Robert Hoehndorf @leechuck

leechuck.de KAUST, Thuwal, Saudi Arabia Joined March 2012

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Robert Hoehndorf @leechuck

4 weeks ago

Our ontology-aware metrics are complementary to CAFA-style protein-level accuracy. Paper: doi.org/10.1093/bib/bb… Code/data: github.com/bio-ontology-r… #CAFA #FunctionCOSI #ProteinFunction 6/6

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We applied the framework to curated annotations from six model organisms and predictions from seven methods. Curated annotations mostly satisfy the constraints; current predictors do not yet produce complete, coherent and consistent genome-scale annotation sets. 5/6

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Robert Hoehndorf @leechuck

4 weeks ago

New in Briefings in Bioinformatics: we use the Gene Ontology @news4go as a logical framework to ask whether genome-scale function annotations are biologically plausible, not only accurate protein by protein. #GeneOntology #Bioinformatics 1/6

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Robert Hoehndorf @leechuck

2 months ago

Work led by Fernando Zhapa-Camacho. Paper: doi.org/10.1093/bioinf… Code: github.com/bio-ontology-r… 5/5

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Robert Hoehndorf @leechuck

2 months ago

A supervised signal from known gene-disease associations makes the embeddings and the similarity measure task-specific. On mouse models of human disease it beats inductive semantic-similarity baselines and matches transductive methods, while staying general. 4/5

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Robert Hoehndorf @leechuck

2 months ago

New in Bioinformatics: INDIGENA, an inductive method to predict disease-gene associations by ranking genes for a set of phenotypes. 🧵 1/5

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Robert Hoehndorf @leechuck

3 months ago

#ESWC2026 paper 3/3 — Robust KG Embedding via Denoising: unified robustness framework treating KGE scoring as energy-based, exploiting the denoising / score-matching link. Adds certified robustness metrics via randomized smoothing. Code: github.com/tewiSong/RKGE

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Robert Hoehndorf @leechuck

3 months ago

#ESWC2026 paper 2/3 — GeometrE: fully geometric multi-hop reasoning on KGs. Every logical operator maps to a pure geometric transform in latent space. Plus a transitive loss preserving r(a,b) ∧ r(b,c) → r(a,c). github.com/bio-ontology-r…

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Robert Hoehndorf @leechuck

3 months ago

3 papers from our group accepted at #ESWC2026 in Dubrovnik next week! Excited to present work on drug-safety knowledge graphs, geometric multi-hop reasoning over KGs, and robust KG embeddings via denoising. See you in Dubrovnik!

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Robert Hoehndorf @leechuck

3 months ago

SIDEKICK: a knowledge graph of drug indications, contraindications & adverse reactions from 50K+ FDA labels via LLM + Graph-RAG, mapped to HPO/MONDO/RxNorm. Beats SIDER & OnSIDES on side-effect-based drug repurposing. At #ESWC2026, Dubrovnik. sidekick.bio2vec.net

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Robert Hoehndorf @leechuck

2 years ago

@KAUST_News @CBRC_KAUST

المحنّا- Faten Dhawi @F_D_Almutiri

2 years ago

#الجينوم #السعودي حققت جامعة الملك عبدالله للعلوم والتقنية (كاوست) إنجازًا علميًا وطنيًا مميزًا من خلال إنتاج أول جينوم سعودي مرجعي عالي الجودة باسم KSA001 و يتميز هذا الجينوم بكونه متاحًا وفق معايير FAIR العالمية التي تضمن سهولة البحث عنه، توفره، قابليته للتشغيل المتبادل،

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Robert Hoehndorf @leechuck

2 years ago

🧬 Proud to share our new paper! A complete genome assembly from Saudi Arabia (KSA001), freely available to all. Special shoutout to @coolmaksat for leading the bioinformatics. Also hard work to get this IRB-approved nature.com/articles/s4159…

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Robert Hoehndorf @leechuck

2 years ago

2nd day of #NeSy2024 is about to start, with a session on neurosymbolic languages. Will be great to see how this work can contribute to reproducibility of NeSy research and experiments.