We meet to discuss a recent paper in neuroscience with a significant modeling or a data analysis component. We hope the journal club will help generate new ideas, foster new collaborations, and keep up-to-date with the literatures.
People interested in computational and theoretical neuroscience (undergraduates, master students, PhD students, post-docs, and faculty) are welcome to attend and are encouraged to present a paper. If you’d like to be added to the email list, visit our Google Group.
(Note: After sending the request for access to the Google Group, please send a reminder to Benjie Miao, the current organizer, via email bmiao@ucsd.edu. This will help ensure the request is processed in time, as the Google Group does not automatically send reminders upon receiving a request.)
Here is our current list of suggested papers.
In the summer, we set up a dedicated topic, Neural geometry and its function in behavioural tasks, and have all the events around this topic. We will study how to use mathematical methods to describe populational neural activities and construct manifolds with certain geometric properties, and how these manifolds become interpretable and relevant to behavioural readouts.
Session 1: Linear separability, manifold geometry, and their applications in mouse visual cortex
Date: Jul 8th. (Wednesday), 1:00-2:30pm
Presenter: Benjie Miao
References:
Cover, T. M., Geometrical and statistical properties of systems of linear inequalities with applications in pattern recognition. IEEE Transactions on Electronic Computers (1965).
Chung, S., Lee, D. D., & Sompolinsky, H. Classification and geometry of general perceptual manifolds. Physical Review X (2018).
Emmanouil Froudarakis, et. al., Object manifold geometry across the mouse cortical visual hierarchy. eLife (2026)
Session 2: Network and topological neuroscience
Date: Jul 15th. (Wednesday), 1:00-2:30pm
Presenters: Stella Yuan
References:
A hands-on tutorial on network and topological neuroscience
Session 3:
Date: Jul 22nd. (Wednesday), 1:00-2:30pm
Presenters: Felix Taschbach
References:
Session 4: Geometry of dynamics in low-rank neural networks
Date: Jul 28th. (Tuesday), 11:30am-1:00pm
Presenters: Caelen Hilty
References:
A theory of multi-task computation and task selection
Linking Connectivity, Dynamics, and Computations in Low-Rank Recurrent Neural Networks
Session 5:
Date: Aug 5th. (Wednesday), 1:00-2:30pm
Presenters: Chuan Tian
References:
Session 6:
Date: Aug 11th. / Aug 12th.
Presenters
Session 7:
Date: Aug 18th. / Aug 19th.
Presenters
Session 8:
Date: Aug 25th. / Aug 26th.
Presenters
Session 9:
Date: Sep 1st. / Sep 2nd.
Presenters
Session 10:
Date: Sep 8th. / Sep 9th.
Presenters
Fall 2020:
Date: Nov. 16th, 2020
Presenter: Mikio Aoi
Paper: Stine et al., (2020). Differentiating between integration and non-integration strategies in perceptual decision making. Elife, 9, e55365
Date: Nov. 23, 2020
Presenter: Marcelo Mattar
Paper: Whittington, Muller, et al (2020). The Tolman-Eichenbaum Machine: Unifying Space and Relational Memory through Generalization in the Hippocampal Formation. Cell 183, 1–15
Date: Nov. 30, 2020
Presenter: Marcus Benna
Paper: Ori Maoz et al. Learning probabilistic neural representations with randomly connected circuits, PNAS(2020).
