Mohammad Ashhad successfully defends MSc thesis on machine learning for survival analysis 1 min read · Tue, May 19 2026 News Biomedical Informatics Neuro-Symbolic AI Congratulations to Mohammad Ashhad, who successfully defended his Master’s thesis “ Machine Learning Methods for Survival Analysis: From Outcome-Conditioned Data Synthesis to Decoupled Ranking and Calibration” on 3 May 2026 in KAUST’s Bioengineering Program. Mohammad will now continue in the group as a PhD student in the Computer Science Program. The thesis tackles two persistent obstacles to building accurate, generalizable survival models from biomedical data: the scarcity of shareable training data, and the trade-off between expressiveness and robustness that classical and deep-learning
New publication at ESWC 2026: Robust knowledge graph embedding via denoising 1 min read · Thu, May 14 2026 News A paper at ESWC 2026 by Tengwei Song, Xudong Ma, Yang Liu, Jie Luo and Robert Hoehndorf introduces a unified framework that hardens knowledge graph embeddings against perturbations in the embedding space, with certified robustness guarantees.
New publication at ESWC 2026: SIDEKICK, a semantically integrated knowledge graph for drug safety 1 min read · Wed, May 13 2026 News SIDEKICK, presented at ESWC 2026 by Mohammad Ashhad, Olga Mashkova, Ricardo Henao (Duke) and Robert Hoehndorf, builds an ontology-aligned knowledge graph of drug indications, contraindications and adverse reactions from 50,000+ FDA drug labels.
New publication at ESWC 2026: Fully geometric multi-hop reasoning on knowledge graphs with transitive relations 1 min read · Tue, May 12 2026 News A new paper by Fernando Zhapa-Camacho and Robert Hoehndorf, presented at ESWC 2026, introduces GeometrE, a fully geometric box-embedding method that performs multi-hop reasoning on knowledge graphs without neural components for logical operations, and preserves transitive relations through an idempotency-enforcing loss.
Asaad Mohammedsaleh earns MSc on genome-scale protein function adjustment 1 min read · Wed, Apr 29 2026 News Asaad Mohammedsaleh has completed his MSc in Computer Science with a thesis on a constraint-optimization framework that repairs the consistency of genome-scale protein function predictions.
Yang Liu earns PhD on reference bias in disease genomics 1 min read · Mon, Apr 27 2026 News Yang Liu has completed her PhD in Bioengineering with a thesis examining how reference genomes and variant interpretation frameworks shape what we can, and cannot, observe in human disease genomics.
Fernando Zhapa-Camacho earns PhD on neuro-symbolic ontology embeddings 1 min read · Sun, Apr 26 2026 News Fernando Zhapa-Camacho has completed his PhD in Computer Science with a thesis on neuro-symbolic methods that embed ontologies into latent spaces and apply them to protein function and gene-disease prediction.
New genetic maps expected to improve personalized medicine for underrepresented populations 1 min read · Wed, Aug 13 2025 News Clip News Press Releases genome genome sequencing precision medicine genetics smart health New pangenome graphs made using exclusively Saudi and Japanese samples give new genetic insights on these two populations
AI tool maps hidden links between diseases 1 min read · Wed, Jan 15 2025 News Clip News AI for healthcare AI Natural Language Processing bioinformatics Understanding how diseases trigger one another could lead to better treatments, prevention strategies and improved genetic risk prediction.
AI tool predicts function of unknown proteins 2 min read · Sun, Feb 18 2024 News artificial intelligence bioinformatics biotechnology Powered by logic and large language models, DeepGO-SE predicts the biological role of proteins and could be used to aid drug discovery.
A new approach to rare disease diagnosis 2 min read · Mon, Oct 23 2023 News bioinformatics artificial intelligence An innovative AI-based tool leverages varied symptom descriptions, along with evidence from the scientific literature and genomic datasets, to pinpoint disease-associated gene variants.
PhD Dissertation Defense | Prioritizing Causative Genomic Variants by Integrating Molecular and Functional Annotations from Multiple Biomedical Ontologies 3 min read · Mon, Jul 24 2023 News Computer science biology artificial intelligence CBRC PhD Student Azza Althagafi successfully defends her dissertation under the supervision of Associate Professor Robert Hoehndorf. She has been a member of the Bio-Ontology Research Group (BORG) since 2016. Her research interest lies in the crossroads of computer science and biology, leveraging AI techniques to explore the human genome's intricacies and its link to various diseases.
