Joined March 2012
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18 Photos and videos
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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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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Work led by Fernando Zhapa-Camacho.
Paper: doi.org/10.1093/bioinformati…
Code: github.com/bio-ontology-rese…
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#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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#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-rese…
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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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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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24 Nov 2024
🧬 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/s41597-0…
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10 Sep 2024
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.
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9 Sep 2024
"Size matters" --- knowledge graphs and ontologies in life sciences are possibly larger than in any other field; they are a formidable challenge for any AI method, symbolic or neural #nesy2024
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9 Sep 2024
Billions of statements in biological knowledge graphs! Millions of nodes, billions of triples.
Neurosymbolic methods are not yet ready to handle this data. (From @CPesquita's keynote at #NeSy2024)
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9 Sep 2024
At the #nesy2024 keynote today, @CPesquita highlights how medical and biological research was one main driver in the developments in logic and AI throughout history - in the words of Galen, "That the best doctor is also a philosopher" #nesy2024
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9 Sep 2024
What can life sciences do for neuro-symbolic AI? Excited for the #bioinformatics-related keynote by @CPesquita at #NeSy2024 - starting soon!
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9 Sep 2024
Happy to be at #NeSy2024 in Barcelona, just opened by @ejimenez_ruiz. First session on #XAI just starting.
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Robert Hoehndorf retweeted
18 Jun 2024
We recently wrote a survey on #ontology #embedding. Great contributions from @leechuck Olga and Fernando from @CBRC_KAUST , @lawhy_AI and Ian Horrocks. #knowledgegraphs #survey #KnowledgeRepresentation. With methods, applications and system (mOWL).
arxiv.org/abs/2406.10964
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3 May 2024
Latest work by my former student @azzathamer on using #neurosymbolicAI and biomedical ontologies to help diagnose #RareDisease is now online: academic.oup.com/bioinformat…
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3 May 2024
Read the article to find out how the neurosymbolic model learns to interpret different types of evidence (from model organism phenotypes over #GeneOntology functions to anatomical site of gene expression) and finally link the variant to #RareDisease phenotypes.
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