Michael Krauthammer

According to our database, Michael Krauthammer authored at least 76 papers between 2000 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis.

Zsolt Balázs, Todor Gitchev, Ivna Ivankovic, Michael Krauthammer

Bioinform., January, 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

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

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

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

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

Simple Contrastive Representation Learning for Time Series Forecasting.

Xiaochen Zheng, Xingyu Chen, Manuel Schürch, Amina Mollaysa, Ahmed Allam, Michael Krauthammer

Proceedings of the IEEE International Conference on Acoustics, 2024

2023

Radiology-Aware Model-Based Evaluation Metric for Report Generation.

Amos Calamida, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, 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

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

Attention-based Multi-task Learning for Base Editor Outcome Prediction.

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

SimTS: Rethinking Contrastive Representation Learning for Time Series Forecasting.

Xiaochen Zheng, Xingyu Chen, Manuel Schürch, Amina Mollaysa, Ahmed Allam, Michael Krauthammer

CoRR, 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

Disfluent Cues for Enhanced Speech Understanding in Large Language Models.

Morteza Rohanian, Farhad Nooralahzadeh, Omid Rohanian, David A. Clifton, Michael Krauthammer

Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2023, 2023

Boosting Radiology Report Generation by Infusing Comparison Prior.

Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer

Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, 2023

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

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

Progressive Transformer-Based Generation of Radiology Reports.

Farhad Nooralahzadeh, Nicolas Perez Gonzalez, Thomas Frauenfelder, Koji Fujimoto, Michael Krauthammer

Proceedings of the Findings of the Association for Computational Linguistics: EMNLP 2021, 2021

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

Reducing Annotation Burden Through Multimodal Learning.

Kevin Lopez, Samah J. Fodeh, Ahmed Allam, Cynthia Brandt, Michael Krauthammer

Frontiers Big Data, 2020

Patient Similarity Analysis with Longitudinal Health Data.

Ahmed Allam, Matthias Dittberner, Anna Sintsova, Dominique Brodbeck, Michael Krauthammer

CoRR, 2020

Iterations for Propensity Score Matching in MonetDB.

Michael H. Böhlen, Oksana Dolmatova, Michael Krauthammer, Alphonse Mariyagnanaseelan, Jonathan Stahl, Timo Surbeck

Proceedings of the Advances in Databases and Information Systems, 2020

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

Prototyping a precision oncology 3.0 rapid learning platform.

Connor Sweetnam, Simone Mocellin, Michael Krauthammer, Nathaniel Knopf, Robert Baertsch, Jeff Shrager

BMC Bioinform., 2018

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

PySeqLab: an open source Python package for sequence labeling and segmentation.

Ahmed Allam, Michael Krauthammer

Bioinform., 2017

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

Proceedings of the Summit on Clinical Research Informatics, 2017

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

Global copy number profiling of cancer genomes.

Xuefeng Wang, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy Ruonan Zhang, R. Scott Powers, Michael Krauthammer

Bioinform., 2016

Controlling testing volume for respiratory viruses using machine learning and text mining.

Mark V. Mai, Michael Krauthammer

Proceedings of the AMIA 2016, 2016

2015

Mutadelic: mutation analysis using description logic inferencing capabilities.

Matthew E. Holford, Michael Krauthammer

Bioinform., 2015

iCyrus: A Semantic Framework for Biomedical Image Discovery.

Syed Ahmad Chan Bukhari, Mate Levente Nagy, Paolo Ciccarese, Michael Krauthammer, Christopher J. O. Baker

Proceedings of the 8th Semantic Web Applications and Tools for Life Sciences International Conference, 2015

Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data.

Tobias Kuhn, Christine Chichester, Michael Krauthammer, Michel Dumontier

Proceedings of the Semantic Web - ISWC 2015, 2015

BIM: an open ontology for the annotation of biomedical images.

Ahmad C. Bukhari, Mate Levente Nagy, Michael Krauthammer, Paolo Ciccarese, Christopher J. O. Baker

Proceedings of the International Conference on Biomedical Ontology, 2015

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

SEBI: An Architecture for Biomedical Image Discovery, Interoperability and Reusability Based on Semantic Enrichment.

Syed Ahmad Chan Bukhari, Michael Krauthammer, Christopher J. O. Baker

Proceedings of the 7th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2014

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

Broadening the Scope of Nanopublications.

Tobias Kuhn, Paolo Emilio Barbano, Mate Levente Nagy, Michael Krauthammer

Proceedings of the Semantic Web: Semantics and Big Data, 10th International Conference, 2013

Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications.

Jamie P. McCusker, Timothy Lebo, Michael Krauthammer, Deborah L. McGuinness

Proceedings of the Data Integration in the Life Sciences - 9th International Conference, 2013

Nanorecords: A Novel Approach to Communicating High-Level Medical Information.

Mark V. Mai, Tobias Kuhn, José Costa, Michael Krauthammer

Proceedings of the AMIA 2013, 2013

2012

Image Mining from Gel Diagrams in Biomedical Publications

Tobias Kuhn, Michael Krauthammer

CoRR, 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

Underspecified Scientific Claims in Nanopublications.

