doc. Mgr. Bc. Vít Nováček, PhD

Curriculum vitae

Name, first names, scientific degrees

• doc. Mgr. et Bc. Vít Nováček, PhD

Department / Faculty / University

• Department of Data Processing and Machine Learning, Faculty of Informatics, Masaryk University
• Masaryk Memorial Cancer Institute

Function, current position

• Associate Professor (at Masaryk University)
• Biomedical AI Consultant (at Masaryk Memorial Cancer Institute)

Education and academic qualifications

• 2011: PhD in computer science at Digital Enterprise Research Institute (DERI), NUI Galway; thesis committee: Stefan Decker, DERI (now RWTH Aachen), Eduard Hovy, Information Sciences Institute, University of Southern California (now Carnegie-Mellon University), Siegfried Handschuh, DERI (now University of St. Gallen)
• 2006: Mgr. (equiv. to MSc) in theoretical computer science at Faculty of Informatics, Masaryk University Brno, Czech Republic
• 2004: Bc. (equiv. to BSc) in theoretical computer science at Faculty of Informatics, Masaryk University Brno, Czech Republic
• 2003: Bc. (equiv. to BA) in political science and philosophy, and journalism and media studies (dual major) at Faculty of Social Sciences, Masaryk University Brno, Czech Republic

Professional experience

• 2022-now: Associate Professor (Faculty of Informatics, Masaryk University)
• 2020-2022: Assistant Professor (Faculty of Informatics, Masaryk University)
• 2020-now: Biomedical AI consultant (Masaryk Memorial Cancer Institute)
• 2015-2023: Research Fellow, group leader (Data Science Institute, National University of Ireland Galway; part-time since September 2020, limited to coordination of the AI activities in the CLARIFY H2020 project)
• 2012-2015: Senior post-doctoral researcher, project leader (Insight, National University of Ireland Galway)
• 2011-2016: Research associate, visiting research fellow (Information Sciences Institute, University of Southern California)
• 2010-2012: Post-doctoral researcher (DERI, National University of Ireland Galway)

Teaching activities

• 2023-now: AI and ML in Healthcare (PV287 at Masaryk University; lectures and labs)
• 2022-now: Computational methods in Bioinformatics and Systems Biology (PB051 at Masaryk University; lectures and labs)
• 2021-now: Natural Language Learning (PA164 at Masaryk University; lectures and labs)
• 2021-now: Computer Science Applications in Biology (IV121 at Masaryk University; teaching lectures and labs)
• 2021-now: Introduction to Machine Learning (IB031 at Masaryk University; teaching labs)
• 2020-now: Artificial Intelligence I (PB016 at Masaryk University; organising and teaching labs)
• 2011: Computer Science (CS102 at National University of Ireland Galway; reshaping the course from scratch, organising and teaching lectures, organising and grading exams)
• 2003-2004: Introduction to the C language (PB071 at Masaryk University; teaching labs)
  
  Supervision experience:
  
• PhD theses supervised: 3 (Sameh K. Mohamed, graduated at NUI Galway in 2020; Emir Munoz, graduated at NUI Galway in 2020; Petr Zelina, started at FI MU in 2023)
• MSc theses supervised: 10+
• BSc theses supervised: 5+
• Post-doctoral fellows supervised: 6
• Research associates supervised: 5+

Research activities

• Artificial Intelligence and Machine Learning
• Medical Informatics
• Discovery Informatics
• Knowledge Graphs
• formerly also Semantic Web (participating for instance in large EU FP6 projects Knowledge Web and NEPOMUK, and in standardisation activities at W3C)

Professional stays abroad

• 2012: Visiting research fellow at Information Sciences Institute, University of Southern California (3 months)
• 2006-2007: Student intern at the Digital Enterprise Research Institute (DERI), National University of Ireland Galway (6 months)

Other academic activities, research projects, grants

• 2024-now: coordinating a team developing multimodal learning and NLP solutions for biomedical data mining in the OP JAK project Salvage aiming at cancer prevention
• 2022-now: coordinating a team responsible for setting up the MMCI local node in a federated data analytics infrastructure developed within the IDEA4RC Horizon Europe project
• 2022-now: team member in an AZV project developing radiomics tools for distinguishing between false and true progressions of brain metastases (responsible for secure data transfer and processing)
• 2021-2023: PI and overall coordinator in the AIcope GAMU Interdisciplinary project
• 2020-2023: local PI and WP leader in the CLARIFY H2020 project
• 2015-now: member of Graduate Research Committee at National University of Ireland Galway
• 2012-2019: PI and overall scientific coordinator in the KI2NA and TOMOE industrial collaboration projects funded by Fujitsu Laboratories Limited at National University of Ireland Galway
• 2006-2008: invited expert at W3C working groups for Semantic Web Deployment and the OWL2 knowledge representation standard

