def test_local_graph(self):
n = 1
f = boolean_map(n)
formula = local_edges(f, {(0,): [(1,1,1)]})
sols = solve(formula, n)
self.assertEqual(len(list(sols)), 1)
n = 2
f = boolean_map(n)
formula = local_edges(f, {(0,0): [(1,2,1), (2,1,-1)]})
sols = solve(formula, n, max_models=10)
for sol in sols:
lig = local_int_graph(sol)
self.assertTrue((1,2,1) in lig[(0,0)])
self.assertTrue((2,1,-1) in lig[(0,0)])
self.assertFalse((1,2,-1) in lig[(0,0)])
self.assertFalse((2,1,+1) in lig[(0,0)])
f = boolean_map(n)
formula = local_edges(f, {(0,0): [(1,2,1), (2,1,-1)], (0,1): [(2,1,1)]}, only=False)
sols = solve(formula, n, max_models=10)
with self.assertRaises(StopIteration):
next(sols)
formula = local_edges(f, {(0,0): [(1,2,1), (2,1,-1)], (1,1): [(2,1,1)]}, only=False)
sols = solve(formula, n, max_models=10)
for sol in sols:
lig = local_int_graph(sol)
self.assertTrue((1,2,1) in lig[(0,0)])
self.assertTrue((2,1,-1) in lig[(0,0)])
def test_global_circuit(self):
n = 4
f = boolean_map(n)
formula = And([Not(is_circuit(f, x, [1,2,3,4])) for x in f] + [is_global_circuit(f, [1,2,3,4])])
sol = next(solve(formula, n, max_models=1))
lcs = local_circuits(sol)
gcs = global_circuits(sol)
self.assertTrue(([1,2,3,4],1) in gcs or ([1,2,3,4],-1) in gcs)
for x in f:
self.assertFalse(([1,2,3,4],1) in lcs[x])
self.assertFalse(([1,2,3,4],-1) in lcs[x])
formula = And([Not(is_circuit(f, x, [2,3,4], -1)) for x in f] + [is_global_circuit(f, [2,3,4], sign=-1)])
sol = next(solve(formula, n, max_models=1))
lcs = local_circuits(sol)
gcs = global_circuits(sol)
self.assertTrue(([2,3,4],-1) in gcs)
for x in f:
self.assertFalse(([2,3,4],-1) in lcs[x])
formula = And([Not(is_circuit(f, x, [1,4,3], +1)) for x in f] + [is_global_circuit(f, [1,4,3], sign=+1)])
sol = next(solve(formula, n, max_models=1))
lcs = local_circuits(sol)
gcs = global_circuits(sol)
self.assertTrue(([1,4,3],+1) in gcs)
for x in f:
self.assertFalse(([1,4,3],+1) in lcs[x])
def test_map_state(self):
f = boolean_map(1)
formula = And(fixed_point(f, (0,)), map_state(f, (0,), (1,)))
self.assertEqual(len(list(solve(formula, 1))), 0)
self.assertEqual(len(list(solve(fixed_point(f, (0,)), 1))), 2)
self.assertEqual(len(list(solve(map_state_set(f, (0,), [(0,), (1,)]), 1))), 4)
self.assertEqual(len(list(solve(map_state_set(f, (0,), [(0,), (1,)]), 1, max_models=3))), 3)
def test_global_graph(self):
n = 3
f = boolean_map(n)
formula = global_edges(f, [(1,2,1), (2,3,1), (3,1,-1)])
sols = solve(formula, n)
k = 0
for sol in sols:
k = k + 1
lig = local_int_graph(sol)
for x in f:
self.assertEqual(lig[x], [(1,2,1), (2,3,1), (3,1,-1)])
self.assertEqual(global_int_graph(sol), [(1,2,1), (2,3,1), (3,1,-1)])
self.assertEqual(k, 1)
formula = global_edges(f, [(1,2,1), (2,3,1)], all_states=False)
sols = solve(formula, n, max_models=3)
for sol in sols:
grg = global_int_graph(sol)
self.assertTrue((1,2,1) in grg)
self.assertTrue((2,3,1) in grg)
self.assertFalse((3,1,-1) in grg)
self.assertFalse((3,1,1) in grg)
self.assertFalse((3,2,-1) in grg)
self.assertFalse((3,2,1) in grg)
formula = global_edges(f, [(1,2,1), (2,3,1), (3,1,-1)], only=False, all_states=False)
sols = solve(formula, n, max_models=3)
for sol in sols:
grg = global_int_graph(sol)
self.assertTrue((1,2,1) in grg)
self.assertTrue((2,3,1) in grg)
self.assertTrue((3,1,-1) in grg)
def test_succ(self):
