Inter-Disciplinary Research

DATA MANAGEMENT + EDUCATION

REFEREED PUBLICATIONS
2 June 2021 Weiguo Wang, Sourav S Bhowmick, Hui Li, Shafiq Joty, Siyuan Liu, Peng Chen

Towards Enhancing Database Education: Natural Language Generation Meets Query Execution Plans

In the Proceedings of 47th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2021)

ACM Press, Xi'an, China.

Technical Report

Video

This paper presents a framework that extends NEURON by exploiting deep learning to generate natural language description of query execution plans of SQL queries to facilitate database education.
1 July 2019 Siyuan Liu, Sourav S Bhowmick, Wanlu Zhang, Shu Wang, Wanyi Huang, Shafiq Joty

NEURON: Query Execution Plan Meets Natural Language Processing For Augmenting DB Education

In the Proceedings of 45th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2019)

ACM Press, Amsterdam, The Netherlands (Demo).

Video

This system generates rule-based natural language description of query execution plans of SQL queries as well as provides a NL-based question-answering framework to facilitate database education. NEURON is currently deployed in database systems courses in NTU and Xidian University.

DATA VISUALIZATION + VISUAL ARTS

REFEREED PUBLICATIONS
2 Oct 2021 Castillo Clarence Fitzgerald Gumtang, Sourav S Bhowmick

Kandinsky Mobile: Abstract Art-Inspired Interactive Visualization of Social Discussions on Mobile Devices.

In Proceedings of 29th ACM International Conference on Multimedia (ACM MM 2021)

ACM Press, Virtual (Interactive Arts Track).

Video

This paper extends our effort on desktop machines to mobile devices. Kandinsky-Mobile is inspired by the paintings of Wassily Kandinsky to interactively visualize social discussion landscapes on mobile devices.
1 July 2019 Christina Lui, Sourav S Bhowmick, Adam Jatowt

KANDINSKY: Abstract Art-Inspired Visualization of Social Discussions

In Proceedings of 42nd international ACM SIGIR conference on Research and Development in Information Retrieval (ACM SIGIR 2019)

ACM Press, Paris, France (Demo).

Video

This paper is inspired by the geometrical form of paintings of the father of abstract art, Wassily Kandinsky, to interactively visualize social discussion landscapes on a desktop.

DATA-CENTRIC COMPUTING + PSYCHOLOGY

REFEREED PUBLICATIONS
10 Aug 2021 Zifeng Yuan, Huey-Eng Chua, Sourav S Bhowmick, Zekun Ye, Wook-Shin Han, Byron Choi

Towards Plug-and-Play Visual Graph Query Interfaces: Data-driven Canned Pattern Selection for Large Networks

In Proceedings of 47th International Conference on Very Large Data Bases (VLDB 2021)

ACM Press, Copenhagen, Denmark.

Technical Report

Video

This work exploits the notion of cognitive load from cognitive psychology to generate canned patterns from large network that are easy to visually intepret by humans to enhance usability of data-driven visual graph query interfaces.
9 June 2021 Kai Huang, Huey-Eng Chua, Sourav S Bhowmick, Byron Choi, Shuigeng Zhou

MIDAS: Towards Efficient and Effective Maintenance of Canned Patterns in Visual Graph Query Interfaces

In the Proceedings of 47th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2021)

ACM Press, Xi'an, China.

Technical Report

Code

This work builds on CATAPULT by exploiting the notion of cognitive load from cognitive psychology to maintain canned patterns in a data-driven visual graph query interface as the underlying graph repository evolves.
8 June 2021 Weiguo Wang, Sourav S Bhowmick, Hui Li, Shafiq Joty, Siyuan Liu, Peng Chen

Towards Enhancing Database Education: Natural Language Generation Meets Query Execution Plans

In the Proceedings of 47th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2021)

ACM Press, Xi'an, China.

Technical Report

Video

This paper presents a AI-based framework that for the first time exploits psychology theories on habituation and boredom to generate natural language (NL) description of query execution plans (QEP) of SQL queries to facilitate database education. This facilitates diversification of NL description of QEPs.
7 June 2020 Hui Li, Hui Li, Sourav S Bhowmick

CHASSIS: Conformity Meets Online Information Diffusion

In the Proceedings of 46th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2020)

ACM Press, Portland, USA.

