Hagit Shatkay

Publication Activity (10 Years)

Years Active: 1996-2023
Publications (10 Years): 40

Top Topics

Temporal Properties

Document Classification

Prostate Cancer

Machine Learning Methods

Top Venues

Database J. Biol. Databases Curation

Publications

Juan Trelles Trabucco, Carla Floricel, Cecilia N. Arighi, Hagit Shatkay, Daniela Raciti, Martin Ringwald, G. Elisabeta Marai
MouseScholar: Evaluating an Image+Text Search System for Biocuration. BIBM (2023)
Shixiao Liang, Aaron Higuera, Christina Peters, Venkat Roy, Waheed U. Bajwa, Hagit Shatkay, Christopher D. Tunnell
Domain-Informed Neural Networks for Interaction Localization Within Astroparticle Experiments. Frontiers Artif. Intell. 5 (2022)
Shijun Zhang, Heng-Yi Wu, Lei Wang, Gongbo Zhang, Luis M. Rocha, Hagit Shatkay, Lang Li
Translational drug-interaction corpus. Database J. Biol. Databases Curation 2022 (2022) (2022)
Kasra Nezamabadi, Jacob Mayfield, Pengyuan Li, Gabriela V. Greenland, Sebastian Rodriguez, Bahadir Simsek, Parvin Mousavi, Hagit Shatkay, M. Roselle Abraham
Toward ECG-based analysis of hypertrophic cardiomyopathy: a novel ECG segmentation method for handling abnormalities. J. Am. Medical Informatics Assoc. 29 (11) (2022)
Shixiao Liang, Aaron Higuera, Christina Peters, Venkat Roy, Waheed U. Bajwa, Hagit Shatkay, Christopher D. Tunnell
Domain-informed neural networks for interaction localization within astroparticle experiments. CoRR (2021)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of SNOMED codes. CoRR (2021)
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
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 (2021)
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
Machine Learning Methods for Identifying Atrial Fibrillation Cases and Their Predictors in Patients With Hypertrophic Cardiomyopathy: The HCM-AF-Risk Model. CoRR (2021)
Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia L. Smith, Martin Ringwald, G. Elisabeta Marai, Cecilia N. Arighi, Hagit Shatkay
Corrigendum to: Utilizing image and caption information for biomedical document classification. Bioinform. 37 (19) (2021)
Pengyuan Li, Xiangying Jiang, Gongbo Zhang, Juan Trelles Trabucco, Daniela Raciti, Cynthia L. Smith, Martin Ringwald, G. Elisabeta Marai, Cecilia N. Arighi, Hagit Shatkay
Utilizing image and caption information for biomedical document classification. Bioinform. 37 (Supplement) (2021)
Juan Trelles Trabucco, Pengyuan Li, Cecilia N. Arighi, Daniela Raciti, Hagit Shatkay, G. Elisabeta Marai
ANIMO: Annotation of Biomed Image Modalities. BIBM (2021)
Xiangying Jiang, Pengyuan Li, James A. Kadin, Judith A. Blake, Martin Ringwald, Hagit Shatkay
Integrating image caption information into biomedical document classification in support of biocuration. Database J. Biol. Databases Curation 2020 (2020)
Juan Trelles Trabucco, Pengyuan Li, Cecilia N. Arighi, Hagit Shatkay, G. Elisabeta Marai
Modality-Classification of Microscopy Images Using Shallow Variants of Deep Networks. BIBM (2020)
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2020 (2020)
Hagit Shatkay, Stanley B. Zdonik
Approximate Queries and Representations for Large Data Sequences. CoRR (2019)
Pengyuan Li, Xiangying Jiang, Hagit Shatkay
Figure and caption extraction from biomedical documents. Bioinform. 35 (21) (2019)
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia N. Arighi, Gongbo Zhang, Hagit Shatkay
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. Database J. Biol. Databases Curation 2019 (2019)
Pengyuan Li, Xiangying Jiang, Hagit Shatkay
Extracting Figures and Captions from Scientific Publications. CIKM (2018)
Pengyuan Li, Xiangying Jiang, Chandra Kambhamettu, Hagit Shatkay
Compound image segmentation of published biomedical figures. Bioinform. 34 (7) (2018)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Co-occurrence of medical conditions: Exposing patterns through probabilistic topic modeling of snomed codes. J. Biomed. Informatics 82 (2018)
