Hagit Shatkay

99 papers A* 2A 5B 1C 2Misc 4Journal 48Unranked 33
YearRankTypeTitle / Venue / Authors
2025 J jnl
BI-LAVA: Biocuration With Hierarchical Image Labelling Through Active Learning and Visual Analytics.
Comput. Graph. Forum
Juan Trelles Trabucco, Andrew Wentzel, William Berrios, Hagit Shatkay, G. Elisabeta Marai
2023 — conf
MouseScholar: Evaluating an Image+Text Search System for Biocuration.
BIBM
Juan Trelles Trabucco, Carla Floricel, Cecilia N. Arighi, Hagit Shatkay, Daniela Raciti, Martin Ringwald, G. Elisabeta Marai
2022 J jnl
Domain-Informed Neural Networks for Interaction Localization Within Astroparticle Experiments.
Frontiers Artif. Intell.
Shixiao Liang, Aaron Higuera, Christina Peters, Venkat Roy, Waheed U. Bajwa, Hagit Shatkay, Christopher D. Tunnell
2022 J jnl
Toward ECG-based analysis of hypertrophic cardiomyopathy: a novel ECG segmentation method for handling abnormalities.
J. Am. Medical Informatics Assoc.
Kasra Nezamabadi, Jacob Mayfield, Pengyuan Li, Gabriela V. Greenland, Sebastian Rodriguez, Bahadir Simsek, Parvin Mousavi, Hagit Shatkay, M. Roselle Abraham
2022 J jnl
Translational drug-interaction corpus.
Database J. Biol. Databases Curation
Shijun Zhang, Heng-Yi Wu, Lei Wang, Gongbo Zhang, Luis M. Rocha, Hagit Shatkay, Lang Li
2021 — conf
ANIMO: Annotation of Biomed Image Modalities.
BIBM
Juan Trelles Trabucco, Pengyuan Li, Cecilia N. Arighi, Daniela Raciti, Hagit Shatkay, G. Elisabeta Marai
2021 J jnl
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of SNOMED codes.
CoRR
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2021 J jnl
Corrigendum to: Utilizing image and caption information for biomedical document classification.
Bioinform.
Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia L. Smith, Martin Ringwald, G. Elisabeta Marai, Cecilia N. Arighi, Hagit Shatkay
2021 J jnl
Domain-informed neural networks for interaction localization within astroparticle experiments.
CoRR
Shixiao Liang, Aaron Higuera, Christina Peters, Venkat Roy, Waheed U. Bajwa, Hagit Shatkay, Christopher D. Tunnell
2021 J jnl
Identifying Ventricular Arrhythmias and Their Predictors by Applying Machine Learning Methods to Electronic Health Records in Patients With Hypertrophic Cardiomyopathy(HCM-VAr-Risk Model).
CoRR
Moumita Bhattacharya, Dai-Yin Lu, Shibani M. Kudchadkar, Gabriela Villarreal Greenland, Prasanth Lingamaneni, Celia P. Corona-Villalobos, Yufan Guan, Joseph E. Marine, Jeffrey E. Olgin, Stefan L. Zimmerman, Theodore P. Abraham, Hagit Shatkay, Maria Roselle Abraham
2021 J jnl
Machine Learning Methods for Identifying Atrial Fibrillation Cases and Their Predictors in Patients With Hypertrophic Cardiomyopathy: The HCM-AF-Risk Model.
CoRR
Moumita Bhattacharya, Dai-Yin Lu, Ioannis Ventoulis, Gabriela V. Greenland, Hulya Yalcin, Yufan Guan, Joseph E. Marine, Jeffrey E. Olgin, Stefan L. Zimmerman, Theodore P. Abraham, M. Roselle Abraham, Hagit Shatkay
2021 J jnl
Utilizing image and caption information for biomedical document classification.
Bioinform.
Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia L. Smith, Martin Ringwald, G. Elisabeta Marai, Cecilia N. Arighi, Hagit Shatkay
2020 J jnl
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).
Database J. Biol. Databases Curation
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay
2020 J jnl
Integrating image caption information into biomedical document classification in support of biocuration.
Database J. Biol. Databases Curation
Xiangying Jiang, Pengyuan Li, James A. Kadin, Judith A. Blake, Martin Ringwald, Hagit Shatkay
2020 — conf
Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks.
