def __init__(self,
grammar,
make_h0,
data,
max_depth=3,
increment_from=None,
yield_partition=False,
steps=Infinity,
grammar_optimize=True,
**kwargs):
"""
Initializer.
*grammar* - what grammar are we using?
*make_h0* - a function to generate h0s. This MUST take a value argument to set the value
*data* - D for P(H|D)
*max_depth*, *max_n* -- only one of these may be specified. Either enumerate up to depth max_depth, or enumerate up to the largest depth such that the number of trees is less than max_N
TODO: We can in principle optimize the grammar by including only one rule of the form NT->TERMiNAL for each NT. This will exponentially speed things up...
"""
partitions = []
# first figure out how many trees we have
# We generate a lot and then replace terminal nodes with their types, because the terminal nodes will
# be the only ones that are allowed to be altered *within* a chain. So this collapses together
# trees that differ only on terminals
seen_collapsed = set() # what have we seen the collapsed forms of?
for t in grammar.increment_tree(x=increment_from, max_depth=max_depth):
ct = trim_leaves(t)
if ct not in seen_collapsed:
seen_collapsed.add(ct)
partitions.append(t)
#print "# Using partitions:", partitions
# Take each partition (h0) and set it to have zero resample_p exact at the leaf
for p in partitions:
print p
for t in p:
if not t.is_terminal():
t.resample_p = 0.0
else:
t.resample_p = 1.0
# initialize each chain
MultipleChainMCMC.__init__(self,
lambda: None,
data,
steps=steps,
nchains=len(partitions),
**kwargs)
# And set each to the partition
for c, p in zip(self.chains, partitions):
c.set_state(make_h0(value=p))
# and store these
self.partitions = map(copy, partitions)
def __init__(self, grammar, make_h0, data, max_N=1000, steps=Infinity, **kwargs):
"""
:param grammar: -- the grammar we use
:param make_h0: -- make a hypothesis
:param data: -- data for the posterior
:param max_N: -- the max number of samples we'll take
:param steps: -- how many steps
:return:
"""
# first figure out the depth we can go to without exceeding max_N
partitions = []
try:
for d in infrange():
#print "# trying ", d
tmp = []
for i, t in enumerate(grammar.enumerate_at_depth(d, leaves=False)):
tmp.append(t)
if i > max_N:
raise BreakException
# this gets set if we successfully exit the loop
# so it will store the last set that didn't exceed size max_N
partitions = tmp
except BreakException:
pass
# Take each partition, which doesn't have leaves, and generate leaves, setting
# it to a random generation (fill in the leaves with random hypotheses)
for p in partitions:
print "# Partition:", p
for n in p.subnodes():
# set to not resample these
n.resample_p = 0.0
# and fill in the missing leaves with a random generation
for i, a in enumerate(n.args):
if grammar.is_nonterminal(a):
n.args[i] = grammar.generate(a)
# initialize each chain
MultipleChainMCMC.__init__(self, lambda: None, data, steps=steps, nchains=len(partitions), **kwargs)
# And set each to the partition
for c, p in zip(self.chains, partitions):
c.set_state(make_h0(value=p))
# and store these
self.partitions = map(copy, partitions)
def __init__(self, grammar, make_h0, data, max_N=1000, steps=Infinity, **kwargs):
"""
:param grammar: -- the grammar we use
:param make_h0: -- make a hypothesis
:param data: -- data for the posterior
:param max_N: -- the max number of samples we'll take
:param steps: -- how many steps
:return:
"""
# first figure out the depth we can go to without exceeding max_N
partitions = []
try:
for d in infrange():
#print "# trying ", d
tmp = []
for i, t in enumerate(grammar.enumerate_at_depth(d, leaves=False)):
tmp.append(t)
if i > max_N:
raise BreakException
# this gets set if we successfully exit the loop
# so it will store the last set that didn't exceed size max_N
partitions = tmp
except BreakException:
pass
assert len(partitions) > 0
# and store these so we can see them later
self.partitions = map(copy, partitions)
# Take each partition, which doesn't have leaves, and generate leaves, setting
# it to a random generation (fill in the leaves with random hypotheses)
for p in partitions:
print "# Initializing partition:", p
for n in p.subnodes():
# set to not resample these
setattr(n, 'resample_p', 0.0) ## NOTE: This is an old version of how proposals were made, but we use it here to store in each node a prob of being resampled
# and fill in the missing leaves with a random generation
for i, a in enumerate(n.args):
if grammar.is_nonterminal(a):
n.args[i] = grammar.generate(a)
print "# Initialized %s partitions" % len(partitions)
# initialize each chain
MultipleChainMCMC.__init__(self, lambdaNone, data, steps=steps, nchains=len(partitions), **kwargs)
# And set each to the partition
for c, p in zip(self.chains, partitions):
# We need to make sure the proposal_function is set to use resample_p, which is set above
v = make_h0(value=p, proposal_function=MyProposal(grammar) )
c.set_state(v, compute_posterior=False) # and make v use the right proposal function
def __init__(self, make_h0, data, within_steps=100, **kwargs):
MultipleChainMCMC.__init__(self, make_h0, data, **kwargs)
self.within_steps = within_steps
self.kwargs = kwargs
self.seen = set()
self.chainZ = [-Infinity for _ in xrange(self.nchains)]
self.nsamples = 0 # How many samples have we drawn?
def __init__(self, make_h0, data, within_steps=100, **kwargs):
MultipleChainMCMC.__init__(self, make_h0, data, **kwargs)
self.within_steps = within_steps
self.kwargs = kwargs
self.seen = set()
self.chainZ = [-Infinity for _ in xrange(self.nchains)]
self.nsamples = 0 # How many samples have we drawn?
