MY RESEARCH  Interests  Projects  Skills Resources Awards Acknowledgement

Interests

• (Graph) data mining and its application in computational sciences
• Applied graph theory, discrete optimization
• Parallel and Distributed computing, modeling and simulation, software engineering
• Scientific Computing

Projects (papers and softwares)

• Condition-Dependent dynamics prediction of protein-protein interaction networks   
  Recent technological advances have produced large data sets of protein-protein interactions (PPI), which construct a static map. However, it fails to represent dynamic aspects of interactions. The dynamics inference of PPI networks is critical for supporting the comprehensibility of the biological systems.
  - Proposed a graph-based conflict-free scheduling algorithm to build a training model, which is a critical component in multi-label classification for predicting dynamics of PPI networks.
  - Explored statistical learning theory and several data mining techniques and tools
  - Anticipated the writing of an extended NSF proposal based on the project.
  - Supplementary materials available

• AlignNets : Network alignment and motif finding  
  Metabolism is a vital cellular process whose understanding is critical to human disease studies and drug discovery. The accumulation of high-throughput genomic, proteomic and metabolical data allows for increasingly accurate modeling and reconstruction of metabolic networks. Alignment of the reconstructed networks can catch model inconsistencies and infer missing elements. Existing alignment tools are mostly based on isomorphic and homeomorphic embedding effectively solving a problem that is NP-complete even when searching a match for a tree in acyclic networks. In this project, I
  - Designed the first polynomial-time algorithm for efficiently finding optimal homo-homeo morphic embedding from multi-source trees into arbitrary networks which allows for enzyme deletions and insertions
  - Extended the algorithm to arbitrary networks even with cycles
  - Proposed a framework of detecting and filling pathway by embedding sequence alignment tools and do database search for missing enzymes and proteins with the matching prosites and the resulted high sequence similarity
  - Implemented a web service tool MetNetAligner which can be used for predicting unknown pathways, comparing and finding conserved patterns, and resolving ambiguous identification of enzymes. The tool supports two alignment algorithms.
  - Published papers: Recomb Satellite'07 paper,  BIBE'07 paper , BIBE'07 slides  ,  ISBRA'07 ,  CSBS 2007 
  -- Tool Website available under request .
   
• iC2mpi : A Platform for Parallel Execution of Graph-Structured Iterative Computations (Paper in PDSEC'07  )  (CSc6310)
  The project aims to studying the parallelization of sequential programs. A unique proof-of-concept prototype platform (iC2mpi) has been proposed for parallelization of a class of applications that have similar computational structure, namely graph-structured iterative applications such as the time-stepped simulation of battlefield management. I
  - Studied static and dynamic load balancing in distributed computing;
  - Implemented Battlefield simulation based on iC2mpi;
   
• MANET : Self Management Routing of Mobile Sensor Network (Paper in SpringSim'06  Slides in SpringSim'06  Paper in Studies in Computational Intelligence'06    ).
  Most existing routing protocols in mobile ad hoc networks mainly focus on addressing the problems of dense and sparse yet connected networks. However, the crisis-driven and geography-driven applications, such as those in ecology forest and modern battlefield, typically challenge current routing protocols in disjoint mobile sensor networks (DMSN) where network partitions can occur and last for a significant period.
  In this project, I
  - Implemented an agent-based simulation for studying the problems of efficient route discovery in the disjoint networks
  - Proposed a novel autonomous messenger-based route discovery and routing protocol for disjoint clusters-based topology in DMSN
  - Proposed another two routing discovery and maintenance protocols which applied genetic fuzzy system and genetic algorithm and improved the performance
  - Software availableHERE.
   
• CrayfishSim : A behavior-model simulation for natural ecology which is based on DEVSJAVA ( Poster in SECABC05 )
  In sea ecology, there exists the mechanism which decide the movement of preys and predators with the dynamics of the environment. The mechanishm can be described as a network of mutually inhibiting centers for specific behaviors. This research aims to study behavioral choice models which account for more of the complexities of animal behavior, including changes in behavioral state, and formation of social dominance hierarchies.
  In this project, I
  - Provided a heap-based implementation of discrete event simulation(DEVS)
  - Studied the behavior-model simulation and its application in sea ecology
  - Designing and implementing a GUI-based controller for the behavior-model simulation which also shows real time behavior analysis data in dynamic charts
  - Software availableHERE.
   
• Optimization Algorithm
  Minimum Linear Arrangement
  - Code is available HERE
  - Report is available HERE
  
  
• Protein Sequence Analysis
  Obesity, as an increasingly serious public healthy disease, has been attracting more and more researchers. INSIG2, as an attractive candidate protein associated with obesity, has been studied recently. The structure prediction and verification have been significantly expected. So our project aim is to identify its structure by employing some popular bioinformatics tools such as PDB, BLAST, ClusterW, RASMOL and AMMP.
  - Slides are available HERE
  - Report is available HERE
  
  
• Task Allocation in Real Team and Multi Robots  (CSc8350) ( .doc)