Pykeen Versions Save

What's Changed

• 🧰♻️ Add Dependency Caching by @mberr in https://github.com/pykeen/pykeen/pull/1239
• ⚖️🗺️ Fix estimate diversity function by @dobraczka in https://github.com/pykeen/pykeen/pull/1242
• 👋🌐 Update Hello World Notebook by @mberr in https://github.com/pykeen/pykeen/pull/1249
• 💾📉 Improve Memory-Efficiency of Converting OGB Datasets to TriplesFactory by @mberr in https://github.com/pykeen/pykeen/pull/1253
• 🔧✍️ Fix CachedTextRepresentation.from_dataset by @mberr in https://github.com/pykeen/pykeen/pull/1259
• 🧬 💾 Add the PharMeBINet dataset by @sbonner0 in https://github.com/pykeen/pykeen/pull/1257
• ⚗️🎯 Fix norm limit regularizers hpo defaults by @mberr in https://github.com/pykeen/pykeen/pull/1274
• 🤔🙅‍♀️ Fix TransH HPO compatability by @mberr in https://github.com/pykeen/pykeen/pull/1277
• 🔥🪞 Fix relation prediction with inverses by @mberr in https://github.com/pykeen/pykeen/pull/1304
• 🧹🧑‍⚖️ add gc_after_trial parameter for optuna by @LizzAlice in https://github.com/pykeen/pykeen/pull/1301
• 🐏🚀 Use torch_max_mem for automatic memory optimization in Evaluator by @mberr in https://github.com/pykeen/pykeen/pull/1261
• ⚓↕️ CSGraphAnchorSearcher: Ensure top-k index array is sorted by @mberr in https://github.com/pykeen/pykeen/pull/1318
• 🔥🧩 Fix NodePiece & Complex Embeddings by @mberr in https://github.com/pykeen/pykeen/pull/1288
• 🥄🧩 Utility to create inductive NodePiece representations by @mberr in https://github.com/pykeen/pykeen/pull/1322
• 🍂🚮 Ensure cleanup of temporary files by @mberr in https://github.com/pykeen/pykeen/pull/1307
• ↔️⭐ Merge BoxE interaction by @mberr in https://github.com/pykeen/pykeen/pull/1180
• 🌅🔪 Early Slicing for Lazy Target Representations by @mberr in https://github.com/pykeen/pykeen/pull/1321
• 🔧🔮 Fix predict_all for inductive inference by @mberr in https://github.com/pykeen/pykeen/pull/1320
• 🏗️🌊 Support resolving non-rank-based metrics by @mberr in https://github.com/pykeen/pykeen/pull/1237
• 📖✨ Update readme by @mberr in https://github.com/pykeen/pykeen/pull/968
• ⁉️⭕ Raise error when encountering a checkpoint_name in the HPO configuration by @mberr in https://github.com/pykeen/pykeen/pull/1324
• 📉☎️ Validation Loss Training Callback by @mberr in https://github.com/pykeen/pykeen/pull/1169
• Relax protobuf requirement by @cthoyt in https://github.com/pykeen/pykeen/pull/1332
• ✅📉 Check Losses' HPO Defaults by @mberr in https://github.com/pykeen/pykeen/pull/1333
• 🔝📐 Bump PyTorch Geometric cpu-build version for CI by @mberr in https://github.com/pykeen/pykeen/pull/1336
• ☑️💸 Update Losses' HPO default range checks by @mberr in https://github.com/pykeen/pykeen/pull/1337
• 🎣🏆 Repo cleanup and fix RGCN's hpo_default by @mberr in https://github.com/pykeen/pykeen/pull/1370

New Contributors

• @LizzAlice made their first contribution in https://github.com/pykeen/pykeen/pull/1301

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.10.1...v1.10.2

What's Changed

• 📚🛗 Update Prediction Migration Guide by @mberr in https://github.com/pykeen/pykeen/pull/1233
• 🚚🪞Make sure inductive representation is on same device by @dobraczka in https://github.com/pykeen/pykeen/pull/1229

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.10.0...v1.10.1

The PyKEEN 1.10 release contains a huge variety of bug fixes, performance improvements, and new features. A few highlights include symmetric sLCWA training loop, evaluation with OGB, biomedical entity representation modules, low-rank representation approximation, and many improvements to the prediction pipeline.

Models and Layers

• 🔧✈️ Fix TransH by @mberr in https://github.com/pykeen/pykeen/pull/1057
• ♚♔ Update ConvKB interaction by @mberr in https://github.com/pykeen/pykeen/pull/1065
• 🐸🫖 Fix QuatE by @mberr in https://github.com/pykeen/pykeen/pull/1056
• 🐸🫖 Fix failing QuatE tests by @mberr in https://github.com/pykeen/pykeen/pull/1070
• 🩹💯 Fix typo in OpenEA graph size by @dobraczka in https://github.com/pykeen/pykeen/pull/1073
• 🌑⛱️ Inductive ERModel base class by @mberr in https://github.com/pykeen/pykeen/pull/1106
• 🏋️ 🔧 Kwargs fix for edge weighting in CompGCNLayer by @migalkin in https://github.com/pykeen/pykeen/pull/1138
• ↔️⭐ Merge ComplEx interaction by @mberr in https://github.com/pykeen/pykeen/pull/1103
• ↔️⭐ Merge AutoSF interaction by @mberr in https://github.com/pykeen/pykeen/pull/1112
• 🦷 🔄 Extract inversion utilities by @cthoyt in https://github.com/pykeen/pykeen/pull/1203

NodePiece

• 📿 🧩 Support disconnected nodes in the Relation tokenizer by @migalkin in https://github.com/pykeen/pykeen/pull/1064
• ⚙️🔢 Fix InductiveNodePiece for parametric aggregations by @mberr in https://github.com/pykeen/pykeen/pull/1104

Documentation

• 🖊️📖 Fix typo in tutorial by @mberr in https://github.com/pykeen/pykeen/pull/1067