BIBM
Juan Trelles Trabucco, Pengyuan Li, Cecilia N. Arighi, Hagit Shatkay, G. Elisabeta Marai
2019 J jnl
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance.
Database J. Biol. Databases Curation
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia N. Arighi, Gongbo Zhang, Hagit Shatkay
2019 J jnl
Approximate Queries and Representations for Large Data Sequences.
CoRR
Hagit Shatkay, Stanley B. Zdonik
2019 — ch.
Biomedical Text Mining.
Encyclopedia of Bioinformatics and Computational Biology (2)
Hagit Shatkay
2019 J jnl
Figure and caption extraction from biomedical documents.
Bioinform.
Pengyuan Li, Xiangying Jiang, Hagit Shatkay
2018 J jnl
Chronic Kidney Disease stratification using office visit records: Handling data imbalance via hierarchical meta-classification.
BMC Medical Informatics Decis. Mak.
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2018 — conf
Co-occurrence of Medical Conditions: Exposing Patterns Through Probabilistic Topic Modeling.
BCB
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2018 J jnl
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of snomed codes.
J. Biomed. Informatics
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2018 J jnl
Compound image segmentation of published biomedical figures.
Bioinform.
Pengyuan Li, Xiangying Jiang, Chandra Kambhamettu, Hagit Shatkay
2018 A conf
Extracting Figures and Captions from Scientific Publications.
CIKM
Pengyuan Li, Xiangying Jiang, Hagit Shatkay
2018 — conf
Identifying Experimental Evidence in Biomedical Abstracts Relevant to Drug-Drug Interactions.
BCB
Gongbo Zhang, Debarati Roychowdhury, Pengyuan Li, Heng-Yi Wu, Shijun Zhang, Lang Li, Hagit Shatkay
2018 J jnl
Stochastic Modeling of Temporal Enhanced Ultrasound: Impact of Temporal Properties on Prostate Cancer Characterization.
IEEE Trans. Biomed. Eng.
Layan Nahlawi, Caroline Barcelos Gonçalves, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Hagit Shatkay, Parvin Mousavi
2017 — conf
Assessing chronic kidney disease from office visit records using hierarchical meta-classification of an imbalanced dataset.
BIBM
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2017 J jnl
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD).
Database J. Biol. Databases Curation
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay
2017 J jnl
Identifying Growth-Patterns in Children by Applying Cluster analysis to Electronic Medical Records.
CoRR
Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay
2017 J jnl
Identifying Patterns of Associated-Conditions through Topic Models of Electronic Medical Records.
CoRR
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2017 — conf
Identifying articles relevant to drug-drug interaction: Addressing class imbalance.
BIBM
Gongbo Zhang, Moumita Bhattacharya, Heng-Yi Wu, Pengyuan Li, Lang Li, Hagit Shatkay
2017 — conf
Models of temporal enhanced ultrasound data for prostate cancer diagnosis: the impact of time-series order.
Image-Guided Procedures
Layan Nahlawi, Caroline Barcelos Gonçalves, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi, Hagit Shatkay
2017 — conf
Segmenting Compound Biomedical Figures into Their Constituent Panels.
CLEF
Pengyuan Li, Xiangying Jiang, Chandra Kambhamettu, Hagit Shatkay
2016 — conf
Identifying patterns of associated-conditions through topic models of Electronic Medical Records.
BIBM
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
2016 A conf
Improved Multi-Label Classification Using Inter-Dependence Structure via a Generative Mixture Model.
ECAI
Ramanuja Simha, Hagit Shatkay
2016 — conf
Prostate Cancer: Improved Tissue Characterization by Temporal Modeling of Radio-Frequency Ultrasound Echo Data.
MICCAI (1)
Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Hagit Shatkay, Parvin Mousavi
2016 — conf
UDEL CIS Working Notes in ImageCLEF 2016.
CLEF (Working Notes)
Pengyuan Li, Scott Sorensen, Abhishek Kolagunda, Xiangying Jiang, Xiaolong Wang, Chandra Kambhamettu, Hagit Shatkay
2015 — conf
CIS UDEL Working Notes on ImageCLEF 2015: Compound Figure Detection Task.
CLEF (Working Notes)
Xiaolong Wang, Xiangying Jiang, Abhishek Kolagunda, Hagit Shatkay, Chandra Kambhamettu
2015 J jnl
Protein (multi-)location prediction: utilizing interdependencies via a generative model.
