Also available on Google Scholar
Recent pre-prints
Moritz Schaefer, Stephan Reichl, Rob ter Horst, Adele M. Nicolas, Thomas Krausgruber, Francesco Piras, Peter Stepper, Christoph Bock, Matthias Samwald.
“Large language models are universal biomedical simulators”
bioRxiv, June 2023. https://doi.org/10.1101/2023.06.16.545235
Konstantin Hebenstreit, Robert Praas, Louis P. Kiesewetter, Matthias Samwald.
“An Automatically Discovered Chain-of-Thought Prompt Generalizes to Novel Models and Datasets”
arXiv, May 2023. https://doi.org/10.48550/arXiv.2305.02897
BigScience Workshop: Teven Le Scao, Angela Fan, Christopher Akiki, Ellie Pavlick, Suzana Ilić, Daniel Hesslow, Roman Castagné, Alexandra Sasha Luccioni, François Yvon, Matthias Gallé, Jonathan Tow, Alexander M. Rush, Stella Biderman, Albert Webson, Pawan Sasanka Ammanamanchi, Thomas Wang, Benoît Sagot, Niklas Muennighoff, Albert Villanova del Moral, Olatunji Ruwase, Rachel Bawden, Stas Bekman, Angelina McMillan-Major, Iz Beltagy, Huu Nguyen, Lucile Saulnier, Samson Tan, Pedro Ortiz Suarez, Victor Sanh, Hugo Laurençon, Yacine Jernite, Julien Launay, Margaret Mitchell, Colin Raffel, […], Matthias Samwald […], Thomas Wolf.
“BLOOM: A 176B-Parameter Open-Access Multilingual Language Model”
arXiv, November 2022. https://doi.org/10.48550/arXiv.2211.05100
Peer-reviewed articles
2023
[125] Konstantin Hebenstreit, Robert Praas, Matthias Samwald.
“A collection of principles for guiding and evaluating large language models”
Socially Responsible Language Modelling Research (SoLaR) workshop
NeurIPS 2023, December 16, 2023
https://doi.org/10.48550/arXiv.2312.10059
[124] Wojciech Kusa, Oscar E. Mendoza, Matthias Samwald, Petr Knoth, Allan Hanbury.
“CSMeD: Bridging the Dataset Gap in Automated Citation Screening for Systematic Literature Reviews”
NeurIPS 2023, December 14, 2023
https://doi.org/10.48550/arXiv.2311.12474
[123] Hoda Memarzadeh, Nasser Ghadiri, Matthias Samwald, Maryam Lotfi Shahreza.
“Applying Unsupervised Keyphrase Methods on Concepts Extracted from Discharge Sheets.”
Pattern Analysis and Applications, September 29, 2023. https://doi.org/10.1007/s10044-023-01198-0
[122] Simon Ott, Konstantin Hebenstreit, Valentin Liévin, Christoffer Egeberg Hother, Milad Moradi, Maximilian Mayrhauser, Robert Praas, Ole Winther, Matthias Samwald.
“ThoughtSource: A Central Hub for Large Language Model Reasoning Data”
Scientific Data 10, no. 1 (August 8, 2023): 528. https://doi.org/10.1038/s41597-023-02433-3
(arXiv version: https://doi.org/10.48550/arXiv.2301.11596)
[121] Jesse J Swen, Cathelijne H van der Wouden, Lisanne EN Manson, Heshu Abdullah-Koolmees, Kathrin Blagec, Tanja Blagus, Stefan Böhringer, Prof Anne Cambon-Thomsen, Erika Cecchin, Ka-Chun Cheung, Vera HM Deneer, Mathilde Dupui, Prof Magnus Ingelman-Sundberg, Siv Jonsson, Candace Joefield-Roka, Katja S Just, Prof Mats O Karlsson, Lidija Konta, Rudolf Koopmann, Marjolein Kriek, Prof Thorsten Lehr, Christina Mitropoulou, Emmanuelle Rial-Sebbag, Victoria Rollinson, Rossana Roncato, Matthias Samwald, Elke Schaeffeler, Maria Skokou, Prof Matthias Schwab, Prof Daniela Steinberger Prof Julia C Stingl, Roman Tremmel, Richard M Turner, Mandy H van Rhenen, Cristina L Dávila Fajardo, Prof Vita Dolžan, Prof George P Patrinos, Prof Munir Pirmohamed, Prof Gere Sunder-Plassmann, Prof Giuseppe Toffoli, Prof Henk-Jan Guchelaar, Ubiquitous Pharmacogenomics Consortium.
“A 12-Gene Pharmacogenetic Panel to Prevent Adverse Drug Reactions: An Open-Label, Multicentre, Controlled, Cluster-Randomised Crossover Implementation Study”
The Lancet 401, no. 10374 (4 February 2023): 347–56. https://doi.org/10.1016/S0140-6736(22)01841-4
[120] Kathrin Blagec, Jakob Kraiger, Wolfgang Frühwirt, Matthias Samwald.
“Benchmark Datasets Driving Artificial Intelligence Development Fail to Capture the Needs of Medical Professionals”
Journal of Biomedical Informatics 137 (1 January 2023): 104274. https://doi.org/10.1016/j.jbi.2022.104274
(arXiv version: http://arxiv.org/abs/2201.07040)
2022
[119] Simon Ott, Adriano Barbosa-Silva, Kathrin Blagec, Jan Brauner, Matthias Samwald.
“Mapping Global Dynamics of Benchmark Creation and Saturation in Artificial Intelligence”
Nature Communications 13, no. 1 (10 November 2022): 6793. https://doi.org/10.1038/s41467-022-34591-0.
(arXiv version: https://arxiv.org/abs/2203.04592)
[118] Kathrin Blagec, Jesse J. Swen, Rudolf Koopmann, Ka-Chun Cheung, Mandy Crommentuijn-van Rhenen, Inge Holsappel, Lidija Konta, Simon Ott, Daniela Steinberger, Hong Xu, Erika Cecchin, Vita Dolžan, Cristina Lucía Dávila-Fajardo, George P. Patrinos, Gere Sunder-Plassmann, Richard M. Turner, Munir Pirmohamed, Henk-Jan Guchelaar, Matthias Samwald, Ubiquitous Pharmacogenomics Consortium.
“Pharmacogenomics Decision Support in the U-PGx Project: Results and Advice from Clinical Implementation across Seven European Countries”
PLOS ONE 17, no. 6 (8 June 2022): e0268534. https://doi.org/10.1371/journal.pone.0268534
[117] 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, Matthias Samwald, Stephen Bach, Stella Biderman, Mario Sänger, Bo Wang, Alison Callahan, Daniel León Periñán, Théo Gigant, Patrick Haller, Jenny Chim, Jose David Posada, John Michael Giorgi, Karthik Rangasai Sivaraman, Marc Pàmies, Marianna Nezhurina, Robert Martin, Michael Cullan, Moritz Freidank, Nathan Dahlberg, Shubhanshu Mishra, Shamik Bose, Nicholas Michio Broad, Yanis Labrak, Shlok S. Deshmukh, Sid Kiblawi, Ayush Singh, Minh Chien Vu, Trishala Neeraj, Jonas Golde, Albert Villanova del Moral, Benjamin Beilharz.