Performance

• 🍭 🚀 Add optional dep for opt_einsum by @mberr in https://github.com/pykeen/pykeen/pull/1058
• ⚽ 🔧 Properly shuttle tensors to CPU in rank-based evaluator by @Allaway11 in https://github.com/pykeen/pykeen/pull/1076
• 🍭🧑‍🚀 Update remaining einsum usages by @mberr in https://github.com/pykeen/pykeen/pull/1068
• ♻️⚙️ Re-use AMO for predict_triples_df by @mberr in https://github.com/pykeen/pykeen/pull/1089

Pipeline and Prediction

• 🔮☕ Custom Prediction Filtering by @mberr in https://github.com/pykeen/pykeen/pull/1090
• 🪓💻 Split Pipeline Code by @mberr in https://github.com/pykeen/pykeen/pull/1075
• 🔮🤔 Upgrade Prediction Consumers by @mberr in https://github.com/pykeen/pykeen/pull/1078
• 🌀 🏴‍☠️ Clean up inverse triples arguments by @cthoyt in https://github.com/pykeen/pykeen/pull/1092
• 🐛🐔 Fixing bug with index-error for predict.consume_scores by @AImenes in https://github.com/pykeen/pykeen/pull/1157

Representation

• 🔵🟦 Approximate other representation with Low-Rank by @mberr in https://github.com/pykeen/pykeen/pull/1091
• 🗿📖 Update text-based representation tutorial by @mberr in https://github.com/pykeen/pykeen/pull/1147
• 📜🔧 Fix labels not being converted to list by @mberr in https://github.com/pykeen/pykeen/pull/1209
• 🪞🧬 Text representation for biomedical entities via PyOBO by @cthoyt in https://github.com/pykeen/pykeen/pull/1055

Training and Negative Sampling

• ☺️🫖 Relax Slicing Check by @mberr in https://github.com/pykeen/pykeen/pull/1216
• 🪞🚆 Symmetric LCWA by @mberr in https://github.com/pykeen/pykeen/pull/1098
• 🫴🔋 Fix to pass any negative sampler kwargs through if present by @sbonner0 in https://github.com/pykeen/pykeen/pull/1119
• 💾🚆 Fix re-loading training triples by @mberr in https://github.com/pykeen/pykeen/pull/1185

Loss

• Remove unnecessary unsqueezing in MRL by @sbonner0 in https://github.com/pykeen/pykeen/pull/1128
• :book: :hammer_and_wrench: Fix losses docs typos by @nicolafan in https://github.com/pykeen/pykeen/pull/1200

Metrics and Evaluation

• 🔍📈 Fix MacroRankBasedEvaluator share precomputed weights for different triples by @mberr in https://github.com/pykeen/pykeen/pull/1079
• 🧮🪞 Rank-Based Metrics with Confidence Estimates via Bootstrapping by @mberr in https://github.com/pykeen/pykeen/pull/1084
• Incremental ranks by @mberr in https://github.com/pykeen/pykeen/pull/1083
• 😮🪑 Add basic support of OGB's evaluation by @mberr in https://github.com/pykeen/pykeen/pull/1088
• 😮🪑 Add OGB Evaluator by @mberr in https://github.com/pykeen/pykeen/pull/948
• 🌪️➰ Evaluation loop and filter triples by @mberr in https://github.com/pykeen/pykeen/pull/1214
• ⛳💌 Separately Expose Clearing of Intermediate Evaluator Results by @mberr in https://github.com/pykeen/pykeen/pull/1195

Lightning

• ⚡🩹 Fix lightning training without validation by @mberr in https://github.com/pykeen/pykeen/pull/1158
• ⚡🧪 Bring back lightning tests by @mberr in https://github.com/pykeen/pykeen/pull/1191

Misc

• 📌🖼️ Fix plotting utility by @mberr in https://github.com/pykeen/pykeen/pull/1072
• ☁️☀️ Fix word cloud by @mberr in https://github.com/pykeen/pykeen/pull/1081
• ✂️⌨️ Remove unused code by @mberr in https://github.com/pykeen/pykeen/pull/1095
• 💲🐚 Remove $ sign from README shell examples by @mberr in https://github.com/pykeen/pykeen/pull/1101
• 🩹🧑‍🏫 Fix scikit-learn dependency by @dobraczka in https://github.com/pykeen/pykeen/pull/1122
• 👷🚇 Fix CI failure due to new versions by @mberr in https://github.com/pykeen/pykeen/pull/1170
• 🩹🪟 Fix Windows installation instructions by @jamesmyatt in https://github.com/pykeen/pykeen/pull/1164
• 🧹🐻 Cleanup before 1.9 release by @cthoyt in https://github.com/pykeen/pykeen/pull/1204
• 🩹⚙️ Include result_tracker field in dict returned by _get_best_study_config() by @AntonisKl in https://github.com/pykeen/pykeen/pull/1206

New Contributors

• @Allaway11 made their first contribution in https://github.com/pykeen/pykeen/pull/1076
• @jamesmyatt made their first contribution in https://github.com/pykeen/pykeen/pull/1164
• @AImenes made their first contribution in https://github.com/pykeen/pykeen/pull/1157
• @nicolafan made their first contribution in https://github.com/pykeen/pykeen/pull/1200
• @AntonisKl made their first contribution in https://github.com/pykeen/pykeen/pull/1206

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.9.0...v1.10.0

The theme of this release of PyKEEN is centered on new and exciting representations to bring more kinds of data (text, image, scalar data) into training in an elegant way. Several of these contribute to new functionality for NodePiece.

