K. Vijay-Shanker

According to our database1, K. Vijay-Shanker authored at least 125 papers between 1985 and 2019.

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Bibliography

2019
Exploring word embedding techniques to improve sentiment analysis of software engineering texts.
Proceedings of the 16th International Conference on Mining Software Repositories, 2019

2018
iPTMnet: an integrated resource for protein post-translational modification network discovery.
Nucleic Acids Research, 2018

Automatic gene annotation using GO terms from cellular component domain.
BMC Med. Inf. & Decision Making, 2018

Identification of key differentially expressed MicroRNAs in cancer patients through pan-cancer analysis.
Comp. in Bio. and Med., 2018

iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.
Database, 2018

DEXTER: Disease-Expression Relation Extraction from Text.
Database, 2018

Protein Complex Mention Recognition with Web-Based Knowledge Learning.
Proceedings of the Emerging Technologies for Education - Third International Symposium, 2018

2017
WebGIVI: a web-based gene enrichment analysis and visualization tool.
BMC Bioinformatics, 2017

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.
Database, 2017

Automatically generating natural language descriptions for object-related statement sequences.
Proceedings of the IEEE 24th International Conference on Software Analysis, 2017

UD_GU_BioTM at TREC 2017: Precision Medicine Track.
Proceedings of The Twenty-Sixth Text REtrieval Conference, 2017

Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

Identifying Comparative Structures in Biomedical Text.
Proceedings of the BioNLP 2017, Vancouver, Canada, August 4, 2017, 2017

2016
miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases.
J. Biomedical Semantics, 2016

BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph.
Database, 2016

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.
Database, 2016

Scalable Text Mining Assisted Curation of PTM Proteoforms in the Protein Ontology.
Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.
IEEE/ACM Trans. Comput. Biology Bioinform., 2015

miRTex: A Text Mining System for miRNA-Gene Relation Extraction.
PLoS Computational Biology, 2015

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system.
Database, 2015

Automatically Mining Negative Code Examples from Software Developer Q & A Forums.
Proceedings of the 30th IEEE/ACM International Conference on Automated Software Engineering Workshops, 2015

Developing a model of loop actions by mining loop characteristics from a large code corpus.
Proceedings of the 2015 IEEE International Conference on Software Maintenance and Evolution, 2015

An extended dependency graph for relation extraction in biomedical texts.
Proceedings of the Workshop on Biomedical Natural Language Processing, BioNLP@IJCNLP 2015, 2015

2014
Automatic Segmentation of Method Code into Meaningful Blocks: Design and Evaluation.
Journal of Software: Evolution and Process, 2014

An empirical study of identifier splitting techniques.
Empirical Software Engineering, 2014

Rapid Adaptation of POS Tagging for Domain Specific Uses.
CoRR, 2014

A Method for Stopping Active Learning Based on Stabilizing Predictions and the Need for User-Adjustable Stopping.
CoRR, 2014

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

An Approach to Reducing Annotation Costs for BioNLP.
CoRR, 2014

A Generalizable NLP Framework for Fast Development of Pattern-based Biomedical Relation Extraction Systems.
BMC Bioinformatics, 2014

RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information.
Database, 2014

iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system.
Database, 2014

2013
A framework for biomedical figure segmentation towards image-based document retrieval.
BMC Systems Biology, 2013

Automatically mining software-based, semantically-similar words from comment-code mappings.
Proceedings of the 10th Working Conference on Mining Software Repositories, 2013

A dataset for evaluating identifier splitters.
Proceedings of the 10th Working Conference on Mining Software Repositories, 2013

JSummarizer: An automatic generator of natural language summaries for Java classes.
Proceedings of the IEEE 21st International Conference on Program Comprehension, 2013

Automatic generation of natural language summaries for Java classes.
Proceedings of the IEEE 21st International Conference on Program Comprehension, 2013

Part-of-speech tagging of program identifiers for improved text-based software engineering tools.
Proceedings of the IEEE 21st International Conference on Program Comprehension, 2013

Differentiating Roles of Program Elements in Action-Oriented Concerns.
Proceedings of the 2013 IEEE International Conference on Software Maintenance, 2013

Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach.
Proceedings of the ACM Conference on Bioinformatics, 2013

An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
The eFIP system for text mining of protein interaction networks of phosphorylated proteins.
Database, 2012

Developing a biocuration workflow for AgBase, a non-model organism database.
Database, 2012

RankPref: Ranking Sentences Describing Relations between Biomedical Entities with an Application.
Proceedings of the 2012 Workshop on Biomedical Natural Language Processing, 2012

Pathway curation: Application of text-mining tools eGIFT and RLIMS-P.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

iSimp: A sentence simplification system for biomedicail text.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

Robust segmentation of biomedical figures for image-based document retrieval.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

Improving interacting residue prediction using long-distance information in hidden Markov models.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine, 2012

2011
Automatic Segmentation of Method Code into Meaningful Blocks to Improve Readability.
Proceedings of the 18th Working Conference on Reverse Engineering, 2011