“BigBIO: A Framework for Data-Centric Biomedical Natural Language Processing”
NeurIPS 2022
(arXiv version: https://doi.org/10.48550/arXiv.2206.15076)
[116] Georg Brandmayr, Manfred Hartmann, Franz Fürbass, Gerald Matz, Matthias Samwald, Tilmann Kluge, Georg Dorffner.
“Relational Local Electroencephalography Representations for Sleep Scoring”
Neural Networks 154 (1 October 2022): 310–22. https://doi.org/10.1016/j.neunet.2022.07.020
[115] Hoda Memarzadeh, Nasser Ghadiri, Matthias Samwald, Maryam Lotfi Shahreza.
“A Study into Patient Similarity through Representation Learning from Medical Records”
Knowledge and Information Systems, 13 September 2022. https://doi.org/10.1007/s10115-022-01740-2
[114] Milad Moradi, Matthias Samwald.
“Improving the Robustness and Accuracy of Biomedical Language Models through Adversarial Training”
Journal of Biomedical Informatics 132 (2022): 104114. https://doi.org/10.1016/j.jbi.2022.104114
[113] Kathrin Blagec, Adriano Barbosa-Silva, Simon Ott, Matthias Samwald.
“A Curated, Ontology-Based, Large-Scale Knowledge Graph of Artificial Intelligence Tasks and Benchmarks”
Scientific Data 9, no. 1 (2022): 322. https://www.nature.com/articles/s41597-022-01435-x
[112] Kathrin Blagec, Georg Dorffner, Milad Moradi, Simon Ott, Matthias Samwald.
“A Global Analysis of Metrics Used for Measuring Performance in Natural Language Processing”
Workshop on Efficient Benchmarking in NLP at ACL 2022, 2022. https://aclanthology.org/2022.nlppower-1.6/
[111] Jason Alan Fries, Natasha Seelam, Gabriel Altay, Leon Weber, Myungsun Kang, Debajyoti Datta, Ruisi Su, Samuele Garda, Bo Wang, Simon Ott, Matthias Samwald, Wojciech Kusa.
“Dataset Debt in Biomedical Language Modeling”
Challenges & Perspectives in Creating Large Language Models workshop at ACL 2022, 2022. https://aclanthology.org/2022.bigscience-1.10/
[110] Simon Ott, Adriano Barbosa-Silva, Matthias Samwald.
“LinkExplorer: Predicting, Explaining and Exploring Links in Large Biomedical Knowledge Graphs”
Bioinformatics, February 2022, btac068. https://doi.org/10.1093/bioinformatics/btac068
[bioRxiv]
2021
[109] Christine Wallisch, Asan Agibetov, Daniela Dunkler, Maria Haller, Matthias Samwald, Georg Dorffner, Georg Heinze.
“The Roles of Predictors in Cardiovascular Risk Models – a Question of Modeling Culture?”
BMC Medical Research Methodology 21, no. 1 (December 18, 2021): 284. https://doi.org/10.1186/s12874-021-01487-4.
[108] Asan Agibetov, Andreas Kammerlander, Franz Duca, Christian Nitsche, Matthias Koschutnik, Carolina Donà, Theresa-Marie Dachs, René Rettl, Alessa Stria, Lore Schrutka, Christina Binder, Johannes Kastner, Hermine Agis, Renate Kain, Michaela Auer-Grumbach, Matthias Samwald, Christian Hengstenberg, Georg Dorffner, Julia Mascherbauer, Diana Bonderman.
“Convolutional Neural Networks for Fully Automated Diagnosis of Cardiac Amyloidosis by Cardiac Magnetic Resonance Imaging”
Journal of Personalized Medicine 11, no. 12 (December 2021): 1268. https://doi.org/10.3390/jpm11121268
[107] Simon Ott, Christian Meilicke, Matthias Samwald.
“SAFRAN: An Interpretable, Rule-Based Link Prediction Method Outperforming Embedding Models”
3rd Conference on Automated Knowledge Base Construction (AKBC 2021), 2021. https://openreview.net/forum?id=jCt9S_3w_S9
[106] Milad Moradi, Matthias Samwald.
“Evaluating the Robustness of Neural Language Models to Input Perturbations”
Conference on Empirical Methods in Natural Language Processing 2021 (EMNLP 2021), accepted.
[105] Milad Moradi, Matthias Samwald.
“Explaining Black-Box Models for Biomedical Text Classification”
IEEE Journal of Biomedical and Health Informatics 25, Nr. 8 (August 2021): 3112–20. https://doi.org/10.1109/JBHI.2021.3056748
[104] Milad Moradi, Matthias Samwald.
“Post-Hoc Explanation of Black-Box Classifiers Using Confident Itemsets”
Expert Systems with Applications 165 (March 2021): 113941. https://doi.org/10.1016/j.eswa.2020.113941
2020
[103] Asan Agibetov, Matthias Samwald.
“Benchmarking neural embeddings for link prediction in knowledge graphs under semantic and structural changes”
Journal of Web Semantics 64 (October 2020): 100590. https://doi.org/10.1016/j.websem.2020.100590
[102] Asan Agibetov, Benjamin Seirer, Theresa-Marie Dachs, Matthias Koschutnik, Daniel Dalos, René Rettl, Franz Duca, Lore Schrutka, Hermine Agis, Renate Kain, Michela Auer-Grumbach, Christina Binder, Julia Mascherbauer, Christian Hengstenberg, Matthias Samwald, Georg Dorffner, Diana Bonderman.
“Machine Learning Enables Prediction of Cardiac Amyloidosis by Routine Laboratory Parameters: A Proof-of-Concept Study”
Journal of Clinical Medicine 9, Nr. 5 (May 2020): 1334. https://doi.org/10.3390/jcm9051334
[101] Anna Breit, Simon Ott, Asan Agibetov, Matthias Samwald.
“OpenBioLink: A benchmarking framework for large-scale biomedical link prediction”
Bioinformatics 36, Nr. 13 (July 2020): 4097–98. https://doi.org/10.1093/bioinformatics/btaa274
[100] Milad Moradi, Maedeh Dashti, Matthias Samwald.
