Lorenzo Contento
Lorenzo Contento
For some parameter values I get a segmentation fault while doing adjoint sensitivity analysis. The problematic point is line 2033 in the following snippet: https://github.com/LLNL/sundials/blob/0c83e0b3f954673b0cf1419cfde1ed4cb3ea1438/src/cvodes/cvodea.c#L2027-L2037 It seems that the index...
The method ``` ForwardDiff.jacobian(f!, y::AbstractArray, x::AbstractArray) ``` throws `UndefRefError` when `y` contains undefined references. For example, ``` using ForwardDiff f!(y, x) = copy!(y, x) x0 = BigFloat[1.0, 1.0] ForwardDiff.jacobian(f!, similar(x0),...
- [x] Added caching of the gradients so that the forward problem is only computed once. * Caching occurs in a wrapped Objective, so that the Theano operators are unmodified...
PyMC3 by default remaps bounded random variables to variables defined on the whole real line, "in order to sample models more efficiently". See, e.g., [https://docs.pymc.io/notebooks/api_quickstart.html#Automatic-transforms-of-bounded-RVs](https://docs.pymc.io/notebooks/api_quickstart.html#Automatic-transforms-of-bounded-RVs) [https://docs.pymc.io/api/bounds.html](https://docs.pymc.io/api/bounds.html) Thus, when the starting...
SymPy offers some simple floating-point optimizations, mainly `exp(1-x) -> expm1(x)` and `log(1+x) -> log1p(x)`. Using them by default should not break anything as far as I can see. Only downside...
The default behaviour when a boost mathematical function overflows or is evaluated outside its domain is to raise an exception. This leads to AMICI crashing ungracefully, which may result e.g....
I get a `SIGABRT` which is apparently due to OpenMP. ``` __pthread_kill 0x00007fff6eac833a pthread_kill 0x00007fff6eb84e60 abort 0x00007fff6ea4f808 __kmp_abort_process 0x0000000120d34440 __kmp_fatal 0x0000000120cf5d17 __kmp_register_library_startup() 0x0000000120cfd500 __kmp_do_serial_initialize() 0x0000000120cf6362 __kmp_get_global_thread_id_reg 0x0000000120cf6321 amici::AmiciApplication::runAmiciSimulations(amici::Solver const&, std::__1::vector...
AMICI uses SymPy for symbolic computation and mathematical formulas from SBML files are converted to strings and loaded with `sympy.sympify`. This function does not produce a faithful representation of the...
When truncating a `Geometric` distributions, `rand` will return different types depending on the bounds chosen. For example, values sampled from `truncated(Geometric(0.6); lower = 2)` are floats, while values sampled from...
~~I have a plot with many facets that I am not able to `paginate` using the `col` and `row` arguments.~~ `paginate(plt; row, col)` called on a plot that has no...