Computer Science

Dr Vit Novácek

Biography

Vit holds a PhD from National University of Ireland Galway and currently leads the Biomedical Discovery Informatics Unit at Data Science Institute, NUI Galway where he also is a Research Fellow and Adjunct Lecturer. His personal research interests revolve around developing machine-aided discovery solutions by means of machine/representation learning, explainable AI and text mining, with a strong focus on biomedical use cases (e.g. prediction of adverse drug effects, protein drug targets or signalling reactions). Vit also has substantial experience with coordinating large industrial collaboration projects (for instance, with Fujitsu Laboratories Limited), is a primary or senior author of over 30 high-impact publications and has acquired over 3M euros in research project funding as of 2020.

Peer Reviewed Journals

	Year	Publication
	(2008)	'Infrastructure for dynamic knowledge integration-Automated biomedical ontology extension using textual resources' Novacek, V,Laera, L,Handschuh, S,Davis, B (2008) 'Infrastructure for dynamic knowledge integration-Automated biomedical ontology extension using textual resources'. Journal Of Biomedical Informatics, 41 :816-828 [DOI] [Details]
	(2010)	'CORAAL-Dive into publications, bathe in the knowledge' Novacek, V;Groza, T;Handschuh, S;Decker, S (2010) 'CORAAL-Dive into publications, bathe in the knowledge'. Journal Of Web Semantics, 8 :176-181 [DOI] [Details]
	(2010)	'Towards Knowledge-Based Life Science Publication Repositories' Novacek, V,Groza, T,Handschuh, S,Chen, H,Wang, Y,Cheung, KH (2010) 'Towards Knowledge-Based Life Science Publication Repositories'. Knowledge Management And Organizational Learning, 11 :309-345 [DOI] [Details]
	(2014)	'SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading' Novacek, V,Burns, GAPC (2014) 'SKIMMR: facilitating knowledge discovery in life sciences by machine-aided skim reading'. Peerj, 2 [DOI] [Details]
	(2014)	'Empirically Grounded Emergent Knowledge' Novacek, V;Handschuh, S (2014) 'Empirically Grounded Emergent Knowledge'. Perspectives On Ontology Learning, 18 :153-172 [Details]
	(2019)	'Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models' Munoz, E,Novacek, V,Vandenbussche, PY (2019) 'Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models'. Brief Bioinform, 20 :190-202 [DOI] [Details]
	(2010)	'CORAAL -- Dive into Publications; Bathe in the Knowledge' Novacek, V., Groza, T., Handschuh, S., Decker, S. (2010) 'CORAAL -- Dive into Publications; Bathe in the Knowledge'. Journal of Web Semantics, :81-104 [Details]
	(2009)	'Eye of the Tiger' Novacek, V., Groza, T., Handschuh, S., Decker, S. (2009) 'Eye of the Tiger'. Technology Ireland Journal, :301-330 [ARAN Link] [Details]
	(2008)	'Infrastructure for Dynamic Knowledge Integration -- Automated Biomedical Ontology Extension Using Textual Resources' Novacek, V., Laera, L., Handschuh, S., Davis, B. (2008) 'Infrastructure for Dynamic Knowledge Integration -- Automated Biomedical Ontology Extension Using Textual Resources'. Journal of Biomedical Informatics, [ARAN Link] [Details]

Book Chapters

	Year	Publication
	(2010)	'Towards Knowledge-Based Life Science Publication Repositories' Novacek, V., Groza, T., Handschuh, S. (2010) 'Towards Knowledge-Based Life Science Publication Repositories' In: Semantic e-Science. [Details]
	(2008)	'Automatic Knowledge Acquisition and Integration Technique: Application to Large Scale Taxonomy Extraction and Document Annotation' Novacek, V. (2008) 'Automatic Knowledge Acquisition and Integration Technique: Application to Large Scale Taxonomy Extraction and Document Annotation' In: Enterprise Information Systems. [Details]

