Vinh Nguyen

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Photo credit to Amit Sheth.

Vinh received her PhD degree (her advisor is Amit Sheth) from Kno.e.sis, Computer Science department, Wright State University. Her research interests are Knowledge Representation and Reasoning, Semantic Web, Knowledge Graph, Knowledge Discovery, and related data management and data integration. She is currently a postdoctoral fellow at the National Library of Medicine, NIH.

Personal info:

  • Email: ntkimvinh7@gmail.com
  • Address: Building 38A, Room 9N912D, 8600 ROCKVILLE PIKE, BETHESDA MD 20894.

Additional pages:


Latest Updates

  • June 6-8, 2018

Attended the High Risk High Reward Symposium, NIH.

  • April 2018

Had the breakout session at the Ontology Summit Symposium

  • Mar 28, 2018

Invited speaker at the Ontology Summit 2018: Contexts in Open Knowledge Network. https://www.slideshare.net/ntkimvinh7/ckg-portal-a-knowledge-publishing-proposal-for-open-knowledge-network

  • Mar 2018

Joining NLM/NIH as a postdoctoral fellow.

  • Feb 2018

Served on the program committee (PC) of ISWC 2018, Resources track

  • Jan 2018

Our workshop proposal for the 1st International Workshop on Contextualized Knowledge Graphs has been accepted at ISWC 2018. I will co-chair this workshop with my advisor Amit Sheth and Jose M. Gimenez-Garcia

Served as Reviewer for ESWC 2018

  • Dec 2017

Defended her dissertation "Semantic Web Foundations for Representing, Reasoning, and Traversing Contextualized Knowledge Graphs"

  • Oct 2017

Attended the Open Knowledge Network invited-only workshop http://ichs.ucsf.edu/open-knowledge-network/

  • July 2017

Gave an invited talk at Web Science Summer School 2017

  • April 2017

Served on the program committee (PC) of ISWC 2017, Resources track

  • March 2017

Selected for the Best Ph.D. Student award by Graduate School at Wright State University.

  • Feb 2017

Invited as a speaker at the Learning Week of Answering Questions using Web Data, Université Jean Monnet Saint-Étienne, France, July 2017.

  • Jan 2017

Served as Reviewer for Knowledge and Information System journal

  • Oct 2016

Received the Best Reviewer award @Resources track at ISWC 2016

  • Served as PC member at ISWC 2016
  • April 30, 2016

Submitted the paper titled RDF Statements about Statements: Leveraging Singleton Property Semantics for Context-Aware Reasoning, to ISWC 2016.

  • Feb 11, 2016

The paper, KnowledgeWiki: An OpenSource Tool for Creating Community-Curated Vocabulary, with a Use Case in Materials Science with AFRL, accepted at Linked Data on the Web, LDOW@WWW 2016.

  • Oct 19, 2015

The paper Exposing Provenance Metadata Using Different RDF Models with NCBI, got accepted at Semantic Web Applications and Tools for Life sciences (SWAT4LS) 2015.

  • Served on the program committee (PC) of ISWC 2015, Datasets and Ontologies track
  • Started the fourth (last!) summer internship at IBM Watson from May to August 2015.
  • Feb 14, 2014

Received a sweet present on Valentine's day with a Google Travel grant.

  • Dec 28, 2013

Our paper "Don't like RDF Reification? Making statements about statements using singleton property" got accepted at Semantic Web track, WWW 2014 with acceptance rate 12.9%.

  • Aug 26, 2013

Finished the third summer internship at Medical Ontology Research group. The first two summers were at this group in 2011 and at Oracle Semantic Technologies group in 2012.


CKG Portal

CKG Portal: A Knowledge Publishing Proposal for Open Knowledge Network.

Dissertation Research

  • Dissertation title (tentative)

Singleton Property: A Formal Approach for Representing, Querying, and Reasoning with RDF Contextualized Triples

  • Background

Semantic Web has emerged as a prominent field with RDF, RDFS, SPARQL, and OWL as W3C standards for knowledge representation and reasoning. Knowledge, considered as a set of facts, is represented as a set of RDF triples in the RDF data model. This simple data model serves as the foundational concept in the syntax and semantics of RDF, RDFS, SPARQL, and OWL. These W3C standards have been continuously improved for meeting demands of practical applications and tools. One major requirement raised by Semantic Web practitioners is the ability to associate the contextual metadata such as provenance, time, or location to a fact, or a triple. This requirement is a challenge to the foundations of Semantic Web, as RDF triple is the foundational concept and currently there is no formal concept to represent the triple itself.