Non-university activities

• 2007-now: program committee member for (selection of international conferences): AAAI Conference on Artificial Intelligence; Conference on Information and Knowledge Management (CIKM); Annual Symposium of American Medical Informatics Association (AMIA); International Semantic Web Conference (ISWC); Computer-Based Medical Systems (CBMS); International Conference on Knowledge Engineering and Knowledge Management (EKAW); ...
• 2014-2016: topic editor in Frontiers in Neuroinformatics (part of Frontiers, an Open Access imprint of the Nature-Springer publishing group; co-editor: Gully Burns (Information Sciences Institute, University of Southern California)
• 2007-now: invited reviewer for (selection of international journals): Artificial Intelligence in Medicine; Journal of Web Semantics; Journal of Biomedical Informatics; Knowledge-Based Systems (all Elsevier journals); The Computer Journal, Bioinformatics, Briefings in Bioinformatics (all Oxford University Press journals); ...
• 2006-now: organised in excess of 10 international events, such as Workshop on Semantic Web Solutions for Large-Scale Biomedical Data Analytics (SeWeBMeDA, collocated with ISWC in 2019 and 2020) or a Special track at IEEE conference on Computer-Based Medical Systems (CBMS) in 2014

Most significant professional accomplishments

• 2023: invited speaker in the Knowledge Graphs and Semantic Computing Series at University of Illinois Urbana-Champaign
• 2013: invited panelist at the IEEE conference on Computer-Based Medical Systems
• 2011: nominated for the best Irish PhD thesis in ICT
• 2010: invited speaker at Znalosti, a premier Czech AI conference
• 2009: winner of the second prize and $15,000 prize money in Elsevier Grand Challenge aimed at knowledge enhancement in life sciences

