Using BLAST, A DNA and Protein Sequence Comparison Tool, for Finding Gene and Protein Names in Journal Articles. - Michael Krauthammer; Andrey Rzhetsky; Pavel Morozov; Carol Friedman (AMIA, 2000)

Knowledge Sharing in the Construction of an Anatomical Navigational Ontology. - Michael Krauthammer; Nina Wacholder; Stephen B. Johnson; Gai Elhanan; Pat Molholt (AMIA, 2000)

Designing a Navigational Ontology for Browsing and Accessing 3D Anatomical Images. - Nina Wacholder; Judith M. Venuti; Michael Krauthammer; Pat Molholt (AMIA, 2000)

A knowledge model for analysis and simulation of regulatory networks. - Andrey Rzhetsky; Tomohiro Koike; Sergey Kalachikov; Shawn M. Gomez; Michael Krauthammer; Sabina H. Kaplan; Pauline Kra; James J. Russo; Carol Friedman (Bioinform., 2000)

A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries. - Michael Krauthammer; George Hripcsak (AMIA, 2001)

Linking Protein Interaction Data to the MESH Hierarchy. - Michael Krauthammer; Pauline Kra; Carol Friedman (AMIA, 2001)

GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. - Andrey Rzhetsky; Michael Krauthammer; Tomohiro Koike; Pauline Kra; Shawn M. Gomez; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; Stephen B. Johnson; Vasileios Hatzivassiloglou; Carol Friedman (German Conference on Bioinformatics, 2001)

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. - Carol Friedman; Pauline Kra; Hong Yu 001; Michael Krauthammer; Andrey Rzhetsky (ISMB (Supplement of Bioinformatics), 2001)

Representing nested semantic information in a linear string of text using XML. - Michael Krauthammer; Stephen B. Johnson; George Hripcsak; David A. Campbell; Carol Friedman (AMIA, 2002)

Of truth and pathways: chasing bits of information through myriads of articles. - Michael Krauthammer; Pauline Kra; Ivan Iossifov; Shawn M. Gomez; George Hripcsak; Vasileios Hatzivassiloglou; Carol Friedman; Andrey Rzhetsky (ISMB, 2002)

A Native XML Database Design for Clinical Document Research. - Stephen B. Johnson; David A. Campbell; Michael Krauthammer; P. Karina Tulipano; Eneida A. Mendonça; Carol Friedman; George Hripcsak (AMIA, 2003)

Probabilistic inference of molecular networks from noisy data sources. - Ivan Iossifov; Michael Krauthammer; Carol Friedman; Vasileios Hatzivassiloglou; Joel S. Bader; Kevin P. White; Andrey Rzhetsky (Bioinform., 2004)

Term identification in the biomedical literature. - Michael Krauthammer; Goran Nenadic (J. Biomed. Informatics, 2004)

GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. - Andrey Rzhetsky; Ivan Iossifov; Tomohiro Koike; Michael Krauthammer; Pauline Kra; Mitzi Morris; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; W. John Wilbur (J. Biomed. Informatics, 2004)

Towards Semantic Role Labeling & IE in the Medical Literature. - Yacov Kogan; Nigel Collier; Serguei V. S. Pakhomov; Michael Krauthammer (AMIA, 2005)

Shallow Semantic Parsing of Randomized Controlled Trial Reports. - Hyung M. Paek; Yacov Kogan; Prem Thomas; Seymour Codish; Michael Krauthammer (AMIA, 2006)

A semantic web approach to biological pathway data reasoning and integration. - Kei-Hoi Cheung; Peishen Qi; David Tuck; Michael Krauthammer (J. Web Semant., 2006)

Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. - Andrew K. Smith; Kei-Hoi Cheung; Michael Krauthammer; Martin H. Schultz; Mark Gerstein (Bioinform., 2007)

Term Mapping Using Matrix Operations. - Michael Krauthammer; Thaibinh Luong (Ontologies and Text Mining for Life Sciences, 2008)

Yale Image Finder (YIF): a new search engine for retrieving biomedical images. - Songhua Xu; Jamie P. McCusker; Michael Krauthammer (Bioinform., 2008)

Enriching PubMed Related Article Search with Sentence Level Co-citations. - Nam Tran; Pedro Alves; Shuangge Ma; Michael Krauthammer (AMIA, 2009)

