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panosalef/README.md

Panos Alefantis

MD. PhD candidate in Cognition and Perception, New York University (Angelaki and Mattar labs).

Interests: computational neuroscience, decision making, reinforcement learning, naturalistic behaviour, LLM agents

Code

Repository What it is
cog-cybernet A file-based cognitive architecture for governing many concurrent LLM-agent projects: central executive over a global workspace, situation model rewritten each session, significance-weighted decay, cross-project consolidation. Protocol, templates, hooks, example fleet.
foraging-allocation-dynamics Analysis pipeline behind the 2026 foraging preprint: matching law, stay/return dynamics against a Poisson null, within-block dynamics, policy epochs (Python and MATLAB).
foragingTaskFMM Object model and import pipeline for the freely moving macaque foraging task: behaviour, motion capture, eye tracking, LFP and sorted units on one clock (MATLAB).
foragingAgent_deepRL Recurrent PPO agent (LSTM actor-critic) that learns a three-patch foraging task with stochastic reward timing and noisy cues (PyTorch).
fireflyTask Perturbation, joystick-gain and optic-flow-density analyses behind the 2022 J Neurosci paper (MATLAB).
NNM_fearConditioning Reimplementation of Armony et al.'s anatomically constrained dual-pathway network of fear conditioning (MATLAB).

Publications

  • Alefantis P., Guo Y., Quazi N., Savin C., Angelaki D.E., Pitkow X., Majaj N.J. (2026). Temporal Structure of Reward Availability and Sensory Uncertainty Modulate Allocation Dynamics in Naturalistic Foraging. bioRxiv. doi:10.64898/2026.04.14.718537
  • Alefantis P., Lakshminarasimhan K., Avila E., Noel J.-P., Pitkow X., Angelaki D.E. (2022). Sensory evidence accumulation using optic flow in a naturalistic navigation task. The Journal of Neuroscience. doi:10.1523/JNEUROSCI.2203-21.2022
  • Noel J.-P., Balzani E., Avila E., Lakshminarasimhan K., Bruni S., Alefantis P., Savin C., Angelaki D.E. (2022). Coding of latent variables in sensory, parietal, and frontal cortices during closed-loop virtual navigation. eLife. doi:10.7554/eLife.80280

Contact

pa77@nyu.edu

Popular repositories Loading

  1. fireflyTask fireflyTask Public

    MATLAB analyses behind Alefantis et al. (2022, J Neurosci): optic-flow perturbation, joystick gain and flow density in the firefly navigation task.

    MATLAB

  2. foragingTaskFMM foragingTaskFMM Public

    MATLAB object model and import pipeline for the freely moving macaque foraging task: behaviour, motion capture, eye tracking, Neuralynx LFP and Kilosort units, aligned on one clock.

    MATLAB

  3. foragingAgent_deepRL foragingAgent_deepRL Public

    Recurrent PPO (LSTM actor-critic) agent that learns a three-patch foraging task with stochastic reward timing and noisy cues. PyTorch.

    Jupyter Notebook

  4. NNM_fearConditioning NNM_fearConditioning Public

    MATLAB reimplementation of the anatomically constrained dual-pathway neural network model of fear conditioning (Armony, Servan-Schreiber, Cohen & LeDoux, 1995).

    MATLAB

  5. foraging-allocation-dynamics foraging-allocation-dynamics Public

    Analysis code (MATLAB and Python) for 'Temporal Structure of Reward Availability and Sensory Uncertainty Modulate Allocation Dynamics in Naturalistic Foraging' (bioRxiv 2026): matching law, stay/re…

    Jupyter Notebook

  6. cp-lab-2025 cp-lab-2025 Public

    Grades Google Forms quizzes against a JSON answer key and a class roster; outputs a per-student CSV. Teaching utility for NYU's Cognition & Perception lab course.

    Jupyter Notebook