Publications

Papers

• Koti, D. S., Phillips, J. L., and Cottle, F. S. (in-press). Contrastive Point Coud Pretraining for Enhanced Transformers. In Proceedings of the 36th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2024). Herndon, VA.
• Romer, A. S., Grisnik, M., Dallas, J. W., Sutton, W., Murray, C. M., Hardman, R. H., Blanchard, T., Hanscom, R. J., Clark, R. W., Godwin, C., Alexander, N. R., Moe, K. C., Cobb, V. A., Eaker, J., Colvin, R., Thames, D., Ogle, C., Campbell, J., Frost, C., Brubaker, R. L., Snyder, S. D., Rurik, A. J., Cummins, C. E., Ludwig, D. W., Phillips, J. L., and Walker, D. M. (2024). Effects of snake fungal disease (ophidiomycosis) on the skin microbiome across two major experimental scales. Conservation Biology. [PDF]
• Givens, K., Ludwig, D. W., and Phillips, J. L. (2024). StrXL: combining Set Transformer and Transformer XL to model sets of arbitrary cardinality. In Proceedings of the 37th International FLAIRS Conference (FLAIRS-2024), Destin, FL. [PDF]
• Mahfooz, A. and Phillips, J. L. (2024). Conditional forecasting of bitcoin prices using exogenous variables. IEEE Access. [PDF]
• Miller, J., Naderi, S., Mullinax, C. B., and Phillips, J. L. (2022). Attention is not enough. In Proceedings of the 44th Annual Meeting of the Cognitive Science Society (CogSci 2022), Toronto, Canada. [PDF] or [preprint-PDF]
• Morton, S. P. and Phillips, J. L. (2021). Computational electrostatics predict variations in SARS-CoV-2 spike and human ACE2 interactions. 2021 IEEE International Conference on Bioinformatics and Biomedicine Workshops (HPC4COVID-19 2021). [PDF] or [preprint-PDF]
• Morton, S. P. and Phillips, J. L. (2021). pH dependent binding energies of broadly neutralizing antibodies. 2021 IEEE International Conference on Bioinformatics and Biomedicine Workshops (CSBW 2021). [PDF] or [preprint-PDF]
• Ludwig, D. W., Remedios, L. W., and Phillips, J. L. (2021). A neurobiologically-inspired deep learning framework for autonomous context learning. In Proceedings of the 33rd IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2021). Bourbakis-Ramamoorthy Best Paper Award. [PDF] or [preprint-PDF]
• Khan, H. and Phillips, J. L. (2021). Language agnostic model: detecting Islamophobic content on social media. In Proceedings of the 2021 ACM Southeast Conference (ACMSE 2021). [PDF] or [PDF]
• Omatu, N. and Phillips, J. L. (2021). Benefits of combining dimensional attention and working memory for partially observable reinforcement learning problems. In Proceedings of the 2021 ACM Southeast Conference (ACMSE 2021). [PDF] or [PDF]
• Dong, Z., Phillips, J. L., Oslund, E., Pettey, C. and Brawner, C. E. (2021). Positive impact of an S-STEM Scholarship Program on Computer Science students' academic performance and retention rate. In Proceedings of the 2021 American Society for Engineering Education Annual Conference and Exposition (ASEE 2021). [LINK] or [preprint-PDF]
• Khan, N. and Phillips, J. L. (2020). Combined model for sensory-based and feedback-based task switching: solving hierarchical reinforcement learning problems statically and dynamically with transfer learning. In Proceedings of the 32nd IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2020). [PDF] or [PDF]
• Syzonenko, I. and Phillips, J. L. (2020). Accelerated protein folding using greedy-proximal A*. Journal of Chemical Theory and Computation. [LINK]
• Williams, A. S. and Phillips, J. L. (2020). Transfer reinforcement learning using output-gated working memory. In Proceedings of the 34th AAAI Conference on Artificial Intelligence, New York, NY. [PDF] or [preprint-PDF]
• Connors, K. A., Beasley, A., Barron, M. G., Belanger, S. E., Bonnell, M., Brill, J. L., de Awart, D., Kienzler, A., Krailler, J., Otter, R., Phillips, J. L., and Embry, M. R. (2019). Creation of a curated aquatic toxicology database: EnviroTox. Environmental Toxicology and Chemistry. [LINK]
• Morton, S. P., Phillips, J. B., and Phillips, J. L. (2019). The molecular basis of pH-modulated HIV gp120 binding revealed. Evolutionary Bioinformatics. [LINK]
• Morton, S. P., Howton, J., and Phillips, J. L. (2018). Sub-class differences of pH-dependent HIV GP120-CD4 interactions. In Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (CSBW), Washington, DC. [PDF] or [preprint-PDF]
• Phillips, J. L., Colvin, M. E., and Newsam, S. (2018). Dimensionality estimation of protein dynamics using polymer models. In Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (CSBW), Washington, DC. [PDF] or [preprint-PDF]
• Syzonenko, I. and Phillips, J. L. (2018). Hybrid spectral/subspace clustering of molecular dynamics simulations. In Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, Washington, DC. [PDF] or [preprint-PDF]
• Jovanovich, M. P. and Phillips, J. L. (2018). N-task learning: solving multiple or unknown numbers of reinforcement learning problems. In Proceedings of the 40th Annual Meeting of the Cognitive Science Society (CogSci 2018), Madison, WI. [PDF]
