Funsor is a tensor-like library for functions and distributions¶

Raises

ValueError

Tensor¶

Einsum(equation, *operands)[source]¶

Wrapper around torch.einsum() or np.einsum() to operate on real-valued Funsors.

Note this operates only on the output tensor. To perform sum-product contractions on named dimensions, instead use + and Reduce.

Parameters

equation (str) – An torch.einsum() or np.einsum() equation.
operands (tuple) – A tuple of input funsors.

class Function(*args, **kwargs)[source]¶

Bases: Funsor

Funsor wrapped by a native PyTorch or NumPy function.

Functions are assumed to support broadcasting and can be eagerly evaluated on funsors with free variables of int type (i.e. batch dimensions).

Function s are usually created via the function() decorator.

Parameters

fn (callable) – A native PyTorch or NumPy function to wrap.
output (type) – An output domain.
args (Funsor) – Funsor arguments.

class Tensor(data, inputs=None, dtype='real')[source]¶

Bases: Funsor

Funsor backed by a PyTorch Tensor or a NumPy ndarray.

This follows the torch.distributions convention of arranging named “batch” dimensions on the left and remaining “event” dimensions on the right. The output shape is determined by all remaining dims. For example:

data = torch.zeros(5,4,3,2)
x = Tensor(data, {"i": Bint[5], "j": Bint[4]})
assert x.output == Reals[3, 2]

Operators like matmul and .sum() operate only on the output shape, and will not change the named inputs.

Parameters

data (numeric_array) – A PyTorch tensor or NumPy ndarray.
inputs (dict) – An optional mapping from input name (str) to datatype (funsor.domains.Domain). Defaults to empty.
dtype (int or the string "real".) – optional output datatype. Defaults to “real”.

item()[source]¶

clamp_finite()[source]¶

property requires_grad¶

align(names)[source]¶

eager_subs(subs)[source]¶

eager_unary(op)[source]¶

eager_reduce(op, reduced_vars)[source]¶

new_arange(name, *args, **kwargs)[source]¶

Helper to create a named torch.arange() or np.arange() funsor. In some cases this can be replaced by a symbolic Slice .

Parameters

name (str) – A variable name.
start (int) –
stop (int) –
step (int) – Three args following slice semantics.
dtype (int) – An optional bounded integer type of this slice.

Return type

Tensor

materialize(x)[source]¶

Attempt to convert a Funsor to a Number or Tensor by substituting arange() s into its free variables.

Parameters: x (Funsor) – A funsor.
Return type: Funsor

align_tensor(new_inputs, x, expand=False)[source]¶

Permute and add dims to a tensor to match desired new_inputs.

Parameters

new_inputs (OrderedDict) – A target set of inputs.
x (funsor.terms.Funsor) – A Tensor or Number .
expand (bool) – If False (default), set result size to 1 for any input of x not in new_inputs; if True expand to new_inputs size.

Returns

a number or torch.Tensor or np.ndarray that can be broadcast to other tensors with inputs new_inputs.

Return type

int or float or torch.Tensor or np.ndarray

align_tensors(*args, **kwargs)[source]¶

Permute multiple tensors before applying a broadcasted op.

This is mainly useful for implementing eager funsor operations.

Parameters

*args (funsor.terms.Funsor) – Multiple Tensor s and Number s.
expand (bool) – Whether to expand input tensors. Defaults to False.

Returns

a pair (inputs, tensors) where tensors are all torch.Tensor s or np.ndarray s that can be broadcast together to a single data with given inputs.

Return type

function(*signature)[source]¶

Decorator to wrap a PyTorch/NumPy function, using either type hints or explicit type annotations.

Example:

# Using type hints:
@funsor.tensor.function
def matmul(x: Reals[3, 4], y: Reals[4, 5]) -> Reals[3, 5]:
    return torch.matmul(x, y)

# Using explicit type annotations:
@funsor.tensor.function(Reals[3, 4], Reals[4, 5], Reals[3, 5])
def matmul(x, y):
    return torch.matmul(x, y)

@funsor.tensor.function(Reals[10], Reals[10, 10], Reals[10], Real)
def mvn_log_prob(loc, scale_tril, x):
    d = torch.distributions.MultivariateNormal(loc, scale_tril)
    return d.log_prob(x)

To support functions that output nested tuples of tensors, specify a nested Tuple of output types, for example:

@funsor.tensor.function
def max_and_argmax(x: Reals[8]) -> Tuple[Real, Bint[8]]:
    return torch.max(x, dim=-1)

Parameters: *signature – A sequence if input domains followed by a final output domain or nested tuple of output domains.

ignore_jit_warnings()[source]¶

tensordot(x, y, dims)[source]¶

Wrapper around torch.tensordot() or np.tensordot() to operate on real-valued Funsors.

Note this operates only on the output tensor. To perform sum-product contractions on named dimensions, instead use + and Reduce.

Arguments should satisfy:

len(x.shape) >= dims
len(y.shape) >= dims
dims == 0 or x.shape[-dims:] == y.shape[:dims]

Parameters

x (Funsor) – A left hand argument.
y (Funsor) – A y hand argument.
dims (int) – The number of dimension of overlap of output shape.

Return type

Funsor

Gaussian¶

class BlockMatrix(shape)[source]¶

Bases: object

Jit-compatible helper to build blockwise matrices. Syntax is similar to torch.zeros()

x = BlockMatrix((100, 20, 20))
x[..., 0:4, 0:4] = x11
x[..., 0:4, 6:10] = x12
x[..., 6:10, 0:4] = x12.transpose(-1, -2)
x[..., 6:10, 6:10] = x22
x = x.as_tensor()
assert x.shape == (100, 20, 20)

as_tensor()[source]¶

class BlockVector(shape)[source]¶

Bases: object

Jit-compatible helper to build blockwise vectors. Syntax is similar to torch.zeros()

x = BlockVector((100, 20))
x[..., 0:4] = x1
x[..., 6:10] = x2
x = x.as_tensor()
assert x.shape == (100, 20)

as_tensor()[source]¶

class Gaussian(white_vec=None, prec_sqrt=None, inputs=None, *, mean=None, info_vec=None, precision=None, scale_tril=None, covariance=None)[source]¶

Bases: Funsor

Funsor representing a batched Gaussian log-density function.

Gaussians are the internal representation for joint and conditional multivariate normal distributions and multivariate normal likelihoods. Mathematically, a Gaussian represents the quadratic log density function:

f(x) = -0.5 * || x @ prec_sqrt - white_vec ||^2
     = -0.5 * < x @ prec_sqrt - white_vec | x @ prec_sqrt - white_vec >
     = -0.5 * < x | prec_sqrt @ prec_sqrt.T | x>
       + < x | prec_sqrt | white_vec > - 0.5 ||white_vec||^2

Internally Gaussians use a square root information filter (SRIF) representation consisting of a square root of the precision matrix prec_sqrt and a vector in the whitened space white_vec. This representation allows space-efficient construction of Gaussians with incomplete information, i.e. with zero eigenvalues in the precision matrix. These incomplete log densities arise when making low-dimensional observations of higher-dimensional hidden state. Sampling and marginalization are supported only for full-rank Gaussians or full-rank subsets of Gaussians. See the rank() and is_full_rank() properties.

Note

Gaussian s are not normalized probability distributions, rather they are canonicalized to evaluate to zero log density at their maximum: f(prec_sqrt \ white_vec) = 0. Not only are Gaussians non-normalized, but they may be rank deficient and non-normalizable, in which case sampling and marginalization are supported only un full-rank subsets of variables.

Parameters

white_vec (torch.Tensor) – An batched white noise vector, where white_vec = prec_sqrt.T @ mean. Alternatively you can specify one of the kwargs mean or info_vec, which will be converted to white_vec.
prec_sqrt (torch.Tensor) – A batched square root of the positive semidefinite precision matrix. This need not be square, and typically has shape prec_sqrt.shape == white_vec.shape[:-1] + (dim, rank), where dim is the total flattened size of real inputs and rank = white_vec.shape[-1]. Alternatively you can specify one of the kwargs precision, covariance, or scale_tril, which will be converted to prec_sqrt.
inputs (OrderedDict) – Mapping from name to Domain .

compression_threshold = 2¶

classmethod set_compression_threshold(threshold: float)[source]¶

Context manager to set rank compression threshold.

To save space Gaussians compress wide prec_sqrt matrices down to square. However compression uses a QR decomposition which can be expensive and which has unstable gradients when the resulting precision matrix is rank deficient. To balance space and time costs and numerical stability, compression is trigger only on prec_sqrt matrices whose width to height ratio is greater than threshold.

Parameters: threshold (float) – Defaults to 2. To optimize for space and deterministic computations, set threshold = 1. To optimize for fewest QR decompositions and numerical stability, set threshold = math.inf.

property rank¶

property is_full_rank¶

log_normalizer()[source]¶

align(names)[source]¶

eager_subs(subs)[source]¶

eager_reduce(op, reduced_vars)[source]¶

align_gaussian(new_inputs, old, expand=False)[source]¶: Align data of a Gaussian distribution to a new inputs shape.

Joint¶

moment_matching_contract_default(*args)[source]¶

moment_matching_contract_joint(red_op, bin_op, reduced_vars, discrete, gaussian)[source]¶

eager_reduce_exp(op, arg, reduced_vars)[source]¶

eager_independent_joint(joint, reals_var, bint_var, diag_var)[source]¶

Contraction¶

class Contraction(*args, **kwargs)[source]¶

Bases: Funsor

Declarative representation of a finitary sum-product operation.

After normalization via the normalize() interpretation contractions will canonically order their terms by type:

Delta, Number, Tensor, Gaussian

align(names)[source]¶

GaussianMixture¶: alias of Contraction

children_contraction(x)[source]¶

eager_contraction_generic_to_tuple(red_op, bin_op, reduced_vars, *terms)[source]¶

eager_contraction_generic_recursive(red_op, bin_op, reduced_vars, terms)[source]¶

eager_contraction_to_reduce(red_op, bin_op, reduced_vars, term)[source]¶

eager_contraction_to_binary(red_op, bin_op, reduced_vars, lhs, rhs)[source]¶

eager_contraction_tensor(red_op, bin_op, reduced_vars, *terms)[source]¶

eager_contraction_gaussian(red_op, bin_op, reduced_vars, x, y)[source]¶

normalize_contraction_commutative_canonical_order(red_op, bin_op, reduced_vars, *terms)[source]¶

normalize_contraction_commute_joint(red_op, bin_op, reduced_vars, other, mixture)[source]¶

normalize_contraction_generic_args(red_op, bin_op, reduced_vars, *terms)[source]¶

normalize_trivial(red_op, bin_op, reduced_vars, term)[source]¶

normalize_contraction_generic_tuple(red_op, bin_op, reduced_vars, terms)[source]¶

binary_to_contract(op, lhs, rhs)[source]¶

reduce_funsor(op, arg, reduced_vars)[source]¶

unary_neg_variable(op, arg)[source]¶

do_fresh_subs(arg, subs)[source]¶

distribute_subs_contraction(arg, subs)[source]¶

normalize_fuse_subs(arg, subs)[source]¶

binary_subtract(op, lhs, rhs)[source]¶

binary_divide(op, lhs, rhs)[source]¶

unary_log_exp(op, arg)[source]¶

unary_contract(op, arg)[source]¶

Integrate¶

class Integrate(log_measure, integrand, reduced_vars)[source]¶

Bases: Funsor

Funsor representing an integral wrt a log density funsor.

Parameters

log_measure (Funsor) – A log density funsor treated as a measure.
integrand (Funsor) – An integrand funsor.
reduced_vars (str, Variable, or set or frozenset thereof.) – An input name or set of names to reduce.

Constant¶

class ConstantMeta(name, bases, dct)[source]¶

Bases: FunsorMeta

Wrapper to convert const_inputs to a tuple.

class Constant(const_inputs, arg)[source]¶

Bases: Funsor

Funsor that is constant wrt const_inputs.

Constant can be used for provenance tracking.

Examples:

a = Constant(OrderedDict(x=Real, y=Bint[3]), Number(0))
a(y=1)  # returns Constant(OrderedDict(x=Real), Number(0))
a(x=2, y=1)  # returns Number(0)

d = Tensor(torch.tensor([1, 2, 3]))["y"]
a + d  # returns Constant(OrderedDict(x=Real), d)

c = Constant(OrderedDict(x=Bint[3]), Number(1))
c.reduce(ops.add, "x")  # returns Number(3)

Parameters

const_inputs (dict) – A mapping from input name (str) to datatype (funsor.domain.Domain).
arg (funsor) – A funsor that is constant wrt to const_inputs.

eager_subs(subs)[source]¶

eager_reduce(op, reduced_vars)[source]¶

align(names)[source]¶

materialize(x)[source]¶

Attempt to convert a Funsor to a Number or Tensor by substituting arange() s into its free variables.

Parameters: x (Funsor) – A funsor.
Return type: Funsor

eager_reduce_add(op, arg, reduced_vars)[source]¶

eager_binary_constant_constant(op, lhs, rhs)[source]¶

eager_binary_constant_tensor(op, lhs, rhs)[source]¶

eager_binary_tensor_constant(op, lhs, rhs)[source]¶

eager_unary(op, arg)[source]¶

Optimizer¶

unfold_contraction_generic_tuple(red_op, bin_op, reduced_vars, terms)[source]¶

unfold_contraction_variadic(r, b, v, *ts)[source]¶

optimize_contraction_variadic(r, b, v, *ts)[source]¶

eager_contract_base(red_op, bin_op, reduced_vars, *terms)[source]¶

optimize_contract_finitary_funsor(red_op, bin_op, reduced_vars, terms)[source]¶

apply_optimizer(x)[source]¶

Adjoint Algorithms¶

class AdjointTape[source]¶

Bases: Interpretation

interpret(cls, *args)[source]¶

adjoint(sum_op, bin_op, root, targets=None, *, batch_vars={})[source]¶

forward_backward(sum_op, bin_op, expr, *, batch_vars=frozenset({}))[source]¶

adjoint(sum_op, bin_op, expr)[source]¶

adjoint_binary(adj_sum_op, adj_prod_op, out_adj, op, lhs, rhs)[source]¶

adjoint_reduce(adj_sum_op, adj_prod_op, out_adj, op, arg, reduced_vars)[source]¶

adjoint_contract_unary(adj_sum_op, adj_prod_op, out_adj, sum_op, prod_op, reduced_vars, arg)[source]¶

adjoint_contract_generic(adj_sum_op, adj_prod_op, out_adj, sum_op, prod_op, reduced_vars, terms)[source]¶

adjoint_contract(adj_sum_op, adj_prod_op, out_adj, sum_op, prod_op, reduced_vars, lhs, rhs)[source]¶

adjoint_cat(adj_sum_op, adj_prod_op, out_adj, name, parts, part_name)[source]¶

adjoint_subs(adj_sum_op, adj_prod_op, out_adj, arg, subs)[source]¶

adjoint_scatter(adj_sum_op, adj_prod_op, out_adj, op, subs, source, reduced_vars)[source]¶

Sum-Product Algorithms¶

partial_unroll(factors, eliminate=frozenset({}), plate_to_step={})[source]¶

Performs partial unrolling of plated factor graphs to standard factor graphs. Only plates with history={0, 1} are supported.

For plates (history=0) unrolling operation appends _{i} suffix to variable names for index i in the plate (e.g., “x”->”x_0” for i=0). For markov dimensions (history=1) unrolling operation renames the suffixes var_prev to var_{i} and var_curr to var_{i+1} for index i (e.g., “x_prev”->”x_0” and “x_curr”->”x_1” for i=0). Markov vars are assumed to have names that follow var_suffix formatting and specifically var_0 for the initial factor (e.g., ("x_0", "x_prev", "x_curr") for history=1).

Parameters

factors (tuple or list) – A collection of funsors.
eliminate (frozenset) – A set of free variables to unroll, including both sum variables and product variable.
plate_to_step (dict) – A dict mapping markov dimensions to step collections that contain ordered sequences of Markov variable names (e.g., {"time": frozenset({("x_0", "x_prev", "x_curr")})}). Plates are passed with an empty step.

Returns

a list of partially unrolled Funsors, a frozenset of partially unrolled variable names, and a frozenset of remaining plates.

partial_sum_product(sum_op, prod_op, factors, eliminate=frozenset({}), plates=frozenset({}), pedantic=False)[source]¶

Performs partial sum-product contraction of a collection of factors.

Returns: a list of partially contracted Funsors.
Return type: list

dynamic_partial_sum_product(sum_op, prod_op, factors, eliminate=frozenset({}), plate_to_step={})[source]¶

Generalization of the tensor variable elimination algorithm of funsor.sum_product.partial_sum_product() to handle higer-order markov dimensions in addition to plate dimensions. Markov dimensions in transition factors are eliminated efficiently using the parallel-scan algorithm in funsor.sum_product.sarkka_bilmes_product(). The resulting factors are then combined with the initial factors and final states are eliminated. Therefore, when Markov dimension is eliminated factors has to contain initial factors and transition factors.

