Publications

Journal Articles

  • A.S. Charles, N. Cermak, R. Affan, B. Scott, J. Schiller, and G. Mishne. GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging.  pdf code
  • A. Song, J.L. Gauthier, J.W. Pillow, D.W. Tank, and A.S. Charles. Neural Anatomy and Optical Microscopy (NAOMi) Simulation for evaluating calcium imaging methods. Journal of Neuroscience Methods 358:109173, 2021. paper link, biorxiv pdf, code, data
  • Q. She, X. Wu, B. Jelfs, A.S. Charles, and R.H.M. Chan. An Efficient and Flexible Spike Train Model via Empirical Bayes. IEEE Transactions of Signal Processing. In Press. 2021. pdf
  • S.A. Koay, A.S. Charles, S.Y. Thiberge, C.D. Brody, and D.W. Tank. Sequential and efficient neural-population coding of complex task information. Submitted. 2021. pdf
  • J.L. Gauthier, S.A. Koay, E.H. Nieh, D.W. Tank, J.W. Pillow, and A.S. Charles. Detecting and Correcting False Transients in Calcium Imaging. Submitted 2020. pdf
  • A.S. Charles, B. Falk, N. Turner, T.D. Pereira, D. Tward, B.D. Pedigo, J. Chung, R. Burns, S.S. Ghosh, J.M. Kebschull, W. Silversmith, and J.T. Vogelstein. Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics. Annual Review of Neuroscience 43(1):441-464, 2020. pdf
  • N.P. Bertrand*, A.S. Charles*, J. Lee*, P.B. Dunn, and C.J. Rozell. Efficient tracking of sparse signals via an Earth mover’s distance regularizer. IEEE Signal Processing Letters 27:1120-1124, 2020. *Equal contribution. IEEE Xplore, pdf.
  • G. Barello, A.S. Charles and J.W. Pillow. Sparse-coding variational auto-encoders. Submitted 2018. pdf .
  • A.S. Charles and C.J. Rozell. Learning dictionaries of dynamics for sparse signal tracking. Submitted 2018.
  • A.S. Charles*, M. Park*, J.P. Weller, G.D. Horwitz, and J.W. Pillow. Dethroning the Fano Factor: a flexible, model-based approach to partitioning neural variability. Neural Computation 30(4):1012-1045 2018. *Joint first author. pdf. code.
  • A. Song*, A.S. Charles*, S.A. Koay, J.L. Gauthier, S.Y. Thiberge, J.W. Pillow, and D.W. Tank. Volumetric Two-Photon Imaging of Neurons Using Spectroscopy (vTwINS). Nature Methods 14(4):420-426, Apr. 2017. *Joint first author. pdf. code.
  • A.S. Charles, D. Yin, and C.J. Rozell. Distributed Sequence Memory of Multidimensional Inputs in Recurrent Networks. Journal of Machine Learning Research 18(7):1-37, Jan 2017. pdf.
  • A.S. Charles, A. Balavoine, and C.J. Rozell. Dynamic Filtering of Time-Varying Sparse Signals via l1 Minimization. IEEE Transactions of Signal Processing 2016, 64(21):5644-5656, November 2016. pdf.
  • A.S. Charles, H.L. Yap, and C.J. Rozell. Short term network memory capacity via the restricted isometry property. Neural Computation, 26(6), June, 2014. pdf.
  • A.S. Charles and C.J. Rozell. Spectral superresolution of hyperspectral imagery using reweighted l1 spatial filtering. IEEE Journal of Geoscience and Remote Sensing Letters, 11(3):602-606, March 2014. pdf.
  • A.S. Charles, P. Garrigues, and C.J. Rozell. A common network architecture efficiently implements a variety of sparsity-based inference problems, Neural Computation, 24(12):3317-3339, December 2012. pdf.
  • S. Shapero, A.S. Charles, C.J. Rozell, and P. Hasler. Low power sparse approximation on reconfigurable analog hardware. IEEE Journal on Emerging and Selected Topics in Circuits and Systems, 2(3):530-541, September 2012. Special Issue on Circuits, Systems and Algorithms for Compressive Sensing. pdf.
  • A.S. Charles, B.A. Olshausen, and C.J. Rozell. Learning sparse codes for hyperspectral images. IEEE Journal of Selected Topics in Signal Processing, 5(5):963-978, September 2011. pdf. code

