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parameter-estimation
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Currently, values for the llh, gradient, the computed trajectories of states and observables, or the sensitivities are checked in unit tests.
Unfortunately, some bugs, such as incorrect Jacobians or switched minus signs in the Newton solver, will not necessarily affect those quantities. However, they will substantially impact solver performance, by causing way too many steps to be taken. Hence, w
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Matplotlib offers various ways of defining colors, in particular via the standard colors cycle ('C0-10'), as hex or as a RBGA tuple https://matplotlib.org/3.1.1/tutorials/colors/colors.html. If I see it correctly, the pypesto visualization routines currently only allow RGBA values. It would be preferable to allow for any color input. This should be rather easily possible by rewriting how passed co
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Use the tempfile....File context managers with delete=True, and yield results in between if necessary.
Build doc during CI
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https://journals.plos.org/ploscompbiol/article?rev=1&id=10.1371/journal.pcbi.1006944
Complexity estimate: medium
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E.g.
(Note both the links are for stochastic gradient descent, but we'd be implementing a simpler, non-stochastic one)
Won't be brilliant, but can be very informa