Sissejuhatus arvutuslikku neuroteadusesse 2014/15 kevad

Projects

Rules

Aim of the project is to analyse real neuroscientific data in order to prove or disprove some theory about inner workings of the brain, find new interesting patterns, which might lead to a new theory, come up with cool visualizations of the data, apply new method or algorithm, etc.

Work will be done in small (1-3) groups. The final result should include:

• The report with ~10 pages of meaningful text.
• The code to produce the results.

Project gives up to 30 points of your final grade: 15 for the content, 7.5 for the appearance and structure of the report and 7.5 for the clearness of the final presentation.

Submit your project here

Topics

Your own project
Come up with an idea of a project related to the field of computational neuroscience and execute it. Before you start working consult with us if your idea is suitable.

• Supervisor: You

Delayed visual feedback (virtual reality, oculus rift)
Is it possible to profoundly confuse the motor cortex by introducing visual lag to visible hand movements? Similar to delayed auditory feedback (speech jamming) - http://en.wikipedia.org/wiki/Delayed_Auditory_Feedback Hardware includes the Oculus Rift VR goggles and leap motion hand tracker.

• Supervisor: Madis Vasser
• Difficulty: hard

Control 10 arms in virtual reality
Body schema remapping - is it possible to assign entirely new functions to existing body parts in VR? The idea is to map each finger of the user to control a separate virtual arm and measure the effectiveness and speed of adoption. Can humans control 10 arms? Research on body schema has shown that this concept is highly mallable -http://en.wikipedia.org/wiki/Body_schema Hardware includes the Oculus Rift VR goggles and leap motion hand tracker.

• Supervisor: Madis Vasser
• Difficulty: hard

Best ways of producing cyber sickness in VR
what happens when you combine the absolute worst possible practices of cyber sickness all in one virtual experience do induce nausea. This could easily sort out the few people from the population who do not get cyber sickness. Then we can investigate if and why these people differ.

• Supervisor: Madis Vasser
• Difficulty: hard

Frequency space visualization for the EEG device in the psychology lab
During the lab visit you've seen the real time EEG signal display. It would be a useful addition to their toolbox if they'd have a real time frequency space visualization. Basically you would need to: take piece of signal from their EEG device (I have code for that in Python), perform FFT on this piece of signal, plot it. And make it fast enough to work in real time.

• Supervisor: Ilya Kuzovkin, Andero Uusberg
• Difficulty: medium

Classification of CIFAR-10 dataset using DeepLearnToolbox
CIFAR-10 consists of 60000 32x32 color images divided into 10 classes: airplane, automobile, bird, cat, deer, dog, frog, horse, ship and truck. It is well-known small enough dataset, that can be trained with just CPU. Your task is to classify CIFAR-10 images using DeepLearnToolbox, the toolkit we used in artificial neural networks practice session.

• Supervisor: Tambet Matiisen
• Difficulty: medium

Directional coherence and conscious perception
It has been suggested recently that cortical activity is more stable when sensory stimuli are consciously perceived (Schurger et al., 2015, PNAS). The aim of this project is to implement the proposed analysis method and apply it to EEG data from a variety of different visual perception paradigms. Results will indicate whether directional coherence is indeed a more selective signature of conscious perception compared to previously used markers.

• Supervisor: Renate Rutiku
• Resources: http://www.pnas.org/content/early/2015/04/01/1418730112.abstract
• Difficulty: easy

Decoding contents of conscious perception from single-trial EEG data
In a visual perception study we presented subjects with fused images of high- and lowpass filtered pictures. The pictures depicted scenes from different categories (ie room/nature/city). Subjects had to indicate which scene category they perceived on every trial. The aim of this project is to use single-trial topographic analysis in order to investigate critical time periods of information processing associated with perceiving either the high- or the lowpass filtered part of a given fused image. Some of the necessary code is already available in MATLAB, but needs testing.

• Supervisor: Renate Rutiku
• Resources: http://www.sciencedirect.com/science/article/pii/S0031320311001440
• Difficulty: medium

Which parameters of pre-stimulus EEG activity best predict conscious perception?
It has been suggested that pre-stimulus alpha power, alpha phase and/or slow negativity contribute to whether the subsequent stimulus is consciously perceived or not. The aim of the present project is to evaluate the individual contribution of each of these parameters on conscious perception within one experiment. The data for this project comes from a visual perception study where many different monochrome line-drawings were presented on threshold contrast. Subjects had to indicate on each trial whether they perceived the stimulus or not.

• Supervisor: Renate Rutiku & Kadi Tulver
• Difficulty: easy

Adaptive methods for estimating non-monotonic psychometric functions Psychophysical paradigms generally assume an underlying psychometric function connecting objective changes in stimulus presentation to changes in perception and behavior. It is oftentimes desirable to estimate said function or one of its parameters (usually the threshold) individually for each participant in order to optimize the experiment. Adaptive methods have been proposed to achieve this goal more reliably and with less sampling than simple staircase methods. But all of these methods fail when the underlying psychometric function is non-monotonic. The aim of the present project is to customize one prominent adaptive method (QUEST) so that it could handle non-monotonic psychometric functions. Code for the original QUEST algorithm is already available in Python.

• Supervisor: Renate Rutiku
• Resources: http://link.springer.com/article/10.3758/BF03202828
• Difficulty: hard

Estimate the age of a person based on her MRI brain scan
The idea of this project is to estimate the age of a person based on her MRI brain scan. To do so the students will download a bunch of MRI data from a public database and apply a regression technique to relate features of the 3d MRI scan to the actual age of the subject. Also, the students will find out and discuss which aspects of the MRI scan are more determinant of the subject age. The project is similar in spirit to this article on face age: http://www.picb.ac.cn/picb-dynamic/admin/pic/Cell%20Research-Jackie.pdf

• Supervisor: Renate Rutiku, Jaan Aru, Ilya Kuzovkin, Raul Vicente
• Difficulty: medium

Is there a purpose for a synaptic failure
The project consists in formulating a computational project on the subject of "synaptic failure"- the fact that in up to 50% of cases a presynaptic signal is not transmitted to the postsynaptic neuron. The goal of the project is to:
1) propose hypothesis why such failure has been selected for during evolution? Is it in some ways metabolically or computationally more efficient?
2) propose a computational model to study the effect of synaptic failure on information transmission.

• Supervisor: Ardi Tampuu
• Difficulty: hard

Hodgkin-Huxley model simulator
This project will revolve around the simulation of the Hodgkin and Huxley model of neuron under many different conditions. In particular, using the graphical simulator HHsim, the student will complete a list of exercises oriented to explore the effects of stimulation, temperature or ion channels in the dynamics of a neuron.

• Supervisor: Raul Vicente
• Resources: http://www.cs.cmu.edu/%7Edst/HHsim/guide.html
• Difficulty: easy