Improving source code search with natural language phrasal representations of method signatures.
Proceedings of the 26th IEEE/ACM International Conference on Automated Software Engineering (ASE 2011), 2011

Generating Parameter Comments and Integrating with Method Summaries.
Proceedings of the 19th IEEE International Conference on Program Comprehension, 2011

Natural Language-Based Software Analyses and Tools for Software Maintenance.
Proceedings of the Software Engineering - International Summer Schools, 2011

Automatically detecting and describing high level actions within methods.
Proceedings of the 33rd International Conference on Software Engineering, 2011

Improving Transmembrane Protein Prediction by Increasing the Utilization of Local Information.
Proceedings of the ISCA 3rd International Conference on Bioinformatics and Computational Biology, 2011

2010
eGIFT: Mining Gene Information from the Literature.
BMC Bioinformatics, 2010

Towards automatically generating summary comments for Java methods.
Proceedings of the ASE 2010, 2010

2009
Taking into Account the Differences between Actively and Passively Acquired Data: The Case of Active Learning with Support Vector Machines for Imbalanced Datasets.
Proceedings of the Human Language Technologies: Conference of the North American Chapter of the Association of Computational Linguistics, Proceedings, May 31, 2009

Mining source code to automatically split identifiers for software analysis.
Proceedings of the 6th International Working Conference on Mining Software Repositories, 2009

Automatically capturing source code context of NL-queries for software maintenance and reuse.
Proceedings of the 31st International Conference on Software Engineering, 2009

A Method for Stopping Active Learning Based on Stabilizing Predictions and the Need for User-Adjustable Stopping.
Proceedings of the Thirteenth Conference on Computational Natural Language Learning, 2009

Information Extraction of Protein Phosphorylation from Biomedical Literature.
Proceedings of the Information Retrieval in Biomedicine, 2009

2008
Analysing source code: looking for useful verbdirect object pairs in all the right places.
IET Software, 2008

AMAP: automatically mining abbreviation expansions in programs to enhance software maintenance tools.
Proceedings of the 2008 International Working Conference on Mining Software Repositories, 2008

Identifying Word Relations in Software: A Comparative Study of Semantic Similarity Tools.
Proceedings of the 16th IEEE International Conference on Program Comprehension, 2008

Mining the Biomedical Literature for Genic Information.
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, 2008

An Approach to Reducing Annotation Costs for BioNLP.
Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, 2008

2007
Sortal Anaphora Resolution in Medline Abstracts.
Computational Intelligence, 2007

Case study: supplementing program analysis with natural language analysis to improve a reverse engineering task.
Proceedings of the 7th ACM SIGPLAN-SIGSOFT Workshop on Program Analysis for Software Tools and Engineering, 2007

Introducing natural language program analysis.
Proceedings of the 7th ACM SIGPLAN-SIGSOFT Workshop on Program Analysis for Software Tools and Engineering, 2007

Exploring the neighborhood with dora to expedite software maintenance.
Proceedings of the 22nd IEEE/ACM International Conference on Automated Software Engineering (ASE 2007), 2007

Building Domain-Specific Taggers without Annotated (Domain) Data.
Proceedings of the EMNLP-CoNLL 2007, 2007

Adaptation of POS Tagging for Multiple BioMedical Domains.
Proceedings of the Biological, translational, and clinical language processing, 2007

Using natural language program analysis to locate and understand action-oriented concerns.
Proceedings of the 6th International Conference on Aspect-Oriented Software Development, 2007

2006
Automated extraction of Tree-Adjoining Grammars from treebanks.
Natural Language Engineering, 2006

An online literature mining tool for protein phosphorylation.
Bioinformatics, 2006

Rapid Adaptation of POS Tagging for Domain Specific Uses.
Proceedings of the Workshop on Linking Natural Language and Biology, 2006

Towards supporting on-demand virtual remodularization using program graphs.
Proceedings of the 5th International Conference on Aspect-Oriented Software Development, 2006

2005
Automatically Generating Tree Adjoining Grammars from Abstract Specifications.
Computational Intelligence, 2005

Literature mining and database annotation of protein phosphorylation using a rule-based system.
Bioinformatics, 2005

Beyond the clause: extraction of phosphorylation information from medline abstracts.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

2004
Using name-internal and contextual features to classify biological terms.
Journal of Biomedical Informatics, 2004

2003
A Biological Named Entity Recognizer.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

An Investigation of Various Information Sources for Classifying Biological names.
Proceedings of the Workshop on Natural Language Processing in Biomedicine, 2003

Generation of Single-sentence Paraphrases from Predicate/Argument Structure using Lexico-grammatical Resources.
Proceedings of the Second International Workshop on Paraphrasing, 2003

2001
Randomized rule selection in transformation-based learning: a comparative study.
Natural Language Engineering, 2001

D-Tree Substitution Grammars.
Computational Linguistics, 2001

2000
Monotonic C-Command: A New Perspective on Tree Adjoining Grammar.
Grammars, 2000

1999
Automatically Selecting Useful Phrases for Dialogue Act Tagging
CoRR, 1999

New Models for Improving Supertag Disambiguation.
Proceedings of the EACL 1999, 1999