Tobias Kuhn, Michael Krauthammer

Proceedings of the Web of Linked Entities Workshop, Boston, USA, November 11, 2012, 2012

Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain.

Samah Jamal Fodeh, Ali Haddad, Cynthia Brandt, Martin H. Schultz, Michael Krauthammer

Proceedings of the Artificial Intelligence Applications and Innovations, 2012

Estimating a gene's mutation burden by the number of observed synonymous base substitutions.

Perry Evans, Michael Krauthammer

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

Finding and Accessing Diagrams in Biomedical Publications.

Tobias Kuhn, Thaibinh Luong, Michael Krauthammer

Proceedings of the AMIA 2012, 2012

2011

MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions.

Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer

Bioinform., 2011

2010

A new pivoting and iterative text detection algorithm for biomedical images.

Songhua Xu, Michael Krauthammer

J. Biomed. Informatics, 2010

Analysis of Cancer Omics Data In A Semantic Web Framework.

Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences, 2010

2009

Structural similarity assessment for drug sensitivity prediction in cancer.

Pavithra Shivakumar, Michael Krauthammer

BMC Bioinform., 2009

Semantic web data warehousing for caGrid.

Jamie P. McCusker, Joshua A. Phillips, Alejandra N. González-Beltrán, Anthony Finkelstein, Michael Krauthammer

BMC Bioinform., 2009

Controlled Natural Language for Clinical Practice Guidelines.

Richard N. Shiffman, George Michel, Michael Krauthammer, Norbert E. Fuchs, Kaarel Kaljurand, Tobias Kuhn

Proceedings of the Pre-Proceedings of the Workshop on Controlled Natural Language (CNL 2009), 2009

Writing Clinical Practice Guidelines in Controlled Natural Language.

Richard N. Shiffman, George Michel, Michael Krauthammer, Norbert E. Fuchs, Kaarel Kaljurand, Tobias Kuhn

Proceedings of the Controlled Natural Language, Workshop on Controlled Natural Language, 2009

Embedding the Guideline Elements Model in Web Ontology Language.

Nam Tran, George Michel, Michael Krauthammer, Richard N. Shiffman

Proceedings of the AMIA 2009, 2009

Enriching PubMed Related Article Search with Sentence Level Co-citations.

Nam Tran, Pedro Alves, Shuangge Ma, Michael Krauthammer

Proceedings of the AMIA 2009, 2009

2008

Yale Image Finder (YIF): a new search engine for retrieving biomedical images.

Songhua Xu, Jamie P. McCusker, Michael Krauthammer

Bioinform., 2008

Term Mapping Using Matrix Operations.

Michael Krauthammer, Thaibinh Luong

Proceedings of the Ontologies and Text Mining for Life Sciences: Current Status and Future Perspectives, 24.03., 2008

2007

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

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

Shallow Semantic Parsing of Randomized Controlled Trial Reports.

Hyung M. Paek, Yacov Kogan, Prem Thomas, Seymour Codish, Michael Krauthammer

Proceedings of the AMIA 2006, 2006

2005

Towards Semantic Role Labeling & IE in the Medical Literature.

Yacov Kogan, Nigel Collier, Serguei V. S. Pakhomov, Michael Krauthammer

Proceedings of the AMIA 2005, 2005

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, Pablo Ariel Duboué, Wubin Weng, W. John Wilbur

J. Biomed. Informatics, 2004

Term identification in the biomedical literature.

Michael Krauthammer, Goran Nenadic

J. Biomed. Informatics, 2004

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

2003

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

Proceedings of the AMIA 2003, 2003

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

Proceedings of the Tenth International Conference on Intelligent Systems for Molecular Biology, 2002

Representing nested semantic information in a linear string of text using XML.

Michael Krauthammer, Stephen B. Johnson, George Hripcsak, David A. Campbell, Carol Friedman

Proceedings of the AMIA 2002, 2002

2001

GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 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, Pablo Ariel Duboué, Wubin Weng, Stephen B. Johnson, Vasileios Hatzivassiloglou, Carol Friedman

Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001

Linking Protein Interaction Data to the MESH Hierarchy.

Michael Krauthammer, Pauline Kra, Carol Friedman

Proceedings of the AMIA 2001, 2001

A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries.

Michael Krauthammer, George Hripcsak

Proceedings of the AMIA 2001, 2001

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

Designing a Navigational Ontology for Browsing and Accessing 3D Anatomical Images.

Nina Wacholder, Judith M. Venuti, Michael Krauthammer, Pat Molholt

Proceedings of the AMIA 2000, 2000

Knowledge Sharing in the Construction of an Anatomical Navigational Ontology.

Michael Krauthammer, Nina Wacholder, Stephen B. Johnson, Gai Elhanan, Pat Molholt

Proceedings of the AMIA 2000, 2000

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

Proceedings of the AMIA 2000, 2000