Bringing Neuroscience to the Semantic Web: The Semantic Synapse Project. - Matthias Samwald; Klaus-Peter Adlassnig (CIMCA/IAWTIC, 2005)

Ontology-Based Data Integration For Biomedical Research. - Vipul Kashyap; Kei-Hoi Cheung; Donald Doherty; Matthias Samwald; M. Scott Marshall; Joanne Luciano; Susie Stephens; Ivan Herman; Raymond Hookway (The Semantic Web: Real-World Applications from Industry, 2007)

Advancing translational research with the Semantic Web. - Alan Ruttenberg; Tim Clark; William J. Bug; Matthias Samwald; Olivier Bodenreider; Helen Chen; Donald Doherty; Kerstin Forsberg; Yong Gao; Vipul Kashyap; June Kinoshita; Joanne Luciano; et al. (BMC Bioinform., 2007)

Previewing Semantic Web Pipes. - Christian Morbidoni; Danh Le Phuoc; Axel Polleres; Matthias Samwald; Giovanni Tummarello (ESWC, 2008)

KiWi - Knowledge in a Wiki. - Sebastian Schaffert; Julia Eder; Matthias Samwald; Andreas Blumauer (ESWC (Posters), 2008)

Simplifying Access to Large-Scale Health Care and Life Sciences Datasets. - Holger Stenzhorn; Kavitha Srinivas; Matthias Samwald; Alan Ruttenberg (ESWC, 2008)

The bio-zen plus ontology. - Matthias Samwald; Klaus-Peter Adlassnig (Appl. Ontology, 2008)

Linking Open Drug Data. - Anja Jentzsch; Jun Zhao 003; Oktie Hassanzadeh; Kei-Hoi Cheung; Matthias Samwald; Bo Andersson (I-SEMANTICS, 2009)

Entrez Neuron RDFa: A Pragmatic Semantic Web Application for Data Integration in Neuroscience Research. - Matthias Samwald; Ernest Lim; Peter Masiar; Luis N. Marenco; Huajun Chen; Thomas M. Morse; Pradeep Mutalik; Gordon M. Shepherd; Perry L. Miller; Kei-Hoi Cheung (MIE, 2009)

Approaches to neuroscience data integration. - Kei-Hoi Cheung; Ernest Lim; Matthias Samwald; Huajun Chen; Luis N. Marenco; Matthew Holford; Thomas M. Morse; Pradeep Mutalik; Gordon M. Shepherd; Perry L. Miller (Briefings Bioinform., 2009)

Life sciences on the Semantic Web: the Neurocommons and beyond. - Alan Ruttenberg; Jonathan Rees; Matthias Samwald; M. Scott Marshall (Briefings Bioinform., 2009)

A journey to Semantic Web query federation in the life sciences. - Kei-Hoi Cheung; H. Robert Frost; M. Scott Marshall; Eric Prud'hommeaux; Matthias Samwald; Jun Zhao 003; Adrian Paschke (BMC Bioinform., 2009)

Federating Distributed Social Data to Build an Interlinked Online Information Society. - Alexandre Passant; Matthias Samwald; John G. Breslin; Stefan Decker (IEEE Intell. Syst., 2009)

Das Semantic Web als Werkzeug in der biomedizinischen Forschung. - Holger Stenzhorn; Matthias Samwald (Social Semantic Web, 2009)

Provenance of Microarray Experiments for a Better Understanding of Experiment Results. - Helena F. Deus; Jun Zhao 003; Satya S. Sahoo; Matthias Samwald; Eric Prud'hommeaux; Michael Miller 001; M. Scott Marshall; Kei-Hoi Cheung (SWPM@ISWC, 2010)

Semantic SenseLab: Implementing the vision of the Semantic Web in neuroscience. - Matthias Samwald; Huajun Chen; Alan Ruttenberg; Ernest Lim; Luis N. Marenco; Perry L. Miller; Gordon M. Shepherd; Kei-Hoi Cheung (Artif. Intell. Medicine, 2010)

