We read and discuss the latest papers in computational neuroscience. The hope is to generate new ideas, foster new collaborations, and keep up-to-date with the literature.

For the spring 2021 semester, we will have four themes (3 weeks per theme). All meetings will be virtual (not recorded). The papers for each theme have been pre-selected to match PNI's interests. The papers reflect authors from a diverse set of backgrounds and from outside of PNI in order to encourage a breadth of perspective.

We encourage participants to spend at least 20 minutes with each paper before coming to club.


If you’d like to be added to the email list, visit our google group, or contact Ben (bcowley [at] princeton.edu) or Iris (istone [at] princeton.edu). If you'd like to present, please also contact Ben and Iris.

Presentation tips

Let’s make our journal club the envy of PNI! Please read the paper before choosing, plan for 35 minutes of presenting (expect plenty of questions!), and follow these tips: presentation_checklist.pdf

Zoom link

We use a recurring Zoom link. You can find the Zoom link in our e-mails. If you need the Zoom link, please join our mailing list or contact Ben or Iris.

Current Meetings (Spring 2021)

Special club for PNI Recruitment

Date Time Presenter Reading
Feb 19 11:30am-12:30pm David Zoltowski Decoding and perturbing decision states in real time.
Peixoto, Verhein, Kiani, ..., Ryu, Shenoy, Newsome (Nature 2021)

Theme 1: Understanding multi-area interactions

Date Time Presenter Reading
Mar 3 3-4pm Ben Cowley Principles of Corticocortical Communication: Proposed Schemes and Design Considerations.
Kohn, Jasper, Semedo, Gokcen, Machens, Yu (Trends in Neuro 2020)
Statistical methods for dissecting interactions between brain areas.
Semedo, Gokcen, Machens, Kohn, Yu (Current Op in Neuro 2020)
Mar 10 3-4pm Rich Pang Inferring brain-wide interactions using data-constrained recurrent neural network models.
Perich, Arlt, Soares, ..., Rudebeck, Harvey, Rajan (bioRxiv 2020)
Mar 17 3-4pm Orren Karniol-Tambour Brain-wide electrical spatiotemporal dynamics encode depression vulnerability.
Hultman, Ulrich, Sachs, ..., Nestler, Carin, Dzirasa (Cell 2018)

Theme 2: Neuroethology: Understanding computation through behavior

Date Time Presenter Reading
Apr 6 3-4pm Jess Breda Computational neuroethology: a call to action.
Datta, Anderson, Branson, Perona, Leifer (Neuron 2019)
Apr 13 3-4pm Jorge Yanar Continuous Whole-Body 3D Kinematic recordings across the rodent behavioral repertoire.
Marshall, Aldarondo, Dunn, Wang, Berman, Olveczky (Neuron 2020)
Apr 20 3-4pm Iris Stone A cortical-hypothalamic circuit decodes social rank and promotes dominance behavior.
Padilla-Coreano, Batra, Patarino, ..., Fiete, Lu, Tye (ResearchSquare 2020)
AlphaTracker: A multi-animal tracking and behavioral analysis tool.
Chen, Zhang, Zhang, ..., Tye, Lu (bioRxiv 2020)

Theme 3: The curious computations of dopamine

Date Time Presenter Reading
May 6 4-5pm Rachel Lee Neural circuitry of reward prediction error.
Watabe-Uchida, Eshel, Uchida (Ann. Review of Neuro. 2017)
May 13 4-5pm Sreejan Kumar Evidence for a neural law of effect.
Athalye, Santos, Carmena, Costa (Science 2018)
May 20 4-5pm Yoel Sanchez Araujo Dopamine enhances signal-to-noise ratio in cortical-brainstem encoding of aversive stimuli.
Vander Weele, Siciliano, Gillian, ..., Wichmann, Wildes, Tye (Nature 2018)