Date: Dec. 7, 2020
Presenter: Yonatan Aljadeff
Paper: Nayebi et al., (2020). Identifying Learning Rules From Neural Network Observables. NeurIPS
Date: Dec. 14, 2020
Presenter: Eran Mukamel
Paper: From deep learning to mechanistic understanding in neuroscience: the structure of retinal prediction (2019) NeurIPS
Winter 2021:
Date: Jan. 12, 2021
Presenter: Gal Mishne
Paper: Russo et al. (2020). Neural Trajectories in the Supplementary Motor Area and Motor Cortex Exhibit Distinct Geometries, Compatible with Different Classes of Computation. Neuron
Date: Jan. 26, 2021
Presenter: Bin Wang
Paper: Stringer et al., (2019) High-dimensional geometry of population responses in visual cortex, Nature
Date: Wednesday Feb 3, 2021 at 5pm (note unusual time)
Presenter: Bin Wang
Paper: Stringer et al., (2019) High-dimensional geometry of population responses in visual cortex, Nature - continued from last week
Date: Feb. 9, 2021
Presenter: Tim Sheehan
Paper: Ruff et al. (2020). Low rank mechanisms underlying flexible visual representations, PNAS
Date: Feb. 16, 2021
Pre-COSYNE poster session
Sign up if you want to do a practice run of you poster before COSYNE-21
Date: Mar. 2nd, 2021
Presenter: Leo Breston
Paper: Gao et al. (2017), A theory of multineuronal dimensionality, dynamics and measurement
Date: Mar. 16th, 2021
Presenter: David Kleinfeld
Paper: Robinson et al. (2020), Targeted activation of hippocampal place cells drives Memory-Guided spatial behavior
Spring 2021:
Date: March 29th 2021, 4pm
Topic: Launch of spring quarter journal club
Date: Monday April 5th, 5:30pm (note irregular time)
Presenter: Brad Theilman (joint with weekly seminar Journal club)
Paper: Kim et al. (2019), Generation of stable heading representations in diverse visual scenes
Date: Monday April 12th, 4pm
Presenter: Jennifer Jensen
Paper: 'Antagonism in olfactory receptor neurons and its implications for the perception of odor mixtures’, DOI: 10.7554/eLife.34958
Date: Monday April 19th, 4pm
Presenter: Homero Esmeraldo
Preprint: Hinton (2021), ‘How to represent part-whole hierarchies in a neural network’.
Date: Monday April 26th, 4pm
Presenter: Yuru Song
Paper: Fundamental law of memory recall. Physical Review Letters, 124(1), 018101. Naim, M., Katkov, M., Romani, S., & Tsodyks, M. (2020).
Date: Monday May 10th, 4pm
Presenter: Ji-An Li
Paper: Goal-Directed Decision Making with Spiking Neurons, https://www.jneurosci.org/content/36/5/1529, J. Friedrich and M. Lengyel (2016).
Date: Monday May 24th, 4pm
Presenter: Felix Taschbach
Paper: Genkin, M., Engel, T.A. Moving beyond generalization to accurate interpretation of flexible models. Nat Mach Intell 2, 674–683 (2020).
Spring 2023:
Date: April 3rd, 2023
Presenter: Bin Wang (Aljadeff Lab)
Paper: Extended Anderson Criticality in Heavy-Tailed Neural Networks, Phys. Rev. Lett. (2022).
Date: April 10th, 2023
Presenter: Stella Yuan (Aoi & Serences Lab)
Date: April 17th, 2023
Presenter: Dhruv Kohli (Mishne & Cloninger Lab)
Paper: Toroidal topology of population activity in grid cells, Nature, (2022)
Date: April 24th, 2023
Presenter: Ji-An Li (Benna & Mattar Lab)
Paper: Residual dynamics resolves recurrent contributions to neural computation, Nat. Neurosci. (2023)
Date: May 1st, 2023
Presenter: Pengcen Jiang (1st year HDSI; Rotating)
Date: May 8th, 2023
Presenter: Meg Robinson (Aoi Lab)
Paper: Movement is governed by rotational neural dynamics in spinal motor networks, Nat. Neurosci. (2022)
Date: May 15th, 2023
Presenter: Yusi Chen (Sejnowski Lab)
Date: June 5th, 2023
Presenter: Felix Taschbach (Benna & Tye Lab)
Paper: Learnable latent embeddings for joint behavioral and neural analysis, Nature (2023)
Date: June 12nd, 2023
Presenter: Johnny Jingze Li (Silva Lab)
Paper: Geometric constraints on human brain function, Nature (2023).
