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- .DS_Store +0 -0
- .gitattributes +9 -0
- benchmark/LICENSE +41 -0
- benchmark/README.md +81 -0
- benchmark/croissant.json +112 -0
- benchmark/diffs/diff_t0_t1.json +59 -0
- benchmark/features/disease_features.csv +0 -0
- benchmark/features/drug_features.csv +0 -0
- benchmark/features/edge_index.pt +3 -0
- benchmark/features/edge_type.pt +3 -0
- benchmark/features/mol_dim.txt +1 -0
- benchmark/features/mol_features.pt +3 -0
- benchmark/features/node_has_mol.pt +3 -0
- benchmark/features/node_has_text.pt +3 -0
- benchmark/features/node_index_map.csv +0 -0
- benchmark/features/text_embeddings.pt +3 -0
- benchmark/features/vocab_sizes.json +1 -0
- benchmark/snapshots/kg_t0.csv +3 -0
- benchmark/snapshots/kg_t1.csv +3 -0
- benchmark/snapshots/t1_build_info.json +53 -0
- benchmark/statistics.json +85 -0
- benchmark/tasks/task_0_base/test.txt +3 -0
- benchmark/tasks/task_0_base/train.txt +3 -0
- benchmark/tasks/task_0_base/valid.txt +3 -0
- benchmark/tasks/task_1_disease_related/test.txt +0 -0
- benchmark/tasks/task_1_disease_related/train.txt +0 -0
- benchmark/tasks/task_1_disease_related/valid.txt +1700 -0
- benchmark/tasks/task_1_drug_related/test.txt +0 -0
- benchmark/tasks/task_1_drug_related/train.txt +0 -0
- benchmark/tasks/task_1_drug_related/valid.txt +0 -0
- benchmark/tasks/task_2_disease_related/test.txt +0 -0
- benchmark/tasks/task_2_disease_related/train.txt +0 -0
- benchmark/tasks/task_2_disease_related/valid.txt +0 -0
- benchmark/tasks/task_2_gene_protein/test.txt +3 -0
- benchmark/tasks/task_2_gene_protein/train.txt +3 -0
- benchmark/tasks/task_2_gene_protein/valid.txt +0 -0
- benchmark/tasks/task_3_gene_protein/test.txt +0 -0
- benchmark/tasks/task_3_gene_protein/train.txt +0 -0
- benchmark/tasks/task_3_gene_protein/valid.txt +0 -0
- benchmark/tasks/task_3_phenotype_related/test.txt +0 -0
- benchmark/tasks/task_3_phenotype_related/train.txt +0 -0
- benchmark/tasks/task_3_phenotype_related/valid.txt +0 -0
- benchmark/tasks/task_4_biological_process/test.txt +0 -0
- benchmark/tasks/task_4_biological_process/train.txt +0 -0
- benchmark/tasks/task_4_biological_process/valid.txt +0 -0
- benchmark/tasks/task_4_phenotype_related/test.txt +0 -0
- benchmark/tasks/task_4_phenotype_related/train.txt +0 -0
- benchmark/tasks/task_4_phenotype_related/valid.txt +0 -0
- benchmark/tasks/task_5_anatomy_pathway/test.txt +3 -0
- benchmark/tasks/task_5_anatomy_pathway/train.txt +3 -0
.DS_Store
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.gitattributes
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benchmark/LICENSE
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PrimeKG-CL Benchmark
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====================
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+
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Code and benchmark configuration files in this release: MIT License.
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+
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Data files derived from PrimeKG and downstream from the source databases:
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licensed under Creative Commons Attribution 4.0 International (CC BY 4.0),
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inheriting PrimeKG's license. Users must respect upstream-database licenses
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where applicable. The t_1 snapshot was reconstructed from these freely
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accessible upstream databases; restrictively licensed databases (DrugBank,
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UMLS, DrugCentral, SIDER, DisGeNET) are NOT re-queried for t_1 and the t_0
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edges from those sources are carried forward unchanged.
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Upstream databases used for t_1 reconstruction:
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Bgee, CTD, Gene Ontology, Gene2GO, HPO, HPOA, MONDO, Uberon, HGNC.
