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2020 – today
- 2024
[j24]Zsolt Balázs
, Todor Gitchev, Ivna Ivankovic, Michael Krauthammer:
Fragmentstein - facilitating data reuse for cell-free DNA fragment analysis. Bioinform. 40(1) (2024)- [c35]Xiaochen Zheng, Xingyu Chen, Manuel Schürch, Amina Mollaysa, Ahmed Allam, Michael Krauthammer:
Simple Contrastive Representation Learning for Time Series Forecasting. ICASSP 2024: 6005-6009 - [i28]Manuel Schürch, Laura Boos, Viola Heinzelmann-Schwarz, Gabriele Gut, Michael Krauthammer, Andreas Wicki, Tumor Profiler Consortium:
Towards AI-Based Precision Oncology: A Machine Learning Framework for Personalized Counterfactual Treatment Suggestions based on Multi-Omics Data. CoRR abs/2402.12190 (2024) - [i27]Xiaochen Zheng, Manuel Schürch, Xingyu Chen, Maria Angeliki Komninou, Reto Schüpbach, Ahmed Allam, Jan Bartussek, Michael Krauthammer:
Clustering of Disease Trajectories with Explainable Machine Learning: A Case Study on Postoperative Delirium Phenotypes. CoRR abs/2405.03327 (2024) - [i26]Cécile Trottet, Manuel Schürch, Ahmed Allam, Imon Barua, Liubov Petelytska, Oliver Distler, Anna-Maria Hoffmann-Vold, Michael Krauthammer, EUSTAR collaborators:
Semi-Supervised Generative Models for Disease Trajectories: A Case Study on Systemic Sclerosis. CoRR abs/2407.11427 (2024) - [i25]Heath Arthur-Loui, Amina Mollaysa, Michael Krauthammer:
Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Goal Directed Generation. CoRR abs/2409.00046 (2024) - [i24]Michael Vollenweider, Manuel Schürch, Chiara Rohrer, Gabriele Gut, Michael Krauthammer, Andreas Wicki:
Learning Personalized Treatment Decisions in Precision Medicine: Disentangling Treatment Assignment Bias in Counterfactual Outcome Prediction and Biomarker Identification. CoRR abs/2410.00509 (2024) - 2023
- [c34]Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer:
Boosting Radiology Report Generation by Infusing Comparison Prior. BioNLP@ACL 2023: 50-61 - [c33]Morteza Rohanian, Farhad Nooralahzadeh, Omid Rohanian, David A. Clifton, Michael Krauthammer:
Disfluent Cues for Enhanced Speech Understanding in Large Language Models. EMNLP (Findings) 2023: 3676-3684 - [i23]Aron N. Horvath, Matteo Berchier, Farhad Nooralahzadeh, Ahmed Allam, Michael Krauthammer:
Exploratory Analysis of Federated Learning Methods with Differential Privacy on MIMIC-III. CoRR abs/2302.04208 (2023) - [i22]Xiaochen Zheng, Xingyu Chen, Manuel Schürch, Amina Mollaysa, Ahmed Allam, Michael Krauthammer:
SimTS: Rethinking Contrastive Representation Learning for Time Series Forecasting. CoRR abs/2303.18205 (2023) - [i21]Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer:
Boosting Radiology Report Generation by Infusing Comparison Prior. CoRR abs/2305.04561 (2023) - [i20]Manuel Schürch, Xiang Li, Ahmed Allam, Giulia Rathmes, Amina Mollaysa, Claudia Cavelti-Weder, Michael Krauthammer:
Generating Personalized Insulin Treatments Strategies with Deep Conditional Generative Time Series Models. CoRR abs/2309.16521 (2023) - [i19]Amina Mollaysa, Ahmed Allam, Michael Krauthammer:
Attention-based Multi-task Learning for Base Editor Outcome Prediction. CoRR abs/2310.02919 (2023) - [i18]Amina Mollaysa, Ahmed Allam, Michael Krauthammer:
Attention-based Multi-task Learning for Base Editor Outcome Prediction. CoRR abs/2311.07636 (2023) - [i17]Xingyu Chen, Xiaochen Zheng, Amina Mollaysa, Manuel Schürch, Ahmed Allam, Michael Krauthammer:
