Publications

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2021	Addressing noise in co-expression network construction. Joshua J R Burns, Benjamin T Shealy, Mitchell S Greer, John A Hadish, Matthew T McGowan, Tyler Biggs, Melissa C Smith, F Alex Feltus, and Stephen P Ficklin. Briefings in Bioinformatics. bbab495.
2021	GPU Acceleration of the HemeLB Code for Lattice Boltzmann Simulations in Sparse Complex Geometries. Benjamin T Shealy, Mehrdad Yousefi, Ashwin T Srinath, Melissa C Smith, and Ulf D Schiller. IEEE Access.
2021	Intelligent Resource Provisioning for Scientific Workflows and HPC. Benjamin T Shealy, F Alex Feltus, and Melissa C Smith. 2021 IEEE Workshop on Workflows in Support of Large-Scale Science (WORKS).
2020	Cellular State Transformations Using Deep Learning for Precision Medicine Applications. Colin Targonski, M Reed Bender, Benjamin T Shealy, Benafsh Husain, Bill Paseman, Melissa C Smith, and F Alex Feltus. Patterns.
2019	A generalized deep learning approach for local structure identification in molecular simulations. Ryan S DeFever, Colin Targonski, Steven W Hall, Melissa C Smith, and Sapna Sarupria. Chemical science 10(32).
2019	Speech Enhancement Using Forked Generative Adversarial Networks with Spectral Subtraction. Ju Lin, Sufeng Niu, Zice Wei, Xiang Lan, Adriaan J Wijngaarden, Melissa C Smith, and Kuang-Ching Wang. Proc. Interspeech 2019.
2019	GPU Implementation of Pairwise Gaussian Mixture Models for Multi-Modal Gene Co-Expression Networks. Benjamin T Shealy, Josh JR Burns, Melissa C Smith, F Alex Feltus, and Stephen P Ficklin. IEEE Access.
2019	Uncovering biomarker genes with enriched classification potential from Hallmark gene sets. Colin A Targonski, Courtney A Shearer, Benjamin T Shealy, Melissa C Smith, and F Alex Feltus. Scientific reports 9(1).
2018	Parallel Power Flow based on OpenMP. Afshin Ahmadi, Shuangshuang Jin, Melissa C Smith, E Randolph Collins, and Arman Goudarzi. 2018 North American Power Symposium (NAPS).
2018	Artificial Intelligence and Deep Learning Applications for Automotive Manufacturing. Andre Luckow, Ken Kennedy, Marcin Ziolkowski, Emil Djerekarov, Matthew Cook, Edward Duffy, Michael Schleiss, Bennie Vorster, Edwin Weill, Ankit Kulshrestha, and others. 2018 IEEE international conference on Big Data (Big Data).
2018	Generalized value iteration networks: Life beyond lattices. Sufeng Niu, Siheng Chen, Hanyu Guo, Colin Targonski, Melissa C Smith, and Jelena Kova{\v{c}}evi{\'c}. Thirty-Second AAAI Conference on Artificial Intelligence.
2016	HPC enabled real-time remote processing of laparoscopic surgery. Zahra Ronaghi, Karan Sapra, Ryan Izard, Edward Duffy, Melissa C Smith, Kuang-Ching Wang, and David M Kwartowitz. Medical Imaging 2016: Image-Guided Procedures, Robotic Interventions, and Modeling.
2015	Enhancing hardware design flows with MyHDL. Keerthan Jaic and Melissa C Smith. Proceedings of the 2015 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays.
2015	Subjective versus objective: classifying analytical models for productive heterogeneous performance prediction. Vivek K Pallipuram, Melissa C Smith, Nilim Sarma, Ranajeet Anand, Edwin Weill, and Karan Sapra. The Journal of Supercomputing 71(1).
2015	HPC Enabled Real-Time Remote Processing of Laparoscopic Surgery. Karan Sapra, Zahra Ronaghi, Ryan Izard, Edward Duffy, Melissa C Smith, Kuang-Ching Wang, and David Kwartowitz. Accepted Poster, Supercomputing (SC).
2014	A practical network intrusion detection system for inline FPGAs on 10GbE network adapters. Keerthan Jaic, Melissa C Smith, and Nilim Sarma. 2014 IEEE 25th International Conference on Application-Specific Systems, Architectures and Processors.
2014	Combining Hadoop and GPU to preprocess large Affymetrix microarray data. Sufeng Niu, Guangyu Yang, Nilim Sarma, Pengfei Xuan, Melissa C Smith, Pradip Srimani, and Feng Luo. 2014 IEEE international conference on big data (Big Data).
2014	A regression-based performance prediction framework for synchronous iterative algorithms on general purpose graphical processing unit clusters. Vivek K Pallipuram, Melissa C Smith, Nimisha Raut, and Xiaoyu Ren. Concurrency and Computation: Practice and Experience 26(2).
2013	Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study. F Alex Feltus, Stephen P Ficklin, Scott M Gibson, and Melissa C Smith. BMC systems biology 7(1).
