def main():
g = DirectedGraph()
for i in range(9):
g.add_vertex(i)
g.add_edge(0, 1, 4)
g.add_edge(0, 7, 8)
g.add_edge(1, 2, 8)
g.add_edge(1, 7, 11)
g.add_edge(2, 3, 7)
g.add_edge(2, 8, 2)
g.add_edge(2, 5, 4)
g.add_edge(3, 4, 9)
g.add_edge(3, 5, 14)
g.add_edge(4, 5, 10)
g.add_edge(5, 6, 2)
g.add_edge(6, 7, 1)
g.add_edge(6, 8, 6)
g.add_edge(7, 8, 7)
print(g)
prim(g)
def main():
n = 10
edges = [((1, 2), 5)]
g = DirectedGraph()
for i in range(9):
g.add_vertex(i)
g.add_edge(0, 1, 4)
g.add_edge(0, 7, 8)
g.add_edge(1, 2, 8)
g.add_edge(1, 7, 11)
g.add_edge(2, 3, 7)
g.add_edge(2, 8, 2)
g.add_edge(2, 5, 4)
g.add_edge(3, 4, 9)
g.add_edge(3, 5, 14)
g.add_edge(4, 5, 10)
g.add_edge(5, 6, 2)
g.add_edge(6, 7, 1)
g.add_edge(6, 8, 6)
g.add_edge(7, 8, 7)
print(bidirectional(g, 0, 8))
def main():
G = DirectedGraph()
G.add_vertex('A')
G.add_vertex('B')
G.add_vertex('C')
G.add_vertex('D')
G.add_vertex('E')
G.add_edge('A', 'B')
G.add_edge('B', 'C')
G.add_edge('B', 'D')
G.add_edge('A', 'E')
print(strongly_connected(G))
class HiddenMarkov(object):
def __init__(self, config_path, transitions=None, emissions=None, start_id='B', end_id='E',
convert_zero=0.000000000001):
"""
:param config_path: to initialize the model path, sample format is available in ../data/hmm.cfg
:param transitions: a list of triplets (from_id, to_id, probability), where from_id and to_id are state labels
:param emissions: a list of triplets (emitter_id, emission_id, probability), where emitter_id is a state label
:param start_id: label for the initial state, (can not emit obs), used for getting the starting probabilities
:param end_id: label for the final state (can not emit obs), only required for the simulations
:param convert_zero: a small number to handle missing or zero entries in the emission and transition data,
if convert_zero is 0 and there is a missing or zero entry in the probabilities, an exception will be raised
"""
self.graph = DirectedGraph(node_t=EmitterNode)
self.emitters = []
self.convert_zero = convert_zero
self.start_id = start_id
self.end_id = end_id
if isinstance(config_path, basestring):
transitions, emissions = load_config(path=config_path) # load from data
else:
assert (transitions is not None and emissions is not None)
self.set_transitions(transitions) # (re)init emitters here
self.starting_ps = {child.id: w for [w, child] in self.graph.nodes[self.start_id].children.values()}
self.set_emissions(emissions)
self.update_emitters()
def set_transitions(self, transitions):
for from_id, to_id, p in transitions:
log_p, converted = try_to_log(p, convert_zero=self.convert_zero) # use log probabilities
if converted:
self.graph.add_vertex(from_id, to_id, log_p)
else:
raise Exception("transition log probability conversion failed for %s" % str(p))
def update_emitters(self):
self.emitters = [state for state_id, state in self.graph.nodes.items() if
len(state.emission_ps.items()) != 0] # list of emitter nodes
def set_emissions(self, emissions):
for node_id, obs_id, p in emissions:
log_p, converted = try_to_log(p, convert_zero=self.convert_zero) # use log probabilities
if converted:
if node_id in self.graph.nodes:
self.graph.nodes[node_id].emission_ps[obs_id] = log_p
else:
raise Exception("emission log probability conversion failed for %s" % str(p))
def is_valid(self):
valid = (self.emitters is not None and len(self.emitters) > 0 and self.starting_ps is not None and len(
self.starting_ps) > 0)
#print(self.emitters is not None, len(self.emitters) > 0, self.starting_ps is not None, len(
# self.starting_ps) > 0)
# valid = valid and other_checks() # Can do more checks here
return valid
def might_not_stop(self, stop_p=0.0000001):
needy_nodes = set()
end_id = self.end_id # end node
for state in self.emitters:
if end_id not in state.children or state.children[end_id][0] < stop_p: # need another node to end
needy_nodes.add(state.id)
for state_id in needy_nodes:
all_needy = True
for p, child in self.graph.nodes[state_id].children.values(): # if all kids are needy, then possible infinite loop
if child.id not in needy_nodes:
all_needy = False
break
if all_needy:
return True
return False
def simulate(self, limit):
if not self.is_valid():
logging.error("The model configuration is not valid, can not simulate..")
if self.might_not_stop():
inp = raw_input("This simulation might get into an infinite loop, continue anyway? (y/n)")
if inp.lower() != 'y':
print("Smart choice!")
return
else:
print("Alright, let's burn some cpu!")
states = self.emitters
p_ranges = [exp(self.starting_ps[s.id]) for s in states]
ix = random_pick(p_ranges)
print(ix)
node = states[ix]
emitted_seq = []
for i in range(limit):
if node.id != self.end_id:
e = node.emit()
print(i, node.id, e)
emitted_seq.append(e)
else:
break
candidates = node.children.values()
p_ranges = [exp(w) for w, _ in candidates]
ix = random_pick(p_ranges)
node = candidates[ix][1]
return emitted_seq