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UNV: Introduction to Neuroscience / Úvod do neurovied

(merged with MTL: MATLAB and neurocognition and VKN: Computational and cognitive neuroscience)
Institute of computer science, Faculty of Science
UPJŠ Košice
Winter semester 2019

Lecturer: Norbert KopčoPerception and cognition laboratorynorbert.kopco@upjs.sk, Jesenná 5, room T2.16, tel. 234 2450
Teaching assistants: Peter Lokša, peterloksa@gmail.com, Jesenná 5, PCL lab (2nd floor), Keerthi Doreswamy, kk.creare@gmail.com, Jesenná 5, PCL lab (2nd floor).
Lectures: Thursday 13:30 – 15:00 in SA1C05 classroom (Jesenná 5)
Labs: Thursday 15:20 – 16:50 in SA1C05 classroom. With the exception of introductional labs and written exams, the labs will be in the form of individual consultations (or, upon agreement).

NEWS AND UPDATES (for old updates, scroll to the end of page)

2019/12/11
– Slides for lecture #13 are online (it also contains parts of lecture 14 as tomorrow is the last lecture). We will meet in the classrom at 13:30 (via skype).
– Assignment #4 is published online. You have until tomorrow (Week #13).
– We received your projects (we’ll grade them soon).
– Final exam will take place the following Thursday 19 Dec at 13:30 in the classroom (the ones who can’t make need to arrange alternative time with Peto). It will cover lectures 8-13.

Class contents

Overview of the anatomy, physiology and cognitive processes in the human brain and mind. Description of neural centers and mechanisms underlying some cortical functions (e.g., visual, auditory and sensorimotor cortex, learning and memory). Basic physiological, psychophysical and computational methods used in neuroscience with emphasis on the application of computational methods in neurophysiological measurements and in the imaging of brain activity (e.g. magnetic resonance). Technical applications of neuroscience research.

Prerequisites

– basics of biology, chemistry, physics
– linear algebra and differential equations
– knowledge of MATLAB or OCTAVE or willingness to learn

Class philosophy and student’s work

The emphasis will be on individual work during the semester. Attendance at lectures is very important (and will be monitored using an attendance sheet). Students’ work in the labs will involve several assignments which the students will work out individually or in small groups. Submitted assignments will be graded and will constitute a part of the final grade. During the semester there will be two compulsory written exams, one in the middle (midterm exam) and one at the end of the semester (final exam). Another requirement is to work on a project (essay, model, small experiment). Based on the points obtained by a student for the assignments, project and written exams, a final overall grade will be proposed after the final exam on the final week of classes. Those who want to improve their grade will have an opportunity to sign up for an additional exam (assuming they passed the course / ak dostali zápočet).

Grading

Contribution of the individual tasks to the final grade:
– active participation at the lectures 7%
– assignments 16% (4 assignments, 4% each)
– project 15% (not compulsory for MTL)
– midterm exam 31%
– final exam 31%
– extra: 5% of the grade can be earned by the participation on the experiments in the Laboratory of perception and cognition. We will keep you informed about the options.

Penalty in grading and ethics

The number of points earned for assignments and projects is reduced by 20% of the maximum value for the assignment/project with each week of delay (i.e., you do not have to bother at all after 5 weeks). Delay begins to count on the day following the labs during which the assignment / project was supposed to be submitted. Each assignment, project, and essay should reflect the work and knowledge of the person who is stated as the author. Questions from the assignments / labs will also appear in the written exams. You can work in groups (up to 2 people) for the assignments, but I expect that everyone who is listed in the assignment as the author actually participated on it. The contribution of the assignments to the final grade is relatively low because I would like each of you (or each group) to try to work on it so that I can give you a feedback on your work (instead of you sending me a copy of the worked-out assignment that you took from someone else without knowing what was there). At random, I will review how the assignment was done for all who are stated as the authors. And if I find that an author does not know how something was done in the assignment, it could mean losing up to 20% of the overall grade for the whole group (i.e., including those who actually did the assignment and can explain how it was done). Once again, I emphasize that the goal is that everyone, not just one person from the group, should do the work on the assignment. Also, I want to motivate those who have completed the assignment to not provide it to others for copying.