Major publications

• BUOSI, Samuele, Mohan TIMILSINA, Adriann JANIK, Luca COSTABELLO, Maria TORRENTE, Mariano PROVENCIO, Dirk FEY a Vít NOVÁČEK. Machine learning estimated probability of relapse in early-stage non-small-cell lung cancer patients with aneuploidy imputation scores and knowledge graph embeddings. Expert Systems with Applications. Elsevier, 2024, roč. 2024, č. 235, s. 121-127. ISSN 0957-4174. Dostupné z: https://dx.doi.org/10.1016/j.eswa.2023.121127. URL info
• BUOSI, Samuele, Mohan TIMILSINA, Maria TORRENTE, Mariano PROVENCIO, Dirk FEY a Vít NOVÁČEK. Boosting predictive models and augmenting patient data with relevant genomic and pathway information. Computers in Biology and Medicine. Pergamon-Elsevier Science Press, 2024, roč. 2024, č. 108398, s. 1-9. ISSN 0010-4825. Dostupné z: https://dx.doi.org/10.1016/j.compbiomed.2024.108398. URL info
• ZELINA, Petr, Jana HALÁMKOVÁ a Vít NOVÁČEK. Extraction, labeling, clustering, and semantic mapping of segments from clinical notes. IEEE TRANSACTIONS ON NANOBIOSCIENCE. UNITED STATES: IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2023, roč. 22, č. 4, s. 781-788. ISSN 1536-1241. Dostupné z: https://dx.doi.org/10.1109/TNB.2023.3275195. URL info
• TIMILSINA, Mohan, Dirk FEY, Samuele BUOSI, Adrianna JANIK, Luca COSTABELLO, Enric CARCERENY, Delvys Rodrıguez ABREU, Manuel COBO, Rafael López CASTRO, Reyes BERNABÉ, Pasquale MINERVINI, Maria TORRENTE, Mariano PROVENCIO a Vít NOVÁČEK. Synergy between imputed genetic pathway and clinical information for predicting recurrence in early stage non-small cell lung cancer. Journal for Biomedical Informatics. Elsevier, 2023, roč. 144, č. 104424, s. 1-12. ISSN 1532-0464. Dostupné z: https://dx.doi.org/10.1016/j.jbi.2023.104424. URL info
• JANIK, Adrianna, Maria TORRENTE, Luca COSTABELLO, Virginia CALVO, Brian WALSH, Carlos CAMPS, Sameh K MOHAMED, Ana L ORTEGA, Vít NOVÁČEK, Bartomeu MASSUTÍ, Pasquale MINERVINI, M Rosario GARCIA CAMPELO, Edel del BARCO, Joaquim BOSCH-BARRERA, Ernestina MENASALVAS, Mohan TIMILSINA a Mariano PROVENCIO. Machine Learning–Assisted Recurrence Prediction for Patients With Early-Stage Non–Small-Cell Lung Cancer. JCO CLINICAL CANCER INFORMATICS. UNITED STATES: LIPPINCOTT WILLIAMS & WILKINS, 2023, roč. 7, e2200062, s. 1-11. ISSN 2473-4276. Dostupné z: https://dx.doi.org/10.1200/CCI.22.00062. URL info
• NOVACEK, Vít. Curing Cancer with Knowledge Graphs (and other Outrageous Ideas). In Knowledge Graphs and Semantic Computing Series at University of Illinois Urbana-Champaign. 2023. URL info
• TIMILSINA, Mohan, Meera TANDAN a Vít NOVÁČEK. Machine learning approaches for predicting the onset time of the adverse drug events in oncology. Machine Learning with Applications. Elsevier, 2022, roč. 2022, č. 9, 14 s. ISSN 2666-8270. URL info
• TIMILSINA, Mohan, Vít NOVÁČEK, Mathieu DAQUIN a Haixuan YANG. Boundary heat diffusion classifier for a semi-supervised learning in a multilayer network embedding. NEURAL NETWORKS. ENGLAND: PERGAMON-ELSEVIER SCIENCE LTD, 2022, roč. 156, č. 1, s. 205-217. ISSN 0893-6080. Dostupné z: https://dx.doi.org/10.1016/j.neunet.2022.10.005. original online article info
• TORRENTE, María, Pedro A SOUSA, Roberto HERNÁNDEZ, Mariola BLANCO, Virginia Calvo Ana COLLAZO, Gracinda R GUERREIRO, Beatriz NÚÑEZ, Joao PIMENTAO, Juan Cristóbal SÁNCHEZ, Manuel CAMPOS, Luca COSTABELLO, Vít NOVÁČEK, Ernestina MENASALVAS, María Esther VIDAL, Mariano PROVENCIO a Virginia CALVO. An Artificial Intelligence-Based Tool for Data Analysis and Prognosis in Cancer Patients: Results from the Clarify Study. CANCERS. SWITZERLAND: MDPI, 2022, roč. 14, č. 16, s. 1-10. ISSN 2072-6694. Dostupné z: https://dx.doi.org/10.3390/cancers14164041. original online article info
• TIMILSINA, Mohan, Dirk FEY, Adrianna JANIK, Maria TORRENTE, Mariano PROVENCIO, Alberto Cruz BERMUDEZ, Enric CARCERENY, Luca COSTABELLO, Delvys Rodrıguez ABREU, Manuel COBO, Rafael Lopez CASTRO, Reyes BERNABE, Maria GUIRADO, Pasquale MINERVINI a Vít NOVÁČEK. Integration of Medical and Genomic Information to Enhance Relapse Prediction in Early Stage Lung Cancer Patients. Online. In Proceedings of the Annual Symposium of the American Medical Informatics Association. Washington, USA: AMIA, 2022, s. 1082-1091. ISSN 1559-4076. URL info