Fall 2023:
Date: Oct 2nd, 2023
Presenter: Teng Fei
Paper: High-resolution image reconstruction with latent diffusion models from human brain activity, bioRxiv
Date: Oct 9th, 2023
Presenter: Pengcen Jiang
Paper: Inferring learning rules from animal decision-making, NeurIPS (2020)
Date: Oct 16th, 2023
Presenter: Palka Puri
Date: Oct 23rd, 2023
Presenter: Stella Yuan
Date: Oct 30th, 2023
Presenter: Dyuthi Sristi
Paper: Multiregion neuronal activity: the forest and the trees, Nat Rev Neurosci (2022)
Date: Nov 6th, 2023
Presenter: Sowmya Manojna
Paper: Preserved neural population dynamics across animals performing similar behaviour, bioRxiv
Date: Nov 20th, 2023
Presenter: Benjie Miao
Paper: A Unified, Scalable Framework for Neural Population Decoding, NeurIPS (2023)
Winter 2024:
Date: Jan 22nd, 2024
Presenter: Stella Yuan (Aoi & Serences Lab)
Paper: Nguyen, N.D., Lutas, A., Amsalem, O. et al. Cortical reactivations predict future sensory responses. Nature (2024).
Date: Jan 29th, 2024
Presenter: Benjie Miao (Rotation Student)
Paper: Nogueira, R., Rodgers, C.C., Bruno, R.M. et al. The geometry of cortical representations of touch in rodents. Nature Neuroscience (2023).
Date: Feb 5th, 2024
Presenter: Mingchen Yao (Sharpee Lab)
Paper: Recanatesi, S., Farrell, M., Lajoie, G. et al. Predictive learning as a network mechanism for extracting low-dimensional latent space representations. Nature Communication (2021).
Date: Feb 12th, 2024
Presenter: Weiheng Qin (Sharpee Lab)
Paper: Kollmorgen, S., Hahnloser, R.H.R. & Mante, V. Nearest neighbours reveal fast and slow components of motor learning. Nature (2020).
Date: Mar 4th, 2024
Presenter: Shiva A. Lindi (Aljadeff Lab)
Paper: Gillett M, Pereira U, Brunel N. Characteristics of sequential activity in networks with temporally asymmetric Hebbian learning. PNAS (2020).
Date: Mar 11th, 2024
Presenter: Mikio Aoi
Paper: Yang JY, O'Connell TF, et al. Restructuring of olfactory representations in the fly brain around odor relationships in natural sources. bioRxiv (2023).
Date: Mar 18th, 2024
Presenter: Iulia Rusu (Rotation Student)
Paper: Van de Ven G M, Tolias A S. Three scenarios for continual learning. arXiv (2019).
Spring 2024:
Date: Apr 8th, 2024
Presenter: Ji-An Li (Benna & Mattar Lab)
Paper: Elia Turner, Omri Barak. The Simplicity Bias in Multi-Task RNNs: Shared Attractors, Reuse of Dynamics, and Geometric Representation. NeurIPS (2023).
Date: Apr 22nd, 2024
Presenter: Sowmya M Narasimha (Prof. Gal Mishne Lab)
Paper: Gerald M Pao, et. al. Experimentally testable whole brain manifolds that recapitulate behavior. Arxiv (2021).
Date: May 13th, 2024
Presenter: Weiheng Qin (Sharpee Lab)
Paper: Wang, H., Zhong, H., Dai, W. P., & Yu, Y. The Functional Role of Pinwheel Topology in the Primary Visual Cortex of High-Order Animals for Complex Natural Image Representation. bioRxiv (2024).
Date: Jun 3rd, 2024
Presenter: Stella Yuan (Aoi & Serences Lab)
Paper: Ratzon, A., Derdikman, D., & Barak, O. Representational drift as a result of implicit regularization. Elife (2024).
Date: Jun 10th, 2024
Presenter: Benjie Miao (Aoi & Augustine Lab)
Paper: Driscoll, L. N., Shenoy, K., & Sussillo, D. Flexible multitask computation in recurrent networks utilizes shared dynamical motifs. Nature Neuroscience (2024).
