Anne Caroline Smith

Academic Papers and Research Interests

My research focuses on applying mathematics and computer science to address challenges in medicine, neuroscience, and engineering.

I have experience analyzing electrophysiological and engineering data using filtering methods and machine learning, applying probabilistic techniques to interpret neural sequence data, and developing software tools for imaging and EEG data analysis.

Recent projects include:

EEG data analysis in both rat and human studies (Python MNE)
Pharmacokinetic-pharmacodynamic modeling in drug development (MATLAB SimBiology)
Longitudinal disease modeling using state-space models (R STAN, pymc3, BUGS, and filtering)
Development of R Shiny and DataBricks applications for correlation analysis in drug development

Neuroscience Publications
1. Smith AC, Wu XB, Levy WB. Controlling activity fluctuations in large,sparsley connected random networks. Network: Computation in Neural Systems 2000; 11 pp 63-81.
2. Smith AC, Gerrard JL, Barnes CA, McNaughton BL. Effect of age on burst firing characteristics of rat hippocampal cells. NeuroReport 2000; 11:2865-71.
3. Smith AC, Brown EN. Estimating a state-space model from point process observations. Neural Computation 2003; 15 pp 965-991.
4. Wirth S, Yanike M, Frank LM, Smith AC, Brown EN, Suzuki WA. Single neurons in the monkey hippocampus and learning of new associations. Science 2003; 300 pp 1578-1581.
5. Smith AC, Frank LM, Wirth S, Yanike M, Hu D, Kubota Y, Graybiel AM, Suzuki WA, Brown EN. Dynamic analysis of learning in behavioral experiments. Journal of Neuroscience 2004; 24(2) pp 447-461. https://github.com/asmith3142
6. Smith AC, Stefani MR, Moghaddam B, Brown EN. Analysis and design of behavioral experiments to characterize population learning. J.Neurophysiology (published online Sept. 29, 2004), 2005, 93 pp 1776-1792.
7. Prerau MK, Smith AC, Eden UT, Yanike M, Suzuki W, Brown EN. A mixed filter algorithm for simultaneously recorded continuous-valued and binary observations. Biological Cybernetics 2008, 99(1) pp 1-14.
8. Law JR, Flanery MA, Wirth S, Yanike M, Suzuki WA, Smith AC, Frank LM, Brown EN, Stark CEL. fMRI activity during the gradual acquisition and expression of paired-associate memory. Journal of Neuroscience 2005, 25(24) pp 5720-5729.
9. Smith AC, Smith P. A set probability technique for detecting relative time order across multiple neurons. Neural Computation 2006, 18(5) pp 1197-1214.
10. Barter LS, Mark LO, Smith AC, Antognini JF. Isoflurane potency in the Northern leopard frog Rana pipiens is similar to that in mammalian species. Vet Res Commun, 2007, 31(6) pp 757-63.
11. Smith AC, Wirth S, Suzuki WA, Brown EN. Bayesian analysis of interleaved learning and response bias in behavioral experiments. Journal of Neurophysiology, 2007, 97(3) pp 2516-24.
12. Yanike M, Wirth S, Smith AC, Brown EN, Suzuki WA. Comparison of associative learning-related signals in the macaque perirhinal cortex and hippocampus. Cerebral Cortex, 2008, 19(5) pp 1064-1078.
13. Kubota Y, Liu J, Hu D, DeCoteau W, Eden UT, Smith AC, Graybiel AM. Stable encoding of task structure coexists with flexible coding of task events in sensorimotor striatum. J Neurophysiol PMCID2774470, 102 pp 2142-2160.
14. Wirth S, Avsar E, Chiu CC, Sharma V, Smith AC, Scalon JD, Brown EN, Suzuki WA. Trial Outcome and Associative Learning Signals in the Monkey Hippocampus. Neuron 2009, 61( 6) pp 930-940.
15. Smith AC, Shah SA, Hudson AE, Purpura KP, Victor JD, Brown EN, Schiff ND. A Bayesian statistical analysis of behavioral facilitation associated with deep brain stimulation. J Neurosci Methods 2009 PMCID2743761, 183(2) pp 267-76.
16. Kubota Y, Liu J, Hu D, DeCoteau WE, Eden UT, Smith AC, Graybiel AM. Stable encoding of task structure coexists with flexible coding of task events in Sensorimotor Striatum. J Neurophysiol 2009 PMCID2774470, 102 pp 2142-2160.
17. Prerau MJ, Smith AC, Eden UT, Kubota Y, Yanike M, Suzuki W, Graybiel AM, Brown EN. Characterizing learning by simultaneous analysis of continuous and binary measures of performance. J Neurophysiol 2009, 102 pp 3060-72.
18. Smith AC, Scalon JD, Wirth S, Yanike M, Suzuki WA, Brown EN. State-space algorithms for estimating spike rate functions. Computational Intelligence and Neuroscience 2009 PMCID2774470, 2010(Article ID 425639).
19. McAssey MP, Hsieh F,Smith AC. Coupling among electroencephalogram gamma signals on a short time scale. Computational Intelligence and Neuroscience, 2010, PMCID2926578.