Establishing a distributed system for the simple representation and integration of diverse scientific assertions. - Matthias Samwald; Holger Stenzhorn (J. Biomed. Semant., 2010)

Towards an Interoperable Information Infrastructure Providing Decision Support for Genomic Medicine. - Matthias Samwald; Holger Stenzhorn; Michel Dumontier; M. Scott Marshall; Joanne Luciano; Klaus-Peter Adlassnig (MIE, 2011)

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside. - Joanne S. Luciano; Bosse Andersson; Colin R. Batchelor; Olivier Bodenreider; Tim Clark; Christine K. Denney; Christopher Domarew; Thomas Gambet; Lee Harland; Anja Jentzsch; Vipul Kashyap; Peter J. Kos; et al. (J. Biomed. Semant., 2011)

Linked open drug data for pharmaceutical research and development. - Matthias Samwald; Anja Jentzsch; Christopher Bouton; Claus Kallesøe; Egon L. Willighagen; Janos G. Hajagos; M. Scott Marshall; Eric Prud'hommeaux; Oktie Hassanzadeh; Elgar Pichler; Susie Stephens (J. Cheminformatics, 2011)

The Arden Syntax standard for clinical decision support: Experiences and directions. - Matthias Samwald; Karsten Fehre; Jeroen S. de Bruin; Klaus-Peter Adlassnig (J. Biomed. Informatics, 2012)

Emerging practices for mapping and linking life sciences data using RDF - A case series. - M. Scott Marshall; Richard D. Boyce; Helena F. Deus; Jun Zhao 003; Egon L. Willighagen; Matthias Samwald; Elgar Pichler; Janos G. Hajagos; Eric Prud'hommeaux; Susie Stephens (J. Web Semant., 2012)

A Formative Evaluation of a Comprehensive Search System for Medical Professionals. - Veronika Stefanov; Alexander Sachs; Marlene Kritz; Matthias Samwald; Manfred Gschwandtner; Allan Hanbury (CLEF, 2013)

Khresmoi - Multilingual Semantic Search of Medical Text and Images. - Niraj Aswani; Thomas Beckers 002; Erich Birngruber; Célia Boyer; Andreas Burner; Jakub Bystron; Khalid Choukri; Sarah Cruchet; Hamish Cunningham; Jan Dedek; Ljiljana Dolamic; René Donner; et al. (MedInfo, 2013)

An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics. - Matthias Samwald; Robert R. Freimuth; Joanne S. Luciano; Simon M. Lin; Robert L. Powers; M. Scott Marshall; Klaus-Peter Adlassnig; Michel Dumontier; Richard D. Boyce (MedInfo, 2013)

Physicians searching the web for medical question answering: A European survey and local user studies. - Matthias Samwald; Marlene Kritz; Manfred Gschwandtner; Veronika Stefanov; Allan Hanbury (MedInfo, 2013)

Genomic CDS: an Example of a Complex Ontology for Pharmacogenetics and Clinical Decision Support. - Matthias Samwald (ORE, 2013)

Pharmacogenomics in the pocket of every patient? A prototype based on quick response codes. - Matthias Samwald; Klaus-Peter Adlassnig (J. Am. Medical Informatics Assoc., 2013)

Towards a Global IT System for Personalized Medicine: the Medicine Safety Code Initiative. - Matthias Samwald; José Antonio Miñarro-Giménez; Kathrin Blagec; Klaus-Peter Adlassnig (eHealth, 2014)

Visualising topic networks in infection control using word vector analysis. - Jeroen S. de Bruin; José Antonio Miñarro-Giménez; Matthias Samwald; Oscar Marín-Alonso (MIE, 2014)

Exploring the Application of Deep Learning Techniques on Medical Text Corpora. - José Antonio Miñarro-Giménez; Oscar Marín-Alonso; Matthias Samwald (MIE, 2014)

An Open-Source, Mobile-Friendly Search Engine for Public Medical Knowledge. - Matthias Samwald; Allan Hanbury (MIE, 2014)