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Citation: see README.md.
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+
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+
----------------------------------------------------------------------
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MIT License (code components)
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+
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Copyright (c) 2026 The PrimeKG-CL authors
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+
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Permission is hereby granted, free of charge, to any person obtaining a copy
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+
of this software and associated documentation files (the "Software"), to deal
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+
in the Software without restriction, including without limitation the rights
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+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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+
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The above copyright notice and this permission notice shall be included in
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all copies or substantial portions of the Software.
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+
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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| 38 |
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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| 39 |
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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| 40 |
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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THE SOFTWARE.
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benchmark/README.md
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# PrimeKG-CL Benchmark v1.0
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+
A continual graph learning benchmark on a real biomedical knowledge graph
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| 4 |
+
with genuine temporal evolution.
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| 5 |
+
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## Snapshots
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| 7 |
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- `snapshots/kg_t0.csv` — June 2021 PrimeKG release. 8,100,498 triples, 129,375 nodes, 30 relations.
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- `snapshots/kg_t1.csv` — July 2023 reconstruction from nine upstream databases (Bgee, CTD, GO, Gene2GO, HPO, HPOA, MONDO, Uberon, HGNC). 13,001,666 triples, 134,211 nodes, 25 relations.
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+
- `snapshots/t1_build_info.json` — provenance / database versions used for the t_1 reconstruction.
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+
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## Temporal diff (t_0 -> t_1)
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+
- Added: 5,760,234 new triples (driven by GO annotations, disease-phenotype refinement, drug-target updates)
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- Removed: 888,848 deprecated triples (retracted associations, ontology corrections)
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+
- Persistent: 7,208,624 triples unchanged across both snapshots
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+
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Full breakdown in `diffs/diff_t0_t1.json`.
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+
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## Continual learning tasks
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10 entity-type-grouped tasks (`tasks/task_*`). Each directory contains
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`train.txt`, `valid.txt`, `test.txt`, one tab-separated triple per line
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(`head_id<TAB>relation<TAB>tail_id`). 70/10/20 train/valid/test split.
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+
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+
```
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+
task_0_base 8,100,498 triples (full t_0)
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+
task_1_disease_related 17,009
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+
task_1_drug_related 125,343
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+
task_2_disease_related 115,382
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+
task_2_gene_protein 2,850,593
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+
task_3_gene_protein 99,761
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| 30 |
+
task_3_phenotype_related 47,997
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+
task_4_biological_process 116,118
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+
task_4_phenotype_related 57,390
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+
task_5_anatomy_pathway 2,752,675
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```
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+
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## Stratified evaluation
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`test_stratification.json` — per-task partition of test triples into
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**persistent** (in both snapshots), **added** (new in t_1), and
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**removed** (only in t_0) strata, supporting stratified-MRR analysis of
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correct retention vs. correct forgetting.
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+
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Task 0's test split: 1,443,243 persistent + 176,856 removed = 1,620,099 total.
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+
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## Multimodal features (`features/`)
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- `text_embeddings.pt` — BiomedBERT [CLS] embeddings projected to 256-d.
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+
Coverage: 36% of entities (those with textual descriptions).
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| 47 |
+
- `mol_features.pt` — Morgan fingerprints (radius 2, 1024 bits) for drugs
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| 48 |
+
with available SMILES. Coverage: 4% of entities.
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- `edge_index.pt`, `edge_type.pt` — R-GCN message-passing tensors for the
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+
full t_0 graph (used by the structural encoder).
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- `node_has_text.pt`, `node_has_mol.pt` — boolean coverage masks.
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- `node_index_map.csv` — global entity_id <-> row_index map.
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- `vocab_sizes.json` — entity / relation vocab sizes.