  • Formal research

My dissertation addresses the above challenge by proposing a formal approach to contextualize RDF triples using singleton property. Singleton property is a special RDF property that represents a specific relationship between two resources within a context. In other words, the triple is contextualized by the contextual metadata associated with its singleton property. For example, the fact that Barack Obama holds the political position PresidentOfUSA in two terms, from 2009-01-20 to 2013-01-20, and from 2013-01-20 to 2017-01-20, can be represented as follows.

Triple type Subject Predicate Object Subject Predicate Object
Singleton triple BarackObama holdsPosition#1 PresidentOfUSA BarackObama holdsPosition#2 PresidentOfUSA
Singleton property defining triple holdsPosition#1 rdf:singletonPropertyOf holdsPosition holdsPosition#2 rdf:singletonPropertyOf holdsPosition
Meta triple holdsPosition#1 starts 2009-01-20 holdsPosition#2 starts 2013-01-20
Meta triple holdsPosition#1 ends 2013-01-20 holdsPosition#2 ends 2017-01-20

In the scope of the dissertation, the singleton property concept is studied further in three aspects.

Representing. As the contextualized triples are also represented in the form of RDF triples, they are compliant with the RDF abstract syntax. The semantics of the singleton property concept is formalized by extending the model-theoretic semantics of RDF and RDFS. The extended semantics maps a singleton property to one and only one pair of ordered resources. This is different from a regular property extension, which is a set of such pairs.

Querying. SPARQL is the RDF query language recommended by W3C. As the singleton property triples are in the form of RDF triples, they are compatible with SPARQL and can be loaded and queried in any triple store.

For more detail and examples about the representing and querying aspects of the approach, and its performance evaluation, please refer to the [slides], which are made out of [SP1].

Reasoning. As entailment rules are derived from the model-theoretic semantics, the extended semantics for singleton property can be leveraged for developing a new reasoning scheme with a set of new entailment rules that involve singleton properties. For more details and examples about the reasoning aspect of the approach, please refer to [SP2] and [SP6].

  • Applied research

In addition to the formal study of the singleton property approach, I also focus on the adoption of this approach in the real world applications and datasets in different domains. As the approach is formalized with a single interpretation, it can be used in any applications, tools, and datasets in any domain. My collaborations with AFRL, NCBI, NLM have led to the adoption of the singleton property approach in several datasets from material sciences to life sciences, such as MatVocab [SP4], PubChem [SP3], Yago2S, and BKR [SP1]. And there are more on-going collaborations! Furthermore, the approach has been adopted by the community and I have compiled a list of datasets implementing our approach. The list will be regularly updated with the new datasets being found or published.

With regard to the evaluation of this approach in practice, different research groups have performed different benchmarks for choosing the most suitable approach for their own application, including PubChem [SP3], [WikiData]. Both benchmarks concluded that the singleton property approach offers the most compact representation and the query performance really depends on the triple store. I believe that the comparison based on a single dataset and its query set is insufficient for recommending the most potential approach to the Semantic Web community. To allow a wider adoption of the singleton property approach in practice, a comprehensive comparison based on the expressiveness and the performance of various aspects is necessary. This is still on-going work for my dissertation.

Related Publications

[SP7]. Singleton Property: A Formal Approach for Representing, Querying, and Reasoning with RDF Contextualized Triples.
  • Vinh Nguyen, Olivier Bodenreider, Amit Sheth.
  • To be submitted.
[SP6]. RDF Statements about Statements: Leveraging Singleton Property Semantics for Context-Aware Reasoning
  • Vinh Nguyen, Amit Sheth
  • Submitted to 15th International Semantic Web Conference (ISWC) 2016.
[SP5]. A formal graph model for RDF and Its Implementation
  • Vinh Nguyen, Jyoti Leeka, Olivier Bodenreider, Amit Sheth.
  • CoRR abs/1606.00480 (2016).
[SP4]. KnowledgeWiki: An Opensource Tool for Creating Community-curated Vocabulary, with a Use Case in Material Science
  • Nishita Jaykumar, PavanKalyan Yallamelli, Vinh Nguyen, Sarasi Latlithena, Krishnaprasad Thirunarayan, Amit Sheth, Clare Paul.
  • In Proceedings of the Linked Data Open on the Web 2016, LDOW@WWW2016.
  • Links: SPARQL endpoing, KnowledgeWiki, Slides