• ZELINA, Petr, Jana HALÁMKOVÁ a Vít NOVÁČEK. Unsupervised extraction, labelling and clustering of segments from clinical notes. Online. In Proceedings of IEEE International Conference on Bioinformatics and Biomedicine (BIBM). USA: IEEE, 2022, s. 1362-1368. ISBN 978-1-6654-6820-6. Dostupné z: https://dx.doi.org/10.1109/BIBM55620.2022.9995229. arXiv preprint info
• NOVACEK, Vít, Marko ŘEHÁČEK, Petr ZELINA a Jana HALÁMKOVÁ. AI for Cancer Patient Empowerment - Interim Results of the AIcope Project. 2022. info
• MOHAMED, Sameh K, Vít NOVACEK a Emir MUNOZ. On Training Knowledge Graph Embedding Models. Information. Switzerland: MDPI, 2021, roč. 12, č. 4, s. 147-165. ISSN 2078-2489. Dostupné z: https://dx.doi.org/10.3390/info12040147. URL info
• TORRENTE, M., F. FRANCO, V. CALVO, A. Collazo LORDUY, E. MENASALVAS, M. E. VIDAL, P. SOUSA, J. PIMENTAO, Vít NOVÁČEK, P. MINERVINI, D. FEY, L. COSTABELLO, M. POCS a M. PROVENCIO. P08. 01 Building Personalized Follow-Up Care Through AI by Bringing the Lung Cancer Patient, Data Scientist and Oncologist Together. Journal of Thoracic Oncology. Elsevier, 2021, roč. 16, č. 10, s. 991-992. ISSN 1556-1380. Dostupné z: https://dx.doi.org/10.1016/j.jtho.2021.08.294. URL info
• MOHAMED, Sameh K., Brian WALSH, Mohan TIMILSINA, Maria TORRENTE, Fabio FRANCO, Mariano PROVENCIO, Adrianna JANIK, Luca COSTABELLO, Pasquale MINERVINI, Pontus STENETORP a Vít NOVÁČEK. On Predicting Recurrence in Early Stage Non-small Cell Lung Cancer. Online. In Adam B. Wilcox, Randi Foraker, Kensaku Kawamoto, Yves A. Lussier, Nadine McCleary. Proceedings of AMIA 2021 Annual Symposium. San Diego: AMIA, 2021, s. 853-862. ISSN 1942-597X. info
• MOHAMED, Sameh K, Ayah NOUNU a Vít NOVÁČEK. Biological applications of knowledge graph embedding models. Briefings in Bioinformatics. Oxford (UK): Oxford University Press, 2021, roč. 22, č. 2, s. 1679-1693. ISSN 1467-5463. Dostupné z: https://dx.doi.org/10.1093/bib/bbaa012. URL info
• NOVÁČEK, Vít, Gavin MCGAURAN, David MATALLANAS, Adrián Vallejo BLANCO, Piero CONCA, Emir MUÑOZ, Luca COSTABELLO, Kamalesh KANAKARAJ, Zeeshan NAWAZ, Brian WALSH, Sameh K MOHAMED, Pierre-Yves VANDENBUSSCHE, Colm J RYAN, Walter KOLCH a Dirk FEY. Accurate prediction of kinase-substrate networks using knowledge graphs. PLoS Computational Biology. Cambridge: PLoS, 2020, roč. 16, č. 12, s. 1-30. ISSN 1553-734X. Dostupné z: https://dx.doi.org/10.1371/journal.pcbi.1007578. URL URL info
• NOVÁČEK, Vít, Loredana LAERA, Siegfried HANDSCHUH a Brian DAVIS. Infrastructure for Dynamic Knowledge Integration -- Automated Biomedical Ontology Extension Using Textual Resources. Journal of Biomedical Informatics. Amsterdam: Elsevier, 2008, roč. 41, č. 5, s. 816-828, 12 s. ISSN 1532-0464. ScienceDirect info
• NOVÁČEK, Vít. Automatic Knowledge Acquisition and Integration Technique: Application to Large Scale Taxonomy Extraction and Document Annotation. In Enterprise Information Systems (ICEIS 2007, revised selected papers). Berlin/Heidelberg: Springer-Verlag, 2008, s. 160-172. IX. ISSN 1865-1348. SpringerLink info
• NOVÁČEK, Vít, Siegfried HANDSCHUH, Loredana LAERA, Diana MAYNARD a Max VOELKEL. Dynamic Ontology Lifecycle Scenario in Translational Medicine. In Proceedings of the 5th European Conference of Computational Biology (ECCB 2006) - Book of Abstracts. Oxford: Oxford University Press, 2007, s. 22-26. ISSN 1460-2059. info
• NOVÁČEK, Vít, Maciej DABROWSKI, Sebastian R. KRUK a Siegfried HANDSCHUH. Extending Community Ontology Using Automatically Generated Suggestions. In Proceedings of FLAIRS 2007. Menlo Park, CA: AAAI Press, 2007, s. 290-295. ISBN 978-1-57735-319-5. info
• NOVÁČEK, Vít. Imprecise Empirical Ontology Refinement: Application to Taxonomy Acquisition. In Proceedings of ICEIS 2007, vol. Artificial Intelligence and Decision Support Systems. Portugal: INSTICC, 2007, s. 31-38. ISBN 978-972-8865-89-4. info
