Syllabus | Class | Computer Lab

Syllabus


Click here for a PDF version of the syllabus:


Class


Prepare yourself for the coursework


In class we will mostly work with review and research articles and excerpts of books rather than a single textbook. Below are some tips how to get most out of reading articles or other texts and getting your mathematical basics up to speed.

Mathematical basics


Two colleagues of mine have taught a "Mathematics Bootcamp" for years. Here is the script they wrote for this class. Please read the parts indicated below.
We will go over this also in class, but in less detail, so it might be helpful for you to have a heads up.

Trigonometric functions (p. 12)
The Basic Rules for Calculating Derivatives (p. 19)
Vector Algebra (p. 29-45)
Complex Number Theory (p. 46-48)




How to read articles efficiently

  • GIST:

    Browse the article first to get the gist.
  • SYSTEM:

    Develop your own system of annotation.
  • ANNOTATE:

    Annotate (if it is your own copy).
  • HIGHLIGHT:

    Highlight (rule of thumb: if you highlight more than 30% you have not understood the contents!).
  • KEYWORDS:

    Jot down a list of keywords and look them up later in books or the internet.
  • QUESTIONS:

    Write down specific questions and ask them to your fellow students or tutor.
  • JUMP:

    If you get stuck, try jumping ahead to the next paragraph or get back to the article later.
  • ESSENCE:

    Write down the essence of the article in 2-3 sentences.

Articles for Student Presentations

Please let me know, in which article from the list below you are interested or if you have a topic or article which you want to present.

1. A Tactile P300 Brain-Computer Interface, Anne-Marie Brouwer and Jan B. F. van Erp, Front Neurosci. 2010; 4: 19.



2. Control of a two-dimensional movement signal by a noninvasive brain-computer interface in humans, Jonathan R. Wolpaw and Dennis J. McFarland, Proc Natl Acad Sci U S A. 2004 December 21; 101(51): 17849-17854. Betzaida




3. A P300-based brain-computer interface for people with amyotrophic lateral sclerosis, F Nijboer, EW Sellers, J Mellinger, MA Jordan, T Matuz, A Furdea, S Halder, U Mochty, DJ Krusienski, TM Vaughan, JR Wolpaw, N Birbaumer, and A Kubler, ClinNeurophysiol. 2008 August; 119(8): 1909-1916. Desree



4. The non-invasive Berlin BrainComputer Interface: Fast acquisition of effective performance in untrained subjects, Benjamin, Blankertz, Guido Dornhege, Matthias Krauledat, Klaus-Robert Mller, Gabriel Curio, 2007, NeuroImage, 37 (2007), 539 - 550. Kathryn



5. An auditory braincomputer interface (BCI), Femke Nijboer, Adrian Furdea, Ingo Gunst, Jurgen Mellinger, Niels Birbaumer, Andrea Kubler, Dennis J. McFarland, 2008, Journal of Neuroscience Methods 167, 43-50. Thomas



6. Temporal classification of multichannel near-infrared spectroscopy signals of motor imagery for developing a brain computer interface, 2007, Ranganatha Sitaram, Haihong Zhang, Cuntai Guan, a Manoj Thulasidas, Yoko Hoshi, Akihiro Ishikawa, Koji, Shimizu, Niels Birbaumer, NeuroImage 34 1416 - 1427.



7. Control of a humanoid robot by a noninvasive braincomputer interface in humans, 2008, Christian J Bell, Pradeep Shenoy, Rawichote Chalodhorn and Rajesh P N Rao, Control of a humanoid robot by a noninvasive braincomputer interface in humans. Adam



8. A novel P300-based braincomputer interface stimulus presentation paradigm: Moving beyond rows and columns, 2010, G.Townsend, B.K. LaPallo, C.B. Boulay, D.J. Krusienski, G.E. Frye, C.K. Hauser, N.E. Schwartz, T.M. Vaughan, J.R. Wolpaw, E.W. Sellers, Clinical Neurophysiology, 121 (7) , 1109-1120. Brett



9. A New Auditory Multi-Class Brain-Computer Interface Paradigm: Spatial Hearing as an Informative Cue, 2010, Schreuder M, Blankertz B, Tangermann M, A N PLoS ONE 5(4): e9813. doi:10.1371/journal.pone.0009813



