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Add GCN-BMP #71
Add GCN-BMP #71
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Generally looks good, typing is missing in certain places. The latest version of black should be used for linting. The auxiliary layers should be in the readme on some name space - also you should consider adding them to the README.
- Chunked iteration of the BMP backbone for better readability
@cthoyt I overtook this. |
@benedekrozemberczki let me know when you're done and I'll take a final pass |
@cthoyt Ready for review. |
Codecov Report
@@ Coverage Diff @@
## main #71 +/- ##
==========================================
+ Coverage 94.01% 94.36% +0.35%
==========================================
Files 29 29
Lines 869 959 +90
==========================================
+ Hits 817 905 +88
- Misses 52 54 +2
Continue to review full report at Codecov.
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* linting * GCNBMP Scatter Reduction fix * Using Rel Conv Layers instead of RGCN Model (avoid unecessary sum readouts) * Added docstrings and fixed highway update implementation * Make number of relationship configurable * little help of black for linting * Cleaning upuseless imports * Sharing attention between right and left side * Adding reference to GCNBMP docstring * Type hinting everything * Fixing docstring in example * - Removing type hints in docstrings as they were added to signatures - Chunked iteration of the BMP backbone for better readability * Ading more-itertools as a dependecy * Using pairwise for encoder construction * Adding missing docstrings * Fixing linting and precommit hook * Fixing the citation back to what is in main * Tests,formatting,example * Tests,formatting,example * GCNBMP * Cleanup Co-authored-by: kcvc236 <kcvc236@seskscpg057.prim.scp> Co-authored-by: Rozemberczki <kmdb028@astrazeneca.net> Co-authored-by: kcvc236 <kcvc236@seskscpg059.prim.scp> Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com>
* CASTER layer implementation - only supervised training stage - input dimensionality assumed to be correct * Apply black and reorganize * Move loss into its own module * Update caster.py * Reduce diff on citation * Implement DeepDrug model (#68) * WIP: model forward pass works, not tested * added dropout and batch norm * WIP: made DeepDrug example, not tested * moved to using layers only, not GCN torchdrug model * docstring * added dropout and made context feats optional * added DeepDrug unit test * deepdrug self attribute fix * docstring update * unpack method update (when no context feats used) * isort * fixed test setting (context_channels) * fixed testing without context * black * RST fix * RST fix * more pythonic loop + swap i to _ * removed context feat support in DeepDrug * removed context handling from testing DeepDrug * fixed examples DeepDrug, no context handling, decreased epochs 100->20 * removed unused import * used a wrapper for calling the same layers on pairs of batches * used a wrapper for calling the same layers on pairs of batches * docstring fix * Abstract process applied to left and right sides * Apply black * Cleanup Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com> * Add GCN-BMP (#71) * linting * GCNBMP Scatter Reduction fix * Using Rel Conv Layers instead of RGCN Model (avoid unecessary sum readouts) * Added docstrings and fixed highway update implementation * Make number of relationship configurable * little help of black for linting * Cleaning upuseless imports * Sharing attention between right and left side * Adding reference to GCNBMP docstring * Type hinting everything * Fixing docstring in example * - Removing type hints in docstrings as they were added to signatures - Chunked iteration of the BMP backbone for better readability * Ading more-itertools as a dependecy * Using pairwise for encoder construction * Adding missing docstrings * Fixing linting and precommit hook * Fixing the citation back to what is in main * Tests,formatting,example * Tests,formatting,example * GCNBMP * Cleanup Co-authored-by: kcvc236 <kcvc236@seskscpg057.prim.scp> Co-authored-by: Rozemberczki <kmdb028@astrazeneca.net> Co-authored-by: kcvc236 <kcvc236@seskscpg059.prim.scp> Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com> * Implement DeepDDI model (#63) * update: Add deepddi model * update: Add deepddi examples * update: Add deepddi test case * Style: deepddi model * Style: deepddi model * Style: deepddi_examples.py * Update deepddi.py * Update deepddi.py Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com> * CASTER review fixes * flake8 fixes * CASTER: typing fix Co-authored-by: Andriy Nikolov <kgsq682@astrazeneca.net> Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com> Co-authored-by: Piotr Grabowski <3966940+kajocina@users.noreply.github.com> Co-authored-by: Michaël Ughetto <michael.ughetto@astrazeneca.com> Co-authored-by: kcvc236 <kcvc236@seskscpg057.prim.scp> Co-authored-by: Rozemberczki <kmdb028@astrazeneca.net> Co-authored-by: kcvc236 <kcvc236@seskscpg059.prim.scp> Co-authored-by: walter <32014404+hzcheney@users.noreply.github.com>
Summary
First draft of implementation for GCN-BMP. Closes Issue #21 .
Changes
Caveats
Differences with the original paper
Performance
Example's ROC AUC: 0.749128