DifferentialEquation Op refactor (#3634)

* addition of test for equality checking of ODE Ops
(not yet implemented)

* WIP: refactoring the DifferentialEquation Op
+ full support for test_values
+ explicit input/output types
+ 2D return shape
+ optional return of sensitivities
+ gradient without helper Op

* fully replace DifferentialEquation Op with the refactored implementation

* align tests with refactored API
+ whitespace & condensed formatting
+ test for equality of identical Ops

* use tt.stack as suggested by DeprecationWarning

* always cast y0 and theta to floatX

* allow some tests to fail on float32
(due to downcast exception)

* don't use f-strings to maintain 3.5 support

* link ODE refactor PR

* renamed ODE notebooks
+ add notebooks to examples index

* use (custom) errors instead of asserts

* move ShapeError to exceptions.py

RELEASE-NOTES.md

@@ -4,7 +4,7 @@
 
 ### New features
 - Implemented robust u turn check in NUTS (similar to stan-dev/stan#2800). See PR [#3605]
-- Add capabilities to do inference on parameters in a differential equation with `DifferentialEquation`. See [#3590](https://github.com/pymc-devs/pymc3/pull/3590).
+- Add capabilities to do inference on parameters in a differential equation with `DifferentialEquation`. See [#3590](https://github.com/pymc-devs/pymc3/pull/3590) and [#3634](https://github.com/pymc-devs/pymc3/pull/3634).
 - Distinguish between `Data` and `Deterministic` variables when graphing models with graphviz. PR [#3491](https://github.com/pymc-devs/pymc3/pull/3491).
 - Sequential Monte Carlo - Approximate Bayesian Computation step method is now available. The implementation is in an experimental stage and will be further improved.
 - Added `Matern12` covariance function for Gaussian processes. This is the Matern kernel with nu=1/2.

docs/source/notebooks/ODE_parameter_estimation.ipynb → docs/source/notebooks/ODE_with_manual_gradients.ipynb

@@ -20,7 +20,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Bayesian inference in non-linear ODEs using PyMC3\n",
+    "# Lotka-Volterra with manual gradients\n",
     "\n",
     "by [Sanmitra Ghosh](https://www.mrc-bsu.cam.ac.uk/people/in-alphabetical-order/a-to-g/sanmitra-ghosh/)"
    ]

docs/source/notebooks/table_of_contents_examples.js

@@ -54,6 +54,7 @@ Gallery.contents = {
     "normalizing_flows_overview": "Variational Inference",
     "gaussian-mixture-model-advi": "Variational Inference",
     "GLM-hierarchical-advi-minibatch": "Variational Inference",
-    "ODE_parameter_estimation": "Inference in ODE models",
-    "ODE_API_parameter_estimation": "Inference in ODE models"
+    "ODE_with_manual_gradients": "Inference in ODE models",
+    "ODE_API_introduction": "Inference in ODE models",
+    "ODE_API_shapes_and_benchmarking": "Inference in ODE models"
 }

pymc3/exceptions.py

@@ -3,6 +3,7 @@
     "IncorrectArgumentsError",
     "TraceDirectoryError",
     "ImputationWarning",
+    "ShapeError"
 ]
 
 
@@ -24,3 +25,12 @@ class ImputationWarning(UserWarning):
     """Warning that there are missing values that will be imputed."""
 
     pass
+
+
+class ShapeError(Exception):
+    """Error that the shape of a variable is incorrect."""
+    def __init__(self, message, actual=None, expected=None):
+        if expected and actual:
+            super().__init__('{} (actual {} != expected {})'.format(message, actual, expected))
+        else:
+            super().__init__(message)

pymc3/ode/ode.py

@@ -1,8 +1,12 @@
+import logging
 import numpy as np
 import scipy
 import theano
 import theano.tensor as tt
-from ..ode.utils import augment_system, ODEGradop
+from ..ode.utils import augment_system
+from ..exceptions import ShapeError
+
+_log = logging.getLogger('pymc3')
 
 
 class DifferentialEquation(theano.Op):
@@ -17,16 +21,16 @@ class DifferentialEquation(theano.Op):
 
     func : callable
         Function specifying the differential equation
-    t0 : float
-        Time corresponding to the initial condition
     times : array
         Array of times at which to evaluate the solution of the differential equation.
     n_states : int
         Dimension of the differential equation.  For scalar differential equations, n_states=1.
         For vector valued differential equations, n_states = number of differential equations in the system.
-    n_odeparams : int
+    n_theta : int
         Number of parameters in the differential equation.
-
+    t0 : float
+        Time corresponding to the initial condition
+    
     .. code-block:: python
 
         def odefunc(y, t, p):
@@ -35,45 +39,49 @@ def odefunc(y, t, p):
        
         times = np.arange(0.5, 5, 0.5)
 