[SP3]. Exposing Provenance Metadata Using Different RDF Models
  • Gang Fu, Evan Bolton, Núria Queralt-Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier
  • In Proceedings of Semantic Web Applications and Tools for Life Science (SWAT4LS), 2015.
[SP2]. On reasoning with RDF statements about statements using Singleton Property Representation
  • Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan, Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura I. Furlong, Amit Sheth.
  • CoRR abs/1509.04513 (2015).
[SP1]. Don't like RDF Reification? Making statements about statements using singleton property
  • Vinh Nguyen, Olivier Bodenreider, Amit Sheth
  • In Proceedings of the 23rd international conference on World wide web (WWW 2014).
  • Links: Slides

Related Datasets Implementing Our Singleton Property Approach (to be frequently updated)

This list contains the datasets that have implemented our singleton property approach in the RDF data model. It is not comprehensive as I may not be aware of every dataset. Please kindly drop me an email at vinh@knoesis.org if you know any dataset not listed here. Much appreciated!!!

KnowledgeWiki

  • Nishita Jaykumar, PavanKalyan Yallamelli, Vinh Nguyen, Sarasi Latlithena, Krishnaprasad Thirunarayan, Amit Sheth, Clare Paul. KnowledgeWiki: An Opensource Tool for Creating Community-curated Vocabulary, with a Use Case in Material Science. In Proceedings of the Linked Data Open on the Web 2016, LDOW@WWW2016.
  • Links: SPARQL endpoint, KnowledgeWiki, Slides

PubChem

  • Gang Fu, Evan Bolton, Núria Queralt-Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier. Exposing Provenance Metadata Using Different RDF Models. In Proceedings of Semantic Web Applications and Tools for Life Science (SWAT4LS), 2015.
  • Download dataset
WikiData
  • Daniel Hernández, Aidan Hogan, and Markus Krötzsch. Reifying RDF: What Works Well With Wikidata? In Proceedings of the 11th International Workshop on Scalable Semantic Web Knowledge Base Systems co-located with 14th International Semantic Web Conference (ISWC 2015), Bethlehem, PA, USA. 2015.
  • Download data, queries, configuration

SRDF

  • Sangha Nam, Younggyun Hahm, Sejin Nam, Key-Sun Choi. SRDF: Korean Open Information Extraction using Singleton Property. In Proceedings of the ISWC 2015 Posters & Demonstrations Track co-located with the 14th International Semantic Web Conference (ISWC-2015).
  • Download at dataset

SingletonMinded

Historical data with DBPedia

  • Norman Weisenburger, Volha Bryl, Simone Paolo Ponzetto. Mining historical data for DBpedia via temporal tagging of Wikipedia infoboxes. In Proceedings of NLP&DBpedia 2014 Workshop @ ISWC 2014.
  • Download slides and dataset

Blog: Neo4j as Graph Database for OpenCog AtomSpace architecture?

BKR

  • A biomedical knowledge repository integrating UMLS and PubMed predications. This dataset represents the provenance of a given predication, whether it is extracted from a PubMed abstract, or UMLS.
  • Download dataset.

Yago2S-SP

  • RDF-compliant dataset converted from Yago2S dataset.
  • Download dataset



Research Projects

The Semantics and Services enabled Problem Solving Environment for Trypanosoma cruzi

This project aims to utilize state-of-the-art semantic technologies for effective querying of multiple databases through creation of a suite of ontologies modeling multiple aspects of T. cruzi research domain.