Fall 2024:
Date: Sep 30th, 2024
Presenter: Benjie Miao (Aoi & Augustine Lab)
Paper: Vinograd, A., Nair, A., Kim, J., Linderman, S. W., & Anderson, D. J. Causal evidence of a line attractor encoding an affective state. Nature (2024)
Date: Oct 14th, 2024
Presenter: Mingchen Yao (Sharpee Lab)
Paper: Chen G, Kang B, Lindsey J, Druckmann S, Li N. Modularity and robustness of frontal cortical networks. Cell (2023)
Date: Oct 21st, 2024
Presenter: Max Weinberg
Paper: Qingyang Wang, Albert Cardona, Marta Zlatic, Joshua Vogelstein, Carey Priebe. Why do we have so many excitatory neurons?. bioRxiv (2024)
Date: Nov 4th, 2024
Presenter: Max Weinberg
Paper: Costa, A. C., Ahamed, T., Jordan, D., & Stephens, G. J. A Markovian dynamics for Caenorhabditis elegans behavior across scales. PNAS (2024)
Date: Nov 18th, 2024
Presenter: Richard Gast (Kennedy Lab)
Paper: Gast, R., Solla, S. A., & Kennedy, A. Neural heterogeneity controls computations in spiking neural networks. PNAS (2024).
Date: Nov 25th, 2024
Presenter: Stella Yuan (Aoi & Augustine Lab)
Paper: Wang, Z., Di Tullio, R. W., Rooke, S., & Balasubramanian, V. Time makes space: Emergence of place fields in networks encoding temporally continuous sensory experiences. bioRxiv (2024).
Date: Dec 9th, 2024
Presenter: Shiva A. Lindi (Aljadeff Lab)
Paper: Kozachkov, L., Kastanenka, K. V., & Krotov, D. Building transformers from neurons and astrocytes. PNAS (2023).
Date: Dec 16th, 2024
Presenter: Keerthana Senthilnathan (First Year MSDS)
Paper: Benjamin, A.S., Zhang, LQ., Qiu, C. et al. Efficient neural codes naturally emerge through gradient descent learning. Nat Commun (2022).
Winter 2025:
Date: Jan 13th, 2025
Presenter: Benjie Miao (Aoi & Augustine Lab)
Paper: Xie, W., Wittig, J.H., Chapeton, J.I. et al. Neuronal sequences in population bursts encode information in human cortex. Nature (2024)
Date: Jan 20th, 2025
Presenter: N/A (Martin Luther King Jr. Day)
Paper: N/A
Date: Jan 27th, 2025
Presenter: Ji-An Li (Benna & Mattar Lab)
Paper: Dohare, S., Hernandez-Garcia, J.F., Lan, Q. et al. Loss of plasticity in deep continual learning. Nature (2024).
Date: Feb 3rd, 2025
Presenter: Jeremy Chung-Yueh Lin (Komiyama Lab)
Paper: Griffin, S., Khanna, P., Choi, H. et al. Ensemble reactivations during brief rest drive fast learning of sequences. Nature (2025).
Date: Feb 10th, 2025
Presenter: Chan Li (Goldenfeld Lab)
Paper: Biroli, G., Bonnaire, T., de Bortoli, V. et al. Dynamical regimes of diffusion models. Nat. Comm. (2024).
Date: Feb 17th, 2025
Presenter: N/A (University Holiday)
Paper: N/A
Date: Feb 24th, 2025
Presenter: Mingchen Yao (Sharpee Lab)
Paper: Noorman, M., Hulse, B.K., Jayaraman, V. et al. Maintaining and updating accurate internal representations of continuous variables with a handful of neurons. Nat Neurosci. (2024).
Date: Mar 3rd, 2025
Presenter: N/A
Paper: N/A
Date: Mar 10th, 2025
Presenter: Richard Gast (Kennedy Lab)
Paper: Genkin, M., Shenoy, K. V., Chandrasekaran, C., & Engel, T. A. The dynamics and geometry of choice in premotor cortex. bioRxiv (2023).
