Update slideflow_fork submodule to include TIFF mpp-detection fix#12

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JurreWeijer wants to merge 234 commits into

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JurreWeijer:pr–mpp-only

Commits on Jul 31, 2024

Commits on Aug 1, 2024

Commits on Aug 6, 2024

added setup, tests
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merge
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removed unnessary files
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fixed tests
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updated requirements
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fixed setup
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added cython to pre-setup
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now sources environment
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test
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test
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set version for ruamel.yaml
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now added pip upgrade
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removed ruamel
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readded ruamel
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test
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fixed requirements
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no specific ruamel ersion
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making sure numpy is installed first
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specific numpy version
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simplified installation
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Commits on Aug 7, 2024

Updated README.md to account for integrated slideflow fork
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added slideflow fork inside main codebase
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added slideflow to main codebase
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Update README.md
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updated slideflow
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Allow custom losses and custom metrics during training
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Update README.md
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survival test now also ttests custom loss/metric import
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fixes
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fix slideflow
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fix fastai in slideflow_fork
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slideflow now correctly parses custom metrics
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Update README.md
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Update README.md
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Commits on Aug 8, 2024

added documentation
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Merge remote-tracking branch 'refs/remotes/origin/main'
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added readthedocs requirements
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updated readthedocs yaml
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fixed readthedocs.yaml
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updated docs
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fixed docs
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fixed bug in optimization, fixes in docs
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minor fix in docs
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updated docs
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Update README.md
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Update README.md
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Update README.md
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Commits on Aug 12, 2024

Update README.md
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updated docs
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Merge remote-tracking branch 'refs/remotes/origin/main'
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updated docs
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updated docs
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updated readthedocs
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updated docs
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update d readthedocs yaml
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test
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fixed readthedocs yaml
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fixed readthedocs
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added imports to __init__ in main directory
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updated docs
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fixed readthedocs yaml
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test
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added better init in pathbench
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updated docs
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added Hibou-L, fixed normalization values feature extractors where these differ from the default
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made it possible to run optimization without pruning, added several new MIL aggregation methods
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added Virchow2
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using lowercase names for new aggregators
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Commits on Aug 13, 2024

started support for augmentations
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renamed test function
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Update README.md
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replaced slideflow clam models with own clam models
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Merge remote-tracking branch 'refs/remotes/origin/main'
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Update README.md
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updated calculate_attention for new clam implementations
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Merge remote-tracking branch 'refs/remotes/origin/main'
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fix readthedocs
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updated all attention to be tensor format
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added sphinx to readthedocs
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updated readthedocs
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updated doc requirements
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Update README.md
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Update README.md
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added augmentations, added additional visualizations optimization mode
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Merge remote-tracking branch 'refs/remotes/origin/main'
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Commits on Aug 14, 2024

fixed lens parameter in attention function
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Commits on Aug 15, 2024

Update README.md
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updated training in slideflow, updated requirements for documentation
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Merge remote-tracking branch 'refs/remotes/origin/main'
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now correctly weights classes
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Update README.md
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Commits on Aug 21, 2024

Commits on Aug 23, 2024

Added EXAONE-Path F, added learnable topk and changed regular topk to pperform aweighted sattention sum
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Commits on Aug 28, 2024

added new aggregators, EXAONE-path FM, approximated feature similarity
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updated conf
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Update README.md
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Commits on Aug 29, 2024

added visualization app
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Merge remote-tracking branch 'refs/remotes/origin/main'
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updated viz app
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Commits on Sep 3, 2024

Commits on Nov 28, 2024

mitigated issues with multiprocessing, changed test files, added report option
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Commits on Jan 30, 2025

Commits on Feb 5, 2025

Added citation
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Commits on Feb 12, 2025

Update README.md
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Commits on Feb 14, 2025

Commits on Feb 17, 2025

Commits on Feb 19, 2025

Commits on Feb 20, 2025

Commits on Feb 21, 2025

now ensures closing all pools in QC
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Commits on Feb 25, 2025

Update README.md
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Commits on Feb 26, 2025

Commits on Mar 6, 2025

Added H0-mini
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Commits on Mar 13, 2025

Commits on Apr 25, 2025

Commits on May 13, 2025

Commits on May 22, 2025

Added uncertainty to inference, updated handling of dataset names, made benchmarking and optimization applicable to multiple test sets
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Commits on May 29, 2025

Fixed survival target casting, more flexible definition of heatmaps, dataset locations, removed uninformative warnings
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Commits on May 31, 2025

Commits on Jun 1, 2025

Commits on Jun 2, 2025

Commits on Jun 4, 2025

fixed patient grouping for slide-level models, assertion on survival prediction metrics, fixed visualization of survival ROC-AUC curve, addition of (fastai, custom) callbacks
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Commits on Jun 8, 2025

Commits on Jun 18, 2025

Update README.md
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Commits on Jun 20, 2025

Update README.md
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Commits on Jul 1, 2025

Update README.md
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Commits on Jul 2, 2025

Update slideflow_fork submodule to include TIFF mpp-detection fix
JurreWeijer
committed