An Update on Genomic CDS, a Complex Ontology for Pharmacogenomics and Clinical Decision Support. - José Antonio Miñarro-Giménez; Matthias Samwald (ORE, 2014)

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery. - Michel Dumontier; Christopher J. O. Baker; Joachim Baran; Alison Callahan; Leonid L. Chepelev; Jose Cruz-Toledo; Nicholas R. Del Rio; Geraint Duck; Laura Inés Furlong; Nichealla Keath; Dana Klassen; Jamie P. McCusker; et al. (J. Biomed. Semant., 2014)

Applying deep learning techniques on medical corpora from the World Wide Web: a prototypical system and evaluation. - José Antonio Miñarro-Giménez; Oscar Marín-Alonso; Matthias Samwald (CoRR, 2015)

Toward a complete dataset of drug-drug interaction information from publicly available sources. - Serkan Ayvaz; John R. Horn; Oktie Hassanzadeh; Qian Zhu 003; Johann Stan; Nicholas P. Tatonetti; Santiago Vilar; Mathias Brochhausen; Matthias Samwald; Majid Rastegar-Mojarad; Michel Dumontier; Richard D. Boyce (J. Biomed. Informatics, 2015)

Pharmacogenomic knowledge representation, reasoning and genome-based clinical decision support based on OWL 2 DL ontologies. - Matthias Samwald; José Antonio Miñarro-Giménez; Richard D. Boyce; Robert R. Freimuth; Klaus-Peter Adlassnig; Michel Dumontier (BMC Medical Informatics Decis. Mak., 2015)

How Many Patients Could Benefit From Pre-emptive Pharmacogenomic Testing and Decision Support? A Retrospective Study Based on Nationwide Austrian Claims Data. - Wolfgang Kuch; Christoph Rinner; Walter Gall; Matthias Samwald (eHealth, 2016)

The Importance of Gene-Drug-Drug-Interactions in Pharmacogenomics Decision Support: An Analysis Based on Austrian Claims Data. - Kathrin Blagec; Wolfgang Kuch; Matthias Samwald (eHealth, 2017)

Effects of Medical Device Regulations on the Development of Stand-Alone Medical Software: A Pilot Study. - Kathrin Blagec; David Jungwirth; Daniela Haluza; Matthias Samwald (eHealth, 2018)

Fast and Scalable Learning of Neuro-Symbolic Representations of Biomedical Knowledge. - Asan Agibetov; Matthias Samwald (DL4KGS@ESWC, 2018)

Global and Local Evaluation of Link Prediction Tasks with Neural Embeddings. - Asan Agibetov; Matthias Samwald (Semdeep/NLIWoD@ISWC, 2018)

We divide, you conquer: from large-scale ontology alignment to manageable subtasks with a lexical index and neural embeddings. - Ernesto Jiménez-Ruiz; Asan Agibetov; Matthias Samwald; Valerie Cross (OM@ISWC, 2018)

Fast and scalable neural embedding models for biomedical sentence classification. - Asan Agibetov; Kathrin Blagec; Hong Xu 016; Matthias Samwald (BMC Bioinform., 2018)

Breaking-down the Ontology Alignment Task with a Lexical Index and Neural Embeddings. - Ernesto Jiménez-Ruiz; Asan Agibetov; Matthias Samwald; Valerie Cross (CoRR, 2018)

Implementing pharmacogenomics decision support across seven European countries: The Ubiquitous Pharmacogenomics (U-PGx) project. - Kathrin Blagec; Rudolf Koopmann; Mandy Crommentuijn-van Rhenen; Inge Holsappel; Cathelijne H. van der Wouden; Lidija Konta; Hong Xu 016; Daniela Steinberger; Enrico Just; Jesse J. Swen; Henk-Jan Guchelaar; Matthias Samwald (J. Am. Medical Informatics Assoc., 2018)

Dividing the Ontology Alignment Task. - Ernesto Jiménez-Ruiz; Asan Agibetov; Jiaoyan Chen 001; Matthias Samwald; Valerie Cross (Zenodo, 2018)

