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SurvSHAP(t) calculation using {treeshap} and fixes for SurvLIME #87

Merged
merged 58 commits into from
Oct 24, 2023
Merged

SurvSHAP(t) calculation using {treeshap} and fixes for SurvLIME #87

merged 58 commits into from
Oct 24, 2023

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krzyzinskim
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  • added new calculation_method for surv_shap() called "treeshap" that use treeshap package (#75)
  • enable to calculate SurvSHAP(t) explanations based on subsample of explainer's data
  • changed default kernel width in SurvLIME from sqrt(p * 0.75) to sqrt(p) * 0.75
  • fixed error in SurvLIME when non-factor categorical_variables were provided

kapsner and others added 30 commits April 4, 2023 17:26
@kapsner
feat: adding support for treeshap calculation of survshap for ranger …
a796a99 
…algorithm
@kapsner
fix: added contraint that new-observation for predict surv_shap has e…
d500fd6 
…xactly one row

due to indexing of y_true to first element and if not using y_true the function produces strange results
@kapsner
chore: updated description
44f56db
@kapsner
chore: merged multirow-support into main
bb47009
@kapsner
chore: comment for clarifying implementation of treeshap
b25c468
@kapsner
chore: moved treeshap and kernelshap to suggests and added respective…
dc7d33c 
… error handling
@kapsner
fix: fixed issues when providing matrix to kernelshap
b8135ee
@kapsner
chore: merged feat-global-survshap into feat-treeshap
de65c4b
@kapsner
feat: fully functional treeshap integration
ad886bb 
including support for global survshap values and unit-tests
@kapsner
feat: code adaptions to treeshap computation using pre-difned surviva…
d2c16a6 
…l times from explain-object

addresses #75
@kapsner
refactor: implemented quality checks and now explicitly control row o…
1329254 
…rder for kernelshap and treeshap
@kapsner
chore: rounding time-points for row names to a maximum of 2 digits
60e3b91
@kapsner
chore: more informative error messages in stopifnot statements
5b1a810
@kapsner
chore: merge into main
f88f794
@kapsner
chore: merged latest global-survshap devs into feat-branch
6cfe2fb
@kapsner
feat: adaptions of treeshap feature branch to new global survshap
6a4c926 
- removed data.table parts
- updated error handling
- added unit tests for treeshap (both, local and global shap)

addresses #75
@kapsner
chore: merged dev-global-survshap into treeshap feature branch
bf5222d
@kapsner
chore: merged upstream changes into kapsner-fork
b08f4d5
@kapsner
chore: merged latest upstream changes into treeshap branch
c251f3b
@kapsner
chore: updated description, namespace and typos
15c689c
@kapsner
chore: updated messages
a9269f0
@kapsner
fix: added missing output_type arguments to switch of calculation met…
0e8c85c 
…hod in surv_shap

which caused error of github action unittests when using 'exact_kernel'
@kapsner
fix: new_observation now as.matrix for kernelshap
40a076e
@kapsner
fix: removed data.frame conversion of explainer in kernelshap
a496a67
@kapsner
fix: another try to fix kernelshap data, now X and bg_X as data.frame
23e57da
@kapsner
Merge branch 'ModelOriented:main' into main
ec6d20e
@kapsner
Merge pull request #2 from kapsner/main
5013883 
update dev branch
@kapsner
Merge branch 'ModelOriented:main' into main
2661ef8
@kapsner
Merge pull request #3 from kapsner/main
160053d 
update upstream commits
@kapsner
Merge pull request #4 from ModelOriented/main
5481675 
collect and update upstream enhancements
@krzyzinskim
Update surv_shap.R description
f61aad5
@krzyzinskim
remove treeshap from Remotes
a3a8311
@krzyzinskim
Update surv_shap.R
885a27b
@krzyzinskim
Update test-predict_parts.R
1d275eb
@krzyzinskim
Merge pull request #85 from kapsner/feat-treeshap
0b2f4f5 
Feature: support SurvSHAP computation with {treeshap}
@krzyzinskim
fix sorting for selection of top variables
1dab770
@krzyzinskim
fix survlime with additional categorical variables
285a1be
@krzyzinskim
bump version number
457aaad
@krzyzinskim
fix kernel width
8617516
@krzyzinskim
fix limiting number of observations
aabb96e
@krzyzinskim
fix documentation
03f8319
@krzyzinskim
Merge branch 'treeshap' into fixes
cca9530
@krzyzinskim
Merge pull request #86 from ModelOriented/fixes
0f6bf31 
hot fixes for predict parts functions
@krzyzinskim
fixes for number of observations in model survshap
313d346
@krzyzinskim
fix kernelshap background data
eb6f82d
@krzyzinskim
enable to pass additional parameters to treeshap function
e43f614
@krzyzinskim
fix swarm plot order
0b123bd
@krzyzinskim
fix documentation for curves plot
b1c1051
@krzyzinskim
fix subtitle spacing
19365d1
@krzyzinskim
update survshap for new version of treeshap
9fbc227
@krzyzinskim
add news
63a7509
@mikolajsp mikolajsp merged commit 371fda2 into main Oct 24, 2023
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@mikolajsp mikolajsp deleted the treeshap branch October 24, 2023 19:06
@mikolajsp mikolajsp mentioned this pull request Oct 24, 2023
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3 participants
@krzyzinskim @mikolajsp @kapsner