PhD Dissertation Defense | Ontology design patterns and methods for integrating phenotype ontologies 3 min read · Sun, Jul 23 2023 News Ontologies Computer science artificial intelligence CBRC PhD student Sarah Alghamdi successfully defended her dissertation last week. She has been an essential member of the Bio-Ontology Research Group (BORG) since 2015.Her research interests include the applications of artificial intelligence and statistical methods to genomics and healthcare.
Employee service awards 2023 1 min read · Sun, May 28 2023 News Congratulations to CBRC members Prof. Stefan Arold, Krishnakumar Sivakumar, Raik Grunberg, Senay Kafkas and Salim Bougouffa who received their 2023 KAUST employee service awards.
MS Thesis Defense | Learning 3D structures for protein function prediction 1 min read · Tue, May 9 2023 News bioinformatics protein function prediction Computer science artificial intelligence Student Nurul Muttakin from the Bio-Ontology Research Group (BORG) under the supervision of Assoc. Prof. Robert Hoehndorf successfully defends his Masters thesis. He presented his research on the topic " Learning 3D structures for protein function prediction".
MS Thesis Defense | Predicting Regulatory and Phenotypic Effects of Non-coding Variants 1 min read · Mon, May 8 2023 News Student Hatoon Ali from the Bio-Ontology Research Group (BORG) under the supervision of Prof. Robert Hoehndorf successfully defends her Masters thesis. She presented her research on the topic " Predicting Regulatory and Phenotypic Effects of Non-coding Variants".
KAUST Commencement 2022 looks to a bright future 2 min read · Sun, Dec 18 2022 News King Abdullah University of Science and Technology (KAUST) celebrated its 13th Commencement on a cool, breezy evening, December 16, 2022, among approximately 380 graduating students and a full audience of supportive families, university community members and distinguished guests. This year CBRC saw many student candidates complete their Postdoctoral and Masters Degrees. CBRC congratulates all students on this great achievement and wishes you even more success in the future.
BORG team win at the KAUST-NVIDIA GPU Hackathon 2022 2 min read · Sun, Oct 16 2022 News machine learning ontology artificial intelligence GPU Congratulations to Senay Kafkas, Maxat Kulmanov and Fernando Zhapa Camacho of the Bio-Ontology Research Group (BORG) on winning at the KAUST-NVIDIA GPU Hackathon 2022. The 8th edition of the Hackathon on Accelerating Scientific Applications using Graphical Processing Units (GPUs) was held at King Abdullah University of Science and Technology (KAUST), twelve teams of students and researchers enjoyed the opportunity to accelerate their codes in GPU’s under the guidance of expert mentors of NVIDIA, Codee, KAUST Supercomputing Lab (KSL) and KAUST core labs.
Appointment of Prof. Xin Gao as Interim Director and Prof. Robert Hoehndorf as Interim Associate Director of CBRC 1 min read · Mon, Oct 3 2022 News The Computational Bioscience Research Center (CBRC) is pleased to announce that Professor Xin Gao has assumed the position of Interim Director and Professor Robert Hoehndorf as Interim Associate Director of the CBRC. Both professors assumed their roles on September 15, 2022.
How much do model organism phenotypes contribute to the computational identification of human disease genes? 1 min read · Sun, Sep 4 2022 News Ontologies phenotype ontologies gene-disease associations PhD Student Sarah M Alghamdi from the Bio-Ontology Research Group (BORG) explains how phenotype ontologies help in identifying disease genes through phenotype comparison. Her research was picked as a highlight in the July 2022 issue of Disease Models and Mechanisms Journal.
MS Thesis Defense: Embedding Ontologies using Category Theory Semantics by Fernando Zhapa Camacho 1 min read · Sun, Apr 10 2022 News Computer science Fernando Patricio Zhapa Camacho an M.S./Ph.D. candidate in the KAUST Bio-Ontology research group under the supervision of Professor Robert Hoehndorf successfully defended his thesis "Embedding Ontologies using Category Theory Semantics".
MS Thesis Defense: Description Logic EL++Embeddings with Intersectional Closure by Xi Peng 1 min read · Thu, Mar 31 2022 News machine learning Knowledge representation and reasoning Xi Peng MS Student under the supervision of Professor Robert Hoehndorf successfully defended his thesis "Description Logic EL++Embeddings with Intersectional Closure"
MS Thesis Defense: Rare variant collapsing analysis on UK Biobank by Yang Liu 1 min read · Thu, Mar 31 2022 News bioinformatics machine learning Yang Liu, M.S./Ph.D. candidate in the Bio-Ontology research group under the supervision of Professor Robert Hoehndorf successfully defended her thesis "Rare variant collapsing analysis on UK Biobank".