20. S mith AC, Nguyen VK, Karlsson MP, Frank LM, Smith P. Probability of repeating patterns in simultaneous neural data. Neural Comput 2010 PMID: 20608872, 22(10) pp 2522–2536.
21. Solomon M, Frank MJ, Smith AC, Ly S, Carter CS. Transitive inference in adults with autism spectrum disorders. Cogn Affect Behav Neurosci 2011, 11(3) pp 437-499.
22. Solomon M, Smith AC, Frank MJ, Ly S, Carter CS. Probabilistic reinforcement learning in adults with autism spectrum disorders. Autism Res 2011, 4(2) pp 109-20.
23. Smith AC, Fall CP, Sornborger AT. Near-real time connectivity estimation for multivariate neural data. Proceedings from the 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC ’11).
24. Poulsen C, Smith AC, Tucker D, Mattson C, Luu P. Learning and the Development of Contexts for Action. Frontiers in Human Neuroscience. Published online: 09 December, 2011. Vol 5 Article 159 pp 1-12.
25. Wong KF, Smith AC, Pierce ET, Harrell PG, Walsh JL, Salazar-Gómez AF, Tavares CL, Purdon PL, Brown EN. Statistical modeling of behavioral dynamics during propofol-induced loss of consciousness. J Neurosci Methods. 2014 Apr 30;227 pp 65-74
26. Purdon PL, Pavone KJ, Akeju O, Smith AC, Sampson AL, Lee J, Zhou, DW, Solt K, Brown, EN The Ageing Brain: Age-dependent changes in the electroencephalogram during propofol and sevoflurane general anaesthesia. British Journal of Anaesthesia, 2015, Jul. Vol: 115 Special Issue: SI, Supplement: 1 pp 46-57.
27. Gray DT, Smith AC, Burke SN, Gazzaley A, Barnes CA. Attentional updating and monitoring and affective shifting are impacted independently by aging in macaque monkeys. Behavioural Brain Research. Available online 28 June 2016.
28. Comrie AE, Gray DT, Smith AC, Barnes CA. Different macaque models of cognitive aging exhibit task-dependent behavioral disparities. Behav Brain Res. 2018 May 15;344 pp 110-119.
29. Malem-Shinitski N, Zhang Y, Gray DT, Burke SN, Smith AC, Barnes CA, Ba D. A Separable Two-Dimensional Random Field Model of Binary Response Data from Multi-Day Behavioral Experiments. 2018. Journal of Neuroscience Methods.
30. Allsop SA, Wichmann R, Mills F, Burgos-Robles A, Chang CJ, Felix-Ortiz AC, Vienne A, Beyeler A, Izadmehr EM, Glober G, Cum MI, Stergiadou J, Anandalingam KK, Farris K, Namburi P, Leppla CA, Weddington JC, Nieh EH, Smith AC, Ba D, Brown EN, Tye KM. Corticoamygdala Transfer of Socially Derived Information Gates Observational Learning. 2018 Cell, May 2018
31. Kapellusch AJ, Lester AW, Schwartz BA, Smith, AC, Barnes, CA. Analysis of Learning Deficits in Aged Rats on the W-Track Continuous Spatial Alternation Task. 2018. Behavioral Neuroscience 132(6).
32. Crittenden JR, Sauvage M, Kitsukawa T, Burguière E, Cepeda C, André VM, Canault M , Thomsen M, Zhang H, Costa C, Martella G, Ghiglieri V, Pescatore KA, Unterwald EM, Jackson W, Housman DE, Caine SB, Sulzer D, Calabresi P, Levine MS, BrefelCourbon C, Smith AC, Alessi M-C, Azulay J-P, Graybiel AM. Mutations in CalDAG-GEFI Lead to Striatal Signaling Deficits and Psychomotor Symptoms in Multiple Species Including Human. 2019. (Bioarchiv).
33. Antonoudiou P, Colmers PLW, Walton NL, Weiss GL, Smith AC, Nguyen DP, Lewis M, Quirk MC, Barros L, Melon LC, Maguire JL. Allopregnanolone Mediates Affective Switching Through Modulation of Oscillatory States in the Basolateral Amygdala. Biol Psychiatry. 2022 Feb 1;91(3):283-293.doi: 10.1016/j.biopsych.2021.07.017.
34. Beckley JT, Aman TK, Ackley MA, Kazdoba TM, Lewis MC, Smith AC, Farley BJ, Deats W, Hoffman E, Robichaud AJ, Doherty JJ, Quirk MC. Pharmacological characterization of SAGE-718, a novel positive allosteric modulator of N-methyl-d-aspartate receptors. Brit Journal of Pharmacology, 2024, 181(7) April. pp 1028-1050. https://bpspubs.onlinelibrary.wiley.com/doi/full/10.1111/bph.16235
Book Chapter
1. Smith AC. State-space modeling for the analysis of behavior in learning experiments. In “Advanced State-Space Methods for Neural and Clinical Data”, 2015. Cambridge University Press. Z. Chen, editor.
Applied Mathematics Publications (PhD work)
1. Smith AC, Roberts WW. Straightening of crimped and hooked fibers in converging transport ducts: Computational modeling. Textile Research Journal 1994; 64(6) pp 325-334.
2. Smith AC, Roberts WW. Computational modeling of fiber formation in spunbonding of polypropylene with crystallization: Comparison with experiments. International Nonwovens Journal 1994; 6(1) pp 31-41.
June 14, 2025

Anne Caroline Smith

Neuroscience Publications

Book Chapter

Applied Mathematics Publications (PhD work)