Bioinform.
Ramanuja Simha, Sebastian Briesemeister, Oliver Kohlbacher, Hagit Shatkay
2015 J jnl
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.
Bioinform.
Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia
2015 — conf
Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancer.
BIBM
Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi, Hagit Shatkay
2015 B conf
Utilizing image-based features in biomedical document classification.
ICIP
Kaidi Ma, Hogyeong Jeong, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu, Hagit Shatkay
2014 — conf
Identifying growth-patterns in children by applying cluster analysis to electronic medical records.
BIBM
Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay
2014 — conf
Identifying hypertrophic cardiomyopathy patients by classifying individual heartbeats from 12-lead ECG signals.
BIBM
Quazi Abidur Rahman, Larisa G. Tereshchenko, Matthew Kongkatong, Theodore Abraham, M. Roselle Abraham, Hagit Shatkay
2014 J jnl
Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework.
Algorithms Mol. Biol.
Ramanuja Simha, Hagit Shatkay
2014 — conf
Using unsupervised learning to determine risk level for left ventricular diastolic dysfunction.
BIBM
Kaidi Ma, Marco Canepa, James B. Strait, Hagit Shatkay
2013 J jnl
Learning Hidden Markov Models with Geometrical Constraints
CoRR
Hagit Shatkay
2013 J jnl
Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework.
CoRR
Ramanuja Simha, Hagit Shatkay
2013 C conf
Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework.
WABI
Ramanuja Simha, Hagit Shatkay
2013 J jnl
Protein Function Prediction using Text-based Features extracted from the Biomedical Literature: The CAFA Challenge.
BMC Bioinform.
Andrew Wong, Hagit Shatkay
2013 — conf
What We Found on Our Way to Building a Classifier: A Critical Analysis of the AHA Screening Questionnaire.
Brain and Health Informatics
Quazi Abidur Rahman, Sivajothi Kanagalingam, Aurelio Pinheiro, Theodore Abraham, Hagit Shatkay
2012 — conf
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia.
BIBM
Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu
2012 J jnl
Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature.
BMC Bioinform.
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha
2012 — conf
Detecting and using document structure in scientific text.
IHI
Anita de Waard, Sophia Ananiadou, Maryann E. Martone, Ágnes Sándor, Hagit Shatkay
2012 — conf
OCR-Based Image Features for Biomedical Image and Article Classification: Identifying Documents Relevant to Genomic Cis-Regulatory Elements.
AAAI Fall Symposium: Information Retrieval and Knowledge Discovery in Biomedical Text
Hagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu
2012 — conf
OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements.
BCB
Hagit Shatkay, Ramya Narayanaswamy, Santosh S. Nagaral, Na Harrington, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Tim Johnstone, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu
2011 J jnl
A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature
CoRR
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha
2011 J jnl
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature.
BMC Bioinform.
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha
2011 — conf
An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents.
BIBM
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Hongzhan Huang, Hagit Shatkay, Cathy H. Wu
2011 J jnl
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap
CoRR
Leslie Pack Kaelbling, Hagit Shatkay
2011 J jnl
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
BMC Bioinform.
Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sérgio Matos, Sun Kim, W. John Wilbur, Luis M. Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
2010 — ed.
Advances in Bioinformatics - 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010), Guimarães, Portugal, 16-18 June 2010
IWPACBB
Miguel P. Rocha, Florentino Fernández Riverola, Hagit Shatkay, Juan M. Corchado
2010 A conf
DTMBIO workshop summary.
CIKM
Hagit Shatkay, Doheon Lee, Min Song, Shamkant B. Navathe
2010 — ed.
Linking Literature, Information, and Knowledge for Biology - Workshop of the BioLink Special Interest Group, ISMB/ECCB 2009, Stockholm, Sweden, June 28-29, 2009, Revised Selected Papers
BioLINK@ISMB/ECCB
Christian Blaschke, Hagit Shatkay
2009 J jnl
An integrative scoring system for ranking SNPs by their potential deleterious effects.
Bioinform.
Phil Hyoun Lee, Hagit Shatkay
2009 J jnl
Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life.
BMC Bioinform.
Phil Hyoun Lee, Jae-Yoon Jung, Hagit Shatkay
2009 J jnl
How to Get the Most out of Your Curation Effort.
PLoS Comput. Biol.
Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur
2008 Misc conf
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location.
Pacific Symposium on Biocomputing
Scott Brady, Hagit Shatkay
2008 J jnl
F-SNP: computationally predicted functional SNPs for disease association studies.
Nucleic Acids Res.
Phil Hyoun Lee, Hagit Shatkay
2008 J jnl
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users.
Bioinform.
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur
2008 — conf
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology.
BioLINK@ISMB/ECCB
Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia
2008 Misc conf
Ranking single nucleotide polymorphisms by potential deleterious effects.
AMIA
Phil Hyoun Lee, Hagit Shatkay
2008 J jnl
Ranking single nucleotide polymorphisms by potential deleterious effects.
BMC Bioinform.
Phil Hyoun Lee, Hagit Shatkay
2008 — conf
Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...).
BioLINK@ISMB/ECCB
Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay
2007 J jnl
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data.
Bioinform.
Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher
2007 C conf
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies.
WABI
Phil Hyoun Lee, Hagit Shatkay
2007 Misc conf
Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders.
AMIA
Jess J. Shen, Phil Hyoun Lee, Jeanette J. A. Holden, Hagit Shatkay
2006 — conf
BNTagger: improved tagging SNP selection using Bayesian networks.
ISMB (Supplement of Bioinformatics)
Phil Hyoun Lee, Hagit Shatkay
2006 — conf
Breast Cancer Prognosis via Gaussian Mixture Regression.
CCECE
Tiago H. Falk, Hagit Shatkay, Wai-Yip Chan
2006 J jnl
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier.
Bioinform.
Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe
2006 J jnl
Discovering semantic features in the literature: a foundation for building functional associations.
BMC Bioinform.
Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano
2006 — conf
Exploring a new space of features for document classification: figure clustering.
CASCON
Nawei Chen, Hagit Shatkay, Dorothea Blostein
2006 — conf
Integrating image data into biomedical text categorization.
ISMB (Supplement of Bioinformatics)
Hagit Shatkay, Nawei Chen, Dorothea Blostein
2006 J jnl
New directions in biomedical text annotation: definitions, guidelines and corpus construction.
BMC Bioinform.
W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay
2006 Misc conf
Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data .
Pacific Symposium on Biocomputing
Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay
2006 — conf
Use of Figures in Literature Mining for Biomedical Digital Libraries.
DIAL
Nawei Chen, Hagit Shatkay, Dorothea Blostein
2005 — conf
Applying Probabilistic Thematic Clustering for Classification in the TREC 2005 Genomics Track.
TREC
Z. H. Zheng, Scott Brady, Akash Garg, Hagit Shatkay
2005 J jnl
Hairpins in bookstacks: Information retrieval from biomedical text.
Briefings Bioinform.
Hagit Shatkay
2005 — ed.
Proceedings of the ACL-ISMB Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics@ISMB 2005, Detroit, MI, USA June 24, 2005
LBLODMBS@ISMB
K. Bretonnel Cohen, Lynette Hirschman, Hagit Shatkay, Christian Blaschke
2004 J jnl
ThurGood: Evaluating Assembly-to-Assembly Mapping.
J. Comput. Biol.
Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton
2003 J jnl
Mining the Biomedical Literature in the Genomic Era: An Overview.
J. Comput. Biol.
Hagit Shatkay, Ronen Feldman
2002 J jnl
Information Retrieval Meets Gene Analysis.
IEEE Intell. Syst.
Hagit Shatkay, Stephen Edwards, Mark Boguski
2002 J jnl
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap.
J. Artif. Intell. Res.
Hagit Shatkay, Leslie Pack Kaelbling
2000 — conf
Finding Themes in Medline Documents: Probabilistic Similarity Search.
ADL
Hagit Shatkay, W. John Wilbur
2000 A conf
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis.
ISMB
Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski
1999 A conf
Learning Hidden Markov Models with Geometrical Constraints.
UAI
Hagit Shatkay
1998 A* conf
Heading in the Right Direction.
ICML
Hagit Shatkay, Leslie Pack Kaelbling
1997 — conf
Learning Topological Maps with Weak Local Odometric Information.
IJCAI (2)
Hagit Shatkay, Leslie Pack Kaelbling
1996 A* conf
Approximate Queries and Representations for Large Data Sequences.
ICDE
Hagit Shatkay, Stanley B. Zdonik