Alumna Imane Boudellioua (PhD ’19, MS ’12) receives KACST prize 1 min read · Mon, Dec 21 2020 News Spotlight Congratulations to Computer Science alumna Imane Boudellioua (Ph.D. ’19, MS ’12) for receiving a prize in the 19th edition of the annual KACST Almarai National Prize for Creative Scientific Work for Students (Ph.D. Level). As a Ph.D. student in the Computational Bioscience Research Center, Dr. Boudellioua worked in machine learning and data mining algorithms, with research targeting the potential to help patients with mysterious ailments find genetic causes for their undiagnosed disease.
Former KAUST VSRP student wins Best Talk Award at ISMB 2020 2 min read · Tue, Aug 18 2020 News bio-ontology ISCB ISMB genome artificial intelligence Runar Reve, a former KAUST Visiting Student Research Program (VSRP) student, recently received the International Society for Computational Biology’s (ISCB) Bio-Ontologies COSI – Best Talk Award at the 28th Conference on Intelligent Systems for Molecular Biology (ISMB) 2020.
Studying COVID-19’s envelope protein 1 min read · Tue, Jul 28 2020 News COVID-19 human health genomics A likeness between genes of the SARS and COVID-19 viruses could inform research into potential treatments.
Robert Hoehndorf promoted to associate professor at KAUST 4 min read · Wed, Jul 1 2020 News bioinformatics biomedical data artificial intelligence KAUST faculty member Robert Hoehndorf was recently promoted from the rank of assistant professor to associate professor. Hoehndorf’s promotion caps a year-long process where the German researcher’s scientific and scholarly output was measured and evaluated by internal and external reviews.
KAUST Prospective student: Fernando Patricio Zhapa Camacho 2 min read · Thu, Jun 25 2020 News Natural Language Processing Fernando is a 23-year-old Information Technology graduate fromYachay Tech University in Urcuquí, Ecuador. He has planned to continue his academic career at KAUST under the supervision of Professor Robert Hoehndorf.
Algorithm turns cancer gene discovery on its head 1 min read · Mon, Jan 20 2020 News human health Computer science cancer A method for finding genes that spur tumor growth takes advantage of machine learning algorithms to sift through reams of molecular data collected from studies of cancer cell lines, mouse models and human patients.
Abeer Almutairi succesfully defends her master's thesis | Unsupervised Method for Disease Named Entity Recognition 1 min read · Mon, Dec 2 2019 News Abeer Almutairi, a student under the supervision of Professor Robert Hoehndorf, defended her Master's thesis "Unsupervised Method for Disease Named Entity Recognition" on November 4, 2019.
Mona Alshahrani Ph.D. Defense | Knowledge Graph Representation Learning: Approaches and Applications in Biomedicine 1 min read · Sun, Dec 1 2019 News Mona Alshahrani a Ph.D. candidate under the supervision of Professor Robert Hoehndorf Defended her Ph.D. thesis "Knowledge Graph Representation Learning: Approaches and Applications in Biomedicine."
Symbol of change for AI development 1 min read · Sun, Oct 20 2019 News artificial intelligence Computer science Bridging the knowledge gap in artificial intelligence requires an embedding function that helps step between different types of "thinking."
Database to support infectious disease research 1 min read · Wed, Sep 11 2019 News machine learning artificial intelligence human health Computer science Linking disease pathogens to clinical signs and symptoms through a database could support research into the molecular mechanisms of infectious diseases.
Imene Boudellioua defended her PhD thesis 1 min read · Tue, Feb 5 2019 News On 5 February, Imene successfully defended her Ph.D. thesis titled "Semantic Prioritization of Novel Causative Variants."
Visualization of brain structures helps to model function 1 min read · Thu, Jan 3 2019 News bioscience Computer simulations and virtual reality are used by KAUST researchers and collaborators in France to visualize the energetic coupling between neurons and astrocytes and to improve understanding of brain metabolism. The human brain uses more energy than any other organ, accounting for around 20 percent of all glucose-derived energy. Neurons can’t meet their own energy requirements: they depend on supporting glial cells and the neurovascular system to supply various forms of sugar fuel. However, it is still unclear how this neuro-glio-vasculature network manages the brain’s energy demands
Sara Althubaiti defends her Master's thesis 1 min read · Tue, Nov 6 2018 News cancer driver mutation bioinformatics text mining machine learning Sara Althubaiti, a student under the supervision of Assistant Professor Robert Hoehndorf, defended her Master's thesis on November 5, 2018.
Azza Althagafi defends her Master's thesis 1 min read · Fri, Nov 2 2018 News bioinformatics artificial intelligence genomics Azza Althagafi, a student under the supervision of Assistant Professor Robert Hoehndorf, defended her Master's thesis on November 1, 2018.