Parameters

sum_op (AssociativeOp) – A semiring sum operation.
prod_op (AssociativeOp) – A semiring product operation.
factors (tuple or list) – A collection of funsors.
eliminate (frozenset) – A set of free variables to eliminate, including both sum variables and product variable.
plate_to_step (dict) – A dict mapping markov dimensions to step collections that contain ordered sequences of Markov variable names (e.g., {"time": frozenset({("x_0", "x_prev", "x_curr")})}). Plates are passed with an empty step.

Returns

a list of partially contracted Funsors.

Return type

list

modified_partial_sum_product(sum_op, prod_op, factors, eliminate=frozenset({}), plate_to_step={})[source]¶

Generalization of the tensor variable elimination algorithm of funsor.sum_product.partial_sum_product() to handle markov dimensions in addition to plate dimensions. Markov dimensions in transition factors are eliminated efficiently using the parallel-scan algorithm in funsor.sum_product.sequential_sum_product(). The resulting factors are then combined with the initial factors and final states are eliminated. Therefore, when Markov dimension is eliminated factors has to contain a pairs of initial factors and transition factors.

Parameters

sum_op (AssociativeOp) – A semiring sum operation.
prod_op (AssociativeOp) – A semiring product operation.
factors (tuple or list) – A collection of funsors.
eliminate (frozenset) – A set of free variables to eliminate, including both sum variables and product variable.
plate_to_step (dict) – A dict mapping markov dimensions to step collections that contain ordered sequences of Markov variable names (e.g., {"time": frozenset({("x_0", "x_prev", "x_curr")})}). Plates are passed with an empty step.

Returns

a list of partially contracted Funsors.

Return type

list

sum_product(sum_op, prod_op, factors, eliminate=frozenset({}), plates=frozenset({}), pedantic=False)[source]¶

Performs sum-product contraction of a collection of factors.

Returns: a single contracted Funsor.
Return type: Funsor

naive_sequential_sum_product(sum_op, prod_op, trans, time, step)[source]¶

sequential_sum_product(sum_op, prod_op, trans, time, step)[source]¶

For a funsor trans with dimensions time, prev and curr, computes a recursion equivalent to:

tail_time = 1 + arange("time", trans.inputs["time"].size - 1)
tail = sequential_sum_product(sum_op, prod_op,
                              trans(time=tail_time),
                              time, {"prev": "curr"})
return prod_op(trans(time=0)(curr="drop"), tail(prev="drop"))            .reduce(sum_op, "drop")

but does so efficiently in parallel in O(log(time)).

Parameters

sum_op (AssociativeOp) – A semiring sum operation.
prod_op (AssociativeOp) – A semiring product operation.
trans (Funsor) – A transition funsor.
time (Variable) – The time input dimension.
step (dict) – A dict mapping previous variables to current variables. This can contain multiple pairs of prev->curr variable names.

mixed_sequential_sum_product(sum_op, prod_op, trans, time, step, num_segments=None)[source]¶

For a funsor trans with dimensions time, prev and curr, computes a recursion equivalent to:

tail_time = 1 + arange("time", trans.inputs["time"].size - 1)
tail = sequential_sum_product(sum_op, prod_op,
                              trans(time=tail_time),
                              time, {"prev": "curr"})
return prod_op(trans(time=0)(curr="drop"), tail(prev="drop"))            .reduce(sum_op, "drop")

by mixing parallel and serial scan algorithms over num_segments segments.

Parameters

sum_op (AssociativeOp) – A semiring sum operation.
prod_op (AssociativeOp) – A semiring product operation.
trans (Funsor) – A transition funsor.
time (Variable) – The time input dimension.
step (dict) – A dict mapping previous variables to current variables. This can contain multiple pairs of prev->curr variable names.
num_segments (int) – number of segments for the first stage

naive_sarkka_bilmes_product(sum_op, prod_op, trans, time_var, global_vars=frozenset({}))[source]¶

sarkka_bilmes_product(sum_op, prod_op, trans, time_var, global_vars=frozenset({}), num_periods=1)[source]¶

class MarkovProductMeta(name, bases, dct)[source]¶

Bases: FunsorMeta

Wrapper to convert step to a tuple and fill in default step_names.

class MarkovProduct(sum_op, prod_op, trans, time, step, step_names=None)[source]¶

Bases: Funsor

Lazy representation of sequential_sum_product() .

Parameters

sum_op (AssociativeOp) – A marginalization op.
prod_op (AssociativeOp) – A Bayesian fusion op.
trans (Funsor) – A sequence of transition factors, usually varying along the time input.
time (str or Variable) – A time dimension.
step (dict) – A str-to-str mapping of “previous” inputs of trans to “current” inputs of trans.
step_names (dict) – Optional, for internal use by alpha conversion.

eager_subs(subs)[source]¶

eager_markov_product(sum_op, prod_op, trans, time, step, step_names)[source]¶

Affine Pattern Matching¶

affine_inputs(fn)[source]¶

Returns a [sound sub]set of real inputs of fn wrt which fn is known to be affine.

Parameters: fn (Funsor) – A funsor.
Returns: A set of input names wrt which fn is affine.
Return type: frozenset

extract_affine(fn)[source]¶

Extracts an affine representation of a funsor, satisfying:

x = ...
const, coeffs = extract_affine(x)
y = sum(Einsum(eqn, coeff, Variable(var, coeff.output))
        for var, (coeff, eqn) in coeffs.items())
assert_close(y, x)
assert frozenset(coeffs) == affine_inputs(x)

The coeffs will have one key per input wrt which fn is known to be affine (via affine_inputs() ), and const and coeffs.values will all be constant wrt these inputs.

The affine approximation is computed by ev evaluating fn at zero and each basis vector. To improve performance, users may want to run under the Memoize() interpretation.

Parameters: fn (Funsor) – A funsor that is affine wrt the (add,mul) semiring in some subset of its inputs.
Returns: A pair (const, coeffs) where const is a funsor with no real inputs and coeffs is an OrderedDict mapping input name to a (coefficient, eqn) pair in einsum form.
Return type: tuple

is_affine(fn)[source]¶

A sound but incomplete test to determine whether a funsor is affine with respect to all of its real inputs.

Parameters: fn (Funsor) – A funsor.
Return type: bool

Funsor Factory¶

class Fresh(fn)[source]¶

Bases: object

Type hint for make_funsor() decorated functions. This provides hints for fresh variables (names) and the return type.

Examples:

Fresh[Real]  # a constant known domain
Fresh[lambda x: Array[x.dtype, x.shape[1:]]  # args are Domains
Fresh[lambda x, y: Bint[x.size + y.size]]

Parameters: fn (callable) – A lambda taking named arguments (in any order) which will be filled in with the domain of the similarly named funsor argument to the decorated function. This lambda should compute a desired resulting domain given domains of arguments.

class Bound[source]¶

Bases: object

Type hint for make_funsor() decorated functions. This provides hints for bound variables (names).

class Has(bound)[source]¶

Bases: object

Type hint for make_funsor() decorated functions.

This hint asserts that a set of Bound variables always appear in the .inputs of the annotated argument.

For example, we could write a named matmul function that asserts that both arguments always contain the reduced input, and cannot be constant with respect to that input:

@make_funsor
def MatMul(
    x: Has[{"i"}],
    y: Has[{"i"}],
    i: Bound,
) -> Fresh[lambda x: x]:
    return (x * y).reduce(ops.add, i)

Here the string "i" in the annotations for x and y refer to the argument i of our MatMul function, which is known to be Bound (i.e it does not appear in the .inputs of evaluating Matmul(x, y, "i").

Warning

This annotation is experimental and may be removed in the future.

Note that because Funsor is inherently extensional, violating a Has constraint only raises a SyntaxWarning rather than a full TypeError and even then only under the reflect() interpretation.

As such, Has annotations should be used sparingly, reserved for cases where the programmer has complete control over the inputs to a function and knows that an argument will always depend on a bound variable, e.g. when writing one-off Funsor terms to describe custom layers in a neural network.

Parameters: bound (set) – A set of strings of names of Bound arguments of a make_funsor() -decorated function.

make_funsor(fn)[source]¶

Decorator to dynamically create a subclass of Funsor, together with a single default eager pattern.

This infers inputs, outputs, fresh, and bound variables from type hints follow the following convention:

Funsor inputs are typed Funsor.
Bound variable inputs (names) are typed Bound.
Fresh variable inputs (names) are typed Fresh together with lambda to compute the dependent domain.
Ground value inputs (e.g. Python ints) are typed Value together with their actual data type, e.g. Value[int].
The return value is typed Fresh together with a lambda to compute the dependent return domain.

For example to unflatten a single coordinate into a pair of coordinates we could define:

@make_funsor
def Unflatten(
    x: Funsor,
    i: Bound,
    i_over_2: Fresh[lambda i: Bint[i.size // 2]],
    i_mod_2: Fresh[lambda: Bint[2]],
) -> Fresh[lambda x: x]:
    assert i.output.size % 2 == 0
    return x(**{i.name: i_over_2 * Number(2, 3) + i_mod_2})

Parameters: fn (callable) – A type annotated function of Funsors.
Return type: subclas of Funsor

Testing Utiltites¶

xfail_if_not_implemented(msg='Not implemented', *, match=None)[source]¶

xfail_if_not_found(msg='Not implemented')[source]¶

requires_backend(*backends, reason=None)[source]¶

excludes_backend(*backends, reason=None)[source]¶

class ActualExpected(actual, expected)[source]¶

Bases: LazyComparison

Lazy string formatter for test assertions.

id_from_inputs(inputs)[source]¶

is_array(x)[source]¶

assert_close(actual, expected, atol=1e-06, rtol=1e-06)[source]¶

check_funsor(x, inputs, output, data=None)[source]¶: Check dims and shape modulo reordering.

xfail_param(*args, **kwargs)[source]¶

make_einsum_example(equation, fill=None, sizes=(2, 3))[source]¶

assert_equiv(x, y)[source]¶: Check that two funsors are equivalent up to permutation of inputs.

rand(*args)[source]¶

randint(low, high, size)[source]¶

randn(*args)[source]¶

random_scale_tril(*args)[source]¶

zeros(*args)[source]¶

ones(*args)[source]¶

empty(*args)[source]¶

random_tensor(inputs, output=Real)[source]¶: Creates a random funsor.tensor.Tensor with given inputs and output.

random_gaussian(inputs)[source]¶: Creates a random funsor.gaussian.Gaussian with given inputs.

random_mvn(batch_shape, dim, diag=False)[source]¶: Generate a random torch.distributions.MultivariateNormal with given shape.

make_plated_hmm_einsum(num_steps, num_obs_plates=1, num_hidden_plates=0)[source]¶

make_chain_einsum(num_steps)[source]¶

make_hmm_einsum(num_steps)[source]¶

iter_subsets(iterable, *, min_size=None, max_size=None)[source]¶

class DesugarGetitem[source]¶

Bases: object

Helper to desugar .__getitem__() syntax.

Example:

>>> desugar_getitem[1:3, ..., None]
(slice(1, 3), Ellipsis, None)

Typing Utiltites¶

class GenericTypeMeta(name, bases, dct)[source]¶

Bases: type

Metaclass to support subtyping with parameters for pattern matching, e.g. Number[int, int].

class Variadic[source]¶

Bases: object

A typing-compatible drop-in replacement for Variadic.

deep_isinstance(obj, cls)[source]¶

Enhanced version of isinstance() that can handle basic structured typing types, including Funsor terms and other GenericTypeMeta instances, Union, Tuple, and FrozenSet.

Does not support TypeVar, arbitrary Generic, forward references, or mutable generic collection types like List. Will attempt to fall back to isinstance() when it encounters an unsupported type in obj or cls.

Usage:

x = (1, ("a", "b"))
assert deep_isinstance(x, typing.Tuple[int, tuple])
assert deep_isinstance(x, typing.Tuple[typing.Any, typing.Tuple[str, ...]])

Parameters

obj – An object that may be an instance of cls.
cls – A class that may be a parent class of obj.

deep_issubclass(subcls, cls)[source]¶

Enhanced version of issubclass() that can handle structured types, including Funsor terms, Tuple, and FrozenSet.

Does not support more advanced typing features such as TypeVar, arbitrary Generic subtypes, forward references, or mutable collection types like List. Will attempt to fall back to issubclass() when it encounters a type in subcls or cls that it does not understand.

Usage:

class A: pass
class B(A): pass

assert deep_issubclass(typing.Tuple[int, B], typing.Tuple[int, A])
assert not deep_issubclass(typing.Tuple[int, A], typing.Tuple[int, B])

assert deep_issubclass(typing.Tuple[A, A], typing.Tuple[A, ...])
assert not deep_issubclass(typing.Tuple[B], typing.Tuple[A, ...])

Parameters

subcls – A class that may be a subclass of cls.
cls – A class that may be a parent class of subcls.

deep_type(obj)[source]¶

deep_type(obj: tuple)

deep_type(obj: frozenset)

An enhanced version of type() that reconstructs structured typing` types for a limited set of immutable data structures, notably tuple and frozenset. Mostly intended for internal use in Funsor interpretation pattern-matching.

Example:

assert deep_type((1, ("a",))) is typing.Tuple[int, typing.Tuple[str]]
assert deep_type(frozenset(["a"])) is typing.FrozenSet[str]

get_args(tp)[source]¶

get_origin(tp)[source]¶

get_type_hints(obj, globalns=None, localns=None)[source]¶

Return type hints for an object.

This is often the same as obj.__annotations__, but it handles forward references encoded as string literals, and if necessary adds Optional[t] if a default value equal to None is set.

The argument may be a module, class, method, or function. The annotations are returned as a dictionary. For classes, annotations include also inherited members.

TypeError is raised if the argument is not of a type that can contain annotations, and an empty dictionary is returned if no annotations are present.

BEWARE – the behavior of globalns and localns is counterintuitive (unless you are familiar with how eval() and exec() work). The search order is locals first, then globals.

If no dict arguments are passed, an attempt is made to use the globals from obj (or the respective module’s globals for classes), and these are also used as the locals. If the object does not appear to have globals, an empty dictionary is used.
If one dict argument is passed, it is used for both globals and locals.
If two dict arguments are passed, they specify globals and locals, respectively.

register_subclasscheck(cls)[source]¶

Decorator for registering a custom __subclasscheck__ method for cls which is only ever invoked in deep_issubclass().

This is primarily intended for working with the typing library at runtime. Prefer overriding __subclasscheck__ in the usual way with a metaclass where possible.

class typing_wrap(tp)[source]¶

Bases: object

Utility callable for overriding the runtime behavior of typing objects.

Recipes using Funsor¶

This module provides a number of high-level algorithms using Funsor.

forward_filter_backward_rsample(factors: Dict[str, Funsor], eliminate: FrozenSet[str], plates: FrozenSet[str], sample_inputs: Dict[str, type] = {}, rng_key=None)[source]¶

A forward-filter backward-batched-reparametrized-sample algorithm for use in variational inference. The motivating use case is performing Gaussian tensor variable elimination over structured variational posteriors.

Parameters

factors (dict) – A dictionary mapping sample site name to a Funsor factor created at that sample site.
frozenset – A set of names of latent variables to marginalize and plates to aggregate.
plates – A set of names of plates to aggregate.
sample_inputs (dict) – An optional dict of enclosing sample indices over which samples will be drawn in batch.
rng_key – A random number key for the JAX backend.

Returns

A pair samples:Dict[str, Tensor], log_prob: Tensor of samples and log density evaluated at each of those samples. If sample_inputs is nonempty, both outputs will be batched.

Return type

forward_filter_backward_precondition(factors: Dict[str, Funsor], eliminate: FrozenSet[str], plates: FrozenSet[str], aux_name: str = 'aux')[source]¶

A forward-filter backward-precondition algorithm for use in variational inference or preconditioning in Hamiltonian Monte Carlo. The motivating use case is performing Gaussian tensor variable elimination over structured variational posteriors, and optionally using the learned posterior to determine momentum in HMC.

Parameters

factors (dict) – A dictionary mapping sample site name to a Funsor factor created at that sample site.
frozenset – A set of names of latent variables to marginalize and plates to aggregate.
plates – A set of names of plates to aggregate.
aux_name (str) – Name of the auxiliary variable containing white noise.

Returns

A pair samples:Dict[str, Tensor], log_prob: Tensor of samples and log density evaluated at each of those samples. Both outputs depend on a vector named by aux_name, e.g. aux: Reals[d] where d is the total number of elements in eliminated variables.