1998
An Investigation of Transformation-Based Learning in Discourse
CoRR, 1998

Dialogue Act Tagging with Transformation-Based Learning
CoRR, 1998

Computing Dialogue Acts from Features with Transformation-Based Learning
CoRR, 1998

Consistent grammar development using partial-tree descriptions for Lexicalized Tree-Adjoining Grammars.
Proceedings of the Fourth International Workshop on Tree Adjoining Grammars and Related Frameworks, 1998

Wh-islands in TAG and related formalisms.
Proceedings of the Fourth International Workshop on Tree Adjoining Grammars and Related Frameworks, 1998

TAG derivation as monotonic C-command.
Proceedings of the Fourth International Workshop on Tree Adjoining Grammars and Related Frameworks, 1998

Motion verbs and semantic features in TAG.
Proceedings of the Fourth International Workshop on Tree Adjoining Grammars and Related Frameworks, 1998

An Investigation of Transformation-Based Learning in Discourse.
Proceedings of the Fifteenth International Conference on Machine Learning (ICML 1998), 1998

Dialogue Act Tagging with Transformation-Based Learning.
Proceedings of the 36th Annual Meeting of the Association for Computational Linguistics and 17th International Conference on Computational Linguistics, 1998

1995
A First-Order Axiomatization of the Theory of Finite Trees.
Journal of Logic, Language and Information, 1995

D-Tree Grammars
CoRR, 1995

Compilation of HPSG to TAG
CoRR, 1995

D-Tree Grammars.
Proceedings of the 33rd Annual Meeting of the Association for Computational Linguistics, 1995

Compilation of HPSG to TAG.
Proceedings of the 33rd Annual Meeting of the Association for Computational Linguistics, 1995

1994
The Equivalence of Four Extensions of Context-Free Grammars.
Mathematical Systems Theory, 1994

Obtaining Trees from their Descriptions: An Application to Tree-Adjoining Grammars.
Computational Intelligence, 1994

1993
Parsing Some Constrained Grammar Formalisms.
Computational Linguistics, 1993

The Use of Shared Forests in Tree Adjoining Grammar Parsing.
Proceedings of the Sixth Conference of the European Chapter of the Association for Computational Linguistics, 1993

1992
Using Descriptions of Trees in a Tree Adjoining Grammar.
Computational Linguistics, 1992

Structure Sharing in Lexicalized Tree-Adjoining Grammars.
Proceedings of the 14th International Conference on Computational Linguistics, 1992

Reasoning with Descriptions of Trees.
Proceedings of the 30th Annual Meeting of the Association for Computational Linguistics, 28 June, 1992

A Functional Approach to Generation with TAG.
Proceedings of the 30th Annual Meeting of the Association for Computational Linguistics, 28 June, 1992

1990
An Interpretation of Negation in Feature Structure Descriptions.
Computational Linguistics, 1990

Embedded Pushdown Automata.
Proceedings of the First International Workshop on Tree Adjoining Grammar and Related Frameworks, 1990

Using Tree Adjoining Grammars Systemic Framework in the.
Proceedings of the Fifth International Workshop on Natural Language Generation, 1990

Polynomial Time Parsing of Combinatory Categorial Grammars.
Proceedings of the 28th Annual Meeting of the Association for Computational Linguistics, 1990

Deterministic Left to Right Parsing of Tree Adjoining Languages.
Proceedings of the 28th Annual Meeting of the Association for Computational Linguistics, 1990

1989
Parsing Tree Adjoining Grammars.
Proceedings of the A Perspective in Theoretical Computer Science, 1989

Recognition of Combinatory Categorial Grammars and Linear Indexed Grammars.
Proceedings of the First International Workshop on Parsing Technologies, 1989

Treatment of Long Distance Dependencies in LFG and TAG: Functional Uncertainty in LFG is a Corollary in TAG.
Proceedings of the 27th Annual Meeting of the Association for Computational Linguistics, 1989

A Three-Valued Interpretation of Negation in Feature Structure Descriptions.
Proceedings of the 27th Annual Meeting of the Association for Computational Linguistics, 1989

1988
Feature structures based Tree Adjoining Grammars.
Proceedings of the 12th International Conference on Computational Linguistics, 1988

1987
Characterizing Structural Descriptions produced by Various Grammatical Formalisms.
Proceedings of the 25th Annual Meeting of the Association for Computational Linguistics, 1987

1986
Tree Adjoining and Head Wrapping.
Proceedings of the 11th International Conference on Computational Linguistics, 1986

The Relationship Between Tree Adjoining Grammars And Head Grammarst.
Proceedings of the 24th Annual Meeting of the Association for Computational Linguistics, 1986

1985
Some Computational Properties of Tree Adjoining Grammars.
Proceedings of the 23rd Annual Meeting of the Association for Computational Linguistics, 1985


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