Gongbo Zhang, Debarati Roychowdhury, Pengyuan Li, Heng-Yi Wu, Shijun Zhang, Lang Li, Hagit Shatkay
Identifying Experimental Evidence in Biomedical Abstracts Relevant to Drug-Drug Interactions. BCB (2018)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Co-occurrence of Medical Conditions: Exposing Patterns Through Probabilistic Topic Modeling. BCB (2018)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Chronic Kidney Disease stratification using office visit records: Handling data imbalance via hierarchical meta-classification. BMC Medical Informatics Decis. Mak. 18 (S-4) (2018)
Layan Nahlawi, Caroline Goncalves, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Hagit Shatkay, Parvin Mousavi
Stochastic Modeling of Temporal Enhanced Ultrasound: Impact of Temporal Properties on Prostate Cancer Characterization. IEEE Trans. Biomed. Eng. 65 (8) (2018)
Pengyuan Li, Xiangying Jiang, Chandra Kambhamettu, Hagit Shatkay
Segmenting Compound Biomedical Figures into Their Constituent Panels. CLEF (2017)
Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay
Identifying Growth-Patterns in Children by Applying Cluster analysis to Electronic Medical Records. CoRR (2017)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Identifying Patterns of Associated-Conditions through Topic Models of Electronic Medical Records. CoRR (2017)
Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay
Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). Database J. Biol. Databases Curation 2017 (2017)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Assessing chronic kidney disease from office visit records using hierarchical meta-classification of an imbalanced dataset. BIBM (2017)
Gongbo Zhang, Moumita Bhattacharya, Heng-Yi Wu, Pengyuan Li, Lang Li, Hagit Shatkay
Identifying articles relevant to drug-drug interaction: Addressing class imbalance. BIBM (2017)
Layan Nahlawi, Caroline Goncalves, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi, Hagit Shatkay
Models of temporal enhanced ultrasound data for prostate cancer diagnosis: the impact of time-series order. Medical Imaging: Image-Guided Procedures (2017)
Pengyuan Li, Scott Sorensen, Abhishek Kolagunda, Xiangying Jiang, Xiaolong Wang, Chandra Kambhamettu, Hagit Shatkay
UDEL CIS Working Notes in ImageCLEF 2016. CLEF (Working Notes) (2016)
Moumita Bhattacharya, Claudine Jurkovitz, Hagit Shatkay
Identifying patterns of associated-conditions through topic models of Electronic Medical Records. BIBM (2016)
Ramanuja Simha, Hagit Shatkay
Improved Multi-Label Classification Using Inter-Dependence Structure via a Generative Mixture Model. ECAI (2016)
Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Hagit Shatkay, Parvin Mousavi
Prostate Cancer: Improved Tissue Characterization by Temporal Modeling of Radio-Frequency Ultrasound Echo Data. MICCAI (1) (2016)
Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Parvin Mousavi, Hagit Shatkay
Using Hidden Markov Models to capture temporal aspects of ultrasound data in prostate cancer. BIBM (2015)
Kaidi Ma, Hogyeong Jeong, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu, Hagit Shatkay
Utilizing image-based features in biomedical document classification. ICIP (2015)
Xiaolong Wang, Xiangying Jiang, Abhishek Kolagunda, Hagit Shatkay, Chandra Kambhamettu
CIS UDEL Working Notes on ImageCLEF 2015: Compound Figure Detection Task. CLEF (Working Notes) (2015)
Ramanuja Simha, Sebastian Briesemeister, Oliver Kohlbacher, Hagit Shatkay
Protein (multi-)location prediction: utilizing interdependencies via a generative model. Bioinform. 31 (12) (2015)
Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. Bioinform. 31 (2) (2015)
Kaidi Ma, Marco Canepa, James B. Strait, Hagit Shatkay
Using unsupervised learning to determine risk level for left ventricular diastolic dysfunction. BIBM (2014)