“Summarization of Biomedical Articles Using Domain-Specific Word Embeddings and Graph Ranking”
Journal of Biomedical Informatics 107 (Juli 2020): 103452. https://doi.org/10.1016/j.jbi.2020.103452
[99] Cathelijne H. van der Wouden, Stefan Böhringer, Erika Cecchin, Ka-Chun Cheung, Cristina Lucía Dávila-Fajardo, Vera H. M. Deneer, Vita Dolžan, Magnus Ingelman-Sundberg, Siv Jönsson, Mats O Karlsson, Marjolein Kriek, Christina Mitropoulou, George P Patrinos, Munir Pirmohamed, Emmanuelle Rial-Sebbag, Matthias Samwald, Matthias Schwab, Daniela Steinberger, Julia Stingl, Gere Sunder-Plassmann, Giuseppe Toffoli, Richard M Turner, Mandy H van Rhenen, Erik van Zwet, Jesse J Swen, Henk-Jan Guchelaar, Ubiquitous Pharmacogenomics Consortium.
“Generating Evidence for Precision Medicine: Considerations Made by the Ubiquitous Pharmacogenomics Consortium When Designing and Operationalizing the PREPARE Study”
Pharmacogenetics and Genomics, 20. April 2020. https://doi.org/10.1097/FPC.0000000000000405
[98] Ernesto Jiménez-Ruiz, Asan Agibetov, Jiaoyan Chen, Matthias Samwald and Valerie Cross.
“Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modules”
24th European Conference on Artificial Intelligence (ECAI 2020), 2020 (conference article)
2019
[97] Milad Moradi, Georg Dorffner, Matthias Samwald.
“Deep contextualized embeddings for quantifying the informative content in biomedical text summarization”
Computer Methods and Programs in Biomedicine 184 (February 1 2020): 105117. https://doi.org/10.1016/j.cmpb.2019.105117
[96] Asan Agibetov, Georg Dorffner, Matthias Samwald.
“Using hyperbolic large-margin classifiers for biological link prediction”
5th Semantic Deep Learning Workshop @ IJCAI. Macao 2019 (conference article)
[95] Kathrin Blagec, Hong Xu, Asan Agibetov, Matthias Samwald.
“Neural sentence embedding models for semantic similarity estimation in the biomedical domain”
BMC Bioinformatics 20, No. 1 (December 2019). https://doi.org/10.1186/s12859-019-2789-2
[94] Asan Agibetov, B. Seirer, S. Aschauer, D. Dalos, R. Rettl, F. Duca, H. Agis, R. Kain, C. Binder, J. Mascherbauer, C. Hengstenberg, Matthias Samwald, Georg Dorffner, Daniela Bonderman.
“Extremely boosted prediction of cardiac amyloidosis by routine laboratory parameters”
European Society of Cardiology Congress 2019. Poster number 86980 (10.3 – Chronic Heart Failure – Diagnostic Methods). Paris (poster abstract)
[93] Asan Agibetov, B. Seirer, S. Aschauer, D. Dalos, R. Rettl, F. Duca, H. Agis, R. Kain, C. Binder, J. Mascherbauer, C. Hengstenberg, Matthias Samwald, Georg Dorffner, Daniela Bonderman.
“Optimal variable selection for simple prediction model of cardiac amyloidosis by routine laboratory parameters”
Jahrestagung der Österreichische Kardiologische Gesellschaft. Postersitzung 20-3. Salzburg (poster abstract)
2018
[92] Asan Agibetov, Kathrin Blagec, Hong Xu, Matthias Samwald.
“Fast and scalable neural embedding models for biomedical sentence classification”
BMC Bioinformatics 19, No. 1 (December 22, 2018): 541. https://doi.org/10.1186/s12859-018-2496-4
[91] Asan Agibetov, Matthias Samwald.
“Global and Local Evaluation of Link Prediction Tasks with Neural Embeddings”
Proceedings of SemDeep-4 and NLIWOD-4, 89–102, 2018, http://ceur-ws.org/Vol-2241/#paper-09 (conference article)
[90] Kathrin Blagec, Rudolf Koopmann, Mandy Crommentuijn – van Rhenen, Inge Holsappel, Cathelijne van der Wouden, Lidija Konta, Hong Xu, Daniela Steinberger, Enrico Just, Jesse J. Swen; Henk-Jan Guchelaar, Matthias Samwald.
“Multi-modal decision support to enable pharmacogenetics-based drug dosing across seven European countries”
In: “ISMD2018 Twelfth International Symposium on Molecular Diagnostics”. Clinical Chemistry and Laboratory Medicine (CCLM) 56, Nr. 6 (24. Mai 2018): eA97–120. https://doi.org/10.1515/cclm-2018-0281 (conference article)
[89] Kathrin Blagec, David Jungwirth, Daniela Haluza, Matthias Samwald.
“Effects of Medical Device Regulations on the Development of Stand-Alone Medical Software: A Pilot Study”
Studies in Health Technology and Informatics, 2018, 180–187. https://doi.org/10.3233/978-1-61499-858-7-180 (conference article)
[88] Asan Agibetov, Matthias Samwald.
“Fast and scalable learning of neuro-symbolic representations of biomedical knowledge”
Workshop on Deep Learning for Knowledge Graphs and Semantic Technologies (DL4KGS), June 2018, Heraklion, Greece (conference article)
[87] Kathrin Blagec, Rudolf Koopmann, Mandy Crommentuijn – van Rhenen, Inge Holsappel, Cathelijne H van der Wouden, Lidija Konta, Hong Xu, Daniela Steinberger, Enrico Just, Jesse J Swen, Henk-Jan Guchelaar, Matthias Samwald.
“Implementing Pharmacogenomics Decision Support across Seven European Countries: The Ubiquitous Pharmacogenomics (U-PGx) Project”
Journal of the American Medical Informatics Association, Feb 9 2018. https://doi.org/10.1093/jamia/ocy005 (journal article)
[86] Ernesto Jiménez-Ruiz, Asan Agibetov, Matthias Samwald, Valerie Cross
“We divide, you conquer: from large-scale ontology alignment to manageable subtasks with a lexical index and neural embeddings”
SemDeep-4_NLIWOD-4 2018, Joint Proceedings ISWC 2018 Workshops SemDeep-4 and NLIWOD-4, October 2018, Monterey, USA (conference article)
[85] Kathrin Blagec, Rudolf Koopmann, Mandy Crommentuijn – van Rhenen, Inge Holsappel, Cathelijne H van der Wouden, Lidija Konta, Hong Xu, Daniela Steinberger, Enrico Just, Jesse J Swen, Henk-Jan Guchelaar, Matthias Samwald.
“Enabling pharmacogenomic decision support across seven European countries with diverse health IT infrastructures”
AMIA 2018 Informatics Summit, March 12-15 2018, San Francisco, USA (poster abstract)
2017
[84] Kathrin Blagec, Rudolf Koopmann, Mandy Crommentuijn – van Rhenen, Inge Holsappel, Cathelijne van der Wouden, Lidija Konta, Daniela Steinberger, Enrico Just, Jesse J. Swen, Henk-Jan Guchelaar, Matthias Samwald.
“Establishing multi-lingual, multi-modal pharmacogenomic decision support across seven European countries”
ESPT 2017 Fourth Conference, October 4 – October 7 2017, Catania, Italy (website, poster)
[83] Kathrin Blagec, Wolfgang Kuch, Matthias Samwald.