Related publications

iExplore: Interactive Browsing and Exploring Biomedical Knowledge

  • Vinh Nguyen, Olivier Bodenreider, Jagannathan Srinivasan, Todd Minning, Thomas Rindesch, Bastien Rance, Ramakanth Kavuluru, Hima Yalamanchili, Krishnaprasad Thirunarayan, Satya Sahoo, and Amit Sheth.
  • Semantic Web Challenge at ISWC 2012, Boston, USA.

iExplore: A provenance-based application for exploring biomedical knowledge

  • Vinh Nguyen, Olivier Bodenreider, Thomas Rindflesch, Amit Sheth.
  • In Poster Proceedings of the Eighth International Conference on Data Integration in the Life Sciences (DILS 2012).

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

  • Priti Parikh, Todd Minning, Vinh Nguyen, Sarasi Lalithsena, Amir Asiaee, Satya Sahoo, Prashant Doshi, Rick Tarleton, Amit Sheth
  • PLOS Neglected Tropical Diseases, Jan 2012.

A unified framework for managing provenance information in translational research

  • Satya Sanket Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth
  • BMC Bioinformatics 12: 461 (2011)

The Knowledge-driven Exploration of Integrated Biomedical Knowledge Sources Facilitates the Generation of New Hypotheses

  • Vinh Nguyen, Olivier Bodenreider, Todd Minning, Amit P. Sheth.
  • Proceedings of the First Workshop on Linked Science, LISC @ISWC 2011.
  • Links: slides, demo video.

Biomedical Ontologies for Parasite Research

  • Vinh Nguyen, Satya Sahoo, Priti Parikh, Todd Minning, Brent Weatherly, Flora Logan, Amit Sheth, Rick Tarleton.
  • Poster in ISMB 2010, July 11-13 2010, Boston, MA, USA.

Managing provenance information in parasite research

  • Vinh Nguyen, Priti Parikh, Satya Sahoo, Amit Sheth.
  • Poster at OCCBIO, Columbus, 6-8 June 2010.



Publications

GoogleScholar

RDF Statements about Statements: Leveraging Singleton Property Semantics for Context-Aware Reasoning

  • Vinh Nguyen, Amit Sheth
  • Submitted to 15th International Semantic Web Conference (ISWC), 2016.

A formal graph model for RDF and Its Implementation

  • Vinh Nguyen, Jyoti Leeka, Olivier Bodenreider, Amit Sheth.
  • CoRR abs/1606.00480 (2016).

KnowledgeWiki: An Opensource Tool for Creating Community-curated Vocabulary, with a Use Case in Material Science

  • Nishita Jaykumar, PavanKalyan Yallamelli, Vinh Nguyen, Sarasi Latlithena, Krishnaprasad Thirunarayan, Amit Sheth, Clare Paul.
  • In Proceedings of the Linked Data Open on the Web 2016, LDOW@WWW2016.

Exposing Provenance Metadata Using Different RDF Models

  • Gang Fu, Evan Bolton, Núria Queralt-Rosinach, Laura Inés Furlong, Vinh Nguyen, Amit P. Sheth, Olivier Bodenreider, Michel Dumontier
  • In Proceedings of Semantic Web Applications and Tools for Life Science (SWAT4LS), 2015.

On reasoning with RDF statements about statements using Singleton Property Representation

  • Vinh Nguyen, Olivier Bodenreider, Krishnaprasad Thirunarayan, Gang Fu, Evan Bolton, Núria Queralt Rosinach, Laura I. Furlong, Amit Sheth.
  • CoRR abs/1509.04513 (2015).

Don't like RDF Reification? Making statements about statements using singleton property

  • Vinh Nguyen, Olivier Bodenreider, Amit Sheth
  • In Proceedings of the 23rd international conference on World wide web (WWW '14).

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

  • Priti Parikh, Todd Minning, Vinh Nguyen, Sarasi Lalithsena, Amir Asiaee, Satya Sahoo, Prashant Doshi, Rick Tarleton, Amit Sheth
  • PLOS Neglected Tropical Diseases, Jan 2012.

A unified framework for managing provenance information in translational research

  • Satya Sanket Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth
  • BMC Bioinformatics 12: 461 (2011)

The Knowledge-driven Exploration of Integrated Biomedical Knowledge Sources Facilitates the Generation of New Hypotheses

  • Vinh Nguyen, Olivier Bodenreider, Todd Minning, Amit P. Sheth.
  • Proceedings of the First Workshop on Linked Science, LISC @ISWC 2011.



