of log-posterior values stored after each node-level update.
- `networks` - list of sampled transition-function matrices. Each element shares the same format as `true_network`.
- `post_edge_prob`- matrix of marginal posterior edge probabilities calculated after discarding burn_in period
- `burn_in`- the `burn_in` ratio returned back to user for posterior reference

### Convergence: trace plot

A trace plot of the log-posterior over MCMC updates evaluates chain behavior. Given that we know the specific ground-truth network, we can further compute the log-posterior of the true network via the package's internal `Error_LLH()` function and graph it as a reference baseline:


``` r
# Evaluate log-posterior value of the true network
# Call the unexported package function to compute a reference log-posterior
# for the ground-truth network.
true_logpost_raw <- BBNI:::Error_LLH(
  TRFUM = true_network, GeneData = simulated_data,
  SampleSize = sample_size, num.node = num_nodes,
  prior_para = prior_para, penalty = penalty,
  timeseries = TRUE
)
# The log-posterior value is the last element of the first returned vector.
true_logpost <- true_logpost_raw[[1]][length(true_logpost_raw[[1]])]

# Draw base trace plot with package function
plot_trace(mcmc_results)

# Add true-network reference value.
abline(h = true_logpost, col = "firebrick", lty = 2, lwd = 2)
legend("bottomleft",
       legend = "True network log-posterior",
       col = "firebrick", lty = 2, lwd = 2, bty = "n")
```

![plot of chunk trace-plot](figures/trace-plot-1.png)

Note that the horizontal axis has units of node-level updates rather than outer MCMC iterations. The convergence of the log-posterior towards the baseline value is an indication of chain success. With statistical variation being inevitable, a perfect match with the true topology and Boolean functions is not expected from a single posterior sample.

### Final sampled network

The final sampled network can be visualized as follows:


``` r
final_network <- tail(mcmc_results$networks, 1)[[1]]
final_layout <- igraph::layout_with_fr(igraph::graph_from_adjacency_matrix(t((final_network > 0) * 1), mode = "directed")) # for graph reproducibility
plot_network(final_network, layout = final_layout)
```

![plot of chunk view-results](figures/view-results-1.png)

### Recovery of the true network

As we know the true network, we can quantify the recovery by comparing the final sampled network with the true edge structure and Boolean transition functions:


``` r
true_edges <- true_network > 0
final_edges <- final_network > 0

true_positive <- sum(true_edges & final_edges) # correctly recovered edges
false_positive <- sum(!true_edges & final_edges) # spurious edges
false_negative <- sum(true_edges & !final_edges) # missed true edges

cat("True edges in the network:       ", sum(true_edges), "\n")
#> True edges in the network:        29
cat("Correctly recovered edges:       ", true_positive, "\n")
#> Correctly recovered edges:        28
cat("Spurious (false positive) edges: ", false_positive, "\n")
#> Spurious (false positive) edges:  0
cat("Missed (false negative) edges:   ", false_negative, "\n")
#> Missed (false negative) edges:    1

# Among the correctly-recovered edges, how many also got the right
# Boolean function?
correct_function_final <- sum(true_edges & final_edges & (true_network == final_network))
cat("...of which function also correct: ", correct_function_final, "out of", true_positive, "\n")
#> ...of which function also correct:  27 out of 28
```

Once again, some deviation is reasonable because this comparison uses only one sample from the end of the Markov chain. A posterior summary across multiple samples may allow a more stable estimate.

### Posterior summarization by Bayesian model averaging

Instead of relying on a single sampled network, we can summarize the posterior distribution by Bayesian model averaging (BMA) over several retained network samples. This allows calculation of posterior edge-inclusion probabilities, which are often more informative than a single end sample. In biological applications, reducing false-positive edges is particularly important, as each predicted interaction may warrant costly experimental validation.

We first discard an initial burn-in period, here set to 75% of the recorded chain to match the burn-in convention used in [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806)'s own simulation studies, instead of `run_bbni()`'s own default `burn_in` value of 70%. This is to reduce the impact of the unpredictability of the arbitrary starting structure. We then retain one network per outer iteration (every `num.node` node-level updates) to account for the strong statistical dependence of within-iteration samples. For each directed edge, the posterior inclusion probability is calculated as the fraction of retained samples in which that edge appears:


``` r
bma_edges <- mcmc_results$post_edge_prob > 0.5
bma_tp <- sum(true_edges & bma_edges)
bma_fp <- sum(!true_edges & bma_edges)
bma_fn <- sum(true_edges & !bma_edges)
cat("Correctly recovered edges:       ", bma_tp, "\n")
#> Correctly recovered edges:        29
cat("Spurious (false positive) edges: ", bma_fp, "\n")
#> Spurious (false positive) edges:  0
cat("Missed (false negative) edges:   ", bma_fn, "\n")
#> Missed (false negative) edges:    0
```

### Visualizing network recovery

The following plot compares the true network and the BMA consensus network. Edges that are structurally correct but assigned the wrong Boolean function are marked differently from edges for which both the parent relation and function are correctly recovered. Only edges with a computed statistical probability of higher than 50% are shown:


``` r
# ensure reproducibility of visualization
combined_adj_layout <- ((mcmc_results$post_edge_prob > 0.5) | (true_network > 0)) * 1
compare_layout <- igraph::layout_with_fr(igraph::graph_from_adjacency_matrix(t(combined_adj_layout), mode = "directed"))
plot_bbni(mcmc_results, true_network = true_network, threshold = 0.5, layout = compare_layout)
```

![plot of chunk visualize-network](figures/visualize-network-1.png)

## Application to real-world biological data

The workflow above uses simulated data so that the inferred network can be compared with a known ground truth. For empirical biological data, the same inference procedure can be applied with an expression matrix that is both binary and in the required `num.node` x `SampleSize` format. Since true topology is generally unknown in real applications, posterior edge-inclusion probabilities, convergence assessment, and biological plausibility should be emphasized over direct recovery metrics.