Date: Mar 17th, 2025, 2:30pm (Note unusual time)
COSYNE practice session I
Presenter: JC Gorman (Gertner Lab), Trevor Supan McPherson (Gertner Lab)
Date: Mar 24th, 2025
COSYNE practice session II
Presenter: Poster presenters
Spring 2025:
Date: Apr 14th, 2025
Presenter: Chan Li (Goldenfeld Lab)
Paper: Nguyen, A., & Reddy, G. (2024). Differential learning kinetics govern the transition from memorization to generalization during in-context learning. ICLR (2025).
Fall 2025:
Date: Sep 29th, 2025
Presenter: Benjie Miao (Augustine/Aoi Lab)
Paper: Raut, R.V., Rosenthal, Z.P., Wang, X. et al. Arousal as a universal embedding for spatiotemporal brain dynamics. Nature (2025).
Date: Oct 20th, 2025
Presenter: Shiva A. Lindi
Paper: Gozel, O., & Doiron, B. Between-area communication through the lens of within-area neuronal dynamics. Science Advances (2024).
Date: Nov 3rd, 2025
Presenter: Caelen Hilty
Paper: Chandra, S., Sharma, S., Chaudhuri, R. et al. Episodic and associative memory from spatial scaffolds in the hippocampus. Nature (2025).
Date: Nov 10th, 2025
Presenter: Stella Yuan
Paper: Kashyap A, Geenjaar E, Bey P, Dhindsa K, Glomb K, Plis S, Keilholz S, Ritter P. Using an ordinary differential equation model to separate rest and task signals in fMRI. Nat Commun (2025).
Date: Dec 1st, 2025
Presenter: Christiano S. Simões
Paper: Special Research Presentation - Topological invariants in the activity of three-dimensional bioprinted neuronal constructs derived from human induced pluripotent stem cells
Date: Dec 15th, 2025
Presenter:Chan Li (Goldenfeld Lab)
Paper: Bonnet, D., Cottart, K., Hirtzlin, T. et al. Bayesian continual learning and forgetting in neural networks. Nat Commun (2025).
Winter 2025:
Date: Jan 26th, 2026
Presenter: Fangxu Cai (Benna Lab)
Paper: Stroud, J. P., Watanabe, K., Suzuki, T., Stokes, M. G., & Lengyel, M. Optimal information loading into working memory explains dynamic coding in the prefrontal cortex. PNAS (2023).
Date: Feb 2nd, 2026
Presenter: Ram Dyuthi Sristi
Topic: Interpretable Representations of Neural Circuit Dynamics Across Regions and Contexts (Thesis defense practice)
Date: Feb 9th, 2026
Presenter: Felix Taschbach (Benna Lab)
Paper: Yi, D., et al. Shared-AE: Automatic Identification of Shared Subspaces in High-dimensional Neural and Behavioral Activity. International Conference on Learning Representations (ICLR) (2026).
Date: Mar 2rd, 2026
Presenter: Sowmya Manojna
Topic: COSYNE 2026 Practice Talk
Date: Mar 9th, 2026
Presenter: Hayoung Song (currently postdoc at Washington University in St. Louis)
Paper: Song, H., Chen, R., Botch, T.L. et al. Geometry of neural dynamics along the cortical attractor landscape reflects changes in attention. Nat Commun (2026).
Date: Mar 23rd, 2026
Presenter: Chuan Tian (Benna Lab)
Paper: Zucchet, N., Meier, R., Schug, S., Mujika, A., & Sacramento, J. (2023). Online learning of long-range dependencies. Advances in Neural Information Processing Systems, 36, 10477-10493.
Spring 2026
Date: Apr 13th, 2026
Presenter: Chan Li
Paper: Sakamoto, K., & Sato, I. (2025). Explaining Grokking and Information Bottleneck through Neural Collapse Emergence. ICLR (2026).
Date: May 18th, 2026
Presenter: Minjun Kang
Paper: Cheon J. & Paik S. (2026). Brain-inspired warm-up training with random noise for uncertainty calibration. Nature.
Date: June 8th, 2026
Presenter: Benjie Miao
Paper: Pachitariu et al. (2026). A critical initialization for biological neural networks. Nature.