Theme 4: Recording from more neurons than we know what to do with

Date Time Presenter Reading
June 9 3-4pm Aditi Jha Towards the neural population doctrine.
Saxena and Cunningham (Current Opinion in Neuro. 2019)
June 16 3-4pm Daniel Greenidge A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex.
de Vries, Lecoq, Buice, ..., Phillips, Reid, Koch (Nat Neuro 2020)
June 23 3-4pm Eleni Papadoyannis Distributed coding of choice, action and engagement across the mouse brain.
Steinmetz, Zatka-Haas, Carandini, Harris (Nature 2019)



Past Meetings (Fall 2020)

Date Time/Room Presenter Reading
Jan 30 4-5pm, PNI 230 David Zoltowski Stimulus-choice (mis)alignment in primate MT cortex.
Zhao, Yates, Levi, Huk, Park (bioRxiv 2019)
Feb 6 3-4pm, PNI 130 Zoë Ashwood Computational noise in reward-guided learning drives behavioral variability in volatile environments.
Findling, Skvortsova, Dromnelle, Palminteri, Wyart. (Nat Neuro 2019)
Feb 13 3-4pm, PNI 130 Daniel Greenidge Structure in neural population recordings: an expected byproduct of simpler phenomena?
Elsayed and Cunningham. (Nat Neuro 2017)
Feb 20 11am-12pm, Psych 404 Brian DePasquale Engineering recurrent neural networks from task-relevant manifolds and dynamics.
Pollock and Jazayeri. (bioRxiv 2019)
Feb 27 No club -- COSYNE
Mar 5 No club -- Unfilled slot
Mar 12 Virtual Lindsay Willmore Deep neuroethology of a virtual rodent.
Merel, Aldarondo, Marshall, Tassa, Wayne, Olveczky. (arXiv 2019)


Past Meetings (Fall 2019)

Date Presenter Reading
Oct 24 Ben Cowley High-dimensional geometry of population responses in visual cortex.
Stringer, Pachitariu, Steinmetz, Carandini, Harris. (Nature 2019)
Oct 31 (not meeting) A spooky paper
Fox (Ann. Reviews 1975)
Nov 7 Ben Cowley What makes a good scientific figure?
Nov 14 Matt Creamer Hierarchical recurrent state space models reveal discrete and continuous dynamics of neural activity in C. elegans
Linderman, Nichols, Blei, Zimmer, Paninski. (bioRxiv 2019)
Nov 21 Sean Bittner (visitor) Interrogating theoretical models of neural computation with deep inference
Bittner, Agostina Palmigiano, Piet, Duan, Brody, Miller, Cunningham. (bioRxiv, 2019)
Dec 5 Matt Panichello Bayesian computation through cortical latent dynamics
Sohn, Narain, Meirhaeghe, Jazayeri (Neuron 2019)
Dec 12 No journal club (PNI holiday party)
Dec 19 Kevin Chen A quantitative model of conserved macroscopic dynamics predicts future motor commands
Brennan, Proekt. (eLife, 2019)


Past Meetings (Spring 2019)

Date Presenter Reading
Jan 17 David Zoltowski Distributed correlates of visually-guided behavior across the mouse brain
Steinmetz et al. (2018)
Feb 5 Brian Depasquale The population dynamics of a canonical cognitive circuit
Chaudhuri et al. (2019)
Feb 12 Robert Yang Task representations in neural networks trained to perform many cognitive tasks
Yang et al. (2019)
Feb 22nd, 11AM Nick Roy A diverse range of factors affect the nature of neural representations underlying short-term memory
Orhan and Ma. (2019)
Feb 26 No Meeting COSYNE
Mar 5 No Meeting COSYNE
Mar 12 Zoe Ashwood Linking Connectivity, Dynamics, and Computations in Low-Rank Recurrent Neural Networks
Mastrogiuseppe and Ostojic. (2018)
Mar 19 Manuel Schottdorf Classification and Geometry of General Perceptual Manifolds
Chung et al. (2018)
Mar 26 Anqi Wu Revealing neural correlates of behavior without behavioral measurements
Rubin et al. (2019)
Apr 2 Kevin Chen The Dynamical Regime of Sensory Cortex: Stable Dynamics around a Single Stimulus-Tuned Attractor Account for Patterns of Noise Variability
Hennequin et al. (2018)
Apr 9 Diksha Gupta Adaptive coding for dynamic sensory inference
Mlyarski and Hermundstad (2018)
Apr 16 Ben Cowley Reversible Inactivation of Different Millimeter-Scale Regions of Primate IT Results in Different Patterns of Core Object Recognition Deficits
Rajalingman and DiCarlo (2019)
Apr 23 Lindsay Willmore Memory without Feedback in a Neural Network
Mark Goldman (2009)
Apr 30 Tyler Boyd-Meredith Computing by Robust Transience: How the Fronto-Parietal Network Performs Sequential, Category-Based Decision
Chaisangmongkon et al. (2017)
May 21 Adam Calhoun and Ben Cowley Evolving Images for Visual Neurons Using a Deep Generative Network Reveals Coding Principles and Neuronal Preferences
Ponce et al. (2019), Bashivan et al. 2019