Conference Papers

  • J. Choi, K. Kumar, M. Khazali, K. Wingel, M. Choudhury, A.S. Charles, and B. Pesaran. Optimal Adaptive Electrode Selection to Maximize Simultaneously Recorded Neuron Yield. Neural Inormation Processing Systems (NeurIPS), Virtual, December 2020.pdf
  • S. Gigante, and A.S. Charles, S. Krishnaswamy, and G. Mishne. Visualizing the PHATE of Neural Networks. Neural Inormation Processing Systems (NeurIPS), Vancouver, Canada, December 2019.pdf
  • G. Mishne and A.S. Charles Learning spatially-correlated temporal dictionaries for calcium imaging. Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Brighton, UK, May 2019 (Selected for oral presentation) pdf.
  • A.S. Charles and J.W. Pillow. Additive continuous-time joint partitioning of neural variability. Proceedings of the Conference on Cognitive Computational Neuroscience (CCN), Philadelphia, PA, USA, September 2018. pdf.
  • A.S. Charles, H.L. Yap, D. Lin and C.J. Rozell. Short-term sequence memory: Compressive effects of recurrent network dynamics. Proceedings of the Conference on Cognitive Computational Neuroscience (CCN), Philadelphia, PA, USA, September 2018. pdf.
  • N.P. Bertrand, J. Lee, A.S. Charles, P. Dunn, and C.J. Rozell. Sparse dynamic filtering via earth mover’s distance regularization. Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), Calgary, Alberta, Canada, April 2018 pdf.
  • M. Shvartsman, N. Sudaram, M.C. Aoi, A.S. Charles, T. L. Wilke, and J. D. Cohen. Matrix-variate models for fMRI analysis. The International Conference on Artificial Intelligence and Statistics (AISTATS), Playa Blanca, Lanzarote, Canary Islands, April 2018. pdf(arxiv), pdf (MLR).
  • A.S. Charles, N.P. Bertrand, J. Lee, and C.J. Rozell. Earth-mover’s distance as a tracking regulaizer. Proceedings the CAMSAP, Curacao, Dutch Antilles, December 2017. pdf
  • A.S. Charles, A. Song, S.A. Koay, D.W. Tank, and J.W. Pillow. Stochastic filtering of two-photon imaging using reweighted l1. Proceedings of the ICASSP New Orleans, Louisiana, March 2017.
  • A.S. Charles and C.J. Rozell, Convergence of basis pursuit de-noising with dynamic filtering. Proceedings of the GlobalSIP Atlanta, Georgia, November 2014. pdf
  • A.S. Charles, Y. Dong and C.J. Rozell, Can random linear networks store multiple long input streams?. Proceedings of the GlobalSIP Atlanta, Georgia, November 2014. pdf
  • A.S. Charles and C.J. Rozell, Dynamic filtering of sparse signals using reweighted l1. Proceedings of the ICASSP Vancouver, Canada, May 2013. pdf
  • A.S. Charles, A. Ahmed, A. Joshi, S. Conover, C. Turnes, and M.A. Davenport, Cleaning up toxic waste: Removing nefarious contributions to recommendation systems. Proceedings of the ICASSP Vancouver, Canada, May 2013. pdf
  • H.L. Yap, A.S. Charles, and C.J. Rozell, The restricted isometry property for echo state networks with applications to sequence memory capacity. Statistical Signal Processing Workshop Ann Arbor, Michigan, August 2012. pdf
  • A.S. Charles, M.S. Asif, J. Romberg, and C.J. Rozell, Sparsity penalties in dynamical system estimation. Proceedings of the CISS Baltimore, Maryland, March 2011. (Selected for oral presentation) pdf
  • M.S. Asif, A.S. Charles, J. Romberg and C.J. Rozell, Estimation and dynamic updating of time-varying signals with sparse variations. Proceedings of the ICASSP, Prague, Czech Republic, May 2011. pdf
  • A.S. Charles, A.A. Kressner and C.J. Rozell, Causal sparse decompositions of audio signals. Proceedings of the IEEE Signal Processing (DSP) Workshop, Sedona, AZ, January 2011. (Nominated for best student paper/Selected for oral presentation) pdf (Nominated for best student paper)
  • A.S. Charles, B.A. Olshausen and C.J. Rozell. Sparse coding for spectral signatures in hyperspectral images. Proceedings of the Asilomar Conference on Signals, Systems and Computers, Pacific Grove, CA, November 2010 pdf , poster

