class DirichletOutputPSP(RandomPSP):
def simulate(self, args):
alpha = args.operandValues()[0]
return simulateDirichlet(alpha, args.np_prng())
def logDensity(self, val, args):
alpha = args.operandValues()[0]
return logDensityDirichlet(val, alpha)
def description(self, name):
return " %s(alphas) samples a simplex point according to the given " \
"Dirichlet distribution." % name
registerBuiltinSP("dirichlet", \
typed_nr(DirichletOutputPSP(),
[t.HomogeneousArrayType(t.PositiveType())], t.SimplexType()))
class SymmetricDirichletOutputPSP(RandomPSP):
def simulate(self, args):
(alpha, n) = args.operandValues()
return simulateDirichlet([float(alpha) for _ in range(int(n))],
args.np_prng())
def logDensity(self, val, args):
(alpha, n) = args.operandValues()
return logDensityDirichlet(val, [float(alpha) for _ in range(int(n))])
def description(self, name):
return " %s(alpha, n) samples a simplex point according to the " \
"""(Deterministic) basic programming SPs"""
import cPickle as pkl
from venture.lite.exception import VentureValueError
from venture.lite.sp import SPType
from venture.lite.sp_help import binaryPred
from venture.lite.sp_help import deterministic_typed
from venture.lite.sp_help import type_test
from venture.lite.sp_registry import registerBuiltinSP
from venture.lite.utils import raise_
import venture.lite.types as t
import venture.lite.value as v
registerBuiltinSP(
"eq",
binaryPred(lambda x, y: x.equal(y),
descr="eq compares its two arguments for equality"))
registerBuiltinSP(
"neq",
binaryPred(lambda x, y: not x.equal(y),
descr="neq checkes whether its arguments are not equal"))
registerBuiltinSP("gt", binaryPred(lambda x,y: x.compare(y) > 0,
descr="gt returns true if its first argument compares greater " \
"than its second"))
registerBuiltinSP("gte", binaryPred(lambda x,y: x.compare(y) >= 0,
descr="gte returns true if its first argument compares greater " \
"than or equal to its second"))
@override(DeterministicPSP)
def canAbsorb(self, _trace, appNode, parentNode):
return parentNode != appNode.operandNodes[2]
@override(DeterministicPSP)
def description(self,name):
return "%s returns its third argument unchanged at runtime, " \
"but tags the subexpression creating the object as being " \
"within the given scope and block." % name
def isTagOutputPSP(thing):
return isinstance(thing, TagOutputPSP) or \
(isinstance(thing, TypedPSP) and isTagOutputPSP(thing.psp))
registerBuiltinSP("tag",
typed_nr(TagOutputPSP(),
[t.AnyType("<scope>"), t.AnyType("<block>"), t.AnyType()],
t.AnyType()))
class TagExcludeOutputPSP(DeterministicPSP):
@override(DeterministicPSP)
def simulate(self,args):
return args.operandValues()[1]
@override(DeterministicPSP)
def gradientOfSimulate(self, _args, _value, direction):
return [0, direction]
@override(DeterministicPSP)
def canAbsorb(self, _trace, appNode, parentNode):
return parentNode != appNode.operandNodes[1]
aux.N += 1
aux.xTotal += x
aux.STotal += x * x.T
def unincorporate(self, x, args):
x = np.mat(x).reshape((self.d, 1))
aux = args.spaux()
aux.N -= 1
aux.xTotal -= x
aux.STotal -= x * x.T
def logDensityOfData(self, aux):
(mN, kN, vN, SN) = self.updatedParams(aux)
term1 = -(aux.N * self.d * math.log(math.pi)) / 2.
term2 = logGenGamma(self.d, vN / 2.)
term3 = -logGenGamma(self.d, self.v0 / 2.)