Aerial Path Planning for Urban Scene Reconstruction: A Continuous Optimization Method and Benchmark 1 min read · Tue, Oct 16 2018 News optimization urban planning Small unmanned aerial vehicles (UAVs) are ideal capturing devices for high-resolution urban 3D reconstructions using multi-view stereo. Nevertheless, practical considerations such as safety usually mean that access to the scan target is often only available for a short amount of time, especially in urban environments. It, therefore, becomes crucial to perform both view and path planning to minimize flight time while ensuring complete and accurate reconstructions. In this work, we address the challenge of automatic view and path planning for UAV-based aerial imaging with the goal of urban
Award-winning algorithm takes search for habitable planets to the next level 1 min read · Tue, Oct 16 2018 News telescope astronomy NVIDIA PASC singular-value-decomposition-MOAO An international team of scientists, including KAUST high performance computing experts and astronomers from the Paris Observatory and the National Astronomical Observatory of Japan (NAOJ), in collaboration with NVIDIA, is taking the search for habitable planets and observation of first epoch galaxies to the next level.
Mona Alshahrani defends her thesis proposal 1 min read · Tue, Oct 16 2018 News data integration machine learning human bioinformatics Mona Alshahrani, a Ph.D. candidate under the supervision of Assistant Professor Robert Hoehndorf, defended her thesis proposal on October 10, 2018.
National Infectious Disease Initiative Workshop brings researchers to KAUST 1 min read · Mon, Oct 8 2018 News infectious disease Representatives from the KAUST Computational Bioscience Research Center (CBRC), King Abdulaziz City for Science and Technology (KACST), King Saud University (KSU), Taibah University, National Guard Health Affairs (NGHA) and the Saudi Arabia Ministry of Health (MOH) met on October 1 to iron out details of a national initiative to fight infectious diseases.
KAUST and KACST join forces to prevent infectious diseases 2 min read · Mon, Oct 1 2018 News The KAUST Computational Bioscience Research Center (CBRC) and King Abdulaziz City for Science and Technology (KACST) have collaborated under the umbrella of the National Infectious Disease Initiative to enrich research...
CBRC goes to ECCB 2018 3 min read · Thu, Aug 9 2018 News Computational biology Nanopore Sequencing cwDTW algorithm ontology phenotypes SmuDGE The European Conference on Computational Biology (ECCB) is one of the most important conferences in the field of bioinformatics and computational biology. Held in a different European city annually, this year's conference will take place in the historic city of Athens, Greece on September 8-12, 2018.
Maxat Kulmanov defends his thesis proposal 1 min read · Tue, Jul 31 2018 News bioinformatics artificial intelligence neural network Semantic web machine learning Maxat Kulmanov, a Ph.D. candidate under the supervision of Assistant Professor Robert Hoehndorf, defended his thesis proposal on July 31, 2018.
BORG members to present at ISMB 2018 1 min read · Sun, May 27 2018 News Three members of the Bio-Ontology Research Group will be presenting their work at the International Society for Computational Biology conference in Chicago, U.S.A.
Exploring science's fourth paradigm 5 min read · Mon, May 7 2018 News computational and statistical interface big data The recent KAUST Research Conference: Computational and Statistical Interface to Big Data brought together leading computer science researchers and statistical experts to discuss the current state and future of data science. Held on campus from March 19 to 21, the conference covered such data science topics as succinct data representation and storage; big data visualization; parallel and distributed algorithms for inference and optimization; and analysis of large graphs and networks.
Sarah Alghamdi defends her master's thesis 1 min read · Sun, May 6 2018 News artificial intelligence bioinformatics computational methods data mining Sarah Alghamdi successfully defended her master's thesis on April 10, 2018. Her project, entitled "Ontology Design Patterns for Combining Pathology and Anatomy: Application to Study Ageing and Longevity in Inbred Mouse Strains", was well-received by a panel of professors that included Professor Vladimir Bajic, Associate Professor Xin Gao and Assistant Professor Robert Hoehndorf.
Assistant Professor Robert Hoehndorf awarded Center Partnership Fund 1 min read · Thu, Apr 19 2018 News CBRC was awarded three Center Partnership Funds by the KAUST Office of Sponsored Research on April 1, 2018.
BORG students present research in KAUST Research Conference on Big Data Analyses in Evolutionary Biology 1 min read · Tue, Dec 12 2017 News Two students from the Bio-Ontology Research Group presented their research at KAUST Research Conference on Big Data Analyses in Evolutionary Biology.