Moumita Bhattacharya, Deborah Ehrenthal, Hagit Shatkay
Identifying growth-patterns in children by applying cluster analysis to electronic medical records. BIBM (2014)
Quazi Abidur Rahman, Larisa G. Tereshchenko, Matthew Kongkatong, Theodore Abraham, M. Roselle Abraham, Hagit Shatkay
Identifying hypertrophic cardiomyopathy patients by classifying individual heartbeats from 12-lead ECG signals. BIBM (2014)
Ramanuja Simha, Hagit Shatkay
Protein (multi-)location prediction: using location inter-dependencies in a probabilistic framework. Algorithms Mol. Biol. 9 (2014)
Ramanuja Simha, Hagit Shatkay
Protein (Multi-)Location Prediction: Using Location Inter-Dependencies in a Probabilistic Framework. CoRR (2013)
Hagit Shatkay
Learning Hidden Markov Models with Geometrical Constraints CoRR (2013)
Ramanuja Simha, Hagit Shatkay
Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework. WABI (2013)
Quazi Abidur Rahman, Sivajothi Kanagalingam, Aurelio Pinheiro, Theodore Abraham, Hagit Shatkay
What We Found on Our Way to Building a Classifier: A Critical Analysis of the AHA Screening Questionnaire. Brain and Health Informatics (2013)
Andrew Wong, Hagit Shatkay
Protein Function Prediction using Text-based Features extracted from the Biomedical Literature: The CAFA Challenge. BMC Bioinform. 14 (S-3) (2013)
Anita de Waard, Sophia Ananiadou, Maryann E. Martone, Ágnes Sándor, Hagit Shatkay
Detecting and using document structure in scientific text. IHI (2012)
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis Mateus Rocha
Correction: A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. BMC Bioinform. 13 (2012)
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
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 (2012)
Xia Bi, Hongzhan Huang, Sherri Matis-Mitchell, Peter B. McGarvey, Manabu Torii, Hagit Shatkay, Cathy H. Wu
Building a classifier for identifying sentences pertaining to disease-drug relationships in tardive dyskinesia. BIBM (2012)
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
OCR-based image features for biomedical image and article classification: identifying documents relevant to cis-regulatory elements. BCB (2012)
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 Mateus Rocha, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinform. 12 (S-8) (2011)
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis Mateus Rocha
A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. BMC Bioinform. 12 (S-8) (2011)
Leslie Pack Kaelbling, Hagit Shatkay
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap CoRR (2011)
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Hongzhan Huang, Hagit Shatkay, Cathy H. Wu
An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents. BIBM (2011)
Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis Mateus Rocha
A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature CoRR (2011)
Hagit Shatkay, Doheon Lee, Min Song, Shamkant B. Navathe
DTMBIO workshop summary. CIKM (2010)
Andrey Rzhetsky, Hagit Shatkay, W. John Wilbur
How to Get the Most out of Your Curation Effort. PLoS Comput. Biol. 5 (5) (2009)
Phil Hyoun Lee, Hagit Shatkay
An integrative scoring system for ranking SNPs by their potential deleterious effects. Bioinform. 25 (8) (2009)
Phil Hyoun Lee, Jae-Yoon Jung, Hagit Shatkay
Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life. BMC Bioinform. 10 (S-13) (2009)
Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia
Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. BioLINK@ISMB/ECCB (2008)
Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay
Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). BioLINK@ISMB/ECCB (2008)
Phil Hyoun Lee, Hagit Shatkay
F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res. 36 (Database-Issue) (2008)
Scott Brady, Hagit Shatkay
EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location. Pacific Symposium on Biocomputing (2008)