“The Importance of Gene-Drug-Drug-Interactions in Pharmacogenomics Decision Support: An Analysis Based on Austrian Claims Data”
Studies in Health Technology and Informatics 236 (2017) doi:10.3233/978-1-61499-759-7-121 (conference article)
[82] Reihaneh Rostami, Sebastian Hofer, Kathrin Blagec, Hong Xu, Rick Kiefer, Matthias Samwald, Robert R. Freimuth.
“Sharing Clinical Pharmacogenomic Test Results via Mobile Devices”
AMIA Joint Summits on Translational Medicine 2017, March 29 2017, San Francisco, USA (link, conference article)
[81] Cathelijne van der Wouden, Anne Cambon-Thomsen, Henk-Jan Guchelaar, Erika Cecchin, Ka-Chun Cheung, Cristina Lucía Dávila-Fajardo, Vera Deneer, Vita Dolzan, Magnus Ingelman-Sundberg, Siv Jönsson, Mats Karlsson, Marjolein Kriek, Christina Mitropoulou, George Patrinos, Munir Pirmohamed, Matthias Samwald, Elke Schaeffeler, Matthias Schwab, Daniela Steinberger, Julia Stingl, Gere Sunder-Plassmann, Giuseppe Toffoli, Richard Turner, Mandy van Rhenen, Jesse Swen, Henk-Jan Guchelaar, on behalf of the Ubiquitous Pharmacogenomics Consortium.
“Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium”
Clinical Pharmacology & Therapeutics 101, no. 3 (March 1, 2017): 341–58. doi:10.1002/cpt.602 (journal article)
2016
[80] Matthias Samwald, Hong Xu, Kathrin Blagec, Philip E. Empey, Daniel C. Malone, Seid Mussa Ahmed, Patrick Ryan, Sebastian Hofer, Richard D. Boyce.
“Incidence of Exposure of Patients in the United States to Multiple Drugs for Which Pharmacogenomic Guidelines Are Available.”
PLOS ONE 11, no. 10 (October 20, 2016): e0164972. doi:10.1371/journal.pone.0164972 (journal article)
[79] Cathelijne H. van der Wouden, Jesse J. Swen, Matthias Samwald, Christina Mitropoulou, Matthias Schwab, Henk-Jan Guchelaar.
“A Brighter Future for the Implementation of Pharmacogenomic Testing.”
European Journal of Human Genetics, August 31, 2016. doi:10.1038/ejhg.2016.116. (journal article)
[78] Fan Zhu, Javier García-García, Eli Stahl, Abhishek Pratap, Gaurav Pandey, Dimitrios Pappas, Daniel Aguilar, Bernat Anton, Jaume Bonet, Ridvan Eksi, Oriol Fornés, Emre Guney, Hongdong Li, Manuel Alejandro Marín, Bharat Panwar, Joan Planas-Iglesias, Daniel Poglayen, Jing Cui, Andre O. Falcao, Christine Suver, Bruce Hoff, Venkat S. K. Balagurusamy, Donna Dillenberger, Elias Chaibub Neto, Thea Norman, Tero Aittokallio, Muhammad Ammad-ud-din, Chloe-Agathe Azencott, Víctor Bellón, Valentina Boeva, Kerstin Bunte, Himanshu Chheda, Lu Cheng, Jukka Corander, Michel Dumontier, Anna Goldenberg, Peddinti Gopalacharyulu, Mohsen Hajiloo, Daniel Hidru, Alok Jaiswal, Samuel Kaski, Beyrem Khalfaoui, Suleiman Ali Khan, Eric R. Kramer, Pekka Marttinen, Aziz M. Mezlini, Bhuvan Molparia, Matti Pirinen, Janna Saarela, Matthias Samwald, Véronique Stoven, Hao Tang, Jing Tang, Ali Torkamani, Jean-Phillipe Vert, Bo Wang, Tao Wang, Krister Wennerberg, Nathan E. Wineinger, Guanghua Xiao, Yang Xie, Rae Yeung, Xiaowei Zhan, Cheng Zhao, Members of the Rheumatoid Arthritis Challenge Consortium, Jeff Greenberg, Joel Kremer, Kaleb Michaud, Anne Barton, Marieke Coenen, Xavier Mariette, Corinne Miceli, Nancy Shadick, Michael Weinblatt, Niek de Vries, Paul P. Tak, Danielle Gerlag, Tom W. J. Huizinga, Fina Kurreeman, Cornelia F. Allaart, S. Louis Bridges Jr., Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan, Lara M. Mangravite, S. Louis Bridges, Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan, Lara M. Mangravite
“Crowdsourced Assessment of Common Genetic Contribution to Predicting Anti-TNF Treatment Response in Rheumatoid Arthritis.”
Nature Communications 7 (August 23, 2016): 12460. doi:10.1038/ncomms12460 (journal article)
[77] Wolfgang Kuch, Christoph Rinner, Walter Gall, Matthias Samwald.
“How Many Patients Could Benefit From Pre-Emptive Pharmacogenomic Testing and Decision Support? A Retrospective Study Based on Nationwide Austrian Claims Data.”
Studies in Health Technology and Informatics 223 (2016): 253–58. doi:10.3233/978-1-61499-645-3-253 (conference article)
[76] Matthias Samwald, Kathrin Blagec, Sebastian Hofer, Robert R. Freimuth.
“One man’s *1 is another man’s *13? Trouble with current nomenclatures in personalized medicine”
Summer school Genomic Medicine – Bridging Research and the Clinic, May 3 – May 7 2016, Portorož, Slovenia (invited conference article) Book of Abstracts
[75] Matthias Samwald.
“Bridging theory and practice: Clinical decision support systems for personalized medicine”,
Summer school Genomic Medicine – Bridging Research and the Clinic, May 3 – May 7 2016, Portorož, Slovenia (invited conference article) Book of Abstracts
[74] Kathrin Blagec, Katrina M. Romagnoli, Richard D. Boyce, Matthias Samwald.
“Examining Perceptions of the Usefulness and Usability of a Mobile-Based System for Pharmacogenomics Clinical Decision Support: A Mixed Methods Study.”
PeerJ 4 (February 8, 2016): e1671. doi:10.7717/peerj.1671 (journal article)
[73] RC Kiefer, DK Sharma, Matthias Samwald, MK Linan D Sottara, KK Wix, Robert R. Freimuth.
“Emerging Resources for Pharmacogenomic Clinical Decision Support.”
Pacific Symposium on Biocomputing (PSB) 2016, January 4 – January 8 2016, Hawaii, USA (poster)
2015
[72] Matthias Samwald, Kathrin Blagec, Sebastian Hofer, Robert R. Freimuth.
“Analysing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data.”
Pharmacogenomics, September 30, 2015. doi:10.2217/pgs.15.108 (journal article)
[71] Sebastian Hofer, Kathrin Blagec, Robert R. Freimuth, Matthias Samwald.
