Vahid S. Bokharaie

Alumni Department Physiology of Cognitive Processes
Alumni of the Department High-Field Magnetic Resonance


I do not update this page anymore. Please check my personal website which can be found here:

I am an applied mathematician, control engineer, and computational neuroscientist. If you want to know more about my projects apart from the brief description below, please look at my homepage

I also have a YouTube Channel in which I share some videos and eye-tracking recordings that I think can be of interest to the general public. Also, a multimedia blog called The Joy of Neuroscience.

I am a big believer in open-source software and what it represents. I have released open-source software, contribute to open-source software projects, and been a reviewer for the Journal of Open-Source Software (JOSS). Details of such contributions can be found in my GitHub account. And here are the links to my Google Scholar and ResearchGate profiles.

Also, I love photography as an art and as a subject for scientific inquiries. You can find my photography portfolio here.

Research interests

  • Insights from Neuroscience to improve AI: Ideas on how to improve a famous applications of AI, based on recent advances in neuroscience, including my own work. More details on this topic can be found here.

  • Analysis of Biomedical Imaging Data: I have analyzed the data collected from different kinds of invasive and non-invasive biomedical imaging experiments. Although my main focus has been on analyzing fMRI data, which lead to this PNAS publication and this Python-based open-source software which I released in JOSS. I have also developed a novel method to analyze EEG data, to compare EEG signals between participants, conditions, stimuli, and channels.

  • Human Gaze Behaviour in Response to Complex Visual Stimuli: In a set of experiments involving simultaneous eye-tracking and EEG recordings, we studied the human gaze behavior and the corresponding changes in brain activity when the participant was exposed to complex visual stimuli. The stimuli included real-world still images, video stimuli, and also Adelson-Movshon grid which can evoke tri-stable perception in humans. This page includes more details.

  • Neuroanatomy: My fascination with neuroanatomy and the respect I have for neuroanatomists is endless. This was partly inspired by reading the works of the late Valentino Breaitenberg and also Prof. Almut Schüz, for example, this great book. Also, after getting to know the works of a group of colleagues, I become interested in an interesting group of neurons called von Economo Neurons. Here is a short review I have written about these neurons. Following that line of thought, I got involved in an effort to classify cell types in the nervous system. Our collaboration led to this report in Nature Neuroscience. And also this publication in Nature Communications, which was a metadata analysis on the publicly available data on neurochemistry experiments.

  • Mathematical Epidemiology: Some thoughts on the topic, based on my previous work on monotone dynamical system, which I thought can be useful for epidemiologists, in particular, in this day and age that we all struggle with a pandemic. I published the study as a paper in PLOS ONE. And an open-source software to simulate the spread of SARS-CoV-2 in an age-stratified population. More details here.


  • PhD in Applied Mathematics from Hamilton Institute, Maynooth, Ireland.
  • MSc in Control Engineering from KNTU, Tehran, Iran.
  • BSc in Electrical Engineering from Ferdowsi Univeristy, Mashhad, Iran. 
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