-        ode_model = DifferentialEquation(func=odefunc, t0=0, times=times, n_states=1, n_odeparams=1)
+        ode_model = DifferentialEquation(func=odefunc, times=times, n_states=1, n_theta=1, t0=0)
     """
-
-    __props__ = ("func", "t0", "times", "n_states", "n_odeparams")
-
-    def __init__(self, func, times, n_states, n_odeparams, t0=0):
+    _itypes = [
+        tt.TensorType(theano.config.floatX, (False,)),                  # y0 as 1D floatX vector
+        tt.TensorType(theano.config.floatX, (False,))                   # theta as 1D floatX vector
+    ]
+    _otypes = [
+        tt.TensorType(theano.config.floatX, (False, False)),            # model states as floatX of shape (T, S)
+        tt.TensorType(theano.config.floatX, (False, False, False)),     # sensitivities as floatX of shape (T, S, len(y0) + len(theta))
+    ]
+    __props__ = ("func", "times", "n_states", "n_theta", "t0")
+
+    def __init__(self, func, times, *, n_states, n_theta, t0=0):
         if not callable(func):
             raise ValueError("Argument func must be callable.")
         if n_states < 1:
             raise ValueError("Argument n_states must be at least 1.")
-        if n_odeparams <= 0:
-            raise ValueError("Argument n_odeparams must be positive.")
+        if n_theta <= 0:
+            raise ValueError("Argument n_theta must be positive.")
 
         # Public
         self.func = func
         self.t0 = t0
         self.times = tuple(times)
+        self.n_times = len(times)
         self.n_states = n_states
-        self.n_odeparams = n_odeparams
+        self.n_theta = n_theta
+        self.n_p = n_states + n_theta
 
         # Private
-        self._n = n_states
-        self._m = n_odeparams + n_states
-
         self._augmented_times = np.insert(times, 0, t0)
-        self._augmented_func = augment_system(func, self._n, self._m)
+        self._augmented_func = augment_system(func, self.n_states, self.n_p)
         self._sens_ic = self._make_sens_ic()
 
-        self._cached_y = None
-        self._cached_sens = None
-        self._cached_parameters = None
-
-        self._grad_op = ODEGradop(self._numpy_vsp)
-
+        # Cache symbolic sensitivities by the hash of inputs
+        self._apply_nodes = {}
+        self._output_sensitivities = {}
+
     def _make_sens_ic(self):
         """
         The sensitivity matrix will always have consistent form.
-        If the first n_odeparams entries of the parameters vector in the simulate call
-        correspond to ode paramaters, then the first n_odeparams columns in
+        If the first n_theta entries of the parameters vector in the simulate call
+        correspond to ode paramaters, then the first n_theta columns in
         the sensitivity matrix will be 0 
 
         If the last n_states entries of the paramters vector in the simulate call
@@ -83,7 +91,7 @@ def _make_sens_ic(self):
         """
 
         # Initialize the sensitivity matrix to be 0 everywhere
-        sens_matrix = np.zeros((self._n, self._m))
+        sens_matrix = np.zeros((self.n_states, self.n_p))
 
         # Slip in the identity matrix in the appropirate place
         sens_matrix[:, -self.n_states :] = np.eye(self.n_states)
@@ -95,89 +103,109 @@ def _make_sens_ic(self):
         return dydp
 
     def _system(self, Y, t, p):
-        """This is the function that will be passed to odeint. Solves both ODE and sensitivities
-
+        """This is the function that will be passed to odeint. Solves both ODE and sensitivities.
         """
-
-        dydt, ddt_dydp = self._augmented_func(Y[: self._n], t, p, Y[self._n :])
+        dydt, ddt_dydp = self._augmented_func(Y[:self.n_states], t, p, Y[self.n_states:])
         derivatives = np.concatenate([dydt, ddt_dydp])
         return derivatives
 
-    def _simulate(self, parameters):
-        # Initial condition comprised of state initial conditions and raveled
-        # sensitivity matrix
-        y0 = np.concatenate([parameters[self.n_odeparams :], self._sens_ic])
+    def _simulate(self, y0, theta):
+        # Initial condition comprised of state initial conditions and raveled sensitivity matrix
+        s0 = np.concatenate([y0, self._sens_ic])
 