“Analysing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data.”
ESPT 2015: Integration of Pharmacogenomics in clinical decision support, October 7 – 9, 2015, Budapest, Hungary (poster)
[70] Sebastian Hofer, Matthias Samwald.
“A tool for rapid aggregation of eQTLs in human cells”
The European Human Genetics Conference 2015 (ESHG 2015), June 6 – 9, Glasgow, UK (poster)
[69] Serkan Ayvaz, John Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas P. Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, Richard D. Boyce.
“Toward a Complete Dataset of Drug–drug Interaction Information from Publicly Available Sources.”
Journal of Biomedical Informatics 55 (June 2015): 206–17. doi:10.1016/j.jbi.2015.04.006 (journal article)
[68] Alexander Pfundner, Tobias Schönberg, John Horn, Richard D Boyce, Matthias Samwald.
“Utilizing the Wikidata System to Improve the Quality of Medical Content in Wikipedia in Diverse Languages: A Pilot Study.”
Journal of Medical Internet Research 17, no. 5 (May 5, 2015): e110. doi:10.2196/jmir.4163 (journal article)
[67] Matthias Samwald, Jose A. Miñarro Giménez, Richard D. Boyce, Robert R. Freimuth, Klaus-Peter Adlassnig, Michel Dumontier.
“Pharmacogenomic Knowledge Representation, Reasoning and Genome-Based Clinical Decision Support Based on OWL 2 DL Ontologies.”
BMC Medical Informatics and Decision Making 15, no. 1 (February 22, 2015): 12. doi:10.1186/s12911-015-0130-1 (journal article)
2014
[66] Matthias Samwald, Veronika Stefanov, Georg Petz, Claus-Dieter Volko, Allan Hanbury.
“Improving the Quality and Findability of Open Medical Information on the Web: Medical Wikidata and the FindMeEvidence Search Engine”
Medicine 2.0’14 Europe, World Congress on Social Media, Mobile Apps, Internet / Web 2.0, October 8 – October 10, 2014, Torremolinos, Spain (conference article) link
[65] Jeroen De Bruin, Jose Miñarro-Giménez, Matthias Samwald, Oscar Marin Alonso.
“Visualising topic networks in infection control using word vector analysis”
Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (poster)
[64] Matthias Samwald, José Antonio Minarro-Giménez, Kathrin Blagec, Klaus-Peter Adlassnig.
“Towards a global IT system for personalized medicine: the Medicine Safety Code initiative“
Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)
[63] José Antonio Minarro-Giménez, Oscar Marín-Alonso, Matthias Samwald.
“Exploring the application of deep learning techniques on medical text corpora”
Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)
[62] Matthias Samwald, Allan Hanbury.
“An open-source, mobile-friendly search engine for public medical knowledge”
Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)
[61] José Antonio Minarro-Giménez, Matthias Samwald.
“An update on Genomic CDS, a complex ontology for pharmacogenomics and clinical decision support”
OWL Reasoner Evaluation Workshop 2014 (ORE2014), Vienna, Austria (conference article)
[60] Jose Antonio Miñarro-Giménez, Kathrin Blagec, Richard D. Boyce, Klaus-Peter Adlassnig, Matthias Samwald.
“An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care.”
PLoS ONE 9, no. 5 (May 2, 2014): e93769. doi:10.1371/journal.pone.0093769. Open access article (journal article)
[59] Serkan Ayvaz, Qian Zhu, Harry Hochheiser, Mathias Brochhausen, John Horn, Michel Dumontier, Matthias Samwald, Richard Boyce.
“Drug-Drug Interaction Data Source Survey and Linking”
AMIA Summit on Translational Bioinformatics, April 7 – April 9, San Francisco, USA(poster)
[58] Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, James P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson, Robert Hoehndorf.
“The Semanticscience Integrated Ontology (SIO) for Biomedical Research and Knowledge Discovery.”
Journal of Biomedical Semantics 5, no. 1 (March 6, 2014): 14. doi:10.1186/2041-1480-5-14 Open access article (journal article)
2013
[57] Matthias Samwald, Robert R Freimuth.
“Making data on essential pharmacogenes available for every patient everywhere: the Medicine Safety Code initiative”
Pharmacogenomics 14, Nr. 13 (October 2013): 1529–1531. doi:10.2217/pgs.13.121 Open access article (journal article; invited editorial)
[56] Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodriguez, Norbert Fuhr, Adam Funk, Alba Garcia Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gomez, R. Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth J. F. Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Iván Martínez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, João Palotti, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecher, Angus Roberts, Patrick Ruch, Alexander Sachs, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel Angel Tinte, Zdenka Uresová, Alejandro Vargas, Dina Vishnyakova.
“Khresmoi-Multilingual Semantic Search of Medical Text and Images.”
Studies in Health Technology and Informatics 192 (2013): 1266.
[55] Veronika Stefanov, Alexander Sachs, Marlene Kritz, Matthias Samwald, Manfred Gschwandtner, Allan Hanbury.
“A Formative Evaluation of a Comprehensive Search System for Medical Professionals.”
In Information Access Evaluation. Multilinguality, Multimodality, and Visualization, edited by Pamela Forner, Henning Müller, Roberto Paredes, Paolo Rosso, and Benno Stein, 81–92. Lecture Notes in Computer Science 8138. Springer Berlin Heidelberg, 2013. link (conference article)
[54] Matthias Samwald
“Genomic CDS: an example of a complex ontology for pharmacogenetics and clinical decision support”
OWL Reasoner Evaluation Workshop 2013 (ORE2013), July 22, Ulm, Germany (conference article)
[53] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury
“Physicians searching the web for medical question answering: A European survey and local user studies”
Medinfo2013, August 20-23, Copenhagen, Denmark (poster)
[52] Matthias Samwald, Robert Freimuth, Joanne S. Luciano, Simon Lin, Robert L. Powers, M. Scott Marshall, Klaus-Peter Adlassnig, Michel Dumontier, Richard D. Boyce.
“An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics”
Medinfo2013, August 20-23, Copenhagen, Denmark (conference article) Open-access preprint version
[51] Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury, Matthias Samwald.
“Utilisation and perceived problems of online medical resources and search tools among different groups of European physicians”
Journal of Medical Internet Research 15, no. 6 (2013): e122. Open-access article (journal article)
[50] Matthias Samwald.
“Semantically Enabling Genetic Medicine to Facilitate Patients and Guidelines Matching and Enhanced Clinical Decision Support”
Proceedings of the Conference on Semantics in Healthcare and Life Sciences 2013 (CSHALS 2013), February 28, 2013, Cambridge/Boston, Massachusetts, USA (conference article)
Slides
[49] Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul Jean Bonnal, Brad Chapman, Peter Cock, Tore Eriksson, Paul Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi.
“The 3rd DBCLS BioHackathon: Improving Life Science Data Integration with Semantic Web Technologies.”
