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Projects

One of your tasks in the UNV+VKN class is to work on a project on a topic of your choice. You can work in groups of up to 2 people (you can also work individually). The project aims to give you the chance to practice:

– searching for scientific information on the web,

– the ability to implement a mathematical model on a computer,

– try what modeling involves (eg, a short simulation to test what happens when model parameters are changed),

– working with text, the ability to read and analyze scientific text, and

– writing grammatically correct and stylistically clear scientific documents.

The project also gives you the opportunity to learn more about the selected topic from the field of neural and cognitive sciences.

The projects can be of two types:

  1. write an essay / research review about a specific problem related to computational and cognitive neuroscience.
  2. implement (and possibly expand) a computational or neural model of any neural process or cognitive function and test it on selected physiological or psychological data.

The following is a list of topics and links to papers that you can choose for your project.

Research review/essay

For research review/essay, you are expected to choose a topic that is of personal interest to you and write a 5-10 page research review/essay on this topic. The difference between these two forms is that the research review does not require a lot of your own contribution as it summarizes the results obtained from different sources (relatively more of them should be stated – at least 3). On the other hand, the essay is expected to include the author’s own view, in addition to summarizing some articles (so there can be a smaller number of cited literature). Ideally, you should find about two to three articles on the topic which are looking at it from a different perspective. In the essay, you should then analyze in what aspects the articles match, in what they do not, and try to provide your own view in the discussion. So your essay can have four parts:

Overview introducing the chosen scientific topic, providing basic information of that topic, its importance etc.

Summary of the results from the articles you have chosen, without comparison and evaluation.

Analysis should include a comparison of aspects in which the articles match one another and those in which they differ.

A discussion in which you should try to link the results of your analysis to the wider context of the research field, summarize your results, and possibly suggest future directions.

In addition, your paper should contain an Abstract, an Introduction, a Conclusion, and a list of References similarly as standard articles.

Important: The essay as well as the research review should contain only text written by you. If you copy the text from some source or if you are citing, you must indicate the source and you must write the text in quotes. For example, your article may include the following paragraph: Juraj Jánošík in 1748 before jumping on the hook shouted “When you’ve baked me …”. If you summarize information from a different article in your article, you must also indicate it appropriately. E.g. “Koncek (2003) asserts that the earth is round …” and at the end of your article in the List of references you will have an entry: “Konček, P. (2003) Modern theory of the shape of the Earth’s surface. Košice: Published by ELFA “. Examples of quoting can be found e.g. in the articles listed on this page, or in an example essay. For more detailed information on citing according to the American Psychological Association standard, visit https://owl.english.purdue.edu/owl/section/2/10/.

Any copy without mentioning the source is plagiarism, and if I find it, your essay will be graded accordingly.

Sample essay

To get a better idea of what I consider as a well-written essay, I’ve put one of my old essays here. It’s in English and the range is a bit bigger than I expect from you. But in terms of form and content, this essay should be a good guide. Note also the structure of this essay (parts such as Introduction, Historic background, Summary, Discussion, References). Also note that this essay does not contain links to some random Web pages of whoever on the Internet, but to scientific journal publications. It would be good if you also took a similar course in your essay.

How to search scientific information on the web

Today, the vast majority of scientific information is available on the web, part free of charge and part for a fee. Our University subscribes to some databases. Additionally, at the Perception and Cognitive Laboratory we have almost unlimited access. Basic resources which you should use when searching for literature:

Electronic resources, books and journals available in the Perception and Cognition Laboratory –
(Bookshelf is at https://pcl.upjs.sk/library/ ).

MIT Encyclopedia of cognitive science (available only with password) this encyclopedia contains basic information about almost every relevant topic.
www.google.com or even better scholar.google.com or books.google.com – e.g. if you are interested in how does so-called short-term memory work, try to google the keyword connectionist model of working memory and you will get to many articles.
Web of Science is a database that contains links to a large number of articles with two-way links also. That is, you have the opportunity to find out not only which articles are cited in particular article but also which articles cited that article.
http://www.ncbi.nlm.nih.gov/PubMed/ – MEDLINE is a database of articles from biomedical field, containing e.g. the abstracts of the articles.
Behavioral and Brain Sciences – open-access journal with articles on various topics related to neural and cognitive sciences.
http://www.upjs.sk/pracoviska/univerzitna-kniznica/katalogy/ – information about databases accessible via UPJS.
MIT CogNet – more that you would ever want to know about brain functioning (paid website)
Books on a selected topic: e.g., there are two recent books on binaural and special hearing, listed in our Bookshelf:

Topics of essays, research reviews and projects based on Workshop we organized

Topics from the workshops on “Cognitive neuroscience of auditory and cross-modal perception”, which we organized. You can choose the topics of individual lecturers from the Speakers section. Each lecturer prepared lectures and assignments for the particular topic and these may be the basis of your work. Some links are still non-functional. Teaching Assistant will provide you with missing documents.