term4 = (self.v0 / 2.) * np.linalg.slogdet(self.S0)[1] # first is sign
term5 = -(vN / 2.) * np.linalg.slogdet(SN)[1]
term6 = (self.d / 2.) * math.log(float(self.k0) / kN)
return term1 + term2 + term3 + term4 + term5 + term6
registerBuiltinSP(
"make_niw_normal",
typed_nr(MakeCMVNOutputPSP(), [
t.HomogeneousArrayType(t.NumberType()),
t.NumberType(),
t.NumberType(),
t.MatrixType()
], SPType([], t.HomogeneousArrayType(t.NumberType()))))
from numbers import Number
import numpy as np
from venture.lite.exception import VentureValueError
from venture.lite.sp_help import deterministic_typed
from venture.lite.sp_help import type_test
from venture.lite.sp_registry import registerBuiltinSP
import venture.lite.value as vv
import venture.lite.types as t
import venture.lite.utils as u
registerBuiltinSP("array",
deterministic_typed(lambda *args: np.array(args),
[t.AnyType()], t.ArrayType(), variadic=True,
sim_grad=lambda args, direction: direction.getArray(),
descr="array returns an array initialized with its arguments"))
registerBuiltinSP("vector",
deterministic_typed(lambda *args: np.array(args),
[t.NumberType()], t.ArrayUnboxedType(t.NumberType()), variadic=True,
sim_grad=lambda args, direction: direction.getArray(),
descr="vector returns an unboxed numeric array initialized with its arguments"))
registerBuiltinSP("is_array", type_test(t.ArrayType()))
registerBuiltinSP("is_vector", type_test(t.ArrayUnboxedType(t.NumberType())))
registerBuiltinSP("to_array",
deterministic_typed(lambda seq: seq.getArray(),
[t.HomogeneousSequenceType(t.AnyType())], t.ArrayType(),
#
# XXX This implementation will suggest to a multi-site proposal
# that there are more distinct possibilities than actually exist,
# if more than one table was emptied by recent unincorporations.
# This is Github issue #462:
# https://github.com/probcomp/Venturecxx/issues/462
if aux.cachedTables:
tables += sorted(aux.cachedTables.values())
else:
tables.append(aux.nextTable)
return tables
registerBuiltinSP(
'make_crp',
typed_nr(MakeCRPOutputPSP(),
[t.NumberType(), t.NumberType()],
SPType([], t.AtomType()),
min_req_args=1))
def draw_crp_samples(n, alpha, np_rng=None):
"""Jointly draw n samples from CRP(alpha).
This returns an assignment of n objects to clusters, given by a
length-n list of cluster ids.
"""
aux = CRPSPAux()
args = MockArgs([], aux, np_rng=np_rng)
psp = CRPOutputPSP(alpha, 0) # No dispersion
def draw_sample():
def logDensity(self, value, args):
n = args.operandValues()[0]
xs = args.spaux().xs
assert len(xs) > n
theta = np.dot(xs[n], self.O)
return math.log(theta[value])
def incorporate(self, value, args):
n = args.operandValues()[0]
os = args.spaux().os
if n not in os: os[n] = []
os[n].append(value)
def unincorporate(self, value, args):
n = args.operandValues()[0]
os = args.spaux().os
del os[n][os[n].index(value)]
if not os[n]: del os[n]
class UncollapsedHMMRequestPSP(DeterministicPSP):
def simulate(self, args):
return Request([], [args.operandValues()[0]])
registerBuiltinSP(
"make_lazy_hmm",
typed_nr(MakeUncollapsedHMMOutputPSP(),
[t.SimplexType(), t.MatrixType(),
t.MatrixType()], SPType([t.CountType()], t.IntegerType())))
vvsum(direction)]),
deterministic_psp(
np.add,
sim_grad=lambda args, direction: [vvsum(direction), direction]),
deterministic_psp(
lambda *args: np.sum(args, axis=0),
sim_grad=lambda args, direction: [direction for _ in args],
descr="add returns the sum of all its arguments"),
deterministic_psp(symbolic_zero_left,
sim_grad=lambda args, direction: [0, direction]),
deterministic_psp(symbolic_zero_right,
sim_grad=lambda args, direction: [direction, 0]),
deterministic_psp(lambda a, b: a + b),
])