Training and Evaluation

• 🔬🔁 Evaluation loop by @mberr in https://github.com/pykeen/pykeen/pull/768
• 🐦🛑 Early stopping: Reload weights from best epoch by @mberr in https://github.com/pykeen/pykeen/pull/961
• 🔬🚪 Update evaluator's evaluate to pass through kwargs by @mberr in https://github.com/pykeen/pykeen/pull/938
• 🌪😿 Fix epoch loss by @mberr in https://github.com/pykeen/pykeen/pull/1021

Datasets

• 🥨🕸️ Add Global Biotic Interactions (GloBI) dataset by @cthoyt in https://github.com/pykeen/pykeen/pull/947
• Fix dataset caching with inverse triples by @mberr in https://github.com/pykeen/pykeen/pull/1034

Models

New

• 🇨🇴🕸️ Add co-occurence filtered meta model by @mberr in https://github.com/pykeen/pykeen/pull/943

Updates

• 📏🤝 Add LineaRE interaction by @mberr in https://github.com/pykeen/pykeen/pull/971
• ✨🤖 Update ERMLP to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/869
• ✨🤖 Update ERMLP-E to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/872
• ✨🤖 Update HolE to ER-Model by @mberr in https://github.com/pykeen/pykeen/pull/953
• ✨🤖 Update TransE to ER-Model by @mberr in https://github.com/pykeen/pykeen/pull/955
• ✨🤖 Update TransH to ER-Model by @mberr in https://github.com/pykeen/pykeen/pull/954
• ✨🤖 Update RESCAL to ER-Model by @mberr in https://github.com/pykeen/pykeen/pull/952
• ✨💀 Phase out old-style model by @mberr in https://github.com/pykeen/pykeen/pull/865
• 🫶 🧨 Update ConvKB & SE to use einsum by @mberr in https://github.com/pykeen/pykeen/pull/978
• 🏎️ 🏴‍☠️ Add efficient RGCN implementation by @mberr in https://github.com/pykeen/pykeen/pull/634
• 🔧➡️ Move Nguyen's TransE configurations into correct directory by @PhaelIshall in https://github.com/pykeen/pykeen/pull/957

Representations

• 👥📝 Wikidata Textual Representations by @mberr in https://github.com/pykeen/pykeen/pull/966
• 🔗🗿 Combined Representation by @mberr in https://github.com/pykeen/pykeen/pull/964
• 🔳🔲 Add PartitionRepresentation by @mberr in https://github.com/pykeen/pykeen/pull/980
• 📋❇️ Generalize Text Encoders & add a simple one by @mberr in https://github.com/pykeen/pykeen/pull/969
• 🚚🗽 Add transformed representation by @mberr in https://github.com/pykeen/pykeen/pull/984
• 👀📇 Simple visual representations by @mberr in https://github.com/pykeen/pykeen/pull/965
• 🏋️🚂 Tensor Train Representation by @mberr in https://github.com/pykeen/pykeen/pull/989

NodePiece

• ⚓🔍 NodePiece: GPU-enabled BFS searcher by @migalkin in https://github.com/pykeen/pykeen/pull/990
• 🏴‍☠️🌊 NodePiece x METIS by @mberr in https://github.com/pykeen/pykeen/pull/988
• ⚓ 📖 NodePiece documentation on MetisAnchorTokenizer by @migalkin in https://github.com/pykeen/pykeen/pull/1026

Documentation

• 😺🇪🇬 Explicitly set Sphinx language by @mberr in https://github.com/pykeen/pykeen/pull/951
• 💥 📒 Add troubleshooting for loading old models by @jas-ho in https://github.com/pykeen/pykeen/pull/963
• 📘 🚀 Update README by @cthoyt in https://github.com/pykeen/pykeen/pull/1039
• 📒 🤡 Fix documentation build by @cthoyt in https://github.com/pykeen/pykeen/pull/946
• 📕 🏴‍☠️ Update docs and deprecations by @mberr in https://github.com/pykeen/pykeen/pull/979
• 📗 🖊️ Update docs about normalizers and constrainers by @mberr in https://github.com/pykeen/pykeen/pull/1047

Loss

• ⚔️⚖️ Add adversarially weighted BCE loss by @mberr in https://github.com/pykeen/pykeen/pull/958
• ⚔️🤔 New procedure for computing AdversarialBCEWithLogits by @migalkin in https://github.com/pykeen/pykeen/pull/997

Predictions

• 🐉🐉 Score multiple tails at once by @mberr in https://github.com/pykeen/pykeen/pull/949
• 🔮〰️ Update Prediction Filtering by @mberr in https://github.com/pykeen/pykeen/pull/1048
• 🔮 🎉 Add inference_mode annotation to get_prediction_df() by @tatiana-iazykova in https://github.com/pykeen/pykeen/pull/1024
• 🔨🧪 Fix the device in _safe_evaluate() by @migalkin in https://github.com/pykeen/pykeen/pull/1041

Meta

• 🤖🖐️ Update GHA by @mberr in https://github.com/pykeen/pykeen/pull/959
• 🦈🧵 Darglint forever by @cthoyt in https://github.com/pykeen/pykeen/pull/985

Misc

• 🚨📊 Cast kwargs as strings in plot_er by @vsocrates in https://github.com/pykeen/pykeen/pull/945
• ⛏📲 Add utility to analyze degree distributions by @mberr in https://github.com/pykeen/pykeen/pull/857
• 🥯✔️ Add max_id/shape verification by @mberr in https://github.com/pykeen/pykeen/pull/983
• Use torch_ppr by @mberr in https://github.com/pykeen/pykeen/pull/995
• ➕🍹 Add ExtraReprMixin by @mberr in https://github.com/pykeen/pykeen/pull/994
• 🛤️🛢️ Add prefix when tracking pipeline metrics by @mberr in https://github.com/pykeen/pykeen/pull/998
• ⭕🔺 Update PyG version for CI by @mberr in https://github.com/pykeen/pykeen/pull/1025
• #️⃣🐍 Allow passing numpy.ndarray to CoreTriplesFactory by @mberr in https://github.com/pykeen/pykeen/pull/1029

New Contributors

• @PhaelIshall made their first contribution in https://github.com/pykeen/pykeen/pull/957
• @jas-ho made their first contribution in https://github.com/pykeen/pykeen/pull/963
• @tatiana-iazykova made their first contribution in https://github.com/pykeen/pykeen/pull/1024

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.8.2...v1.9.0

Datasets

• Add the PrimeKG dataset by @sbonner0 in https://github.com/pykeen/pykeen/pull/915
• 🌀🔗 Extend EA datasets to allow loading a unified graph by @mberr in https://github.com/pykeen/pykeen/pull/871
• 🎺🎷 Fix wk3l loading by @mberr in https://github.com/pykeen/pykeen/pull/907

