autograd_extended.py

"""
From Appendix B in the paper
Implementation of autograd
"""

import scipy.integrate

import autograd.numpy as np
from autograd.extend import primitive, defvjp_argnums
from autograd import make_vjp
from autograd.misc import flatten
from autograd.builtins import tuple

odeint = primitive(scipy.integrate.odeint)


def grad_odeint_all(yt, func, y0, t, func_args, **kwargs):
	"""
	Extended from "Scalable Inference of Ordinary Differential"
	Equation Models of Biochemical Processes". Sec. 2.4.2
	Fabian Froehlich, Carolin Loos, Jan Hasenauer, 2017
	https://arxiv.org/pdf/1711.08079.pdf
	"""

	T, D = np.shape(yt)
	flat_args, unflatten = flatten(func_args)

	def flat_func(y, t, flat_args):
		return func(y, t, *unflatten(flat_args))


	def unpack(x):
		#	   y, 		vjp_y,		vjp_t, 		vjp_args
		return x[0:D],	x[D:2 * D],	x[2 * D],	x[2 * D + 1:]


	def augmented_dynamics(augmented_state, t, flat_args):
		# Original system augemented with vjp_y, vjp_t and vjp_args
		y, vjp_y, _, _ = unpack(augmented_state)
		vjp_all, dy_dt = make_vjp(flat_func, argnum=(0, 1, 2))(y, t, flat_args)
		vjp_y, vjp_t, vjp_args = vjp_all(-vjp_y)
		return np.hstack((dy_dt, vjp_y, vjp_t, vjp_args))


	def vjp_all(g, **kwargs):
		vjp_y = g[-1, :]
		vjp_t0 = 0
		time_vjp_list = []
		vjp_args = np.zeros(np.size(flat_args))

		for i in range(T - 1, 0, -1):
			# Compute effect of moving current time.
			vjp_cur_t = np.dot(func(yt[i, :], t[i], *func_args), g[i, :])
			time_vjp_list.append(vjp_cur_t)
			vjp_t0 = vjp_t0 - vjp_cur_t

			# Run augmented system backwards to the previous observation
			aug_y0 = np.hstack((yt[i, :], vjp_y, vjp_t0, vjp_args))
			aug_ans = odeint(augmented_dynamics, aug_y0,
							 np.array(t[i], t[i - 1]), tuple((flat_args,)), **kwargs)
			_, vjp_y, vjp_t0, vjp_args = unpack(aug_ans[1])

			# Add gradient from current output
			vjp_y = vjp_y + g[i - 1, :]

		time_vjp_list.append(vjp_t0)
		vjp_times = np.hstack(time_vjp_list)[::-1]

		return None, vjp_y, vjp_times, unflatten(vjp_args)

	return vjp_all


def grad_argnums_wrapper(all_vjp_builder):
	"""
	A generic autograd helper funciton. Takes a function that
	builds vjps for all arguments, and wraps it to return only required vjps.
	"""
	def build_selected_vjps(argnums, ans, combined_args, kwargs):
		vjp_func = all_vjp_builder(ans, *combined_args, **kwargs)

		def chosen_vjps(g):
			# Return whichever vjps were asked for
			all_vjps = vjp_func(g)
			return [all_vjps[argnum] for argnum in argnums]

		return chosen_vjps

	return build_selected_vjps


if __name__ == '__main__':
print(defvjp_argnums(odeint, grad_argnums_wrapper(grad_odeint_all)))