Conference Abstracts

  • J. Choi, M. Khazali, A.S. Charles, and B. Pesaran. Multi-scale measurements of primate motor cortex during free reaching. Brain Initiative Investigators Meeting, June 2021
  • S. Keeley*, D. Zoltowski*, A.S. Charles, J.W. Pillow. Improved estimation of neural encoding models from calcium imaging data. Brain Initiative Investigator’s Meeting, June, 2020. *Equal contribution 
  • A.S. Charles, N. Cermak, J. Shiller, and G. Mishne. Calcium imaging analysis with graph filtered temporal dictionary learning. Society for Neuroscience (SfN), Chicago, Illinois, October 2019
  • A.S. Charles and J. W. Pillow. Continuous-time partitioning of neural variability. Society for Neuroscience (SfN), Chicago, Illinois, October 2019
  • G. Mishne, N. Cermak, J. Shiller, and A.S. Charles. Spatially-filtered temporal dictionary learning for calcium imaging analysis. Signal Processing with Adaptive Sparse Structured Representations (SPARS), Toulouse, France, June 2019
  • G. Mishne, B. Scott, S. Thiberge, N. Cermak, J. Schiller, D.W. Tank, and A.S. Charles. Graph-filtered temporal dictionary learning for calcium imaging analysis. Computational Neuroscience Meeting (CNS), Barcelona, Spain, July 2019 (Selected for oral presentation)
  • J.L. Gauthier, S.A. Koay, E. Nieh, D.W. Tank, J.W. Pillow, and A.S. Charles. Sparse-coding variational auto-encoders. Computational and Systems Neuroscience (CoSyNe), Lisbon, Portugal, July 2019
  • G. Mishne, B. Scott, S. Thiberge, N. Cermak, J. Schiller, D.W. Tank, and A.S. Charles. Temporal dictionary learning for calcium imaging analysis. Computational and Systems Neuroscience (CoSyNe), Lisbon, Portugal, July 2019
  • G. Barello, A.S. Charles, and J.W. Pillow. Sparse-coding variational auto-encoders. Computational and Systems Neuroscience (CoSyNe), Lisbon, Portugal, July 2019
  • A.S. Charles, H. L. Yap, D. Yin, and C. J. Rozell. Rigorous guarantees on sequence memory capacity in recurrent neural networks using randomized dimensionality reduction. Theoretical Foundation of Deep Learning, Atlanta, Georgia, October 2018
  • J.L. Gauthier, A.S. Charles, D.W. Tank, and J.W. Pillow. Robust identification and removal of falsetransients in calcium fluorescence imaging data. Society for Neuroscience (SfN), San Diego, California, September 2018
  • M. Shvartsman, N. Sudaram, M.C. Aoi, A.S. Charles, T.L. Wilke, and J.D. Cohen. Matrix-normal models for fMRI analysis. Organization for Human Brain Mapping (OHBM), Singapore, June 2018
  • M. Shvartsman, N. Sudaram, M.C. Aoi, A.S. Charles, T.L. Wilke, and J.D. Cohen. Matrix-normal models for fMRI analysis. Computational and Systems Neuroscience (CoSyNe), Denver, Colorodo, March 2018
  • J. Lee, A.S. Charles, N.P. Bertrand, and C.J. Rozell. An optimal transport tracking regularizer. Neural Information Processing Systems (NIPS) Workshops, Long Beach, California, December 2017
  • M. Shvartsman, N. Sudaram, M.C. Aoi, A.S. Charles, T.L. Wilke, and J.D. Cohen. Matrix-variate models for fMRI analysis. Neural Information Processing Systems (NIPS) Workshops, Long Beach, California, December 2017
  • A. Song, A.S. Charles, S.Y. Thiberge, J.L. Gauther, S.A. Koay, J.W. Pillow, and D.W. Tank. Volumetric two-photon imaging via stereoscopy and two-photon calcium imaging simulator. Emerging Tools for Acquisition and Interpretation of Whole-Brain Functional Data, Ashburn, Virginia, November 2017
  • J.L. Gauthier, A.S. Charles, D.W. Tank, and J.W. Pillow. Robust estimation of calcium transients by modeling contamination. SFN Washington DC., June 2017.
  • A. Song, A.S. Charles, D.W. Tank and J.W. Pillow. A two-photon microscopy simulation framework for optimizing optics and benchmarking cell-finding algorithms. SFN Washington DC., June 2017.
  • A.S. Charles, A. Song, S.A. Koay, J.L. Gauthier, S.Y. Thiberge, D.W. Tank, and J.W. Pillow. Adaptive orthogonal basis pursuit for volumetric two-photon microscopy. SPARS Lisbon, Portugal, June 2017.
  • A.S. Charles, D. Yin, and C.J. Rozell. Compression of multiple input streams into recursive neural networks. SPARS Lisbon, Portugal, June 2017.
  • A.S. Charles, J. Lee, N.P. Bertrand, and C.J. Rozell. Dynamic filtering with earth mover’s distance regularization. SPARS Lisbon, Portugal, June 2017.
  • A.S. Charles and J.W. Pillow. Continuous-time partitioning of binned spike counts. CoSyNe Salt Lake City, Utah, February 2017.