registerBuiltinSP("add", no_request(generic_add))
generic_sub = dispatching_psp([
SPType([t.NumberType(), t.NumberType()], t.NumberType()),
SPType([t.ArrayUnboxedType(t.NumberType()),
t.NumberType()], t.ArrayUnboxedType(t.NumberType())),
SPType([t.NumberType(), t.ArrayUnboxedType(t.NumberType())],
t.ArrayUnboxedType(t.NumberType())),
SPType([
t.ArrayUnboxedType(t.NumberType()),
t.ArrayUnboxedType(t.NumberType())
], t.ArrayUnboxedType(t.NumberType()))
], [
deterministic_psp(
lambda x, y: x - y,
sim_grad=lambda args, direction: [direction, -direction],
class MakeMSPOutputPSP(DeterministicPSP):
def simulate(self, args):
sharedOperatorNode = args.operandNodes[0]
return VentureSPRecord(
SP(MSPRequestPSP(sharedOperatorNode), ESRRefOutputPSP()))
def description(self, name):
return "%s returns the stochastically memoized version of the input SP." % name
class MSPRequestPSP(DeterministicPSP):
def __init__(self, sharedOperatorNode):
self.sharedOperatorNode = sharedOperatorNode
def simulate(self, args):
vals = args.operandValues()
id = str(vals)
exp = ["memoizedSP"] + [["quote", val] for val in vals]
env = VentureEnvironment(None, ["memoizedSP"],
[self.sharedOperatorNode])
return Request([ESR(id, exp, addr.req_frame(id), env)])
registerBuiltinSP(
"mem",
typed_nr(MakeMSPOutputPSP(),
[SPType([t.AnyType("a")], t.AnyType("b"), variadic=True)],
SPType([t.AnyType("a")], t.AnyType("b"), variadic=True)))
else:
args.append(VentureArray(flat_args[i:i + s]))
i += s
assert i == len(flat_args)
return args
class ApplyFunctionOutputPSP(DeterministicPSP):
def simulate(self, args):
vals = args.operandValues()
function = vals[0]
arguments = vals[1:]
sp_type = function.sp_type
unwrapped_args = sp_type.unwrap_arg_list(arguments)
#print sp_type.name(), unwrapped_args
returned = function.f(*unwrapped_args)
wrapped_return = sp_type.wrap_return(returned)
return wrapped_return
def description(self, _name=None):
return "Apply a VentureFunction to arguments."
# TODO Add type signature. Look at signature of apply?
applyFunctionSP = SP(NullRequestPSP(), ApplyFunctionOutputPSP())
registerBuiltinSP("apply_function", applyFunctionSP)
def simulate(self, args):
(operator, operands) = args.operandValues()
exp = [operator] + operands
env = VentureEnvironment()
return Request([ESR(args.node, exp, addr.req_frame(0), env)])
def description(self, name):
return "%s(func, vals) returns the result of applying a variadic" \
" function to an array of operands" % name
registerBuiltinSP(
"apply",
esr_output(
TypedPSP(
ApplyRequestPSP(),
SPType([
SPType([t.AnyType("a")], t.AnyType("b"), variadic=True),
t.HomogeneousArrayType(t.AnyType("a"))
], t.RequestType("b")))))
class ArrayMapRequestPSP(DeterministicPSP):
def simulate(self, args):
(operator, operands) = args.operandValues()
exps = [[operator, e.quote(operand)] for operand in operands]
env = VentureEnvironment()
return Request([
ESR((args.node, i), exp, addr.req_frame(i), env)
for i, exp in enumerate(exps)
])
else:
return [True, False]
def description(self, name):
return ' {name}(p) returns true with probability p and false otherwise. '\
'If omitted, p is taken to be 0.5. '\
'If you are tempted to write ({name} (exp x)),'\
' write (log_{name} x) instead. '\
'If you are tempted to write ({name} (logistic x)),'\
' write (log_odds_{name} x) instead.'\
.format(name=name)
registerBuiltinSP(
"flip",
typed_nr(BernoulliOutputPSP(), [t.ProbabilityType()],
t.BoolType(),
min_req_args=0))
registerBuiltinSP(
"bernoulli",
typed_nr(BernoulliOutputPSP(), [t.ProbabilityType()],
t.IntegerType(),
min_req_args=0))
class LogBernoulliOutputPSP(DiscretePSP):
def simulate(self, args):
logp = args.operandValues()[0]
return math.log(args.py_prng().random()) < logp
# (at your option) any later version.
#
# Venture is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Venture. If not, see <http://www.gnu.org/licenses/>.
import numpy as np
from venture.lite.sp import SPType
from venture.lite.sp_help import deterministic_psp
from venture.lite.sp_help import dispatching_psp
from venture.lite.sp_help import no_request
from venture.lite.sp_registry import registerBuiltinSP
import venture.lite.types as t
generic_biplex = dispatching_psp(
[SPType([t.BoolType(), t.AnyType(), t.AnyType()], t.AnyType()),
SPType([t.ArrayUnboxedType(t.NumberType()), t.ArrayUnboxedType(t.NumberType()), t.ArrayUnboxedType(t.NumberType())], t.ArrayUnboxedType(t.NumberType()))],
[deterministic_psp(lambda p, c, a: c if p else a,
sim_grad=lambda args, direction: [0, direction, 0] if args[0] else [0, 0, direction],
descr="biplex returns either its second or third argument, depending on the first."),
deterministic_psp(np.where,
# TODO sim_grad
descr="vector-wise biplex")])
registerBuiltinSP("biplex", no_request(generic_biplex))
return self._name or '<covariance>'
def distribution(self, base, **kwargs):
return None
def gradient_type(self):
return t.ArrayUnboxedType(t.NumericArrayType())
makeGPType = SPType(
[GPMeanType('mean function'),
GPCovarianceType('covariance kernel')], gpType)
makeGPSP = SP(NullRequestPSP(), TypedPSP(MakeGPOutputPSP(), makeGPType))
registerBuiltinSP('make_gp', makeGPSP)
xType = t.NumericArrayType('x')
oType = t.NumberType('o')
def _mean_sp(F, argtypes):
def mean_gradientOfSimulate(args, direction):
return parameter_nest(F(*args).parameters, direction.getArray())
return deterministic_typed(F,
argtypes,
GPMeanType(),
sim_grad=mean_gradientOfSimulate,
descr=F.__doc__)
from venture.lite.psp import DeterministicPSP
from venture.lite.psp import TypedPSP
from venture.lite.request import ESR
from venture.lite.request import Request
from venture.lite.sp import SPType
from venture.lite.sp_help import esr_output
from venture.lite.sp_help import type_test
from venture.lite.sp_help import typed_func
from venture.lite.sp_help import typed_nr
from venture.lite.sp_registry import registerBuiltinSP
import venture.lite.address as addr
import venture.lite.env as env
import venture.lite.types as t
registerBuiltinSP("get_current_environment",
typed_func(lambda args: args.env, [], env.EnvironmentType(),
descr="get_current_environment returns the lexical environment of its invocation site"))
registerBuiltinSP("get_empty_environment",
typed_func(lambda args: env.VentureEnvironment(), [], env.EnvironmentType(),
descr="get_empty_environment returns the empty environment"))
registerBuiltinSP("is_environment", type_test(env.EnvironmentType()))
class ExtendEnvOutputPSP(DeterministicPSP):
def simulate(self,args):
(en, sym, _) = args.operandValues()
node = args.operandNodes[2]
return env.VentureEnvironment(en,[sym],[node])
def description(self,name):
return "%s returns an extension of the given environment where the given symbol is bound to the given object" % name
def register_record(name, *fields):
(tester, constructor, accessors) = record(name, len(fields))
registerBuiltinSP(name, constructor)
registerBuiltinSP("is_" + name, tester)
for (f, a) in zip(fields, accessors):
registerBuiltinSP(f, a)