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+
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## Files
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+
```
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LICENSE MIT (code) + CC BY 4.0 (data)
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| 58 |
+
croissant.json MLCommons Croissant metadata
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| 59 |
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README.md this file
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| 60 |
+
statistics.json benchmark-level summary
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| 61 |
+
test_stratification.json per-task persistent/added/removed counts
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| 62 |
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diffs/diff_t0_t1.json full t_0->t_1 diff with per-relation breakdown
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| 63 |
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snapshots/ kg_t0.csv, kg_t1.csv, build provenance
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tasks/ 10 task directories with train/valid/test splits
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features/ multimodal node features
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+
```
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+
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## Citation
|
| 69 |
+
```
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| 70 |
+
@inproceedings{primekgcl2026,
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| 71 |
+
title={PrimeKG-CL: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs},
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author={Anonymous},
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| 73 |
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booktitle={NeurIPS Datasets and Benchmarks Track},
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year={2026}
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}
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```
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## License
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- Code components: MIT.
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- Data files: CC BY 4.0, inheriting PrimeKG's license; users must respect upstream-database licenses where applicable.
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- See `LICENSE` for details.
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benchmark/croissant.json
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{
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"@context": {
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"@language": "en",
|
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"@vocab": "https://schema.org/",
|
| 5 |
+
"citeAs": "cr:citeAs",
|
| 6 |
+
"column": "cr:column",
|
| 7 |
+
"conformsTo": "dct:conformsTo",
|
| 8 |
+
"cr": "http://mlcommons.org/croissant/",
|
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"data": {
|
| 10 |
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"@id": "cr:data",
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"@type": "@json"
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+
},
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"dataType": {
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"@id": "cr:dataType",
|
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"@type": "@vocab"
|
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+
},
|
| 17 |
+
"dct": "http://purl.org/dc/terms/",
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| 18 |
+
"examples": {
|
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"@id": "cr:examples",
|
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+
"@type": "@json"
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+
},
|
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"extract": "cr:extract",
|
| 23 |
+
"field": "cr:field",
|
| 24 |
+
"fileProperty": "cr:fileProperty",
|
| 25 |
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"fileObject": "cr:fileObject",
|
| 26 |
+
"fileSet": "cr:fileSet",
|
| 27 |
+
"format": "cr:format",
|
| 28 |
+
"includes": "cr:includes",
|
| 29 |
+
"isLiveDataset": "cr:isLiveDataset",
|
| 30 |
+
"jsonPath": "cr:jsonPath",
|
| 31 |
+
"key": "cr:key",
|
| 32 |
+
"md5": "cr:md5",
|
| 33 |
+
"parentField": "cr:parentField",
|
| 34 |
+
"path": "cr:path",
|
| 35 |
+
"recordSet": "cr:recordSet",
|
| 36 |
+
"references": "cr:references",
|
| 37 |
+
"regex": "cr:regex",
|
| 38 |
+
"repeated": "cr:repeated",
|
| 39 |
+
"replace": "cr:replace",
|
| 40 |
+
"sc": "https://schema.org/",
|
| 41 |
+
"separator": "cr:separator",
|
| 42 |
+
"source": "cr:source",
|
| 43 |
+
"subField": "cr:subField",
|
| 44 |
+
"transform": "cr:transform"
|
| 45 |
+
},
|
| 46 |
+
"@type": "sc:Dataset",
|
| 47 |
+
"name": "PrimeKG-CL",
|
| 48 |
+
"description": "PrimeKG-CL is a continual graph learning benchmark on a real biomedical knowledge graph with genuine temporal evolution. It contains two temporal snapshots reconstructed from nine asynchronously updating biomedical databases (June 2021 and July 2023), with 129K+ entities, 8.1M+ edges, 10 entity-type-grouped continual learning tasks, multimodal node features (textual via BiomedBERT, molecular via Morgan fingerprints, structural via R-GCN), and three evaluation tracks (continual biomedical relationship prediction, biomedical entity classification, biomedical KGQA).",
|
| 49 |
+
"license": "https://creativecommons.org/licenses/by/4.0/",
|
| 50 |
+
"url": "https://github.com/yradwan147/Yousef_PrimeKG-CL_NeurIPS2026",
|
| 51 |
+
"version": "1.0",
|
| 52 |
+
"datePublished": "2026-04-25",
|
| 53 |
+
"citeAs": "@inproceedings{primekgcl2026, title={{PrimeKG-CL}: A Continual Graph Learning Benchmark on Evolving Biomedical Knowledge Graphs}, author={Anonymous}, booktitle={NeurIPS Datasets and Benchmarks Track}, year={2026}}",
|
| 54 |
+
"conformsTo": "http://mlcommons.org/croissant/1.0",
|
| 55 |
+
"distribution": [
|
| 56 |
+
{
|
| 57 |
+
"@type": "cr:FileObject",
|
| 58 |
+
"@id": "snapshot-t0",
|
| 59 |
+
"name": "kg_t0.csv",
|
| 60 |
+
"contentUrl": "snapshots/kg_t0.csv",
|
| 61 |
+
"encodingFormat": "text/csv",
|
| 62 |
+
"description": "Snapshot t_0 (June 2021): 8,100,498 triples across 129,375 nodes and 30 relation types."
