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3df3fe4
PathBench alpha 0.1
Jul 31, 2024
fecb76f
Added logo
Sbrussee Jul 31, 2024
83b22cb
Update README.md
Sbrussee Jul 31, 2024
74018c6
Update README.md
Sbrussee Jul 31, 2024
c48419b
Update README.md
Sbrussee Jul 31, 2024
27bd578
Update README.md
Sbrussee Jul 31, 2024
373b0d9
Update README.md
Sbrussee Jul 31, 2024
d09d396
Update README.md
Sbrussee Jul 31, 2024
97cee95
Update README.md
Sbrussee Jul 31, 2024
8c389a2
Update README.md
Sbrussee Jul 31, 2024
1ed4a81
Update README.md
Sbrussee Jul 31, 2024
cfa1e02
Update README.md
Sbrussee Jul 31, 2024
fb2eec4
Update README.md
Sbrussee Jul 31, 2024
fdb2a04
rem keys
Jul 31, 2024
e8bf45d
test
Jul 31, 2024
5ab5e7a
Update README.md
Sbrussee Jul 31, 2024
38f3c65
Update README.md
Sbrussee Jul 31, 2024
537bdce
Update README.md
Sbrussee Jul 31, 2024
63d937c
Update README.md
Sbrussee Jul 31, 2024
f5cf2d8
Update README.md
Sbrussee Jul 31, 2024
58a16df
Update LICENSE
Sbrussee Aug 1, 2024
8fa31ae
Moved functions to appropriate locations
Aug 1, 2024
9ee98b5
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 1, 2024
3f05432
added dynamic weight directory
Aug 1, 2024
72d43f8
Update README.md
Sbrussee Aug 1, 2024
47ba76e
Update README.md
Sbrussee Aug 1, 2024
f4fa219
added setup, tests
Aug 6, 2024
780121c
merge
Aug 6, 2024
6e4b65f
removed unnessary files
Aug 6, 2024
9e08272
fixed tests
Aug 6, 2024
9c87e5d
updated requirements
Aug 6, 2024
d735d6c
fixed setup
Aug 6, 2024
134a50b
added cython to pre-setup
Aug 6, 2024
4caee2a
now sources environment
Aug 6, 2024
9ff8cd2
test
Aug 6, 2024
424b096
test
Aug 6, 2024
fbc1dba
set version for ruamel.yaml
Aug 6, 2024
c6896c3
now added pip upgrade
Aug 6, 2024
458bcfc
removed ruamel
Aug 6, 2024
74f0003
readded ruamel
Aug 6, 2024
00d825c
test
Aug 6, 2024
518f99f
fixed requirements
Aug 6, 2024
3fe230a
no specific ruamel ersion
Aug 6, 2024
15f6864
making sure numpy is installed first
Aug 6, 2024
456e83d
specific numpy version
Aug 6, 2024
03f2b47
simplified installation
Aug 6, 2024
9a089b2
Updated README.md to account for integrated slideflow fork
Sbrussee Aug 7, 2024
40d5750
added slideflow fork inside main codebase
Aug 7, 2024
9ad7848
added slideflow to main codebase
Aug 7, 2024
e0c66ed
Update README.md
Sbrussee Aug 7, 2024
df5fa96
updated slideflow
Aug 7, 2024
9d6d146
Allow custom losses and custom metrics during training
Aug 7, 2024
fe21880
Update README.md
Sbrussee Aug 7, 2024
c062f3f
survival test now also ttests custom loss/metric import
Aug 7, 2024
db1a547
fixes
Aug 7, 2024
42410b9
fix slideflow
Aug 7, 2024
054da15
fix fastai in slideflow_fork
Aug 7, 2024
2ec99e9
slideflow now correctly parses custom metrics
Aug 7, 2024
7087276
Update README.md
Sbrussee Aug 7, 2024
55c3129
Update README.md
Sbrussee Aug 7, 2024
487538e
added documentation
Aug 8, 2024
3614bbb
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 8, 2024
50c6590
added readthedocs requirements
Aug 8, 2024
afc6566
updated readthedocs yaml
Aug 8, 2024
f0fc49b
fixed readthedocs.yaml
Aug 8, 2024
a787ad3
updated docs
Aug 8, 2024
1877f23
fixed docs
Aug 8, 2024
e371deb
fixed bug in optimization, fixes in docs
Aug 8, 2024
beedb9f
minor fix in docs
Aug 8, 2024
3cd0d41
updated docs
Aug 8, 2024
38f81bb
Update README.md
Sbrussee Aug 8, 2024
0048706
Update README.md
Sbrussee Aug 8, 2024
bed5332
Update README.md
Sbrussee Aug 8, 2024
b9774e4
Update README.md
Sbrussee Aug 12, 2024
37e0ad3
updated docs
Aug 12, 2024
91cb91c
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 12, 2024
dc24796
updated docs
Aug 12, 2024
a71f6ab
updated docs
Aug 12, 2024
75a75e6
updated readthedocs
Aug 12, 2024
5ec5701
updated docs
Aug 12, 2024
473f6be
update d readthedocs yaml
