OLE - A New Ontology Learning Platform. - Vít Novácek; Pavel Smrz (RANLP Text Mining Workshop, 2005)

Empirical Merging of Ontologies - A Proposal of Universal Uncertainty Representation Framework. - Vít Novácek; Pavel Smrz (ESWC, 2006)

Text Mining for Semantic Relations as a Support Base of a Scientific Portal Generator. - Vít Novácek; Pavel Smrz; Jan Pomikálek (LREC, 2006)

Ontology Acquisition for Automatic Building of Scientific Portals. - Pavel Smrz; Vít Novácek (SOFSEM, 2006)

Inferential Ontology Learning. - Vít Novácek (KWEPSY, 2007)

Extending Community Ontology Using Automatically Generated Suggestions. - Vít Novácek; Maciej Dabrowski; Sebastian Ryszard Kruk; Siegfried Handschuh (FLAIRS, 2007)

Imprecise Empirical Ontology Refinement - Application to Taxonomy Acquisition. - Vít Novácek (ICEIS (2), 2007)

Automatic Knowledge Acquisition and Integration Technique: Application to Large Scale Taxonomy Extraction and Document Annotation. - Vít Novácek (ICEIS (Selected Papers), 2007)

EUREEKA: Deepening the Semantic Web by More Efficient Emergent Knowledge Representation and Processing. - Vít Novácek (ISWC (Posters & Demos), 2008)

Relaxing the Basic KR&R Principles to Meet the Emergent Semantic Web! - Vít Novácek (URSW, 2008)

Infrastructure for dynamic knowledge integration - Automated biomedical ontology extension using textual resources. - Vít Novácek; Loredana Laera; Siegfried Handschuh; Brian Davis 001 (J. Biomed. Informatics, 2008)

CORAAL - Towards Deep Exploitation of Textual Resources in Life Sciences. - Vít Novácek; Tudor Groza; Siegfried Handschuh (AIME, 2009)

Knowledge-based search for oncological literature. - Vít Novácek; Tudor Groza; Siegfried Handschuh (CBMS, 2009)

Towards Lightweight and Robust Large Scale Emergent Knowledge Processing. - Vít Novácek; Stefan Decker (ISWC, 2009)

Biomedical Publication Knowledge Acquisition, Processing and Dissemination with CORAAL. - Vít Novácek; Siegfried Handschuh (OTM Conferences (2), 2010)

CORAAL - Dive into publications, bathe in the knowledge. - Vít Novácek; Tudor Groza; Siegfried Handschuh; Stefan Decker (J. Web Semant., 2010)

Towards Knowledge-Based Life Science Publication Repositories. - Vít Novácek; Tudor Groza; Siegfried Handschuh (Semantic e-Science, 2010)

Getting the Meaning Right: A Complementary Distributional Layer for the Web Semantics. - Vít Novácek; Siegfried Handschuh; Stefan Decker (ISWC (1), 2011)

Distributional Framework for Emergent Knowledge Acquisition and its Application to Automated Document Annotation - Vít Novácek (CoRR, 2012)

Linking the scientific and clinical data with KI2NA-LHC - An outline. - Vít Novácek; Aisha Naseer (CBMS, 2013)

SKIMMR: machine-aided skim-reading. - Vít Novácek; Gully Burns (IUI Companion, 2013)

Technical report: Linking the scientific and clinical data with KI2NA-LHC - Vít Novácek; Aisha Naseer (CoRR, 2013)

A Method for Building Burst-Annotated Co-Occurrence Networks for Analysing Trends in Textual Data. - Yutaka Mitsuishi; Vít Novácek; Pierre-Yves Vandenbussche (LREC, 2014)

SemanTex: Semantic Text Exploration Using Document Links Implied by Conceptual Networks Extracted from the Texts. - Suad Aldarra; Emir Muñoz; Pierre-Yves Vandenbussche; Vít Novácek (ISWC (Posters & Demos), 2014)

A Methodology for Empirical Analysis of LOD Datasets. - Vít Novácek (CoRR, 2014)

Formalising Hypothesis Virtues in Knowledge Graphs: A General Theoretical Framework and its Validation in Literature-Based Discovery Experiments. - Vít Novácek (CoRR, 2015)

Using Drug Similarities for Discovery of Possible Adverse Reactions. - Emir Muñoz; Vít Novácek; Pierre-Yves Vandenbussche (AMIA, 2016)

Identifying Equivalent Relation Paths in Knowledge Graphs. - Sameh K. Mohamed; Emir Muñoz; Vít Novácek; Pierre-Yves Vandenbussche (LDK, 2017)

Regularizing Knowledge Graph Embeddings via Equivalence and Inversion Axioms. - Pasquale Minervini; Luca Costabello; Emir Muñoz; Vít Novácek; Pierre-Yves Vandenbussche (ECML/PKDD (1), 2017)

Knowledge base completion using distinct subgraph paths. - Sameh K. Mohamed; Vít Novácek; Pierre-Yves Vandenbussche (SAC, 2018)

Finding Explanations of Entity Relatedness in Graphs: A Survey. - Raoul Biagioni; Pierre-Yves Vandenbussche; Vít Novácek (CoRR, 2018)

Link Prediction Using Multi Part Embeddings. - Sameh K. Mohamed; Vít Novácek (ESWC, 2019)

Loss Functions in Knowledge Graph Embedding Models. - Sameh K. Mohamed; Vít Novácek; Pierre-Yves Vandenbussche; Emir Muñoz (DL4KG@ESWC, 2019)