Journal of Biomedical Semantics 4, no. 1 (February 11, 2013): 6. doi:10.1186/2041-1480-4-6
[48] Matthias Samwald, Klaus-Peter Adlassnig.
“Pharmacogenomics in the pocket of every patient? A prototype based on Quick Response (QR) codes”
Journal of the American Medical Informatics Association 20, no. 3 (January 5, 2013): 409–412. http://dx.doi.org/10.1136/amiajnl-2012-001275 (journal article) Open access preprint version
2012
[47] Matthias Samwald, Zhan Ye, Daniel A Vasco, Steven Schrodi, Murray Brilliant, Simon Lin.
“Pharmacogenomics in the Pocket of Every Patient? – A Prototype Card with Quick Response (QR) Code”
Critical Assessment of Massive Data Analysis 2012 (CAMDA2012), co-located with the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012) (conference article)
[46] Gökhan Karakülah, Asli Suner, Klaus-Peter Adlassnig, Matthias Samwald.
“A data-driven living review for pharmacogenomic decision support in cancer treatment“
Studies in Health Technology and Informatics 180 (2012): 688–692.(conference article)
[45] Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodríguez, Norbert Fuhr, Adam Funk, Alba García Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gómez, Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Ivan Martinez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecherc, Angus Roberts, Patrick Ruch, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel A. Tinte, Zdenka Urešová, Alejandro Vargas, Dina Vishnyakova.
“Khresmoi: Multimodal Multilingual Medical Information Search”
Medical Informatics Europe 2012 (MIE2012) (poster and presentation booth)
[44] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Allan Hanbury.
“A curated index of high-quality web resources for medical practitioners”
Medical Informatics Europe 2012 (MIE2012) (poster)
[43] Matthias Samwald, Karsten Fehre, Jeroen de Bruin, Klaus-Peter Adlassnig.
“The Arden Syntax Standard for Clinical Decision Support: Experiences and Directions.”
Journal of Biomedical Informatics 45, no. 4 (August 2012): 711–718 (journal article) Open access preprint version
[42] M. Scott Marshall, Richard Boyce, Helena F. Deus, Jun Zhao, Egon L. Willighagen, Matthias Samwald, Elgar Pichler, Janos Hajagos, Eric Prud’hommeaux, Susie Stephens.
“Emerging Practices for Mapping and Linking Life Sciences Data Using RDF — A Case Series.”
Web Semantics: Science, Services and Agents on the World Wide Web 14 (July 2012): 2–13. (journal article)
[41] Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S. Luciano, Robert R. Freimuth, Frederick Whipple, Elgar Pichler, Eric Prud’hommeaux, Michel Dumontier, M. Scott Marshall.
“Semantically enabling pharmacogenomic data for the realization of personalized medicine”
Pharmacogenomics 13, no. 2 (January 2012): 201–212.(journal article) Open access preprint version
[40] Matthias Samwald, Adrien Coulet, Robert R. Freimuth, Iker Huerga, Joanne Luciano, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Frederick Whipple, Michael Marshall, Michel Dumontier.
“An informatics infrastructure for translating pharmacogenomic knowledge into clinical practice”
In 2012 AMIA Summit on Translational Bioinformatics, 2012 Joint Summits on Translational Science, San Francisco, California, March 19, 2012 – March 23, 2012 Manuscript ID AMIA-077-T2012 (conference article)
2011
[39] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury.
“An open, trustworthy and multilingual search engine for medical practitioners”
In 23rd International Conference of the European Federation for Medical Informatics (MIE2011), User Centred Networked Health Care – A. Moen et al. (Eds.), MIE 2011 / CD / Short Communications, 2011 (conference article)
[38] Matthias Samwald, Holger Stenzhorn, Michel Dumontier, M. Scott Marshall, Joanne Luciano, Klaus-Peter Adlassnig.
“Towards an interoperable information infrastructure providing decision support for genomic medicine”
Studies in Health Technology and Informatics 169 (2011): 165-169. Proceedings of Medical Informatics Europe 2011 (MIE2011). (conference article)
PDF, Link to publisher
[37] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury.
“Towards an open, trustworthy and multilingual search engine for medical practitioners: News from the European Khresmoi project”
In Schreier, G., Hayn, D. & Ammenwerth, E. (Eds.) Tagungsband der eHealth2011 – Health Informatics meets eHealth – von der Wissenschaft zur Anwendung und zurück, Grenzen überwinden – Continuity of Care, 26.–27. Mai 2011, Wien, Österreichische Computer Gesellschaft, Wien, 135 – 140 (conference article)
PDF
[36] Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M. Scott Marshall, Eric Prud’hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens.
“Linked open drug data for pharmaceutical research and development”
Journal of Cheminformatics 3, no. 1 (2011): 19. (journal article)
[35] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud?hommeaux, Matthias Samwald, Lynn Schriml, Petev J. Tonellato, Patricia L. Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier.
“The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside”
Journal of Biomedical Semantics 2, no. 2 (2011): S1. (journal article)
[34] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christine Domarew, Thomas Gambet, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Timothy Lebo, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Patricia L. Wletzel, Jun Zhao, Susie Stephens, Michel Dumontier.
“The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration”
In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (conference article)
Conference proceedings
[33] Matthias Samwald, Jun Zhao, Michel Dumontier, M. Scott Marshall, Kei Cheung, Joanne S. Luciano.
“Translating ethnopharmacological findings into novel drug leads: the potential roles of linked open data and ontologies”
In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (poster)
Conference proceedings
2010
[32] Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud’hommeaux, Michael Miller, M.Scott Marshall, Kei-Hoi Cheung.
“Provenance of Microarray Experiments for a Better Understanding of Experiment Results”
Proceedings of Second International Workshop on the role of Semantic Web in Provenance Management (SWPM-2010), Shanghai, China (conference article)
[31] Matthias Samwald, Michel Dumontier, Jun Zhao, Joanne Luciano, M Scott Marshall, Kei-Hoi Cheung.
“Integrating findings from traditional medicine into modern pharmaceutical research: the potential role of linked open data”
Chinese Medicine 5, No. 1 (2010): 43. (journal article)
[30] Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D Karp, Chris Sander, Gary D Bader.
“The BioPAX community standard for pathway data sharing.”
Nature Biotechnology 28, Nr. 9 (9, 2010): 935-942. (journal article)
[29] Kei-Hoi Cheung, Matthias Samwald, Raymond K. Auerbach, Mark B. Gerstein.
“Structured digital tables on the Semantic Web: toward a structured digital literature”
Nature Molecular Systems Biology 6 (August 24, 2010): 403. (journal article)
[28] Michel Dumontier, Bosse Andersson, Colin Batchelor, Christine Denney, Christopher Domarew, Anja Jentzsch, Joanne Luciano, Elgar Pichler, Eric Prud’hommeaux, Patricia Whetzel, Olivier Bodenreider, Tim Clark, Lee Harland, Vipul Kashyap, Peter Kos, Julia Kozlovsky, James McGurk, Chimezie Ogbuji, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Jun Zhao, Susie Stephens.
