Cognitive Computational Neuroscience

Open positions

Postdoc PhD positions

We do not have any open postdoc or PhD positions at the moment. Please contact Athina Tzovara for inquiries.

Master theses

Deep learning techniques to study neural functions in coma patients

Computational techniques are increasingly used in the field of neuroscience. Signal processing and machine learning have promising clinical applications in automating the detection and characterisation of pathological patterns of neural activiy.

One tool that is commonly used to measure neural functions is electroencephalography -EEG-. EEG is a non-invasive technique that measures time-series of electric activity of the brain, though electrodes placed on the scalp. EEG is used as a diagnostic tool in neurological disorders, like epilepsy or coma. EEG recordings in coma patients carry information about the integrity of neural functions in the absence of consciousness, and can be used to predict the patients’ outcome and chances of survival. Recent work from our group has characterised patterns of EEG resposnes to sounds during the first day of coma. We showed that neural synchrony of EEG activity is predictive of patients’ outcome 3 months later, and that neural complexity is indicative of consciousness levels. However, it is not known how the synchrony and complexity of neural responses evolve over time.

This master thesis will use signal processing and machine learning techniques to analyse a rich EEG dataset of coma patients recorded over the first two days of coma. The goal is to evaluate how neural signals of coma patients evolve over time, and establish clinical predictors of their outcome.

The student working on this project will gain experience in signal processing of time series data, machine learning algorithms for biomedical data, and in the development of clinical biomarkers.

For more infomration please contact:

Sigurd Alnes: sigurd.alnes@inf.unibe.ch

Athina Tzovara: athina.tzovara@inf.unibe.ch

Forecasting epileptic seizures

Interested in doing a master thesis in computational neuroscience ? We are about to start a prospective trial of forecasting seizures for people with epilepsy and we need your help. Please convince us that you are the passionate student who can bring the required coding competences and motivation to crack an important clinical problem.

At the University hospital of Bern (Inselspital) and the University of Geneva we are starting a new seizure forecasting project in 2022, duration 6-12 months, to be agreed upon. Part-time home-based work is possible, weekly meetings in Bern or Geneva are expected. The team is young and dynamic and includes engineers, biologists, physicists, and neurologists. The candidate will be trained conjointly by a computational neuroscientist (T. Proix; https://ndlab.ch/) and a neurologist (M. Baud, www.neuro-elab.com) who both specialize in quantitative neuroscience research. The candidate will mostly work on computational problems, but, if language skills allow (German or French) will have opportunities to interact directly with chronic epilepsy patients in the neurology department for the acquisition of intracranial EEG recordings. The task at hand will combine software development, EEG signal processing and machine learning.

Required qualifications

Preferred qualifications

Your tasks

Please send us your complete application (CV, motivation letter, references, etc…) to:

Actigraphy analysis in REM sleep behavior disorder

Potential follow-up tool and disease progression marker?!

Isolated REM-sleep behavior disorder (iRBD) is an early stage of alpha-synucleinopathy and may occur in isolation more than 10 years before the diagnosis of PD or as part of its symptomatology, then termed secondary. Clinically, it is characterized by vivid dreams and their acting out during sleep. Currently, there is no available biomarker indicating disease progression of iRBD or its conversion to Parkinson’s disease. In analogy to Alzheimer’s disease, we know that a disturbance of the sleep-wake rhythm and circadian regulation occurs before the onset of full-blown Parkinson’s disease.

A method that can detect subtle early signs is actigraphy. Actigraphy uses continuous measurement of movement (acceleration moments) per minute over several days. Advantages of this method are numerous: on one hand its clinical reliability as well as good acceptance by patients, and on the other hand, the objective reliability and subsequent statistical evaluation of the measured values.

The goal of this master thesis is to analyze a rich actigraphy dataset. The student will then use this method retrospectively in a mixed cohort of patients with isolated and secondary RBD in order to examine the analysis results of the clinical subgroups in comparison to the control group and, in the case of several measurements of individual patients, to analyze the data over the course of the disease follow up. For this project programming skills in Python, Matlab or R are needed and interest in analyzing actigraphy data, recorded from wearable devices. The student that will work in this project will gain experience analyzing rich actigraphy datasets, and will have the opportunity to apply advanced data analysis methods on a clinical application. For more information, please contact:

Dr. Carolin Schäfer, Oberärztin, SWEZ, Neurologie, Inselspital : Carolin.schaefer@insel.ch

Prof. Athina Tzovara: athina.tzovara@inf.unibe.ch

Clustering human single neuron data during sleep

When we sleep, we process auditory stimuli from the environment around us. However, the neural mechanisms that allow the human brain to process stimuli during sleep are under-explored. We are collecting single-unit and local field potential (LFP) responses from patients with epilepsy, with intracranially implanted electrodes, with the aim of better characterizing how the auditory response is modulated by sleep.

This project, suitable for a master or bachelors thesis, will primarily focus on spike sorting of single-unit data and analysing firing rates and local field potentials in response to auditory stimuli.

The student working on it will gain experience with processing and analysis of a rich electrophysiological dataset and contribute to expanding the understanding of how information processing is altered by the absence of consciousness. This thesis will give experience with Python/matlab programming, processing and visualizing time-series signals.

For more infomration please contact:

Sigurd Alnes: sigurd.alnes@inf.unibe.ch

Athina Tzovara: athina.tzovara@inf.unibe.ch

Information theory techniques to study neural functions in sleep

When we sleep, we process auditory stimuli from the environment around us. However, the neural mechanisms that allow the human brain to process stimuli during sleep are under-explored. Recent studies suggest that responsiveness to external stimuli in sleep is related to complexity of neural activity and levels of neuronal noise.

Tools from the field of computer science, such as information theory or machine learning can be used to quantify the complexity of neural signals, recorded through electroencephalography (EEG). EEG is a non-invasive technique that measures electric activity of the brain through electrodes on the scalp. Measures of scale-free dynamics of neural activity can be applied on time-series of EEG signals to quantify the complexity of neural responses, or levels of neuronal noise. Interestingly, past studies suggest that the compexity of ongoing neural activity is modulated by sleep. However, it remains unknown how changes in neural complexity during sleep affect sensory processing of external stimuli (e.g. sounds).

The focus of this thesis will be on using techniques from information theory to study complexity of EEG responses to sounds during sleep and wakefulness. The student working on this project will analyse a dataset of high-density sleep EEG recordings using signal processing and information theory techniques. Also, the student will gain experience with Python programming, processing and visualizing time-series signals. No previous experience with sleep or EEG is necessary.

For more infomration please contact:

Sigurd Alnes: sigurd.alnes@inf.unibe.ch

Athina Tzovara: athina.tzovara@inf.unibe.ch