K. Vijay-Shanker

ORCID

Publication Activity (10 Years)

Years Active: 1985-2023
Publications (10 Years): 31

Top Venues

CoRR

Database J. Biol. Databases Curation

ICPC

BMC Bioinform.

Publications

Sultan Alrowili, K. Vijay-Shanker
ArTrivia: Harvesting Arabic Wikipedia to Build A New Arabic Question Answering Dataset. ArabicNLP (2023)
Mehmet Efruz Karabulut, K. Vijay-Shanker
Sectioning biomedical abstracts using pointer networks. BCB (2023)
Sultan Alrowili, K. Vijay-Shanker
Exploring Biomedical Question Answering with BioM-Transformers At BioASQ10B challenge: Findings and Techniques. CLEF (Working Notes) (2022)
Peng Su, K. Vijay-Shanker
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction. BMC Bioinform. 23 (1) (2022)
Bashar Alhafni, Nizar Habash, Houda Bouamor, Ossama Obeid, Sultan Alrowili, Daliyah Alzeer, Khawlah M. Alshanqiti, Ahmed ElBakry, Muhammad N. ElNokrashy, Mohamed Gabr, Abderrahmane Issam, Abdelrahim Qaddoumi, K. Vijay-Shanker, Mahmoud Zyate
The Shared Task on Gender Rewriting. CoRR (2022)
Mehmet Efruz Karabulut, K. Vijay-Shanker
Sectioning of Biomedical Abstracts: A Sequence of Sequence Classification Task. CoRR (2022)
Peng Su, Yifan Peng, K. Vijay-Shanker
Improving BERT Model Using Contrastive Learning for Biomedical Relation Extraction. BioNLP@NAACL-HLT (2021)
Mehmet Efruz Karabulut, K. Vijay-Shanker, Yifan Peng
CU-UD: text-mining drug and chemical-protein interactions with ensembles of BERT-based models. CoRR (2021)
Peng Su, Yifan Peng, K. Vijay-Shanker
Improving BERT Model Using Contrastive Learning for Biomedical Relation Extraction. CoRR (2021)
Debarati Roychowdhury, Samir Gupta, Xihan Qin, Cecilia N. Arighi, K. Vijay-Shanker
emiRIT: a text-mining-based resource for microRNA information. Database J. Biol. Databases Curation 2021 (2021)
Peng Su, K. Vijay-Shanker
Adversarial Learning for Supervised and Semi-supervised Relation Extraction in Biomedical Literature. CoRR (2020)
Peng Su, K. Vijay-Shanker
Investigation of BERT Model on Biomedical Relation Extraction Based on Revised Fine-tuning Mechanism. BIBM (2020)
Eeshita Biswas, Mehmet Efruz Karabulut, Lori L. Pollock, K. Vijay-Shanker
Achieving Reliable Sentiment Analysis in the Software Engineering Domain using BERT. ICSME (2020)
Peng Su, K. Vijay-Shanker
Investigation of BERT Model on Biomedical Relation Extraction Based on Revised Fine-tuning Mechanism. CoRR (2020)
Eeshita Biswas, K. Vijay-Shanker, Lori L. Pollock
Exploring word embedding techniques to improve sentiment analysis of software engineering texts. MSR (2019)
Hongzhan Huang, Cecilia N. Arighi, Karen E. Ross, Jia Ren, Gang Li, Sheng-Chih Chen, Qinghua Wang, Julie Cowart, K. Vijay-Shanker, Cathy H. Wu
iPTMnet: an integrated resource for protein post-translational modification network discovery. Nucleic Acids Res. 46 (Database-Issue) (2018)
Yu Hu, Hayley Dingerdissen, Samir Gupta, Robel Y. Kahsay, K. Vijay-Shanker, Quan Wan, Cheng Yan, Raja Mazumder
Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis. Comput. Biol. Medicine 103 (2018)
Jia Ren, Gang Li, Karen Ross, Cecilia N. Arighi, Peter B. McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K. Vijay-Shanker, Cathy H. Wu
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. Database J. Biol. Databases Curation 2018 (2018)
Ruoyao Ding, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker
Automatic gene annotation using GO terms from cellular component domain. BMC Medical Informatics Decis. Mak. 18 (S-5) (2018)
Ruoyao Ding, Xiaoyi Pan, Yingying Qu, Cathy H. Wu, K. Vijay-Shanker
Protein Complex Mention Recognition with Web-Based Knowledge Learning. SETE@ICWL (2018)
Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker
DEXTER: Disease-Expression Relation Extraction from Text. Database J. Biol. Databases Curation 2018 (2018)
Gang Li, Cathy H. Wu, K. Vijay-Shanker
Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction. BioNLP (2017)
Xiaoran Wang, Lori L. Pollock, K. Vijay-Shanker
Automatically generating natural language descriptions for object-related statement sequences. SANER (2017)
Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H. Wu, K. Vijay-Shanker, Cecilia N. Arighi
eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. Database J. Biol. Databases Curation 2017 (2017)
A. S. M. Ashique Mahmood, Gang Li, Shruti Rao, Peter B. McGarvey, Cathy H. Wu, Subha Madhavan, K. Vijay-Shanker
UD_GU_BioTM at TREC 2017: Precision Medicine Track. TREC (2017)
Liang Sun, Yongnan Zhu, A. S. M. Ashique Mahmood, Catalina O. Tudor, Jia Ren, K. Vijay-Shanker, Jian Chen, Carl J. Schmidt
WebGIVI: a web-based gene enrichment analysis and visualization tool. BMC Bioinform. 18 (1) (2017)
Samir Gupta, A. S. M. Ashique Mahmood, Karen Ross, Cathy H. Wu, K. Vijay-Shanker
Identifying Comparative Structures in Biomedical Text. BioNLP (2017)
Karen E. Ross, Darren A. Natale, Cecilia N. Arighi, Sheng-Chih Chen, Hongzhan Huang, Gang Li, Jia Ren, Michael Wang, K. Vijay-Shanker, Cathy H. Wu
Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology. ICBO/BioCreative (2016)
Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker
miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases. J. Biomed. Semant. 7 (2016)
Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016)
Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. Database J. Biol. Databases Curation 2016 (2016)
Yifan Peng, Samir Gupta, Cathy H. Wu, K. Vijay-Shanker
An extended dependency graph for relation extraction in biomedical texts. BioNLP@IJCNLP (2015)
Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu, Cecilia N. Arighi
Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system. Database J. Biol. Databases Curation 2015 (2015)
Ryan Serva, Zachary R. Senzer, Lori L. Pollock, K. Vijay-Shanker
Automatically Mining Negative Code Examples from Software Developer Q & A Forums. ASE Workshops (2015)
Manabu Torii, Cecilia N. Arighi, Gang Li, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (1) (2015)
Xiaoran Wang, Lori L. Pollock, K. Vijay-Shanker
Developing a model of loop actions by mining loop characteristics from a large code corpus. ICSME (2015)
Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker
miRTex: A Text Mining System for miRNA-Gene Relation Extraction. PLoS Comput. Biol. 11 (9) (2015)
Michael Bloodgood, K. Vijay-Shanker
An Approach to Reducing Annotation Costs for BioNLP. CoRR (2014)
Michael Bloodgood, K. Vijay-Shanker
Taking into Account the Differences between Actively and Passively Acquired Data: The Case of Active Learning with Support Vector Machines for Imbalanced Datasets. CoRR (2014)
Emily Hill, David W. Binkley, Dawn J. Lawrie, Lori L. Pollock, K. Vijay-Shanker
An empirical study of identifier splitting techniques. Empir. Softw. Eng. 19 (6) (2014)
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. Database J. Biol. Databases Curation 2014 (2014)
Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. Database J. Biol. Databases Curation 2014 (2014)
Yifan Peng, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems. BMC Bioinform. 15 (2014)
Xiaoran Wang, Lori L. Pollock, K. Vijay-Shanker
Automatic Segmentation of Method Code into Meaningful Blocks: Design and Evaluation. J. Softw. Evol. Process. 26 (1) (2014)
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
Rapid Adaptation of POS Tagging for Domain Specific Uses. CoRR (2014)
Michael Bloodgood, K. Vijay-Shanker
A Method for Stopping Active Learning Based on Stabilizing Predictions and the Need for User-Adjustable Stopping. CoRR (2014)
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Catalina O. Tudor, Manabu Torii, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
A framework for biomedical figure segmentation towards image-based document retrieval. BMC Syst. Biol. 7 (S-4) (2013)
Laura Moreno, Andrian Marcus, Lori L. Pollock, K. Vijay-Shanker
JSummarizer: An automatic generator of natural language summaries for Java classes. ICPC (2013)
David W. Binkley, Dawn J. Lawrie, Lori L. Pollock, Emily Hill, K. Vijay-Shanker
A dataset for evaluating identifier splitters. MSR (2013)
Samir Gupta, Sana Malik, Lori L. Pollock, K. Vijay-Shanker
