Dr. Vahid S. Bokharaie

Department High-field Magnetic Resonance
+49 7071 601 1644
+49 7071 601 652


For my ongoing work on modelling the spread of COVID-19, please look at this page

I am an applied mathematician and a control engineer and a data-scientist. I have worked in different and mostly unrelated fields of science and engineering and at the moment, working mainly in the fascinating field of systems neuroscience.

I have a habit of working on different projects at the same time; a habit which has always been a source of joy and pain. I spend time on a few projects that have very little in common, except that I enjoy working on them and that my skills as a mathematician and as a data scientist helps me to make a meaningful impact in each. The more notable ones are:

  • Analysis of Molecular fMRI data: This is a collaboration with a group of colleagues who have designed a smart contrast agent to detect the changes in calcium concentration at the onset of ischaemia using fMRI signals. It led to this PNAS publication. As part of this project, I developed a code to analysis the fMRI data which I have released as an open-source python library in here.

  • Data Science and Machine Learning in Neuroscience: A big part of what I do can be categorised as Data Science. In almost every project I work on, I have to deal with multi-dimensional data of various sizes and then use various mathematical tools to analyse the data and find the answers to the questions of interest. One project which is done and published, is summarised in this paper published in Nature Communications, which is a meta-analysis of the effects of different drugs on different neurotransmitters in various regions of rat brain. 
  • Individual Differences in Gaze Behaviour in humans: Motivated by my interest in photography, I have designed a project to study how we humans look at photographs, and how different compositional elements, such as contrast, colour, depth of fields, etc., can affect that process. I am using photographs of a master photographer as the visual stimuli. I use an Eye-tracking system to record the gaze behaviour of the participants when they look at the selected photographs. I also record their brain activity using Electroencephalography (EEG) recordings. The aim of the project is to improve our understanding of how we humans look at and perceive a photograph, and how our gaze behaviour is affected by various compositional elements and the contents of the photograph. The photographer I collaborate with in this project, Mr. Bruce Barnbaum, has written two books on this subject, from the perspective of the artist. His photographs provide a suitable benchmark to compare the results of my experiments with the widely accepted theories of composition in visual arts.

  • Adaptive Learning and the role of LCNE activity: When an animal is faced with a change in the environment, how does it react to such changes? What happens when there is an Intra or Extra-dimensional shift in the reward stimulus? To answer such questions, I have started a collaboration in a behavioural study. In particular, I am interested to discover the role that Locus Coeruleus Noradrenergic (LCNE) activity plays in regulating the arousal state of the animals when a change in their environment occurs. Collaborating with a group of colleagues, we look into the pupil diameter data of a number of rats as a proxy for their LCNE activity while at the same time using data provided by a 32 channel EEG system to discover the changes in the activities in different brain regions in such paradigms.

  • Effects of Time-delay in a Cell assembly: A purely theoretical project which is inspired by my interest in a fascinating group of neurons called von Economo Neurons (VENs). Among their properties, a prominent one, supported by indirect evidence, is that they provide fast and long-range projections. And they are also known to be targeted specifically in diseases that affect social graces. And so far they have been found in Anterior Insular and Cingulate Cortices (AIC, ACC) in human, primates and other mammals with large brains. Given all that evidence, the question that comes to mind is what role time-delay (or lack thereof) plays in such cognitive functions. And which evolutionary force has led to the genesis of this groups of neurons. If you are curious to know more about VENs, you can read this introductory document I have written.


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