Phil Hyoun Lee, Hagit Shatkay
Ranking single nucleotide polymorphisms by potential deleterious effects. BMC Bioinform. 9 (S-10) (2008)
Phil Hyoun Lee, Hagit Shatkay
Ranking single nucleotide polymorphisms by potential deleterious effects. AMIA (2008)
Hagit Shatkay, Fengxia Pan, Andrey Rzhetsky, W. John Wilbur
Multi-dimensional classification of biomedical text: Toward automated, practical provision of high-utility text to diverse users. Bioinform. 24 (18) (2008)
Hagit Shatkay, Annette Höglund, Scott Brady, Torsten Blum, Pierre Dönnes, Oliver Kohlbacher
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data. Bioinform. 23 (11) (2007)
Jess J. Shen, Phil Hyoun Lee, Jeanette J. A. Holden, Hagit Shatkay
Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders. AMIA (2007)
Phil Hyoun Lee, Hagit Shatkay
Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies. WABI (2007)
Malik Yousef, Michael Nebozhyn, Hagit Shatkay, Stathis Kanterakis, Louise C. Showe, Michael K. Showe
Combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier. Bioinform. 22 (11) (2006)
Nawei Chen, Hagit Shatkay, Dorothea Blostein
Use of Figures in Literature Mining for Biomedical Digital Libraries. DIAL (2006)
Tiago H. Falk, Hagit Shatkay, Wai-Yip Chan
Breast Cancer Prognosis via Gaussian Mixture Regression. CCECE (2006)
Phil Hyoun Lee, Hagit Shatkay
BNTagger: improved tagging SNP selection using Bayesian networks. ISMB (Supplement of Bioinformatics) (2006)
Nawei Chen, Hagit Shatkay, Dorothea Blostein
Exploring a new space of features for document classification: figure clustering. CASCON (2006)
Monica Chagoyen, Pedro Carmona-Saez, Hagit Shatkay, José María Carazo, Alberto D. Pascual-Montano
Discovering semantic features in the literature: a foundation for building functional associations. BMC Bioinform. 7 (2006)
Annette Höglund, Torsten Blum, Scott Brady, Pierre Dönnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay
Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . Pacific Symposium on Biocomputing (2006)
W. John Wilbur, Andrey Rzhetsky, Hagit Shatkay
New directions in biomedical text annotation: definitions, guidelines and corpus construction. BMC Bioinform. 7 (2006)
Hagit Shatkay, Nawei Chen, Dorothea Blostein
Integrating image data into biomedical text categorization. ISMB (Supplement of Bioinformatics) (2006)
Z. H. Zheng, Scott Brady, A. Garg, Hagit Shatkay
Applying Probabilistic Thematic Clustering for Classification in the TREC 2005 Genomics Track. TREC (2005)
Hagit Shatkay
Hairpins in bookstacks: Information retrieval from biomedical text. Briefings Bioinform. 6 (3) (2005)
Hagit Shatkay, Jason R. Miller, Clark M. Mobarry, Michael Flanigan, Shibu Yooseph, Granger G. Sutton
ThurGood: Evaluating Assembly-to-Assembly Mapping. J. Comput. Biol. 11 (5) (2004)
Hagit Shatkay, Ronen Feldman
Mining the Biomedical Literature in the Genomic Era: An Overview. J. Comput. Biol. 10 (6) (2003)
Hagit Shatkay, Leslie Pack Kaelbling
Learning Geometrically-Constrained Hidden Markov Models for Robot Navigation: Bridging the Topological-Geometrical Gap. J. Artif. Intell. Res. 16 (2002)
Hagit Shatkay, Stephen Edwards, Mark Boguski
Information Retrieval Meets Gene Analysis. IEEE Intell. Syst. 17 (2) (2002)
Hagit Shatkay, W. John Wilbur
Finding Themes in Medline Documents: Probabilistic Similarity Search. ADL (2000)
Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski
Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. ISMB (2000)
Hagit Shatkay
Learning Hidden Markov Models with Geometrical Constraints. UAI (1999)
Hagit Shatkay, Leslie Pack Kaelbling
Heading in the Right Direction. ICML (1998)
Hagit Shatkay, Leslie Pack Kaelbling
Learning Topological Maps with Weak Local Odometric Information. IJCAI (2) (1997)
Hagit Shatkay, Stanley B. Zdonik
Approximate Queries and Representations for Large Data Sequences. ICDE (1996)