  • J.L. Gauthier, A.S. Charles, J.W. Pillow, and D.W. Tank. Robust estimation of calcium transients by modeling contamination. CoSyNe Salt Lake City, Utah, February 2017.
  • A. Song, A.S. Charles, J.L. Gauthier, S.A. Koay, D.W. Tank, and J.W. Pillow. Two-photon microscopy simulation for optics optimization and benchmarking. CoSyNe Salt Lake City, Utah, February 2017.
  • A.S. Charles, H.L. Yap, D. Yin, and C.J. Rozell. Short-term sequence memory in recurrent networks. NIPS Workshops Barcelona, Spain, December 2016.
  • N.P. Bertrand, H.L. Yap, A.S. Charles, and C.J. Rozell. Efficient randomized filtering for dimensionality reduction in electrophysiology data. NIPS Workshops Barcelona, Spain, December 2016.
  • A. Song, A.S. Charles, S.Y. Thiberge, J.L. Gauthier, S.A. Koay, J.W. Pillow, and D.W. Tank. Two-photon imaging of neurons using stereoscopy (TwINS). SfN San Diego, California, December 2016.
  • A.S. Charles and C.J. Rozell, Learning a dynamics dictionary for time-varying sparse signals. SPARS Cambridge, United Kingdom, July 2015.
  • A.S. Charles and C.J. Rozell, Robust estimation of sparse time-varying signals. Information Theory and Applications La Jolla, California, February 2015.
  • C.J. Rozell, M. Zhu, A.S. Charles, H.L. Yap, and M. Norko, The role of sparsity in visual perception. BICA Cambridge, Massachusetts, November 2014.
  • A.S. Charles, C.J. Rozell, and N. Tufillaro, Sparsity based spectral super-resolution and applications to water color. IGARSS Quebec, Canada, May 2014. pdf
  • A.S. Charles and C.J. Rozell. Stochastic filtering via reweighted l1. SPARS, Lausanne, Switzerland, July 2013. pdf, poster
  • A.S. Charles, H.L. Yap, and C.J. Rozell. Using compressed sensing to study sequence memory capacity in networked systems. SPARS, Lausanne, Switzerland, July 2013 pdf
  • A.A. Kressner, A.S. Charles, and C.J. Rozell. Causal locally competitive algorithm for the sparse decomposition of audio signals. IEEE Womens Workshop on Communications and Signal Processing, Ban, Canada, July 2012
  • A.S. Charles, H.L. Yap, , and C.J. Rozell. Short term memory in neural networks via the restricted isometry property. Computational Neuroscience Meeting Workshop on Methods of Information Theory in Computational Neuroscience, Atlanta, GA, July 2012
  • H.L. Yap, A.S. Charles, and C.J. Rozell, Short-term memory capacity in recurrent Networks via compressed sensing. Challenges in Geometry, Analysis and Computation: High-Dimensional Synthesis, Yale University, June 2012 abstract
  • C.J. Rozell and A.S. Charles. Spectral super-resolution of hyperspectral images. SIAM Conference on Imaging Science, Philadelphia, PA, May 2012
  • C.J. Rozell and A.S. Charles. Recursive estimation of dynamic signals with sparsity models via re-weighted l1 minimization. Janelia Farm Conference on Machine Learning, Statistical Inference, and Neuroscience, Ashburn, VA, May 2012
  • A.S. Charles, H.L. Yap, and C.J. Rozell, Short-term memory capacity in recurrent Networks via compressed sensing. Janelia Farm Conference on Machine Learning,Statistical Inference and Neuroscience, Ashburn, Virginia, 2012 poster
  • A.S. Charles, H.L. Yap, and C.J. Rozell, Short-term memory capacity in recurrent Networks via compressed sensing. Proceedings of COSYNE, Salt Lake City, Utah, 2012 pdf, poster
  • A.S. Charles, B.A. Olshausen, and C.J. Rozell. Learning sparse codes for hyperspectral images. Duke Workshop on Sensing and Analysis of High-Dimensional Data (SAHD), Durham, NC, July 2011 poster
  • A.S. Charles and C.J. Rozell, A hierarchical re-weighted-l1 approach for dynamic sparse signal estimation. SPARS, Edinburgh, Scotland UK, 2011 (Selected for oral presentation) pdf, slides

Other publications

  • A.S. Charles, Interpreting Deep Learning: The Machine Learning Rorschach Test? Society for Industrial and Applied Mathematics (SIAM) News, Jul. 2018. link, extended pdf
  • M. Shvartsman, N. Sundaram, M.C. Aoi, A.S. Charles, T.C. Wilke, and J.D. Cohen. Matrix-normal models for fMRI analysis. arXiv:1711.03058 Nov. 2017. pdf
  • A.S. Charles. Dynamics and correlations in sparse signal acquisition. PhD thesis, Georgia Institute of Technology, 2015. pdf
  • A.S. Charles. Adjustable Subband Allocation Algorithm for Critically Sampled Subband Adaptive Filters. Master’s Thesis. The Cooper Union for the Advancement of Science and Art. April 2009. pdf