Using hyperbolic large-margin classifiers for biological link prediction. - Asan Agibetov; Georg Dorffner; Matthias Samwald (SemDeep@IJCAI, 2019)

Neural sentence embedding models for semantic similarity estimation in the biomedical domain. - Kathrin Blagec; Hong Xu 016; Asan Agibetov; Matthias Samwald (BMC Bioinform., 2019)

Clustering of Deep Contextualized Representations for Summarization of Biomedical Texts. - Milad Moradi; Matthias Samwald (CoRR, 2019)

OpenBioLink: A resource and benchmarking framework for large-scale biomedical link prediction. - Anna Breit; Asan Agibetov; Matthias Samwald (CoRR, 2019)

Dividing the Ontology Alignment Task. - Ernesto Jiménez-Ruiz; Asan Agibetov; Jiaoyan Chen 001; Matthias Samwald; Valerie Cross (Zenodo, 2019)

Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-Based Modules. - Ernesto Jiménez-Ruiz; Asan Agibetov; Jiaoyan Chen 001; Matthias Samwald; Valerie Cross (ECAI, 2020)

OpenBioLink: a benchmarking framework for large-scale biomedical link prediction. - Anna Breit; Simon Ott; Asan Agibetov; Matthias Samwald (Bioinform., 2020)

Deep contextualized embeddings for quantifying the informative content in biomedical text summarization. - Milad Moradi; Georg Dorffner; Matthias Samwald (Comput. Methods Programs Biomed., 2020)

A critical analysis of metrics used for measuring progress in artificial intelligence. - Kathrin Blagec; Georg Dorffner; Milad Moradi; Matthias Samwald (CoRR, 2020)

Explaining black-box text classifiers for disease-treatment information extraction. - Milad Moradi; Matthias Samwald (CoRR, 2020)

Scalable and interpretable rule-based link prediction for large heterogeneous knowledge graphs. - Simon Ott; Laura Graf 002; Asan Agibetov; Christian Meilicke; Matthias Samwald (CoRR, 2020)

Summarization of biomedical articles using domain-specific word embeddings and graph ranking. - Milad Moradi; Maedeh Dashti; Matthias Samwald (J. Biomed. Informatics, 2020)

Benchmarking neural embeddings for link prediction in knowledge graphs under semantic and structural changes. - Asan Agibetov; Matthias Samwald (J. Web Semant., 2020)

SAFRAN: An interpretable, rule-based link prediction method outperforming embedding models. - Simon Ott; Christian Meilicke; Matthias Samwald (AKBC, 2021)

Evaluating the Robustness of Neural Language Models to Input Perturbations. - Milad Moradi; Matthias Samwald (EMNLP (1), 2021)

Deep learning models are not robust against noise in clinical text. - Milad Moradi; Kathrin Blagec; Matthias Samwald (CoRR, 2021)

GPT-3 Models are Poor Few-Shot Learners in the Biomedical Domain. - Milad Moradi; Kathrin Blagec; Florian Haberl; Matthias Samwald (CoRR, 2021)

A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks. - Kathrin Blagec; Adriano Barbosa-Silva; Simon Ott; Matthias Samwald (CoRR, 2021)

Post-hoc explanation of black-box classifiers using confident itemsets. - Milad Moradi; Matthias Samwald (Expert Syst. Appl., 2021)

Explaining Black-Box Models for Biomedical Text Classification. - Milad Moradi; Matthias Samwald (IEEE J. Biomed. Health Informatics, 2021)

BigBio: A Framework for Data-Centric Biomedical Natural Language Processing. - Jason A. Fries; Leon Weber; Natasha Seelam; Gabriel Altay; Debajyoti Datta; Samuele Garda; Sunny Kang; Rosaline Su; Wojciech Kusa; Samuel Cahyawijaya; Fabio Barth; Simon Ott; et al. (NeurIPS, 2022)

LinkExplorer: predicting, explaining and exploring links in large biomedical knowledge graphs. - Simon Ott; Adriano Barbosa-Silva; Matthias Samwald (Bioinform., 2022)