2013	Massive-scale gene co-expression network construction and robustness testing using random matrix theory. Scott M Gibson, Stephen P Ficklin, Sven Isaacson, Feng Luo, Frank A Feltus, and Melissa C Smith. PloS one 8(2).
2013	Circumventing keyloggers and screendumps. Karan Sapra, Benafsh Husain, Richard Brooks, and Melissa Smith. 2013 8th International Conference on Malicious and Unwanted Software:" The Americas"(MALWARE).
2012	Parallelizing principal component analysis for robust facial recognition using CUDA. Todd Goodall, Scott Gibson, and Melissa C Smith. 2012 Symposium on Application Accelerators in High Performance Computing.
2012	A comparative study of GPU programming models and architectures using neural networks. Vivek K Pallipuram, Mohammad Bhuiyan, and Melissa C Smith. The Journal of Supercomputing 61(3).
2012	Exploring multi-level parallelism for large-scale spiking neural networks. Vivek K Pallipuram, Melissa C Smith, Nimisha Raut, and Xiaoyu Ren. Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA).
2012	A multi-node GPGPU implementation of non-linear anisotropic diffusion filter. Vivek K Pallipuram, Nimisha Raut, Xiaoyu Ren, Melissa C Smith, and Sumedh Naik. 2012 Symposium on Application Accelerators in High Performance Computing.
2012	Optimization of shared high-performance reconfigurable computing resources. Melissa C Smith and Gregory D Peterson. ACM Transactions on Embedded Computing Systems (TECS) 11(2).
2011	Performance, optimization, and fitness: Connecting applications to architectures. Mohammad A Bhuiyan, Melissa C Smith, and Vivek K Pallipuram. Concurrency and Computation: Practice and Experience 23(10).
2011	An analytical model for multilevel performance prediction of Multi-FPGA systems. Brian Holland, Alan D George, Herman Lam, and Melissa C Smith. ACM Transactions on Reconfigurable Technology and Systems (TRETS) 4(3).
2011	Evaluation of GPU architectures using spiking neural networks. Vivek K Pallipuram, Mohammad A Bhuiyan, and Melissa C Smith. 2011 Symposium on Application Accelerators in High-Performance Computing.
2011	Heterogeneous Accelerated Bioinformatics-Perspectives for Cancer Research. E Stahlberg, T Steinke, MC Smith, S Chandrasekaran, and B Chapman. Proceedings of the International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA).
2011	An End-to-End Tool Flow for FPGA-Accelerated Scientific Computing. Greg Stitt, Alan George, Herman Lam, Melissa Smith, Vikas Aggarwal, Gongyu Wang, Casey Reardon, Brian Holland, Seth Koehler, and James Coole. IEEE Design \& Test of Computers 28(4).
2010	Acceleration of spiking neural networks in emerging multi-core and GPU architectures. Mohammad A Bhuiyan, Vivek K Pallipuram, Melissa C Smith, Tarek Taha, and Rommel Jalasutram. 2010 IEEE International Symposium on Parallel \& Distributed Processing, Workshops and Phd Forum (IPDPSW).
2010	Optimization and performance study of large-scale biological networks for reconfigurable computing. Mohammad A Bhuiyan, Ananth Nallamuthu, Melissa C Smith, and Vivek K Pallipuram. 2010 Fourth International Workshop On High-Performance Reconfigurable Computing Technology And Applications (Hprcta).
2010	Energy efficient biomolecular simulations with FPGA-based reconfigurable computing. Ananth Nallamuthu, Melissa C Smith, Scott Hampton, Pratul K Agarwal, and Sadaf R Alam. Proceedings of the 7th ACM international conference on Computing frontiers.
2009	FPGA implementation of Izhikevich spiking neural networks for character recognition. Kenneth L Rice, Mohammad A Bhuiyan, Tarek M Taha, Christopher N Vutsinas, and Melissa C Smith. 2009 International Conference on Reconfigurable Computing and FPGAs.
2008	Strategic challenges for application development productivity in reconfigurable computing. Saumil G Merchant, Brian M Holland, Casey Reardon, Alan D George, Herman Lam, Greg Stitt, Melissa C Smith, Nahid Alam, Ivan Gonzalez, Esam El-Araby, and others. 2008 IEEE National Aerospace and Electronics Conference.
2007	Using FPGA devices to accelerate biomolecular simulations. Sadaf R Alam, Pratul K Agarwal, Melissa C Smith, Jeffrey S Vetter, and David Caliga. Computer 40(3).
2005	Accelerating scientific applications with the SRC-6 reconfigurable computer: Methodologies and analysis. Melissa C Smith, Jeffrey S Vetter, and Xuejun Liang. 19th IEEE International Parallel and Distributed Processing Symposium.
2005	Parallel application performance on shared high performance reconfigurable computing resources. Melissa C Smith and Gregory D Peterson. Performance Evaluation 60(1-4).
2005	Scientific computing beyond CPUs: FPGA implementations of common scientific kernels. Melissa C Smith, Jeffrey S Vetter, and Sadaf R Alam. 2005 MAPLD International Conference.