Computational Neuroscience

We investigate the cognitive and neural mechanisms underlying learning and memory using computational methods. We highly welcome bright students who would like to pursue a Bachelor/Master thesis in our group. The main language of communication is English.


A particular focus of our research is understanding the function of a brain region, called the hippocampus. It is involved in storing and retrieving episodic memories and in generating representations of space. However, it remains unclear why these two functions go together and how these functions are implemented in the hippocampus. To address these two questions, we employ a number of computational and theoretical approaches, including

  • biologically realistic neural network models, which nonetheless are highly simplified, that capture the essence of the neural circuit mechanism underlying learning and memory.
  • algorithmic models of the storage and retrieval of episodic memories.
  • conceptual models of the nature of episodic memory.
  • robotics simulations of spatial memory in rodents.

The two projects described below exemplify the approach of our group.

 Modeling spatial learning and navigation

Rodents are known to perform extremely well when navigating complex environments and to adapt rapidly to novel situations. They maneuver through dark sewers while looking for food or fleeing from predators and seem to know exactly where they are and where to go. We are modeling the spatial behavior of rodents using a robot model. A particular interesting question is how animals learn to navigate novel environments and to perform new tasks. We are studying this question using a machine learning approach called reinforcement learning. Within this framework, we implement the neural circuitry of the hippocampus to study how the neural mechanisms underlying spatial learning and navigation. For more details see the "Projects" tab above.


Neural sequences in the hippocampus

The Nobel Prize in Physiology or Medicine in 2014 was awarded to John O’Keefe for the discovery of place cells and to May-Britt Moser and Edvard Moser for the discovery of grid cells. Place cells are found in the hippocampus and they respond, or “spike”, when an animal is located in a particular place, called a “place field”. The timing of spiking is such that, during one cycle of the theta oscillation (8 – 12Hz), groups of place cells spike in a sequence that corresponds to the order of their place fields in space (theta sequences). Intriguingly, the same place cells also spike in sequential order afterwards, when the animal is resting or sleeping (replay sequences). We are developing neural network models to help us understand how theta and replay sequences are generated and what role they play in learning and memory. 

International collaborations:

  • Kamran Diba, University of Michigan, USA

  • Chengyu Li, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China

  • Edison Pignaton de Freitas, Federal University of Rio Grande do Sul, Brazil

  • Bailu Si, Shenyang Institute of Automation, Chinese Academy of Sciences, China

  • Patrick Crotty, Colgate University, USA

  • Yuri Dabaghian, Baylor College of Medicine, USA

  • Lynn Nadel, University of Arizona, USA

  • Thomas Suddendorf, University of Queensland, Australia

  • Alireza Valizadeh, Institute of Advanced Studies, Zanjan, Iran


Major depressive disorder (MDD) is a disabling condition that adversely affects a person general health, work or school life, sleeping and eating habits, and person's family. Despite intense research efforts, the response rate of antidepressant treatments are relatively low and the etiology and progression of MDD remain poorly understood. To advance our understanding of MDD, we use computational modelling as described in our article.

For further information consult the  project page (see above).

The model to simulate the dynamics of disease states in depression can be downloaded as a zip File and can be used with Matlab.



With Parametric Anatomical Modeling (PAM), we propose a technique and a Python implementation to create artificial neural networks that meet connectivity patterns and connection lengths of large scale neural networks.

The basic idea of PAM is to trace neural, synaptic and intermediate layers from anatomical data and relate those layers to each other. With a set of mapping techniques, complex relationships between those layers can be defined to determine how axonal and dendritic projections traverse through space and where synapses are formed.

For further information consult the project page (see above).

PAM is available as an Addon for Blender and can be downloaded from a repository on Github. An importer for the neural network simulator NEST is available in a separate repository.



Our group aims to provide neuroscientific community with a collection of high-quality SVG-figures for free use in publications, presentations, websites etc. via GitHub.

All SVG-files in the repository underlie the Create Commons Attribution 4.0 International License.

A ZIP-file containing all of the currently available figures as well as additional information concerning their creation can be downloaded here.

Modeling the Dynamics of Disease States in Depression

We study under what conditions the model can account for the occurrence and recurrence of depressive episodes and how we can model the effects of antidepressant treatments and cognitive behavioral therapy within the same dynamical systems model through changing a small subset of parameters.

Parametric Anatomical Modeling (PAM)

With Parametric Anatomical Modeling (PAM), we propose a technique and a Python implementation to create artificial neural networks that meet connectivity patterns and connection lengths of large scale neural networks.