Deep Learning, Natural Language Processing, and Explainable Artificial Intelligence in the Biomedical Domain. - Milad Moradi; Matthias Samwald (CoRR, 2022)

Mapping global dynamics of benchmark creation and saturation in artificial intelligence. - Adriano Barbosa-Silva; Simon Ott; Kathrin Blagec; Jan Brauner; Matthias Samwald (CoRR, 2022)

A global analysis of metrics used for measuring performance in natural language processing. - Kathrin Blagec; Georg Dorffner; Milad Moradi; Simon Ott; Matthias Samwald (CoRR, 2022)

BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing. - Jason Alan Fries; Leon Weber; Natasha Seelam; Gabriel Altay; Debajyoti Datta; Samuele Garda; Myungsun Kang; Ruisi Su; Wojciech Kusa; Samuel Cahyawijaya; Fabio Barth; Simon Ott; et al. (CoRR, 2022)

Improving the robustness and accuracy of biomedical language models through adversarial training. - Milad Moradi; Matthias Samwald (J. Biomed. Informatics, 2022)

A study into patient similarity through representation learning from medical records. - Hoda Memarzadeh; Nasser Ghadiri; Matthias Samwald; Maryam Lotfi Shahreza (Knowl. Inf. Syst., 2022)

Relational local electroencephalography representations for sleep scoring. - Georg Brandmayr; Manfred Martin Hartmann; Franz Fürbass; Gerald Matz; Matthias Samwald; Tilmann Kluge; Georg Dorffner (Neural Networks, 2022)

CSMeD: Bridging the Dataset Gap in Automated Citation Screening for Systematic Literature Reviews. - Wojciech Kusa; Óscar E. Mendoza; Matthias Samwald; Petr Knoth; Allan Hanbury (NeurIPS, 2023)

ThoughtSource: A central hub for large language model reasoning data. - Simon Ott; Konstantin Hebenstreit; Valentin Liévin; Christoffer Egeberg Hother; Milad Moradi; Maximilian Mayrhauser; Robert Praas; Ole Winther; Matthias Samwald (CoRR, 2023)

An automatically discovered chain-of-thought prompt generalizes to novel models and datasets. - Konstantin Hebenstreit; Robert Praas; Louis P. Kiesewetter; Matthias Samwald (CoRR, 2023)

A collection of principles for guiding and evaluating large language models. - Konstantin Hebenstreit; Robert Praas; Matthias Samwald (CoRR, 2023)

Benchmark datasets driving artificial intelligence development fail to capture the needs of medical professionals. - Kathrin Blagec; Jakob Kraiger; Wolfgang Frühwirt; Matthias Samwald (J. Biomed. Informatics, 2023)

Applying unsupervised keyphrase methods on concepts extracted from discharge sheets. - Hoda Memarzadeh; Nasser Ghadiri; Matthias Samwald; Maryam Lotfi Shahreza (Pattern Anal. Appl., 2023)

GPT-4 as a biomedical simulator. - Moritz Schaefer; Stephan Reichl; Rob ter Horst; Adele M. Nicolas; Thomas Krausgruber; Francesco Piras; Peter Stepper; Christoph Bock; Matthias Samwald (Comput. Biol. Medicine, 2024)

Exploring the landscape of large language models: Foundations, techniques, and challenges. - Milad Moradi; Ke Yan; David Colwell; Matthias Samwald; Rhona Asgari (CoRR, 2024)

TRIAGE: Ethical Benchmarking of AI Models Through Mass Casualty Simulations. - Nathalie Maria Kirch; Konstantin Hebenstreit; Matthias Samwald (CoRR, 2024)

Model-agnostic explainable artificial intelligence for object detection in image data. - Milad Moradi; Ke Yan; David Colwell; Matthias Samwald; Rhona Asgari (Eng. Appl. Artif. Intell., 2024)

A comparison of chain-of-thought reasoning strategies across datasets and models. - Konstantin Hebenstreit; Robert Praas; Louis P. Kiesewetter; Matthias Samwald (PeerJ Comput. Sci., 2024)