Embedding the Guideline Elements Model in Web Ontology Language. - Nam Tran; George Michel; Michael Krauthammer; Richard N. Shiffman (AMIA, 2009)

Writing Clinical Practice Guidelines in Controlled Natural Language. - Richard N. Shiffman; George Michel; Michael Krauthammer; Norbert E. Fuchs; Kaarel Kaljurand; Tobias Kuhn (CNL, 2009)

Controlled Natural Language for Clinical Practice Guidelines. - Richard N. Shiffman; George Michel; Michael Krauthammer; Norbert E. Fuchs; Kaarel Kaljurand; Tobias Kuhn (CNL (Pre-Proceedings), 2009)

Semantic web data warehousing for caGrid. - Jamie P. McCusker; Joshua A. Phillips; Alejandra N. González-Beltrán; Anthony Finkelstein; Michael Krauthammer (BMC Bioinform., 2009)

Structural similarity assessment for drug sensitivity prediction in cancer. - Pavithra Shivakumar; Michael Krauthammer (BMC Bioinform., 2009)

Analysis of Cancer Omics Data In A Semantic Web Framework. - Matthew Holford; Jamie P. McCusker; Kei-Hoi Cheung; Michael Krauthammer (SWAT4LS, 2010)

A new pivoting and iterative text detection algorithm for biomedical images. - Songhua Xu; Michael Krauthammer (J. Biomed. Informatics, 2010)

MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions. - Vijay Garla; Yong Kong; Sebastian Szpakowski; Michael Krauthammer (Bioinform., 2011)

Finding and Accessing Diagrams in Biomedical Publications. - Tobias Kuhn; Thaibinh Luong; Michael Krauthammer (AMIA, 2012)

Estimating a gene's mutation burden by the number of observed synonymous base substitutions. - Perry Evans; Michael Krauthammer (BIBM, 2012)

Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain. - Samah Jamal Fodeh; Ali Haddad; Cynthia Brandt; Martin H. Schultz; Michael Krauthammer (AIAI (1), 2012)

Underspecified Scientific Claims in Nanopublications. - Tobias Kuhn; Michael Krauthammer (WoLE@ISWC, 2012)

A semantic web framework to integrate cancer omics data with biological knowledge. - Matthew Holford; Jamie P. McCusker; Kei-Hoi Cheung; Michael Krauthammer (BMC Bioinform., 2012)

Image Mining from Gel Diagrams in Biomedical Publications - Tobias Kuhn; Michael Krauthammer (CoRR, 2012)

Nanorecords: A Novel Approach to Communicating High-Level Medical Information. - Mark V. Mai; Tobias Kuhn; José Costa; Michael Krauthammer (AMIA, 2013)

Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications. - Jamie P. McCusker; Timothy Lebo; Michael Krauthammer; Deborah L. McGuinness (DILS, 2013)

Broadening the Scope of Nanopublications. - Tobias Kuhn; Paolo Emilio Barbano; Mate Levente Nagy; Michael Krauthammer (ESWC, 2013)

Complementary ensemble clustering of biomedical data. - Samah Jamal Fodeh; Cynthia Brandt; Thaibinh Luong; Ali Haddad; Martin H. Schultz; Terrence Murphy; Michael Krauthammer (J. Biomed. Informatics, 2013)

SEBI: An Architecture for Biomedical Image Discovery, Interoperability and Reusability Based on Semantic Enrichment. - Syed Ahmad Chan Bukhari; Michael Krauthammer; Christopher J. O. Baker (SWAT4LS, 2014)

Mining images in biomedical publications: Detection and analysis of gel diagrams. - Tobias Kuhn; Mate Levente Nagy; Thaibinh Luong; Michael Krauthammer (J. Biomed. Semant., 2014)

BIM: an open ontology for the annotation of biomedical images. - Ahmad C. Bukhari; Mate Levente Nagy; Michael Krauthammer; Paolo Ciccarese; Christopher J. O. Baker (ICBO, 2015)

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data. - Tobias Kuhn; Christine Chichester; Michael Krauthammer; Michel Dumontier (ISWC (1), 2015)

iCyrus: A Semantic Framework for Biomedical Image Discovery. - Syed Ahmad Chan Bukhari; Mate Levente Nagy; Paolo Ciccarese; Michael Krauthammer; Christopher J. O. Baker (SWAT4LS, 2015)