def __init__(self, make_h0, data, temperatures=[1.0, 1.1, 1.5], within_steps=50, swaps=1, yield_only_t0=False, **kwargs):
self.yield_only_t0 = yield_only_t0 #whether we yield all samples, or only from the lowest temperature
self.within_steps = within_steps
self.swaps = swaps
assert 'nchains' not in kwargs
MultipleChainMCMC.__init__(self, make_h0, data, nchains=len(temperatures), **kwargs)
# and set the temperatures
for i, t in enumerate(temperatures):
self.chains[i].likelihood_temperature = t
def __init__(self, make_h0, data, temperatures=[1.0, 1.1, 1.5], within_steps=10, swaps=1, yield_only_t0=False, **kwargs):
self.yield_only_t0 = yield_only_t0 #whether we yield all samples, or only from the lowest temperature
self.within_steps = within_steps
self.swaps=swaps
assert 'nchains' not in kwargs
MultipleChainMCMC.__init__(self, make_h0, data, nchains=len(temperatures), **kwargs)
# and set the temperatures
for i,t in enumerate(temperatures):
self.chains[i].likelihood_temperature = t
def __init__(self, grammar, make_h0, data, max_depth=3, increment_from=None, yield_partition=False, steps=Infinity, grammar_optimize=True, **kwargs):
"""
Initializer.
*grammar* - what grammar are we using?
*make_h0* - a function to generate h0s. This MUST take a value argument to set the value
*data* - D for P(H|D)
*max_depth*, *max_n* -- only one of these may be specified. Either enumerate up to depth max_depth, or enumerate up to the largest depth such that the number of trees is less than max_N
TODO: We can in principle optimize the grammar by including only one rule of the form NT->TERMiNAL for each NT. This will exponentially speed things up...
"""
partitions = []
# first figure out how many trees we have
# We generate a lot and then replace terminal nodes with their types, because the terminal nodes will
# be the only ones that are allowed to be altered *within* a chain. So this collapses together
# trees that differ only on terminals
seen_collapsed = set() # what have we seen the collapsed forms of?
for t in grammar.increment_tree(x=increment_from, max_depth=max_depth):
ct = trim_leaves(t)
if ct not in seen_collapsed:
seen_collapsed.add(ct)
partitions.append(t)
#print "# Using partitions:", partitions
# Take each partition (h0) and set it to have zero resample_p exact at the leaf
for p in partitions:
print p
for t in p:
if not t.is_terminal():
t.resample_p = 0.0
else:
t.resample_p = 1.0
# initialize each chain
MultipleChainMCMC.__init__(self, lambda: None, data, steps=steps, nchains=len(partitions), **kwargs)
# And set each to the partition
for c,p in zip(self.chains, partitions):
c.set_state(make_h0(value=p))
# and store these
self.partitions = map(copy, partitions)
def next(self):
nxt = MultipleChainMCMC.next(self) # get the next one
idx = self.chain_idx
if nxt not in self.seen:
self.chainZ[idx] = logplusexp(self.chainZ[idx], nxt.posterior_score)
self.seen.add(nxt)
# # Process the situation where we need to re-organize
if self.nsamples % (self.within_steps * self.nchains) == 0 and self.nsamples > 0:
self.refresh()
self.nsamples += 1
return nxt
def next(self):
nxt = MultipleChainMCMC.next(self) # get the next one
idx = self.chain_idx
if nxt not in self.seen:
self.chainZ[idx] = logplusexp(self.chainZ[idx],
nxt.posterior_score)
self.seen.add(nxt)
# # Process the situation where we need to re-organize
if self.nsamples % (self.within_steps *
self.nchains) == 0 and self.nsamples > 0:
self.refresh()
self.nsamples += 1
return nxt
def __init__(self,
grammar,
make_h0,
data,
max_N=1000,
steps=Infinity,
**kwargs):
"""
:param grammar: -- the grammar we use
:param make_h0: -- make a hypothesis
:param data: -- data for the posterior
:param max_N: -- the max number of samples we'll take
:param steps: -- how many steps
:return:
"""
# first figure out the depth we can go to without exceeding max_N
partitions = []
try:
for d in infrange():
#print "# trying ", d
tmp = []
for i, t in enumerate(
grammar.enumerate_at_depth(d, leaves=False)):
tmp.append(t)
if i > max_N:
raise BreakException
# this gets set if we successfully exit the loop
# so it will store the last set that didn't exceed size max_N
partitions = tmp
except BreakException:
pass
assert len(partitions) > 0
# and store these so we can see them later
self.partitions = map(copy, partitions)
# Take each partition, which doesn't have leaves, and generate leaves, setting
# it to a random generation (fill in the leaves with random hypotheses)
for p in partitions:
print "# Initializing partition:", p
for n in p.subnodes():
# set to not resample these
setattr(
n, 'resample_p', 0.0
) ## NOTE: This is an old version of how proposals were made, but we use it here to store in each node a prob of being resampled
# and fill in the missing leaves with a random generation
for i, a in enumerate(n.args):
if grammar.is_nonterminal(a):
n.args[i] = grammar.generate(a)
print "# Initialized %s partitions" % len(partitions)
# initialize each chain
MultipleChainMCMC.__init__(self,
lambdaNone,
data,
steps=steps,
nchains=len(partitions),
**kwargs)
# And set each to the partition
for c, p in zip(self.chains, partitions):
# We need to make sure the proposal_function is set to use resample_p, which is set above
v = make_h0(value=p, proposal_function=MyProposal(grammar))
c.set_state(v, compute_posterior=False
) # and make v use the right proposal function