The primary focus of the Biomedical Discovery Informatics unit at Data Science Institute of NUI Galway are cutting-edge AI and machine learning solutions motivated by and validated within a wide range of practically-relevant life science use cases. This research falls under the general umbrella of discovery informatics that has recently emerged as a field that explores the potential of applying various computer science technologies like Semantic Web, big data analytics, AI or machine learning to interdisciplinary challenges in turning data and information into actual knowledge. Life sciences are one of the most relevant application areas of discovery informatics, both in terms of interesting research problems and societal impact opportunities. This is reflected by the strategic vision of the unit that is to deliver novel scientific results with substantial impact potential in life sciences and healthcare.
The core research topics of the unit are as follows: Representation learning for biomedical data (including networked data, protein/gene sequences, etc.); Network analytics for biomedical data; Supervised, semi-supervised, unsupervised and reinforcement learning models for sparsely annotated and/or noisy data (primarily focusing on open biomedical data); Knowledge graph generation (transformation of legacy data into knowledge graphs, integration, cleansing); Knowledge graph embeddings (statistical relational learning models, focused primarily on link prediction and knowledge base completion, but also on more advanced issues like discovery of causal relationships); Mixed embedding models for knowledge graph and unstructured (primarily text) data; Explainable AI (with special focus on hybrid approaches combining latent and graph feature models); Informing explainable / predictive models with background domain knowledge; Augmenting standard deep learning models by knowledge graphs.
Selected application areas include: Drug repurposing and discovery; Prediction of adverse drug effects (including polypharmacy scenarios); Cellular signalling prediction (with specific focus on pathways prevalent in cancer and neurodegenerative diseases); General-purpose predictive “shells” and/or software libraries for processing biomedical data; Survival analysis (with specific focus on models based on integrated multi-omics data); Clinical decision support systems (with specific focus on precision medicine).
Areas of work:
Knowledge graphs, Network analytics for biomedical data, Explainable ai, Reinforcement learning, Representation learning,
Unit Leader:
Unit Members:
Publications:

Sameh K. Mohamed, Vit Novacek, Aayah Nounu
34th Annual ACM Symposium on Applied Computing

Sameh K. Mohamed, Vit Novacek, Aayah Nounu
34th Annual ACM Symposium on Applied Computing

The 16th Extended Semantic Web Conference

Sameh K. Mohamed and Vit Novacek and Pierre-Yves Vandenbussche
33rd Annual ACM Symposium on Applied Computing

Sameh K. Mohamed and Vit Novacek and Pierre-Yves Vandenbussche
33rd Annual ACM Symposium on Applied Computing

Sameh K. Mohamed and Vit Novacek and Pierre-Yves Vandenbussche
33rd Annual ACM Symposium on Applied Computing

Sameh K. Mohamed and Vit Novacek and Pierre-Yves Vandenbussche
33rd Annual ACM Symposium on Applied Computing

Pasquale Minervini and Luca Costabello and Emir Muñoz and Vít Nováček and Pierre-Yves Vandenbussche
MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2017, PT I

Sameh K. Mohamed and Emir Muñoz and Vít Nováček and Pierre-Yves Vandenbussche
1st Conference on Language Data and Knowledge


2013 IEEE 26TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS)

SEMANTIC WEB - ISWC 2011, PT I

Novacek, Groza, Handschuh, Chen, Wang, Cheung, KH
Knowledge Management And Organizational Learning

Novacek, V., Groza, T., Handschuh, S.
Semantic e-Science

Novacek, V., Groza, T., Handschuh, S., Decker, S.
Journal Of Web Semantics

Novacek, Groza, Handschuh, Decker
Journal Of Web Semantics


ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS: OTM 2010, PT II


ARTIFICIAL INTELLIGENCE IN MEDICINE, PROCEEDINGS

2009 22ND IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS

SEMANTIC WEB - ISWC 2009, PROCEEDINGS

Novacek, Laera, Handschuh, Davis
Journal Of Biomedical Informatics

Novacek, V., Laera, L., Handschuh, S., Davis, B.
Journal Of Biomedical Informatics

ENTERPRISE INFORMATION SYSTEMS-BOOKS

Proceedings of ICEIS 2007; Artificial Intelligence and Decision Support Systems