Past Meetings (Fall 2018)

Date Presenter Reading
Oct 25th, 3PM Jonathan Pillow Efficient coding explains the universal law of generalization in human perception
Chris R. Sims (2018)
Nov 1st Anqi Wu Uncovering hidden brain state dynamics that regulate performance and decision-making during cognition
Taghia et al. (2018)
Nov 8th No Meeting, SFN
Nov 15th Manuel Schottdorf Distributed network interactions and their emergence in developing neocortex
Smith et al. (2018)
Nov 22nd No Meeting, Thanksgiving
Nov 29th Sue Ann Koay Shaping Neural Circuits by High Order Synaptic Interactions
Tannenbaum et al. (2018)
Dec 6th No Meeting, NIPS


Past Meetings (Spring 2018)

Date Presenter Reading
Jan 16 Thomas Luo Mixed selectivity morphs population codes in prefrontal cortex
Parthasarathy et al. (2017)
Jan 23 Ashok Litwin-Kumar Optimal degrees of synaptic connectivity
Litwin-Kumar et al. (2017)
Jan 30 David Zoltowski A Switching Observer for Human Perceptual Estimation
Laquitaine & Gardner (2017)
Feb 7 Jonathan Pillow Unified theory of efficient, predictive, and sparse coding
Chalk et al. (2017)
Feb 14 Stephen Keeley Eigen-Distortions of Hierarchical Representations
Berardino et al. (2017)
Feb 23 (Fri, 11AM in room 130!) Adrian Bondy Perceptual decision-making as probabilistic inference by neural sampling.
Haefner, Berkes, & Fiser. (2016)
Feb 28 Diksha Gupta Optimal compensation for neuron loss
Barrett, Deneve and Machens (2016)
Mar 14 Nick Roy Evidence for a neural law of effect
Athalye, Santos, Carmena, and Costa.(2017)
Mar 21 No meeting - Snow Day
Mar 28 Morgan Gustison Modular Deconstruction Reveals the Dynamical and Physical Building Blocks of a Locomotion Motor Program
Bruno, Frost, and Humphries. (2015)
Apr 4 Adam Charles Unsupervised discovery of temporal sequences in high-dimensional datasets, with applications to neuroscience.
Mackevicius et al.
Apr 11 Camille Rullan Computational Account of Spontaneous Activity as a Signature of Predictive Coding
Koren and Daneve(2017)
Apr 18 Mikio Aoi Flexible timing by temporal scaling of cortical responses
Wang, Narain, Hosseini, Jazayeri (2018)
Apr 25 Mike Morais Optimal Control of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements
Hennequin, Vogels, Gerstner (2014)
May 2 Brain DePasquale Choice History Biases Subsequent Evidence Accumulation
Urai et al. (2018)
May 9 Adam Calhoun Spontaneous behaviors drive multidimensional, brain-wide population activity
Carsen Stringer, Marius Pachitariu, Nicholas Steinmetz, Charu Bai Reddy, Matteo Carandini, Kenneth D. Harris (2018)