|
| 63 |
+
},
|
| 64 |
+
{
|
| 65 |
+
"@type": "cr:FileObject",
|
| 66 |
+
"@id": "snapshot-t1",
|
| 67 |
+
"name": "kg_t1.csv",
|
| 68 |
+
"contentUrl": "snapshots/kg_t1.csv",
|
| 69 |
+
"encodingFormat": "text/csv",
|
| 70 |
+
"description": "Snapshot t_1 (July 2023): 13,001,666 triples across 134,211 nodes and 25 relation types."
|
| 71 |
+
},
|
| 72 |
+
{
|
| 73 |
+
"@type": "cr:FileSet",
|
| 74 |
+
"@id": "task-files",
|
| 75 |
+
"name": "tasks",
|
| 76 |
+
"description": "10 entity-type-grouped continual learning tasks; each contains train.txt, valid.txt, test.txt with one tab-separated triple per line.",
|
| 77 |
+
"encodingFormat": "text/plain",
|
| 78 |
+
"includes": "tasks/*/*.txt"
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"@type": "cr:FileObject",
|
| 82 |
+
"@id": "stratification",
|
| 83 |
+
"name": "test_stratification.json",
|
| 84 |
+
"contentUrl": "test_stratification.json",
|
| 85 |
+
"encodingFormat": "application/json",
|
| 86 |
+
"description": "Per-task partition of test triples into persistent / added / removed strata for stratified evaluation."
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"@type": "cr:FileSet",
|
| 90 |
+
"@id": "features",
|
| 91 |
+
"name": "features",
|
| 92 |
+
"description": "Multimodal node features: text_embeddings.pt (BiomedBERT 768-d -> 256-d), mol_features.pt (Morgan 1024-bit), edge_index.pt and edge_type.pt for R-GCN message passing.",
|
| 93 |
+
"encodingFormat": "application/octet-stream",
|
| 94 |
+
"includes": "features/*"
|
| 95 |
+
}
|
| 96 |
+
],
|
| 97 |
+
"recordSet": [
|
| 98 |
+
{
|
| 99 |
+
"@type": "cr:RecordSet",
|
| 100 |
+
"@id": "triples-t0",
|
| 101 |
+
"name": "triples-t0",
|
| 102 |
+
"description": "Triples in snapshot t_0.",
|
| 103 |
+
"field": [
|
| 104 |
+
{"@type": "cr:Field", "@id": "triples-t0/relation", "name": "relation", "dataType": "sc:Text"},
|
| 105 |
+
{"@type": "cr:Field", "@id": "triples-t0/x_id", "name": "x_id", "dataType": "sc:Text"},
|
| 106 |
+
{"@type": "cr:Field", "@id": "triples-t0/y_id", "name": "y_id", "dataType": "sc:Text"},
|
| 107 |
+
{"@type": "cr:Field", "@id": "triples-t0/x_type", "name": "x_type", "dataType": "sc:Text"},
|
| 108 |
+
{"@type": "cr:Field", "@id": "triples-t0/y_type", "name": "y_type", "dataType": "sc:Text"}
|
| 109 |
+
]
|
| 110 |
+
}
|
| 111 |
+
]
|
| 112 |
+
}
|
benchmark/diffs/diff_t0_t1.json
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"old_snapshot": {
|
| 3 |
+
"path": "data/benchmark/snapshots/kg_t0.csv",
|
| 4 |
+
"num_triples": 8100498,
|
| 5 |
+
"num_entities": 129312,
|
| 6 |
+
"num_relations": 30
|
| 7 |
+
},
|
| 8 |
+
"new_snapshot": {
|
| 9 |
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"path": "data/benchmark/snapshots/kg_t1.csv",
|
| 10 |
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"num_triples": 13001666,
|
| 11 |
+
"num_entities": 132914,
|
| 12 |
+
"num_relations": 25
|
| 13 |
+
},
|
| 14 |
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"diff": {
|
| 15 |
+
"added_triples": 5760234,
|
| 16 |
+
"removed_triples": 888848,
|
| 17 |
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"persistent_triples": 7208624,
|
| 18 |