• NOVÁČEK, Vít, Loredana LAERA a Siegfried HANDSCHUH. Dynamic Integration of Medical Ontologies in Large Scale. In Proceedings of WWW2007/HCLSDI. New York: ACM Press, 2007, s. 2-11. ISBN 978-1-59593-654-7. info
• NOVÁČEK, Vít, Loredana LAERA a Siegfried HANDSCHUH. Semi-automatic Integration of Learned Ontologies into a Collaborative Framework. In Proceedings of IWOD/ESWC 2007. Innsbruck: Springer Verlag, 2007, s. 13-26. info
• NOVÁČEK, Vít, Loredana LAERA a Siegfried HANDSCHUH. Aiding the Data Integration in Medicinal Settings by Means of Semantic Technologies. In Making Semantics Work for Business. Vienna: Semantic Technology Institutes International, 2007, s. 10-15. info
• NOVÁČEK, Vít. A Non-traditional Inference Paradigm for Learned Ontologies. In Proceedings of ESWC 2007 PhD Symposium. Innsbruck: CEUR Workshop Proceedings, 2007, s. 57-62. ISSN 1613-0073. info
• NOVÁČEK, Vít. D2.3.9 Theoretical Aspects for Ontology Lifecycle. Innsbruck, Austria: Knowledge Web EU NoE, 2007, 51 s. Knowledge Web EU NoE deliverable D2.3.9. URL info
• NOVÁČEK, Vít. D2.3.8v2 Report and Prototype of Dynamics in the Ontology Lifecycle. Innsbruck, Austria: Knowledge Web EU NoE, 2007, 85 s. Knowledge Web EU NoE deliverable D2.3.8v2. URL info
• NOVÁČEK, Vít a Pavel SMRŽ. Ontology Acquisition for Automatic Building of Scientific Portals. In Lecture Notes in Computer Science 3831. Berlin: Springer, 2006, s. 493-500. ISBN 3-540-31198-X. URL info
• NOVÁČEK, Vít. Ontology Learning. Brno: Faculty of Informatics, Masaryk University, 2006, 65 s. Diploma Thesis. URL info
• NOVÁČEK, Vít. Motivations of Extensive Incorporation of Uncertainty in OLE Ontologies. In SOFSEM 2006: Theory and Practice of Computer Science: 32nd Conference on Current Trends in Theory and Practice of Computer Science. Student Research Forum Proceedings. Prague: Institute of Computer Science, Academy of Sciences of the Czech Republic, 2006, s. 145-154. ISBN 80-903298-4-5. URL info
• NOVÁČEK, Vít, Pavel SMRŽ a Jan POMIKÁLEK. Text Mining for Semantic Relations as a Support Base of a Scientific Portal Generator. In Proceedings of LREC 2006 - 5th International Conference on Language Resources and Evaluation. Paris: ELRA, 2006, s. 1338-1343. ISBN 2-9517408-2-4. URL info
• NOVÁČEK, Vít a Pavel SMRŽ. Empirical Merging of Ontologies A Proposal of Universal Uncertainty Representation Framework. In The Semantic Web: Research and Applications (Lecture notes in Computer Science 4011 / 2006 - Proceedings of ESWC'06 - 3rd European Semantic Web Conference). Berlin: Springer Verlag, 2006, s. 65-79, 14 s. ISBN 3-540-34544-2. URL info
• NOVÁČEK, Vít, Siegfried HANDSCHUH, Diana MAYNARD, Loredana LAERA, Sebastian KRUK, Max VOELKEL, Tudor GROZA a Valentina TAMMA. Report and Prototype of Dynamics in the Ontology Lifecycle. Galway, Ireland: Knowledge Web, 2006, 49 s. D2.3.8v1. info
• NOVÁČEK, Vít. Ontology Acquisition Supported by Imprecise Conceptual Refinement - New Results and Reasoning Perspectives. In Inteligentní modely, algoritmy, metody a nástroje pro vytváření sémantického webu. Praha: Ústav informatiky AV ČR, 2006, s. 91-101, 10 s. ISBN 80-903298-7-X. info
• NOVÁČEK, Vít a Pavel SMRŽ. OLE - A New Ontology Learning Platform. In International Workshop on Text Mining Research, Practice and Opportunities - Proceedings. Shoumen, Bulgaria: Incoma Ltd., 2005, s. 12-16. ISBN 954-91743-1-X. URL info
• NOVÁČEK, Vít a Pavel SMRŽ. BOLE - A New Bio-Ontology Learning Platform. In Proceedings of International Workshop on Biomedical Ontologies and Text Processing (held in conjunction with 4th European Conference on Computational Biology). Madrid: INB, 2005, s. 36-39. URL info
• NOVÁČEK, Vít. Implementace lexikálních pravidel v Prologu: Systém pro vzájmený převod českých vět v aktivní a pasivní formě. Brno: Fakulta informatiky, Masarykova univerzita, 2004, 48 s. URL info
• NOVÁČEK, Vít. Od rovných práv k dekonstrukci: Feminismus a perspektivy poststrukturalismu. Brno: Fakulta sociálních studií, Masarykova univerzita, 2003, 57 s. info
• NOVÁČEK, Vít. Specifika online žurnalistiky. Brno: Fakulta sociálních studií, Masarykova univerzita, 2002, 46 s. info

2024/01/19