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New interpolation schemes, modified filtering, and added tests #79

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merged 44 commits into from
Dec 5, 2023
Merged

New interpolation schemes, modified filtering, and added tests #79

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f893638
Attempting to replicate PE with a simplified version, preparing for a…
orebas Jul 30, 2023
a1bc43c
started SPE, trying optimization method first.
orebas Jul 31, 2023
f2a8a01
added some examples to delete later
orebas Aug 3, 2023
2063723
last changes before back to main
orebas Aug 4, 2023
5087349
First draft of replacing interpolation with AAA interpolation.
orebas Aug 4, 2023
aa7d670
Just added one super simple example
orebas Aug 7, 2023
6aeeecf
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.jl
orebas Aug 7, 2023
240664b
First cut which uses AAA and FH interpolation and a reduced interpola…
orebas Aug 21, 2023
f2b2058
added all models file in benchmarks folder.
orebas Sep 15, 2023
8a38a0a
added results.txt, had to force because normally ignored.
orebas Sep 15, 2023
0ad3727
added result.txt renamed
orebas Sep 15, 2023
8d8eea4
amended result.read
orebas Sep 15, 2023
5dea4dc
starting to fix IC time
orebas Sep 28, 2023
4af24da
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.…
orebas Oct 2, 2023
1c3f513
small modifications
orebas Oct 3, 2023
0f7267a
Merge pull request #2 from orebas/orebas/SPE
orebas Oct 4, 2023
43263d4
starting to add backsolving.
orebas Oct 4, 2023
8027ab4
syncing with laptop
orebas Oct 4, 2023
569adbf
first test of backsolving
orebas Oct 6, 2023
08339ca
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.jl
orebas Oct 6, 2023
8e24b16
first run of backwards.
orebas Oct 6, 2023
326b4e0
added precompilation workflows.
orebas Oct 19, 2023
2c3abb0
model file change
orebas Oct 19, 2023
2b1190d
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.jl
orebas Oct 19, 2023
383d8ae
tried to speed up using statement
orebas Oct 23, 2023
adede29
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.jl
orebas Oct 23, 2023
bbdab14
added some debug statements, remove them later
orebas Oct 26, 2023
c833359
removed almost all filtering. Will reintroduce filtering at a later …
orebas Nov 5, 2023
497465d
fixed small bug.
orebas Nov 5, 2023
714be8d
changed tolerances everywhere to 1e-12. Removed some stray files.
orebas Nov 7, 2023
eea2b8a
added parameter and ic_constraints
orebas Nov 7, 2023
fc24e37
Merge branch 'main' of https://github.com/iliailmer/ParameterEstimati…
orebas Nov 7, 2023
b9c1196
added support for bigfloat and arbfloat and other numerics.
orebas Nov 9, 2023
d56fa31
fixed error calculation. sorted results by error. added "where t=...…
orebas Nov 19, 2023
5e57f75
Fixed error output. testing new filtering.
orebas Nov 19, 2023
bad094c
removed some bad examples
orebas Nov 20, 2023
511c931
removed some more junk files
orebas Nov 20, 2023
40280ed
removed a few more junk files
orebas Nov 20, 2023
bd6d7b0
wokring on testing framework.
orebas Dec 4, 2023
eba0c45
fixed old tests, ahead of adding new tests
orebas Dec 4, 2023
8453671
added a number of tests (parameter recovery for more serious systems,…
orebas Dec 5, 2023
a0cf213
Merge branch 'main' into main
orebas Dec 5, 2023
ac52e55
changed updated version and some compat versions.
orebas Dec 5, 2023
d3edb6c
Merge branch 'main' of https://github.com/orebas/ParameterEstimation.jl
orebas Dec 5, 2023
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4 changes: 2 additions & 2 deletions .gitignore
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Expand Up @@ -31,8 +31,8 @@ Manifest.toml
*.code-workspace
.vscode
benchmarks/matlab*/src
*.txt
!benchmarks/matlab*/iqm/*/*/*/*.txt
#*.txt
#!benchmarks/matlab*/iqm/*/*/*/*.txt
timecommand
objf*.m
sharable
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4 changes: 4 additions & 0 deletions ParamterEstimation/Project.toml
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@@ -0,0 +1,4 @@
[deps]
BaryRational = "91aaffc3-5777-4842-85b7-5d3d5d6a3494"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
25 changes: 14 additions & 11 deletions Project.toml
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@@ -1,11 +1,13 @@
name = "ParameterEstimation"
uuid = "b4cd1eb8-1e24-11e8-3319-93036a3eb9f3"
authors = ["Soo Go <[email protected]>", "Hoon Hong <[email protected]>", "Ilia Ilmer <[email protected]>", "Alexey Ovchinnikov <[email protected]>", "Pedro Soto <[email protected]>", "Chee Yap <[email protected]>"]
version = "0.2.1"
authors = ["Oren Bassik <[email protected]>", "Soo Go <[email protected]>", "Hoon Hong <[email protected]>", "Ilia Ilmer <[email protected]>", "Alexey Ovchinnikov <[email protected]>", "Pedro Soto <[email protected]>", "Chee Yap <[email protected]>"]
version = "0.3.0"

[deps]
BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
ArbNumerics = "7e558dbc-694d-5a72-987c-6f4ebed21442"
BaryRational = "91aaffc3-5777-4842-85b7-5d3d5d6a3494"
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Groebner = "0b43b601-686d-58a3-8a1c-6623616c7cd4"
HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Expand All @@ -14,28 +16,29 @@ Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
Oscar = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
SIAN = "cf7bdac0-b945-4905-b5ad-bc3f1a757483"
StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
Suppressor = "fd094767-a336-5f1f-9728-57cf17d0bbfb"
Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
TaylorDiff = "b36ab563-344f-407b-a36a-4f200bebf99c"
TaylorSeries = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
TestSetExtensions = "98d24dd4-01ad-11ea-1b02-c9a08f80db04"

[compat]
BenchmarkTools = "1"
DifferentialEquations = "7"
Groebner = "0.2, 0.3, 0.4, 0.5"
Groebner = "0.2, 0.3, 0.4 - 0.5"
HomotopyContinuation = "2"
LinearSolve = "1, 2"
LinearSolve = "2"
ModelingToolkit = "8"
OrderedCollections = "1"
Oscar = "0.10, 0.11, 0.12, 0.13"
Oscar = "0.10 - 0.20"
ProgressMeter = "1"
SIAN = "1.4.1"
StructuralIdentifiability = "0.4.9, 0.5"
SIAN = "1 - 1.5.10"
StructuralIdentifiability = "0.4.9 - 0.5.30"
Symbolics = "4, 5"
TaylorSeries = "0.12, 0.13, 0.14, 0.15"
TaylorSeries = "0.12 - 0.30"
TestSetExtensions = "2"
julia = "1"
8 changes: 5 additions & 3 deletions README.md
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Expand Up @@ -17,17 +17,19 @@ Currently is installable via
```julia

using Pkg
Pkg.add("ParameterEstimation.jl")
Pkg.add(url="https://github.com/orebas/ParameterEstimation.jl")
```

or
The production version of this fork is installable via

```julia

using Pkg
Pkg.add(url="https://github.com/iliailmer/ParameterEstimation.jl")
Pkg.add("ParameterEstimation.jl")
```



## Toy Example

```julia
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