Return type

Pyro-Compatible Distributions¶

This interface provides a number of PyTorch-style distributions that use funsors internally to perform inference. These high-level objects are based on a wrapping class: FunsorDistribution which wraps a funsor in a PyTorch-distributions-compatible interface. FunsorDistribution objects can be used directly in Pyro models (using the standard Pyro backend).

FunsorDistribution Base Class¶

class FunsorDistribution(funsor_dist, batch_shape=torch.Size([]), event_shape=torch.Size([]), dtype='real', validate_args=None)[source]¶

Bases: TorchDistribution

Distribution wrapper around a Funsor for use in Pyro code. This is typically used as a base class for specific funsor inference algorithms wrapped in a distribution interface.

Parameters

funsor_dist (funsor.terms.Funsor) – A funsor with an input named “value” that is treated as a random variable. The distribution should be normalized over “value”.
batch_shape (torch.Size) – The distribution’s batch shape. This must be in the same order as the input of the funsor_dist, but may contain extra dims of size 1.
event_shape – The distribution’s event shape.

arg_constraints = {}¶

property support¶

log_prob(value)[source]¶

sample(sample_shape=torch.Size([]))[source]¶

rsample(sample_shape=torch.Size([]))[source]¶

expand(batch_shape, _instance=None)[source]¶

funsordistribution_to_funsor(pyro_dist, output=None, dim_to_name=None)[source]¶

Hidden Markov Models¶

class DiscreteHMM(initial_logits, transition_logits, observation_dist, validate_args=None)[source]¶

Hidden Markov Model with discrete latent state and arbitrary observation distribution. This uses [1] to parallelize over time, achieving O(log(time)) parallel complexity.

The event_shape of this distribution includes time on the left:

event_shape = (num_steps,) + observation_dist.event_shape

This distribution supports any combination of homogeneous/heterogeneous time dependency of transition_logits and observation_dist. However, because time is included in this distribution’s event_shape, the homogeneous+homogeneous case will have a broadcastable event_shape with num_steps = 1, allowing log_prob() to work with arbitrary length data:

# homogeneous + homogeneous case:
event_shape = (1,) + observation_dist.event_shape

This class should be interchangeable with pyro.distributions.hmm.DiscreteHMM .

References:

[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019): “Temporal Parallelization of Bayesian Filters and Smoothers” https://arxiv.org/pdf/1905.13002.pdf

Parameters

initial_logits (Tensor) – A logits tensor for an initial categorical distribution over latent states. Should have rightmost size state_dim and be broadcastable to batch_shape + (state_dim,).
transition_logits (Tensor) – A logits tensor for transition conditional distributions between latent states. Should have rightmost shape (state_dim, state_dim) (old, new), and be broadcastable to batch_shape + (num_steps, state_dim, state_dim).
observation_dist (Distribution) – A conditional distribution of observed data conditioned on latent state. The .batch_shape should have rightmost size state_dim and be broadcastable to batch_shape + (num_steps, state_dim). The .event_shape may be arbitrary.

property has_rsample¶

log_prob(value)[source]¶

expand(batch_shape, _instance=None)[source]¶

class GaussianHMM(initial_dist, transition_matrix, transition_dist, observation_matrix, observation_dist, validate_args=None)[source]¶

Hidden Markov Model with Gaussians for initial, transition, and observation distributions. This adapts [1] to parallelize over time to achieve O(log(time)) parallel complexity, however it differs in that it tracks the log normalizer to ensure log_prob() is differentiable.

This corresponds to the generative model:

z = initial_distribution.sample()
x = []
for t in range(num_steps):
    z = z @ transition_matrix + transition_dist.sample()
    x.append(z @ observation_matrix + observation_dist.sample())

The event_shape of this distribution includes time on the left:

event_shape = (num_steps,) + observation_dist.event_shape

This distribution supports any combination of homogeneous/heterogeneous time dependency of transition_dist and observation_dist. However, because time is included in this distribution’s event_shape, the homogeneous+homogeneous case will have a broadcastable event_shape with num_steps = 1, allowing log_prob() to work with arbitrary length data:

event_shape = (1, obs_dim)  # homogeneous + homogeneous case

This class should be compatible with pyro.distributions.hmm.GaussianHMM , but additionally supports funsor adjoint algorithms.

References:

[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019): “Temporal Parallelization of Bayesian Filters and Smoothers” https://arxiv.org/pdf/1905.13002.pdf

Variables

hidden_dim (int) – The dimension of the hidden state.
obs_dim (int) – The dimension of the observed state.

Parameters

initial_dist (MultivariateNormal) – A distribution over initial states. This should have batch_shape broadcastable to self.batch_shape. This should have event_shape (hidden_dim,).
transition_matrix (Tensor) – A linear transformation of hidden state. This should have shape broadcastable to self.batch_shape + (num_steps, hidden_dim, hidden_dim) where the rightmost dims are ordered (old, new).
transition_dist (MultivariateNormal) – A process noise distribution. This should have batch_shape broadcastable to self.batch_shape + (num_steps,). This should have event_shape (hidden_dim,).
transition_matrix – A linear transformation from hidden to observed state. This should have shape broadcastable to self.batch_shape + (num_steps, hidden_dim, obs_dim).
observation_dist (MultivariateNormal or Independent of Normal) – An observation noise distribution. This should have batch_shape broadcastable to self.batch_shape + (num_steps,). This should have event_shape (obs_dim,).

has_rsample = True¶

arg_constraints = {}¶

class GaussianMRF(initial_dist, transition_dist, observation_dist, validate_args=None)[source]¶

Temporal Markov Random Field with Gaussian factors for initial, transition, and observation distributions. This adapts [1] to parallelize over time to achieve O(log(time)) parallel complexity, however it differs in that it tracks the log normalizer to ensure log_prob() is differentiable.

The event_shape of this distribution includes time on the left:

event_shape = (num_steps,) + observation_dist.event_shape

This distribution supports any combination of homogeneous/heterogeneous time dependency of transition_dist and observation_dist. However, because time is included in this distribution’s event_shape, the homogeneous+homogeneous case will have a broadcastable event_shape with num_steps = 1, allowing log_prob() to work with arbitrary length data:

event_shape = (1, obs_dim)  # homogeneous + homogeneous case

This class should be compatible with pyro.distributions.hmm.GaussianMRF , but additionally supports funsor adjoint algorithms.

References:

[1] Simo Sarkka, Angel F. Garcia-Fernandez (2019): “Temporal Parallelization of Bayesian Filters and Smoothers” https://arxiv.org/pdf/1905.13002.pdf

Variables

hidden_dim (int) – The dimension of the hidden state.
obs_dim (int) – The dimension of the observed state.

Parameters

initial_dist (MultivariateNormal) – A distribution over initial states. This should have batch_shape broadcastable to self.batch_shape. This should have event_shape (hidden_dim,).
transition_dist (MultivariateNormal) – A joint distribution factor over a pair of successive time steps. This should have batch_shape broadcastable to self.batch_shape + (num_steps,). This should have event_shape (hidden_dim + hidden_dim,) (old+new).
observation_dist (MultivariateNormal) – A joint distribution factor over a hidden and an observed state. This should have batch_shape broadcastable to self.batch_shape + (num_steps,). This should have event_shape (hidden_dim + obs_dim,).

has_rsample = True¶

class SwitchingLinearHMM(initial_logits, initial_mvn, transition_logits, transition_matrix, transition_mvn, observation_matrix, observation_mvn, exact=False, validate_args=None)[source]¶

pyro.distributions.MultivariateNormal

Switching Linear Dynamical System represented as a Hidden Markov Model.

This corresponds to the generative model:

z = Categorical(logits=initial_logits).sample()
y = initial_mvn[z].sample()
x = []
for t in range(num_steps):
    z = Categorical(logits=transition_logits[t, z]).sample()
    y = y @ transition_matrix[t, z] + transition_mvn[t, z].sample()
    x.append(y @ observation_matrix[t, z] + observation_mvn[t, z].sample())

Viewed as a dynamic Bayesian network:

z[t-1] ----> z[t] ---> z[t+1]         Discrete latent class
   |  \       |  \       |   \
   | y[t-1] ----> y[t] ----> y[t+1]   Gaussian latent state
   |   /      |   /      |   /
   V  /       V  /       V  /
x[t-1]       x[t]      x[t+1]         Gaussian observation

Let class be the latent class, state be the latent multivariate normal state, and value be the observed multivariate normal value.

Parameters

initial_logits (Tensor) – Represents p(class[0]).
initial_mvn (MultivariateNormal) – Represents p(state[0] | class[0]).
transition_logits (Tensor) – Represents p(class[t+1] | class[t]).
transition_matrix (Tensor) –
transition_mvn (MultivariateNormal) – Together with transition_matrix, this represents p(state[t], state[t+1] | class[t]).
observation_matrix (Tensor) –
observation_mvn (MultivariateNormal) – Together with observation_matrix, this represents p(value[t+1], state[t+1] | class[t+1]).
exact (bool) – If True, perform exact inference at cost exponential in num_steps. If False, use a moment_matching() approximation and use parallel scan algorithm to reduce parallel complexity to logarithmic in num_steps. Defaults to False.

has_rsample = True¶

arg_constraints = {}¶

log_prob(value)[source]¶

expand(batch_shape, _instance=None)[source]¶

filter(value)[source]¶

Compute posterior over final state given a sequence of observations.

Parameters: value (Tensor) – A sequence of observations.
Returns: A posterior distribution over latent states at the final time step, represented as a pair (cat, mvn), where Categorical distribution over mixture components and mvn is a MultivariateNormal with rightmost batch dimension ranging over mixture components. This can then be used to initialize a sequential Pyro model for prediction.
Return type: tuple

Conversion Utilities¶

This module follows a convention for converting between funsors and PyTorch distribution objects. This convention is compatible with NumPy/PyTorch-style broadcasting. Following PyTorch distributions (and Tensorflow distributions), we consider “event shapes” to be on the right and broadcast-compatible “batch shapes” to be on the left.

This module also aims to be forgiving in inputs and pedantic in outputs: methods accept either the superclass torch.distributions.Distribution objects or the subclass pyro.distributions.TorchDistribution objects. Methods return only the narrower subclass pyro.distributions.TorchDistribution objects.

tensor_to_funsor(tensor, event_inputs=(), event_output=0, dtype='real')[source]¶

Convert a torch.Tensor to a funsor.tensor.Tensor .

Note this should not touch data, but may trigger a torch.Tensor.reshape() op.

Parameters

tensor (torch.Tensor) – A PyTorch tensor.
event_inputs (tuple) – A tuple of names for rightmost tensor dimensions. If tensor has these names, they will be converted to result.inputs.
event_output (int) – The number of tensor dimensions assigned to result.output. These must be on the right of any event_input dimensions.

Returns

A funsor.

Return type

funsor.tensor.Tensor

funsor_to_tensor(funsor_, ndims, event_inputs=())[source]¶

Convert a funsor.tensor.Tensor to a torch.Tensor .

Note this should not touch data, but may trigger a torch.Tensor.reshape() op.

Parameters

funsor (funsor.tensor.Tensor) – A funsor.
ndims (int) – The number of result dims, == result.dim().
event_inputs (tuple) – Names assigned to rightmost dimensions.

Returns

A PyTorch tensor.

Return type

torch.Tensor

dist_to_funsor(pyro_dist, event_inputs=())[source]¶

Convert a PyTorch distribution to a Funsor.

Parameters: torch.distribution.Distribution – A PyTorch distribution.
Returns: A funsor.
Return type: funsor.terms.Funsor

mvn_to_funsor(pyro_dist, event_inputs=(), real_inputs={})[source]¶

Convert a joint torch.distributions.MultivariateNormal distribution into a Funsor with multiple real inputs.

This should satisfy:

sum(d.num_elements for d in real_inputs.values())
  == pyro_dist.event_shape[0]

Parameters

pyro_dist (torch.distributions.MultivariateNormal) – A multivariate normal distribution over one or more variables of real or vector or tensor type.
event_inputs (tuple) – A tuple of names for rightmost dimensions. These will be assigned to result.inputs of type Bint.
real_inputs (OrderedDict) – A dict mapping real variable name to appropriately sized Real. The sum of all .numel() of all real inputs should be equal to the pyro_dist dimension.

Returns

A funsor with given real_inputs and possibly additional Bint inputs.

Return type

funsor.terms.Funsor

funsor_to_mvn(gaussian, ndims, event_inputs=())[source]¶

Convert a Funsor to a pyro.distributions.MultivariateNormal , dropping the normalization constant.

Parameters

gaussian (funsor.gaussian.Gaussian or funsor.joint.Joint) – A Gaussian funsor.
ndims (int) – The number of batch dimensions in the result.
event_inputs (tuple) – A tuple of names to assign to rightmost dimensions.

Returns

a multivariate normal distribution.

Return type

funsor_to_cat_and_mvn(funsor_, ndims, event_inputs)[source]¶

Converts a labeled gaussian mixture model to a pair of distributions.

Parameters

funsor (funsor.joint.Joint) – A Gaussian mixture funsor.
ndims (int) – The number of batch dimensions in the result.

Returns

A pair (cat, mvn), where cat is a Categorical distribution over mixture components and mvn is a MultivariateNormal with rightmost batch dimension ranging over mixture components.

matrix_and_mvn_to_funsor(matrix, mvn, event_dims=(), x_name='value_x', y_name='value_y')[source]¶

Convert a noisy affine function to a Gaussian. The noisy affine function is defined as:

y = x @ matrix + mvn.sample()

The result is a non-normalized Gaussian funsor with two real inputs, x_name and y_name, corresponding to a conditional distribution of real vector y` given real vector ``x.

Parameters

matrix (torch.Tensor) – A matrix with rightmost shape (x_size, y_size).
mvn (torch.distributions.MultivariateNormal or torch.distributions.Independent of torch.distributions.Normal) – A multivariate normal distribution with event_shape == (y_size,).
event_dims (tuple) – A tuple of names for rightmost dimensions. These will be assigned to result.inputs of type Bint.
x_name (str) – The name of the x random variable.
y_name (str) – The name of the y random variable.

Returns

A funsor with given real_inputs and possibly additional Bint inputs.

Return type

funsor.terms.Funsor

Distribution Funsors¶

This interface provides a number of standard normalized probability distributions implemented as funsors.

class Distribution(*args, **kwargs)[source]¶

Bases: Funsor

Funsor backed by a PyTorch/JAX distribution object.

Parameters: *args – Distribution-dependent parameters. These can be either funsors or objects that can be coerced to funsors via to_funsor() . See derived classes for details.

dist_class = 'defined by derived classes'¶

eager_reduce(op, reduced_vars)[source]¶

property has_enumerate_support¶

classmethod eager_log_prob(*params)[source]¶

enumerate_support(expand=False)[source]¶

entropy()[source]¶

mean()[source]¶

variance()[source]¶

class Beta(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Beta

class Cauchy(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Cauchy

class Chi2(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Chi2

class BernoulliProbs(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of _PyroWrapper_BernoulliProbs

class BernoulliLogits(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of _PyroWrapper_BernoulliLogits

class Binomial(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Binomial

class Categorical(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Categorical

class CategoricalLogits(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of _PyroWrapper_CategoricalLogits

class Delta(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Delta

class Dirichlet(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Dirichlet

class DirichletMultinomial(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of DirichletMultinomial

class Exponential(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Exponential

class Gamma(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Gamma

class GammaPoisson(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of GammaPoisson

class Geometric(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Geometric

class Gumbel(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Gumbel

class HalfCauchy(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of HalfCauchy

class HalfNormal(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of HalfNormal

class Laplace(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Laplace

class Logistic(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Logistic

class LowRankMultivariateNormal(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of LowRankMultivariateNormal

class Multinomial(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Multinomial

class MultivariateNormal(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of MultivariateNormal

class NonreparameterizedBeta(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of NonreparameterizedBeta

class NonreparameterizedDirichlet(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of NonreparameterizedDirichlet

class NonreparameterizedGamma(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of NonreparameterizedGamma

class NonreparameterizedNormal(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of NonreparameterizedNormal

class Normal(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Normal

class Pareto(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Pareto

class Poisson(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Poisson

class StudentT(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of StudentT

class Uniform(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of Uniform

class VonMises(*args, **kwargs)¶

Bases: Distribution

dist_class¶: alias of VonMises

Mini-Pyro Interface¶

This interface provides a backend for the Pyro probabilistic programming language. This interface is intended to be used indirectly by writing standard Pyro code and setting pyro_backend("funsor"). See examples/minipyro.py for example usage.

Mini Pyro¶

This file contains a minimal implementation of the Pyro Probabilistic Programming Language. The API (method signatures, etc.) match that of the full implementation as closely as possible. This file is independent of the rest of Pyro, with the exception of the pyro.distributions module.

An accompanying example that makes use of this implementation can be found at examples/minipyro.py.

class Distribution(funsor_dist, sample_inputs=None)[source]¶

Bases: object

log_prob(value)[source]¶

expand_inputs(name, size)[source]¶

get_param_store()[source]¶

class Messenger(fn=None)[source]¶

Bases: object

process_message(msg)[source]¶

postprocess_message(msg)[source]¶

class trace(fn=None)[source]¶

Bases: Messenger

postprocess_message(msg)[source]¶

get_trace(*args, **kwargs)[source]¶

class replay(fn, guide_trace)[source]¶

Bases: Messenger

process_message(msg)[source]¶

class block(fn=None, hide_fn=<function block.<lambda>>)[source]¶

Bases: Messenger

process_message(msg)[source]¶

class seed(fn=None, rng_seed=None)[source]¶: Bases: Messenger

class CondIndepStackFrame(name, size, dim)¶

Bases: tuple

property dim¶: Alias for field number 2

property name¶: Alias for field number 0

property size¶: Alias for field number 1

class PlateMessenger(fn, name, size, dim)[source]¶

Bases: Messenger

process_message(msg)[source]¶

tensor_to_funsor(value, cond_indep_stack, output)[source]¶

class log_joint(fn=None)[source]¶

Bases: Messenger

process_message(msg)[source]¶

postprocess_message(msg)[source]¶

apply_stack(msg)[source]¶

sample(name, fn, obs=None, infer=None)[source]¶

param(name, init_value=None, constraint=Real(), event_dim=None)[source]¶

plate(name, size, dim)[source]¶

class PyroOptim(optim_args)[source]¶: Bases: object

class Adam(optim_args)[source]¶

Bases: PyroOptim

TorchOptimizer¶: alias of Adam

class ClippedAdam(optim_args)[source]¶

Bases: PyroOptim

TorchOptimizer¶: alias of ClippedAdam

class SVI(model, guide, optim, loss)[source]¶

Bases: object

step(*args, **kwargs)[source]¶

Expectation(log_probs, costs, sum_vars, prod_vars)[source]¶

elbo(model, guide, *args, **kwargs)[source]¶

class ELBO(**kwargs)[source]¶: Bases: object

class Trace_ELBO(**kwargs)[source]¶: Bases: ELBO

class TraceMeanField_ELBO(**kwargs)[source]¶: Bases: ELBO

class TraceEnum_ELBO(**kwargs)[source]¶: Bases: ELBO

class Jit(fn, **kwargs)[source]¶: Bases: object

class Jit_ELBO(elbo, **kwargs)[source]¶: Bases: ELBO

JitTrace_ELBO(**kwargs)[source]¶

JitTraceMeanField_ELBO(**kwargs)[source]¶

JitTraceEnum_ELBO(**kwargs)[source]¶

Einsum Interface¶

This interface implements tensor variable elimination among tensors. In particular it does not implement continuous variable elimination.

naive_contract_einsum(eqn, *terms, **kwargs)[source]¶: Use for testing Contract against einsum

naive_einsum(eqn, *terms, **kwargs)[source]¶: Implements standard variable elimination.

naive_plated_einsum(eqn, *terms, **kwargs)[source]¶

Implements Tensor Variable Elimination (Algorithm 1 in [Obermeyer et al 2019])

[Obermeyer et al 2019] Obermeyer, F., Bingham, E., Jankowiak, M., Chiu, J.,: Pradhan, N., Rush, A., and Goodman, N. Tensor Variable Elimination for Plated Factor Graphs, 2019

einsum(eqn, *terms, **kwargs)[source]¶

Top-level interface for optimized tensor variable elimination.

Parameters

equation (str) – An einsum equation.
*terms (funsor.terms.Funsor) – One or more operands.
plates (set) – Optional keyword argument denoting which funsor dimensions are plate dimensions. Among all input dimensions (from terms): dimensions in plates but not in outputs are product-reduced; dimensions in neither plates nor outputs are sum-reduced.

Compiler & Tracer¶

lower(expr: Funsor) → Funsor[source]¶

Lower a funsor expression: - eliminate bound variables - convert Contraction to Binary

Parameters: expr (Funsor) – An arbitrary funsor expression.
Returns: A lowered funsor expression.
Return type: Funsor

trace_function(fn, kwargs: dict, *, allow_constants=False)[source]¶

Traces function to an OpProgram that runs on backend values.

Example:

# Create a function involving ops.
def fn(a, b, x):
    return ops.add(ops.matmul(a, x), b)

# Evaluate via Funsor substitution.
data = dict(a=randn(3, 3), b=randn(3), x=randn(3))
expected = fn(**data)

# Alternatively evaluate via a program.
program = trace_function(expr, data)
actual = program(**data)
assert (acutal == expected).all()

Parameters: expr (Funsor) – A funsor expression to evaluate.
Returns: An op program.
Return type: OpProgram

class OpProgram(constants, inputs, operations)[source]¶

Bases: object

Backend program for evaluating a symbolic funsor expression.

Programs depend on the funsor library only via funsor.ops and op registrations; program evaluation does not involve funsor interpretation or rewriting. Programs can be pickled and unpickled.

Parameters

expr (iterable) – A list of built-in constants (leaves).
inputs (iterable) – A list of string names of program inputs (leaves).
operations (iterable) – A list of program operations defining non-leaf nodes in the program dag. Each operations is a tuple (op, arg_ids) where op is a funsor op and arg_ids is a tuple of positions of values, starting from zero and counting: constants, inputs, and operation outputs.

as_code(name='program')[source]¶

Returns Python code text defining a straight-line function equivalent to this program.

Parameters: name (str) – Optional name for the function, defaults to “program”.
Returns: A string defining a python function equivalent to this program.
Return type: str

Interactive online version:

Named tensor notation with funsors (Part 1)¶

Introduction¶

Mathematical notation with named axes introduced in Named Tensor Notation (Chiang, Rush, Barak 2021) improves the readability of mathematical formulas involving multidimensional arrays. This includes tensor operations such as elementwise operations, reductions, contractions, renaming, indexing, and broadcasting. In this tutorial we translate examples from Named Tensor Notation into funsors to demonstrate the implementation of these operations in funsor library and familiarize readers with funsor syntax. Part 1 covers examples from 2 Informal Overview, 3.4.2 Advanced Indexing, and 5 Formal Definitions.

First, let’s import some dependencies.

[ ]:

!pip install funsor[torch]@git+https://github.com/pyro-ppl/funsor

[1]:

from torch import tensor

import funsor
import funsor.ops as ops
from funsor import Number, Tensor, Variable
from funsor.domains import Bint

funsor.set_backend("torch")

Named Tensors¶

Each tensor axis is given a name:

\[\begin{split}\begin{aligned} A &\in \mathbb{R}^{\mathsf{\vphantom{fg}height}[3] \times \mathsf{\vphantom{fg}width}[3]} = \mathbb{R}^{\mathsf{\vphantom{fg}width}[3] \times \mathsf{\vphantom{fg}height}[3]} \\ A &= \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} 3 & 1 & 4 \\ 1 & 5 & 9 \\ 2 & 6 & 5 \end{bmatrix}\end{array} = \mathsf{\vphantom{fg}width} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}height}\\\begin{bmatrix} 3 & 1 & 2 \\ 1 & 5 & 6 \\ 4 & 9 & 5 \end{bmatrix}\end{array}. \end{aligned}\end{split}\]

[2]:

A = Tensor(tensor([[3, 1, 4], [1, 5, 9], [2, 6, 5]]))["height", "width"]

Access elements of \(A\) using named indices:

\[A_{\mathsf{\vphantom{fg}height}(1), \mathsf{\vphantom{fg}width}(3)} = A_{\mathsf{\vphantom{fg}width}(3), \mathsf{\vphantom{fg}height}(1)} = 4\]

[3]:

# A(height=0, width=2) =
A(width=2, height=0)

[3]:

Tensor(tensor(4))

Partial indexing:

\[\begin{split}\begin{aligned} A_{\mathsf{\vphantom{fg}height}(1)} &= \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\ \begin{bmatrix} 3 & 1 & 4 \end{bmatrix}\end{array} & A_{\mathsf{\vphantom{fg}width}(3)} &= \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}height}\\ \begin{bmatrix} 4 & 9 & 5 \end{bmatrix}\end{array}. \end{aligned}\end{split}\]

[4]:

A(height=0)

[4]:

Tensor(tensor([3, 1, 4]), {'width': Bint[3]})

[5]:

A(width=2)

[5]:

Tensor(tensor([4, 9, 5]), {'height': Bint[3]})

Named tensor operations¶

Elementwise operations and broadcasting¶

Elementwise operations:

\[\begin{split}\frac1{1+\exp(-A)} = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\ \begin{bmatrix} \frac 1{1+\exp(-3)} & \frac 1{1+\exp(-1)} & \frac 1{1+\exp(-4)} \\[1ex] \frac 1{1+\exp(-1)} & \frac 1{1+\exp(-5)} & \frac 1{1+\exp(-9)} \\[1ex] \frac 1{1+\exp(-2)} & \frac 1{1+\exp(-6)} & \frac 1{1+\exp(-5)} \end{bmatrix}\end{array}.\end{split}\]

[6]:

# A.sigmoid() =
# ops.sigmoid(A) =
# 1 / (1 + ops.exp(-A)) =
1 / (1 + (-A).exp())

[6]:

Tensor(tensor([[0.9526, 0.7311, 0.9820],
               [0.7311, 0.9933, 0.9999],
               [0.8808, 0.9975, 0.9933]]), {'height': Bint[3], 'width': Bint[3]})

Tensors with different shapes are automatically broadcasted against each other before an operation is applied. Let

\[\begin{split}\begin{aligned} x &\in \mathbb{R}^{\mathsf{\vphantom{fg}height}[3]} & y &\in \mathbb{R}^{\mathsf{\vphantom{fg}width}[3]} \\ x &= \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\\ \begin{bmatrix} 2 \\ 7 \\ 1 \end{bmatrix}\end{array} & y &= \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} 1 & 4 & 1 \end{bmatrix}\end{array}. \end{aligned}\end{split}\]

[7]:

x = Tensor(tensor([2, 7, 1]))["height"]

y = Tensor(tensor([1, 4, 1]))["width"]

Binary addition operation:

\[\begin{split}\begin{aligned} A + x &= \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} 3+2 & 1+2 & 4+2 \\ 1+7 & 5+7 & 9+7 \\ 2+1 & 6+1 & 5+1 \end{bmatrix}\end{array} & A + y &= \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} 3+1 & 1+4 & 4+1 \\ 1+1 & 5+4 & 9+1 \\ 2+1 & 6+4 & 5+1 \end{bmatrix}\end{array}. \end{aligned}\end{split}\]

[8]:

# ops.add(A, x) =
A + x

[8]:

Tensor(tensor([[ 5,  3,  6],
               [ 8, 12, 16],
               [ 3,  7,  6]]), {'height': Bint[3], 'width': Bint[3]})

[9]:

# ops.add(A, y) =
A + y

[9]:

Tensor(tensor([[ 4,  5,  5],
               [ 2,  9, 10],
               [ 3, 10,  6]]), {'height': Bint[3], 'width': Bint[3]})

Binary multiplication operation:

\[\begin{split}A \odot x = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} 3\cdot2 & 1\cdot2 & 4\cdot2 \\ 1\cdot7 & 5\cdot7 & 9\cdot7 \\ 2\cdot1 & 6\cdot1 & 5\cdot1 \end{bmatrix}\end{array}\end{split}\]

[10]:

# ops.mul(A, x) =
A * x

[10]:

Tensor(tensor([[ 6,  2,  8],
               [ 7, 35, 63],
               [ 2,  6,  5]]), {'height': Bint[3], 'width': Bint[3]})

Binary maximum operation:

\[\begin{split}\max(A, y) = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\\begin{bmatrix} \max(3, 1) & \max(1, 4) & \max(4, 1) \\ \max(1, 1) & \max(5, 4) & \max(9, 1) \\ \max(2, 1) & \max(6, 4) & \max(5, 1) \end{bmatrix}\end{array}.\end{split}\]

[11]:

ops.max(A, y)

[11]:

Tensor(tensor([[3, 4, 4],
               [1, 5, 9],
               [2, 6, 5]]), {'height': Bint[3], 'width': Bint[3]})

Reductions¶

Named axes can be reduced over by calling the .reduce method and specifying the reduction operator and names of reduced axes. Note that reduction is defined only for operators that are associative and commutative.

\[\begin{split}\sum\limits_{\substack{\mathsf{\vphantom{fg}height}}} A = \sum_i A_{\mathsf{\vphantom{fg}height}(i)} = \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\ \begin{bmatrix} 3+1+2 & 1+5+6 & 4+9+5 \end{bmatrix}\end{array}.\end{split}\]

[12]:

A.reduce(ops.add, "height")

[12]:

Tensor(tensor([ 6, 12, 18]), {'width': Bint[3]})

\[\begin{split}\sum\limits_{\substack{\mathsf{\vphantom{fg}width}}} A = \sum_j A_{\mathsf{\vphantom{fg}width}(j)} = \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}height}\\ \begin{bmatrix} 3+1+4 & 1+5+9 & 2+6+5 \end{bmatrix}\end{array}.\end{split}\]

[13]:

A.reduce(ops.add, "width")

[13]:

Tensor(tensor([ 8, 15, 13]), {'height': Bint[3]})

Reduction over multiple axes:

\[\begin{split}\sum\limits_{\substack{\mathsf{\vphantom{fg}height}\\ \mathsf{\vphantom{fg}width}}} A = \sum_i \sum_j A_{\mathsf{\vphantom{fg}height}(i),\mathsf{\vphantom{fg}width}(j)} = 3+1+4+1+5+9+2+6+5.\end{split}\]

[14]:

A.reduce(ops.add, {"height", "width"})

[14]:

Tensor(tensor(36))

Multiplication reduction:

\[\begin{split}\prod\limits_{\substack{\mathsf{\vphantom{fg}height}}} A = \prod_i A_{\mathsf{\vphantom{fg}height}(i)} = \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\ \begin{bmatrix} 3\cdot1\cdot2 & 1\cdot5\cdot6 & 4\cdot9\cdot5 \end{bmatrix}\end{array}.\end{split}\]

[15]:

A.reduce(ops.mul, "height")

[15]:

Tensor(tensor([  6,  30, 180]), {'width': Bint[3]})

Max reduction:

\[\begin{split}\max\limits_{\substack{\mathsf{\vphantom{fg}height}}} A = \max \{A_{\mathsf{\vphantom{fg}height}(i)} \mid 1 \leq i \leq n\} = \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width}\\ \begin{bmatrix} \max(3, 1, 2) & \max(1, 5, 6) & \max(4, 9, 5) \end{bmatrix}\end{array}.\end{split}\]

[16]:

A.reduce(ops.max, "height")

[16]:

Tensor(tensor([3, 6, 9]), {'width': Bint[3]})

Contraction¶

Contraction operation can be written as elementwise multiplication followed by summation over an axis:

\[\begin{split}A \mathbin{\underset{\substack{\mathsf{\vphantom{fg}width}}}{\vphantom{fg}\odot}} y = \sum_j A_{\mathsf{\vphantom{fg}width}(j)} \, y_{\mathsf{\vphantom{fg}width}(j)} = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\\\begin{bmatrix} 3\cdot 1 + 1\cdot 4 + 4\cdot 1 \\ 1\cdot 1 + 5\cdot 4 + 9\cdot 1 \\ 2\cdot 1 + 6\cdot 4 + 5\cdot 1 \end{bmatrix}\end{array}.\end{split}\]

[17]:

(A * y).reduce(ops.add, "width")

[17]:

Tensor(tensor([11, 30, 31]), {'height': Bint[3]})

Some other operations from linear algebra:

\[x \mathbin{\underset{\substack{\mathsf{\vphantom{fg}height}}}{\vphantom{fg}\odot}} x = \sum_i x_{\mathsf{\vphantom{fg}height}(i)} \, x_{\mathsf{\vphantom{fg}height}(i)} \qquad \text{inner product}\]

[18]:

(x * x).reduce(ops.add, "height")

[18]:

Tensor(tensor(54))

\[[x \odot y]_{\mathsf{\vphantom{fg}height}(i), \mathsf{\vphantom{fg}width}(j)} = x_{\mathsf{\vphantom{fg}height}(i)} \, y_{\mathsf{\vphantom{fg}width}(j)} \qquad \text{outer product}\]

[19]:

x * y

[19]:

Tensor(tensor([[ 2,  8,  2],
               [ 7, 28,  7],
               [ 1,  4,  1]]), {'height': Bint[3], 'width': Bint[3]})

\[A \mathbin{\underset{\substack{\mathsf{\vphantom{fg}width}}}{\vphantom{fg}\odot}} y = \sum_i A_{\mathsf{\vphantom{fg}width}(i)} \, y_{\mathsf{\vphantom{fg}width}(i)} \qquad \text{matrix-vector product}\]