Technical Report

Talk

CHASSIS marries a social psychology theory (conformity) with online information diffusion model for superior predictive power.
6 June 2020 Sourav S Bhowmick, Kai Huang, Huey Eng Chua, Zifeng Yuan, Byron Choi, Shuigeng Zhou

AURORA: Data-driven Construction of Visual Graph Query Interfaces for Graph Databases

In the Proceedings of 46th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2020)

ACM Press, Portland, USA (Demo).

Video

AURORA is a demonstration of a data-driven visual graph query interface whose components are grounded on the principles of cognitive psychology. Specifically, it exploits CATAPULT for displaying cognitive load-conscious canned patterns on the GUI.
5 July 2019 Kai Huang, Huey Eng Chua, Sourav S Bhowmick, Byron Choi, Shuigeng Zhou

CATAPULT: Data-driven Selection of Canned Patterns for Efficient Visual Graph Query Formulation

In the Proceedings of 45th ACM SIGMOD International Conference on Management of Data (ACM SIGMOD 2019)

ACM Press, Amsterdam, The Netherlands.

Code

This is the first work that exploits the notion of cognitive load from cognitive psychology for selecting canned patterns in a data-driven visual graph query interface from a large collection of small- or medium-sized data graphs. The idea is to maintain the existing patterns with those which are visually easy to intepret by humans (i.e., low cognitive load).
4 Oct 2015 Sourav S Bhowmick, Curtis Dyreson, Byron Choi, Min-Hwee Ang

Interruption-Sensitive Empty Result Feedback: Rethinking the Visual Query Feedback Paradigm for Semistructured Data

In the Proceedings of 24th ACM International Conference on Information and Knowledge Management (CIKM 2015)

ACM Press, Melbourne, Australia

This paper integrates the impact of interruption, a concept well-studied in cognitive psychology, with query feedback in the context of semistructured data. In particular, the adverse effect of interruption during query processing has not be investigated in data management prior to this work.
3 Jan 2015 Hui Li, Sourav S Bhowmick, Aixin Sun, J Cui

Conformity-aware Influence Maximization in Online Social Networks

The VLDB Journal, 24(1), Springer-Verlag.

This paper is an extension of CINEMA and integrates the notion of conformity from social psychology into online influence maximization problem.
2 Mar 2013 Hui Li, Sourav S Bhowmick, Aixin Sun

CINEMA: Conformity-Aware Greedy Algorithm for Influence Maximization in Online Social Networks

In the Proceedings of 16th International Conference on Extending Database Technology (EDBT 2013)

ACM Press, Genoa, Italy

This paper is the first work that integrates the notion of conformity from social psychology into online influence maximization problem leading to superior influence spread prediction.
1 Oct 2011 Hui Li, Sourav S Bhowmick, Aixin Sun

CASINO: Towards Conformity-Aware Social Influence Analysis in Online Social Networks

In the Proceedings of 20th ACM Conference of Information and Knowledge Management (ACM CIKM 2011)

ACM Press, Glasgow, Scotland (Short)

Extended version

This is the first work that marries conformity from social pyschology with online social influence.

DATA-CENTRIC COMPUTING + SYSTEM BIOLOGY

REFEREED PUBLICATIONS
27 Jan 2018 Huey Eng Chua, Sourav S Bhowmick, Jie Zheng

TROVE: A User-friendly Tool for Visualizing and Analyzing Cancer Hallmarks in Signaling Networks

Bioinformatics, 34(2), Oxford Univ Press.

Video

A software framework for visualizing and analyzing cancer hallmarks in cancer-related signaling neworks.
26 Oct 2017 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

Synergistic Target Combination Prediction From Curated Signaling Networks: Machine Learning Meets Systems Biology and Pharmacology

Methods, Vol 129, Elsevier Science (Invited Paper)

One of the early work that is at the intersection of Machine Learning, Systems Biology, and Pharmacology for predicting synergistic target combinations from curated disease-related signaling networks to advance combination therapy.
25 Aug 2017 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking

In the Proceedings of 8th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2017)

ACM Press, Boston, USA

This work is one of the first that aims to rank signaling networks by exploiting target characteristics.
24 May 2017 Sourav S Bhowmick, Boon-Siew Seah Summarizing Biological Networks

Springer Verlag, ISBN 978-3-319-54620-9, Pages: 146.