Aug 12, 2024
6943d96
test
Aug 12, 2024
03b83b2
fixed readthedocs yaml
Aug 12, 2024
d6ea88b
fixed readthedocs
Aug 12, 2024
ef9f276
added imports to __init__ in main directory
Aug 12, 2024
b917d02
updated docs
Aug 12, 2024
4145b05
fixed readthedocs yaml
Aug 12, 2024
0942463
test
Aug 12, 2024
13859c7
added better init in pathbench
Aug 12, 2024
e4164ba
updated docs
Aug 12, 2024
356a576
added Hibou-L, fixed normalization values feature extractors where th…
Aug 12, 2024
1575112
made it possible to run optimization without pruning, added several n…
Aug 12, 2024
7ec34c0
added Virchow2
Aug 12, 2024
07457c3
using lowercase names for new aggregators
Aug 12, 2024
15abe4b
started support for augmentations
Aug 13, 2024
b84e585
renamed test function
Aug 13, 2024
b76b2db
Update README.md
Sbrussee Aug 13, 2024
f3124be
replaced slideflow clam models with own clam models
Aug 13, 2024
830b5da
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 13, 2024
0ad1fd8
Update README.md
Sbrussee Aug 13, 2024
90323da
updated calculate_attention for new clam implementations
Aug 13, 2024
2927f83
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 13, 2024
9aef664
fix readthedocs
Aug 13, 2024
0dce69e
updated all attention to be tensor format
Aug 13, 2024
0daf373
added sphinx to readthedocs
Aug 13, 2024
39a77d3
updated readthedocs
Aug 13, 2024
751b08b
updated doc requirements
Aug 13, 2024
07b4521
Update README.md
Sbrussee Aug 13, 2024
e670a6c
Update README.md
Sbrussee Aug 13, 2024
df73e53
added augmentations, added additional visualizations optimization mode
Aug 13, 2024
cb2905f
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 13, 2024
e17e895
fixed lens parameter in attention function
Aug 14, 2024
5d520fe
Update README.md
Sbrussee Aug 15, 2024
479a5d7
updated training in slideflow, updated requirements for documentation
Aug 15, 2024
0864b04
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 15, 2024
0ffee4b
now correctly weights classes
Aug 15, 2024
a5965ab
Update README.md
Sbrussee Aug 15, 2024
2a2e63d
added custom losses, mil-friendly augmentantions, speciable QC and sp…
Aug 21, 2024
98beff7
Update README.md
Sbrussee Aug 21, 2024
f7916b1
Update README.md
Sbrussee Aug 21, 2024
3b0bd8e
fixed QC bug
Aug 21, 2024
2f6573a
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 21, 2024
717c18d
Added EXAONE-Path F, added learnable topk and changed regular topk to…
Aug 23, 2024
0c8ed46
added new aggregators, EXAONE-path FM, approximated feature similarity
Aug 28, 2024
03780d2
updated conf
Aug 28, 2024
0856880
Update README.md
Sbrussee Aug 28, 2024
06eb647
added visualization app
Aug 29, 2024
4317b30
Merge remote-tracking branch 'refs/remotes/origin/main'
Aug 29, 2024
826d054
updated viz app
Aug 29, 2024
43efe80
added similarity matrix calculation, experimental ensemble model crea…
Sbrussee Sep 3, 2024
cf1923f
Update README.md
Sbrussee Sep 3, 2024
ce49275
Update README.md
Sbrussee Sep 3, 2024
6db267a
Removed slideflow_fork from index instead adding it as a submodule
Sbrussee Sep 18, 2024
372f725
added slideflow_fork as submoudle
Sbrussee Sep 18, 2024
a626bd7
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Sep 18, 2024
455d6d2
Update README.md
Sbrussee Sep 18, 2024
a716e04
updated requirements to fix install
Sbrussee Sep 18, 2024
0cecea2
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Sep 18, 2024
1578415
added CONCH, phikon_v2 and ensemble mode
Sbrussee Sep 18, 2024
fb1cd1e
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Sep 18, 2024
961184c
testing survival loss
Sbrussee Sep 19, 2024
3d0656e
added conch to requirements
Sbrussee Sep 19, 2024
070b9b2
Update README.md
Sbrussee Sep 19, 2024
e209931