Conference Publications

	Year	Publication
	(2007)	*ICEIS 2007: PROCEEDINGS OF THE NINTH INTERNATIONAL CONFERENCE ON ENTERPRISE INFORMATION SYSTEMS* Novacek, V (2007) Imprecise empirical ontology refinement - Application to taxonomy acquisition ICEIS 2007: PROCEEDINGS OF THE NINTH INTERNATIONAL CONFERENCE ON ENTERPRISE INFORMATION SYSTEMS , pp.31-38 [Details]
	(2008)	*ENTERPRISE INFORMATION SYSTEMS-BOOKS* Novacek, V (2008) Automatic Knowledge Acquisition and Integration Technique: Application to Large Scale Taxonomy Extraction and Document Annotation ENTERPRISE INFORMATION SYSTEMS-BOOKS , pp.160-172 [Details]
	(2009)	*2009 22ND IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS* Novacek, V;Groza, T;Handschuh, S (2009) Knowledge-Based Search for Oncological Literature 2009 22ND IEEE INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS [Details]
	(2009)	*ARTIFICIAL INTELLIGENCE IN MEDICINE, PROCEEDINGS* Novacek, V;Groza, T;Handschuh, S (2009) CORAAL - Towards Deep Exploitation of Textual Resources in Life Sciences ARTIFICIAL INTELLIGENCE IN MEDICINE, PROCEEDINGS , pp.206-215 [Details]
	(2009)	*SEMANTIC WEB - ISWC 2009, PROCEEDINGS* Novacek, V;Decker, S (2009) Towards Lightweight and Robust Large Scale Emergent Knowledge Processing SEMANTIC WEB - ISWC 2009, PROCEEDINGS , pp.456-472 [Details]
	(2010)	*ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS: OTM 2010, PT II* Novacek, V;Handschuh, S (2010) Biomedical Publication Knowledge Acquisition, Processing and Dissemination with CORAAL ON THE MOVE TO MEANINGFUL INTERNET SYSTEMS: OTM 2010, PT II [Details]
	(2011)	*SEMANTIC WEB - ISWC 2011, PT I* Novacek, V;Handschuh, S;Decker, S (2011) Getting the Meaning Right: A Complementary Distributional Layer for the Web Semantics SEMANTIC WEB - ISWC 2011, PT I , pp.504-519 [Details]
	(2013)	*2013 IEEE 26TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS)* Novacek, V;Naseer, A (2013) Linking the Scientific and Clinical Data with KI2NA-LHC - An Outline 2013 IEEE 26TH INTERNATIONAL SYMPOSIUM ON COMPUTER-BASED MEDICAL SYSTEMS (CBMS) , pp.540-541 [Details]
	(2017)	*MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2017, PT I* Minervini, P,Costabello, L,Munoz, E,Novacek, V,Vandenbussche, PY,Ceci, M,Hollmen, J,Todorovski, L,Vens, C,Dzeroski, S (2017) Regularizing Knowledge Graph Embeddings via Equivalence and Inversion Axioms MACHINE LEARNING AND KNOWLEDGE DISCOVERY IN DATABASES, ECML PKDD 2017, PT I , pp.668-683 [DOI] [Details]
	(2017)	*LANGUAGE, DATA, AND KNOWLEDGE, LDK 2017* Mohamed, SK,Munoz, E,Novacek, V,Vandenbussche, PY,Gracia, J,Bond, F,McCrae, JP,Buitelaar, P,Chiarcos, C,Hellmann, S (2017) Identifying Equivalent Relation Paths in Knowledge Graphs LANGUAGE, DATA, AND KNOWLEDGE, LDK 2017 , pp.299-314 [DOI] [Details]
	(2018)	*33rd Annual ACM Symposium on Applied Computing* Mohamed, SK;Novacek, V;Vandenbussche, PY (2018) Knowledge Base Completion Using Distinct Subgraph Paths 33rd Annual ACM Symposium on Applied Computing , pp.1992-1999 [DOI] [ARAN Link] [Details]
	(2010)	*Proceedings of Znalosti* Novacek, V. (2010) Can We Deal with Emergent Knowledge Yet? Proceedings of Znalosti [Details]
	(2009)	*Proceedings of AIME* Novacek, V., Groza, T., Handschuh, S. (2009) CORAAL -- Towards Deep Exploitation of Textual Resources in Life Sciences Proceedings of AIME [Details]
	(2009)	*Proceedings of CBMS* Novacek, V., Groza, T., Handschuh, S. (2009) Knowledge-Based Search for Oncological Literature: Technical Architecture and User Perspectives Proceedings of CBMS [ARAN Link] [Details]
	(2009)	*Proceedings of ISWC* Novacek, V., Decker, S. (2009) Towards Lightweight and Robust Large Scale Emergent Knowledge Processing Proceedings of ISWC [ARAN Link] [Details]
	(2007)	*Proceedings of ICEIS 2007; Artificial Intelligence and Decision Support Systems* Novacek, V. (2007) Imprecise Empirical Ontology Refinement: Application to Taxonomy Acquisition Proceedings of ICEIS 2007; Artificial Intelligence and Decision Support Systems Funchal; Madeira; Portugal, [ARAN Link] [Details]
	(2007)	*Proceedings of FLAIRS* Novacek, V., Dabrowski, M., Ryszard Kruk, S., Handschuh, S. (2007) Extending Community Ontology Using Automatically Generated Suggestions Proceedings of FLAIRS Key West; Florida; USA, [ARAN Link] [Details]

