Skip to content

Hopse sparse: added sparse implementations for feature encodings#296

Open
Coerulatus wants to merge 13 commits intohopsefrom
hopse_sparse
Open

Hopse sparse: added sparse implementations for feature encodings#296
Coerulatus wants to merge 13 commits intohopsefrom
hopse_sparse

Conversation

@Coerulatus
Copy link
Copy Markdown
Collaborator

Checklist

  • My pull request has a clear and explanatory title.
  • My pull request passes the Linting test.
  • I added appropriate unit tests and I made sure the code passes all unit tests. (refer to comment below)
  • My PR follows PEP8 guidelines. (refer to comment below)
  • My code is properly documented, using numpy docs conventions, and I made sure the documentation renders properly.
  • I linked to issues and PRs that are relevant to this PR.

Description

  • Added sparse implementations on GPU for feature and positional encodings. Default for positional encodings is to run on cpu with the old implementation (it could be decided based on the data which implementation is best but for now the old one seems to be better with big graphs like mantra).
  • Changed PreProcessor to support GPU preprocessing.
  • Fixed default hydra path for logging runs. Before runs started at the same second would override each other.
  • Fixed data preprocessing with ultiple runs. The first process to reach the preprocessing step locks down the computation for the others so they wait for the preprocessed data to be saved to disk.

@review-notebook-app
Copy link
Copy Markdown

Check out this pull request on  ReviewNB

See visual diffs & provide feedback on Jupyter Notebooks.


Powered by ReviewNB

@codecov
Copy link
Copy Markdown

codecov bot commented Apr 1, 2026

Codecov Report

❌ Patch coverage is 44.16961% with 316 lines in your changes missing coverage. Please review.
✅ Project coverage is 82.26%. Comparing base (6899e1c) to head (656b331).
⚠️ Report is 2 commits behind head on hopse.

Files with missing lines Patch % Lines
...sforms/data_manipulations/random_walk_encodings.py 28.22% 89 Missing ⚠️
...forms/data_manipulations/khop_feature_encodings.py 35.71% 45 Missing ⚠️
...orms/data_manipulations/electrostatic_encodings.py 26.31% 42 Missing ⚠️
...ansforms/data_manipulations/laplacian_encodings.py 50.00% 40 Missing ⚠️
.../transforms/data_manipulations/hkdiag_encodings.py 43.54% 35 Missing ⚠️
...nsforms/data_manipulations/hk_feature_encodings.py 52.94% 32 Missing ⚠️
...sforms/data_manipulations/ppr_feature_encodings.py 62.29% 23 Missing ⚠️
...ns/combined_positional_and_structural_encodings.py 63.15% 7 Missing ⚠️
topobench/data/preprocessor/preprocessor.py 88.00% 3 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##            hopse     #296      +/-   ##
==========================================
- Coverage   85.64%   82.26%   -3.38%     
==========================================
  Files         208      208              
  Lines        8282     8759     +477     
==========================================
+ Hits         7093     7206     +113     
- Misses       1189     1553     +364     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants