Molecular Graphics and Modeling Select Publications

2011
Aaron Smalter, Jun Huan, Gerry Lushington. 
Similarity Boosting for Label Noise Tolerance in Protein-Chemical Interaction Prediction. In Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB'11), 2011.

Xiaohong Wang, Jun Huan, Aaron Smalter, and Gerald Lushington.
G-hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases. Graph Data Management: Techniques and Applications, Sherif Sakr and Eric Pardede edt, IGI Global, ISBN 161350053X, 2011

2010
Aaron Smalter, Jun Huan, Gerald Lushington.
GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No.2, pp. 197-207, 2010

Xiaohong Wang, Jun Huan, Aaron Smalter, Gerald Lushington.
Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases. BMC Bioinformatics, Vol. 11 (Suppl. 3), 2010.

The MicroArray Quality Control (MAQC) Consortium.
The MAQC-II Project: A Comprehensive Study of Common Practices for the Development and Validation of Microarray-based Predictive Models. Nature Biotechnology, 2010.

2009
Aaron Smalter, Jun Huan, Gerald Lushington.
Feature Selection in the Feature Tensor Product Space. Proceedings of the 9th IEEE International Conference on Data Mining (ICDM'09), 2009.

Aaron Smalter, Jun Huan, and Gerald Lushington.
GPD: A Graph Pattern Diffusion Kernel for Accurate Graph Classification with Applications in Cheminformatics. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2009.

Aaron Smalter, Jun Huan, Gerald Lushington.
Feature Selection in the Feature Tensor Product Space. Proceedings of the 9th IEEE International Conference on Data Mining (ICDM'09), 2009.

Aaron Smalter, Jun Huan, Gerald Lushington.
Graph Wavelet Alignment Kernels for Drug Virtual Screening. Journal of Bioinformatics and Computational Biology, Vol. 7 (3), pp. 473-497, 2009.

Xiaohong Wang, Jun Huan, Aaron Smalter, Gerald Lushington.
Application of Kernel Functions for Accurate Similarity Search in Large Chemical Databases. In Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM'09), 2009.

Xiaohong Wang, Aaron Smalter, Jun Huan, and Gerald Lushington.
G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases. In Proceedings of the 12th International Conference on Extending Database Technology, 2009.


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