         # perform the integration
         sol = scipy.integrate.odeint(
-            func=self._system, y0=y0, t=self._augmented_times, args=(parameters,)
+            func=self._system, y0=s0, t=self._augmented_times, args=(np.concatenate([theta, y0]),)
         )
         # The solution
-        y = sol[1:, : self.n_states]
+        y = sol[1:, :self.n_states]
 
         # The sensitivities, reshaped to be a sequence of matrices
-        sens = sol[1:, self.n_states :].reshape(len(self.times), self._n, self._m)
+        sens = sol[1:, self.n_states:].reshape(self.n_times, self.n_states, self.n_p)
 
         return y, sens
 
-    def _cached_simulate(self, parameters):
-        if np.array_equal(np.array(parameters), self._cached_parameters):
-
-            return self._cached_y, self._cached_sens
-
-        return self._simulate(np.array(parameters))
-
-    def _state(self, parameters):
-        y, sens = self._cached_simulate(np.array(parameters))
-        self._cached_y, self._cached_sens, self._cached_parameters = y, sens, parameters
-        return y.ravel()
-
-    def _numpy_vsp(self, parameters, g):
-        _, sens = self._cached_simulate(np.array(parameters))
-
-        # Each element of sens is an nxm sensitivity matrix
-        # There is one sensitivity matrix per time step, making sens a (len(times), n_states, len(parameter))
-        # dimensional array.  Reshaping the sens array in this way is like stacking each of the elements of sens on top
-        # of one another.
-        numpy_sens = sens.reshape((self.n_states * len(self.times), len(parameters)))
-        # The dot product here is equivalent to np.einsum('ijk,jk', sens, g)
-        # if sens was not reshaped and if g had the same shape as yobs
-        return numpy_sens.T.dot(g)
-
-    def make_node(self, odeparams, y0):
-        if len(odeparams) != self.n_odeparams:
-            raise ValueError(
-                "odeparams has too many or too few parameters.  Expected {a} parameter(s) but got {b}".format(
-                    a=self.n_odeparams, b=len(odeparams)
-                )
-            )
-        if len(y0) != self.n_states:
-            raise ValueError(
-                "y0 has too many or too few parameters.  Expected {a} parameter(s) but got {b}".format(
-                    a=self.n_states, b=len(y0)
-                )
+    def make_node(self, y0, theta):
+        inputs = (y0, theta)
+        _log.debug('make_node for inputs {}'.format(hash(inputs)))
+        states = self._otypes[0]()
+        sens = self._otypes[1]()
+
+        # store symbolic output in dictionary such that it can be accessed in the grad method
+        self._output_sensitivities[hash(inputs)] = sens
+        return theano.Apply(self, inputs, (states, sens))
+
+    def __call__(self, y0, theta, return_sens=False, **kwargs):
+        # convert inputs to tensors (and check their types)
+        y0 = tt.cast(tt.unbroadcast(tt.as_tensor_variable(y0), 0), theano.config.floatX)
+        theta = tt.cast(tt.unbroadcast(tt.as_tensor_variable(theta), 0), theano.config.floatX)
+        inputs = [y0, theta]
+        for i, (input, itype) in enumerate(zip(inputs, self._itypes)):
+            if not input.type == itype:
+                raise ValueError('Input {} of type {} does not have the expected type of {}'.format(i, input.type, itype))
+
+        # use default implementation to prepare symbolic outputs (via make_node)
+        states, sens = super(theano.Op, self).__call__(y0, theta, **kwargs)
+
+        if theano.config.compute_test_value != 'off':
+            # compute test values from input test values
+            test_states, test_sens = self._simulate(
+                y0=self._get_test_value(y0),
+                theta=self._get_test_value(theta)
             )
 