A book that consolidates all major efforts related to summarizing biological networks. It show cases works and opportunities that lie at the intersection of network analytics and biological networks.
23 Dec 2016 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, and C Forbes Dewey, Jr

TENET: A Machine Learning-based System for Target Characterization in Signaling Networks

In the Proceedings of 16th IEEE Conference on Data Mining (IEEE ICDM 2016)

IEEE CS, Barcelona, Spain (Demo)

Software prototype of ML-based target characterization in signaling networks.
22 Dec 2016 Boon Siew Seah, Sourav S Bhowmick, Huey Eng Chua, Mengxuan Chen, and C Forbes Dewey, Jr

FacetsViewer: A Tool for Multi-faceted Decomposition of Complex Networks

In the Proceedings of 16th IEEE Conference on Data Mining (IEEE ICDM 2016)

IEEE CS, Barcelona, Spain (Demo)

Video

Software prototype of FACET, a mult-faceted decomposition technique of biological networks.
21 Oct 2016 Huey Eng Chua, Sourav S Bhowmick, Zheng Jie, Lisa Tucker-Kellogg

TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks

In the Proceedings of 7th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2016)

ACM Press, Seattle, USA

Software

TAPESTRY exploits data analytics to prioritize targets in disease-related signaling networks. This is an improved version of our prior work (PANI).
20 Oct 2016 Shital K Mishra, Sourav S Bhowmick, Huey Eng Chua, Zheng Jie

Predictive Modeling of Drug Effects on Signaling Pathways in Diverse Cancer Cell Lines

In the Proceedings of 7th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2016)

ACM Press, Seattle, USA

The paper presents a computational model for predicting effects of drugs on cancer-related signaling networks.
19 March 2016 Sourav S Bhowmick, Boon Siew Seah

Clustering and Summarizing Protein-Protein Interaction Networks: A Survey

IEEE Transactions on Data and Knowledge Engineering (TKDE), 28(3), IEEE CS

A survey paper that exhaustively reviews work on clustering and summarizing PPI networks.
18 Oct 2015 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, C F Dewey, Jr

TENET: Topological Feature-based Target Characterization in Signaling Networks

Bioinformatics, 31(20), Oxford Univ Press.

Technical Report

Software

A software that exploits machine learning to characterize topological features of nodes in signaling networks.
17 January 2015 Shital K Mishra, Sourav S Bhowmick, Huey Eng Chua, Fan Zhang, Jie Zheng

Computational Cell Fate Modelling for Discovery of Rewiring in Apoptotic Network for Enhanced Cancer Drug Sensitivity

BMC Systems Biology, 9:S4, Biomed Central.

The paper presents a computational model for discovering rewiring in apoptotic network, which plays an important role in cancer.
16 Oct 2014 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.

DiffNet: Automatic Differential Functional Summarization of dE-MAP Networks

Methods (IF 4.15), 69, Elsevier Science (Invited Paper)

This work takes a data-driven approach to find differential functional summaries in a differential network from two static gene interaction networks in order to map the interaction differences between them under environment or condition change.
15 Sep 2014 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg

One Feature Doesn’t Fit All: Characterizing Topological Features of Targets in Signaling Networks

In the Proceedings of 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM BCB 2014)

ACM Press, Newport Beach, California, USA

This work exploits machine learning to characterize topological features of nodes in signaling networks.
14 Sep 2014 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.


DualAligner: A Dual Alignment-based Strategy to Align Protein Interaction Networks

Bioinformatics (IF 5.32), 30(18), Oxford Univ Press

Software

This is a novel biological network alignment technique that exploits ideas from data management search to generate more efficient but high quality alignment.
13 Jan 2014 Sourav S Bhowmick, Huey Eng Chua, Jie Zheng

INGOT: Towards Network-driven In Silico Combination Therapy

In the Proceedings of 1st International Conference on Big Data and Smart Computing (BigComp 2014)

IEEE CS, Bangkok, Thailand (Invited Paper)

A vision paper that lays down the vision of opportunities and challenges for in silico target combination prediction for combination therapy.
12 Nov 2012 Boon-Siew Seah, Sourav S Bhowmick, C. Forbes Dewey, Jr.