Lightning

• 🔥⚡ PyTorch Lightning by @mberr in https://github.com/pykeen/pykeen/pull/905
• 🔥⚡ PyTorch Lightning - Part 2 by @mberr in https://github.com/pykeen/pykeen/pull/917
• 🚅⚡ Test Training with PyTorch Lightning by @mberr in https://github.com/pykeen/pykeen/pull/930

Losses

• 📉🧑‍🤝‍🧑 Fix default loss of PairRE by @mberr in https://github.com/pykeen/pykeen/pull/925
• ℹ️🦭 Add InfoNCE loss by @mberr in https://github.com/pykeen/pykeen/pull/926
• ℹ️🚀 Update InfoNCE LCWA implementation by @mberr in https://github.com/pykeen/pykeen/pull/928

Representations

• 🎲🚶 Random Walk Positional Encoding by @mberr in https://github.com/pykeen/pykeen/pull/918
• 🏛️👨 Weisfeiler-Lehman Features by @mberr in https://github.com/pykeen/pykeen/pull/920

Other great stuff that isn't the previous commit (it's after 5PM)

• 🧫🐍 Update scipy minimum version by @mberr in https://github.com/pykeen/pykeen/pull/891
• ♻️☎️ Re-use optimized batch-size in evaluation callback by @mberr in https://github.com/pykeen/pykeen/pull/886
• 🖥️🦎 Fix complex initialization by @mberr in https://github.com/pykeen/pykeen/pull/888
• 📦📚 Update BoxE reproducibility configurations by @mberr in https://github.com/pykeen/pykeen/pull/631
• 🫓🪁 Improve loading of triples with nan strings by @SenJia in https://github.com/pykeen/pykeen/pull/883
• 🪵 ✨ Update flake8 ignores by @cthoyt in https://github.com/pykeen/pykeen/pull/897
• 👯‍♂️👯‍♀️ Unique hashes in the NodePiece representation by @migalkin in https://github.com/pykeen/pykeen/pull/896
• 📐📨 PyTorch Geometric Message Passing Representations by @mberr in https://github.com/pykeen/pykeen/pull/894
• 🪛📁 Fix directory path normalization by @mberr in https://github.com/pykeen/pykeen/pull/890
• 🧛🇪🇺 Implement more graph pair unification approaches by @mberr in https://github.com/pykeen/pykeen/pull/893
• 🔙🌙 Backwards Compatibility for init phases by @mberr in https://github.com/pykeen/pykeen/pull/899
• 📔✅ Update Docstring Coverage check by @mberr in https://github.com/pykeen/pykeen/pull/892
• 🪄🖊️ Class resolver type annotations by @mberr in https://github.com/pykeen/pykeen/pull/904
• 📋➡️ Move listing experiments from epilog to own command by @mberr in https://github.com/pykeen/pykeen/pull/903
• 🔧📜 Update hpo tutorial about grid search by @mberr in https://github.com/pykeen/pykeen/pull/902
• 📖 🛠️ Fix typo in prediction docs by @mberr in https://github.com/pykeen/pykeen/pull/912
• ✂️🌰 Extract triple-independent information from CoreTriplesFactory by @mberr in https://github.com/pykeen/pykeen/pull/908
• 🐍👍 Increase Minimum Python Version to 3.8 by @mberr in https://github.com/pykeen/pykeen/pull/921
• 🧚💾 Extend save to directory doc by @mberr in https://github.com/pykeen/pykeen/pull/916
• 🧠🏷️ Maximize memory utilization for label based initialization by @mberr in https://github.com/pykeen/pykeen/pull/898
• ✏️🇮🇳 Rename inductive representation methods by @mberr in https://github.com/pykeen/pykeen/pull/929
• 👾 ⚽ Add missing device by @vsocrates in https://github.com/pykeen/pykeen/pull/936

New Contributors

• @SenJia made their first contribution in https://github.com/pykeen/pykeen/pull/883
• @vsocrates made their first contribution in https://github.com/pykeen/pykeen/pull/936

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.8.1...v1.8.2

PyKEEN 1.8.1 contains a few critical bug fixes along with some other cool updates.

Evaluation

• ⚖️🌡️ Weighted Rank-Based Metrics by @mberr in https://github.com/pykeen/pykeen/pull/837
• 🌌🧐 Macro evaluation by @mberr in https://github.com/pykeen/pykeen/pull/850

Inductive Models

• ⚓🧍 NodePiece Anchor Searching via PPR by @mberr in https://github.com/pykeen/pykeen/pull/870

Transductive Models

• ✨🤖 Update DistMult to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/874
• ✨🤖 Update ProjE to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/876
• ✨🤖 Update RotatE to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/877
• ✨🤖 Update ConvE to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/875
• 🚛®️ Update TuckER to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/866
• ✨🦜 Upgrade TransR to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/868

New Datasets

• 🌪️ 📖 Add ILPC datasets and inductive dataset resolver by @cthoyt in https://github.com/pykeen/pykeen/pull/848
• 👑🤑 Add aristo-v4 dataset by @mberr in https://github.com/pykeen/pykeen/pull/855

Documentation

• 📗✨ Update documentation to better reflect new-style models by @mberr in https://github.com/pykeen/pykeen/pull/879
• 👣 📚 Correct typos in "First Steps" tutorial by @andreasala98 in https://github.com/pykeen/pykeen/pull/846

Bug Fixes

• 🔧#️⃣ Fix arange dtype and clip variances by @mberr in https://github.com/pykeen/pykeen/pull/881
• 🪄⚖️ Fix pop_regularization_term by @mberr in https://github.com/pykeen/pykeen/pull/849
• 🧑‍🏭🔢 Fix numeric triples factory by @mberr in https://github.com/pykeen/pykeen/pull/862
• 🍔 🪓 Ensure reproducible splits for all datasets by @mberr in https://github.com/pykeen/pykeen/pull/856
• 🚫🏋 Raise explicit error if no training batch was available by @mberr in https://github.com/pykeen/pykeen/pull/860
• 🚚💻 Fix TransformerEncoder tokens' device by @mberr in https://github.com/pykeen/pykeen/pull/861

Misc

• 🔎🏋️ Resolve optimizer, LR-scheduler & tracker in training loop by @mberr in https://github.com/pykeen/pykeen/pull/852
• 🎯🪜 Update default batch size HPO range by @mberr in https://github.com/pykeen/pykeen/pull/864
• ♻️🔥 Use torch builtin broadcast by @mberr in https://github.com/pykeen/pykeen/pull/873

New Contributors

• @andreasala98 made their first contribution in https://github.com/pykeen/pykeen/pull/846

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.8.0...v1.8.1

Among a ton of updates since the beginning of the year, PyKEEN v1.8.0 has three major themes:

1. The introduction of the inductive link prediction pipeline and the NodePiece model. We highly suggest checking out An Open Challenge for Inductive Link Prediction on Knowledge Graphs to go along with this new pipeline and models.
2. The introduction of new rank-based evaluation metrics to go along with A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs
3. Major internal refactoring of negative sampling to better use PyTorch's data loaders and support multi-CPU generation (special thanks to @Koenkalle for help testing this)

NodePiece and Inductive Link Prediction

• 🦆🐍 Inductive LP framework by @migalkin in https://github.com/pykeen/pykeen/pull/722
• 🌙🐺 Add mode parameter by @cthoyt in https://github.com/pykeen/pykeen/pull/769
• 🍸✌️ Mixed tokenization for NodePiece by @mberr in https://github.com/pykeen/pykeen/pull/770
• ☮️⚓ NodePiece with anchors by @mberr in https://github.com/pykeen/pykeen/pull/755
• 🥒🏴‍☠️ Precomputed Tokenization for NodePiece by @mberr in https://github.com/pykeen/pykeen/pull/822
• 🦜📖 Refactor NodePiece and improve documentation by @cthoyt in https://github.com/pykeen/pykeen/pull/833
• ⚓ 🔧 NodePiece MixtureAnchorSelection unique anchor IDs fix + PageRank fix by @migalkin in https://github.com/pykeen/pykeen/pull/776
• 🧩🧪 NodePiece experimental configs by @migalkin in https://github.com/pykeen/pykeen/pull/771
• 👀 🏋️ Attention edge weighting by @migalkin in https://github.com/pykeen/pykeen/pull/734

Models

New

• ⛟↔️ Add (multi-)linear Tucker interaction by @mberr in https://github.com/pykeen/pykeen/pull/751
• 🍦 🎸 Soft inverse triples baseline by @mberr in https://github.com/pykeen/pykeen/pull/543

Updated

• 🤖 ⛑️ Fix device for FixedModel by @mberr in https://github.com/pykeen/pykeen/pull/725
• 🧀 🏹 Unify usage of slice_size by @cthoyt in https://github.com/pykeen/pykeen/pull/729
• 📟 ✂️ Remove device from model by @cthoyt in https://github.com/pykeen/pykeen/pull/730
• 💃 🪥 Cleanup model argument passing by @cthoyt in https://github.com/pykeen/pykeen/pull/762

Training and Evaluation

• ✂️ ⏰ Split early stopping logic from evaluation by @mberr in https://github.com/pykeen/pykeen/pull/355
• 🎲🎚️ Sampled Rank-Based Evaluator by @mberr in https://github.com/pykeen/pykeen/pull/733
• ⛏©️ Fix Checkpointing by @mberr in https://github.com/pykeen/pykeen/pull/740
• 🌋 🗺️ Switch evaluator from dataclass to dict by @cthoyt in https://github.com/pykeen/pykeen/pull/780
• 🌀 ⚖️ Simplify evaluate by @mberr in https://github.com/pykeen/pykeen/pull/767
• 🛤️ 🔁 Store result tracker inside loop by @mberr in https://github.com/pykeen/pykeen/pull/793

Callbacks

• 📞🔙 Evaluation callback by @mberr in https://github.com/pykeen/pykeen/pull/765
• 🥊 ☎️ Early stopping via training callback by @mberr in https://github.com/pykeen/pykeen/pull/354

Data and Datasets

New

• 🪢🤔 Add OpenEA datasets by @dobraczka in https://github.com/pykeen/pykeen/pull/784
• 💉8️⃣ Add the PharmKG8k dataset by @sbonner0 in https://github.com/pykeen/pykeen/pull/797
• 🧪💉 Add PharmKG full dataset by @sbonner0 in https://github.com/pykeen/pykeen/pull/806
• ♻️ 2️⃣ Replace OGB's WikiKG by WikiKG2 by @mberr in https://github.com/pykeen/pykeen/pull/809

Updates

• 📌🧠 Use pinned memory for training data loader by @mberr in https://github.com/pykeen/pykeen/pull/747
• 🧮💃 Add property for number of parameters by @mberr in https://github.com/pykeen/pykeen/pull/804
• 💾 ♻️ Refactor dataset utility code by @cthoyt in https://github.com/pykeen/pykeen/pull/830
• 💾 🐕 Update dataset registration by @cthoyt in https://github.com/pykeen/pykeen/pull/832
• 💾 🚀 Update dataset statistics by @cthoyt in https://github.com/pykeen/pykeen/pull/834
• 😴🐲 Ignore create_inverse_triples for caching hash digest by @mberr in https://github.com/pykeen/pykeen/pull/813
• 🖇️ 📊 Use Figshare link for OpenEA dataset by @dobraczka in https://github.com/pykeen/pykeen/pull/838
• 📦 💾 Batch data loader by @mberr in https://github.com/pykeen/pykeen/pull/817
• 📥 🏭 Save Training Triples Factory by @mali-git in https://github.com/pykeen/pykeen/pull/655
• 🦞 💿 Negative sampling in data loader by @mberr in https://github.com/pykeen/pykeen/pull/417
• 💾💽 Change serialization format by @mberr in https://github.com/pykeen/pykeen/pull/785
• 🧰 📥 Cache dataset loading by @mberr in https://github.com/pykeen/pykeen/pull/569

Metrics

• 📏🪕 Compute Candidate Set Sizes by @mberr in https://github.com/pykeen/pykeen/pull/732
• 🏆 🍱 Update rank data structure by @cthoyt in https://github.com/pykeen/pykeen/pull/758
• 📐 🍱 Update metric key data structure by @cthoyt in https://github.com/pykeen/pykeen/pull/759
• 🐳 😃 Reorganize metrics and expectation functions by @cthoyt in https://github.com/pykeen/pykeen/pull/763
• 🏛️ 👽 Add improved indicator constructor by @cthoyt in https://github.com/pykeen/pykeen/pull/781
• 🏛️ 🥾 Improve metrics data structures by @cthoyt in https://github.com/pykeen/pykeen/pull/782
• 🎩 🎸 Class-Based Rank-Based Metrics by @mberr in https://github.com/pykeen/pykeen/pull/786
• ⚙️🌡️ Add more adjusted metrics by @cthoyt in https://github.com/pykeen/pykeen/pull/814
• 🪡🗜️ Refactor derived metrics by @mberr in https://github.com/pykeen/pykeen/pull/835
• 🔢 🐎 Update value range & docstring of adjusted metrics by @mberr in https://github.com/pykeen/pykeen/pull/823
• ➕🌍 Add option to add all default rank-based metrics by @mberr in https://github.com/pykeen/pykeen/pull/827
• 🪛💡 Fix RankBasedMetricResults.iter_rows by @mberr in https://github.com/pykeen/pykeen/pull/792

Prediction

• 🙃👓 Predict workflow with inverse relations by @mberr in https://github.com/pykeen/pykeen/pull/726

Representations

• 🪛🔗 Change interactions' shape by @mberr in https://github.com/pykeen/pykeen/pull/736
• 🍝 🛰️ Update constrainer, initializer, and normalizer resolution by @mberr in https://github.com/pykeen/pykeen/pull/742
• 🦄 🔢 Only get representations for unique indices by @mberr in https://github.com/pykeen/pykeen/pull/743
• ⛔💠 Remove get in canonical shape by @mberr in https://github.com/pykeen/pykeen/pull/745
• ⏩🛌 Fix dtype forwarding in Embedding by @mberr in https://github.com/pykeen/pykeen/pull/746
• 📏🕳️ Move normalization to base representation by @mberr in https://github.com/pykeen/pykeen/pull/818
• ✏️📏 Unify representation module nomenclature by @mberr in https://github.com/pykeen/pykeen/pull/811
• ✨💤 Resolve Representations by @mberr in https://github.com/pykeen/pykeen/pull/803

Trackers

• Add loss kwargs to ResultTracker by @Rodrigo-A-Pereira in https://github.com/pykeen/pykeen/pull/741
• 🪡💻 Fix typo in ConsoleTracker.log_metrics by @mberr in https://github.com/pykeen/pykeen/pull/787

Fixes

• 🍌🍍 Fix ValueError during size probing on GPU machines by @mberr in https://github.com/pykeen/pykeen/pull/821
• 🪄➰ Fix device error in training loop by @mberr in https://github.com/pykeen/pykeen/pull/774
• ☕📱 Fix filterer's device by @mberr in https://github.com/pykeen/pykeen/pull/801
• ⛵💻 Make sure indices are moved to device by @mberr in https://github.com/pykeen/pykeen/pull/800

Documentation, Typing, and Packaging

• 🌊 👋 Goodbye to setup.py and Makefile for building the docs by @cthoyt in https://github.com/pykeen/pykeen/pull/761
• 🌌 🥛 Update Constants and Types by @mberr in https://github.com/pykeen/pykeen/pull/754
• 🔫 🐈‍⬛ Update black by @cthoyt in https://github.com/pykeen/pykeen/pull/764
• 🐍 💪 Add Python 3.10 support by @cthoyt in https://github.com/pykeen/pykeen/pull/831
• 🥰 📙 Update argument passing and documentation by @cthoyt in https://github.com/pykeen/pykeen/pull/842
• 🍊 ⌨️ Typing Updates by @cthoyt in https://github.com/pykeen/pykeen/pull/760
• ⚙️📚 Fix HPO doc by @mberr in https://github.com/pykeen/pykeen/pull/820
• 📖🔪 Extend documentation on subbatching and slicing by @mberr in https://github.com/pykeen/pykeen/pull/810

Misc

• ✉️ ♻️ Add list of available configurations to usage message of reproduction by @mberr in https://github.com/pykeen/pykeen/pull/753
• 🦎⚡ Update class-resolver by @cthoyt in https://github.com/pykeen/pykeen/pull/775

Full Changelog: https://github.com/pykeen/pykeen/compare/v1.7.0...v1.8.0

New Models

• Add BoxE by @ralphabb in https://github.com/pykeen/pykeen/pull/618
• Add TripleRE by @mberr in https://github.com/pykeen/pykeen/pull/712
• Add AutoSF by @mberr in https://github.com/pykeen/pykeen/pull/713
• Add Transformer by @mberr in https://github.com/pykeen/pykeen/pull/714
• Add Canonical Tensor Decomposition by @mberr in https://github.com/pykeen/pykeen/pull/663
• Add (novel) Fixed Model by @cthoyt in https://github.com/pykeen/pykeen/pull/691
• Add NodePiece model by @mberr in https://github.com/pykeen/pykeen/pull/621

Updated Models

• Update R-GCN configuration by @mberr in https://github.com/pykeen/pykeen/pull/610
• Update ConvKB to ERModel by @cthoyt in https://github.com/pykeen/pykeen/pull/425
• Update ComplEx to ERModel by @mberr in https://github.com/pykeen/pykeen/pull/639
• Rename TranslationalInteraction to NormBasedInteraction by @mberr in https://github.com/pykeen/pykeen/pull/651
• Fix generic slicing dimension by @mberr in https://github.com/pykeen/pykeen/pull/683
• Rename UnstructuredModel to UM and StructuredEmbedding to SE by @cthoyt in https://github.com/pykeen/pykeen/pull/721
• Allow to pass unresolved loss to ERModel's __init__ by @mberr in https://github.com/pykeen/pykeen/pull/717