n = 3
f = boolean_map(n)
formula = succ(f, (0,0,0), (0,1,0))
sols = solve(formula, n, max_models=4)
for sol in sols:
self.assertEqual(sol[(0,0,0)][1], 1)
formula = succ_set(f, (1,1,0), [(0,1,0), (1,1,1)])
sols = solve(formula, n, max_models=4)
for sol in sols:
self.assertTrue(sol[(1,1,0)][0]==0 or sol[(1,1,0)][2]==1)
def test_multilevel(self):
ms = [2,1,4]
n = sum(ms)
f = boolean_map(n)
rg = [(1,1,1), (2,1,-1)]
rgl = [((1,1),(1,2),1), ((2,1),(1,1),-1)]
mltb = multi_level_to_bool(ms)
formula = And(multilevel(f, ms), global_edges(f, [(mltb[j],mltb[i],s) for j,i,s in rgl], all_states=False, only=False))
sol = boolean_to_multi(next(solve(formula, n, max_models=1)), ms)
self.assertTrue(all(e in global_int_graph(sol) for e in rg))
formula = And(formula, stepwise(f, ms))
sol = boolean_to_multi(next(solve(formula, n, max_models=1)), ms)
self.assertTrue(all(e in global_int_graph(sol) for e in rg))
self.assertTrue(is_stepwise(sol))
def test_trap_set(self):
n = 3
f = boolean_map(n)
xs = [(0,0,0), (0,1,0), (1,1,1)]
formula = trap_set(f, xs)
sol = next(solve(formula, n, max_models=1))
self.assertTrue(is_trap_domain(sol, xs))
def test_orbit(self):
n = 3
f = boolean_map(n)
formula = orbit(f, [(0,0,0), (0,1,0), (1,1,0), (1,0,0)])
sol = next(solve(formula, n, max_models=1))
self.assertEqual(sol[(0,0,0)][1], 1)
self.assertEqual(sol[(0,1,0)][0], 1)
self.assertEqual(sol[(1,1,0)][1], 0)
with self.assertRaises(ValueError):
orbit(f, [(1,1,0), (1,0,0), (1,1,1), (0,1,1)])
n = 4
f = boolean_map(n)
c = [(0,1,0,0), (0,1,1,0), (0,1,1,1), (1,1,1,1), (1,1,0,1), (1,1,0,0), (0,1,0,0)]
formula = orbit(f, c)
sol = solve(formula, n, max_models=1)
self.assertEqual(next(sol)[(0,1,0,0)][2], 1)
def test_edge(self):
n, ms = 3, [1]*3
f = boolean_map(n)
formula = And(edge(f, (0,0,1), 2, 3, -1),
edge(f, (0,0,0), 3, 1, 0),
edge(f, (0,1,1), 1, 1, +1))
sols = solve(formula, n, max_models=10)
for sol in sols:
self.assertTrue(sol[(0,0,1)][2]==1 and sol[(0,1,1)][2]==0)
self.assertTrue(sol[(0,0,0)][0]==sol[(0,0,1)][0])
self.assertTrue(sol[(0,1,1)][0]==0 and sol[(1,1,1)][0]==1)
self.assertTrue((2,3,-1) in local_int_graph_state(sol, (0,0,1), ms))
self.assertTrue((3,1,-1) not in local_int_graph_state(sol, (0,0,0), ms))
self.assertTrue((3,1,+1) not in local_int_graph_state(sol, (0,0,0), ms))
self.assertTrue((1,1,+1) in local_int_graph_state(sol, (0,1,1), ms))
with self.assertRaises(ValueError):
solve(edge(f, (0,1,1), 2, 3, 2), n)
def test_circuit_signs(self):
n = 4
f = boolean_map(n)
formula = is_circuit(f, (0,1,0,0), [1,4,2])
sol = next(solve(formula, n, max_models=1))
self.assertTrue((([1,4,2],-1) in local_circuits(sol)[(0,1,0,0)]) or \
(([1,4,2],1) in local_circuits(sol)[(0,1,0,0)]))
formula = And([is_circuit(f, x, [2,3,4], sign=-1) for x in f])
sol = next(solve(formula, n, max_models=1))
lcs = local_circuits(sol)
for x in f:
self.assertTrue(([2,3,4],-1) in lcs[x])
formula = And([is_circuit(f, x, [1,2,3,4], sign=+1) for x in f])
sol = next(solve(formula, n, max_models=1))
lcs = local_circuits(sol)
for x in f:
self.assertTrue(([1,2,3,4],1) in lcs[x])
def test_attractive_cycle(self):
n = 4
f = boolean_map(n)
with self.assertRaises(ValueError):
attractive_cycle(f, [(1,1,0), (1,0,0), (1,1,1), (0,1,1)])
c = [(0,1,0,0), (0,1,1,0), (0,1,1,1), (1,1,1,1), (1,1,0,1), (1,1,0,0), (0,1,0,0)]
