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UNV: Computational and Cognitive Neuroscience I / Výpočtová a kognitívna neuroveda I

(formerly Intro to neuroscience. Merged with MTL: MATLAB and neurocognition and VKN: Computational and cognitive neuroscience II)
Institute of computer science, Faculty of Science
UPJŠ Košice
Winter semester 2022

Lecturer: Norbert KopčoPerception and cognition laboratorynorbert.kopco@upjs.sk, Jesenná 5, room T2.16, tel. 234 2450
Teaching assistants (TA): UNV Ondrej Spišák, MTL: Udbhav Singhal, VKN: Keerthi Doreswamy, Jesenná 5, PCL lab (4th floor).
Lectures: Mon 13:30-15:00 via Skype or in person in VKM (Jesenná 5)
Labs: UNV+MTL: Tue 14:25 – 15:55 SA1C05 (classrooms with matlab available for individual use also on: Wed 8:00 – 9:30 in SA1C04 classroom, Mon 13:30-15:00 SA1C04, VKN: Tue 9:50-11:20 SA1C04). With the exception of the initial lab sessions and written exams, the labs will be in the form of individual consultations (or, upon agreement with TAs).

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

2021/12/19
– Lecture 14 slides were included with last week lectures (however, they will NOT be included in the final exam). You can also watch a video lecture by Daniel Dennett.
– We are still grading your assignments #3, 4 & 5.
– Tuesday: Final exam will take place during the lab via skype. Format similar to the midterm exam. Topics will include lectures 8-13 (not 14) and Assignments #3-5 (you can choose to only answer questions for Assignment #4 or 5 for a full grade, but you will get extra credit if you answer both).
– Your current grading is in the excel sheet shared a couple of weeks ago. The final grade will be proposed based on it, hopefully by 24 Dec.
2021/12/10
– you can fill out the course evaluation here

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 6%
– assignments 20% (5 assignments, 4% each)
– project 14% (not compulsory for MTL)
– midterm exam 30%
– final exam 30%
– 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 9: project submitted (80% of the grade)

Schedule of lectures:

Week 1: 21.9. 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: 28.9. 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: 5.10. 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: 12.10. 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: 19.10. 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: 26.10. 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: 2.11. 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 online course The Brain and Space

Week 8: 9.11. 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: 16.11. 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: 23.11. 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“
Supplementary links:
Video introduction to auditory research our lab
Deutch D (2020) Musical Illusions and Phantom Words. Video presented at 2020 meeting of LA chapter of Acoustical Society of America.
Dr. William Brownell- ‘From Sound to Action Potentials – A Tour of the Inner Ear’ Association for Research in Otolaryngology seminar (abstract).
Auditory mailing-list’s list of CDs and webs with auditory demonstrations and illusions. 
We have several demo CDs in the lab:
1. Brian Moore’s book Perceptual consequences of cochlear damage
2. Diana Deutsch Musical Illusions And_Paradoxes
3. Duda Auditory localization demonstrations
4. Houtsma_Auditory_demonstrations (some available here)

Week 11: 30.11. Language, psycholinguistics, production and perception of speech. (slides in PDF EN, SK)
Literature: CSAI chapter 6, MITECS keywords Speech processing, RKN chapter 4.
Gick B & Derrick D Aero-tactile integration in speech perception. Nature 462, 502-504.

Week 12: 7.12. 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.
Michael Posner on the anatomy of attentional networks – a historical perspective (Youtube video)
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 : 14.12. 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
Talk: Amedi A (2022) Healing the brain via Multisensory technologies and using these technologies to better understand the brain 
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
Kopčo N, Lokša P, Lin I-F, Groh J, Shinn-Cunningham B (2019). Hemisphere-Specific Properties of the Ventriloquism Aftereffect. Journal of the Acoustical Society of America, 146, EL177 doi.org/10.1121/1.5123176

Week 14: 21.12. 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: 21.12. individually videolecture by Daniel Dennett “From Bacteria to Bach and Back” 30.10.2017 in Prague

Schedule of labs

Week 1: Introduction to Matlab: Matlab Onramp (also see Getting Started videos or Get started web; or see resources in Useful links)
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), convolution in Matlab , linear regression
Week 3: discussion related to projects – description of electronical sources;
Week 4: work on project; submit the assignment 1
Week 5: assignment 2 (sk) (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 (sk) (to be submitted by the beginning of the labs in week 10)
Week 9: submit the project
Week 10: submit the assignment 3; assignment 4 (sk) (to be submitted by the beginning of the labs in week 12)
Week 11: assignment 5 (sk) (to be submitted by week 13)
Week 12: submit assignment 4
Week 13: submit the assignment 5
Week 14: written exam 2, final grades

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

2021/09/20
– 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 Computation and Cognitive Neuroscience I class (including Matlab and neurocognition and Computational and cognitive neuroscience II – these three courses will be merged). The class will be held in English this semester (but the lectures, labs, assignments, and exams are also offered in Slovak and the students can choose in which language they work during the semester). The class webpage is in English. However, there is a Slovak version of the class webpage and the lecture notes in case you prefer to follow it in Slovak (however not all the information must be up to date there). The students will be allowed to take exams in Slovak or in English, and they can communicate with us in English or Slovak.
– UNV, MTL and VKN will be merged mainly because too few students signed up for each of the classes.
– Lecture slides in PDF are now published online in the Schedule of Lectures list below (password will be provided via email and at lecture).
– Lab1 took place today (MTL) or on Wednesday (UNV) – will cover intro to Matlab.