Rodents perform extremely well in navigating complex environments like dark sewers while looking for food or fleeing from predators. The role of the hippocampus in such spatial navigation efforts has interested researchers from the neuroscience domain for decades: in 1971 so-called ‘place cells’ had been discovered in the rat’s hippocampus. While these cell-types allow the animals to swiftly self-localize in a given environment (cognitive mapping), rodents also seem to rely on grid cells (discovered 2005 in the rat’s hippocampus) for path planning and spatial navigation. In addition, recent publications postulate a relationship between theta waves generated in the hippocampus and decision making in spatial navigation tasks.

Walther, T., & Würtz, R. P.. (2018). Unsupervised Acquisition of Human Body Models. Cognitive Systems Research, 47, 68–84.
Fang, J., Rüther, N., Bellebaum, C., Wiskott, L., & Cheng, S.. (2017). The Interaction between Semantic Representation and Episodic Memory. Neural Computation, 1–40.
Walther, T., & Würtz, R. P.. (2017). Unsupervised Acquisition of Human Body Models using Principles of Organic Computing. ArXiv e-prints. Retrieved from
Cheng, S. (2017). Gedächtnisverbesserung: Möglichkeiten und kritische Betrachtung. In F. Hüttemann & Liggieri, K. (Eds.), Die Grenze . Diskurse des Transhumanismus. (p. invited contribution). Bielefeld: transcript Verlag.
Cheng, S. (2017). Consolidation of Episodic Memory: An Epiphenomenon of Semantic Learning. In N. Axmacher & Rasch, B. (Eds.), Cognitive Neuroscience of Memory Consolidation (pp. 57–72). Cham, Switzerland: Springer International Publishing.
Neher, T., Azizi, A. H., & Cheng, S.. (2017). From grid cells to place cells with realistic field sizes. PLoS ONE, 12(7), e0181618.
Werning, M., & Cheng, S.. (2017). Taxonomy and Unity of Memory. In S. Bernecker & Michaelian, K. (Eds.), The Routledge Handbook of Philosophy of Memory (p. forthcoming). London: Routledge.
Werning, M., & Cheng, S.. (2017). No need for meta-representation: How scenario construction explains the epistemic generativity and privileged epistemic status of episodic memory. Behavioral and Brain Sciences, in press.
Babichev, A., Cheng, S., & Dabaghian, Y. A. (2016). Topological Schemas of Cognitive Maps and Spatial Learning. Frontiers in Computational Neuroscience, 10, 18.
Cheng, S., & Werning, M. (2016). What is episodic memory if it is a natural kind? Synthese, 193(5), 1345–1385.
Cheng, S., Werning, M., & Suddendorf, T. (2016). Dissociating memory traces and scenario construction in mental time travel. Neuroscience & Biobehavioral Reviews, 60, 82–89.
Bayati, M., Valizadeh, A., Abbassian, A., & Cheng, S.. (2015). Self-organization of synchronous activity propagation in neuronal networks driven by local excitation. Frontiers in Computational Neuroscience, 9, 69.
Neher, T., Cheng, S., & Wiskott, L.. (2015). Memory Storage Fidelity in the Hippocampal Circuit: The Role of Subregions and Input Statistics. PLoS Computational Biology, 11(5), e1004250.
Demic, S., & Cheng, S.. (2014). Modeling the Dynamics of Disease States in Depression. PLOS ONE, 9(10), 1–14.
Azizi, A. H., Schieferstein, N., & Cheng, S.. (2014). The transformation from grid cells to place cells is robust to noise in the grid pattern. Hippocampus, 24(8), 912–919.
Pyka, M., Klatt, S., & Cheng, S.. (2014). Parametric Anatomical Modeling: a method for modeling the anatomical layout of neurons and their projections. Frontiers in Neuroanatomy, 8, 91.
Werning, M., & Cheng, S.. (2014). Is Episodic Memory a Natural Kind?-A Defense of the Sequence Analysis. In P. Bello, Guarini, M., McShane, M., & Scassellati, B. (Eds.), Proceedings of the 36th Annual Conference of the Cognitive Science Society (Vol. 2, pp. 964–69). Austin, TX: Cognitive Science Society. Retrieved from
Cheng, S., & Werning, M. (2013). Composition and replay of mnemonic sequences: The contributions of REM and slow-wave sleep to episodic memory. Behavioral and Brain Sciences, 36(06), 610–611.
Azizi, A. H., Wiskott, L., & Cheng, S.. (2013). A computational model for preplay in the hippocampus. Frontiers in Computational Neuroscience, 7, 161.
Cheng, S. (2013). The CRISP theory of hippocampal function in episodic memory. Frontiers in Neural Circuits, 7, 88.
Helduser, S., Cheng, S., & Güntürkün, O. (2013). Identification of two forebrain structures that mediate execution of memorized sequences in the pigeon. Journal of Neurophysiology, 109(4), 958–968.
Bayati, M., & Valizadeh, A. (2012). Effect of synaptic plasticity on the structure and dynamics of disordered networks of coupled neurons. Phys. Rev. E, 86(1), 011925.
Crotty, P., Lasker, E., & Cheng, S.. (2012). Constraints on the synchronization of entorhinal cortex stellate cells. Phys. Rev. E, 86(1), 011908.
Buhry, L., Azizi, A. H., & Cheng, S.. (2011). Reactivation, Replay, and Preplay: How It Might All Fit Together. Neural Plasticity, 2011, 1–11.
Cheng, S., & Frank, L. M. (2011). The structure of networks that produce the transformation from grid cells to place cells . Neuroscience , 197, 293–306.
Cheng, S., & Frank, L. M. (2008). New Experiences Enhance Coordinated Neural Activity in the Hippocampus . Neuron , 57(2), 303–313.
Cheng, S., & Sabes, P. N. (2007). Calibration of Visually Guided Reaching Is Driven by Error-Corrective Learning and Internal Dynamics. Journal of Neurophysiology, 97(4), 3057–3069.
Cheng, S., & Sabes, P. N. (2006). Modeling Sensorimotor Learning with Linear Dynamical Systems. Neural Computation, 18(4), 760–793.
Cheng, S., Petriconi, S., Pratt, S., Skoby, M., Gale, C., Jeon, S., et al. (2004). Statistical and dynamic models of charge balance functions. Phys. Rev. C, 69(5), 054906.
Pratt, S., & Cheng, S.. (2003). Removing distortions from charge balance functions. Phys. Rev. C, 68(1), 014907.
Cheng, S., & Pratt, S. (2003). Isospin fluctuations from a thermally equilibrated hadron gas. Phys. Rev. C, 67(4), 044904.
Cheng, S. (2002). Statistical physics in a finite volume with absolute conservation laws.
Cheng, S. (2002). Modeling Relativistic Heavy Ion Collisions.
Cheng, S., Pratt, S., Csizmadia, P., Nara, Y., Molnár, D., Gyulassy, M., et al. (2002). Effect of finite-range interactions in classical transport theory. Phys. Rev. C, 65(2), 024901.
Cheng, S., & Pratt, S. (2001). Quantum corrections for pion correlations involving resonance decays. Phys. Rev. C, 63(5), 054904.
Computational Studies of the Role of Semantic Representation in Episodic Memory