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"emerged_entities": 36653,
|
| 19 |
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"disappeared_entities": 33051,
|
| 20 |
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"emerged_relations": 0,
|
| 21 |
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"disappeared_relations": 5
|
| 22 |
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},
|
| 23 |
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"added_by_relation": {
|
| 24 |
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"anatomy_protein_present": 4763650,
|
| 25 |
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"anatomy_protein_absent": 698316,
|
| 26 |
+
"bioprocess_protein": 89080,
|
| 27 |
+
"molfunc_protein": 61502,
|
| 28 |
+
"cellcomp_protein": 52758,
|
| 29 |
+
"phenotype_phenotype": 47334,
|
| 30 |
+
"exposure_protein": 35880,
|
| 31 |
+
"disease_disease": 16346,
|
| 32 |
+
"bioprocess_bioprocess": 9322,
|
| 33 |
+
"anatomy_anatomy": 4676,
|
| 34 |
+
"molfunc_molfunc": 4256,
|
| 35 |
+
"disease_phenotype_positive": 1322,
|
| 36 |
+
"cellcomp_cellcomp": 870,
|
| 37 |
+
"disease_phenotype_negative": 4
|
| 38 |
+
},
|
| 39 |
+
"added_by_x_type": {
|
| 40 |
+
"gene/protein": 2850593,
|
| 41 |
+
"anatomy": 2735659,
|
| 42 |
+
"biological_process": 53862,
|
| 43 |
+
"effect/phenotype": 47997,
|
| 44 |
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"molecular_function": 35007,
|
| 45 |
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"cellular_component": 27249,
|
| 46 |
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"exposure": 17940,
|
| 47 |
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"disease": 17009
|
| 48 |
+
},
|
| 49 |
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"added_by_y_type": {
|
| 50 |
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"gene/protein": 2850593,
|
| 51 |
+
"anatomy": 2735659,
|
| 52 |
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"biological_process": 53862,
|
| 53 |
+
"effect/phenotype": 47997,
|
| 54 |
+
"molecular_function": 35007,
|
| 55 |
+
"cellular_component": 27249,
|
| 56 |
+
"exposure": 17940,
|
| 57 |
+
"disease": 17009
|
| 58 |
+
}
|
| 59 |
+
}
|
benchmark/features/disease_features.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
benchmark/features/drug_features.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
benchmark/features/edge_index.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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|
| 3 |
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size 364992190
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benchmark/features/edge_type.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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|
| 3 |
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size 182496887
|
benchmark/features/mol_dim.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
1024
|
benchmark/features/mol_features.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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|
| 3 |
+
size 505448012
|
benchmark/features/node_has_mol.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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oid sha256:a671501d1f338655c9d098b5730b67b1a0c22fea8247860d6a0738eadf83c401