Part-of-speech tagging of program identifiers for improved text-based software engineering tools. ICPC (2013)
Matthew J. Howard, Samir Gupta, Lori L. Pollock, K. Vijay-Shanker
Automatically mining software-based, semantically-similar words from comment-code mappings. MSR (2013)
Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii, K. Vijay-Shanker, Hongzhan Huang, Cathy H. Wu
An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. BCB (2013)
Emily Hill, David C. Shepherd, Lori L. Pollock, K. Vijay-Shanker
Differentiating Roles of Program Elements in Action-Oriented Concerns. ICSM (2013)
Manabu Torii, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. BCB (2013)
Laura Moreno, Jairo Aponte, Giriprasad Sridhara, Andrian Marcus, Lori L. Pollock, K. Vijay-Shanker
Automatic generation of natural language summaries for Java classes. ICPC (2013)
Colin Kern, Alvaro J. González, Li Liao, K. Vijay-Shanker
Improving interacting residue prediction using long-distance information in hidden Markov models. BIBM (2012)
Catalina O. Tudor, K. Vijay-Shanker
RankPref: Ranking Sentences Describing Relations between Biomedical Entities with an Application. BioNLP@HLT-NAACL (2012)
Lakshmi R. Pillai, Philippe Chouvarine, Catalina O. Tudor, Carl J. Schmidt, K. Vijay-Shanker, Fiona M. McCarthy
Developing a biocuration workflow for AgBase, a non-model organism database. Database J. Biol. Databases Curation 2012 (2012)
Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker
The eFIP system for text mining of protein interaction networks of phosphorylated proteins. Database J. Biol. Databases Curation 2012 (2012)
Carl J. Schmidt, Liang Sun, Cecilia N. Arighi, Keith Decker, K. Vijay-Shanker, Manabu Torii, Catalina O. Tudor, Cathy H. Wu, Peter D'Eustachio
Pathway curation: Application of text-mining tools eGIFT and RLIMS-P. BIBM Workshops (2012)
Luis D. Lopez, Jingyi Yu, Catalina O. Tudor, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu
Robust segmentation of biomedical figures for image-based document retrieval. BIBM (2012)
Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker
iSimp: A sentence simplification system for biomedicail text. BIBM (2012)
Lori L. Pollock, K. Vijay-Shanker, Emily Hill, Giriprasad Sridhara, David C. Shepherd
Natural Language-Based Software Analyses and Tools for Software Maintenance. ISSSE (2011)
Xiaoran Wang, Lori L. Pollock, K. Vijay-Shanker
Automatic Segmentation of Method Code into Meaningful Blocks to Improve Readability. WCRE (2011)
Colin Kern, Li Liao, K. Vijay-Shanker
Improving Transmembrane Protein Prediction by Increasing the Utilization of Local Information. BICoB (2011)
Giriprasad Sridhara, Lori L. Pollock, K. Vijay-Shanker
Generating Parameter Comments and Integrating with Method Summaries. ICPC (2011)
Giriprasad Sridhara, Lori L. Pollock, K. Vijay-Shanker
Automatically detecting and describing high level actions within methods. ICSE (2011)
Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Improving source code search with natural language phrasal representations of method signatures. ASE (2011)
Giriprasad Sridhara, Emily Hill, Divya Muppaneni, Lori L. Pollock, K. Vijay-Shanker
Towards automatically generating summary comments for Java methods. ASE (2010)
Catalina O. Tudor, Carl J. Schmidt, K. Vijay-Shanker
eGIFT: Mining Gene Information from the Literature. BMC Bioinform. 11 (2010)
Eric Enslen, Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Mining source code to automatically split identifiers for software analysis. MSR (2009)
Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Automatically capturing source code context of NL-queries for software maintenance and reuse. ICSE (2009)
Michael Bloodgood, K. Vijay-Shanker
A Method for Stopping Active Learning Based on Stabilizing Predictions and the Need for User-Adjustable Stopping. CoNLL (2009)
Michael Bloodgood, K. Vijay-Shanker
Taking into Account the Differences between Actively and Passively Acquired Data: The Case of Active Learning with Support Vector Machines for Imbalanced Datasets. HLT-NAACL (Short Papers) (2009)
