Domain Applications

OptimShortestPaths provides built-in support for common application domains, particularly in pharmaceutical and healthcare optimization.

Drug-Target Networks

Analyze drug-target interactions and selectivity.

Creating a Network

using OptimShortestPaths

drugs = ["Aspirin", "Ibuprofen", "Celecoxib"]
targets = ["COX1", "COX2"]

# Binding affinities (0-1 scale, higher = stronger binding)
affinity_matrix = [
    0.85  0.45;  # Aspirin: strong COX1 (0.85), moderate COX2 (0.45)
    0.30  0.90;  # Ibuprofen: moderate COX1 (0.30), strong COX2 (0.90)
    0.05  0.95   # Celecoxib: weak COX1 (0.05), very strong COX2 (0.95) - selective!
]

network = create_drug_target_network(drugs, targets, affinity_matrix)

Finding Paths

# Find shortest path from drug to target
distance, path = find_drug_target_paths(network, "Aspirin", "COX2")
println("Binding affinity: ", distance)

Analyzing Selectivity

# Compare Ibuprofen affinity for COX1 vs COX2
drug_idx = network.drug_indices["Ibuprofen"]
cox1_idx = network.target_indices["COX1"]
cox2_idx = network.target_indices["COX2"]

ratio = calculate_distance_ratio(network.graph, drug_idx, cox1_idx, cox2_idx)
println("COX2/COX1 selectivity ratio: ", ratio)

# Analyze overall connectivity
stats = analyze_drug_connectivity(network, "Celecoxib")
println("Reachable targets: ", stats)

Metabolic Pathways

Optimize biochemical reaction pathways.

Creating a Pathway

metabolites = ["Glucose", "G6P", "F6P", "F16BP", "DHAP", "G3P", "PEP", "Pyruvate"]

reactions = ["Hexokinase", "PGI", "PFK", "Aldolase", "TPI", "GAPDH", "PK"]
reaction_costs = [1.0, 0.0, 1.0, 0.0, 0.0, 0.2, 0.2]  # Encode energy usage as non-negative costs
reaction_network = [
    ("Glucose", "Hexokinase", "G6P"),
    ("G6P",    "PGI",        "F6P"),
    ("F6P",    "PFK",        "F16BP"),
    ("F16BP",  "Aldolase",   "DHAP"),
    ("DHAP",   "TPI",        "G3P"),
    ("G3P",    "GAPDH",      "PEP"),
    ("PEP",    "PK",         "Pyruvate"),
]

pathway = create_metabolic_pathway(metabolites, reactions, reaction_costs, reaction_network)

Finding Optimal Pathways

# Find pathway from substrate to product
pathway_cost, pathway_steps = find_metabolic_pathway(pathway, "Glucose", "Pyruvate")
println("Total pathway cost: ", pathway_cost)
println("Pathway: ", pathway_steps)

Treatment Protocols

Optimize clinical treatment sequences.

Creating a Protocol

treatments = ["Initial", "ChemoA", "ChemoB", "Surgery", "Radiation", "Remission"]

# Costs in thousands of dollars
costs = [0.0, 50.0, 60.0, 100.0, 40.0, 0.0]

# Efficacy weights (higher = better outcome)
efficacy = [0.0, 0.6, 0.7, 0.8, 0.5, 1.0]

# Valid treatment transitions (from, to, additional_risk)
transitions = [
    ("Initial", "ChemoA", 0.1),
    ("Initial", "Surgery", 0.3),
    ("ChemoA", "ChemoB", 0.05),
    ("ChemoA", "Surgery", 0.2),
    ("ChemoB", "Radiation", 0.15),
    ("Surgery", "Radiation", 0.1),
    ("Radiation", "Remission", 0.05),
]

protocol = create_treatment_protocol(treatments, costs, efficacy, transitions)

Optimizing Sequences

# Find lowest-cost path to remission
total_cost, sequence = optimize_treatment_sequence(protocol, "Initial", "Remission")

println("Total cost: \$", total_cost * 1000)
println("Optimal sequence: ", sequence)

Supply Chain Optimization

For custom domains like supply chain, use the generic interface:

# Entities: Factories, warehouses, distribution centers
# Edges: Transportation links
# Weights: Shipping cost + inventory holding cost

factories = 3
warehouses = 4
dist_centers = 5
n_vertices = factories + warehouses + dist_centers

edges = Edge[]
weights = Float64[]

# Use a fixed RNG seed so the illustrative costs match the example script.
using Random
rng = MersenneTwister(42)

# Factory → Warehouse links
for f in 1:factories
    for w in 1:warehouses
        from = f
        to = factories + w
        transport_cost = rand(rng, 10:20)
        push!(edges, Edge(from, to, length(edges)+1))
        push!(weights, float(transport_cost))
    end
end

# Warehouse → Distribution center links
for w in 1:warehouses
    for d in 1:dist_centers
        from = factories + w
        to = factories + warehouses + d
        cost = rand(rng, 5:15)
        push!(edges, Edge(from, to, length(edges)+1))
        push!(weights, float(cost))
    end
end

graph = DMYGraph(n_vertices, edges, weights)

# Find optimal route from factory 1 to distribution center 5
target = factories + warehouses + 5
distances = dmy_sssp!(graph, 1)
println("Minimum cost to DC 5: \$", distances[target])

Generic Pattern

All domain applications follow this pattern:

Define entities (metabolites, drugs, locations, etc.)
Define relationships (reactions, bindings, routes, etc.)
Assign costs/weights (affinities, times, distances, etc.)
Create graph using domain constructor or generic DMYGraph
Run algorithm to find optimal solutions