Dynamic Local Attention with Hierarchical Patching for Irregular Clinical Time Series. CoRR abs/2311.07744 (2023) - [i16]Cécile Trottet, Manuel Schürch, Ahmed Allam, Imon Barua, Liubov Petelytska, Oliver Distler, Anna-Maria Hoffmann-Vold, Michael Krauthammer, EUSTAR collaborators:
Modeling Complex Disease Trajectories using Deep Generative Models with Semi-Supervised Latent Processes. CoRR abs/2311.08149 (2023) - [i15]Amos Calamida, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Michael Krauthammer:
Radiology-Aware Model-Based Evaluation Metric for Report Generation. CoRR abs/2311.16764 (2023) - 2022
- [i14]Kyriakos Schwarz, Alicia Pliego-Mendieta, Lara Planas-Paz, Chantal Pauli, Ahmed Allam, Michael Krauthammer:
DDoS: A Graph Neural Network based Drug Synergy Prediction Algorithm. CoRR abs/2210.00802 (2022) - 2021
- [j23]Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez, Michael Krauthammer:
AttentionDDI: Siamese attention-based deep learning method for drug-drug interaction predictions. BMC Bioinform. 22(1): 412 (2021) - [c32]Farhad Nooralahzadeh, Nicolas Perez Gonzalez, Thomas Frauenfelder, Koji Fujimoto, Michael Krauthammer:
Progressive Transformer-Based Generation of Radiology Reports. EMNLP (Findings) 2021: 2824-2832 - [i13]Farhad Nooralahzadeh, Nicolas Perez Gonzalez, Thomas Frauenfelder, Koji Fujimoto, Michael Krauthammer:
Progressive Transformer-Based Generation of Radiology Reports. CoRR abs/2102.09777 (2021) - 2020
- [j22]Kevin Lopez, Samah J. Fodeh, Ahmed Allam, Cynthia Brandt, Michael Krauthammer:
Reducing Annotation Burden Through Multimodal Learning. Frontiers Big Data 3: 19 (2020) - [j21]Laura Kinkead, Ahmed Allam, Michael Krauthammer:
AutoDiscern: rating the quality of online health information with hierarchical encoder attention-based neural networks. BMC Medical Informatics Decis. Mak. 20(1): 104 (2020) - [c31]Michael H. Böhlen, Oksana Dolmatova, Michael Krauthammer, Alphonse Mariyagnanaseelan, Jonathan Stahl, Timo Surbeck:
Iterations for Propensity Score Matching in MonetDB. ADBIS 2020: 189-203 - [i12]Ahmed Allam, Matthias Dittberner, Anna Sintsova, Dominique Brodbeck, Michael Krauthammer:
Patient Similarity Analysis with Longitudinal Health Data. CoRR abs/2005.06630 (2020) - [i11]Kyriakos Schwarz, Ahmed Allam, Nicolas Andres Perez Gonzalez, Michael Krauthammer:
AttentionDDI: Siamese Attention-based Deep Learning method for drug-drug interaction predictions. CoRR abs/2012.13248 (2020)
2010 – 2019
- 2019
- [i10]Laura Kinkead, Ahmed Allam, Michael Krauthammer:
AutoDiscern: Rating the Quality of Online Health Information with Hierarchical Encoder Attention-based Neural Networks. CoRR abs/1912.12999 (2019) - 2018
- [j20]Connor Sweetnam, Simone Mocellin, Michael Krauthammer, Nathaniel Knopf, Robert Baertsch, Jeff Shrager:
Prototyping a precision oncology 3.0 rapid learning platform. BMC Bioinform. 19(1): 341:1-341:19 (2018) - [i9]Ahmed Allam, Mate Levente Nagy, George R. Thoma, Michael Krauthammer:
Neural networks versus Logistic regression for 30 days all-cause readmission prediction. CoRR abs/1812.09549 (2018) - 2017
- [j19]Ahmed Allam, Michael Krauthammer:
PySeqLab: an open source Python package for sequence labeling and segmentation. Bioinform. 33(21): 3497-3499 (2017) - [j18]Ahmed Allam, Peter Johannes Schulz, Michael Krauthammer:
