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Work led by Fernando Zhapa-Camacho. Paper: doi.org/10.1093/bioinf… Code: github.com/bio-ontology-r… 5/5
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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
New in Bioinformatics: INDIGENA, an inductive method to predict disease-gene associations by ranking genes for a set of phenotypes. 🧵 1/5
#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
#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…
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!
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
@KAUST_News @CBRC_KAUST
🧬 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…
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.
@CPesquita How do you determine whether a prediction is (scientifically) interesting? Is it just novelty, or is there a role for causality? #NeSy2024
Ontologies model a consensus, not reality. (@CPesquita at #NeSy2024)
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)
"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
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
What can life sciences do for neuro-symbolic AI? Excited for the #bioinformatics-related keynote by @CPesquita at #NeSy2024 - starting soon!
Happy to be at #NeSy2024 in Barcelona, just opened by @ejimenez_ruiz. First session on #XAI just starting.
Robert Hoehndorf retweeted
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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Mo @Mo_Li_KAUST
897 Followers 214 Following Associate Professor @KAUST, Stem cell biologist interested in regeneration & aging, developer of single-cell long-read sequencing technologies
Kingsley Uyi Idehen @kidehen
9K Followers 8K Following Founder & CEO, OpenLink Software. 🔗 https://t.co/sTt5T5d1uA 🔗 https://t.co/VGVHGUGEHq 🔗 https://t.co/owcnsohhvA 🔗 https://t.co/FtJLPA3IDl
UniProt @uniprot
11K Followers 564 Following UniProt is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation.
Larry Hunter @ProfLHunter
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ESWC Conferences @eswc_conf
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596 Followers 479 Following Manager, Research Communication; Follow @KAUSTResearch to engage with our research stories!
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591 Followers 513 Following @[email protected] Developer sparql & https://t.co/bAMEzo5jH3
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3K Followers 838 Following Prof @CedarsSinai making drugs safer 1B data points at a time. @Stanford BMI PhD; @Columbia DBMI; @tatonetti.bsky.social; EiC BioData Mining; he/they 🏳️🌈
Pavel Klinov 🇪🇺 @klinovp
737 Followers 508 Following Database engineer @StardogHQ. Graph query planning, optimisations, evaluation -- all that stuff. University of Manchester alum. Endurance cyclist. Immigrant.
KAUST CEMSE @KAUST_CEMSE
5K Followers 109 Following The official account of the Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division at KAUST.
Gene Ontology @go@gen... @news4go
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Catia Pesquita @CPesquita
632 Followers 376 Following Professor @DIemCiencias. Senior researcher in SW and Bioinformatics @lasige. Views my own.
DICE Research Group @DiceResearch
2K Followers 1K Following Data Science Research Group with a focus on #knowledgegraphs @unipb. #linkeddata #machinelearning #webscience #openscience #NLG
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SEMANTiCS Conference @SemanticsConf
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661 Followers 3K Following Ghent University in Belgium, Ghent University Global Campus in Korea. Deep machine learning, biological sequence analysis, and visual content processing.
Mochammad Ichsan @ichsanomics
674 Followers 5K Following Mediator kinases | Bone biology in health & diseases | osteoblastogenic & anti-osteoclastogenic compounds | ML & chembioinformatics | NAD+ | RT≠endorsement
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619 Followers 61 Following Welcome to the official StruBE lab twitter account! Here you will find relevant news about our group's work and activities. For more info visit our website!
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194 Followers 842 Following PostDoc in 'Computational Biology' | @thehuwslabs_QUB & @creeveylab | @QUBelfast
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