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Merged
melvinbarbaux merged 5 commits into from
Jan 13, 2026
Merged

refactor(preprocess): move graph embeddings into preprocessing and drop legacy transductive configs #24

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• refactor(preprocess): move graph embeddings into preprocessing and …
melvinbarbaux Jan 13, 2026
06c2bdf
update index dooc
melvinbarbaux Jan 13, 2026
88d12d3
fix ci
melvinbarbaux Jan 13, 2026
ff73b43
fix test
melvinbarbaux Jan 13, 2026
102a08a
fix
melvinbarbaux Jan 13, 2026
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2 changes: 1 addition & 1 deletion .github/workflows/docs.yml
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Expand Up @@ -3,7 +3,7 @@ name: Docs
on:
push:
branches: ["main"]
tags: ["v*"]
tags: ["v*", "[0-9]*"]
paths:
- "docs/**"
- "mkdocs.yml"
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2 changes: 1 addition & 1 deletion .github/workflows/release.yml
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Expand Up @@ -3,7 +3,7 @@ name: Release
on:
push:
branches: ["main"]
tags: ["v*"]
tags: ["v*", "[0-9]*"]
paths:
- "src/**"
- "pyproject.toml"
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.

The format is based on "Keep a Changelog", and this project adheres to Semantic Versioning.

## 0.1.1
- Bump version metadata and docs.
- Allow docs/release workflows to run on numeric tags.

## 0.1.0
- Contains all desired transductive methods and marks a stable benchmark release.

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42 changes: 0 additions & 42 deletions bench/configs/experiments/best/README_by_dataset.md
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54 changes: 0 additions & 54 deletions bench/configs/experiments/best/README_by_method.md
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Expand Up @@ -810,33 +810,6 @@ python -m bench.main --config bench/configs/experiments/best/transductive/chebne
python -m bench.main --config bench/configs/experiments/best/transductive/chebnet/vision/svhn.yaml > log/transductive/chebnet/vision/svhn.log 2>&1
```

## transductive/dgi

```
mkdir -p log/transductive/dgi/audio log/transductive/dgi/graph log/transductive/dgi/tabular log/transductive/dgi/text log/transductive/dgi/vision
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/audio/speechcommands.yaml > log/transductive/dgi/audio/speechcommands.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/audio/yesno.yaml > log/transductive/dgi/audio/yesno.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/graph/citeseer.yaml > log/transductive/dgi/graph/citeseer.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/graph/cora.yaml > log/transductive/dgi/graph/cora.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/graph/pubmed.yaml > log/transductive/dgi/graph/pubmed.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/tabular/adult.yaml > log/transductive/dgi/tabular/adult.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/tabular/breast_cancer.yaml > log/transductive/dgi/tabular/breast_cancer.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/tabular/iris.yaml > log/transductive/dgi/tabular/iris.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/tabular/toy.yaml > log/transductive/dgi/tabular/toy.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/ag_news.yaml > log/transductive/dgi/text/ag_news.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/amazon_polarity.yaml > log/transductive/dgi/text/amazon_polarity.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/amazon_reviews_multi_en.yaml > log/transductive/dgi/text/amazon_reviews_multi_en.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/dbpedia_14.yaml > log/transductive/dgi/text/dbpedia_14.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/imdb.yaml > log/transductive/dgi/text/imdb.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/yelp_polarity.yaml > log/transductive/dgi/text/yelp_polarity.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/text/yelp_review_full.yaml > log/transductive/dgi/text/yelp_review_full.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/vision/cifar10.yaml > log/transductive/dgi/vision/cifar10.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/vision/cifar100.yaml > log/transductive/dgi/vision/cifar100.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/vision/mnist.yaml > log/transductive/dgi/vision/mnist.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/vision/stl10.yaml > log/transductive/dgi/vision/stl10.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/dgi/vision/svhn.yaml > log/transductive/dgi/vision/svhn.log 2>&1
```

## transductive/dynamic_label_propagation

```
Expand Down Expand Up @@ -1242,33 +1215,6 @@ python -m bench.main --config bench/configs/experiments/best/transductive/n_gcn/
python -m bench.main --config bench/configs/experiments/best/transductive/n_gcn/vision/svhn.yaml > log/transductive/n_gcn/vision/svhn.log 2>&1
```

## transductive/node2vec

```
mkdir -p log/transductive/node2vec/audio log/transductive/node2vec/graph log/transductive/node2vec/tabular log/transductive/node2vec/text log/transductive/node2vec/vision
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/audio/speechcommands.yaml > log/transductive/node2vec/audio/speechcommands.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/audio/yesno.yaml > log/transductive/node2vec/audio/yesno.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/graph/citeseer.yaml > log/transductive/node2vec/graph/citeseer.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/graph/cora.yaml > log/transductive/node2vec/graph/cora.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/graph/pubmed.yaml > log/transductive/node2vec/graph/pubmed.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/tabular/adult.yaml > log/transductive/node2vec/tabular/adult.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/tabular/breast_cancer.yaml > log/transductive/node2vec/tabular/breast_cancer.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/tabular/iris.yaml > log/transductive/node2vec/tabular/iris.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/tabular/toy.yaml > log/transductive/node2vec/tabular/toy.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/ag_news.yaml > log/transductive/node2vec/text/ag_news.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/amazon_polarity.yaml > log/transductive/node2vec/text/amazon_polarity.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/amazon_reviews_multi_en.yaml > log/transductive/node2vec/text/amazon_reviews_multi_en.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/dbpedia_14.yaml > log/transductive/node2vec/text/dbpedia_14.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/imdb.yaml > log/transductive/node2vec/text/imdb.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/yelp_polarity.yaml > log/transductive/node2vec/text/yelp_polarity.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/text/yelp_review_full.yaml > log/transductive/node2vec/text/yelp_review_full.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/vision/cifar10.yaml > log/transductive/node2vec/vision/cifar10.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/vision/cifar100.yaml > log/transductive/node2vec/vision/cifar100.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/vision/mnist.yaml > log/transductive/node2vec/vision/mnist.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/vision/stl10.yaml > log/transductive/node2vec/vision/stl10.log 2>&1
python -m bench.main --config bench/configs/experiments/best/transductive/node2vec/vision/svhn.yaml > log/transductive/node2vec/vision/svhn.log 2>&1
```

## transductive/p_laplace_learning

```
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90 changes: 0 additions & 90 deletions bench/configs/experiments/best/transductive/dgi/audio/speechcommands.yaml
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90 changes: 0 additions & 90 deletions bench/configs/experiments/best/transductive/dgi/audio/yesno.yaml
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68 changes: 0 additions & 68 deletions bench/configs/experiments/best/transductive/dgi/graph/citeseer.yaml
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