[20]:

(A * y).reduce(ops.add, "width")

[20]:

Tensor(tensor([11, 30, 31]), {'height': Bint[3]})

\[\begin{split}x \mathbin{\underset{\substack{\mathsf{\vphantom{fg}height}}}{\vphantom{fg}\odot}} A = \sum_i x_{\mathsf{\vphantom{fg}height}(i)} \, A_{\mathsf{\vphantom{fg}height}(i)} \qquad \text{vector-matrix product} \\\end{split}\]

[21]:

(x * A).reduce(ops.add, "height")

[21]:

Tensor(tensor([15, 43, 76]), {'width': Bint[3]})

\[A \mathbin{\underset{\substack{\mathsf{\vphantom{fg}width}}}{\vphantom{fg}\odot}} B = \sum_i A_{\mathsf{\vphantom{fg}width}(i)} \odot B_{\mathsf{\vphantom{fg}width}(i)} \qquad \text{matrix-matrix product}~(B \in \mathbb{R}^{\mathsf{\vphantom{fg}width}\times \mathsf{\vphantom{fg}width2}})\]

[22]:

B = Tensor(
    tensor([[3, 2, 5], [5, 4, 0], [8, 3, 6]]),
)["width", "width2"]

(A * B).reduce(ops.add, "width")

[22]:

Tensor(tensor([[ 46,  22,  39],
               [100,  49,  59],
               [ 76,  43,  40]]), {'height': Bint[3], 'width2': Bint[3]})

Contraction can be generalized to other binary and reduction operations:

\[\begin{split}\max_{\mathsf{\vphantom{fg}width}} (A + y) = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\\\begin{bmatrix} \max(3+1, 1+4, 4+1) \\ \max(1+1, 5+4, 9+1) \\ \max(2+1, 6+4, 5+1) \end{bmatrix}\end{array}.\end{split}\]

[23]:

(A + y).reduce(ops.max, "width")

[23]:

Tensor(tensor([ 5, 10, 10]), {'height': Bint[3]})

Renaming and reshaping¶

Renaming funsors is simple:

\[\begin{split}A_{\mathsf{\vphantom{fg}height}\rightarrow\mathsf{\vphantom{fg}height2}} = \mathsf{\vphantom{fg}height2} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width} \\\begin{bmatrix} 3 & 1 & 4 \\ 1 & 5 & 9 \\ 2 & 6 & 5 \\ \end{bmatrix}\end{array}.\end{split}\]

[24]:

# A(height=Variable("height2", Bint[3]))
A(height="height2")

[24]:

Tensor(tensor([[3, 1, 4],
               [1, 5, 9],
               [2, 6, 5]]), {'height2': Bint[3], 'width': Bint[3]})

\[\begin{split}A_{(\mathsf{\vphantom{fg}height},\mathsf{\vphantom{fg}width})\rightarrow\mathsf{\vphantom{fg}layer}} = \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}layer}\\ \begin{bmatrix} 3 & 1 & 4 & 1 & 5 & 9 & 2 & 6 & 5 \end{bmatrix}\end{array}\end{split}\]

[25]:

layer = Variable("layer", Bint[9])

A_layer = A(height=layer // Number(3, 4), width=layer % Number(3, 4))
A_layer

[25]:

Tensor(tensor([3, 1, 4, 1, 5, 9, 2, 6, 5]), {'layer': Bint[9]})

\[\begin{split}A_{\mathsf{\vphantom{fg}layer}\rightarrow(\mathsf{\vphantom{fg}height},\mathsf{\vphantom{fg}width})} = \mathsf{\vphantom{fg}height} \begin{array}[b]{@{}c@{}}\mathsf{\vphantom{fg}width} \\\begin{bmatrix} 3 & 1 & 4 \\ 1 & 5 & 9 \\ 2 & 6 & 5 \\ \end{bmatrix}\end{array}.\end{split}\]

[26]:

height = Variable("height", Bint[3])
width = Variable("width", Bint[3])

A_layer(layer=height * Number(3, 4) + width % Number(3, 4))

[26]:

Tensor(tensor([[3, 1, 4],
               [1, 5, 9],
               [2, 6, 5]]), {'height': Bint[3], 'width': Bint[3]})

Advanced indexing¶

All of advanced indexing can be achieved through name substitutions in funsors.

\[\begin{split}\mathop{\underset{\substack{\mathsf{\vphantom{fg}ax}}}{\vphantom{fg}\mathrm{index}}} \colon \mathbb{R}^{\mathsf{\vphantom{fg}ax}[n]} \times [n] \rightarrow \mathbb{R}\\ \mathop{\underset{\substack{\mathsf{\vphantom{fg}ax}}}{\vphantom{fg}\mathrm{index}}}(A, i) = A_{\mathsf{\vphantom{fg}ax}(i)}.\end{split}\]

\[\begin{split}\begin{aligned} E &\in \mathbb{R}^{\mathsf{\vphantom{fg}vocab}[n] \times \mathsf{\vphantom{fg}emb}} \\ i &\in [n] \\ I &\in [n]^{\mathsf{\vphantom{fg}seq}} \\ P &\in \mathbb{R}^{\mathsf{\vphantom{fg}seq}\times \mathsf{\vphantom{fg}vocab}[n]} \end{aligned}\end{split}\]

Partial indexing \(\mathop{\underset{\substack{\mathsf{\vphantom{fg}vocab}}}{\vphantom{fg}\mathrm{index}}}(E,i)\):

[27]:

E = Tensor(
    tensor([[2, 1, 5], [3, 4, 2], [1, 3, 7], [1, 4, 3], [5, 9, 2]]),
)["vocab", "emb"]

E(vocab=2)

[27]:

Tensor(tensor([1, 3, 7]), {'emb': Bint[3]})

Integer array indexing \(\mathop{\underset{\substack{\mathsf{\vphantom{fg}vocab}}}{\vphantom{fg}\mathrm{index}}}(E,I)\):

[28]:

I = Tensor(tensor([3, 2, 4, 0]), dtype=5)["seq"]

E(vocab=I)

[28]:

Tensor(tensor([[1, 4, 3],
               [1, 3, 7],
               [5, 9, 2],
               [2, 1, 5]]), {'seq': Bint[4], 'emb': Bint[3]})

Gather operation \(\mathop{\underset{\substack{\mathsf{\vphantom{fg}vocab}}}{\vphantom{fg}\mathrm{index}}}(P,I)\):

[29]:

P = Tensor(
    tensor([[6, 2, 4, 2], [8, 2, 1, 3], [5, 5, 7, 0], [1, 3, 8, 2], [5, 9, 2, 3]]),
)["vocab", "seq"]

P(vocab=I)

[29]:

Tensor(tensor([1, 5, 2, 2]), {'seq': Bint[4]})

Indexing with two integer arrays:

\[\begin{split}\begin{aligned} |\mathsf{\vphantom{fg}seq}| &= m \\ I_1 &= [m]^\mathsf{\vphantom{fg}subseq}\\ I_2 &= [n]^\mathsf{\vphantom{fg}subseq}\\ S &= \mathop{\underset{\substack{\mathsf{\vphantom{fg}vocab}}}{\vphantom{fg}\mathrm{index}}}(\mathop{\underset{\substack{\mathsf{\vphantom{fg}seq}}}{\vphantom{fg}\mathrm{index}}}(P, I_1), I_2) \in \mathbb{R}^{\mathsf{\vphantom{fg}subseq}} \\ S_{\mathsf{\vphantom{fg}subseq}(i)} &= P_{\mathsf{\vphantom{fg}seq}(I_{\mathsf{\vphantom{fg}subseq}(i)}), \mathsf{\vphantom{fg}vocab}(I_{\mathsf{\vphantom{fg}subseq}(i)})}. \end{aligned}\end{split}\]

[30]:

I1 = Tensor(tensor([1, 2, 0]), dtype=4)["subseq"]
I2 = Tensor(tensor([3, 0, 4]), dtype=5)["subseq"]

P(seq=I1, vocab=I2)

[30]:

Tensor(tensor([3, 4, 5]), {'subseq': Bint[3]})

Note

Click here to download the full example code

Example: Adam optimizer¶

import argparse

import torch

import funsor
import funsor.ops as ops
from funsor.adam import Adam
from funsor.domains import Real, Reals
from funsor.tensor import Tensor
from funsor.terms import Variable


def main(args):
    funsor.set_backend("torch")

    # Problem definition.
    N = 100
    P = 10
    data = Tensor(torch.randn(N, P))["n"]
    true_weight = Tensor(torch.randn(P))
    true_bias = Tensor(torch.randn(()))
    truth = true_bias + true_weight @ data

    # Model.
    weight = Variable("weight", Reals[P])
    bias = Variable("bias", Real)
    pred = bias + weight @ data
    loss = (pred - truth).abs().reduce(ops.add, "n")

    # Inference.
    with Adam(args.num_steps, lr=args.learning_rate, log_every=args.log_every) as optim:
        loss.reduce(ops.min, {"weight", "bias"})

    print(f"True bias\n{true_bias}")
    print("Learned bias\n{}".format(optim.param("bias")))
    print(f"True weight\n{true_weight}")
    print("Learned weight\n{}".format(optim.param("weight")))


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Linear regression example using Adam interpretation"
    )
    parser.add_argument("-P", "--num-features", type=int, default=10)
    parser.add_argument("-N", "--num-data", type=int, default=100)
    parser.add_argument("-n", "--num-steps", type=int, default=201)
    parser.add_argument("-lr", "--learning-rate", type=float, default=0.05)
    parser.add_argument("--log-every", type=int, default=20)
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: Discrete HMM¶

import argparse
from collections import OrderedDict

import torch

import funsor
import funsor.ops as ops
import funsor.torch.distributions as dist
from funsor.interpreter import reinterpret
from funsor.optimizer import apply_optimizer


def main(args):
    funsor.set_backend("torch")

    # Declare parameters.
    trans_probs = torch.tensor([[0.2, 0.8], [0.7, 0.3]], requires_grad=True)
    emit_probs = torch.tensor([[0.4, 0.6], [0.1, 0.9]], requires_grad=True)
    params = [trans_probs, emit_probs]

    # A discrete HMM model.
    def model(data):
        log_prob = funsor.to_funsor(0.0)

        trans = dist.Categorical(
            probs=funsor.Tensor(
                trans_probs,
                inputs=OrderedDict([("prev", funsor.Bint[args.hidden_dim])]),
            )
        )

        emit = dist.Categorical(
            probs=funsor.Tensor(
                emit_probs,
                inputs=OrderedDict([("latent", funsor.Bint[args.hidden_dim])]),
            )
        )

        x_curr = funsor.Number(0, args.hidden_dim)
        for t, y in enumerate(data):
            x_prev = x_curr

            # A delayed sample statement.
            x_curr = funsor.Variable("x_{}".format(t), funsor.Bint[args.hidden_dim])
            log_prob += trans(prev=x_prev, value=x_curr)

            if not args.lazy and isinstance(x_prev, funsor.Variable):
                log_prob = log_prob.reduce(ops.logaddexp, x_prev.name)

            log_prob += emit(latent=x_curr, value=funsor.Tensor(y, dtype=2))

        log_prob = log_prob.reduce(ops.logaddexp)
        return log_prob

    # Train model parameters.
    data = torch.ones(args.time_steps, dtype=torch.long)
    optim = torch.optim.Adam(params, lr=args.learning_rate)
    for step in range(args.train_steps):
        optim.zero_grad()
        if args.lazy:
            with funsor.interpretations.lazy:
                log_prob = apply_optimizer(model(data))
            log_prob = reinterpret(log_prob)
        else:
            log_prob = model(data)
        assert not log_prob.inputs, "free variables remain"
        loss = -log_prob.data
        loss.backward()
        optim.step()


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Kalman filter example")
    parser.add_argument("-t", "--time-steps", default=10, type=int)
    parser.add_argument("-n", "--train-steps", default=101, type=int)
    parser.add_argument("-lr", "--learning-rate", default=0.05, type=float)
    parser.add_argument("-d", "--hidden-dim", default=2, type=int)
    parser.add_argument("--lazy", action="store_true")
    parser.add_argument("--filter", action="store_true")
    parser.add_argument("--xfail-if-not-implemented", action="store_true")
    args = parser.parse_args()

    if args.xfail_if_not_implemented:
        try:
            main(args)
        except NotImplementedError:
            print("XFAIL")
    else:
        main(args)

Note

Click here to download the full example code

Example: Switching Linear Dynamical System EEG¶

We use a switching linear dynamical system [1] to model a EEG time series dataset. For inference we use a moment-matching approximation enabled by funsor.interpretations.moment_matching.

References

[1] Anderson, B., and J. Moore. “Optimal filtering. Prentice-Hall, Englewood Cliffs.” New Jersey (1979).

import argparse
import time
from collections import OrderedDict
from os.path import exists
from urllib.request import urlopen

import numpy as np
import pyro
import torch
import torch.nn as nn

import funsor
import funsor.ops as ops
import funsor.torch.distributions as dist
from funsor.pyro.convert import (
    funsor_to_cat_and_mvn,
    funsor_to_mvn,
    matrix_and_mvn_to_funsor,
    mvn_to_funsor,
)


# download dataset from UCI archive
def download_data():
    if not exists("eeg.dat"):
        url = "http://archive.ics.uci.edu/ml/machine-learning-databases/00264/EEG%20Eye%20State.arff"
        with open("eeg.dat", "wb") as f:
            f.write(urlopen(url).read())


class SLDS(nn.Module):
    def __init__(
        self,
        num_components,  # the number of switching states K
        hidden_dim,  # the dimension of the continuous latent space
        obs_dim,  # the dimension of the continuous outputs
        fine_transition_matrix=True,  # controls whether the transition matrix depends on s_t
        fine_transition_noise=False,  # controls whether the transition noise depends on s_t
        fine_observation_matrix=False,  # controls whether the observation matrix depends on s_t
        fine_observation_noise=False,  # controls whether the observation noise depends on s_t
        moment_matching_lag=1,
    ):  # controls the expense of the moment matching approximation

        self.num_components = num_components
        self.hidden_dim = hidden_dim
        self.obs_dim = obs_dim
        self.moment_matching_lag = moment_matching_lag
        self.fine_transition_noise = fine_transition_noise
        self.fine_observation_matrix = fine_observation_matrix
        self.fine_observation_noise = fine_observation_noise
        self.fine_transition_matrix = fine_transition_matrix

        assert moment_matching_lag > 0
        assert (
            fine_transition_noise
            or fine_observation_matrix
            or fine_observation_noise
            or fine_transition_matrix
        ), (
            "The continuous dynamics need to be coupled to the discrete dynamics in at least one way [use at "
            + "least one of the arguments --ftn --ftm --fon --fom]"
        )

        super(SLDS, self).__init__()

        # initialize the various parameters of the model
        self.transition_logits = nn.Parameter(
            0.1 * torch.randn(num_components, num_components)
        )
        if fine_transition_matrix:
            transition_matrix = torch.eye(hidden_dim) + 0.05 * torch.randn(
                num_components, hidden_dim, hidden_dim
            )
        else:
            transition_matrix = torch.eye(hidden_dim) + 0.05 * torch.randn(
                hidden_dim, hidden_dim
            )
        self.transition_matrix = nn.Parameter(transition_matrix)
        if fine_transition_noise:
            self.log_transition_noise = nn.Parameter(
                0.1 * torch.randn(num_components, hidden_dim)
            )
        else:
            self.log_transition_noise = nn.Parameter(0.1 * torch.randn(hidden_dim))
        if fine_observation_matrix:
            self.observation_matrix = nn.Parameter(
                0.3 * torch.randn(num_components, hidden_dim, obs_dim)
            )
        else:
            self.observation_matrix = nn.Parameter(
                0.3 * torch.randn(hidden_dim, obs_dim)
            )
        if fine_observation_noise:
            self.log_obs_noise = nn.Parameter(
                0.1 * torch.randn(num_components, obs_dim)
            )
        else:
            self.log_obs_noise = nn.Parameter(0.1 * torch.randn(obs_dim))

        # define the prior distribution p(x_0) over the continuous latent at the initial time step t=0
        x_init_mvn = pyro.distributions.MultivariateNormal(
            torch.zeros(self.hidden_dim), torch.eye(self.hidden_dim)
        )
        self.x_init_mvn = mvn_to_funsor(
            x_init_mvn,
            real_inputs=OrderedDict([("x_0", funsor.Reals[self.hidden_dim])]),
        )