• Williams, A. S. and Phillips, J. L. (2018). Multilayer context reasoning in a neurobiologically inspired working memory model for cognitive robots. In Proceedings of the 40th Annual Meeting of the Cognitive Science Society (CogSci 2018), Madison, WI. [PDF]
• Mueller, R. T., Travers, T., Cha H.-J., Phillips, J., Gnanakaran, S., and Pos, K. M. (2017). Switch loop flexibility affects substrate transport of the AcrB efflux pump. Journal of Molecular Biology, 429 (24), 3863-3874. [PDF]
• Morton, S. P., Phillips, J. B., and Phillips, J. L. (2017). High-throughput structural modeling of the HIV transmission bottleneck. 2017 IEEE International Conference on Bioinformatics and Biomedicine Workshops, Kansas City, MO. [PDF] or [preprint-PDF]
• Howton, J. and Phillips, J. L. (2017). Computational modeling of pH-dependent gp120-CD4 interactions in founder and chronic HIV strains. Proceedings of the 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (CSBW), Boston, MA. [PDF] or [PDF]
• DuBois, G. M. and Phillips, J. L. (2017). Working memory concept encoding using holographic reduced representations. Proceedings of the 28th Modern Artificial Intelligence and Cognitive Science Conference (MAICS 2017), Fort Wayne, IN. [PDF]
• Phillips, J. L., and Gnanakaran, S. (2015). A data-driven approach to modeling the tripartite structure of multidrug resistance efflux pumps. Proteins: Structure, Function, and Bioinformatics, 83 (1), 46-65. [PDF]
• Gottardo, R., Bailer, R. T., Korber, B T., Gnanakaran, S., Phillips, J., Shen, X., Tomaras, G. D., Turk, E., Imholte, G., Eckler, L., Wenschuh, H., Zerweck, J., Greene, K., Gao, H., Berman, P. W., Francis, D., Sinangil, F., Lee, C., Nitayaphan, S., Rerks-Ngarm, S., Kaewkungwal, J., Pitisuttithum, P., Tartaglia, J., Robb, M. L., Michael, N. L., Kim, J. H., Zolla-Pazner, S., Haynes, B. F., Mascola, J. R., Self, S., Gilbert, P., Montefiori, D. C. (2013). Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial. PLoS One. [PDF]
• Stieh, D., Phillips J. L., Rogers P. M., King, D. F., Cianci, G. C., Jeffs, S. A., Gnanakaran, S., and Shattock, R. J. (2013). Dynamic electrophoretic fingerprinting of the HIV-1 envelope glycoprotein. Retrovirology, 10 (33). [PDF]
• Phillips, J. L., Colvin, M. E., and Newsam, S. (2011). Validating clustering of molecular dynamics simulations using polymer models. BMC Bioinformatics, 12 (1), 445. [PDF]
• Yamada, J., Phillips, J. L., Patel, S., Goldfien, G., Calestagne-Morelli, A., Huang, H., Reza, R., Acheson, J., Krishnan, V. V., Newsam, S., Gopinathan, A., Lau, E. Y., Colvin, M. E., Uversky V. N., and Rexach M. F. (2010). A bimodal distribution of two distinct categories of instrinsically-disordered structures with separate functions in FG nucleoporins. Molecular and Cellular Proteomics, 9, 2205-2224. [PDF]
• Lau, E. Y., Phillips, J. L., and Colvin, M. E. (2009). Molecular dynamics simulations of highly charged green fluorescent proteins. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 107 (8), 1233-1241. [PDF]
• Phillips, J. L., Colvin, M. E., Lau, E. Y., and Newsam, S. (2008). Analyzing dynamical simulations of intrinsically disordered proteins using spectral clustering. In IEEE BIBM 2008 Workshop on Computational Structural Bioinformatics, Philadelphia, PA. [PDF]
• Tugcu, M., Wang, X., Hunter, J. E., Phillips, J., Noelle, D., and Wilkes, D. M. (2007). A computational neuroscience model of working memory with application to robot perceptual learning. In Proceedings of the 3rd International Conference on Computational Intelligence, Banff, Alberta, Canada. [PDF]
• Phillips, J. L., and Noelle, D. C. (2006). Working memory for robots: inspirations from computational neuroscience. In Proceedings of the 5th International Conference on Development and Learning, Bloomington, IN. [PDF]
• Phillips, J. L., and Noelle, D. C. (2005). A biologically inspired working memory framework for robots. In Proceedings of the 14th IEEE International Workshop on Robot and Human Interactive Communication, Nashville, TN. [PDF]
• Phillips, J. L., Kogekar, S., and Adams, J. A. (2004). Emergency automated response system (EARS). In Proceedings of the 48 Annual Meeting of the Human Factors and Ergonomics Society, New Orleans, LA. [PDF]
• Phillips, J. L., and Noelle, D. C. (2004). Reinforcement learning of dimensional attention for categorization. In Proceedings of the 26th Annual Meeting of the Cognitive Science Society (CogSci 2004), Chicago, IL. [PDF]

Ph.D. Dissertation

• Phillips, J. L. (2012). Validation of computational approaches for studying disordered and unfolded protein dynamics using polymer models. University of California, Merced. [PDF]

M.S. Thesis

• Phillips, J. L. (2004). Reinforcement learning of dimensional attention for categorization. Vanderbilt University. [PDF]