10. Hochberg, L.R., Bacher, D, Jarosiewicz, B, Masse, N.Y., Simeral, J.D., Vogel, J, Haddadin, S., Liu, J., van der Smagt, P., Donoghue, J.P.
Reach and grasp by people with tetraplegia using a neurally controlled robotic arm. Nature. 2012 May 17; 485 (7398): 372-5. ​Rodrigo



11. "Control of an Electrical Prosthesis With an SSVEP-Based BCI," Muller-Putz, G.R.; Pfurtscheller, G., Biomedical Engineering, IEEE Transactions on , vol.55, no.1, pp.361-364, Jan. 2008. Monique



Directions for the presentations

  • Presentation time: 15 min, Time for questions: 5 min (= 20 min. in total)
  • Presentations will count 33% towards your grade, if you are an undergraduate, and 45% if you are a graduate student.
  • Number of slides: 10-30 depending on how much you put on your slides.
  • "A picture says more than 1000 words" (most times).
  • Suggested outline of your presentation: (1) Introduction and Background (What is the article about? What is the central research question or problem it tackles? What has been done in the literature? (go briefly over other articles cited by your article, one representative image or sentence per other article you want to mention is usually enough)) (2) Methods and Results (What where the methods used in the article? How do they work? What were the results?) (3) Discussion and Conclusion (What were the main findings of the article? How do the results advance the field? What questions do the results raise? How could one go from there?)
  • Feel free to include your own opinions in the discussion (but mark them as such)
  • I want to see that you have understood the article (or your chosen topic) and the methods used therein.
  • Please contact me with any questions or concerns you might have.

Please click here to sign up for a time slot.

Computer Lab


MATLAB

If you have never programmed in MATLAB please work through the tutorials:


Research report

  • Your research report should have 2-4 pages of text and 2-3 pages of figures and 1-2 pages of references = 5-9 pages in total.
  • Contents:
  1. Title: Choose a title for your research report and add your name as the author.
  2. Abstract: 200-300 words describing the basic research questions and results of your report (basically a very condensed form of the report). The abstract should be self-explanatory!
  3. Introduction: Using the literature (the article of Dr. Furdea as well as references from your web searches), give some background about BCI for ALS patients and mention challenges in creating BCIs for this group of patients (attention, sleep, CLIS) and describe shortly the data. State the research question of our project: How can we achieve a BCI for this patient (search for features in EEG not yet analyzed, exclusion of trials where the subject was not attentive)
  4. Methods: Write about the analysis methods used and what they do. (selection of epochs, band-pass filter, event related potentials (ERP) i.e. the curves, time-frequency analysis)
  5. Results: Describe the results we obtained using the figures we saved in the computer lab.
  6. Discussion: Compare the results obtained to the literature, draw conclusions and discuss potential further steps that you could take if this was a long-term project.

Suggestions on how to write the research report:
  • Think of the report as a (non-fictional) story. The introduction sets the stage (i.e. describes the research that has been done so far and what research question(s) are tackled in the report). The methods and results section is kind of where the "action" is happening. The discussion then relates your results to the results in the literature and gives a wrap-up of the report to the reader.
  • Take some of the scientific papers you encountered during the program as example of how to write your report.
  • For the introduction, use Dr. Furdea's article and the literature from the references of your web search. You are also encouraged to find more related references on the web and cite them in your report.
  • You are encouraged to work on the research reports in groups, however, every student needs to turn in his or her own research report in his or her own words (identical paragraphs are not acceptable!)!
  • With your report you show that you have understood the methods we have been using on the data and that you can extract the relevant information from the results and set them into perspective.
  • State personal opinions only in the discussion (and to a limited extent (e.g. we believe'') in the abstract). Indicate that it is your opinion.</li><li>Do not use contractions like don't'', isn't'', it's'', etc.
  • Every abbreviation has to be explained at its first use, e.g. electroencephalography (EEG).


Please submit your report as e-mail attachment (in PDF format) to me.
EXTENDED Deadline: Saturday, June 22, 11:59 pm EDT (Florida time)