Representations and Initialization

• Add low-rank embeddings by @mberr in https://github.com/pykeen/pykeen/pull/680
• Add NodePiece representation by @mberr in https://github.com/pykeen/pykeen/pull/621
• Add label-based initialization using a transformer (e.g., BERT) by @mberr in https://github.com/pykeen/pykeen/pull/638 and https://github.com/pykeen/pykeen/pull/652
• Add label-based representation (e.g., to update language model using KGEM) by @mberr in https://github.com/pykeen/pykeen/pull/652
• Remove literal representations (use label-based initialization instead) by @mberr in https://github.com/pykeen/pykeen/pull/679

Training

• Fix displaying previous epoch's loss by @mberr in https://github.com/pykeen/pykeen/pull/627
• Fix kwargs transmission on MultiTrainingCallback by @Rodrigo-A-Pereira in https://github.com/pykeen/pykeen/pull/645
• Extend Callbacks by @mberr in https://github.com/pykeen/pykeen/pull/609
• Add gradient clipping by @mberr in https://github.com/pykeen/pykeen/pull/607
• Fix negative score shape for sLCWA by @mberr in https://github.com/pykeen/pykeen/pull/624
• Fix epoch loss for loss reduction != "mean" by @mberr in https://github.com/pykeen/pykeen/pull/623
• Add sLCWA support for Cross Entropy Loss by @mberr in https://github.com/pykeen/pykeen/pull/704

Inference

• Add uncertainty estimate functions via MC dropout by @mberr in https://github.com/pykeen/pykeen/pull/688
• Fix predict top k by @mberr in https://github.com/pykeen/pykeen/pull/690
• Fix indexing in predict_* methods when using inverse relations by @mberr in https://github.com/pykeen/pykeen/pull/699
• Move tensors to device for predict_* methods by @mberr in https://github.com/pykeen/pykeen/pull/658

Trackers

• Fix wandb logging by @mberr in https://github.com/pykeen/pykeen/pull/647
• Add multi-result tracker by @mberr in https://github.com/pykeen/pykeen/pull/682
• Add Python result tracker by @mberr in https://github.com/pykeen/pykeen/pull/681
• Update file trackers by @cthoyt in https://github.com/pykeen/pykeen/pull/629

Evaluation

• Store rank count by @mberr in https://github.com/pykeen/pykeen/pull/672
• Extend evaluate() for easier relation filtering by @mberr in https://github.com/pykeen/pykeen/pull/391
• Rename sklearn evaluator and refactor evaluator code by @cthoyt in https://github.com/pykeen/pykeen/pull/708
• Add additional classification metrics via rexmex by @cthoyt in https://github.com/pykeen/pykeen/pull/668

Triples and Datasets

• Add helper dataset with internal batching for Schlichtkrull sampling by @mberr in https://github.com/pykeen/pykeen/pull/616
• Refactor splitting code and improve documentation by @mberr in https://github.com/pykeen/pykeen/pull/709
• Switch np.loadtxt to pandas.read_csv by @mberr in https://github.com/pykeen/pykeen/pull/695
• Add binary I/O to triples factories @cthoyt in https://github.com/pykeen/pykeen/pull/665

Torch Usage

• Use torch.finfo to determine suitable epsilon values by @mberr in https://github.com/pykeen/pykeen/pull/626
• Use torch.isin instead of own implementation by @mberr in https://github.com/pykeen/pykeen/pull/635
• Switch to using torch.inference_mode instead of torch.no_grad by @sbonner0 in https://github.com/pykeen/pykeen/pull/604

Miscellaneous

• Add YAML experiment format by @mberr in https://github.com/pykeen/pykeen/pull/612
• Add comparison with reproduction results during replication, if available by @mberr in https://github.com/pykeen/pykeen/pull/642
• Adapt hello_world notebook to API changes by @dobraczka in https://github.com/pykeen/pykeen/pull/649
• Add testing configuration for Jupyter notebooks by @mberr in https://github.com/pykeen/pykeen/pull/650
• Add empty default loss_kwargs by @mali-git in https://github.com/pykeen/pykeen/pull/656
• Optional extra config for reproduce by @mberr in https://github.com/pykeen/pykeen/pull/692
• Store pipeline configuration in pipeline result by @mberr in https://github.com/pykeen/pykeen/pull/685
• Fix upgrade to sequence by @mberr in https://github.com/pykeen/pykeen/pull/697
• Fix pruner use in hpo_pipeline by @mberr in https://github.com/pykeen/pykeen/pull/724

Housekeeping

• Automatically lint with black by @cthoyt in https://github.com/pykeen/pykeen/pull/605
• Documentation and style guide cleanup by @cthoyt in https://github.com/pykeen/pykeen/pull/606

This release is only compatible with PyTorch 1.9+. Because of some changes, it's now pretty non-trivial to support both, so moving forwards PyKEEN will continue to support the latest version of PyTorch and try its best to keep backwards compatibility.

New Models

• DistMA (https://github.com/pykeen/pykeen/pull/507)
• TorusE (https://github.com/pykeen/pykeen/pull/510)
• Frequency Baselines (https://github.com/pykeen/pykeen/pull/514)
• Gated Distmult Literal (https://github.com/pykeen/pykeen/pull/591, thanks @Rodrigo-A-Pereira)

New Datasets

• WD50K (https://github.com/pykeen/pykeen/pull/511)
• Wikidata5M (https://github.com/pykeen/pykeen/pull/528)
• BioKG (https://github.com/pykeen/pykeen/pull/585, thanks @sbonner0)

New Losses

• Double Margin Loss (https://github.com/pykeen/pykeen/pull/539)
• Focal Loss (https://github.com/pykeen/pykeen/pull/542)
• Pointwise Hinge Loss (https://github.com/pykeen/pykeen/pull/540)
• Soft Pointwise Hinge Loss (https://github.com/pykeen/pykeen/pull/540)
• Pairwise Logistic Loss (https://github.com/pykeen/pykeen/pull/540)