    # we construct the various funsors used to compute the marginal log probability and other model quantities.
    # these funsors depend on the various model parameters.
    def get_tensors_and_dists(self):
        # normalize the transition probabilities
        trans_logits = self.transition_logits - self.transition_logits.logsumexp(
            dim=-1, keepdim=True
        )
        trans_probs = funsor.Tensor(
            trans_logits, OrderedDict([("s", funsor.Bint[self.num_components])])
        )

        trans_mvn = pyro.distributions.MultivariateNormal(
            torch.zeros(self.hidden_dim), self.log_transition_noise.exp().diag_embed()
        )
        obs_mvn = pyro.distributions.MultivariateNormal(
            torch.zeros(self.obs_dim), self.log_obs_noise.exp().diag_embed()
        )

        event_dims = (
            ("s",) if self.fine_transition_matrix or self.fine_transition_noise else ()
        )
        x_trans_dist = matrix_and_mvn_to_funsor(
            self.transition_matrix, trans_mvn, event_dims, "x", "y"
        )
        event_dims = (
            ("s",)
            if self.fine_observation_matrix or self.fine_observation_noise
            else ()
        )
        y_dist = matrix_and_mvn_to_funsor(
            self.observation_matrix, obs_mvn, event_dims, "x", "y"
        )

        return trans_logits, trans_probs, trans_mvn, obs_mvn, x_trans_dist, y_dist

    # compute the marginal log probability of the observed data using a moment-matching approximation
    @funsor.interpretations.moment_matching
    def log_prob(self, data):
        (
            trans_logits,
            trans_probs,
            trans_mvn,
            obs_mvn,
            x_trans_dist,
            y_dist,
        ) = self.get_tensors_and_dists()

        log_prob = funsor.Number(0.0)

        s_vars = {-1: funsor.Tensor(torch.tensor(0), dtype=self.num_components)}
        x_vars = {}

        for t, y in enumerate(data):
            # construct free variables for s_t and x_t
            s_vars[t] = funsor.Variable(f"s_{t}", funsor.Bint[self.num_components])
            x_vars[t] = funsor.Variable(f"x_{t}", funsor.Reals[self.hidden_dim])

            # incorporate the discrete switching dynamics
            log_prob += dist.Categorical(trans_probs(s=s_vars[t - 1]), value=s_vars[t])

            # incorporate the prior term p(x_t | x_{t-1})
            if t == 0:
                log_prob += self.x_init_mvn(value=x_vars[t])
            else:
                log_prob += x_trans_dist(s=s_vars[t], x=x_vars[t - 1], y=x_vars[t])

            # do a moment-matching reduction. at this point log_prob depends on (moment_matching_lag + 1)-many
            # pairs of free variables.
            if t > self.moment_matching_lag - 1:
                log_prob = log_prob.reduce(
                    ops.logaddexp,
                    {
                        s_vars[t - self.moment_matching_lag],
                        x_vars[t - self.moment_matching_lag],
                    },
                )

            # incorporate the observation p(y_t | x_t, s_t)
            log_prob += y_dist(s=s_vars[t], x=x_vars[t], y=y)

        T = data.shape[0]
        # reduce any remaining free variables
        for t in range(self.moment_matching_lag):
            log_prob = log_prob.reduce(
                ops.logaddexp,
                {
                    s_vars[T - self.moment_matching_lag + t],
                    x_vars[T - self.moment_matching_lag + t],
                },
            )

        # assert that we've reduced all the free variables in log_prob
        assert not log_prob.inputs, "unexpected free variables remain"

        # return the PyTorch tensor behind log_prob (which we can directly differentiate)
        return log_prob.data

    # do filtering, prediction, and smoothing using a moment-matching approximation.
    # here we implicitly use a moment matching lag of L = 1. the general logic follows
    # the logic in the log_prob method.
    @torch.no_grad()
    @funsor.interpretations.moment_matching
    def filter_and_predict(self, data, smoothing=False):
        (
            trans_logits,
            trans_probs,
            trans_mvn,
            obs_mvn,
            x_trans_dist,
            y_dist,
        ) = self.get_tensors_and_dists()

        log_prob = funsor.Number(0.0)

        s_vars = {-1: funsor.Tensor(torch.tensor(0), dtype=self.num_components)}
        x_vars = {-1: None}

        predictive_x_dists, predictive_y_dists, filtering_dists = [], [], []
        test_LLs = []

        for t, y in enumerate(data):
            s_vars[t] = funsor.Variable(f"s_{t}", funsor.Bint[self.num_components])
            x_vars[t] = funsor.Variable(f"x_{t}", funsor.Reals[self.hidden_dim])

            log_prob += dist.Categorical(trans_probs(s=s_vars[t - 1]), value=s_vars[t])

            if t == 0:
                log_prob += self.x_init_mvn(value=x_vars[t])
            else:
                log_prob += x_trans_dist(s=s_vars[t], x=x_vars[t - 1], y=x_vars[t])

            if t > 0:
                log_prob = log_prob.reduce(
                    ops.logaddexp, {s_vars[t - 1], x_vars[t - 1]}
                )

            # do 1-step prediction and compute test LL
            if t > 0:
                predictive_x_dists.append(log_prob)
                _log_prob = log_prob - log_prob.reduce(ops.logaddexp)
                predictive_y_dist = y_dist(s=s_vars[t], x=x_vars[t]) + _log_prob
                test_LLs.append(
                    predictive_y_dist(y=y).reduce(ops.logaddexp).data.item()
                )
                predictive_y_dist = predictive_y_dist.reduce(
                    ops.logaddexp, {f"x_{t}", f"s_{t}"}
                )
                predictive_y_dists.append(funsor_to_mvn(predictive_y_dist, 0, ()))

            log_prob += y_dist(s=s_vars[t], x=x_vars[t], y=y)

            # save filtering dists for forward-backward smoothing
            if smoothing:
                filtering_dists.append(log_prob)

        # do the backward recursion using previously computed ingredients
        if smoothing:
            # seed the backward recursion with the filtering distribution at t=T
            smoothing_dists = [filtering_dists[-1]]
            T = data.size(0)

            s_vars = {
                t: funsor.Variable(f"s_{t}", funsor.Bint[self.num_components])
                for t in range(T)
            }
            x_vars = {
                t: funsor.Variable(f"x_{t}", funsor.Reals[self.hidden_dim])
                for t in range(T)
            }

            # do the backward recursion.
            # let p[t|t-1] be the predictive distribution at time step t.
            # let p[t|t] be the filtering distribution at time step t.
            # let f[t] denote the prior (transition) density at time step t.
            # then the smoothing distribution p[t|T] at time step t is
            # given by the following recursion.
            # p[t-1|T] = p[t-1|t-1] <p[t|T] f[t] / p[t|t-1]>
            # where <...> denotes integration of the latent variables at time step t.
            for t in reversed(range(T - 1)):
                integral = smoothing_dists[-1] - predictive_x_dists[t]
                integral += dist.Categorical(
                    trans_probs(s=s_vars[t]), value=s_vars[t + 1]
                )
                integral += x_trans_dist(s=s_vars[t], x=x_vars[t], y=x_vars[t + 1])
                integral = integral.reduce(
                    ops.logaddexp, {s_vars[t + 1], x_vars[t + 1]}
                )
                smoothing_dists.append(filtering_dists[t] + integral)

        # compute predictive test MSE and predictive variances
        predictive_means = torch.stack([d.mean for d in predictive_y_dists])  # T-1 ydim
        predictive_vars = torch.stack(
            [d.covariance_matrix.diagonal(dim1=-1, dim2=-2) for d in predictive_y_dists]
        )
        predictive_mse = (predictive_means - data[1:, :]).pow(2.0).mean(-1)

        if smoothing:
            # compute smoothed mean function
            smoothing_dists = [
                funsor_to_cat_and_mvn(d, 0, (f"s_{t}",))
                for t, d in enumerate(reversed(smoothing_dists))
            ]
            means = torch.stack([d[1].mean for d in smoothing_dists])  # T 2 xdim
            means = torch.matmul(means.unsqueeze(-2), self.observation_matrix).squeeze(
                -2
            )  # T 2 ydim

            probs = torch.stack([d[0].logits for d in smoothing_dists]).exp()
            probs = probs / probs.sum(-1, keepdim=True)  # T 2

            smoothing_means = (probs.unsqueeze(-1) * means).sum(-2)  # T ydim
            smoothing_probs = probs[:, 1]

            return (
                predictive_mse,
                torch.tensor(np.array(test_LLs)),
                predictive_means,
                predictive_vars,
                smoothing_means,
                smoothing_probs,
            )
        else:
            return predictive_mse, torch.tensor(np.array(test_LLs))


def main(args):
    funsor.set_backend("torch")

    # download and pre-process EEG data if not in test mode
    if not args.test:
        download_data()
        N_val, N_test = 149, 200
        data = np.loadtxt("eeg.dat", delimiter=",", skiprows=19)
        print(f"[raw data shape] {data.shape}")
        data = data[::20, :]
        print(f"[data shape after thinning] {data.shape}")
        eye_state = [int(d) for d in data[:, -1].tolist()]
        data = torch.tensor(data[:, :-1]).float()
    # in test mode (for continuous integration on github) so create fake data
    else:
        data = torch.randn(10, 3)
        N_val, N_test = 2, 2

    T, obs_dim = data.shape
    N_train = T - N_test - N_val

    np.random.seed(0)
    rand_perm = np.random.permutation(N_val + N_test)
    val_indices = rand_perm[0:N_val]
    test_indices = rand_perm[N_val:]

    data_mean = data[0:N_train, :].mean(0)
    data -= data_mean
    data_std = data[0:N_train, :].std(0)
    data /= data_std

    print(f"Length of time series T: {T}   Observation dimension: {obs_dim}")
    print(f"N_train: {N_train}  N_val: {N_val}  N_test: {N_test}")

    torch.manual_seed(args.seed)

    # set up model
    slds = SLDS(
        num_components=args.num_components,
        hidden_dim=args.hidden_dim,
        obs_dim=obs_dim,
        fine_observation_noise=args.fon,
        fine_transition_noise=args.ftn,
        fine_observation_matrix=args.fom,
        fine_transition_matrix=args.ftm,
        moment_matching_lag=args.moment_matching_lag,
    )

    # set up optimizer
    adam = torch.optim.Adam(
        slds.parameters(),
        lr=args.learning_rate,
        betas=(args.beta1, 0.999),
        amsgrad=True,
    )
    scheduler = torch.optim.lr_scheduler.ExponentialLR(adam, gamma=args.gamma)
    ts = [time.time()]

    report_frequency = 1

    # training loop
    for step in range(args.num_steps):
        nll = -slds.log_prob(data[0:N_train, :]) / N_train
        nll.backward()

        if step == 5:
            scheduler.base_lrs[0] *= 0.20

        adam.step()
        scheduler.step()
        adam.zero_grad()

        if step % report_frequency == 0 or step == args.num_steps - 1:
            step_dt = ts[-1] - ts[-2] if step > 0 else 0.0
            pred_mse, pred_LLs = slds.filter_and_predict(
                data[0 : N_train + N_val + N_test, :]
            )
            val_mse = pred_mse[val_indices].mean().item()
            test_mse = pred_mse[test_indices].mean().item()
            val_ll = pred_LLs[val_indices].mean().item()
            test_ll = pred_LLs[test_indices].mean().item()

            stats = "[step %03d] train_nll: %.5f val_mse: %.5f val_ll: %.5f test_mse: %.5f test_ll: %.5f\t(dt: %.2f)"
            print(
                stats % (step, nll.item(), val_mse, val_ll, test_mse, test_ll, step_dt)
            )

        ts.append(time.time())

    # plot predictions and smoothed means
    if args.plot:
        assert not args.test
        (
            predicted_mse,
            LLs,
            pred_means,
            pred_vars,
            smooth_means,
            smooth_probs,
        ) = slds.filter_and_predict(data, smoothing=True)

        pred_means = pred_means.data.numpy()
        pred_stds = pred_vars.sqrt().data.numpy()
        smooth_means = smooth_means.data.numpy()
        smooth_probs = smooth_probs.data.numpy()

        import matplotlib

        matplotlib.use("Agg")  # noqa: E402
        import matplotlib.pyplot as plt

        f, axes = plt.subplots(4, 1, figsize=(12, 8), sharex=True)
        T = data.size(0)
        N_valtest = N_val + N_test
        to_seconds = 117.0 / T

        for k, ax in enumerate(axes[:-1]):
            which = [0, 4, 10][k]
            ax.plot(to_seconds * np.arange(T), data[:, which], "ko", markersize=2)
            ax.plot(
                to_seconds * np.arange(N_train),
                smooth_means[:N_train, which],
                ls="solid",
                color="r",
            )

            ax.plot(
                to_seconds * (N_train + np.arange(N_valtest)),
                pred_means[-N_valtest:, which],
                ls="solid",
                color="b",
            )
            ax.fill_between(
                to_seconds * (N_train + np.arange(N_valtest)),
                pred_means[-N_valtest:, which] - 1.645 * pred_stds[-N_valtest:, which],
                pred_means[-N_valtest:, which] + 1.645 * pred_stds[-N_valtest:, which],
                color="lightblue",
            )
            ax.set_ylabel(f"$y_{which + 1}$", fontsize=20)
            ax.tick_params(axis="both", which="major", labelsize=14)

        axes[-1].plot(to_seconds * np.arange(T), eye_state, "k", ls="solid")
        axes[-1].plot(to_seconds * np.arange(T), smooth_probs, "r", ls="solid")
        axes[-1].set_xlabel("Time (s)", fontsize=20)
        axes[-1].set_ylabel("Eye state", fontsize=20)
        axes[-1].tick_params(axis="both", which="major", labelsize=14)

        plt.tight_layout(pad=0.7)
        plt.savefig("eeg.pdf")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Switching linear dynamical system")
    parser.add_argument("-n", "--num-steps", default=3, type=int)
    parser.add_argument("-s", "--seed", default=15, type=int)
    parser.add_argument("-hd", "--hidden-dim", default=5, type=int)
    parser.add_argument("-k", "--num-components", default=2, type=int)
    parser.add_argument("-lr", "--learning-rate", default=0.5, type=float)
    parser.add_argument("-b1", "--beta1", default=0.75, type=float)
    parser.add_argument("-g", "--gamma", default=0.99, type=float)
    parser.add_argument("-mml", "--moment-matching-lag", default=1, type=int)
    parser.add_argument("--plot", action="store_true")
    parser.add_argument("--fon", action="store_true")
    parser.add_argument("--ftm", action="store_true")
    parser.add_argument("--fom", action="store_true")
    parser.add_argument("--ftn", action="store_true")
    parser.add_argument("--test", action="store_true")
    args = parser.parse_args()

    main(args)

Note

Click here to download the full example code

Example: Forward-Backward algorithm¶

import argparse
from collections import OrderedDict
from typing import Dict, List, Tuple

import funsor.ops as ops
from funsor import Funsor, Tensor
from funsor.adjoint import AdjointTape
from funsor.domains import Bint
from funsor.testing import assert_close, random_tensor


def forward_algorithm(
    factors: List[Funsor],
    step: Dict[str, str],
) -> Tuple[Funsor, List[Funsor]]:
    """
    Calculate log marginal probability using the forward algorithm:
    Z = p(y[0:T])

    Transition and emission probabilities are given by init and trans factors:
    init = p(y[0], x[0])
    trans[t] = p(y[t], x[t] | x[t-1])

    Forward probabilities are computed inductively:
    alpha[t] = p(y[0:t], x[t])
    alpha[0] = init
    alpha[t+1] = alpha[t] @ trans[t+1]
    """
    step = OrderedDict(sorted(step.items()))
    drop = tuple("_drop_{}".format(i) for i in range(len(step)))
    prev_to_drop = dict(zip(step.keys(), drop))
    curr_to_drop = dict(zip(step.values(), drop))
    reduce_vars = frozenset(drop)

    # base case
    alpha = factors[0]
    alphas = [alpha]
    # inductive steps
    for trans in factors[1:]:
        alpha = (alpha(**curr_to_drop) + trans(**prev_to_drop)).reduce(
            ops.logaddexp, reduce_vars
        )
        alphas.append(alpha)
    else:
        Z = alpha(**curr_to_drop).reduce(ops.logaddexp, reduce_vars)
    return Z


def forward_backward_algorithm(
    factors: List[Funsor],
    step: Dict[str, str],
) -> List[Tensor]:
    """
    Calculate marginal probabilities:
    p(x[t], x[t-1] | Y)
    """
    step = OrderedDict(sorted(step.items()))
    drop = tuple("_drop_{}".format(i) for i in range(len(step)))
    prev_to_drop = dict(zip(step.keys(), drop))
    curr_to_drop = dict(zip(step.values(), drop))
    reduce_vars = frozenset(drop)

    # Base cases
    alpha = factors[0]  # alpha[0] = p(y[0], x[0])
    beta = Tensor(
        ops.full_like(alpha.data, 0.0), alpha(x_curr="x_prev").inputs
    )  # beta[T] = 1