Mutadelic: mutation analysis using description logic inferencing capabilities. - Matthew E. Holford; Michael Krauthammer (Bioinform., 2015)

Controlling testing volume for respiratory viruses using machine learning and text mining. - Mark V. Mai; Michael Krauthammer (AMIA, 2016)

Global copy number profiling of cancer genomes. - Xuefeng Wang; Mengjie Chen; Xiaoqing Yu; Natapol Pornputtapong; Hao Chen 064; Nancy Ruonan Zhang; R. Scott Powers; Michael Krauthammer (Bioinform., 2016)

Decentralized provenance-aware publishing with nanopublications. - Tobias Kuhn; Christine Chichester; Michael Krauthammer; Núria Queralt-Rosinach; Ruben Verborgh; George Giannakopoulos; Axel-Cyrille Ngonga Ngomo; Raffaele Viglianti; Michel Dumontier (PeerJ Prepr., 2016)

A Clinical Decision Support System for Monitoring Post-Colonoscopy Patient Follow-Up and Scheduling. - Roxanne Wadia; Mark A. Shifman; Forrest W. Levin; Luis N. Marenco; Cynthia Brandt; Kei-Hoi Cheung; Tamar H. Taddei; Michael Krauthammer (CRI, 2017)

PySeqLab: an open source Python package for sequence labeling and segmentation. - Ahmed Allam; Michael Krauthammer (Bioinform., 2017)

Toward automated assessment of health Web page quality using the DISCERN instrument. - Ahmed Allam; Peter Johannes Schulz; Michael Krauthammer (J. Am. Medical Informatics Assoc., 2017)

Prototyping a precision oncology 3.0 rapid learning platform. - Connor Sweetnam; Simone Mocellin; Michael Krauthammer; Nathaniel Knopf; Robert Baertsch; Jeff Shrager (BMC Bioinform., 2018)

Neural networks versus Logistic regression for 30 days all-cause readmission prediction. - Ahmed Allam; Mate Levente Nagy; George R. Thoma; Michael Krauthammer (CoRR, 2018)

Iterations for Propensity Score Matching in MonetDB. - Michael H. Böhlen; Oksana Dolmatova; Michael Krauthammer; Alphonse Mariyagnanaseelan; Jonathan Stahl; Timo Surbeck (ADBIS, 2020)

Patient Similarity Analysis with Longitudinal Health Data. - Ahmed Allam; Matthias Dittberner; Anna Sintsova; Dominique Brodbeck; Michael Krauthammer (CoRR, 2020)

Reducing Annotation Burden Through Multimodal Learning. - Kevin Lopez; Samah J. Fodeh; Ahmed Allam; Cynthia Brandt; Michael Krauthammer (Frontiers Big Data, 2020)

AutoDiscern: rating the quality of online health information with hierarchical encoder attention-based neural networks. - Laura Kinkead; Ahmed Allam; Michael Krauthammer (BMC Medical Informatics Decis. Mak., 2020)

Progressive Transformer-Based Generation of Radiology Reports. - Farhad Nooralahzadeh; Nicolas Perez Gonzalez; Thomas Frauenfelder; Koji Fujimoto; Michael Krauthammer (EMNLP (Findings), 2021)

AttentionDDI: Siamese attention-based deep learning method for drug-drug interaction predictions. - Kyriakos Schwarz; Ahmed Allam; Nicolas Andres Perez Gonzalez; Michael Krauthammer (BMC Bioinform., 2021)

Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task. - Joseph Cornelius; Oscar Lithgow-Serrano; Vani Kanjirangat; Fabio Rinaldi 001; Koji Fujimoto; Mizuho Nishio; Osamu Sugiyama; Kana Ichikawa; Farhad Nooralahzadeh; Aron N. Horvath; Michael Krauthammer (NTCIR, 2022)

Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. - Koji Fujimoto; Mizuho Nishio; Osamu Sugiyama; Kana Ichikawa; Joseph Cornelius; Oscar Lithgow-Serrano; Vani Kanjirangat; Fabio Rinaldi 001; Aron N. Horvath; Farhad Nooralahzadeh; Michael Krauthammer (NTCIR, 2022)

DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. - Kyriakos Schwarz; Alicia Pliego-Mendieta; Lara Planas-Paz; Chantal Pauli; Ahmed Allam; Michael Krauthammer (CoRR, 2022)

Boosting Radiology Report Generation by Infusing Comparison Prior. - Sanghwan Kim; Farhad Nooralahzadeh; Morteza Rohanian; Koji Fujimoto; Mizuho Nishio; Ryo Sakamoto; Fabio Rinaldi 001; Michael Krauthammer (BioNLP@ACL, 2023)

Disfluent Cues for Enhanced Speech Understanding in Large Language Models. - Morteza Rohanian; Farhad Nooralahzadeh; Omid Rohanian; David A. Clifton; Michael Krauthammer (EMNLP (Findings), 2023)

Classification of cancer TNM stage from Japanese radiology report using on-premise LLM at NTCIR-17 MedNLP-SC RR-TNM subtask. - Koji Fujimoto; Mizuho Nishio; Chikako Tanaka; Morteza Rohanian; Farhad Nooralahzadeh; Michael Krauthammer; Fabio Rinaldi 001 (NTCIR, 2023)

Zero-shot classification of TNM staging for Japanese radiology report using ChatGPT at RR-TNM subtask of NTCIR-17 MedNLP-SC. - Mizuho Nishio; Hidetoshi Matsuo; Takaaki Matsunaga; Koji Fujimoto; Morteza Rohanian; Farhad Nooralahzadeh; Fabio Rinaldi 001; Michael Krauthammer (NTCIR, 2023)

Exploratory Analysis of Federated Learning Methods with Differential Privacy on MIMIC-III. - Aron N. Horvath; Matteo Berchier; Farhad Nooralahzadeh; Ahmed Allam; Michael Krauthammer (CoRR, 2023)

SimTS: Rethinking Contrastive Representation Learning for Time Series Forecasting. - Xiaochen Zheng; Xingyu Chen; Manuel Schürch; Amina Mollaysa; Ahmed Allam; Michael Krauthammer (CoRR, 2023)

Generating Personalized Insulin Treatments Strategies with Deep Conditional Generative Time Series Models. - Manuel Schürch; Xiang Li; Ahmed Allam; Giulia Rathmes; Amina Mollaysa; Claudia Cavelti-Weder; Michael Krauthammer (CoRR, 2023)

Attention-based Multi-task Learning for Base Editor Outcome Prediction. - Amina Mollaysa; Ahmed Allam; Michael Krauthammer (CoRR, 2023)

Dynamic Local Attention with Hierarchical Patching for Irregular Clinical Time Series. - Xingyu Chen; Xiaochen Zheng; Amina Mollaysa; Manuel Schürch; Ahmed Allam; Michael Krauthammer (CoRR, 2023)

Modeling Complex Disease Trajectories using Deep Generative Models with Semi-Supervised Latent Processes. - Cécile Trottet; Manuel Schürch; Ahmed Allam; Imon Barua; Liubov Petelytska; Oliver Distler; Anna-Maria Hoffmann-Vold; Michael Krauthammer; EUSTAR collaborators (CoRR, 2023)

Radiology-Aware Model-Based Evaluation Metric for Report Generation. - Amos Calamida; Farhad Nooralahzadeh; Morteza Rohanian; Koji Fujimoto; Mizuho Nishio; Michael Krauthammer (CoRR, 2023)

DDoS: A Graph neural Network Based Drug Synergy Prediction Algorithm. - Kyriakos Schwarz; Alicia Pliego-Mendieta; Amina Mollaysa; Lara Planas-Paz; Chantal Pauli; Ahmed Allam; Michael Krauthammer (CHIL, 2024)

Simple Contrastive Representation Learning for Time Series Forecasting. - Xiaochen Zheng; Xingyu Chen; Manuel Schürch; Amina Mollaysa; Ahmed Allam; Michael Krauthammer (ICASSP, 2024)

Learning Personalized Treatment Decisions in Precision Medicine: Disentangling Treatment Assignment Bias in Counterfactual Outcome Prediction and Biomarker Identification. - Michael Vollenweider; Manuel Schürch; Chiara Rohrer; Gabriele Gut; Michael Krauthammer; Andreas Wicki (ML4H@NeurIPS, 2024)

