Changhe Yuan and Brandon Malone, "Learning Optimal Bayesian Networks: A Shortest Path Perspective," Journal of Artificial Intelligence Research, vol. 48, pp. 23 - 65., October 2013.
Babi Ramesh Reddy Nallamilli, Jian Zhang, Hana Mujahid, Brandon M. Malone, Susan M. Bridges and Zhaohua Peng, “Polycomb Group Gene OsFIE2 Regulates Rice (Oryza sativa) Seed Development and Grain Filling via a Mechanism Distinct from Arabidopsis,” PLoS Genetics, 9(3): e1003322. doi:10.1371/journal.pgen.1003322, March 2013.
William Sanders, Nan Wang, Susan Bridges, Brandon Malone, Yoginder Dandass, Fiona McCarthy, Bindu Nanduri, Mark Lawrence and Shane Burgess. “The Proteogenomic Mapping Tool,” BMC Bioinformatics, vol. 12, no. 115, April 2011.
Brandon Malone, Kustaa Kangas, Matti Jarvisalo, Mikko Koivisto and Petri Myllymaki. "Predicting the Hardness of Learning Bayesian Networks," 28th AAAI Conference on Artificial Intelligence. Quebec City, Canada. July 2014.
Xiannian Fan, Changhe Yuan and Brandon Malone. "Tightening Bounds for Bayesian Network Structure Learning," 28th AAAI Conference on Artificial Intelligence. Quebec City, Canada. July 2014.
Xiannian Fan, Brandon Malone and Changhe Yuan. "Finding Optimal Bayesian Network Structures with Constraints Learned from Data," 30th Conference on Uncertainty in Artificial Intelligence. Quebec City, Canada. July 2014.
Jeremias Berg, Matti Jarvisalo and Brandon Malone. "Learning Optimal Bounded Treewidth Bayesian Networks via Maximum Satisfiability," 17th International Conference on Artificial Intelligence and Statistics. Reykjavik, Iceland. April 2014.
Brandon Malone and Changhe Yuan, "Evaluating Anytime Algorithms for Learning Optimal Bayesian Networks," 29th Conference on Uncertainty in Artificial Intelligence, Bellevue, Washington, July 2013.
Srishti Srivastava, Brandon Malone, Nitin Sukhija, Ioana Banicescu, Florina Ciorba, "Predicting the Flexibility of Dynamic Loop Scheduling Using an Artificial Neural Network," 12th International Symposium on Parallel and Distributed Computing, Bucharest, Romania, June 2013.
Changhe Yuan and Brandon Malone. "An Improved Admissible Heuristic for Finding Optimal Bayesian Networks," 28th Conference on Uncertainty in Artificial Intelligence, Catalina Island, California, August 2012.
Brandon Malone, Changhe Yuan and Eric Hansen. “Memory-Efficient Dynamic Programming for Learning Optimal Bayesian Networks,” 25th AAAI Conference on Artificial Intelligence, San Francisco, California, August 2011.
Brandon Malone, Changhe Yuan, Eric Hansen and Susan Bridges. “Improving the Scalability of Optimal Bayesian Network Learning with Frontier Breadth-First Branch and Bound Search,” 27th Conference on Uncertainty in Artificial Intelligence, Barcelona, Catalonia, Spain, July 2011.
Changhe Yuan, Brandon Malone and Xiaojian Wu. “Learning Optimal Bayesian Networks Using A* Search,” 22nd International Joint Conference on Artificial Intelligence, Barcelona, Catalonia, Spain, July 2011.
Brandon Malone, Travis Atkison, Martha Kosa and Frank Hadlock. “Pedagogically effective effortless algorithm visualization with a PCIL,” 39th IEEE International Conference on Frontiers in Education, San Antonio, TX, October 2009.
Brandon Malone and Ambareen Siraj. “Tracking requirements and threats for secure software development,” 46th ACM Southeast Conference, Auburn, Alabama, March 2008.
Michael Baldwin and Brandon Malone, “Utilizing smart cards for authentication and compliance tracking in a diabetes case management system,” 46th ACM Southeast Conference, Auburn, Alabama, March 2008.
Frank Hadlock and Brandon Malone, “The Frequency Median Sequence and its Construction,” International Conference on Artificial Intelligence 2006, Las Vegas, Nevada, pp. 509-513, June 2006.
Conference and Workshop Papers Published as Special Issues of Journals
Nitin Sukhija, Brandon Malone, Srishti Srivastava, Ioana Banicescu and Florina Ciorba. "Portfolio-based Selection of Robust Dynamic Loop Scheduling Algorithms using Machine Learning," 3rd International Workshop on Parallel and Distributed Computing for Large Scale Machine Learning and Big Data Analytics. Phoenix, Arizona. May 2014. (Preprint. To appear in IEEE International Symposium on Parallel & Distributed Processing, Workshops and PhD Forum (IPDPSW)). Best Paper Award.
Brandon Malone and Changhe Yuan, "A Depth-first Branch and Bound Algorithm for Learning Optimal Bayesian Networks," Graph Structures for Knowledge Representation and Reasoning, Lecture Notes in Computer Science, vol. 8323, pp. 111-122. 2014.
Zhifa Liu, Brandon Malone and Changhe Yuan. "Empirical Evaluation of Scoring Functions for Bayesian Network Model Selection," BMC Bioinformatics, vol. 13, suppl. 15, September 2012.
Brandon Malone, Andy Perkins and Susan Bridges. “Integrating phenotype and gene expression data for predicting gene function,” BMC Bioinformatics, vol. 10, suppl. 11, October 2009.
Frank Hadlock, Robert Fly and Brandon Malone. “A Comprehensive Problem for Algorithm and Paradigm Visualization,” The Journal of Computing Sciences in Colleges, vol. 22, no. 2, pp. 189 – 196, December 2006.
Brandon Malone and Changhe Yuan. "A Bounded Error, Anytime, Parallel Algorithm for Exact Bayesian Network Structure Learning," 6th European Workshop on Probabilistic Graphical Models, Granada, Spain, September 2012.