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Graph embedding and graph backbones #592

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merged 205 commits into from
Nov 9, 2021
Merged

Graph embedding and graph backbones #592

merged 205 commits into from
Nov 9, 2021

Commits on Jul 12, 2021

  1. Initial structure of GraphClassification model.py

    pablo authored and PabloAMC committed Jul 12, 2021
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  2. Improvement of model.py. Still need to debug etc

    pablo authored and PabloAMC committed Jul 12, 2021
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  3. BasicDataset Implemented

    pablo authored and PabloAMC committed Jul 12, 2021
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  4. Create __init__.py

    pablo authored and PabloAMC committed Jul 12, 2021
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  5. Implemented dataset and DataModule as for image processing 

    Lacking Pipeline and it is possible that division in raw and processed folders might be needed.
    pablo authored and PabloAMC committed Jul 12, 2021
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  6. Pipeline taken from images. 

    I'm unsure how to adapt
    pablo authored and PabloAMC committed Jul 12, 2021
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  7. Initial structure of GraphClassification model.py

    pablo authored and PabloAMC committed Jul 12, 2021
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  8. Improvement of model.py. Still need to debug etc

    pablo authored and PabloAMC committed Jul 12, 2021
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  9. BasicDataset Implemented

    pablo authored and PabloAMC committed Jul 12, 2021
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  10. Implemented dataset and DataModule as for image processing 

    Lacking Pipeline and it is possible that division in raw and processed folders might be needed.
    pablo authored and PabloAMC committed Jul 12, 2021
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  11. Pipeline taken from images. 

    I'm unsure how to adapt
    pablo authored and PabloAMC committed Jul 12, 2021
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  12. Choice of model implemented (you can pass a model to GraphClassifier) 

    The class BasicGraphDataset in graphClassification/data.py is probably unneded
    pablo authored and PabloAMC committed Jul 12, 2021
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  14. Initial readaptation of the structure

    pablo committed Jul 12, 2021
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  16. Minimal structure of how to structure data.py files

    pablo committed Jul 12, 2021
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  18. Minor corrections

    pablo committed Jul 12, 2021
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  19. update

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    tchaton authored and PabloAMC committed Jul 12, 2021
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  20. i

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  21. update

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  23. Added auto_dataset.num_features

    pablo committed Jul 12, 2021
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  24. Deleted manually included num_features so that it is extracted from G… 

    …raphDatasetSource()
    pablo committed Jul 12, 2021
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  25. Test for GraphClassification implemented

    pablo committed Jul 12, 2021
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  26. Documentation for GraphClassification included

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  28. Creation of from_pygdatasequence method in DataModule and GraphSequen… 

    …ceDataSource()
    pablo committed Jul 12, 2021
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  29. Update graph_classification.py

    PabloAMC committed Jul 12, 2021
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  30. Update datatype_graph.txt

    PabloAMC committed Jul 12, 2021
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  31. Tests and docs for the from_pygdatasequence method

    pablo committed Jul 12, 2021
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  33. Graph requirements

    pablo committed Jul 12, 2021
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  35. Update CHANGELOG.md

    pablo committed Jul 12, 2021
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  36. Update requirements with pytorch geometric libraries

    pablo committed Jul 12, 2021
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  37. Simplified, version with only the DataSource

    PabloAMC committed Jul 12, 2021
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  39. Minor tweaks

    PabloAMC committed Jul 12, 2021
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  40. Merge branch 'master' of https://github.com/PabloAMC/lightning-flash

    PabloAMC committed Jul 12, 2021
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  41. Update the flash_example to reflect the new template

    PabloAMC committed Jul 12, 2021
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  43. Delete IMDB-BINARY_A.txt

    PabloAMC authored Jul 12, 2021
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  44. Delete IMDB-BINARY_graph_indicator.txt

    PabloAMC authored Jul 12, 2021
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  45. Delete IMDB-BINARY_graph_labels.txt

    PabloAMC authored Jul 12, 2021
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  46. Class method from_pygdatasequence from flash/core/data/data_module.py

