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refactoring to handle (very) degenerate beliefs #15

Merged
merged 76 commits into from
Mar 9, 2025
Merged

refactoring to handle (very) degenerate beliefs #15

merged 76 commits into from
Mar 9, 2025

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cecileane
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  • not complete: more work needed
  • used for a simulation study that did not have degenerate factors

bstkj and others added 30 commits May 18, 2024 16:43
@bstkj
generalized beliefs: start
ea8411f
@bstkj
generalized beliefs: marginalization + tests
c5052a6
@bstkj
integratebelief! for generalizedBelief
a460691
@bstkj
propagate_belief! for generalizedBelief
6551af2
@cecileane
adhere to code style blue; new abstract type
22089da
@cecileane
Belief → CanonicalBelief
e162701
@bstkj
Fix div!
39dad1b
@bstkj
Fix mult!
9405101
@bstkj
Use svd instead of qr in marg!
2c6e86d
@bstkj
Edits to extend!
6a51789
@bstkj
propagate_belief! between generalized and canonical beliefs
cc22e5a
@bstkj
refactor init_beliefs_allocate, init_beliefs_assignfactors start
97d4503
@bstkj
refactor init_beliefs_allocate, init_beliefs_assignfactors: cont
1bd5c6f
@bstkj
Merge remote-tracking branch 'origin' into degenerate_factor
e173f53
@bstkj
small edits
5fa404e
@bstkj
Small edits
fe3bddf
@bstkj
allocate mix of generalized and canonical beliefs
e055e8c
@bstkj
Note on marginalizing out variables with no data below
4573c89
@bstkj
assign mix of degen and non-degen factors: start
204f7c9
@bstkj
clique tree calibration w/ non-det and det factors
678d330
@bstkj
move degenerate.jl into beliefs.jl and beliefupdates.jl
faedb90
@bstkj
tidy up beliefupdates.jl
6a8be4f
@bstkj
update score.jl
5f56829
@bstkj
AbstractFactorBelief -> AbstractFactor
dc5d9da
@bstkj
proper test suite for generalized beliefs: start
1329008
@bstkj
Add network for generalized beliefs tests
ffb80ff
@bstkj
Adjust other tests: start
6556251
@bstkj
Adjust other tests: continue
2f0f7b3
@bstkj
Bug fix. All tests pass
62ed7ed
@bstkj
small edits
4888d7b
cecileane and others added 19 commits October 9, 2024 15:39
@cecileane
check for no missing intermediate node: start
9971bb5
@bstkj
Fix bug in extend, gen belief MvBM tests pass
3ba6cb2
@bstkj
use node2fixed in allocatebeliefs
5f0f06a
@bstkj
clean up allocatebeliefs
01d5be0
@bstkj
clean up beliefs, beliefupdates
f85124c
@cecileane
check for no missing intermediate node: cont
94eb1ee
@bstkj
Store Q, R params in same matrix
f8f6bc1
@bstkj
debug marginalize noninscope variables in factor: start
4954636
@cecileane
no missing intermediate node check: test started
1ab8509
@cecileane
no missing intermediate node check: done
d2fa8b9
@bstkj
marginalize noninscope variables in factor: add test
0a16f3c
@bstkj
LKJ trans for MvFullBM optimization
8358229
@bstkj
LKJ trans debug
b209234
@bstkj
log-cholesky param for variance-rate
7660634
@bstkj
Hack to adjust optimization stepsize
b97b165
@bstkj
reduce StaticArrays for homogeneousBM, beliefs
d2f242c
@bstkj
terminate calibration early: start
c9f6bf1
@bstkj
Handle non-positive variance exception in optimize
dccbae9
@bstkj
adjust calibration threshold
bf4fba5
@cecileane cecileane requested a review from bstkj March 5, 2025 14:57
@codecov Codecov
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codecov bot commented Mar 6, 2025 •
edited
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Codecov Report

Attention: Patch coverage is 91.17647% with 60 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
src/beliefs.jl 89.79% 20 Missing ⚠️
src/calibration.jl 63.46% 19 Missing ⚠️
src/score.jl 33.33% 14 Missing ⚠️
src/beliefupdates.jl 97.99% 6 Missing ⚠️
src/utils.jl 96.29% 1 Missing ⚠️
Files with missing lines Coverage Δ
src/clustergraphbeliefs.jl 87.78% <100.00%> (ø)
src/evomodels/evomodels.jl 68.91% <100.00%> (ø)
src/evomodels/homogeneousbrownianmotion.jl 96.77% <100.00%> (+1.81%) ⬆️
src/utils.jl 97.67% <96.29%> (-0.64%) ⬇️
src/beliefupdates.jl 96.85% <97.99%> (+4.00%) ⬆️
src/score.jl 74.13% <33.33%> (-15.45%) ⬇️
src/calibration.jl 90.20% <63.46%> (-7.45%) ⬇️
src/beliefs.jl 92.28% <89.79%> (+3.31%) ⬆️

... and 2 files with indirect coverage changes

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@bstkj bstkj merged commit f801d07 into main Mar 9, 2025
4 of 6 checks passed
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@bstkj bstkj bstkj approved these changes

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@cecileane @bstkj