formula = attractive_cycle(f, c)
sols = solve(formula, n, max_models=10)
for sol in sols:
self.assertEqual(sol[(0,1,0,0)][2], 1)
self.assertTrue(any(sorted(a)==sorted(c[:-1]) for a in attractive_cycles(sol)))
def test_circuit_path(self):
n = 3
f = boolean_map(n)
path = [(0,0,0),(0,1,0),(0,1,1),(1,1,1)]
path1 = [(0,0,0),(1,0,0)]
formula = is_path_circuit(f, path, [1,2,3], +1)
formula = And(formula, And([Not(is_path_circuit(f, path, c)) for c in circuits(n) if len(c)<3]))
formula = And(formula, Not(f[(1,1,1)][2]))
formula = And(formula, is_path_circuit(f, path1, [1], -1))
formula = And(formula, Not(is_path_circuit(f, path1, [3])))
sols = solve(formula, n, max_models=2)
for sol in sols:
cs = path_circuits(sol, path)
self.assertTrue(all(len(c[0])>=3 for c in cs))
self.assertTrue(([1,2,3], +1) in cs)
self.assertTrue(([1], -1) in path_circuits(sol, path1))
self.assertTrue(([1], -1) in path_circuits(sol, path1, sign=-1))
self.assertEqual(path_graph(sol, []), [])
self.assertEqual(path_graph(sol, [(1,0),(1,1)]), [])
import os
sys.path.insert(
0, os.path.join(os.path.dirname(os.path.realpath(__file__)), '..'))
from pprint import pprint
from pysmt.shortcuts import And
from dinpy.din import attractors
from dinpy.interaction_graphs import global_int_graph, local_int_graph
from dinpy.find_din import boolean_map, global_edges, local_edges, solve, orbit
# find Boolean networks with a given interaction graph
n = 4
f = boolean_map(n)
edges = [(1, 2, 1), (2, 3, -1), (3, 4, 1), (4, 1, -1)]
print("Imposing global interaction graph: {}".format(edges))
sols = solve(global_edges(f, edges), n)
for g in sols:
print("Interaction graph: {}".format(global_int_graph(g)))
print("Attractors: {}".format(list(attractors(g))))
edges = [(1, 3, 1), (3, 2, 1), (3, 4, 1), (4, 1, -1)]
print("Imposing global interaction graph: {}".format(edges))
sols = solve(global_edges(f, edges), n)
for g in sols:
print("Interaction graph: {}".format(global_int_graph(g)))
print("Attractors: {}".format(list(attractors(g))))
# find Boolean networks with given local graphs and orbit
edges = {(0, 0, 0, 1): [], (1, ) * n: [(1, 1, -1)]}
print("Imposing local interaction graph: {}".format(edges))
path = [(0, ) * n, (0, 1, 0, 0), (1, 1, 0, 0), (1, 0, 0, 0)]
from dinpy.find_din import boolean_map, solve, circuits, attractive_cycle, is_circuit
from dinpy.find_din import multilevel, stepwise, fixed_point
from dinpy.multi_to_boolean import boolean_to_multi
def no_local_neg_circuits(f, n):
return [Not(is_circuit(f, x, c, sign=-1)) for x in f for c in circuits(n)]
# find a Boolean network with an antipodal attractive cycle and no local negative circuits
n = 6
f = boolean_map(n)
nolnc = no_local_neg_circuits(f, n)
antip_cycle = [(1,)*k+(0,)*(n-k) for k in range(n)] + [(0,)*k+(1,)*(n-k) for k in range(n)] + [(0,)*n]
attr_cycle = attractive_cycle(f, antip_cycle)
print("Formula created.")
sols = solve(And(nolnc+[attr_cycle]), n, max_models=1)
try:
g = next(sols)
pprint(g)
pprint(polys(g))
lc = local_circuits(g)
print("Signs of local circuits: {}".format(set([s for x in lc for c, s in lc[x]])))
print("Attractors: {}".format(list(attractors(g))))
except StopIteration:
print("No solutions.")
# find a multilevel network with no local negative circuits
ms = [3,3]
n = sum(ms)
f = boolean_map(n)
formula = And(no_local_neg_circuits(f, n) +