    # Backward algorithm
    # beta[t] = p(y[t+1:T] | x[t])
    # beta[t] = trans[t+1] @ beta[t+1]
    betas = [beta]
    for trans in factors[:0:-1]:
        beta = (trans(**curr_to_drop) + beta(**prev_to_drop)).reduce(
            ops.logaddexp, reduce_vars
        )
        betas.append(beta)
    else:
        init = factors[0]
        Z = (init(**curr_to_drop) + beta(**prev_to_drop)).reduce(
            ops.logaddexp, reduce_vars
        )
    betas.reverse()

    # Forward algorithm & Marginal computations
    marginal = alpha + betas[0](**{"x_prev": "x_curr"}) - Z  # p(x[0] | Y)
    marginals = [marginal]
    # inductive steps
    for trans, beta in zip(factors[1:], betas[1:]):
        # alpha[t-1] * trans[t] = p(y[0:t], x[t-1], x[t])
        alpha_trans = alpha(**{"x_curr": "x_prev"}) + trans
        # alpha[t] = p(y[0:t], x[t])
        alpha = alpha_trans.reduce(ops.logaddexp, "x_prev")
        # alpha[t-1] * trans[t] * beta[t] / Z = p(x[t-1], x[t] | Y)
        marginal = alpha_trans + beta(**{"x_prev": "x_curr"}) - Z
        marginals.append(marginal)

    return marginals


def main(args):
    """
    Compute marginal probabilities p(x[t], x[t-1] | Y) for an HMM:

    x[0] -> ... -> x[t-1] -> x[t] -> ... -> x[T]
     |              |         |             |
     v              v         v             v
    y[0]           y[t-1]    y[t]           y[T]

    Z = p(y[0:T])
    alpha[t] = p(y[0:t], x[t])
    beta[t] = p(y[t+1:T] | x[t])
    trans[t] = p(y[t], x[t] | x[t-1])

    p(x[t], x[t-1] | Y) = alpha[t-1] * beta[t] * trans[t] / Z

    d Z / d trans[t] = alpha[t-1] * beta[t]

    **References:**

    [1] Jason Eisner (2016)
        "Inside-Outside and Forward-Backward Algorithms Are Just Backprop
        (Tutorial Paper)"
        https://www.cs.jhu.edu/~jason/papers/eisner.spnlp16.pdf
    [2] Zhifei Li and Jason Eisner (2009)
        "First- and Second-Order Expectation Semirings
        with Applications to Minimum-Risk Training on Translation Forests"
        http://www.cs.jhu.edu/~zfli/pubs/semiring_translation_zhifei_emnlp09.pdf
    """

    # transition and emission probabilities
    init = random_tensor(OrderedDict([("x_curr", Bint[args.hidden_dim])]))
    factors = [init]
    for t in range(args.time_steps - 1):
        factors.append(
            random_tensor(
                OrderedDict(x_prev=Bint[args.hidden_dim], x_curr=Bint[args.hidden_dim])
            )
        )

    # Compute marginal probabilities using the forward-backward algorithm
    marginals = forward_backward_algorithm(factors, {"x_prev": "x_curr"})
    # Compute marginal probabilities using backpropagation
    with AdjointTape() as tape:
        Z = forward_algorithm(factors, {"x_prev": "x_curr"})
    result = tape.adjoint(ops.logaddexp, ops.add, Z, factors)
    adjoint_terms = list(result.values())

    t = 0
    for expected, adj, trans in zip(marginals, adjoint_terms, factors):
        # adjoint returns dZ / dtrans = alpha[t-1] * beta[t]
        # marginal = alpha[t-1] * beta[t] * trans / Z
        actual = adj + trans - Z
        assert_close(expected, actual.align(tuple(expected.inputs)), rtol=1e-4)
        print("")
        print(f"Marginal term: p(x[{t}], x[{t-1}] | Y)")
        print("Forward-backward algorithm:\n", expected.data)
        print("Differentiating forward algorithm:\n", actual.data)
        t += 1


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Forward-Backward Algorithm Is Just Backprop"
    )
    parser.add_argument("-t", "--time-steps", default=10, type=int)
    parser.add_argument("-d", "--hidden-dim", default=3, type=int)
    args = parser.parse_args()

    main(args)

Note

Click here to download the full example code

Example: Kalman Filter¶

import argparse

import torch

import funsor
import funsor.ops as ops
import funsor.torch.distributions as dist
from funsor.interpreter import reinterpret
from funsor.optimizer import apply_optimizer


def main(args):
    funsor.set_backend("torch")

    # Declare parameters.
    trans_noise = torch.tensor(0.1, requires_grad=True)
    emit_noise = torch.tensor(0.5, requires_grad=True)
    params = [trans_noise, emit_noise]

    # A Gaussian HMM model.
    def model(data):
        log_prob = funsor.to_funsor(0.0)

        x_curr = funsor.Tensor(torch.tensor(0.0))
        for t, y in enumerate(data):
            x_prev = x_curr

            # A delayed sample statement.
            x_curr = funsor.Variable("x_{}".format(t), funsor.Real)
            log_prob += dist.Normal(1 + x_prev / 2.0, trans_noise, value=x_curr)

            # Optionally marginalize out the previous state.
            if t > 0 and not args.lazy:
                log_prob = log_prob.reduce(ops.logaddexp, x_prev.name)

            # An observe statement.
            log_prob += dist.Normal(0.5 + 3 * x_curr, emit_noise, value=y)

        # Marginalize out all remaining delayed variables.
        log_prob = log_prob.reduce(ops.logaddexp)
        return log_prob

    # Train model parameters.
    torch.manual_seed(0)
    data = torch.randn(args.time_steps)
    optim = torch.optim.Adam(params, lr=args.learning_rate)
    for step in range(args.train_steps):
        optim.zero_grad()
        if args.lazy:
            with funsor.interpretations.lazy:
                log_prob = apply_optimizer(model(data))
            log_prob = reinterpret(log_prob)
        else:
            log_prob = model(data)
        assert not log_prob.inputs, "free variables remain"
        loss = -log_prob.data
        loss.backward()
        optim.step()
        if args.verbose and step % 10 == 0:
            print("step {} loss = {}".format(step, loss.item()))


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Kalman filter example")
    parser.add_argument("-t", "--time-steps", default=10, type=int)
    parser.add_argument("-n", "--train-steps", default=101, type=int)
    parser.add_argument("-lr", "--learning-rate", default=0.05, type=float)
    parser.add_argument("--lazy", action="store_true")
    parser.add_argument("--filter", action="store_true")
    parser.add_argument("-v", "--verbose", action="store_true")
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: Mini Pyro¶

import argparse

import torch
from pyroapi import distributions as dist
from pyroapi import infer, optim, pyro, pyro_backend
from torch.distributions import constraints

import funsor
from funsor.montecarlo import MonteCarlo


def main(args):
    funsor.set_backend("torch")

    # Define a basic model with a single Normal latent random variable `loc`
    # and a batch of Normally distributed observations.
    def model(data):
        loc = pyro.sample("loc", dist.Normal(0.0, 1.0))
        with pyro.plate("data", len(data), dim=-1):
            pyro.sample("obs", dist.Normal(loc, 1.0), obs=data)

    # Define a guide (i.e. variational distribution) with a Normal
    # distribution over the latent random variable `loc`.
    def guide(data):
        guide_loc = pyro.param("guide_loc", torch.tensor(0.0))
        guide_scale = pyro.param(
            "guide_scale", torch.tensor(1.0), constraint=constraints.positive
        )
        pyro.sample("loc", dist.Normal(guide_loc, guide_scale))

    # Generate some data.
    torch.manual_seed(0)
    data = torch.randn(100) + 3.0

    # Because the API in minipyro matches that of Pyro proper,
    # training code works with generic Pyro implementations.
    with pyro_backend(args.backend), MonteCarlo():
        # Construct an SVI object so we can do variational inference on our
        # model/guide pair.
        Elbo = infer.JitTrace_ELBO if args.jit else infer.Trace_ELBO
        elbo = Elbo()
        adam = optim.Adam({"lr": args.learning_rate})
        svi = infer.SVI(model, guide, adam, elbo)

        # Basic training loop
        pyro.get_param_store().clear()
        for step in range(args.num_steps):
            loss = svi.step(data)
            if args.verbose and step % 100 == 0:
                print(f"step {step} loss = {loss}")

        # Report the final values of the variational parameters
        # in the guide after training.
        if args.verbose:
            for name in pyro.get_param_store():
                value = pyro.param(name).data
                print(f"{name} = {value.detach().cpu().numpy()}")

        # For this simple (conjugate) model we know the exact posterior. In
        # particular we know that the variational distribution should be
        # centered near 3.0. So let's check this explicitly.
        assert (pyro.param("guide_loc") - 3.0).abs() < 0.1


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Minipyro demo")
    parser.add_argument("-b", "--backend", default="funsor")
    parser.add_argument("-n", "--num-steps", default=1001, type=int)
    parser.add_argument("-lr", "--learning-rate", default=0.02, type=float)
    parser.add_argument("--jit", action="store_true")
    parser.add_argument("-v", "--verbose", action="store_true")
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: PCFG¶

import argparse
import math
from collections import OrderedDict

import torch

import funsor
import funsor.ops as ops
from funsor.delta import Delta
from funsor.domains import Bint
from funsor.tensor import Tensor
from funsor.terms import Number, Stack, Variable


def Uniform(components):
    components = tuple(components)
    size = len(components)
    if size == 1:
        return components[0]
    var = Variable("v", Bint[size])
    return Stack(var.name, components).reduce(ops.logaddexp, var.name) - math.log(size)


# @of_shape(*([Bint[2]] * size))
def model(size, position=0):
    if size == 1:
        name = str(position)
        return Uniform((Delta(name, Number(0, 2)), Delta(name, Number(1, 2))))
    return Uniform(
        model(t, position) + model(size - t, t + position) for t in range(1, size)
    )


def main(args):
    funsor.set_backend("torch")
    torch.manual_seed(args.seed)

    print_ = print if args.verbose else lambda msg: None
    print_("Data:")
    data = torch.distributions.Categorical(torch.ones(2)).sample((args.size,))
    assert data.shape == (args.size,)
    data = Tensor(data, OrderedDict(i=Bint[args.size]), dtype=2)
    print_(data)

    print_("Model:")
    m = model(args.size)
    print_(m.pretty())

    print_("Eager log_prob:")
    obs = {str(i): data(i) for i in range(args.size)}
    log_prob = m(**obs)
    print_(log_prob)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="PCFG example")
    parser.add_argument("-s", "--size", default=3, type=int)
    parser.add_argument("--seed", default=0, type=int)
    parser.add_argument("-v", "--verbose", action="store_true")
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: Biased Kalman Filter¶

import argparse
import itertools
import math
import os

import pyro.distributions as dist
import torch
import torch.nn as nn
from torch.optim import Adam

import funsor
import funsor.ops as ops
import funsor.torch.distributions as f_dist
from funsor.domains import Reals
from funsor.pyro.convert import dist_to_funsor, funsor_to_mvn
from funsor.tensor import Tensor, Variable

# We use a 2D continuous-time NCV dynamics model throughout.
# See http://webee.technion.ac.il/people/shimkin/Estimation09/ch8_target.pdf
TIME_STEP = 1.0
NCV_PROCESS_NOISE = torch.tensor(
    [
        [1 / 3, 0.0, 1 / 2, 0.0],
        [0.0, 1 / 3, 0.0, 1 / 2],
        [1 / 2, 0.0, 1.0, 0.0],
        [0.0, 1 / 2, 0.0, 1.0],
    ]
)
NCV_TRANSITION_MATRIX = torch.tensor(
    [
        [1.0, 0.0, 0.0, 0.0],
        [0.0, 1.0, 0.0, 0.0],
        [1.0, 0.0, 1.0, 0.0],
        [0.0, 1.0, 0.0, 1.0],
    ]
)


@torch.no_grad()
def generate_data(num_frames, num_sensors):
    """
    Generate data from a damped NCV dynamics model
    """
    dt = TIME_STEP
    bias_scale = 4.0
    obs_noise = 1.0
    trans_noise = 0.3

    # define dynamics
    z = torch.cat([10.0 * torch.randn(2), torch.rand(2)])  # position  # velocity
    damp = 0.1  # damp the velocities
    f = torch.tensor(
        [
            [1, 0, 0, 0],
            [0, 1, 0, 0],
            [dt * math.exp(-damp * dt), 0, math.exp(-damp * dt), 0],
            [0, dt * math.exp(-damp * dt), 0, math.exp(-damp * dt)],
        ]
    )
    trans_dist = dist.MultivariateNormal(
        torch.zeros(4),
        scale_tril=trans_noise * torch.linalg.cholesky(NCV_PROCESS_NOISE),
    )

    # define biased sensors
    sensor_bias = bias_scale * torch.randn(2 * num_sensors)
    h = torch.eye(4, 2).unsqueeze(-1).expand(-1, -1, num_sensors).reshape(4, -1)
    obs_dist = dist.MultivariateNormal(
        sensor_bias, scale_tril=obs_noise * torch.eye(2 * num_sensors)
    )

    states = []
    observations = []
    for t in range(num_frames):
        z = z @ f + trans_dist.sample()
        states.append(z)

        x = z @ h + obs_dist.sample()
        observations.append(x)

    states = torch.stack(states)
    observations = torch.stack(observations)
    assert observations.shape == (num_frames, num_sensors * 2)
    return observations, states, sensor_bias


class Model(nn.Module):
    def __init__(self, num_sensors):
        super(Model, self).__init__()
        self.num_sensors = num_sensors

        # learnable params
        self.log_bias_scale = nn.Parameter(torch.tensor(0.0))
        self.log_obs_noise = nn.Parameter(torch.tensor(0.0))
        self.log_trans_noise = nn.Parameter(torch.tensor(0.0))

    def forward(self, observations, add_bias=True):
        obs_dim = 2 * self.num_sensors
        bias_scale = self.log_bias_scale.exp()
        obs_noise = self.log_obs_noise.exp()
        trans_noise = self.log_trans_noise.exp()

        # bias distribution
        bias = Variable("bias", Reals[obs_dim])
        assert not torch.isnan(bias_scale), "bias scales was nan"
        bias_dist = dist_to_funsor(
            dist.MultivariateNormal(
                torch.zeros(obs_dim),
                scale_tril=bias_scale * torch.eye(2 * self.num_sensors),
            )
        )(value=bias)

        init_dist = dist.MultivariateNormal(
            torch.zeros(4), scale_tril=100.0 * torch.eye(4)
        )
        self.init = dist_to_funsor(init_dist)(value="state")

        # hidden states
        prev = Variable("prev", Reals[4])
        curr = Variable("curr", Reals[4])
        self.trans_dist = f_dist.MultivariateNormal(
            loc=prev @ NCV_TRANSITION_MATRIX,
            scale_tril=trans_noise * torch.linalg.cholesky(NCV_PROCESS_NOISE),
            value=curr,
        )

        state = Variable("state", Reals[4])
        obs = Variable("obs", Reals[obs_dim])
        observation_matrix = Tensor(
            torch.eye(4, 2)
            .unsqueeze(-1)
            .expand(-1, -1, self.num_sensors)
            .reshape(4, -1)
        )
        assert observation_matrix.output.shape == (
            4,
            obs_dim,
        ), observation_matrix.output.shape
        obs_loc = state @ observation_matrix
        if add_bias:
            obs_loc += bias
        self.observation_dist = f_dist.MultivariateNormal(
            loc=obs_loc, scale_tril=obs_noise * torch.eye(obs_dim), value=obs
        )

        logp = bias_dist
        curr = "state_init"
        logp += self.init(state=curr)
        for t, x in enumerate(observations):
            prev, curr = curr, "state_{}".format(t)
            logp += self.trans_dist(prev=prev, curr=curr)
            logp += self.observation_dist(state=curr, obs=x)
            # marginalize out previous state
            logp = logp.reduce(ops.logaddexp, prev)
        # marginalize out bias variable
        logp = logp.reduce(ops.logaddexp, "bias")

        # save posterior over the final state
        assert set(logp.inputs) == {"state_{}".format(len(observations) - 1)}
        posterior = funsor_to_mvn(logp, ndims=0)

        # marginalize out remaining variables
        logp = logp.reduce(ops.logaddexp)
        assert isinstance(logp, Tensor) and logp.shape == (), logp.pretty()
        return logp.data, posterior


def track(args):
    results = {}  # keyed on (seed, bias, num_frames)
    for seed in args.seed:
        torch.manual_seed(seed)
        observations, states, sensor_bias = generate_data(
            max(args.num_frames), args.num_sensors
        )
        for bias, num_frames in itertools.product(args.bias, args.num_frames):
            print(
                "tracking with seed={}, bias={}, num_frames={}".format(
                    seed, bias, num_frames
                )
            )
            model = Model(args.num_sensors)
            optim = Adam(model.parameters(), lr=args.lr, betas=(0.5, 0.8))
            losses = []
            for i in range(args.num_epochs):
                optim.zero_grad()
                log_prob, posterior = model(observations[:num_frames], add_bias=bias)
                loss = -log_prob
                loss.backward()
                losses.append(loss.item())
                if i % 10 == 0:
                    print(loss.item())
                optim.step()