updated test with better annotation files
Sbrussee Sep 19, 2024
0d768aa
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Sep 19, 2024
84b6e21
Removed __pycahce__ and compiled python files from tracking
Sbrussee Sep 19, 2024
14a5a20
Update README.md
Sbrussee Sep 19, 2024
2ded008
updated the way datasets are handled, tried to solve problems with mu…
Sbrussee Sep 20, 2024
4602055
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Sep 20, 2024
5c935aa
mitigated multiprocessing problem in slideflow_fork
Sbrussee Sep 20, 2024
8d7a7e2
added new dataset handling to ensemble and optimization mode
Sbrussee Sep 20, 2024
4ac5465
Update README.md
Sbrussee Sep 20, 2024
ee48708
fixed multiprocessing problem, removed untested features
Sbrussee Oct 1, 2024
70d6e94
added pretrained_weights default
Sbrussee Oct 1, 2024
1aa472e
Update README.md
Sbrussee Oct 1, 2024
4670530
updated docs
Sbrussee Oct 1, 2024
1037151
updated docs
Sbrussee Oct 1, 2024
9ebc638
updated docs
Sbrussee Oct 1, 2024
845b313
mitigated issues with multiprocessing, changed test files, added repo…
Sbrussee Nov 28, 2024
56a341f
Update README.md
Sbrussee Jan 30, 2025
af4e553
Update README.md
Sbrussee Jan 30, 2025
2be5c61
Added citation
Sbrussee Feb 5, 2025
f5f9f4a
Update README.md
Sbrussee Feb 12, 2025
2600663
Create pathbench_mil.dockerfile
Sbrussee Feb 13, 2025
2bd0428
Update README.md to include docker instructions
Sbrussee Feb 13, 2025
7d17efb
Rename pathbench_mil.dockerfile to pathbench_mil.Dockerfile
Sbrussee Feb 13, 2025
2656734
Rename pathbench_mil.Dockerfile to pathbench-gpu.Dockerfile
Sbrussee Feb 13, 2025
b053b17
Update README.md
Sbrussee Feb 13, 2025
c542790
Update README.md
Sbrussee Feb 14, 2025
3c84049
Update README.md
Sbrussee Feb 14, 2025
b1a2789
updated test datasets, losses, visualizations, added discrete surviva…
Sbrussee Feb 17, 2025
7f59055
Update README.md
Sbrussee Feb 17, 2025
75d801f
Update README.md
Sbrussee Feb 17, 2025
bf8921f
Update README.md
Sbrussee Feb 19, 2025
3a7d1bd
fixed small error in benchmark.py calculate_results
Sbrussee Feb 19, 2025
93f3735
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Feb 19, 2025
1e9bf05
fixed Huggingface token bug
Sbrussee Feb 20, 2025
abe4a88
Update README.md
Sbrussee Feb 20, 2025
82354cf
MPP missing error only appears once now
Sbrussee Feb 20, 2025
913f6f7
now ensures closing all pools in QC
Sbrussee Feb 21, 2025
91f7a4b
fixed bug where weight was not defined in training script
Sbrussee Feb 24, 2025
ce2b986
Set cache dir to specified weights dir
Sbrussee Feb 24, 2025
73458cd
Update pathbench-gpu.Dockerfile
Sbrussee Feb 24, 2025
c1dbf41
Update README.md for correct Docker instructions
Sbrussee Feb 24, 2025
c7674e4
added support for per-dataset test output
Sbrussee Feb 24, 2025
88c7885
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Feb 24, 2025
8b0df10
Update README.md
Sbrussee Feb 25, 2025
baae7a0
Update README.md
Sbrussee Feb 26, 2025
afb609e
Added inference mode for saved models
Sbrussee Feb 26, 2025
6eac644
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Feb 26, 2025
16ebbe7
Added site-preserved k-split and default configurations for each task
Sbrussee Feb 26, 2025
bda4308
Update README.md
Sbrussee Feb 26, 2025
2660fcd
Update README.md
Sbrussee Feb 26, 2025
6082b66
Add example of visualization dashboard
Sbrussee Feb 26, 2025
69f3d23
Update README.md to account for visualization application
Sbrussee Feb 26, 2025
40e3cbf
Update vis_app.py
Sbrussee Feb 26, 2025
ccaf8bc
updated visualization app
Sbrussee Feb 26, 2025
1b4c7b8
Added H0-mini
Sbrussee Mar 6, 2025
3c7c30b
Update README.md for better docker support
Sbrussee Mar 13, 2025
4e8f7b4
fixed bug with None HF-token and bug in optimization mode when config…