The following list contains more suggestions for the essay/review topics. For each one, I’m mentioning an article which can be the basis for your essay. If you can not get to the article, let us know and Peter will provide it.

Theories about human brain functioning. In your essay, you can think about questions such as: How good theories about the functioning of the human brain should look like. What experiments (behavioral or physiological) can help us understand the functioning of the brain. How the development of the theories about human mind is influenced by technical advances.

References: Churchland P. S. (1986) Theories of Brain Function (Chapter 10 from the book Neurophilosophy: Toward a Unified Science of the Mind-Brain).

Daugman J. G. (1990) Brain Metaphor and Brain Theory (Chapter 2 from the book Computational Neuroscience by Eric Schwartz)

Theories about functioning of human memory and learning. Topics of your essays can be e.g.: What neural models of learning exist? What are the basic theories about memory functioning? Is memory rather examplar-based or prototype-based?

References: Carpenter GA Neural-network models of learning and memory: leading questions and an emerging framework. TRENDS COGN SCI 5 (3): 114-118 MAR 2001

Auditory perception. What is the role of space and time in hearing? How is auditory cortex organized?

References: Shamma S On the role of space and time in auditory processing, TRENDS in Cognitive Sciences Vol. 5 No. 8, August 2001.

Rauschecker J.P. and Tian B. Mechanisms and streams for processing of ‘‘what’’ and ‘‘where’’ in auditory cortex. PNAS 97, 11800–11806

How can you study human brain using imaging techniques? And how can we model it? 

Horwitz B, Tagamets MA, McIntosh AR. Neural modeling, functional brain imaging, and cognition. Trends in Cognitive Science 3:91-98, 1999.

How speech is processed in the brain? How can this process be modeled by a neural net? 

McClelland, J.L. & Rumelhart, D.E. (1981). An interactive activation model of context effects in letter perception: Part 1. Psychological Review, 5, 375-407.

How are the objects which we perceive visually represented in the brain?

Edelman S. (1998) Representation is representation of similarities. Behavioral and Brain Sciences, Volume 21, Issue 04. August 1998. pp449-467

Other possible topics:

Hearing:

  • An overview of the topics of current research can be made, for example, based on contributions from a recent conference
  • The pitch perception theory
  • Current hypotheses about the organization of the primary auditory cortex
  • Perception of sound source distance
  • Overview of cell types in the cochlear nucleus

Vision:

  • Representation of color in visual pathway
  • Theory of function of individual layers of neurons (laminar organization) in the primary visual area (V1, 17)
  • Perception of three-dimensional space

Methods:

  • Overview of the current optical imaging methods

Various topics mentioned e.g. in Encyclopedia of cognitive science or in the other books related to our class.

If you have caught some interesting news about cognitive and neural science in the media (newspapers, television, radio, internet), it can also motivate you. E.g. here are two such recent reports:

In the essay you should summarize some research papers on this topic, not newspaper sources.

Models

The second alternative for your project is to implement a computational model of some cognitive function or neural process, and compare your implementation with the results described in some article. So the procedure will be such that you can find an article (more articles) in which the model is described. You implement this model (preferably in MATLAB) and generate graphs that should resemble what is described in the selected article. The models are very different in terms of their implementation difficulty and I will take this into account during evaluation. So, potentially, a person can get more points for a not fully implemented complex model than for a simple model he tested on many data.

Examples of models which you can choose for implementation

These models mostly cover areas of my interest. You can also choose other models. A disadvantage (or perhaps an advantage) for you is that I will understand them less.

Colburn’s model of how binaural hearing helps us in listening to sounds in noisy environments

References: Kopco N and BG Shinn-Cunningham (2003) Spatial unmasking of nearby pure-tone targets in a simulated anechoic environment, J Acoust Soc Am, 114, 2856-2870.