Past Meetings (Fall 2017)

Date Presenter Reading
Sep 26 Mike Morais Lawful relation between perceptual bias and discriminability
Wei & Stocker (2017)
Oct 3 Alex Hyafil Attention stabilizes the shared gain of V4 populations
Rabinowitz et al. (2015)
Oct 10 Jamal Williams Brains on Beats
Guclu et al. (2016)
Oct 17 Adam Charles Fundamental bound on the persistence and capacity of short-term memory stored as graded persistent activity
Koyluoglu, et al. eLife (2017)
Oct 24 Adam Calhoun A brain wide circuit model of heat evoked swimming behavior in larval zebrafish
Haesemeyer et al. (2017)
Oct 31 Michael Berry A Theory of Canonical Computations in the Neocortical Microcircuit
Nov 28 Brian DePasquale Optimal degrees of synaptic connectivity
Litwin-Kumar et al. (2017)


Past Meetings (Summer 2017)

Date Presenter Reading
Jun 22 Scott Linderman Using computational theory to constrain statistical models of neural data
Linderman & Gershman (2017)


Past Meetings (Spring 2017)

Date Presenter Reading
Jan 17 Stephen Keeley The hippocampus as a predictive map
Stachenfeld, Botvinick, and Gershman (2016)
Jan 24 Sam Lewallen Training recurrent networks to generate hypotheses about how the brain solves hard navigation problems
Kanitscheider and Fiete (2016)
Jan 31 Adam Charles Predictive Ensemble Decoding of Acoustical Features Explains Context-Dependent Receptive Fields
Yildiz, Mesgarani and Deneve J. Neuroscience (2016)
Feb 07 Mikio/Jonathan/Adam Demixed principal component analysis of neural population data Kobak et al. eLife (2016).
Feb 14 Anne Mennen Unmasking Latent Inhibitory Connections in Human Cortex to Reveal Dormant Cortical Memories Barron et al. Neuron (2016).
Feb 21 Nick Roy Building Machines That Learn and Think Like People Lake et al. (2016).
Mar 3 Mikio Aoi Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1 Seeley at al. PLOS Comp. Bio. (2016).
Mar 28 Jonathan Pillow A probabilistic approach to demixing odors Grabska-Barwinska et al. Nature Neuro. (2017).
Apr 04 Alex Piet Memory replay in balanced recurrent networks Chenkov, Sprekeler & Kempter PLOS Comp. Bio. (2017).
Apr 11 Brian DePasquale Building functional networks of spiking model neurons Abbott at al. Nature Neuro. (2016).
Apr 18 Adrianna Loback STDP installs in winner-take-all circuits an online approximation to hidden markov model learning Kappel, Nessler & Maass PLOS Comp. Bio. (2014).
Apr 25 Diksha Gupta Dynamic control of response criterion in premotor cortex during perceptual detection under temporal uncertainty Carnevale et al. Neuron (2015).
May 02 Nick Roy Stable population coding for working memory coexists with heterogeneous neural dynamics in prefrontal cortex Murray et al. PNAS (2017).
May 09 Alex Libby Information Capacity and Transmission Are Maximized in Balanced Cortical Networks with Neuronal Avalanches Shew et al. J. Neuroscience (2011).


Past Meetings (Fall 2016)

Date Presenter Reading
Oct 4 Nicholas Roy Adaptive optimal training of animal behavior
Bak et al. NIPS (2016)
Oct 11 Adam Calhoun Reading out olfactory receptors: Feedforward circuits detect odors in mixtures without demixing
Mathis, Rokni, Kapoor, Bethge, and Murthy Neuron (2016)
Oct 18 Adam Charles Visual Nonclassical Receptive Field Effects Emerge from Sparse Coding in a Dynamical System
Zhu and Rozell PLOS Computational Biology (2013)
Oct 25 Brian DePasquale Hybrid computing using a neural network with dynamic external memory
Graves et al. Nature (2016)
Nov 1 Mingbo Cai Automatic Construction and Natural-Language Description of Nonparametric Regression Models
Lloyd et al.
Nov 29 Hamza Giaffar Primacy Model of Olfactory Coding
Dec 6 David Zoltowski Reorganization between preparatory and movement population responses in motor cortex
Elsayed, Lara, Kaufman, Churchland and Cunningham Nature Communications (2016)
Dec 13 Mikio Aoi What must a global theory of cortex explain?
Valiant Current Opinion in Neurobiology (2014)