2021/09/26
– Based on the agreement from last week, we will hold the lectures on Mondays at 13:30 and the labs for both MTL and UNV on Tuesdays at 14:25. The lectures will be in the VKM room (but that is not confirmed yet, if it’s not available, we will meet in SA1C05). I will be via skype again.
– Lecture 2 PDF is now available online, we will also finish Lecture 1.
– Lab: will be held on Tuesday and you should come as Udbhav will present some mathematical concepts needed for Assignment 1, as well as introduce Assignment 1 (which is now available below).

2021/10/5
– Next lecture will be on Tuesday 12 Oct at 14:25 (I am traveling on Monday).
2021/10/3
– Lecture 3 is now online.
– Lab: we will start with discussion of the projects – only for UNV/VKN.

2021/10/11
– Lecture 4 will be on Tuesday 12 Oct at 14:25.
– Lecture 4 slides are now online. We will also finish Lecture 3.
– Lab: individual work on project, submit Assignment #1.

2021/10/17
– Lecture 5 slides are now online.
– Assignment #1 was due last week,
– Assignment #2 is now online (we will introduce it during the lecture, in-person lab ),
– Project proposal for UNV is due Tuesday,
– Midterm exam will happen in week 8 during the lab (coordinate with the TAs if that time does not work for you).

2021/10/25
– Lecture 7 slides are now online. We will meet tomorrow at 14:25 to go through it (and to finish Lecture 6).
2021/10/24
– Lecture 6 slides are now online. We will start by finishing lecture 5.
– Assignment #1 grading will be announced soon, project proposals have been graded.
– lab this week is individual work on Assignment #2 and on the project,
– Midterm exam will happen in week 8 during the lab (coordinate with the TAs if that time does not work for you).

2021/11/7
– Lecture 8 slides are now online.
– Assignment #3 is now published. You have 2 weeks to complete it.
– Assignment #2 was due last week.
– Udbhav completed grading of Assignment #1. We will share it soon.
– Tuesday during the lab you will write the midterm exam. For UNV and VKN it will cover all the lectures and labs up to week 7. For MTL it will only cover information from the labs and assignments. The exams are prepared in Slovak or English. You can choose in which language you will write your exam.
2021/11/2
– reminder that if you are interested in 5% credit for the class, you can participate in one of the experiments (you can participate in more than one). Currently, Lucia is collecting data, so you can contact her.
2021/11/14
– Lecture 9 slides are now online.
– UNV project is due tomorrow.
– Assignment #2 grading is in progress.
– Assignment #3 – you have 1 week left to complete it.
– Grading of UNV exam is complete, MTL will be completed soon.
– Discussion of organization for the rest of semester.
– Shared grading.
2021/11/22
– As we agreed today, you are only required to do Assignment #4 or #5, so that you only need to complete 4 assignments to get full credit.
2021/11/21
– Lecture 10 slides are online. We will start by finishing Lecture 9.
– Assignment #4 is published. You can consult Udbhav and Ondrej if you have any questions.
– Assignment #3 is due today (also project is due).
– You received an email with a link to the excel sheet with your grading.
2021/11/15
– Project due date is extended by a week.
– Additional midterm exam will be next Tuesday.

2021/11/28
– Tomorrow’s lecture is going to go from 13:00 until 14:30.
– Lecture 11 slides are online. We will start by finishing Lecture 10.
– Assignment #5 is online (as we agreed, you are required to only hand in #4 or #5, but extra credit will be given if you do both). Also, questions from both will be on the exams.
– Assignment #4 – you have another week.
– Assignment #3 – Udbhav is grading it.
– Project was due last week.
– I’m working on grading your Replacement Midterm exam.

2021/12/5
– Lecture 12 slides are online. We will start by catching up on Lecture 11.
– Assignment #3 and replacement midterm for MTL – still working on grading.
– Assignment #4 due this week, #5 next (you can choose to work on only one of them).
– Project – still waiting for 1 student.
– If you participated in any experiments, ask Lucia to let me know for 5% grade credit. You can also agree with Maria and Matej to participate in theirs once they are ready. It will also give you 5% credit for each experiment.

2021/12/11
– Slides for combined lectures 13 & 14 are online (lecture 14 individually).
– We are still grading your assignments #3 & 4.
– Assignemnt #5 due this week.
– Next week: Final exam during the lab (unless you agree with your TA on a different date/time) via skype. Format similar to the Midtermexam.
– Your current grading is in the excel sheet shared a couple of weeks ago. The final grade will be proposed based on it.