How can neurons perform the multiplication operation?

References: Doron Tal and Eric L. Schwartz. Computing with the leaky integrate-and-fire neuron: Logarithmic computation and multiplicationNeural Computation, 9(2):305-318, Feb. 15 1997.

What the project proposal should look like

It must be clear from the project proposal that you have already looked at the topic and that you know at least roughly what resources you will use. So, besides the title of the topic, a good proposal should include a paragraph (4-5 sentences) describing what the project will be about, what the project’s goal is and what sources you will use.

These sources don’t have to be final, but each of you should include at least 3 links to the articles (full citation: Author, Year, Title, Journal / Book, and link) which you have found and which you would like to use. This also applies to those who have chosen one of the topics specified by me (whether an essay or model). I want to see that you have looked at the sources of the scientific information that are mentioned in the instructions for the project. So, all of you should state at least 1-2 articles you’ve searched out by yourself.

Here is an example of a good proposal from one of the previous years. More articles were listed than was necessary, and moreover, the links to most of them are missing. Otherwise, I was satisfied with this example.

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We chose a research review on the Brain-Computer Interface topic. It refers to acquisition, processing and application of the processed information from the brain using a computer. In the introduction we will discuss reasons for choosing this particular topic. We will briefly summarize the historical progress in this area and look at the basic knowledge about this issue. We will specify the types and methods of acquisition, processing and application of acquired information. We will take a closer look on the current research and experiments in this area, and in the conclusion we will try to indicate the potential future directions of this research.

The references which we plan to use:

  1. J. Vidal, “Toward direct brain-computer communication,” Annu Rev Biophys Bioeng, vol. 2, pp. 157-80, 1973.

Wolpaw JR, Birbaumer N, Heetderks WJ, McFarland DJ, Peckham PH, Schalk G, Donchin E, Quatrano LA, Robinson CJ, Vaughan TM. “ Brain-computer interface technology: a review of the first international meeting“. IEEE Trans Rehab Engin 8:164-173, 2000.

J.R. Wolpaw et al. “ Brain–computer interfaces for communication and control“/ Clinical Neurophysiology 113 (2002) 767–791

Wickelgren ,“Tapping the Mind “.VOL 299 SCIENCE 496-499, 24 JANUARY 2003

Melody M. Moore, Philip R. Kennedy,“ Human Factors Issues in the Neural Signals Direct Brain-Computer Interface“ ASSETS 2000: 114-120. 9. EE

Melody M. Moore “Real-World Applications for Brain–Computer Interface Technology”IEEE Trans Rehab Engin 11, NO. 2, JUNE 2003:162-165. Jeffrey Krasner, “Approval sought to test brain implant; Neuron-fired device would aid paralyzed people, state firm says,” boston.com, 6 Nov 2003.

Carmena, J.M., Lebedev, M.A., Crist, R.E., O’Doherty, J.E., Santucci, D.M., Dimitrov, D.F., Patil, P.G., Henriquez, C.S., Nicolelis, M.A.L.“Learning to control a brain-machine interface for reaching and grasping by primates. “ PLoS Biology, 1: 193-208. (2003)

Opé Tomori, Melody Moore “The Neurally Controllable Internet Browser (BrainBrowser)” CHI 2003: 796-797

The list of people working on this topic: … .

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Schedule and evaluation

week 5 (or see the main class webpage): approved topic of the project (20% of the grade). Each group will write an email with information on who are its members, what topic they chose, and what sources they plan to use. Only when I approve your topic can you work on it.

week 9 (or see the class webpage): submitted conducted project (80% of the grade)

Other links to sources of scientific information:

– regarding cognitive and neural sciences: study programme Cognitive science at Comenius University, within Middle European Interdisciplinary Master Programme in Cognitive Sciencevisual cognitionauditory cognitionBehavioral and Brain Sciencescogprints, citeseer

– slovak language: Short dictionary of slovak language

– english language: www.bartleby.comwww.m-w.com

– organizations: Cognitive Science SocietySociety for NeuroscienceCognitive Neuroscience Society

– journals: Behavioral and Brain SciencesNeural NetworksNeurocomputingNeural computation

– discussion groups: Connectionists mailing list (archive), Auditory mailing list (archive)