CDCgov / CDCgov/DynODE

Chaining `InferenceProcess` together

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Dominant language
Python
Stars
13
Forks
3
Avg merge
19h 43m
Merged PRs (30d)
1

Description

build away for the output of one InferenceProcess to inform the beginning of another.

two examples of where this may be used.

  1. chaining inference together into successive epochs (fitting one year of flu at a time for example)
  2. initialize an MCMC process using the learned parameters from a faster SVI fit.

Both of these problems require one process to flow into the next, in slightly different ways. 1. requires the loading of a previous fit's final compartments into the initial state of the next epoch. 2 requires moving the mass matrix from SVI into MCMC to speed up fitting.

This feels like two similar but slightly different problems that may be solved in a single interface, but this ticket may need to be split into two if we find the problems to be different enough from one another.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the InferenceProcess entry point and reading how an inference run exposes its final compartments, learned parameters, and mass matrix. Compare the successive-epoch and SVI-to-MCMC flows to determine whether one interface can support both or whether the issue should be split. Done means one process can provide the required state or mass matrix to the next process.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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