Hi everyone,
I’m trying to get the SunODE package to work with PyMC3.
I’m currently following the Lotka Volterra example given here: Quickstart with PyMC3 — sunode documentation.
However, at the following part, when assigning random parameters to tensor objects, I’m getting a NotImplementedError by Theano/Aesara.
Does anyone know how I could best deal with this?
I’m running Python 3.9.1 on Mac OS Big Sur, with PyMC3 3.8 , SunODE version 0.2, Aesara version 2.0.10, and Theano-PyMC version 1.1.2. I believe I don’t have Theano installed.
with model:
from sunode.wrappers.as_theano import solve_ivp
solution, *_ = solve_ivp(
y0=y0,
params=params,
rhs=lotka_volterra,
# The time points where we want to access the solution
tvals=times,
t0=times[0],
)
For reference, here’s the complete error.
NotImplementedError Traceback (most recent call last)
<ipython-input-48-cb2e836fc4d6> in <module>
1 with model:
2 from sunode.wrappers.as_theano import solve_ivp
----> 3 solution, *_ = solve_ivp(
4 y0=y0,
5 params=params,
~/opt/miniconda3/lib/python3.9/site-packages/sunode/wrappers/as_theano.py in solve_ivp(t0, y0, params, tvals, rhs, derivatives, coords, make_solver, derivative_subset, solver_kwargs, simplify)
81
82 y0_dims = read_dict(y0)
---> 83 params_dims = read_dict(params)
84
85 if derivative_subset is None:
~/opt/miniconda3/lib/python3.9/site-packages/sunode/wrappers/as_theano.py in read_dict(vals, name)
53 def read_dict(vals, name=None):
54 if isinstance(vals, dict):
---> 55 return {name: read_dict(item, name) for name, item in vals.items()}
56 else:
57 if isinstance(vals, tuple):
~/opt/miniconda3/lib/python3.9/site-packages/sunode/wrappers/as_theano.py in <dictcomp>(.0)
53 def read_dict(vals, name=None):
54 if isinstance(vals, dict):
---> 55 return {name: read_dict(item, name) for name, item in vals.items()}
56 else:
57 if isinstance(vals, tuple):
~/opt/miniconda3/lib/python3.9/site-packages/sunode/wrappers/as_theano.py in read_dict(vals, name)
66 if isinstance(dim_names, (str, int)):
67 dim_names = (dim_names,)
---> 68 tensor = aet.as_tensor_variable(tensor)
69 if tensor.ndim != len(dim_names):
70 raise ValueError(
~/opt/miniconda3/lib/python3.9/site-packages/aesara/tensor/__init__.py in as_tensor_variable(x, name, ndim, **kwargs)
39
40 """
---> 41 return _as_tensor_variable(x, name, ndim, **kwargs)
42
43
~/opt/miniconda3/lib/python3.9/functools.py in wrapper(*args, **kw)
875 '1 positional argument')
876
--> 877 return dispatch(args[0].__class__)(*args, **kw)
878
879 funcname = getattr(func, '__name__', 'singledispatch function')
~/opt/miniconda3/lib/python3.9/site-packages/aesara/tensor/__init__.py in _as_tensor_variable(x, name, ndim, **kwargs)
46 x, name: Optional[str], ndim: Optional[int], **kwargs
47 ) -> NoReturn:
---> 48 raise NotImplementedError(f"Cannot convert {x} to a tensor variable.")
49
50
NotImplementedError: Cannot convert alpha ~ Normal to a tensor variable.
with model:
# We can access the individual variables of the solution using the
# variable names.
pm.Deterministic('hares_mu', solution['hares'])
pm.Deterministic('lynxes_mu', solution['lynxes'])
sd = pm.HalfNormal('sd')
pm.Lognormal('hares', mu=solution['hares'], sd=sd, observed=hare_data)
pm.Lognormal('lynxes', mu=solution['lynxes'], sd=sd, observed=lynx
PyMC3 3.8 is too old to begin with. Try the current version 3.11.2