Conference Paper

	Year	Publication
	(2010)	Invited Talk: Can We Deal with Emergent Knowledge Yet?. Proceedings of Znalosti 2010, VSE Prague, 2010. Vit Novacek, (2010) Invited Talk: Can We Deal with Emergent Knowledge Yet?. Proceedings of Znalosti 2010, VSE Prague, 2010. Conference Paper [ARAN Link] [Details]
	(2009)	CORAAL - Towards Deep Exploitation of Textual Resources in Life Sciences. Proceedings of AIME 2009, Springer Verlag, 2009. Vit Novacek, Tudor Groza, Siegfried Handschuh in Carlo Combi, Yuval Shahar (editors) (2009) CORAAL - Towards Deep Exploitation of Textual Resources in Life Sciences. Proceedings of AIME 2009, Springer Verlag, 2009. Conference Paper [ARAN Link] [Details]

Workshops

	Year	Publication
	(2009)	System Description: Reaching Deeper into the Life Science Bibliome with CORAAL. Proceedings of the Semantic Web Applications in Scientific Discourse Workshop. Novacek, V., Groza, T., Handschuh, S. (2009) System Description: Reaching Deeper into the Life Science Bibliome with CORAAL. Proceedings of the Semantic Web Applications in Scientific Discourse Workshop. Workshops [Details]
	(2009)	Towards a Practical Emergent Knowledge Exploitation. Proceedings of IJCAI. Novacek, V. (2009) Towards a Practical Emergent Knowledge Exploitation. Proceedings of IJCAI. Workshops [ARAN Link] [Details]
	(2008)	Relaxing the Basic KR&R Principles to Meet the Emergent Semantic Web. Proceedings of the Fourth International Workshop on Uncertainty Reasoning for Semantic Web. Novacek, V. (2008) Relaxing the Basic KR&R Principles to Meet the Emergent Semantic Web. Proceedings of the Fourth International Workshop on Uncertainty Reasoning for Semantic Web. Workshops [ARAN Link] [Details]
	(2008)	EUREEKA: Deepening the Semantic Web by More Efficient Emergent Knowledge Representation and Processing. Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference. Novacek, V. (2008) EUREEKA: Deepening the Semantic Web by More Efficient Emergent Knowledge Representation and Processing. Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference. Workshops [ARAN Link] [Details]
	(2007)	Dynamic Integration of Medical Ontologies in Large Scale. Proceedings of WWW2007/HCLSDI. Novacek, V., Laera, L., Handschuh, S. (2007) Dynamic Integration of Medical Ontologies in Large Scale. Proceedings of WWW2007/HCLSDI. Workshops [Details]
	(2007)	A Non-traditional Inference Paradigm for Learned Ontologies. Proceedings of ESWC 2007 PhD Symposium. Novacek, V. (2007) A Non-traditional Inference Paradigm for Learned Ontologies. Proceedings of ESWC 2007 PhD Symposium. Workshops [ARAN Link] [Details]
	(2007)	Dynamic Ontology Lifecycle Scenario in Translational Medicine. Proceedings of the 5th European Conference of Computational Biology - Book of Abstracts. Novacek, V., Handschuh, S., Laera, L., Maynard, D., Voelkel, M. (2007) Dynamic Ontology Lifecycle Scenario in Translational Medicine. Proceedings of the 5th European Conference of Computational Biology - Book of Abstracts. Workshops [ARAN Link] [Details]
	(2007)	Semi-automatic Integration of Learned Ontologies into a Collaborative Framework. Proceedings of IWOD/ESWC 2007. Novacek, V., Laera, L., Handschuh, S. (2007) Semi-automatic Integration of Learned Ontologies into a Collaborative Framework. Proceedings of IWOD/ESWC 2007. Workshops [ARAN Link] [Details]
	(2007)	Aiding the Data Integration in Medicinal Settings by Means of Semantic Technologies. Making Semantics Work for Business. Novacek, V., Laera, L., Handschuh, S. (2007) Aiding the Data Integration in Medicinal Settings by Means of Semantic Technologies. Making Semantics Work for Business. Workshops [ARAN Link] [Details]