Literature

(some texts are available in the electronic form in this folder, accessible with the password mentioned at the lecture)

Primary source of information are the PDF slides of lectures and the book (in Slovak)
Kopčo Norbert (2011) Výpočtová neuroveda (Úvod do modelovania neurofyziologických a behaviorálnych dát), Vydavateľ: Technická univerzita v Košiciach. (abbreviation KVN)

Additional sources:
Gazzaniga M. (ed.): The New Cognitive Neurosciences. 2nd ed. MIT Press. 1999 (available electronically – upon request. Alternatively, for $15 you can get 5-days access and download whichever of more than 400 books available on CogNet. Printed version of the book is in my office)
Purves et al.: Neuroscience. 2nd ed., Sinauer Associates, 1991 (available in fulltext electronically. It is not possible to orient in the book from the contents but you can view the contents and then search for the title of the chapter)
Dayan P and LF Abbott: Theoretical Neuroscience – Computational and Mathematical Modeling of Neural Systems. MIT Press, 2001 (further referred to as TN, available electronically)
Gerstner et al.: Neuronal Dynamics: From single neurons to networks and models of cognition. Camb Univ Press 2014 (free online).
Stillings et al.: Cognitive Science: An Introduction, 2nd ed., MIT Press, 1995 (referred to as CSAI, available electronically)
Wilson RA a FC Keil: The MIT Encyclopedia of the Cognitive Sciences. MIT Press, 1999 (MITECS available electronically)
Rybár J, Beňušková Ľ a Kvasnička V: Kognitívne vedy. Kalligram, 2002 (referred to as RKV, the copy is in my office)
Posner, M: Foundations of Cognitive Science. MIT Press, 1989 (the copy is in my office)
Kandel ER, Schwartz JH a TM Jessell: Principles of Neural Science. McGraw -Hill, 2000 (the copy is in my office)
Novák M, Faber J a O Kufudaki: Neuronové sítě a informační systémy živých organismů. Grada, 1993 (referred to as NS, available electronically)
Marek Dobeš: Základy neuropsychológie.(available electronically)
Levine DS: Introduction to neural and cognitive modeling. Lawrence Erlbaum 1991 (the copy is in my office)
Hertz J, Krogh A and Palmer RG: Introduction to the theory of neural computation. Addison-Wesley 1991 (HKP, the copy is in my office)
Kopčo Norbert (2011) Výpočtová a kognitívna neuroveda (Návody na cvičenia), Vydavateľ: Technická univerzita v Košiciach.
Kvasnička V and Clementis L (2014) Kognitívna veda v kontexte informatických vied. Slovenská technická univerzita v Bratislave

Projects

Detailed information regarding projects can be found here.
Schedule and grading:
Week 5: Approved topic of the project (20% of the grade). Each group will write what topic they have chosen and what sources they plan to use. Only when I approve the topic you can work on it.

Week 12: project submitted (80% of the grade)

Schedule of lectures:

Week 1: 19.9. (postponed to 26.9.) Introduction to neuroscience and cognitive science (slides in PDF EN; SK; animations/demos mentioned in the lectures are available in protected folder)
Structure of the class and requirements, What is neuroscience, What is cognitive psychology and cognitive science,
What is computational neuroscience and neural modeling, Examples of neural models at different levels
Literature: KVN (Chapter 1 Introduction, possibly also Chapter 2), TN (Preface), Preface to RKV, Chapter by M. Dobeš about Cognitive psychologyCSAI chapter 1 (possibly also chapters 2 a 3)