“The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench”
Bio-Ontologies 2010, Proceedings of the 13th Annual Bio-Ontologies Meeting, Boston, USA (conference article)
[27] Patricia L. Whetzel, Colin Batchelor, Elgar Pichler, Bosse Andersson, Olivier Bodenreider, Tim Clark, Christopher Domarew, Michel Dumontier, Anja Jentzsch, Vipul Kashyap, Julia Kozlovsky, Joanne Luciano, Chimezie Ogbuji, Matthias Samwald, Jun Zhao, Susie Stephens.
“Translational Medicine Ontology: A Patient-Centric Ontology for Drug Development and Clinical Practice”
Proceedings of the Summit on Translational Bioinformatics 2010, San Francisco, USA. (poster)
[26] Matthias Samwald, Holger Stenzhorn.
“Establishing a distributed system for the simple representation and integration of diverse scientific assertions.”
Journal of Biomedical Semantics 1, Nr. 1 (2010): S5. (journal article)
[25] Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd, Kei-Hoi Cheung.
“Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience”
Artificial Intelligence in Medicine 48, no. 1 (January 2010): 21-28. (journal article)
2009
[24] Anita de Waard, Simon Buckingham Shum, Annamaria Carusi, Jack Park, Matthias Samwald, Ágnes Sándor.
“Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims”
Proceedings of the Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), co-located with the 8th International Semantic Web Conference (ISWC-2009). (conference article)
Conference Proceedings
[23] Matthias Samwald, Holger Stenzhorn.
“Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards”
Bio-Ontologies 2009, co-located with ISMB2009. (conference article)
Article PDF, Presentation PDF
[22] Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke.
“A Journey to Semantic Web Query Federation in Life Sciences”
BMC Bioinformatics, 10, no. Suppl 10 (2009): S10 (journal article)
[21] Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis Marenco, Matthew E. Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller.
“Approaches to Neuroscience Data Integration”
Briefings in Bioinformatics, 10, no. 4 (July 2009): 345-353 (journal article)
[20] Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, M. Scott Marshall.
“Life sciences on the semantic web: the neurocommons and beyond”
Briefings in Bioinformatics, 10, no. 2 (March 2009): 193-204 (journal article)
[19] Anja Jentzsch, Jun Zhao, Oktie Hassanzadeh, Kei-Hoi Cheung, Matthias Samwald, Bo Andersson.
“Linking Open Drug Data”
In Proceedings of Linking Open Data Triplification Challenge at the I-Semantics 2009, 2009. (conference paper)
Article PDF
[18] Jun Zhao, Anja Jentzsch, Matthias Samwald, Kei-Hoi Cheung.
“Linked Data for Connecting Traditional Chinese Medicine and Western Medicine”
The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)
[17] Christine Denney, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, John Hill, Joanne Luciano, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Holger Stenzhorn, Trish Whetzel, Elizabeth Wu, Susie Stephens.
“Creating a Translational Medicine Ontology”
The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)
[16] Christine Denney, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, Jon Hill, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Patricia L. Whetzel, Elizabeth Wu, Susie Stephens.
“Creating a Translational Medicine Ontology”
Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164 (poster)
[15] Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller, Kei-Hoi Cheung.
“Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience research”
Studies in Health Technology and Informatics/150 (2009): 317-321. Presented at the International Conference of the European Federation for Medical Informatics, 2009 (conference article)
Link, Article PDF
[14] Alexandre Passant, Matthias Samwald, John Breslin, Stefan Decker.
“Federating Distributed Social Data to Build an Interlinked Online Information Society.”
In Proceedings of the WebSci’09: Society On-Line, 2009. (conference article)
Link, Article PDF
2008
[12] Matthias Samwald, Klaus-Peter Adlassnig.
“The bio-zen plus ontology.”
Applied Ontology 3, no. 4 (Januar 1, 2008): 213-217. (journal article)
Link
[11] Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg.
“Simplifying Access to Large-Scale Health Care and Life Sciences Datasets.”
In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)
[10] Matthias Samwald, Kei-Hoi Cheung.
“Experiences with the conversion of SenseLab databases to RDF/OWL (W3C Interest Group Note).”
World Wide Web Consortium, 6, 2008. http://www.w3.org/TR/hcls-senselab/. (W3C interest group note)
[9] Sebastian Schaffert, Julia Eder, Matthias Samwald, Andreas Blumauer.
“KiWi – Knowledge in a Wiki.”
5th European Semantic Web Conference (ESWC2008), Tenerife, Spain, 6, 2008. (poster)
[8] Christian Morbidoni, Danh Le Phuoc, Axel Polleres, Matthias Samwald, Giovanni Tummarello.
“Previewing Semantic Web Pipes.”
In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)
2007
[7] Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, et al.
“Advancing translational research with the Semantic Web.” BMC
Bioinformatics 8 Suppl 3 (2007): S2. doi:1471-2105-8-S3-S2. (journal article)
[6] Matthias Samwald, William Bug, Jonathan Rees, Chris Mungall, John Barkley, Ray Hookway, et al.
“The Semantic Web Health Care and Life Sciences Interest Group work in progress: A large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies.”
International Conference on Intelligent Systems for Molecular Biology (ISMB2007), Vienna, Austria, 2007. (poster)
2006
[4] Matthias Samwald.
“Classes Versus Individuals: Fundamental Design Issues for Ontologies on the Biomedical Semantic Web.”
In Proceedings of the European Federation for Medical Informatics, Special Topic Conference. Timisoara, Romania, 2006. (conference article)
Article PDF
[3] Matthias Samwald, Isabella Hinterleitner, Klaus-Peter Adlassnig.
“Semantic web technology for database integration in neuroscience.”
In FENS Forum Abstracts, 3: Vienna, Austria, 2006. (conference article)
[2] Matthias Samwald, Alan Ruttenberg.
“Representation and resolution of digital resources on the semantic web – an ontology-based approach.”
Athens, Georgia, USA, 2006. (conference article)
2005
[1] Matthias Samwald, Klaus-Peter Adlassnig.
“Bringing Neuroscience to the Semantic Web: The Semantic Synapse Project.”
In Proceedings of the International Conference on Intelligent Agents, Web Technologies & Internet Commerce. Vienna, Austria, 2005. (conference article)
Invited talks
Matthias Samwald. “Aligning Human and Machine Intelligence”, Bio-Ontologies @ ISMB/ECCB 2021, July 26, 2021, online.
Matthias Samwald. “From Data to Knowledge to Cure”, Artificial Intelligence in Clinical and Preclinical Settings symposion, November 12, 2019, Medical University of Vienna, Vienna, Austria.
Matthias Samwald. “Towards Transformative Artificial Intelligence in Life Science and Health Care”, International Symposium on Health Informatics and Bioinformatics 2019 (HIBIT 2019), October 18, 2019, Izmir, Turkey.