            # Collect evaluation metrics.
            final_state_true = states[num_frames - 1]
            assert final_state_true.shape == (4,)
            final_pos_true = final_state_true[:2]
            final_vel_true = final_state_true[2:]

            final_state_est = posterior.loc
            assert final_state_est.shape == (4,)
            final_pos_est = final_state_est[:2]
            final_vel_est = final_state_est[2:]
            final_pos_error = float(torch.norm(final_pos_true - final_pos_est))
            final_vel_error = float(torch.norm(final_vel_true - final_vel_est))
            print("final_pos_error = {}".format(final_pos_error))

            results[seed, bias, num_frames] = {
                "args": args,
                "observations": observations[:num_frames],
                "states": states[:num_frames],
                "sensor_bias": sensor_bias,
                "losses": losses,
                "bias_scale": float(model.log_bias_scale.exp()),
                "obs_noise": float(model.log_obs_noise.exp()),
                "trans_noise": float(model.log_trans_noise.exp()),
                "final_state_estimate": posterior,
                "final_pos_error": final_pos_error,
                "final_vel_error": final_vel_error,
            }
        if args.metrics_filename:
            print("saving output to: {}".format(args.metrics_filename))
            torch.save(results, args.metrics_filename)
    return results


def main(args):
    funsor.set_backend("torch")
    if (
        args.force
        or not args.metrics_filename
        or not os.path.exists(args.metrics_filename)
    ):
        # Increase compression threshold for numerical stability.
        with funsor.gaussian.Gaussian.set_compression_threshold(3):
            results = track(args)
    else:
        results = torch.load(args.metrics_filename)

    if args.plot_filename:
        import matplotlib

        matplotlib.use("Agg")
        import numpy as np
        from matplotlib import pyplot

        seeds = set(seed for seed, _, _ in results)
        X = args.num_frames
        pyplot.figure(figsize=(5, 1.4), dpi=300)

        pos_error = np.array(
            [
                [results[s, 0, f]["final_pos_error"] for s in seeds]
                for f in args.num_frames
            ]
        )
        mse = (pos_error**2).mean(axis=1)
        std = (pos_error**2).std(axis=1) / len(seeds) ** 0.5
        pyplot.plot(X, mse**0.5, "k--")
        pyplot.fill_between(
            X, (mse - std) ** 0.5, (mse + std) ** 0.5, color="black", alpha=0.15, lw=0
        )

        pos_error = np.array(
            [
                [results[s, 1, f]["final_pos_error"] for s in seeds]
                for f in args.num_frames
            ]
        )
        mse = (pos_error**2).mean(axis=1)
        std = (pos_error**2).std(axis=1) / len(seeds) ** 0.5
        pyplot.plot(X, mse**0.5, "r-")
        pyplot.fill_between(
            X, (mse - std) ** 0.5, (mse + std) ** 0.5, color="red", alpha=0.15, lw=0
        )

        pyplot.ylabel("Position RMSE")
        pyplot.xlabel("Track Length")
        pyplot.xticks((5, 10, 15, 20, 25, 30))
        pyplot.xlim(5, 30)
        pyplot.tight_layout(0)
        pyplot.savefig(args.plot_filename)


def int_list(args):
    result = []
    for arg in args.split(","):
        if "-" in arg:
            beg, end = map(int, arg.split("-"))
            result.extend(range(beg, 1 + end))
        else:
            result.append(int(arg))
    return result


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Biased Kalman filter")
    parser.add_argument(
        "--seed",
        default="0",
        type=int_list,
        help="random seed, comma delimited for multiple runs",
    )
    parser.add_argument(
        "--bias",
        default="0,1",
        type=int_list,
        help="whether to model bias, comma deliminted for multiple runs",
    )
    parser.add_argument(
        "-f",
        "--num-frames",
        default="5,10,15,20,25,30",
        type=int_list,
        help="number of sensor frames, comma delimited for multiple runs",
    )
    parser.add_argument("--num-sensors", default=5, type=int)
    parser.add_argument("-n", "--num-epochs", default=50, type=int)
    parser.add_argument("--lr", default=0.1, type=float)
    parser.add_argument("--metrics-filename", default="", type=str)
    parser.add_argument("--plot-filename", default="", type=str)
    parser.add_argument("--force", action="store_true")
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: Switching Linear Dynamical System¶

import argparse

import torch

import funsor
import funsor.ops as ops
import funsor.torch.distributions as dist


def main(args):
    funsor.set_backend("torch")

    # Declare parameters.
    trans_probs = funsor.Tensor(
        torch.tensor([[0.9, 0.1], [0.1, 0.9]], requires_grad=True)
    )
    trans_noise = funsor.Tensor(
        torch.tensor(
            [0.1, 1.0],  # low noise component  # high noisy component
            requires_grad=True,
        )
    )
    emit_noise = funsor.Tensor(torch.tensor(0.5, requires_grad=True))
    params = [trans_probs.data, trans_noise.data, emit_noise.data]

    # A Gaussian HMM model.
    @funsor.interpretations.moment_matching
    def model(data):
        log_prob = funsor.Number(0.0)

        # s is the discrete latent state,
        # x is the continuous latent state,
        # y is the observed state.
        s_curr = funsor.Tensor(torch.tensor(0), dtype=2)
        x_curr = funsor.Tensor(torch.tensor(0.0))
        for t, y in enumerate(data):
            s_prev = s_curr
            x_prev = x_curr

            # A delayed sample statement.
            s_curr = funsor.Variable(f"s_{t}", funsor.Bint[2])
            log_prob += dist.Categorical(trans_probs[s_prev], value=s_curr)

            # A delayed sample statement.
            x_curr = funsor.Variable(f"x_{t}", funsor.Real)
            log_prob += dist.Normal(x_prev, trans_noise[s_curr], value=x_curr)

            # Marginalize out previous delayed sample statements.
            if t > 0:
                log_prob = log_prob.reduce(ops.logaddexp, {s_prev.name, x_prev.name})

            # An observe statement.
            log_prob += dist.Normal(x_curr, emit_noise, value=y)

        log_prob = log_prob.reduce(ops.logaddexp)
        return log_prob

    # Train model parameters.
    torch.manual_seed(0)
    data = torch.randn(args.time_steps)
    optim = torch.optim.Adam(params, lr=args.learning_rate)
    for step in range(args.train_steps):
        optim.zero_grad()
        log_prob = model(data)
        assert not log_prob.inputs, "free variables remain"
        loss = -log_prob.data
        loss.backward()
        optim.step()
        if args.verbose and step % 10 == 0:
            print(f"step {step} loss = {loss.item()}")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="Switching linear dynamical system")
    parser.add_argument("-t", "--time-steps", default=10, type=int)
    parser.add_argument("-n", "--train-steps", default=101, type=int)
    parser.add_argument("-lr", "--learning-rate", default=0.01, type=float)
    parser.add_argument("--filter", action="store_true")
    parser.add_argument("-v", "--verbose", action="store_true")
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: Talbot’s method for numerical inversion of the Laplace transform¶

import argparse
import math

import torch

import funsor
import funsor.ops as ops
from funsor.adam import Adam
from funsor.domains import Real
from funsor.factory import Bound, Fresh, Has, make_funsor
from funsor.interpretations import StatefulInterpretation
from funsor.tensor import Tensor
from funsor.terms import Funsor, Variable
from funsor.util import get_backend


@make_funsor
def InverseLaplace(
    F: Has[{"s"}], t: Funsor, s: Bound  # noqa: F821
) -> Fresh[lambda F: F]:
    """
    Inverse Laplace transform of function F(s).

    There is no closed-form solution for arbitrary F(s). However, we can
    resort to numerical approximations which we store in new interpretations.
    For example, see Talbot's method below.

    :param F: function of s.
    :param t: times at which to evaluate the inverse Laplace transformation of F.
    :param s: s Variable.
    """
    return None


class Talbot(StatefulInterpretation):
    """
    Talbot's method for numerical inversion of the Laplace transform.

    Reference
    Abate, Joseph, and Ward Whitt. "A Unified Framework for Numerically
    Inverting Laplace Transforms." INFORMS Journal of Computing, vol. 18.4
    (2006): 408-421. Print. (http://www.columbia.edu/~ww2040/allpapers.html)

    Implementation here is adapted from the MATLAB implementation of the algorithm by
    Tucker McClure (2021). Numerical Inverse Laplace Transform
    (https://www.mathworks.com/matlabcentral/fileexchange/39035-numerical-inverse-laplace-transform),
    MATLAB Central File Exchange. Retrieved April 4, 2021.

    :param num_steps: number of terms to sum for each t.
    """

    def __init__(self, num_steps):
        super().__init__("talbot")
        self.num_steps = num_steps


@Talbot.register(InverseLaplace, Funsor, Funsor, Variable)
def talbot(self, F, t, s):
    if get_backend() == "torch":
        import torch

        k = torch.arange(1, self.num_steps)
        delta = torch.zeros(self.num_steps, dtype=torch.complex64)
        delta[0] = 2 * self.num_steps / 5
        delta[1:] = (
            2 * math.pi / 5 * k * (1 / (math.pi / self.num_steps * k).tan() + 1j)
        )

        gamma = torch.zeros(self.num_steps, dtype=torch.complex64)
        gamma[0] = 0.5 * delta[0].exp()
        gamma[1:] = (
            1
            + 1j
            * math.pi
            / self.num_steps
            * k
            * (1 + 1 / (math.pi / self.num_steps * k).tan() ** 2)
            - 1j / (math.pi / self.num_steps * k).tan()
        ) * delta[1:].exp()

        delta = Tensor(delta)["num_steps"]
        gamma = Tensor(gamma)["num_steps"]
        ilt = 0.4 / t * (gamma * F(**{s.name: delta / t})).reduce(ops.add, "num_steps")

        return Tensor(ilt.data.real, ilt.inputs)
    else:
        raise NotImplementedError(f"Unsupported backend {get_backend()}")


def main(args):
    """
    Reference for the n-step sequential model used here:

    Aaron L. Lucius et al (2003).
    "General Methods for Analysis of Sequential ‘‘n-step’’ Kinetic Mechanisms:
    Application to Single Turnover Kinetics of Helicase-Catalyzed DNA Unwinding"
    https://www.sciencedirect.com/science/article/pii/S0006349503746487
    """

    funsor.set_backend("torch")

    # Problem definition.
    true_rate = 20
    true_nsteps = 4
    rate = Variable("rate", Real)
    nsteps = Variable("nsteps", Real)
    s = Variable("s", Real)
    time = Tensor(torch.arange(0.04, 1.04, 0.04))["timepoint"]
    noise = Tensor(torch.randn(time.inputs["timepoint"].size))["timepoint"] / 500
    data = (
        Tensor(1 - torch.igammac(torch.tensor(true_nsteps), true_rate * time.data))[
            "timepoint"
        ]
        + noise
    )
    F = rate**nsteps / (s * (rate + s) ** nsteps)
    # Inverse Laplace.
    pred = InverseLaplace(F, time, "s")

    # Loss function.
    loss = (pred - data).abs().reduce(ops.add, "timepoint")
    init_params = {
        "rate": Tensor(torch.tensor(5.0, requires_grad=True)),
        "nsteps": Tensor(torch.tensor(2.0, requires_grad=True)),
    }

    with Talbot(num_steps=args.talbot_num_steps):
        # Fit the data
        with Adam(
            args.num_steps,
            lr=args.learning_rate,
            log_every=args.log_every,
            params=init_params,
        ) as optim:
            loss.reduce(ops.min, {"rate", "nsteps"})
        # Fitted curve.
        fitted_curve = pred(rate=optim.param("rate"), nsteps=optim.param("nsteps"))

    print(f"Data\n{data}")
    print(f"Fit curve\n{fitted_curve}")
    print(f"True rate\n{true_rate}")
    print("Learned rate\n{}".format(optim.param("rate").item()))
    print(f"True number of steps\n{true_nsteps}")
    print("Learned number of steps\n{}".format(optim.param("nsteps").item()))


if __name__ == "__main__":
    parser = argparse.ArgumentParser(
        description="Numerical inversion of the Laplace transform using Talbot's method"
    )
    parser.add_argument("-N", "--talbot-num-steps", type=int, default=32)
    parser.add_argument("-n", "--num-steps", type=int, default=501)
    parser.add_argument("-lr", "--learning-rate", type=float, default=0.1)
    parser.add_argument("--log-every", type=int, default=20)
    args = parser.parse_args()
    main(args)

Note

Click here to download the full example code

Example: VAE MNIST¶

import argparse
import os
import typing
from collections import OrderedDict

import torch
import torch.utils.data
from torch import nn, optim
from torch.nn import functional as F
from torchvision import transforms
from torchvision.datasets import MNIST

import funsor
import funsor.ops as ops
import funsor.torch.distributions as dist
from funsor.domains import Bint, Reals

REPO_PATH = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
DATA_PATH = os.path.join(REPO_PATH, "data")


class Encoder(nn.Module):
    def __init__(self):
        super(Encoder, self).__init__()
        self.fc1 = nn.Linear(784, 400)
        self.fc21 = nn.Linear(400, 20)
        self.fc22 = nn.Linear(400, 20)

    def forward(self, image: Reals[28, 28]) -> typing.Tuple[Reals[20], Reals[20]]:
        image = image.reshape(image.shape[:-2] + (-1,))
        h1 = F.relu(self.fc1(image))
        loc = self.fc21(h1)
        scale = self.fc22(h1).exp()
        return loc, scale


class Decoder(nn.Module):
    def __init__(self):
        super(Decoder, self).__init__()
        self.fc3 = nn.Linear(20, 400)
        self.fc4 = nn.Linear(400, 784)

    def forward(self, z: Reals[20]) -> Reals[28, 28]:
        h3 = F.relu(self.fc3(z))
        out = torch.sigmoid(self.fc4(h3))
        return out.reshape(out.shape[:-1] + (28, 28))


def main(args):
    funsor.set_backend("torch")

    # XXX Temporary fix after https://github.com/pyro-ppl/pyro/pull/2701
    import pyro

    pyro.enable_validation(False)

    encoder = Encoder()
    decoder = Decoder()

    # These rely on type hints on the .forward() methods.
    encode = funsor.function(encoder)
    decode = funsor.function(decoder)

    @funsor.montecarlo.MonteCarlo()
    def loss_function(data, subsample_scale):
        # Lazily sample from the guide.
        loc, scale = encode(data)
        q = funsor.Independent(
            dist.Normal(loc["i"], scale["i"], value="z_i"), "z", "i", "z_i"
        )

        # Evaluate the model likelihood at the lazy value z.
        probs = decode("z")
        p = dist.Bernoulli(probs["x", "y"], value=data["x", "y"])
        p = p.reduce(ops.add, {"x", "y"})

        # Construct an elbo. This is where sampling happens.
        elbo = funsor.Integrate(q, p - q, "z")
        elbo = elbo.reduce(ops.add, "batch") * subsample_scale
        loss = -elbo
        return loss

    train_loader = torch.utils.data.DataLoader(
        MNIST(DATA_PATH, train=True, download=True, transform=transforms.ToTensor()),
        batch_size=args.batch_size,
        shuffle=True,
    )

    encoder.train()
    decoder.train()
    optimizer = optim.Adam(
        list(encoder.parameters()) + list(decoder.parameters()), lr=1e-3
    )
    for epoch in range(args.num_epochs):
        train_loss = 0
        for batch_idx, (data, _) in enumerate(train_loader):
            subsample_scale = float(len(train_loader.dataset) / len(data))
            data = data[:, 0, :, :]
            data = funsor.Tensor(data, OrderedDict(batch=Bint[len(data)]))

            optimizer.zero_grad()
            loss = loss_function(data, subsample_scale)
            assert isinstance(loss, funsor.Tensor), loss.pretty()
            loss.data.backward()
            train_loss += loss.item()
            optimizer.step()
            if batch_idx % 50 == 0:
                print(f"  loss = {loss.item()}")
                if batch_idx and args.smoke_test:
                    return
        print(f"epoch {epoch} train_loss = {train_loss}")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="VAE MNIST Example")
    parser.add_argument("-n", "--num-epochs", type=int, default=10)
    parser.add_argument("--batch-size", type=int, default=8)
    parser.add_argument("--smoke-test", action="store_true")
    args = parser.parse_args()
    main(args)