Paper List for Neural Dynamics

How does higher-order behavior emerge from billions of neurons firing?

The papers below explore neural dynamics in theoretical and experimental contexts, with a focus on interpreting higher-level behaviors from multiple single-neuron recordings.

This list is originally from the Dynamics in Cognition course taught by David Tank at Princeton.

Basic Concepts

Neural Dynamics: A Primer (Hopfield Networks)

Persistent Activity and Attractors

• J.J. Hopfield. Neural networks and physical systems with emergent collective computational abilities. 1982. Notes here.
• H.S. Seung. How the brain keeps the eyes still. 1996.

Attractors and Path Integration

• A. Samsonovich and B. L. McNaughton. Path integration and cognitive mapping in a continuous attractor neural network model. 1997.

Attractors and Grid Cells

• Torkel Hafting, Marianne Fyhn, Sturla Molden, May-Britt Moser, and Edvard I. Moser. Microstructure of a spatial map in the entorhinal cortex. 2005.
• KiJung Yoon, Michael A. Buice, Caswell Barry, Robin Hayman, Neil Burgess, and Ila R. Fiete. Specific evidence of low-dimensional continuous attractor dynamics in grid cells. 2013.

Attractors and Head Direction Cells

• William E. Skaggs, James J. Knierim, Hemant S. Kudrimoti, and Bruce L. McNaughton. A Model of the Neural Basis of the Rat’s Sense of Direction. 1995.
• K. Zhang. Representation of spatial orientation by the intrinsic dynamics of the head-direction cell ensemble: a theory. 1996.
• Sung Soo Kim, Herve Rouault, Shaul Druckmann, and Vivek Jayaraman. Ring attractor dynamics in the Drosophila central brain. 2017.
• Adrien Peyrache, Marie M. Lacroix, Peter C. Petersen, and György Buzsáki. Internally organized mechanisms of the head direction sense. 2015.

Attractors and Decision-Making

• Valerio Mante, David Sussillo, Krishna V. Shenoy, and William T. Newsome. Context-dependent computation by recurrent dynamics in prefrontal cortex. 2013.
• R. Romo, C. D. Brody, A. Hernández, and L. Lemus. Neuronal correlates of parametric working memory in the prefrontal cortex. 1999.

Sequences

Sequences in Songbirds

• Richard H. R. Hahnloser, Alexay A. Kozhevnikov, and Michale S. Fee. An ultra-sparse code underlies the generation of neural sequences in a songbird. 2002.
• Michael A Long and Michale S Fee. Using temperature to analyse temporal dynamics in the songbird motor pathway. 2008.
• Ila R. Fiete, Walter Senn, Claude Z. H. Wang, and Richard H. R. Hahnloser. Spike-timedependent plasticity and heterosynaptic competition organize networks to produce long scalefree sequences of neural activity. 2010.
• Tatsuo S. Okubo, Emily L. Mackevicius, Hannah L. Payne, Galen F. Lynch, and Michale S. Fee. Growth and splitting of neural sequences in songbird vocal development. 2015.

Sequences in Mammals

• Christopher D. Harvey, Philip Coen, and David W. Tank. Choice-specific sequences in parietal cortex during a virtual-navigation decision task. 2012.
• Vladimir Itskov, Carina Curto, Eva Pastalkova, and Gyorgy Buzsaki. Cell Assembly Sequences Arising from Spike Threshold Adaptation Keep Track of Time in the Hippocampus. 2011.

Modeling Sequences

• D. Kleinfeld and H. Sompolinsky. Associative neural network model for the generation of temporal patterns. Theory and application to central pattern generators. 1988.
• Mark S Goldman. Memory without feedback in a neural network. 2009.

Oscillations

Oscillations and Binding

• György Buzsáki and Andreas Draguhn. Neuronal Oscillations in Cortical Networks. 2004.
• Michael Wehr and Gilles Laurent. Odour encoding by temporal sequences of firing in oscillating neural assemblies. 1996.
• Mark Stopfer and Gilles Laurent. Short-term memory in olfactory network dynamics. 1999.

Rotations in State Space

• Mark M. Churchland, John P. Cunningham, Matthew T. Kaufman, Justin D. Foster, Paul Nuyujukian, Stephen I. Ryu, and Krishna V. Shenoy. Neural population dynamics during reaching. 2012.
• Sergey D. Stavisky, Jonathan C. Kao, Stephen I. Ryu, and Krishna V. Shenoy. Motor Cortical Visuomotor Feedback Activity Is Initially Isolated from Downstream Targets in Output Null Neural State Space Dimensions. 2017.

Representations in the Brain

Mismatch Negativity and Predictive Coding

• Jan Homann, Sue Ann Koay, Alistair M. Glidden, David W. Tank, and Michael J. Berry. Predictive Coding of Novel versus Familiar Stimuli in the Primary Visual Cortex. 2017.

Locomotion

• Saul Kato, Harris S. Kaplan, Tina Schrödel, Susanne Skora, Theodore H. Lindsay, Eviatar Yemini, Shawn Lockery, and Manuel Zimmer. Global brain dynamics embed the motor command sequence of Caenorhabditis elegans. 2015.

Visual Representations

• Le Chang and Doris Y. Tsao. The Code for Facial Identity in the Primate Brain. 2017.

Comparing Artificial and Biological Neural Nets

• Daniel L. K. Yamins, Ha Hong, Charles F. Cadieu, Ethan A. Solomon, Darren Seibert, and James J. DiCarlo. Performance-optimized hierarchical models predict neural responses in higher visual cortex. 2014.
• Daniel L. K. Yamins and James J. DiCarlo. Using goal-driven deep learning models to understand sensory cortex. 2016.