Week 2: 26.9. (postponed to 3.10.) Overview of the anatomy and of the functions of central nervous system (CNS) (slides in PDF EN, SK)
Overview of the anatomy, functions and historical theories about CNS funtioning. Introduction to mathematical methods of modeling of neurophysiological data.
Literature: KVN (Chapters 2,3), NS (pages 19-35, 142-150), PNS (Chapters 1 and 19),
R. Wessel, C. Koch, F. Gabbiani (1996) Coding of time-varying electric field amplitude modulations in a wave-type electric fish. J Neurophysiol 75:2280-93 (1996),
Daugman J (2001) “Brain metaphor and brain theory.”
Additional literature:
Web book Neuroscience: The Organization of the Nervous SystemNeural SystemsThe Subdivisions of the Central Nervous System
PNS (Chapter 1 The brain and behavior and 19 Integration of sensory and motor function)

Hubel DH and Wiesel TN (1959) Receptive fields of single neurones in the cat’s striate cortex. The Journal of Physiology 148, 574–591
DENISE GELLENE David Hubel, Nobel-Winning Scientist, Dies at 87, New York Times

Week 3: 3.10. Methods of study in neuroscience. Sensory, motor and association brain areas. (slides in PDF EN, SK)
Literature: NS (Chapter 1 Mozek a metody zkoumani…)
Videos from the celebration of the 25th anniversary of the introduction of fMRI in cognitive neuroscience in 2016 containing also an explanation of the method
Demo Videos of Visual Cognitive Disordes including from Bob Rafal

Week 4: 10.10. Neuron: Anatomy and types, action potential (slides in PDF EN, SK)
Literatúra: KVN (Chapter 4)
Additional literature: D. Johnston and S. Miao-Sin Wu, Foundations of Cellular Neurophysiology, Chapter 2, The MIT Press (1995)

Week 5: 17.10. Neuron: Models of activation of neuron, Spreading of signals in neuron (slides in PDF EN, SK)
Literature: TN (Chapters 5.2, 5.3, 5.5, 5.8).

Week 6: 24.10. Neuron: neural coding, synaptic transmission (slides in PDF EN, SK)
Vyskočil (2001) Pomalý synaptický přenos. Vesmír (80), 13-15
lectures by Christof Koch about neural coding ( local copynon-functional original source)

Week 7: 31.10. Synaptic plasticity– neural basis of learning and memory (slides in PDF EN, SK)
PNS chapters 64,65. Knudsen EI (2002) Instructed learning in the auditory localization pathway of the barn owl. Nature 417: 322-328
Wilson RA a FC Keil (1999) The MIT Encyclopedia of the Cognitive Sciences. Keywords: „Memory”, “Memory: Animal Studies”, “Memory: Human Neurophysiology” a „Hippocampus“
Jedlicka P, Benuskova L, Macakova J, Ostatnikova D (2002) Molekulove mechanizmy ucenia a pamati. In: Hulin I (ed) Patofyziologia, 6. vydanie. Slovak Academic Press (SAP), s.r.o, Bratislava, pp. 1183-1199.
Kelemen E, Pašťalková E (2000) O studiu paměti u lidí a zvířat Prostorová orientace u potkanů jako model pro studium paměti u savců. Vesmír.

Youtube lecture of Jennifer Groh: Space and Memory from onlince course The Brain and Space

Week 8: 7.11. Psychology of memory and learning (slides in PDF EN, SK)
Gluck MA, Myers CE (2000) Gateway to Memory. MIT Press. Chapter 2: Introduction
Corkin, S. (2002) What’s new with the amnesic patient H.M.? Nature Reviews Neuroscience 3, 153-160.
Articles related to current controversy about patient H.M.
New York Timesreaction of MIT BCS.
Christopher Nolan (2000) Memento. Quite interesting (action) movie about the man suffering from anterograde amnesia (he will lose the ability to remember anything new in long term)

Week 9: 14.11. Sight and vision: Introduction. Perception of brightness, contours, color. BCS/FCS model. Perception of size and distance.  (slides in PDF EN, SK)
Literature: CSAI chapters 12.1, 12.3, 12.5
Web: Flash demo with series of visual illusions and explanations what they tell us about processing of visual information in the brain (from University in Bangore, original link), Large collection of visual illusions IllusionWorks
Grossberg, S. and Todorovic, D. (1988). Neural dynamics of 1-D and 2-D brightness perception: A unified model of classical and recent phenomena.Perception & Psychophysics, 43, 241-277