Sbrussee Mar 13, 2025
f591d4c
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee Mar 13, 2025
ed5c55f
Added Slide-level feature extractors, inference mode, major code refa…
Sbrussee Apr 25, 2025
2e5ec15
Update README.md
Sbrussee Apr 25, 2025
0388c3e
Update README.md
Sbrussee Apr 25, 2025
5014c1a
fixed label recognition for survival/regression tasks
Sbrussee May 13, 2025
744080e
Merge remote-tracking branch 'refs/remotes/origin/main'
Sbrussee May 13, 2025
1048da7
Fixed feature extraction using mSTAR, added option for forcing re-ext…
Sbrussee May 19, 2025
f2a26bf
Update README.md
Sbrussee May 19, 2025
ad0f1ce
Update README.md
Sbrussee May 19, 2025
5787df9
Update README.md
Sbrussee May 19, 2025
ddf0593
Update README.md
Sbrussee May 19, 2025
01c4cca
Update README.md
Sbrussee May 19, 2025
b93fd02
Added uncertainty to inference, updated handling of dataset names, ma…
Sbrussee May 22, 2025
93c0d5c
Fixed survival target casting, more flexible definition of heatmaps, …
Sbrussee May 29, 2025
81601b5
Workaround for tile extraction not working if num_workers<=1 + handle…
Falcury May 31, 2025
d7524e0
Fix log: K-fold splits written to {splits_file}
Falcury May 31, 2025
088fab2
Fix skip_feature_extraction option having the reverse effect
Falcury May 31, 2025
dfe5171
Fix balancing info not being saved
Falcury Jun 1, 2025
fc1583e
Fix test datasets not being looped over correctly
Falcury Jun 1, 2025
1090c84
Fix exception handling in benchmark.py
Falcury Jun 1, 2025
8abb0f1
Merge pull request #9 from Falcury/fixes-pieter
Sbrussee Jun 2, 2025
1fb33e6
Update README.md
Sbrussee Jun 2, 2025
666748f
fixed patient grouping for slide-level models, assertion on survival …
Sbrussee Jun 4, 2025
bf67c82
Reapply fixes from PR #9
Falcury Jun 7, 2025
4db556b
Fix mil_name unresolved reference in find_and_apply_best_model()
Falcury Jun 7, 2025
0b11ed9
Don't plot benchmarking output if no combinations were successfully t…
Falcury Jun 7, 2025
ff13973
Fix specified loss not actually used
Falcury Jun 7, 2025
59ad8ca
Require Python 3.10
Falcury Jun 8, 2025
f5d562d
Apply slide_level when calling set_mil_config()
Falcury Jun 8, 2025
3958f47
Merge pull request #10 from Falcury/fixes-pieter
Sbrussee Jun 8, 2025
53a3fea
Update README.md
Sbrussee Jun 18, 2025
891c11a
Update README.md
Sbrussee Jun 20, 2025
c73d331
Update README.md
Sbrussee Jul 1, 2025
db173a3
Update slideflow_fork submodule to include TIFF mpp-detection fix
JurreWeijer Jul 2, 2025
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11 changes: 11 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
__pycache__/
*.py[cod]
*.out
*.log
*.pth
*.bin
*.safetensors
pretrained_weights/*
!pretrained_weights/readme.txt
experiments/
.cache/
6 changes: 3 additions & 3 deletions .gitmodules
Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
[submodule "slideflow"]
path = slideflow
url = https://github.com/Sbrussee/slideflow_fork.git
[submodule "slideflow_fork"]
path = slideflow_fork
url = https://github.com/Sbrussee/slideflow_fork
25 changes: 25 additions & 0 deletions .readthedocs.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,25 @@
version: 2

# Build documentation in the main branch
build:
os: ubuntu-22.04
tools:
python: "3.9"
apt_packages:
- libblas-dev
- liblapack-dev
- gfortran

# Define the necessary Python dependencies
python:
install:
- requirements: docs/requirements.txt

formats:
- pdf
- htmlzip
- epub

# Build the documentation
sphinx:
configuration: docs/source/conf.py
674 changes: 674 additions & 0 deletions LICENSE

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Binary file added PathBench-logo-gecentreerd.png
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