├── .gitignore ├── .gitmodules ├── LICENSE.md ├── README.md ├── data.ipynb ├── elembedding.ipynb ├── elembeddings ├── graph-transe.ipynb ├── graph-walks.ipynb ├── onto2vec_opa2vec.ipynb ├── requirements.txt ├── semantic-similarity.ipynb ├── siamese_nn.ipynb └── slides ├── 01-introduction.pdf ├── 01-introduction.tex ├── 02-ontologies-and-graphs.pdf ├── 02-ontologies-and-graphs.tex ├── 03-semantic-similarity.pdf ├── 03-semantic-similarity.tex ├── 04-ontology-embeddings.pdf ├── 04-ontology-embeddings.tex ├── DTI_ANN_all.pdf ├── HD.png ├── Human_Disease.png ├── Ind_ANN_all.pdf ├── OPA2Vec-tutorial.pdf ├── YSTUnsuper1.png ├── YeastPPINetwork.png ├── YstUnsup2.png ├── aber-owl-plague.png ├── aristo.png ├── bcellapoptosis.png ├── ellosses.pdf ├── ellosses.png ├── embeds-frame-0.png ├── embeds-frame-1.png ├── embeds-frame-10.png ├── embeds-frame-11.png ├── embeds-frame-12.png ├── embeds-frame-13.png ├── embeds-frame-14.png ├── embeds-frame-15.png ├── embeds-frame-16.png ├── embeds-frame-17.png ├── embeds-frame-18.png ├── embeds-frame-19.png ├── embeds-frame-2.png ├── embeds-frame-20.png ├── embeds-frame-21.png ├── embeds-frame-22.png ├── embeds-frame-23.png ├── embeds-frame-24.png ├── embeds-frame-25.png ├── embeds-frame-26.png ├── embeds-frame-27.png ├── embeds-frame-28.png ├── embeds-frame-29.png ├── embeds-frame-3.png ├── embeds-frame-30.png ├── embeds-frame-31.png ├── embeds-frame-32.png ├── embeds-frame-33.png ├── embeds-frame-34.png ├── embeds-frame-35.png ├── embeds-frame-36.png ├── embeds-frame-37.png ├── embeds-frame-38.png ├── embeds-frame-39.png ├── embeds-frame-4.png ├── embeds-frame-40.png ├── embeds-frame-41.png ├── embeds-frame-42.png ├── embeds-frame-43.png ├── embeds-frame-44.png ├── embeds-frame-45.png ├── embeds-frame-46.png ├── embeds-frame-47.png ├── embeds-frame-48.png ├── embeds-frame-49.png ├── embeds-frame-5.png ├── embeds-frame-50.png ├── embeds-frame-51.png ├── embeds-frame-52.png ├── embeds-frame-53.png ├── embeds-frame-54.png ├── 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├── embeds-frame-93.png ├── embeds-frame-94.png ├── embeds-frame-95.png ├── embeds-frame-96.png ├── embeds-frame-97.png ├── embeds-frame-98.png ├── embeds-frame-99.png ├── go-figure1.jpg ├── graph-tsne.png ├── kaust_logo3.png ├── loss-functions-kg.png ├── model-human-obesity-slide.pdf ├── moesin-1.png ├── moesin-2.png ├── multimodal_workflow.pdf ├── network-eps-converted-to.pdf ├── onto2vecflow.png ├── opaworkflow16.png ├── part1.tex ├── part2.tex ├── pato-eval1.png ├── pato-eval2.png ├── pato-eval3.png ├── plant-ontology-sample.png ├── pmi-auc-plot.pdf ├── ppi1.png ├── ppi2.png ├── ppi3.png ├── pvp.pdf ├── pvp.png ├── rdf-walking-datasets.png ├── roc-omim-mgi-1.png ├── t-cell-activation.png ├── t-cell-aggregation.png ├── transe-algorithm.png ├── transe-figure.png ├── transh-figure.png ├── transr-figure.png ├── updtsne.jpg ├── word2vec-example.png └── workflow.png /.gitignore: -------------------------------------------------------------------------------- 1 | data/ 2 | venv/ 3 | 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