Week 10: 21.11. Hearing and auditory cognition (slides in PDF EN, SK)
Literature: Grantham, D.W. (1995). Spatial hearing and related phenomena. In B.C.J. Moore (ed.), Hearing. Academic: London, pp. 297-345
Hartman, W.M. (1999) How We Localize Sound. Physics Today.
Fechner GT (1860) Elements of psychophysics
Wilson RA a FC Keil (1999) The MIT Encyclopedia of the Cognitive Sciences. Keywords: „Auditory physiology:, „Audition“ 
List of CDs and webs with auditory demonstrations and illusions.
 We have plenty of them in the lab:
CD acompanying the book Brian_Moore__Perceptual_consequences_of_cochlear_damageDiana_Deutsch_Musical_Illusions_And_ParadoxesDuda_Auditory_localization_demonstrationsHoutsma_Auditory_demonstrations (some available here)

Week 11: 28.11. Language, psycholinguistics, production and perception of speech. (slides in PDF EN, SK)
Literature: CSAI chapter 6, The brain and language, MITECS keywords Speech processing, RKN chapter 4.
Gick B & Derrick D Aero-tactile integration in speech perception. Nature 462, 502-504.

Week 12: 5.12. Attention (slides in PDF EN, SK)
Literature: Pashler HE (1997) Psychology of Attention. MIT Press. Chapter 1: Introduction. Chapter 2: Selective attention.
Behrmann, M. & Haimson, C. (1999) The cognitive neuroscience of visual attention. Curr Opin Neurobiol 9, 158-63
Parasuraman R (2000) The Attentive Brain. Kapitola 1: The attentive brain: Issues and prospects. MIT Press.
Kopčo, N, A Ler, and B Shinn-Cunningham (2001). “Effect of auditory cuing on azimuthal localization accuracy,” J. Acoust. Soc. Am. 109(5), 2377 ( poster in PDF)
Zatorre RJ, Mondor TA and Evans AC (1999) Auditory Attention to Space and Frequency Activates Similar Cerebral Systems. NeuroImage 10:544-554
James W. (1890) The Principles of Psychology. Chapter 11: Attention.
Lavanya Viswanathan and Ennio Mingolla Attention in Depth
Rensink’s demos of the „change blindness“ effect

Phylishin Z (2000) Situating vision in the world. Trends in Cognitive Sciences. 4(5):197-207.
Web: Demos of visual attention from Visual Attention Lab at Rutgers.
DVD demos in the lab: Visual Awareness Demonstrations from Dan Simons lab

Week 13 : 12.12. Crossmodal interactions (hearing, vision, touch). (slides in PDF EN, SK)
Literature:
Web: Seeing through Sound.
Bor et al. (2014) Adults Can Be Trained to Acquire Synesthetic Experiences. Nature Scientific Reports, 4, Article number: 7089
Additional literature: Our paper about crossmodal interactions / ventriloquism effect in humans and apes:
Kopco, N, I-F Lin, BG Shinn-Cunningham, and JM Groh 
(2009). Reference frame of the ventriloquism aftereffect. Journal of Neuroscience, 29(44):13809-13814

Week 14: 19.12. (or combined w/ Lecture 13) Other topics of study of brain and mind (consciousness, emotions, motivation, decision making, reasoning)
Literature: Keyword Emotions from Purves et al.: Neuroscience.
PICARD, R. W. (1997) Affective Computing. The MIT Press.
Chapter by M. Dobeš about Cognitive psychology

(Week 14: 19.12. individually videolecture by Daniel Dennet from 30.10.2017 in Prague)

Schedule of labs (preliminary)

