Cold Spring Harbor Laboratory

Papers and research supported in part or in whole by The Swartz Foundation

Farhad Pashakhanloo, Alexei Koulakov.
"Stochastic Gradient Descent-Induced Drift of Representation in a Two-Layer Neural Network," Proceedings of the 40th International Conference on Machine Learning (ICML 2023), Honolulu, Hawaii, USA.

Sergey A. Shuvaev, Evgeny M Amelchenko, Dmitry Smagin, Natalia Kudryavtseva, Grigori Enikolopov, Alexei A. Koulakov.
"A normative theory of social conflict," Proceedings of the 37th Conference on Neural Information Processing Systems (NeurIPS 2023), New Orleans, USA

Pashakhanloo, F., Koulakov A.
"Stochastic Gradient Descent-induced drift of representation in a two-layer neural network," arXiv:2302.02563 (2023).

Langdon, C. & Engel, T. A.
"Latent circuit inference from heterogeneous neural responses during cognitive tasks," bioRxiv 2022.01.23.477431 (2022)

Shen, Y., Dasgupta, S., & Navlakha, S. (2021).
Algorithmic insights on continual learning from fruit flies. arXiv preprint arXiv:2107.07617.

Yang Shena, Sanjoy Dasguptab, and Saket Navlakhaa.
Habituation as a neural algorithm for online odor discrimination, PNAS June 2, 2020 117 (22) 12402-12410

Yang Shen, Julia Wang, and Saket Navlakha.
A correspondence between normalization strategies in artificial and biological neural networks, 2020 BioRxiv 10.1101/2020.07.17.197640

Yan-Liang Shi, Nicholas A. Steinmetz, Tirin Moore, Kwabena Boahen, and Tatiana A. Engel.
Influence of On-Off dynamics and selective attention on the spatial pattern of correlated variability in neocortex, 2020 bioRxiv 0.1101/2020.09.02.279893


Dmitri B. Chklovskii

Quan Wen, Armen Stepanyants, Guy N. Elston, Alexander Y. Grosberg, and Dmitri B. Chklovskii. Maximization of the connectivity repertoire as a statistical principle governing the shapes of dendritic arbors. PNAS, July 28, 2009; Vol. 106 , No. 30:12536-12541. Available online at:


Adam Kepecs

Kepecs A, Uchida N, Zariwala HA, Mainen ZF (2008) Neural correlates, computation and behavioural impact of decision confidence.

Nature Sep 11;455(7210):227-31.



Kepecs, Uchida and Mainen (2008) How uncertainty boosts learning: Dynamics updating of decision-strategies.  NeuroEconomics Conference.


Kepecs, Uchida and Mainen (2008) Graded prediction error signal drives behavioral choice biases in rats. Computational and Systems Neuroscience (CoSyNe) Conference


Alexei Koulakov

Encinas JM, Michurina T, Tordo J, Peterson D, Fishell G., Koulakov A, Enikolopov G.N., Disposable Stem Cells: Division-Coupled Astrocytic Differentiation of Neural Stem Cells Determines Age-Related Decline In Hippocampal Neurogenesis.  Nature in review.


Koulakov A., Hromadka T., Zador A., Correlated connectivity and the distribution of firing rates in the neocortex.  Journal of Neuroscience, in review.


Nikitchenko M, Koulakov A. (2008) Neural integrator: a sandpile model.

Neural Computation 20(10): 2379-417.


Tsigankov D, Koulakov A, Sperry versus Hebb: Topographic mapping in Isl2/EphA3 mutant mice. Submitted to Network: Computation in the neural systems (


Tsigankov D, Optimal axonal and dendritic branching strategies during the development of neural circuitry. To be submitted to PLOS computational biology (


Zachary Mainen

Felsen G, Mainen ZF (2008) Neural substrates of sensory-guided locomotor decisions in the rat superior colliculus. Neuron 60:137-48.


Huber D, Petreanu L, Ghitani N, Ranade S, Hromádka T, Mainen Z, Svoboda K (2008) Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature 451:61-64.


Uchida N, Mainen ZF (2007) Odor concentration invariance by chemical ratio coding. Front Syst Neurosci 1:3.



Felsen G, Klein R, Mainen ZF (2008) Movement selection and initiation in the rat superior colliculus. Cosyne Abstr I-49.


Felsen G, Mainen ZF (2008) The role of the superior colliculus sensory-guided spatial decisions in rats. Soc Neurosci Abstr 34, 22.1.


Kepecs A, Uchida N, Mainen ZF (2008) Graded prediction error signal drives behavioral choice biases in rats. Cosyne Abstr I-65.


Kepecs A, Uchida N, Mainen ZF (2008) How uncertainty boosts learning: Dynamic updating of decision strategies. Soc Neurosci Abstr 34, 98.1.


Khan AG, Bhalla US, Mainen ZF (2008) Odour mixture processing in the rat olfactory cortex. FENS Abstr 4, A019.13.


Mainen ZF, Kepecs A, Zariwala H, Uchida N (2008) Uncertainty representation in the orbitofrontal cortex during decision making in rats. FENS Abstr 4, A157.3.


Miura K, Mainen ZF, Uchida N (2008) Dynamic odor representation in rat piriform cortex during active sensation. Soc Neurosci Abstr 34, 117.7.


Murakami M, Mainen ZF (2008) Role of medial prefrontal cortex and secondary motor cortex in withholding impulsive action. Cosyne Abstr III-67


Tony Zador

Asari H, Zador A (2008) Long-lasting context dependence constrains neural encoding models in rodent auditory cortex.  Nature Precedings.   


Hromadka T, DeWeese MR, Zador AM.  Sparse representations of sounds in the unanesthetized auditory cortex.  PLoS Biology 2008; 6(1): e16.


Santiago Jaramillo and Anthony M Zador. The auditory cortex mediates the perceptual effects of acoustic temporal expectation. Nature Neuroscience. Published online 19 December 2010 | doi:10.1038/nn.2688 at


Yang Y, DeWeese MR, Otazu G, Zador AM.  Millisecond-scale differences in neural activity in auditory cortex can drive decisions.  Nature Neuroscience. 11: 1262-3.



Jaramillo S. and Zador AM.  A behavioral paradigm for probing the auditory system of freely moving rats under different behavioral contexts. Cosyne 2008, Salt Lake City, UT.


Otazu GH, Zador AM.  Task-dependent suppression of evoked responses in auditory cortex.  Cosyne 2008, Salt Lake City, UT.


Jaramillo S. and Zador AM. Effects of temporal expectation on the processing of auditory stimuli: characterization of behavioral and single-cell responses. Program No. 710.1. 2008 Neuroscience Meeting Planner. Washington, DC: Society for Neuroscience, 2008. Online.


Otazu GH, Tai L, Zador AM. Engaging in an auditory task suppresses responses in rat auditory cortex. Program No. 851.13. 2008 Neuroscience Meeting Planner. Washington, D.C: Society for Neuroscience, 2008. Online.



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