Toward automated assessment of health Web page quality using the DISCERN instrument. J. Am. Medical Informatics Assoc. 24(3): 481-487 (2017) - [c30]Roxanne Wadia, Mark A. Shifman, Forrest W. Levin, Luis N. Marenco, Cynthia Brandt, Kei-Hoi Cheung, Tamar H. Taddei, Michael Krauthammer:
A Clinical Decision Support System for Monitoring Post-Colonoscopy Patient Follow-Up and Scheduling. CRI 2017 - 2016
- [j17]Xuefeng Wang, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy Ruonan Zhang, R. Scott Powers, Michael Krauthammer:
Global copy number profiling of cancer genomes. Bioinform. 32(6): 926-928 (2016) - [j16]Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier:
Decentralized provenance-aware publishing with nanopublications. PeerJ Comput. Sci. 2: e78 (2016) - [c29]Mark V. Mai, Michael Krauthammer:
Controlling testing volume for respiratory viruses using machine learning and text mining. AMIA 2016 - [i8]Tobias Kuhn, Christine Chichester, Michael Krauthammer, Núria Queralt-Rosinach, Ruben Verborgh, George Giannakopoulos, Axel-Cyrille Ngonga Ngomo, Raffaele Viglianti, Michel Dumontier:
Decentralized provenance-aware publishing with nanopublications. PeerJ Prepr. 4: e1760 (2016) - 2015
- [j15]Matthew E. Holford, Michael Krauthammer:
Mutadelic: mutation analysis using description logic inferencing capabilities. Bioinform. 31(23): 3742-3747 (2015) - [c28]Ahmad C. Bukhari, Mate Levente Nagy, Michael Krauthammer, Paolo Ciccarese, Christopher J. O. Baker:
BIM: an open ontology for the annotation of biomedical images. ICBO 2015 - [c27]Tobias Kuhn, Christine Chichester, Michael Krauthammer, Michel Dumontier:
Publishing Without Publishers: A Decentralized Approach to Dissemination, Retrieval, and Archiving of Data. ISWC (1) 2015: 656-672 - [c26]Syed Ahmad Chan Bukhari, Mate Levente Nagy, Paolo Ciccarese, Michael Krauthammer, Christopher J. O. Baker:
iCyrus: A Semantic Framework for Biomedical Image Discovery. SWAT4LS 2015: 13-22 - 2014
- [j14]Tobias Kuhn, Mate Levente Nagy, Thaibinh Luong, Michael Krauthammer:
Mining images in biomedical publications: Detection and analysis of gel diagrams. J. Biomed. Semant. 5: 10 (2014) - [c25]Syed Ahmad Chan Bukhari, Michael Krauthammer, Christopher J. O. Baker:
SEBI: An Architecture for Biomedical Image Discovery, Interoperability and Reusability Based on Semantic Enrichment. SWAT4LS 2014 - [i7]Tobias Kuhn, Mate Levente Nagy, Thaibinh Luong, Michael Krauthammer:
Mining Images in Biomedical Publications: Detection and Analysis of Gel Diagrams. CoRR abs/1402.2073 (2014) - [i6]Tobias Kuhn, Christine Chichester, Michel Dumontier, Michael Krauthammer:
Publishing without Publishers: a Decentralized Approach to Dissemination, Retrieval, and Archiving of Data. CoRR abs/1411.2749 (2014) - 2013
- [j13]Samah Jamal Fodeh, Cynthia Brandt, Thaibinh Luong, Ali Haddad, Martin H. Schultz, Terrence Murphy, Michael Krauthammer:
Complementary ensemble clustering of biomedical data. J. Biomed. Informatics 46(3): 436-443 (2013) - [c24]Mark V. Mai, Tobias Kuhn, José Costa, Michael Krauthammer:
Nanorecords: A Novel Approach to Communicating High-Level Medical Information. AMIA 2013 - [c23]Jamie P. McCusker, Timothy Lebo, Michael Krauthammer, Deborah L. McGuinness:
Next Generation Cancer Data Discovery, Access, and Integration Using Prizms and Nanopublications. DILS 2013: 105-112 - [c22]Tobias Kuhn, Paolo Emilio Barbano, Mate Levente Nagy, Michael Krauthammer:
Broadening the Scope of Nanopublications. ESWC 2013: 487-501 - [i5]Tobias Kuhn, Paolo Emilio Barbano, Mate Levente Nagy, Michael Krauthammer:
Broadening the Scope of Nanopublications. CoRR abs/1303.2446 (2013) - 2012
- [j12]Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer:
A semantic web framework to integrate cancer omics data with biological knowledge. BMC Bioinform. 13(S-1): S10 (2012) - [c21]Tobias Kuhn, Thaibinh Luong, Michael Krauthammer:
Finding and Accessing Diagrams in Biomedical Publications. AMIA 2012 - [c20]Perry Evans, Michael Krauthammer:
Estimating a gene's mutation burden by the number of observed synonymous base substitutions. BIBM 2012: 1-6 - [c19]Samah Jamal Fodeh, Ali Haddad, Cynthia Brandt, Martin H. Schultz, Michael Krauthammer:
Enhancing Clustering by Exploiting Complementary Data Modalities in the Medical Domain. AIAI (1) 2012: 357-367 - [c18]Tobias Kuhn, Michael Krauthammer:
Underspecified Scientific Claims in Nanopublications. WoLE@ISWC 2012: 29-32 - [i4]Tobias Kuhn, Michael Krauthammer:
Image Mining from Gel Diagrams in Biomedical Publications. CoRR abs/1209.1481 (2012) - [i3]Tobias Kuhn, Michael Krauthammer:
Underspecified Scientific Claims in Nanopublications. CoRR abs/1209.1483 (2012) - 2011
- [j11]Vijay Garla, Yong Kong, Sebastian Szpakowski, Michael Krauthammer:
MU2A - reconciling the genome and transcriptome to determine the effects of base substitutions. Bioinform. 27(3): 416-418 (2011) - 2010
- [j10]Songhua Xu, Michael Krauthammer:
A new pivoting and iterative text detection algorithm for biomedical images. J. Biomed. Informatics 43(6): 924-931 (2010) - [c17]Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer:
Analysis of Cancer Omics Data In A Semantic Web Framework. SWAT4LS 2010 - [i2]Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer:
Analysis Of Cancer Omics Data In A Semantic Web Framework. CoRR abs/1012.1648 (2010)
2000 – 2009
- 2009
- [j9]Jamie P. McCusker, Joshua A. Phillips, Alejandra N. González-Beltrán, Anthony Finkelstein, Michael Krauthammer:
Semantic web data warehousing for caGrid. BMC Bioinform. 10(S-10): 2 (2009) - [j8]Pavithra Shivakumar, Michael Krauthammer:
Structural similarity assessment for drug sensitivity prediction in cancer. BMC Bioinform. 10(S-9): 17 (2009) - [c16]Nam Tran, Pedro Alves, Shuangge Ma, Michael Krauthammer:
Enriching PubMed Related Article Search with Sentence Level Co-citations. AMIA 2009 - [c15]Nam Tran, George Michel, Michael Krauthammer, Richard N. Shiffman:
Embedding the Guideline Elements Model in Web Ontology Language. AMIA 2009 - [c14]Richard N. Shiffman, George Michel, Michael Krauthammer, Norbert E. Fuchs, Kaarel Kaljurand, Tobias Kuhn:
Writing Clinical Practice Guidelines in Controlled Natural Language. CNL 2009: 265-280 - [c13]Richard N. Shiffman, George Michel, Michael Krauthammer, Norbert E. Fuchs, Kaarel Kaljurand, Tobias Kuhn:
Controlled Natural Language for Clinical Practice Guidelines. CNL (Pre-Proceedings) 2009 - 2008
- [j7]Songhua Xu, Jamie P. McCusker, Michael Krauthammer:
Yale Image Finder (YIF): a new search engine for retrieving biomedical images. Bioinform. 24(17): 1968-1970 (2008) - [i1]Michael Krauthammer, Thaibinh Luong:
Term Mapping Using Matrix Operations. Ontologies and Text Mining for Life Sciences 2008 - 2007
- [j6]Andrew K. Smith, Kei-Hoi Cheung, Michael Krauthammer, Martin H. Schultz, Mark Gerstein:
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics. Bioinform. 23(22): 3073-3079 (2007) - 2006
- [j5]Kei-Hoi Cheung, Peishen Qi, David Tuck, Michael Krauthammer:
A semantic web approach to biological pathway data reasoning and integration. J. Web Semant. 4(3): 207-215 (2006) - [c12]Hyung M. Paek, Yacov Kogan, Prem Thomas, Seymour Codish, Michael Krauthammer:
Shallow Semantic Parsing of Randomized Controlled Trial Reports. AMIA 2006 - 2005
- [c11]Yacov Kogan, Nigel Collier, Serguei V. S. Pakhomov, Michael Krauthammer:
Towards Semantic Role Labeling & IE in the Medical Literature. AMIA 2005 - 2004
- [j4]Ivan Iossifov, Michael Krauthammer, Carol Friedman, Vasileios Hatzivassiloglou, Joel S. Bader, Kevin P. White, Andrey Rzhetsky:
Probabilistic inference of molecular networks from noisy data sources. Bioinform. 20(8): 1205-1213 (2004) - [j3]Andrey Rzhetsky, Ivan Iossifov, Tomohiro Koike, Michael Krauthammer, Pauline Kra, Mitzi Morris, Hong Yu, Pablo Ariel Duboué, Wubin Weng, W. John Wilbur:
GeneWays: a system for extracting, analyzing, visualizing, and integrating molecular pathway data. J. Biomed. Informatics 37(1): 43-53 (2004) - [j2]Michael Krauthammer, Goran Nenadic:
Term identification in the biomedical literature. J. Biomed. Informatics 37(6): 512-526 (2004) - 2003
- [c10]Stephen B. Johnson, David A. Campbell, Michael Krauthammer, P. Karina Tulipano, Eneida A. Mendonça, Carol Friedman, George Hripcsak:
A Native XML Database Design for Clinical Document Research. AMIA 2003 - 2002
- [c9]Michael Krauthammer, Stephen B. Johnson, George Hripcsak, David A. Campbell, Carol Friedman:
Representing nested semantic information in a linear string of text using XML. AMIA 2002 - [c8]Michael Krauthammer, Pauline Kra, Ivan Iossifov, Shawn M. Gomez, George Hripcsak, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky:
Of truth and pathways: chasing bits of information through myriads of articles. ISMB 2002: 249-257 - 2001
- [c7]Michael Krauthammer, George Hripcsak:
A knowledge model for the interpretation and visualization of NLP-parsed discharged summaries. AMIA 2001 - [c6]Michael Krauthammer, Pauline Kra, Carol Friedman:
Linking Protein Interaction Data to the MESH Hierarchy. AMIA 2001 - [c5]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:
GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. German Conference on Bioinformatics 2001: 2-5 - [c4]Carol Friedman, Pauline Kra, Hong Yu, Michael Krauthammer, Andrey Rzhetsky:
GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles. ISMB (Supplement of Bioinformatics) 2001: 74-82 - 2000
- [j1]Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James J. Russo, Carol Friedman:
A knowledge model for analysis and simulation of regulatory networks. Bioinform. 16(12): 1120-1128 (2000) - [c3]Michael Krauthammer, Andrey Rzhetsky, Pavel Morozov, Carol Friedman:
Using BLAST, A DNA and Protein Sequence Comparison Tool, for Finding Gene and Protein Names in Journal Articles. AMIA 2000 - [c2]Michael Krauthammer, Nina Wacholder, Stephen B. Johnson, Gai Elhanan, Pat Molholt:
Knowledge Sharing in the Construction of an Anatomical Navigational Ontology. AMIA 2000 - [c1]Nina Wacholder, Judith M. Venuti, Michael Krauthammer, Pat Molholt:
Designing a Navigational Ontology for Browsing and Accessing 3D Anatomical Images. AMIA 2000
Coauthor Index
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