The goal of this project is to extend these results to new object types and classes of objects. A good command of Python is required.

Generically trained SFA networks for cognitive mapping in simulated rodents

This project will assess potential advantages of generically trained SFA networks in cognitive mapping of virtual environments. An excellent command of Python (including numpy, matplotlib, scipy) and C/C++ is required. Experience with the Blender simulation environment would be advantageous.

Modeling Enhanced Replay of Neuronal Sequences in the Hippocampus

Modeling Enhanced Replay of Neuronal Sequences in the Hippocampus

Necessary and Sufficient Behavioral Evidence for Episodic Memory Traces

The goal of this project is to identify what behavioral evidence would be necessary and sufficient to claim that a nonhuman species possesses episodic memory traces. The project requires background knowledge of memory and experience in developing philosophical analyses.

Processing of Spatial Information in the Hippocampal Circuit

In this project, we study whether the responses of neurons in the hippocampal sublayers (DG, CA3, and CA1) resemble the responses of recorded place cells. Knowledge of the programming language Python is required.

Robust Generation of Spatio-temporal Activity Patterns in Neuronal Networks

The goal of this project is to better understand the sensitivity of the various neural network models to noise.

Self-organization of spatially tuned neural activity in volumetric virtual environments

This project is is geared towards extending work of Franzius et al. (2007) to cope with volumetric cognitive mapping based on Slow Feature Analysis methods. An excellent command of Python (including numpy, matplotlib, scipy) and C/C++ is required. Experience with the Blender simulation environment would be advantageous.

The causal relationship between phase precession and theta sequential activity

In this project we investigate the casual relationship between the quality of theta sequences and phase precession of the activity of place cells in the hippocampus.