Zachary P. Fry, David C. Shepherd, Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Analysing source code: looking for useful verbdirect object pairs in all the right places. IET Softw. 2 (1) (2008)
Michael Bloodgood, K. Vijay-Shanker
An Approach to Reducing Annotation Costs for BioNLP. BioNLP (2008)
Catalina O. Tudor, K. Vijay-Shanker, Carl J. Schmidt
Mining the Biomedical Literature for Genic Information. BioNLP (2008)
Giriprasad Sridhara, Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Identifying Word Relations in Software: A Comparative Study of Semantic Similarity Tools. ICPC (2008)
Emily Hill, Zachary P. Fry, Haley Boyd, Giriprasad Sridhara, Yana Novikova, Lori L. Pollock, K. Vijay-Shanker
AMAP: automatically mining abbreviation expansions in programs to enhance software maintenance tools. MSR (2008)
Manabu Torii, K. Vijay-Shanker
Sortal Anaphora Resolution in Medline Abstracts. Comput. Intell. 23 (1) (2007)
John E. Miller, Manabu Torii, K. Vijay-Shanker
Building Domain-Specific Taggers without Annotated (Domain) Data. EMNLP-CoNLL (2007)
Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Exploring the neighborhood with dora to expedite software maintenance. ASE (2007)
John E. Miller, Manabu Torii, K. Vijay-Shanker
Adaptation of POS Tagging for Multiple BioMedical Domains. BioNLP@ACL (2007)
Lori L. Pollock, K. Vijay-Shanker, David C. Shepherd, Emily Hill, Zachary P. Fry, Kishen Maloor
Introducing natural language program analysis. PASTE (2007)
David C. Shepherd, Lori L. Pollock, K. Vijay-Shanker
Case study: supplementing program analysis with natural language analysis to improve a reverse engineering task. PASTE (2007)
David C. Shepherd, Zachary P. Fry, Emily Hill, Lori L. Pollock, K. Vijay-Shanker
Using natural language program analysis to locate and understand action-oriented concerns. AOSD (2007)
John E. Miller, Michael Bloodgood, Manabu Torii, K. Vijay-Shanker
Rapid Adaptation of POS Tagging for Domain Specific Uses. BioNLP@NAACL-HLT (2006)
David C. Shepherd, Lori L. Pollock, K. Vijay-Shanker
Towards supporting on-demand virtual remodularization using program graphs. AOSD (2006)
John Chen, Srinivas Bangalore, K. Vijay-Shanker
Automated extraction of Tree-Adjoining Grammars from treebanks. Nat. Lang. Eng. 12 (3) (2006)
X. Yuan, Zhang-Zhi Hu, H. T. Wu, Manabu Torii, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu
An online literature mining tool for protein phosphorylation. Bioinform. 22 (13) (2006)
Fei Xia, Martha Palmer, K. Vijay-Shanker
Automatically Generating Tree Adjoining Grammars from Abstract Specifications. Comput. Intell. 21 (3) (2005)
Zhang-Zhi Hu, Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker, Cathy H. Wu
Literature mining and database annotation of protein phosphorylation using a rule-based system. Bioinform. 21 (11) (2005)
Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker
Beyond the clause: extraction of phosphorylation information from medline abstracts. ISMB (Supplement of Bioinformatics) (2005)
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
Using name-internal and contextual features to classify biological terms. J. Biomed. Informatics 37 (6) (2004)
Meenakshi Narayanaswamy, K. E. Ravikumar, K. Vijay-Shanker
A Biological Named Entity Recognizer. Pacific Symposium on Biocomputing (2003)
Raymond Kozlowski, Kathleen F. McCoy, K. Vijay-Shanker
Generation of Single-sentence Paraphrases from Predicate/Argument Structure using Lexico-grammatical Resources. IWP@ACL (2003)
Manabu Torii, Sachin Kamboj, K. Vijay-Shanker
An Investigation of Various Information Sources for Classifying Biological names. BioNLP@ACL (2003)
Owen Rambow, K. Vijay-Shanker, David J. Weir
D-Tree Substitution Grammars. Comput. Linguistics 27 (1) (2001)
Sandra Carberry, K. Vijay-Shanker, Andrew Wilson, Ken Samuel
Randomized rule selection in transformation-based learning: a comparative study. Nat. Lang. Eng. 7 (2) (2001)
John Chen, K. Vijay-Shanker
Automated Extraction of TAGs from the Penn Treebank. IWPT (2000)

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Publication Activity (10 Years)

Top Topics

Top Venues

K. Vijay-Shanker