The original study by [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806) applied the Bayesian Boolean network framework to yeast cell-cycle expression data and compared the inferred relationships with a reference cell-cycle network. A package-level empirical example can follow the same structure: load a binary expression matrix, run `run_bbni()`, examine trace behavior, summarize posterior edge probabilities, and interpret high-probability interactions in relation to existing biological knowledge.


``` r
# Load the included binary yeast cell-cycle data (14 genes x 385 complete pooled
# conditions); see ?yeast_data for source and preprocessing details.
data("yeast_data")

# Use same priors as earlier simulated example
yeast_prior_para <- matrix(3, nrow = nrow(yeast_data) + 1, ncol = 2)
yeast_prior_para[nrow(yeast_data) + 1, 1] <- 2
yeast_prior_para[nrow(yeast_data) + 1, 2] <- 100

set.seed(303)
run_start <- Sys.time()

# Run in independent mode: these 385 pooled columns include many distinct experimental
# conditions (MMS exposure, gamma radiation, heat shock, etc.), not a single
# continuous time series, so timeseries = FALSE is the correct model here.
yeast_results <- run_bbni(
  GeneData = yeast_data,
  prior_para = yeast_prior_para,
  num_update = 10000,
  penalty = 0.1,
  prop.ratio = 0.1,
  timeseries = FALSE,
  burn_in = 0.3,
  verbose = FALSE
)

run_end <- Sys.time()
```
The time and number of iterations are outputted below:

``` r
# Duration of chain
cat(
  "Sampler completed", 10000, "iterations (",
  nrow(yeast_data) * 10000, "node updates) in",
  round(as.numeric(difftime(run_end, run_start, units = "mins")), 2), "minutes\n"
)
#> Sampler completed 10000 iterations ( 140000 node updates) in 2.04 minutes
```
The results of the MCMC chain are visualized with the following trace plot and network plot:

``` r
# Visualize results
plot_trace(yeast_results, every = nrow(yeast_data))
```

![plot of chunk yeast-trace](figures/yeast-trace-1.png)

``` r
yeast_layout <- igraph::layout_with_fr(igraph::graph_from_adjacency_matrix(t((yeast_results$post_edge_prob > 0.5) * 1), mode = "directed")) # for graph reproducibility
plot_bbni(yeast_results, node_names = rownames(yeast_data), threshold = 0.5, layout = yeast_layout)
```

![plot of chunk yeast-plot](figures/yeast-plot-1.png)

Running BBNI on the pooled yeast cell-cycle dataset recovers a biologically consistent subnetwork, matching the specific relationships emphasized in the original [Han et al. (2014)](https://doi.org/10.1371/journal.pone.0115806) paper's real-data analysis.
The model identifies CLB2 as a direct regulator of SWI5, matching the paper's reported finding. It also recovers all three "coupled" gene pairs that the original paper specifically mentions — CLN1/CLN2, CLB1/CLB2, and CLB5/CLB6 — as directly linked.
The original paper acknowledges that "12.82% of the links in the reference yeast cell-cycle network... are identified in 100% of the posterior samples." Similarly, the inferred network here is intentionally sparse rather than dense with interconnected genes. Furthermore, several genes (SIC1, CDH1, MCM1) show no high-confidence links in this dataset, reflecting the partial-recovery limitation of real biological data that the original authors reported.

## Next steps

This vignette demonstrates the core `BBNI` workflow on simulated data. From here:

- See `?run_bbni`, `?GenerateNetwork`, and `?GenerateSample` for function-level documentation.
- The simulated example runs 5000 iterations on a 20-node network. Larger networks, noisier data, or higher-precision posterior summaries may require significantly more iterations.
- For user-supplied expression data, format `GeneData` as a binary `num.node` x `SampleSize` matrix, as described above.
- The current model assumes binary data, a directed acyclic graph, and maximum in-degree two. For real data, run multiple chains or sensitivity analysis when possible.

## Session information


``` r
sessionInfo()
#> R version 4.6.0 (2026-04-24 ucrt)
#> Platform: x86_64-w64-mingw32/x64
#> Running under: Windows 11 x64 (build 28020)
#> 
#> Matrix products: default
#>   LAPACK version 3.12.1
#> 
#> locale:
#> [1] LC_COLLATE=Spanish_Latin America.utf8  LC_CTYPE=Spanish_Latin America.utf8    LC_MONETARY=Spanish_Latin America.utf8 LC_NUMERIC=C                           LC_TIME=Spanish_Latin America.utf8    
#> 
#> time zone: America/Chicago
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] BBNI_0.2.2
#> 
#> loaded via a namespace (and not attached):
#>  [1] igraph_2.3.3    R6_2.6.1        xfun_0.60       magrittr_2.0.5  knitr_1.51      pkgconfig_2.0.3 lifecycle_1.0.5 ps_1.9.3        cli_3.6.6       processx_3.9.0  pak_0.10.0      callr_3.7.6    
#> [13] compiler_4.6.0  tools_4.6.0     evaluate_1.0.5  otel_0.2.0      rlang_1.3.0
```