    PabloAMC committed Jul 12, 2021
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  47. Merge branch 'master' of https://github.com/PabloAMC/lightning-flash

    PabloAMC committed Jul 12, 2021
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Commits on Jul 14, 2021

  1. Creating backbones

    PabloAMC committed Jul 14, 2021
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  2. Merge branch 'master' into master

    @ethanwharris
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  3. Changing GRAPH_BACKBONES to GRAPH_CLASSIFICATION_BACKBONES

    PabloAMC committed Jul 14, 2021
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  4. Update docs

    @ethanwharris
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  5. Merge branch 'master' into master

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  6. fix imports.py

    @ethanwharris
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  7. remove unused imports

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  8. clean init.py

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  9. updates

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  10. Minor tweaks in the docs and change from Graph_backbones to graph_cla… 

    …ssification_backbones
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  11. Updates

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  12. Updates

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  13. Updates

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  14. Graph embedding task implemented, modulo corrections

    PabloAMC committed Jul 14, 2021
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  15. Error corrections

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  16. Merge branch 'master' into task_a_thon

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  17. Updates

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  18. Update docs

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  19. Update docs

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  20. Update docs

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  21. fix tests

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  22. fix tests

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  23. Add API reference

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  24. Try fix

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  25. Merge branch 'master' into task_a_thon

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  26. Included Networkx as requirement for graph library

    PabloAMC committed Jul 14, 2021
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  27. Try fix

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  28. Try fix

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  29. Merge branch 'master' into task_a_thon

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  30. batch = (batch[DefaultDataKeys.INPUT], batch[DefaultDataKeys.TARGET])… 

    … to batch = (batch, batch.y)
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  31. Update flash/core/data/auto_dataset.py

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  32. Update docstring

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  33. Correction of minor errors

    PabloAMC committed Jul 14, 2021
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  34. Updating docs

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  35. Merge branch 'master' into task_a_thon

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  36. Update graph_embedding docs

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  37. Minor tweaks

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Commits on Jul 15, 2021

  1. Merge remote-tracking branch 'upstream/master' into task_a_thon

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  3. Correct documentation

    PabloAMC committed Jul 15, 2021
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  4. Creating a head suited for PyG backbones

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  6. Update the head of the embedding model

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  7. Merge branch 'task_a_thon' of https://github.com/PabloAMC/lightning-f… 

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  8. Update graph_classification example

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Commits on Jul 16, 2021

  1. Update backbones to match how they will work in Pytorch Geometric

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Commits on Jul 17, 2021

  1. Update CHANGELOG.md

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  3. Update graph requirements

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  5. Update test_model.py

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  7. Update data_module.py

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  8. Update data_module.py

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  10. Update test_model.py

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  11. Merge branch 'task_a_thon' of https://github.com/PabloAMC/lightning-f… 

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  12. _TORCH_GEOMETRIC_AVAILABLE to _GRAPH_AVAILABLE

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  14. Adding num_features to uses of backbones

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  16. Update graph_classification.py

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  18. Update test_model.py

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  19. Merge branch 'task_a_thon' of https://github.com/PabloAMC/lightning-f… 

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  21. Backbone kwargs default changed from None to {}

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  26. Update model.py

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  27. Small error correction

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Commits on Jul 21, 2021

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  3. models adapted to torch geometric basic models

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  4. Updating minor corrections

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  6. Eliminating needless stuff

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  7. Changed descriptions

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Commits on Sep 23, 2021

  1. Update CHANGELOG.md 

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  2. Update flash/graph/embedding/__init__.py 

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  3. Update flash_examples/graph_classification.py 

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  4. Update docs/source/reference/graph_embedding.rst 

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  5. Updates based on ethan comments

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  14. Eliminating pretrained option

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Commits on Sep 24, 2021

  1. Minor correction in model.py

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  3. self.backbone(x.x, x.edge_index)

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Commits on Sep 27, 2021

  1. update

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  14. Fix reqs.

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  16. Fixes

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  17. Multiple pooling functions

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  18. Fixes

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  19. Fixes

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  20. Try fix

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  21. Speed up CI

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