-        if np.ndim(odeparams) > 1:
-            odeparams = np.ravel(odeparams)
-        if np.ndim(y0) > 1:
-            y0 = np.ravel(y0)
-
-        odeparams = tt.as_tensor_variable(odeparams)
-        y0 = tt.as_tensor_variable(y0)
-        parameters = tt.concatenate([odeparams, y0])
-        return theano.Apply(self, [parameters], [parameters.type()])
+            # check types of simulation result
+            if not test_states.dtype == self._otypes[0].dtype:
+                raise TypeError('Simulated states have the wrong type')
+            if not test_sens.dtype == self._otypes[1].dtype:
+                raise TypeError('Simulated sensitivities have the wrong type')
+
+            # check shapes of simulation result
+            expected_states_shape = (self.n_times, self.n_states)
+            expected_sens_shape = (self.n_times, self.n_states, self.n_p)
+            if not test_states.shape == expected_states_shape:
+                raise ShapeError('Simulated states have the wrong shape.', test_states.shape, expected_states_shape)
+            if not test_sens.shape == expected_sens_shape:
+                raise ShapeError('Simulated sensitivities have the wrong shape.', test_sens.shape, expected_sens_shape)
+
+            # attach results as test values to the outputs
+            states.tag.test_value = test_states
+            sens.tag.test_value = test_sens
+
+        if return_sens:
+            return states, sens
+        return states
 
     def perform(self, node, inputs_storage, output_storage):
-        parameters = inputs_storage[0]
-        out = output_storage[0]
-        # get the numerical solution of ODE states
-        out[0] = self._state(parameters)
+        y0, theta = inputs_storage[0], inputs_storage[1]
+        # simulate states and sensitivities in one forward pass
+        output_storage[0][0], output_storage[1][0] = self._simulate(y0, theta)
 
-    def grad(self, inputs, output_grads):
-        x = inputs[0]
-        g = output_grads[0]
-        # pass the VSP when asked for gradient
-        grad_op_apply = self._grad_op(x, g)
+    def infer_shape(self, node, input_shapes):
+        s_y0, s_theta = input_shapes
+        output_shapes = [(self.n_times, self.n_states), (self.n_times, self.n_states, self.n_p)]
+        return output_shapes
 
-        return [grad_op_apply]
+    def grad(self, inputs, output_grads):
+        _log.debug('grad w.r.t. inputs {}'.format(hash(tuple(inputs))))
+
+        # fetch symbolic sensitivity output node from cache
+        ihash = hash(tuple(inputs))
+        if ihash in self._output_sensitivities:
+            sens = self._output_sensitivities[ihash]
+        else:
+            _log.debug('No cached sensitivities found!')
+            _, sens = self.__call__(*inputs, return_sens=True)
+        ograds = output_grads[0]
+
+        # for each parameter, multiply sensitivities with the output gradient and sum the result
+        # sens is (n_times, n_states, n_p)
+        # ograds is (n_times, n_states)
+        grads = [
+            tt.sum(sens[:,:,p] * ograds)
+            for p in range(self.n_p)
+        ]
+
+        # return separate gradient tensors for y0 and theta inputs
+        result = tt.stack(grads[:self.n_states]), tt.stack(grads[self.n_states:])
+        return result

pymc3/ode/utils.py

@@ -45,41 +45,26 @@ def augment_system(ode_func, n, m):
 
     dydp = dydp_vec.reshape((n, m))
 
-    # Stack the results of the ode_func
-    f_tensor = tt.stack(ode_func(t_y, t_t, t_p))
+    # Stack the results of the ode_func into a single tensor variable
+    yhat = ode_func(t_y, t_t, t_p)
+    if not isinstance(yhat, (list, tuple)):
+        yhat = (yhat,)
+    t_yhat = tt.stack(yhat, axis=0)
 
     # Now compute gradients
-    J = tt.jacobian(f_tensor, t_y)
+    J = tt.jacobian(t_yhat, t_y)
 
     Jdfdy = tt.dot(J, dydp)
 
-    grad_f = tt.jacobian(f_tensor, t_p)
+    grad_f = tt.jacobian(t_yhat, t_p)
 
     # This is the time derivative of dydp
     ddt_dydp = (Jdfdy + grad_f).flatten()
 
     system = theano.function(
         inputs=[t_y, t_t, t_p, dydp_vec],
-        outputs=[f_tensor, ddt_dydp],
+        outputs=[t_yhat, ddt_dydp],
         on_unused_input="ignore",
     )
 
     return system
-
-
-class ODEGradop(theano.Op):
-    def __init__(self, numpy_vsp):
-        self._numpy_vsp = numpy_vsp
-
-    def make_node(self, x, g):
-
-        x = theano.tensor.as_tensor_variable(x)
-        g = theano.tensor.as_tensor_variable(g)
-        node = theano.Apply(self, [x, g], [g.type()])
-        return node
-
-    def perform(self, node, inputs_storage, output_storage):
-        x = inputs_storage[0]
-        g = inputs_storage[1]
-        out = output_storage[0]
-        out[0] = self._numpy_vsp(x, g)  # get the numerical VSP