FACETS: Multi-faceted Functional Decomposition of Protein Interaction Networks

Bioinformatics (IF 5.47), 28(20), Oxford Univ Press

Software

Network summarization techniques in computer science typically generate one summary for a given input. This work presents an algorithm called FACET to generate multi-faceted functional summaries of PPI networks, which is more meaningful in biology.
11 Oct 2012 Huey Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, C. F. Dewey, Jr

STEROID: In Silico Heuristic Target Combination Identification for Disease-Related Signaling Networks

In the Proceedings of 3rd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2012)

ACM Press, Orlando, Florida, USA

Extended version

One of the early computational efforts to predict target combinations in disease-related signaling networks for combination therapy.
10 Sept 2012 L. Venkatraman, Ser-Mien Chia, B. C. Narmada, Jacob K White, Sourav S Bhowmick, C. Forbes Dewey, Jr., Peter So, Lisa Tucker-Kellogg, Hanry Yu

Plasmin Triggers a Switch-like Decrease in Thrombospondin-Dependent Activation of TGF-beta1

Biophysical Journal, 103(5), Elsevier Science (IF 4.22)

A computational model of the role of plasmin on TGF-Beta1 activation that is verified with wet lab experiments.
9 Mar 2012 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey,Jr, Hanry Yu

FUSE: A Profit Maximization Approach for Functional Summarization of Biological Networks

BMC Bioinformatics, 13(S3), Biomed Central (IF 3.03)

(Special Issue on Best Papers of ACM BCB 2011)

Extended version of the FUSE paper that integrates network summarization with PPI networks.
8 Jan 2012 Huey-Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, Qing Zhao, C F Dewey, Hanry Yu

In Silico Identification of Endo16 Regulators in the Sea Urchin Endomesoderm Gene Regulatory Network

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA

This work takes a data analytics-driven approach to identify Endo16 regulators in a gene regulatory network.
7 Jan 2012   Huey-Eng Chua, Sourav S Bhowmick, Lisa Tucker-Kellogg, Yingqi Wang, C F Dewey, Hanry Yu

PANI: An Interactive Data-Driven Tool for Target Prioritization in Signaling Networks

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA (Demo)

Video

Software protype that demonstrates data analytics-driven prioritizing of targets in disease-related signaling networks.
6 Jan 2012 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey, Hanry Yu

FUSE: A System for Data-Driven Multi-Level Functional Summarization of Protein Interaction Networks

In the Proceedings of 2nd ACM SIGHIT International Health Informatics Symposium

ACM Press, Miami, Florida, USA (Demo)

Video

Software prototype of functional summarization of PPI networks that bridges graph summarization with biological networks.
5 2011 L Venkatraman, Huipeng Li, C. F. Dewey, J. K. White, Sourav S Bhowmick, Hanry Yu, Lisa Tucker-Kellogg

The Steady States and Dynamics of Urokinase-mediated Plasmin Activation In Silico and In Vitro

Biophysical Journal, 101(8), Elsevier Science (IF 4.2)

This paper uses a computational model to understand the steady states and dynamics of plasmin activation, which is verified using wet lab. This is a more complete version of the PSB paper.
4  Aug 2011 Boon-Siew Seah, Sourav S Bhowmick, C F Dewey, Jr, Hanry Yu  

FUSE: Towards Multi-Level Functional Summarization of Protein Interaction Networks

In the Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011)

ACM Press, Chicago, USA

Best Paper Award

This paper for the first time brings together network summarization and protein-protein interaction networks under one umbrella to understand functional roles of different components of the network.
3 Aug 2011 Huey-Eng Chua, Sourav S Bhowmick, Qing Zhao, L Tucker-Kellogg, C F Dewey, Jr, Hanry Yu

PANI: A Novel Algorithm for Fast Discovery of Putative Target Nodes in Signaling Networks

In the Proceedings of 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB 2011)

ACM Press, Chicago, USA (Short)

Extended version

PANI uses a data analytics framework to discover putative target nodes in disease-related signaling networks.
2

March

2010

W.-X. Zhang, Lisa Tucker-Kellogg, B.C. Narmada, L. Venkatraman, S. Chang, Y. Lu, Nancy Tan, J. White, C. F. Dewey, S S Bhowmick, Peter So, S Shen, Hanry Yu

Cell Delivery Therapeutics for Liver Regeneration

Advanced Drug Delivery Reviews (ADDR)
62(7-8), Elsevier Science (IF 8.3)

This is a review work on liver regeneration.
1 Jan 2010 L Venkatraman, Hanry Yu, Sourav S Bhowmick, C F Dewey, Jr, L Tucker-Kellogg

The Steady States and Dynamics of Urokinase Mediated Plasmin Activation

In the Proceedings of 15th Pacific Symposium of Biocomputing (PSB 2010)  Hawai, USA.

This paper uses a computational model to understand the steady states and dynamics of plasmin activation.

 

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