Bias correction#79
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micahwoodard wants to merge 9 commits into
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May 3, 2026
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From the schema point of view, it looks good. I did not check the business logic, as I am not familiar with the algorithm.
| readme = {file = "README.md", content-type = "text/markdown"} | ||
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| dependencies = [ | ||
| "aind-dynamic-foraging-models>=0.13.1", |
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https://github.com/AllenNeuralDynamics/aind-dynamic-foraging-models
Package made by Han, Alex, Xinxin and contains the bias calculation.
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I would be somewhat careful with bringing in that as a core dependency. If you must, go ahead, but there are quite a number of additional transitive dependencies you would be adding:
'numpy',
'matplotlib',
'scikit-learn',
'scipy',
'pydantic',
I will leave it up to you!
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yeah maybe it would be better to reimplement. I started and then figured I didn't want to duplicate code multiple places
…/block_based_trial_generator.py Co-authored-by: Bruno Cruz <7049351+bruno-f-cruz@users.noreply.github.com>
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Adds bias correction to block based trial generator. Algorithm explained in #78. I wrote it so bias overrides autowater but need to follow up w/ scis to make sure this is the desired outcome.
I'm calculating bias synchronously in the next function, but fit_logistic_regression from aind_dynamic_foraging_models may take longer than the iti period. Need to benchmark