Week 1: Introduction to Matlab: MATLAB Onramp (or check also „Getting Started“ video)Basic MATLAB commands from teaching assistant  (additional sources: older introduction to MATLAB/OCTAVEIntro from MITGetting Started from Matworks (PDF), sources/handbooks listed in the Useful links section – also in czech)
Week 2: matlab and assignment 1 (sk) (info related to assignment 1 is here (SK), to be submitted by the beginning of the labs in week 4)
Week 3: matlab and assignment 1
Week 4: discussion related to projects – description of electronical sources; submit the assignment 1
Week 5: assignment 2 (to be submitted by the beginning of the labs in week 7); submit the project proposal;
Week 6: work on assignment 2
Week 7: work on the project, submit the assignment 2
Week 8: written exam 1, assignment 3 (to be submitted by the beginning of the labs in week 10)
Week 9: work on the project
Week 10: submit the assignment 3
Week 11: assignment 4 (to be submitted by the beginning of the labs in week 13)
Week 12: submit the project
Week 13: submit the assignment 4
Week 14: written exam 2, finalizing the grading

Useful links (if you find other useful links, you can send them to me)

World organizations: Cognitive neuroscience societyCognitive science societySociety for neuroscienceHuman Brain Mapping, auditory and multimodal: Association for research in otolaryngologyAcoustical Society of AmericaEuropean Acoustics AssociationInternational Multisensory Research Forum
Slovak/czech/central-european related links: Cognitive science at UKom (+ http://www.meicogsci.eu/ with Vienna / BP / Ljublana), Neuroscience at Neurobio institute at SAV KE (also at Institute of social sciences and Institute of expermental physics) KE, Conference Cognition and artificial lifehttp://cognitivescience.cz/Society for cognitive science and philosophy.
Neuroscience in general: facts and figuresmore factsbiophysicsNobel prizessimulator of Goldmann’s equationelectrophysiology,
Hearing: EarLab
Vision: spatiotemporal receptive fields in LGN and V1sensitivity to orientation
Neuroanatomy:  3D anatomy of the brainbrain museumbrain anatomy
Modeling: overview of the simulation softwareGenesis The Virtual BrainTwo Ears
Guide to MATLABOCTAVE (free software compatible with MATLAB): interactive introduction to MATLAB Onramp (click on the image in the section “Learn Interactively”)original documentationvideo Getting startedshort intro in czech languagefrom MIT in english.
Mathematics: statistics (in slovak)MathWorldNumerical recipes
Language hints: Short dictionary of slovak languageMedical dictionary (in czech)English-czech medical dictionary (not always available)
Interviews and popularization lectures: Fresh Air with Oliver Sacks (author of the book The man who mistook his wife for a hat)

OLDER NEWS

2019/12/4
– Slides for lecture #12 are online. We will meet in the classrom at 13:30 (no skype).
– Assignment #4 is published online. You have until tomorrow (Week #13).
– Projects were due next week (week #12).
– Assignment #3 was due last week. Peto graded it. I updated the grading excel sheet accordingly.
2019/11/27
– Slides for lecture #11 are online. We will meet over skype at 13:30 (standard lecture time) in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #4 is published online. You have until Week #13.
– Projects are due next week (week #12).
– Assignment #3 was due last week (we’ll let you know once we corrected them).

2019/11/20
– Slides for lecture #10 are online. We will meet over skype at 13:30 (standard lecture time) in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #3 is due tomorrow.
– An interesting conference in Kosice happening these days Art & Tech Days 2019.

2019/11/13
– Slides for lecture #9 are online. We will meet over skype at 15:00 (during lab) in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #3 is now online. It is due in week 10.
– Midterm exam is now graded. See your grade in the excel to which I sent you a link earlier. Peto will bring the graded exams to the class. Also, Assignment #2 is now graded.
– An interesting conference in Kosice next week Art & Tech Days 2019.

2019/11/6
– We will start with the midterm exam – during lecture. Then, lecture will be given during the lab (or, as early as everybody is done with the exam).
– Slides for lecture #8 are online (I’m also planning to add #9 so that we can at least start it). We will meet over skype in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #3 is now online. It is due in week 10.
– Assignment #2 was due last week (I’ll check with Peto about the.
– Lecture #9 cannot happen at standard time. We either do it on Thursday during the lab (starting 3p or later) via skype, or this Friday or Monday (time is flexible). I think the best option is Monday 1:30p. But I’m flexible. You (mainly the UNV students) can email me your preferred and available times Friday, Monday or Thursday.