|
| 3 |
+
size 125004
|
benchmark/features/node_has_text.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:bd5b5c1cdecc5e5c809260f4f6e5fcfeef721638dbe38ddcc53eecf7184aeeb8
|
| 3 |
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size 125011
|
benchmark/features/node_index_map.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
benchmark/features/text_embeddings.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
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oid sha256:9b7607715b18bfda1cf24269e7a3ea943f6220bf29df53324c5cc25f1d39cd5b
|
| 3 |
+
size 379086433
|
benchmark/features/vocab_sizes.json
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
{"num_entities": 123400, "num_relations": 30}
|
benchmark/snapshots/kg_t0.csv
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:c3edc235ea071be13873fe9597498988236d2106f6f1664148fe93e1921443bb
|
| 3 |
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size 888336264
|
benchmark/snapshots/kg_t1.csv
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:84768dfa496b4a6cbf9dd977ef2f37b88f05699ed1d10b9129a659fbba4bae71
|
| 3 |
+
size 1577153470
|
benchmark/snapshots/t1_build_info.json
ADDED
|
@@ -0,0 +1,53 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"build_time_seconds": 302.7,
|
| 3 |
+
"enabled_databases": [
|
| 4 |
+
"bgee",
|
| 5 |
+
"ctd",
|
| 6 |
+
"gene_ontology",
|
| 7 |
+
"gene2go",
|
| 8 |
+
"hpo",
|
| 9 |
+
"hpoa",
|
| 10 |
+
"mondo",
|
| 11 |
+
"uberon",
|
| 12 |
+
"gene_names"
|
| 13 |
+
],
|
| 14 |
+
"disabled_databases": [
|
| 15 |
+
"reactome",
|
| 16 |
+
"disgenet",
|
| 17 |
+
"drugbank",
|
| 18 |
+
"umls",
|
| 19 |
+
"drugcentral",
|
| 20 |
+
"sider",
|
| 21 |
+
"ppi"
|
| 22 |
+
],
|
| 23 |
+
"carried_drug_edges_from": "data/benchmark/snapshots/kg_t0.csv",
|
| 24 |
+
"total_edges": 13001666,
|
| 25 |
+
"relation_types": 25,
|
| 26 |
+
"edge_counts": {
|
| 27 |
+
"anatomy_protein_present": 7529620,
|
| 28 |
+
"drug_drug": 2672628,
|
| 29 |
+
"anatomy_protein_absent": 730884,
|
| 30 |
+
"protein_protein": 642150,
|
| 31 |
+
"bioprocess_protein": 276812,
|
| 32 |
+
"cellcomp_protein": 190278,
|
| 33 |
+
"molfunc_protein": 187464,
|
| 34 |
+
"disease_protein": 160822,
|
| 35 |
+
"drug_effect": 129568,
|
| 36 |
+
"pathway_protein": 85292,
|
| 37 |
+
"bioprocess_bioprocess": 83448,
|
| 38 |
+
"contraindication": 61350,
|
| 39 |
+
"drug_protein": 51306,
|
| 40 |
+
"phenotype_phenotype": 47354,
|
| 41 |
+
"exposure_protein": 35880,
|
| 42 |
+
"anatomy_anatomy": 29346,
|
| 43 |
+
"molfunc_molfunc": 24824,
|
| 44 |
+
"indication": 18776,
|
| 45 |
+
"disease_disease": 16346,
|
| 46 |
+
"cellcomp_cellcomp": 9326,
|
| 47 |
+
"phenotype_protein": 6660,
|
| 48 |
+
"off-label use": 5136,
|
| 49 |
+
"pathway_pathway": 5070,
|
| 50 |
+
"disease_phenotype_positive": 1322,
|
| 51 |
+
"disease_phenotype_negative": 4
|
| 52 |
+
}
|
| 53 |
+
}
|
benchmark/statistics.json
ADDED
|
@@ -0,0 +1,85 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"benchmark_version": "1.0",
|
| 3 |
+
"strategy": "entity_type",
|
| 4 |
+
"seed": 42,
|
| 5 |
+
"val_ratio": 0.1,
|
| 6 |
+
"test_ratio": 0.2,