Demos and Posters

iExplore: Interactive Browsing and Exploring Biomedical Knowledge

  • Vinh Nguyen, Olivier Bodenreider, Jagannathan Srinivasan, Todd Minning, Thomas Rindesch, Bastien Rance, Ramakanth Kavuluru, Hima Yalamanchili, Krishnaprasad Thirunarayan, Satya Sahoo, and Amit Sheth.
  • Semantic Web Challenge at ISWC 2012, Boston, USA.

iExplore: A provenance-based application for exploring biomedical knowledge

  • Vinh Nguyen, Olivier Bodenreider, Thomas Rindflesch, Amit Sheth.
  • In Poster Proceedings of the Eighth International Conference on Data Integration in the Life Sciences (DILS 2012).

Twitris 2.0: Semantically Empowered System for Understanding Perceptions From Social Data

  • Ashutosh Jadhav, Hemant Purohit, Pavan Kapanipathi, Pramod Ananthram, Ajith Ranabahu, Vinh Nguyen, Pablo Mendes, Alan Gary Smith, Michael Cooney, Amit Sheth.
  • Demo at 9th International Semantic Web Conference, ISWC 2010, Shanghai, China, November 7-11, 2010.

Biomedical Ontologies for Parasite Research

  • Vinh Nguyen, Satya Sahoo, Priti Parikh, Todd Minning, Brent Weatherly, Flora Logan, Amit Sheth, Rick Tarleton.
  • Poster in ISMB 2010, July 11-13 2010, Boston, MA, USA.

Managing provenance information in parasite research

  • Vinh Nguyen, Priti Parikh, Satya Sahoo, Amit Sheth.
  • Poster at OCCBIO, Columbus, 6-8 June 2010.

Twitris: Socially Influenced Browsing

  • Ashutosh Jadhav, Wenbo Wang, Raghava Mutharaju, Pramod Anantharam, Vinh Nguyen, Amit P. Sheth, Karthik Gomadam, Meenakshi Nagarajan, and Ajith Ranabahu.
  • Semantic Web Challenge 2009, 8th International Semantic Web Conference, Oct. 25-29 2009, Washington, DC, USA.



Professional Activities

Invited Talks

  • Invited speaker at the Learning Week of Answering Questions using Web Data, Université Jean Monnet Saint-Étienne, France, 2017.

Reviewers/Program Committee Members

  • 17th International Semantic Web Conference (ISWC 2018)
  • 15th Extended Semantic Web Conference (ESWC 2018)
  • 16th International Semantic Web Conference (ISWC 2017)
  • Knowledge and Information Systems journal, (KAIS 2017
  • 15th International Semantic Web Conference (ISWC 2016)
  • 14th International Semantic Web Conference (ISWC 2015)

Sub-reviewer

  • 26rd International World Wide Web Conference (WWW 2017)
  • 23rd International World Wide Web Conference (WWW 2014)
  • 13th International Semantic Web Conference (ISWC 2014)
  • 9th Extended Semantic Web Conference (ESWC 2014)



Honors & Awards

  • Best PhD student award, 2017.
  • Best Reviewer award at ISWC 2016
  • Google Travel Award to WWW 2014 conference.
  • Selected for NSF travel award to ISWC 2011 conference.



Work Experience

Graduate Research Assistant, Kno.e.sis, Wright State University

  • September 2009 - current

Graduate Teaching Assistant, CS department, Wright State University

  • September 2012 - April 2013

Summer intern, IBM Watson

  • May - August, 2015

Develop the analytics store for the Watson Discovery Advisor for Life Science.

Summer intern, NLM/NIH

  • June - August, 2013

Develop the singleton property approach for using RDF in representing the occurrences of MeSH descriptors within PubMed articles.

Summer intern, Oracle

  • June - August, 2012

Developed a prototype for publishing RDF Quads as relational views.

Summer intern, NLM/NIH

  • June - August, 2011

Integrated several resources leveraging Semantic Web technologies, and developed the tool iExplore for exploring the linked datasets and formulating hypothesis.



Education

Doctor of Philosophy

  • Computer Science department, Wright State University
  • September 2009 - current

Bachelor of Science

  • University of Technology, Ho Chi Minh City, Vietnam
  • September 2002 - April 2007