Semi-Supervised Generative Models for Disease Trajectories: A Case Study on Systemic Sclerosis. - Cécile Trottet; Manuel Schürch; Ahmed Allam; Imon Barua; Liubov Petelytska; Oliver Distler; Anna-Maria Hoffmann-Vold; Michael Krauthammer (MLHC, 2024)

Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data. - Manuel Schürch; Laura Boos; Viola Heinzelmann-Schwarz; Gabriele Gut; Michael Krauthammer; Andreas Wicki; Tumor Profiler Consortium (CoRR, 2024)

Clustering of Disease Trajectories with Explainable Machine Learning: A Case Study on Postoperative Delirium Phenotypes. - Xiaochen Zheng; Manuel Schürch; Xingyu Chen; Maria Angeliki Komninou; Reto Schüpbach; Ahmed Allam; Jan Bartussek; Michael Krauthammer (CoRR, 2024)

Semi-Supervised Generative Models for Disease Trajectories: A Case Study on Systemic Sclerosis. - Cécile Trottet; Manuel Schürch; Ahmed Allam; Imon Barua; Liubov Petelytska; Oliver Distler; Anna-Maria Hoffmann-Vold; Michael Krauthammer; EUSTAR collaborators (CoRR, 2024)

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation. - Heath Arthur-Loui; Amina Mollaysa; Michael Krauthammer (CoRR, 2024)

Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis. - Zsolt Balázs; Todor Gitchev; Ivna Ivankovic; Michael Krauthammer (Bioinform., 2024)

NTCIR-18 RadNLP 2024 Overview: Dataset and Solutions forAutomated Lung Cancer Staging. - Yuta Nakamura; Koji Fujimoto; Jonas Kluckert; Michael Krauthammer; Jun Kanzawa; Akira Katayama; Tomohiro Kikuchi; Ryo Kurokawa; Wataru Gonoi; Yuki Tashiro; Shouhei Hanaoka; Shuntaro Yada; et al. (NTCIR, 2025)

A consensus statement on the use of digital twins in medicine. - Jeffrey David Iqbal; Michael Krauthammer; Claudia M. Witt; Nikola Biller-Andorno; Markus Christen (npj Digit. Medicine, 2025)

TAMER: A Test-Time Adaptive MoE-Driven Framework for EHR Representation Learning. - Yinghao Zhu; Xiaochen Zheng; Ahmed Allam; Michael Krauthammer (CoRR, 2025)

A Variational Perspective on Generative Protein Fitness Optimization. - Lea Bogensperger; Dominik Narnhofer; Ahmed Allam; Konrad Schindler; Michael Krauthammer (CoRR, 2025)

RadVLM: A Multitask Conversational Vision-Language Model for Radiology. - Nicolas Deperrois; Hidetoshi Matsuo; Samuel Ruipérez-Campillo; Moritz Vandenhirtz; Sonia Laguna; Alain Ryser; Koji Fujimoto; Mizuho Nishio; Thomas M. Sutter; Julia E. Vogt; Jonas Kluckert; Thomas Frauenfelder; et al. (CoRR, 2025)

Uncertainty Modeling in Multimodal Speech Analysis Across the Psychosis Spectrum. - Morteza Rohanian; Roya M. Hüppi; Farhad Nooralahzadeh; Noemi Dannecker; Yves Pauli; Werner Surbeck; Iris Sommer; Wolfram Hinzen; Nicolas Langer; Michael Krauthammer; Philipp Homan (CoRR, 2025)

Towards Scalable and Cross-Lingual Specialist Language Models for Oncology. - Morteza Rohanian; Tarun Mehra; Nicola Miglino; Farhad Nooralahzadeh; Michael Krauthammer; Andreas Wicki (CoRR, 2025)

Leveraging the Structure of Medical Data for Improved Representation Learning. - Andrea Agostini; Sonia Laguna; Alain Ryser; Samuel Ruipérez-Campillo; Moritz Vandenhirtz; Nicolas Deperrois; Farhad Nooralahzadeh; Michael Krauthammer; Thomas M. Sutter; Julia E. Vogt (CoRR, 2025)