Drug target discovery using knowledge graph embeddings. - Sameh K. Mohamed; Aayah Nounu; Vít Novácek (SAC, 2019)

Facilitating prediction of adverse drug reactions by using knowledge graphs and multi-label learning models. - Emir Muñoz; Vít Novácek; Pierre-Yves Vandenbussche (Briefings Bioinform., 2019)

BioKG: A Knowledge Graph for Relational Learning On Biological Data. - Brian Walsh; Sameh K. Mohamed; Vít Novácek (CIKM, 2020)

Discovering protein drug targets using knowledge graph embeddings. - Sameh K. Mohamed; Vít Novácek; Aayah Nounu (Bioinform., 2020)

Accurate prediction of kinase-substrate networks using knowledge graphs. - Vít Novácek; Gavin McGauran; David Matallanas; Adrián Vallejo Blanco; Piero Conca; Emir Muñoz; Luca Costabello; Kamalesh Kanakaraj; Muhammad Zeeshan Nawaz; Brian Walsh; Sameh K. Mohamed; Pierre-Yves Vandenbussche; et al. (PLoS Comput. Biol., 2020)

On Predicting Recurrence in Early Stage Non-small Cell Lung Cancer. - Sameh K. Mohamed; Brian Walsh; Mohan Timilsina; Vít Novácek; Maria Torrente; Fabio Franco; Mariano Provencio; Adrianna Janik; Luca Costabello; Pontus Stenetorp; Pasquale Minervini (AMIA, 2021)

Biological applications of knowledge graph embedding models. - Sameh K. Mohamed; Aayah Nounu; Vít Novácek (Briefings Bioinform., 2021)

On Training Knowledge Graph Embedding Models. - Sameh K. Mohamed; Emir Muñoz; Vít Novácek (Inf., 2021)

Integration of Clinical Information and Imputed Aneuploidy Scores to Enhance Relapse Prediction in Early Stage Lung Cancer Patients. - Mohan Timilsina; Samuele Bousi; Dirk Fey; Adrianna Janik; Maria Torrente; Mariano Provencio; Alberto Bermúdez; Enric Carcereny; Luca Costabello; Delvys Rodriguez Abreu; Manuel Cobo; Rafael Castro; et al. (AMIA, 2022)

Unsupervised extraction, labelling and clustering of segments from clinical notes. - Petr Zelina; Jana Halámková; Vít Novácek (BIBM, 2022)

Machine Learning-Assisted Recurrence Prediction for Early-Stage Non-Small-Cell Lung Cancer Patients. - Adrianna Janik; Maria Torrente; Luca Costabello; Virginia Calvo; Brian Walsh; Carlos Camps; Sameh K. Mohamed; Ana L. Ortega; Vít Novácek; Bartomeu Massutí; Pasquale Minervini; M. Rosario Garcia Campelo; et al. (CoRR, 2022)

Boundary heat diffusion classifier for a semi-supervised learning in a multilayer network embedding. - Mohan Timilsina; Vít Novácek; Mathieu d'Aquin; Haixuan Yang (Neural Networks, 2022)

Unsupervised extraction, classification and visualization of clinical note segments using the MIMIC-III dataset. - Petr Zelina; Jana Halámková; Vít Novácek (BIBM, 2023)

Machine Learning Survival Models for Relapse Prediction in a Early Stage Lung Cancer Patient. - Mohan Timilsina; Samuele Buosi; Adrianna Janik; Pasquale Minervini; Luca Costabello; Maria Torrente; Mariano Provencio; Virginia Calvo; Carlos Camps; Ana L. Ortega; Bartomeu Massutí; M. Rosario Garcia Campelo; et al. (IJCNN, 2023)

Synergy between imputed genetic pathway and clinical information for predicting recurrence in early stage non-small cell lung cancer. - Mohan Timilsina; Dirk Fey; Samuele Buosi; Adrianna Janik; Luca Costabello; Enric Carcereny; Delvys Rodriguez Abreu; Manuel Cobo; Rafael Castro; Reyes Bernabé; Pasquale Minervini; Maria Torrente; et al. (J. Biomed. Informatics, 2023)

Boosting predictive models and augmenting patient data with relevant genomic and pathway information. - Samuele Buosi; Mohan Timilsina; Maria Torrente; Mariano Provencio; Dirk Fey; Vít Novácek (Comput. Biol. Medicine, 2024)

Machine learning estimated probability of relapse in early-stage non-small-cell lung cancer patients with aneuploidy imputation scores and knowledge graph embeddings. - Samuele Buosi; Mohan Timilsina; Adrianna Janik; Luca Costabello; Maria Torrente; Mariano Provencio; Dirk Fey; Vít Novácek (Expert Syst. Appl., 2024)

Computing Patient Similarity Based on Unstructured Clinical Notes. - Petr Zelina; Marko Rehácek; Jana Halámková; Lucia Bohovicová; Martin Rusinko; Vít Novácek (TSD (2), 2025)

Integration, Cataloguing and Management of Biobanking and Clinical Data Using FAIR Genomes Metadata Schema. - Radoslava Kacová; Tomás Houfek; Ondrej Horký; Jan Kurán; Radovan Tomásik; Michal Ruzicka; Roman Hrstka; Vít Novácek; Zdenka Dudová (Data Intell., 2025)

Large language model vs. traditional machine learning: Evaluating predictive models for early detection of tumor relapse. - Mohan Timilsina; Samuele Buosi; Maria Torrente; Mariano Provencio; Manuel Cobo; Delvys Rodriguez Abreu; Rafael Castro; Enric Carcereny; Edward Curry; Vít Novácek (Expert Syst. Appl., 2025)