ValueError: Numerical integration does not play well with the chosen bin functionals, choose new ones.
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Hi LoganThanks for reporting this, I've cc'ed Max Dylla and Saurabh Bajaj who implemented that descriptor.Or let me know if you just want to submit a pull request for the patch and I will merge it in. That way the patch can be properly attributed to your Github account.Best,Anubhav
On Thu, Jun 21, 2018 at 12:58 PM <ldwi...@umich.edu> wrote:
Hello,I ran into a bug while testing the GRDF in the mat miner.featurizers.site module. The GeneralizedRadialDistributionFunction.from_preset defines bins using lambda functions in a loop, but they all take the final value instead of being defined with the value of the variable at each step of the loop. The lambda functions need to define a local variable instead of taking the variable from the outer scope to have the proper behavior.This line of code: lambda d: np.exp(-width * (d - center)**2.)))should be like this: lambda d, center=center: np.exp(-width * (d - center)**2.)))and similarly for the lambda in the histogram preset.However, with this bug fix, the default values for the preset (cutoff=10.0; width=0.5; spacing=0.5) produce the following error for Gaussian functions:ValueError: Numerical integration does not play well with the chosen bin functionals, choose new ones.
Broader bin values of (cutoff=10.0; width=1.0; spacing=1.0) will run for both Gaussian and Histogram preset functions.The Histogram preset does sometimes produce values of "inf" for some bins though, and I have not explored the cause of this behavior.Best,Logan Williams
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I will defer this to Max Dylla who I think implemented the latest version of this descriptor(?)Saurabh
On Thu, Jun 21, 2018 at 4:24 PM, Anubhav Jain <AJ...@lbl.gov> wrote:
Hi LoganThanks for reporting this, I've cc'ed Max Dylla and Saurabh Bajaj who implemented that descriptor.Or let me know if you just want to submit a pull request for the patch and I will merge it in. That way the patch can be properly attributed to your Github account.Best,Anubhav
On Thu, Jun 21, 2018 at 12:58 PM <ldwi...@umich.edu> wrote:
Hello,I ran into a bug while testing the GRDF in the mat miner.featurizers.site module. The GeneralizedRadialDistributionFunction.from_preset defines bins using lambda functions in a loop, but they all take the final value instead of being defined with the value of the variable at each step of the loop. The lambda functions need to define a local variable instead of taking the variable from the outer scope to have the proper behavior.This line of code: lambda d: np.exp(-width * (d - center)**2.)))should be like this: lambda d, center=center: np.exp(-width * (d - center)**2.)))and similarly for the lambda in the histogram preset.However, with this bug fix, the default values for the preset (cutoff=10.0; width=0.5; spacing=0.5) produce the following error for Gaussian functions:ValueError: Numerical integration does not play well with the chosen bin functionals, choose new ones.
Broader bin values of (cutoff=10.0; width=1.0; spacing=1.0) will run for both Gaussian and Histogram preset functions.The Histogram preset does sometimes produce values of "inf" for some bins though, and I have not explored the cause of this behavior.Best,Logan Williams
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Anubhav
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I could see a few steps forward around this issue with the bins and step functions:
Personally, I’d pick with option #2. Adding defaults could lead to additional stability and performance by avoiding numerical integration, allow for easier pickling / multiprocessing by avoiding lambda functions, and still preserve the original functionality. Many classes in scikit-learn (e.g., GridSearchCV) allows users to pass either strings for hard-coded options or a callable to do something advanced, and I think that could also work well here.
Logan
Max
Saurabh Bajaj
Data Engineer | Citrine Informatics
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Best,
Anubhav
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