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Use systematic resampling in SMCFilter #2488

Merged
merged 4 commits into from
May 18, 2020
Merged

Use systematic resampling in SMCFilter #2488

merged 4 commits into from
May 18, 2020

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fritzo
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@fritzo fritzo commented May 16, 2020 •
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Addresses #2426

This PR

  1. switches from multinomial resampling to systematic resampling (i.e. quasi-random sampling) in the SMCFilter, increasing sample diversity.
  2. switches from ValueError to a new exception SMCFailed and uses retry logic in CompartmentalModel in case of failure.

Tested

  • added a unit test for _systematic_sample()
  • behavior change is covered by existing tests
  • ensured retry logic works on a hard test case

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fritzo commented May 18, 2020

Thanks for reviewing!

@martinjankowiak martinjankowiak merged commit 28dde74 into dev May 18, 2020
@fritzo fritzo deleted the smc-systematic-resample branch June 5, 2020 15:31
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@martinjankowiak martinjankowiak martinjankowiak approved these changes

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