Past Meetings (Summer 2016)

Date Presenter Reading
Jun 14 Athena Akrami & Adam Charles
Could a neuroscientist understand a microprocessor?
Jonas & Koerding. biorxiv (2016)
Jun 23 Ben Machta Perspective: Sloppiness and Emergent Theories in Physics, Biology, and Beyond
Transtrum, Machta, Brown, Daniels, Myers, and Sethna. J. Chem. Phys. (2015)
Jun 30 Ahmed Hl Hady Cell Types, Network Homeostasis, and Pathological Compensation from a Biologically Plausible Ion Channel Expression Model
O’Leary, Williams, Franci, and Marder. Neuron (2014)
Jul 7 Leenoy Meshulam Sloppiness in Spontaneously Active Neuronal Networks
Panas1, Amin, Maccione, Muthmann1, van Rossum, Berdondini, and Hennig. J. Neurosci. (2015)
Jul 21 Adam Charles Assessing the distinguishability of models and the informativeness of data Navarro et al. Cognitive Psychology (2004)
Aug 23 Ido Kanter Low-firing rates, cortical oscillations and neuronal ?s precision stem from neuronal plasticity: Experiment and theory
Sep 13 Yonatan Aljadeff Optimal population coding by mixed-dimensionality neurons


Past Meetings (Fall-Spring 2015-16)

Date Presenter Reading
Nov 24 Jonathan Pillow
Inferring learning rules from distributions of firing rates in cortical neurons
Lim, McKee, Woloszyn, Amit, Freedman, Sheinberg, & Brunel.
Nature Neuroscience (2015). [summary]
Dec 1 Adam Calhoun Global Brain Dynamics Embed the Motor Command Sequence of Caenorhabditis elegans.
Kato, Kaplan, Schrödel, Skora, Lindsay, Yemini, Lockery, & Zimmer.
Cell (2015)
Dec 8 Mark Ioffe
readers: Alex Piet & DJ Strouse
A thesaurus for a neural population code.
Ganmor, Segev, & Schneidman. eLife (2015).
Dec 15 DJ Strouse
readers: Mark Ioffe & Mingbo Cai
A Bayesian observer model constrained by efficient coding can explain 'anti-Bayesian' percepts.
Wei & Stocker, Nat Neurosci (2015).
Jan 19 Mikio Aoi
readers: Adam Calhoun & Jonathan Pillow.
Cortical activity in the null space: permitting preparation without movement. Kaufman, Churchland, Ryu, & Shenoy, Nat Neurosci 2014.
Jan 29
Sina Tafazoli
readers: Adam Charles & Mikio Aoi
A neural network that finds a naturalistic solution for the production of muscle activity. Sussillo, Churchland, Kaufman, & Shenoy, Nat Neurosci 2015
Feb 2 Mingbo Cai
readers: Becket Ebitz & Nick Roy
Human representation of visuo-motor uncertainty as mixtures of orthogonal basis distributions. Zhang, Daw, Maloney, Nat Neurosci 2015.
Feb 9 Angela Langdon
readers: Jane Keung, Diksha Gupta, Tyler Boyd-Meredith
A neural mechanism for sensing and reproducing a time interval. Jazayeri & Shadlen, Current Biology 2015.
Feb 16 cancelled
Feb 23 Nick Roy
reader: Lea Duncker
The nature of shared cortical variability. Lin, Okun, Carandini, & Harris, Neuron 2015.
Mar 1 ( cosyne workshops)
Mar 8 Diksha Gupta
reader: Tyler Boyd-Meredith
The Inevitability of Probability: Probabilistic Inference in Generic Neural Networks Trained with Non-Probabilistic Feedback A. Emin Orhan & Wei Ji Ma. arxiv 2016.
Mar 15 ( spring break )
Mar 22 cancelled
Mar 29 Sam Lewallen
reader: Ahmed El Hady
Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex. Schottdorf, Wolfgang Keil, Coppola, White, & Wolf. PloS Comp Bio 2015.
Apr 5 Adam Charles Neuronal Circuits Underlying Persistent Representations Despite Time Varying Activity. Druckmann & Chklovskii, Current Biol (2012). [blog summary]
Apr 12 Anqi Wu
readers: Mikio & Nick
Sensory uncertainty decoded from visual cortex predicts behavior. Bergen, Ma, Pratte, & Jehee, Nat Neurosci (2015).
Apr 19 David Deutsch
readers: Diksha & Jonathan
Active sensing in the categorization of visual patterns. Yang, Lengyel, & Wolpert. eLIFE 2016.
Apr 26 Lea Duncker
readers: Adam Charles, Matt Panichello
Robust neuronal dynamics in premotor cortex during motor planning.
Li, Daie, Svoboda, & Druckmann. Nature (2016).
May 3 Alex Piet
readers: Angela Langdon & Sam Lewallen
Robust timing and motor patterns by taming chaos in recurrent neural networks.
Rodrigo Laje & Dean V Buonomano, Nature Neurosci (2013).
May 10 Tyler Boyd-Meredith
readers: Angela L and Alex P
Orbitofrontal Cortex Is Required for Optimal Waiting Based on Decision Confidence.
Lak, Costa, Romberg, Koulakov, Mainen, & Kepecs, Neuron (2014).