2019/10/30
– Slides for lecture #7 are online (we’ll also finish lecture #6). We will meet over skype in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #1 was graded (Peto sent you your grades).
– The grading table based on which I will grade you in this course is now published. See the link in my email, and ask if you have any questions.
– Assignment #2 is now online. It is due tomorrow (week 7).
– I received your project proposals. I will send you my feedback.
– Week 8: midterm exam – during lecture. Then, lecture during lab (I will be in Kosice).
– Move lecture #9 to Monday/Friday/Thursday (when I’m in Kosice)?

2019/10/23
– slides for lecture #6 are online. We will meet over skype in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #1 was due last week (I’ll check its status with Peto).
– Assignment #2 is now online. It is due in week 7.
– project proposals are due tomorrow (week 6).
– Week 8: midterm exam – during lecture? Then, lecture during lab?
– Move lecture #9 to Monday/Friday/Thursday (when I’m in Kosice)?

2019/10/16
– slides for lecture #5 are online. We will meet over skype in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #1 was due last week (I’ll check its status with Peto).
– Assignment #2 is now online. It is due in week 7. It will be introduced during the lecture (+ you can ask Peto questions).
– Since last week you guys discussed Assignment #1, this week Peto will introduce you to work with scientific information resources and give you basic information about your class projects (project proposals deadline is therefore extended to week 6).
– If you are interested in participating in an experiment for the credit of 5%, let me know (or contact directly Ondrej Spišák at spisakon@gmail.com ).2019/10/9
– slides for lecture #4 are online. We will meet over skype in the classroom (if you want to connect remotely, you can use my skype ID nkopco).
– Assignment #1 is due tomorrow at the beginning of the lab.
– During the lab, Peto will introduce you to work with scientific information resources and give you basic information about your class projects (project proposals are due next week).2019/10/2
– slides for lectures #2 and 3 are online. We will go through both of them tomorrow, using lab time to catch up with the schedule.
– your current lab activity is to go through the intro to Matlab and to work on Assignment #1. You can agree on individual consultation with Peto if you need one after we’re done with the lectures.2019/09/25
– slides for lectures #1 and 2 are online. We will go through #1 and a part of lecture 2 (the intro related to assignment #1).
– assignment #1 is now online. Peto will give you intro to Matlab and to Assignment #1.

2019/09/23
– Welcome to the new semester. Please, read carefully the contents of this web – it will serve as the default mode of communication between the teaching stuff and the students of the Intro to neuroscience class (including Matlab and neurocognition and Computational and cognitive neuroscience – these three courses will be merged). The class will be held in English this semester (unless any of you has a problem with following it in English). However, there is a Slovak version of the class webpage and the lecture notes as well as the lab assignments are available in English and in Slovak. And the students will be allowed to take exams in Slovak or in English. And, any time a Slovak student will have a question about a lecture / lab / assignment / exam, they can ask it in Slovak.
– UNV, MTL and VKN will be merged mainly because too few students signed up for each of the classes.
– Lecture 1 will take place 26 Sept, following the schedule of UNV. Lecture slides in PDF will be published online soon in the Schedule of Lectures list below (password will be provided via email and at lecture).
– The lecture will be followed by Lab1 during which Peťo Lokša (teaching assistant) will give you intro to MATLAB.
– Next week (Oct 3) we will try to go through 2 lectures (Lecture 2 and 3) to catch up on the lecture we missed last week. So, we will use Lab time (15:20 – 16:50) to go through Lecture 3.
– One of you has a conflict and cannot attend the lecture during the scheduled time. So, we need to push it to another time, idelly earlier on Thursday (eg, starting at 12:30). Let me know via email how early can you start the Thursday lectures.
– Note that many lectures this semester will be via skype as I will be traveling a lot. Students will be able to join via skype and not attend the lecture.