Matthias Samwald. “AI: From data to knowledge to radical progress”, Conference “Is Artificial Intelligence a Force for Good? Current Opportunities and Challenges Within the Artificial Intelligence Ecosystem”, September 26, 2019, Vienna Austria.
Matthias Samwald. “Implementing pharmacogenomics decision support across Europe: The Ubiquitous Pharmacogenomics (U-PGx) Project”, 26th Scientific Congress of the Austrian Pharmaceutical Society (ÖPhG), June 26, 2019, Graz, Austria.
Matthias Samwald. “Driving radical biomedical progress through AI”, 1st Vienna Symposium Machine Learning in Medicine & Biology, June 6, 2019, Vienna, Austria.
Matthias Samwald. “Enabling 21st Century Medicine: From Semantic Technologies to AI”, PractiKPharma project workshop, May 23, 2019, Montpellier, France.
Matthias Samwald “Transforming Pharma and Medicine through AI: A macrostrategic view”, AI in Pharma Summit 2019, February 22, 2019, Munich, Germany.
Matthias Samwald. “The Medication Safety Code (MSC) Initiative”, 2nd SGAIM spring congress, May 3, 2017, Lausanne, Switzerland.
Gere Sunder-Plassmann, Matthias Samwald. “Making pharmacogenetic treatment optimization accessible across Europe”, Transplant Forum of the Medical University of Vienna, October 27, 2016, Medical University of Vienna, Vienna, Austria.
Matthias Samwald. “Semantic Technologies for Biomedical Decision Support“, EMBL-EBI Industry Programme Workshop, European Bioinformatics Institute, May 18, 2011, Hinxton/Cambridge, UK.
Matthias Samwald. “High-level knowledge representation on the Semantic Web: the Concept Web Alliance and related efforts”, BioHackathon Symposium 2010, February 2010, Tokyo, Japan.
Matthias Samwald. “Scientific Information Integration”, Hypotheses, Evidence and Relations (Hyp-ER) project meeting, May 2009, Elsevier Offices, Amsterdam, Netherlands.
Articles published without peer-review & book chapters
Milad Moradi, Matthias Samwald.
“Deep Learning, Natural Language Processing, and Explainable Artificial Intelligence in the Biomedical Domain”.
ArXiv:2202.12678 [Cs], 25 February 2022. http://arxiv.org/abs/2202.12678
Kathrin Blagec, Adriano Barbosa-Silva, Simon Ott, Matthias Samwald.
“A curated, ontology-based, large-scale knowledge graph of artificial intelligence tasks and benchmarks”.
arXiv:2110.01434 [cs], 6. Oktober 2021. http://arxiv.org/abs/2110.01434
Milad Moradi, Kathrin Blagec, Florian Haberl, Matthias Samwald.
“GPT-3 Models are Poor Few-Shot Learners in the Biomedical Domain”.
arXiv:2109.02555 [cs.CL], September 2021. https://arxiv.org/abs/2109.02555
Milad Moradi, Matthias Samwald.
“Evaluating the Robustness of Neural Language Models to Input Perturbations”.
arXiv:2108.12237 [cs.CL], August 2021. https://arxiv.org/abs/2108.12237
Milad Moradi, Kathrin Blagec, Matthias Samwald.
“Deep learning models are not robust against noise in clinical text”.
arXiv:2108.12242 [cs.CL], August 2021. https://arxiv.org/abs/2108.12242
Simon Ott, Laura Graf, Asan Agibetov, Christian Meilicke, Matthias Samwald.
“Scalable and interpretable rule-based link prediction for large heterogeneous knowledge graphs”.
arXiv:2012.05750 [cs.LG], December 2020. https://arxiv.org/abs/2012.05750
Milad Moradi and Matthias Samwald.
“Explaining black-box text classifiers for disease-treatment information extraction”.
arXiv:2010.10873 [cs.AI], October 2020. https://arxiv.org/abs/2010.10873
Kathrin Blagec, Georg Dorffner, Milad Moradi and Matthias Samwald.
“A critical analysis of metrics used for measuring progress in artificial intelligence”.
arXiv:2008.02577 [cs], August 2020. http://arxiv.org/abs/2008.02577
Simon Ott, Laura Graf, Asan Agibetov, Christian Meilicke and Matthias Samwald.
“Scalable and interpretable rule-based link prediction for large heterogeneous knowledge graphs”.
arXiv:2012.05750 [cs], December 2020. http://arxiv.org/abs/2012.05750
Aniwaa Owusu Obeng, Matthias Samwald and Stuart A. Scott.
“Reactive, Point-of-Care, Preemptive, and Direct-to-Consumer Pharmacogenomics Testing”
In Pharmacogenomics: Challenges and Opportunities in Therapeutic Implementation, Second Edition Academic Press, 2018, ISBN 0128126264 (book chapter)
Jose Antonio Miñarro-Giménez, Oscar Marín-Alonso, and Matthias Samwald.
“Applying Deep Learning Techniques on Medical Corpora from the World Wide Web: A Prototypical System and Evaluation.”
arXiv:1502.03682 [cs], February 12, 2015. http://arxiv.org/abs/1502.03682
Matthias Samwald.
“Suchen und Finden” Das Österreichische Gesundheitswesen – ÖKZ, Ausgabe 52.JG 7, 2011. Article PDF
Alexandre Passant, Matthias Samwald, John G. Breslin, Stefan Decker.
“Federating Distributed Social Data to Build an Interlinked Online Information Society.” IEEE Intelligent Systems 24, no. 6 (11, 2009): 44-48.
Holger Stenzhorn, Matthias Samwald.
“Das Semantic Web als Werkzeug in der biomedizinischen Forschung.” In Social Semantic Web: Web 2.0 – Was nun? Heidelberg, Germany: Springer, 2009. (book chapter)
Matthias Samwald.
“Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research” September 2009. Available from Nature Precedings: http://precedings.nature.com/documents/3775/version/1 (pre-print article)
Vipul Kashyap, Kei-Hoi Cheung, Donald Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, et al.
“Ontology-Based Data Integration For Biomedical Research.” In The Semantic Web: Real-World Applications from Industry, 97-122, 2007. (book chapter)
Matthias Samwald.
“Branchenreport: Semantische Technologien in den Life Sciences (Industry Report: Semantic Technologies in the Life Sciences).” Branchenreport der Semantic Web School. Vienna, Austria: Semantic Web School, 2007. (industry white paper)
Matthias Samwald.
“Review: Dystroglycan in the Nervous System” June 2007. Available from Nature Precedings: http://precedings.nature.com/documents/196/version/1 (pre-print article)
Master’s and doctoral theses
Matthias Samwald. “Semantic Web Technology in Neuroscience and Biomedicine. “ University of Vienna; Medical University of Vienna, 2007. (doctoral thesis)
Matthias Samwald. “Neuromuscular Synapses of the Sympathetic Nervous System” University of Vienna; Medical University of Vienna, 2005. (master’s thesis)