|
| 7 |
+
"min_triples": 100,
|
| 8 |
+
"snapshots": {
|
| 9 |
+
"t0": {
|
| 10 |
+
"path": "data/benchmark/snapshots/kg_t0.csv",
|
| 11 |
+
"num_triples": 8100498
|
| 12 |
+
},
|
| 13 |
+
"t1": {
|
| 14 |
+
"path": "data/benchmark/snapshots/kg_t1.csv",
|
| 15 |
+
"num_triples": 13001666
|
| 16 |
+
}
|
| 17 |
+
},
|
| 18 |
+
"diff": {
|
| 19 |
+
"added_triples": 5760234,
|
| 20 |
+
"removed_triples": 888848,
|
| 21 |
+
"persistent_triples": 7208624,
|
| 22 |
+
"emerged_entities": 36653,
|
| 23 |
+
"disappeared_entities": 33051,
|
| 24 |
+
"emerged_relations": 0,
|
| 25 |
+
"disappeared_relations": 5
|
| 26 |
+
},
|
| 27 |
+
"tasks": {
|
| 28 |
+
"task_0_base": {
|
| 29 |
+
"num_triples": 8100498,
|
| 30 |
+
"splits": {
|
| 31 |
+
"train": 5670350,
|
| 32 |
+
"val": 810049,
|
| 33 |
+
"test": 1620099
|
| 34 |
+
}
|
| 35 |
+
},
|
| 36 |
+
"task_1_disease_related": {
|
| 37 |
+
"num_triples": 17009,
|
| 38 |
+
"splits": {
|
| 39 |
+
"train": 11908,
|
| 40 |
+
"val": 1700,
|
| 41 |
+
"test": 3401
|
| 42 |
+
}
|
| 43 |
+
},
|
| 44 |
+
"task_2_gene_protein": {
|
| 45 |
+
"num_triples": 2850593,
|
| 46 |
+
"splits": {
|
| 47 |
+
"train": 1995416,
|
| 48 |
+
"val": 285059,
|
| 49 |
+
"test": 570118
|
| 50 |
+
}
|
| 51 |
+
},
|
| 52 |
+
"task_3_phenotype_related": {
|
| 53 |
+
"num_triples": 47997,
|
| 54 |
+
"splits": {
|
| 55 |
+
"train": 33599,
|
| 56 |
+
"val": 4799,
|
| 57 |
+
"test": 9599
|
| 58 |
+
}
|
| 59 |
+
},
|
| 60 |
+
"task_4_biological_process": {
|
| 61 |
+
"num_triples": 116118,
|
| 62 |
+
"splits": {
|
| 63 |
+
"train": 81284,
|
| 64 |
+
"val": 11611,
|
| 65 |
+
"test": 23223
|
| 66 |
+
}
|
| 67 |
+
},
|
| 68 |
+
"task_5_anatomy_pathway": {
|
| 69 |
+
"num_triples": 2753599,
|
| 70 |
+
"splits": {
|
| 71 |
+
"train": 1926873,
|
| 72 |
+
"val": 275267,
|
| 73 |
+
"test": 550535
|
| 74 |
+
}
|
| 75 |
+
}
|
| 76 |
+
},
|
| 77 |
+
"features": {
|
| 78 |
+
"num_drugs": 7957,
|
| 79 |
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"drugs_with_text": 4752,
|
| 80 |
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"num_diseases": 17080,
|
| 81 |
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"diseases_with_text": 16673,
|
| 82 |
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"total_nodes": 129312
|
| 83 |
+
},
|
| 84 |
+
"build_time_seconds": 173.0
|
| 85 |
+
}
|
benchmark/tasks/task_0_base/test.txt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:359e0890371b949fe8d31cf100768e54ad7d8cb48eaf06d3350610b954407038
|
| 3 |
+
size 50571695
|
benchmark/tasks/task_0_base/train.txt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:f8f54df0005689efb402a7ea1acc4d34d04c2575217c518550c4bbe82f09a2af
|
| 3 |
+
size 176971128
|
benchmark/tasks/task_0_base/valid.txt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:d4ea299a101f59e3110211b34769726ff292234b221f1b288590467b03af6a07
|
| 3 |
+
size 25284374
|
benchmark/tasks/task_1_disease_related/test.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
benchmark/tasks/task_1_disease_related/train.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
benchmark/tasks/task_1_disease_related/valid.txt
ADDED
|
@@ -0,0 +1,1700 @@
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