My research work in MSc (2004-2006) and PhD (2007-2010) has been focused on the design and performance analysis of stochastic local search algorithms for solving combinatorial optimization problems. One underlying theme of the work is to achieve a balance between search efficiency (e.g. runtime cost) and solution quality, which in particular, involves the performance tuning of the designed algorithms and the empirical comparison among them. Besides classical local search algorithms, I am interested in cooperative & distributed search frameworks such as ant colony optimization (ACO) and particle swarm optimization (PSO) which has demonstrated to solve hard problems in a more efficient and effective manner. My other interest in the area involves applying probabilistic models to the optimization domain by integrating reasoning & learning models as a way to improve the overall search results (e.g. Estimation of Distribution Algorithm and Bayesian Optimization Algorithms).

In my MSc., I conducted a comparative study of several metaheuristic algorithms to solve a fertilizer blends optimization problem for Western Ag. Inc. (Saskatoon, Canada). In my PhD study, I focused on developing local search algorithms for solving the RNA Secondary Structure Design (SSD) problem in Bioinformatics. A novel local search algorithm “rnaDesign” has been developed that solved the RNA design problem and is compared with existing literature solutions. A regression model framework has also been designed which is capable of predicting algorithm performance on the RNA design problem with good accuracy. Both works are accepted for the IEEE Computational Intelligence conference in 2009.


Journal Articles

  • H. A. Ebhardt, H. H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bostan and Richard P. Fahlman. “Meta-analysis of small RNA sequencing errors reveals ubiquitous and tissue specific post transcriptional RNA modifications.” Nucleic Acids Research, Oxford Journals, 1-10, 2009 (NCBI)

Conference Papers

  • Herbert H. Tsang and Denny C. Dai, “RNA-DV: an interactive tool for editing and visualizing RNA secondary structures”. BCB ’12 Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine. 2012 (ACM)
  • Denny C. Dai and Kay C. Wiese, “Performance Prediction for RNA Design Using Parametric and Non-Parametric Regression Model”. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Nashville, TN, USA, April 2009. (IEEE)(slide)
  • Denny C. Dai, Herbert H. Tsang and Kay C. Wiese. “rnaDesign: Local Search for RNA Secondary Structure Design”. IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, Nashville, TN, USA, April 2009. (IEEE)(slide)
  • Denny C. Dai, Herbert H. Hsang and Kay C. Wiese, “An Incremental Redundancy Estimation for the Sequence Neighborhood Boundary”. The 4th Canadian Student Conference on Biomedical Computing and Bioinformatics, Vancouver, Canada (Mar. 2009) (RG)


  • A Comparative Study of Metaheuristic Algorithms for the Fertilizer Optimization Problem. M.Sc. Thesis, Department of Computer Science, University of Saskatchewan, 2006. Supervisor: Dr. Michael C. Horsch (USASK)
  • Multi-Agent Robotic Soccer Design for the RoboCup Simulation Platform. B.Sc. Undergrad Thesis (distinguished), GuangDong University of Technology, China, 2004. Supervisor: Dr. Zeng, Bi

Technical Survey

  • RNA Design Optimization: A Survey and Recent Advances, Denny C. Dai. School of Computing Science, Simon Fraser University, 2009. (RG)



demo github sourceforge

RNA-DV is an interactive design and visualization tool for researchers working in the field of RNA secondary structure. I collaborated with my SFU colleague Dr. Herbert Tsang on the project since 2008. I implemented the app in Java using Netbean IDE. RNA-DV is bundled into both a desktop version and a java applet version that can be run directly from the browser.