dot-simulated_annealing: Run the simulated annealing active subnetwork search

In pathfindR: Enrichment Analysis Utilizing Active Subnetworks

Run the simulated annealing active subnetwork search

Description

The candidate solution starts either with all positive-z-score nodes on (when params$start_with_all_positives) or with each node switched on independently with probability params$gene_init_prob. A random node is toggled each step and the resulting subnetworks are compared rank-by-rank against the current ones, accepting the change with a temperature-dependent probability. The temperature decays geometrically from sa_initial_temp to sa_final_temp over sa_iterations steps.

Usage

.simulated_annealing(network, sc, params, verbose = FALSE)

Arguments

network	A network from build_network() (provides the CSR adjacency csr_offsets / csr_nbrs).
sc	A score context from build_score_context().
params	A list of run parameters.
verbose	Logical; emit progress messages.

Details

The search loop runs in C++ (run_simulated_annealing) and reproduces the Java reference exactly: the same java.util.Random stream (seeded with params$seed), the same initial-state draw order (node order), the same nextInt-based node toggling, and the same acceptance walk over the score-ranked subnetworks (advance to the next pair when a worse move passes its Boltzmann draw; accept on a >0.001 improvement; otherwise reject).

Value

A list of subnetwork objects (all connected components of the final solution, sorted by score descending).

pathfindR documentation built on July 2, 2026, 1:06 a.m.