Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

skeleton for LR encoding ED model with extension of estimator #44

Merged
merged 22 commits into from
Nov 7, 2021

Conversation

davidsebfischer
Copy link
Contributor

@davidsebfischer davidsebfischer commented Oct 12, 2021

Added estimators that yield neighbrouhood tensors of features and avoid using the full adjacency matrix, this can be used for single layer embeddings and breaks the scaling of attention coefficient computation with number of nodes in graph.

The core design feature of the models contributed here is that the models receive two feature input tensors (batch, target nodes, features), (batch, target nodes, neighbors, features), where neighbors is padded to be constant (the max neighborhood size in data set). The adjacency matrix is then just a padding indicator (batch, target nodes, neighbors). For neighbors << max nodes this can result in desirable reduction in data communitcation to GPU and desirable intermediate tensor sizes before masking is applied via the adjacenc matrix, e.g. for attention. This only works fo rmodels with a single graph embedding layer. This implementation can be kept in parallel to the more general implementation that we already have. I recreated the Max and Gcn model layers for this type of input.

  • extract gene names in estimator .set_input_features
  • enable extraction of LR-pairwise activations (embedding) and relate to output weights in linear decoder setting.
  • add unit test for new models

added estimators that yield neighbrouhood tensors of features and avoid using the full adjacency matrix, this can be used for single layer embeddings and breaks the scaling of attention coefficient computation with number of nodes in graph
@davidsebfischer davidsebfischer marked this pull request as draft October 12, 2021 11:15
@github-actions github-actions bot added the enhancement New feature or request label Oct 12, 2021
@review-notebook-app
Copy link

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@AnnaChristina AnnaChristina marked this pull request as ready for review October 14, 2021 12:24
@AnnaChristina AnnaChristina merged commit 92647bf into development Nov 7, 2021
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

2 participants