Added

• Tutorial in using checkpoints when bringing your own data (https://github.com/pykeen/pykeen/pull/498)
• Learning rate scheduling (https://github.com/pykeen/pykeen/pull/492)
• Checkpoints include entity/relation maps (https://github.com/pykeen/pykeen/pull/498)
• QuatE reproducibility configurations (https://github.com/pykeen/pykeen/pull/486)

Changed

• Reimplment SE (https://github.com/pykeen/pykeen/pull/521) and NTN (https://github.com/pykeen/pykeen/pull/522) with new-style models
• Generalize pairwise loss and pointwise loss hierarchies (https://github.com/pykeen/pykeen/pull/540)
• Update to use PyTorch 1.9 functionality (https://github.com/pykeen/pykeen/pull/489)
• Generalize generator strategies in LCWA (https://github.com/pykeen/pykeen/pull/602)

Fixed

• FileNotFoundError on Windows/Anaconda (https://github.com/pykeen/pykeen/pull/503, thanks @Hao-666)
• Fixed docstring for ComplEx interaction (https://github.com/pykeen/pykeen/pull/504)
• Make DistMult the default interaction function for R-GCN (https://github.com/pykeen/pykeen/pull/548)
• Fix gradient error in CompGCN buffering (https://github.com/pykeen/pykeen/pull/573)
• Fix splitting of numeric triples factories (https://github.com/pykeen/pykeen/pull/594, thanks @Rodrigo-A-Pereira)
• Fix determinism in spitting of triples factory (https://github.com/pykeen/pykeen/pull/500)
• Fix documentation and improve HPO suggestion (https://github.com/pykeen/pykeen/pull/524, thanks @kdutia)

New Metrics

• Adjusted Arithmetic Mean Rank Index (https://github.com/pykeen/pykeen/pull/378)
• Add harmonic, geometric, and median rankings (https://github.com/pykeen/pykeen/pull/381)

New Trackers

• Console Tracker (https://github.com/pykeen/pykeen/pull/440)
• Tensorboard Tracker (https://github.com/pykeen/pykeen/pull/416; thanks @sbonner0)

New Models

• QuatE (https://github.com/pykeen/pykeen/pull/367)
• CompGCN (https://github.com/pykeen/pykeen/pull/382)
• CrossE (https://github.com/pykeen/pykeen/pull/467)
• Reimplementation of LiteralE with arbitrary combination (g) function (https://github.com/pykeen/pykeen/pull/245)

New Negative Samplers

• Pseudo-typed Negative Sampler (https://github.com/pykeen/pykeen/pull/412)

Datasets

• Removed invalid datasets (OpenBioLink filtered sets; https://github.com/pykeen/pykeen/pull/https://github.com/pykeen/pykeen/pull/439)
• Added WK3k-15K (https://github.com/pykeen/pykeen/pull/403)
• Added WK3l-120K (https://github.com/pykeen/pykeen/pull/403)
• Added CN3l (https://github.com/pykeen/pykeen/pull/403)

Added

• Documentation on using PyKEEN in Google Colab and Kaggle (https://github.com/pykeen/pykeen/pull/379, thanks @jerryIsHere)
• Pass custom training loops to pipeline (https://github.com/pykeen/pykeen/pull/334)
• Compatibility later for the fft module (https://github.com/pykeen/pykeen/pull/288)
• Official Python 3.9 support, now that PyTorch has it (https://github.com/pykeen/pykeen/pull/223)
• Utilities for dataset analysis (https://github.com/pykeen/pykeen/pull/16, https://github.com/pykeen/pykeen/pull/392)
• Filtering of negative sampling now uses a bloom filter by default (https://github.com/pykeen/pykeen/pull/401)
• Optional embedding dropout (https://github.com/pykeen/pykeen/pull/422)
• Added more HPO suggestion methods and docs (https://github.com/pykeen/pykeen/pull/446)
• Training callbacks (https://github.com/pykeen/pykeen/pull/429)
• Class resolver for datasets (https://github.com/pykeen/pykeen/pull/473)

Updated

• R-GCN implementation now uses new-style models and is super idiomatic (https://github.com/pykeen/pykeen/pull/110)
• Enable passing of interaction function by string in base model class (https://github.com/pykeen/pykeen/pull/384, https://github.com/pykeen/pykeen/pull/387)
• Bump scipy requirement to 1.5.0+
• Updated interfaces of models and negative samplers to enforce kwargs (https://github.com/pykeen/pykeen/pull/445)
• Reorganize filtering, negative sampling, and remove triples factory from most objects (https://github.com/pykeen/pykeen/pull/400, https://github.com/pykeen/pykeen/pull/405, https://github.com/pykeen/pykeen/pull/406, https://github.com/pykeen/pykeen/pull/409, https://github.com/pykeen/pykeen/pull/420)
• Update automatic memory optimization (https://github.com/pykeen/pykeen/pull/404)
• Flexibly define positive triples for filtering (https://github.com/pykeen/pykeen/pull/398)
• Completely reimplemented negative sampling interface in training loops (https://github.com/pykeen/pykeen/pull/427)
• Completely reimplemented loss function in training loops (https://github.com/pykeen/pykeen/pull/448)
• Forward-compatibility of embeddings in old-style models and updated docs on how to use embeddings (https://github.com/pykeen/pykeen/pull/474)

Fixed

• Regularizer passing in the pipeline and HPO (https://github.com/pykeen/pykeen/pull/345)
• Saving results when using multimodal models (https://github.com/pykeen/pykeen/pull/349)
• Add missing diagonal constraint on MuRE Model (https://github.com/pykeen/pykeen/pull/353)
• Fix early stopper handling (https://github.com/pykeen/pykeen/pull/419)
• Fixed saving results from pipeline (https://github.com/pykeen/pykeen/pull/428, thanks @kantholtz)
• Fix OOM issues with early stopper and AMO (https://github.com/pykeen/pykeen/pull/433)
• Fix ER-MLP functional form (https://github.com/pykeen/pykeen/pull/444)