Past Meetings (Summer 2015)

Date Presenter Reading
Topic #1: Information theory and the brain (Adam Calhoun)
June 9 Jonathan Pillow

June 16 Adam Calhoun
June 23 Chris Baldassano
June 30 Ida Momennejad
Topic #2: Neural Codes in Noisy Cortical Circuits (Alex Piet & Ahmed El Hady)
July 14 Leenoy Meshulam
July 21 Alex Piet
July 28 Sam Lewallen
Aug 4 Athena Akrami
Aug 11 Ahmed El Hady
Aug 18 Sam Lewallen


Past Meetings (Spring 2015)

Date Presenter and readers Reading
Mar 18 Jonathan Pillow
readers: Jason P. & Jamal W.
Partitioning Neuronal Variability.
Goris, Movshon & Simoncelli Nature Neurosci (2014).

Apr 01 Michael Berry
readers: Angela L. & Sam L.
Predictive coding of dynamical variables in balanced spiking networks.
Boerlin, Machens & Deneve, PLoS Comp Biol (2013).
Apr 08 DJ Strouse
readers: Jonathan P. & Adam C.
Predictive information in a sensory population.
Palmer, Marre, Berry, & Bialek. arXiv:1307.0225
Apr 15 Mikio Aoi
readers: Alex P. & Ashley L.
Neural constraints on learning. Sadtler, Quick, Golub, Chase, Ru, Tyler-Kabara, Yu & Batista. Nature (2014).
Apr 22 Adrianna Loback
readers: Jonathan P. & DJ S.
A Simple Model of Optimal Population Coding for Sensory Systems. Doi & Lewicki, PLOS Comp. Biol. (2014)
Apr 29 Chris Baldassano
readers: Jamal W. & Ida M.
Human-level control through deep reinforcement learning. Mnih et al, Nature (2015).
May 06 Sam Lewallen
reader: Stephanie Chan
Performance-optimized hierarchical models predict neural responses in higher visual cortex", Yamins, Hong, Cadieu, Solomon, Seibert, & DiCarlo, PNAS (2014).
May 13 Jane Keung
readers: Alex Piet & Mikio Aoi
Signals in inferotemporal and perirhinal cortex suggest an untangling of visual target information. Pagan, Urban, Wohl, & Rust, Nature Neurosci (2013).