====== bam33nin -- Neuroinformatika / Neuroinformatics ====== ====== Výuka | Course info ====== /* **Online výuka (přednášky) probíhají dle rozvrhu na tomto odkazu [[https://meet.google.com/ehc-shyf-aic|https://meet.google.com/ehc-shyf-aic]] ** */ [[https://cw.fel.cvut.cz/b192/courses/bam33nin/podminky|Podmínky předmětu a způsob hodnocení]] [[https://intranet.fel.cvut.cz/cz/education/rozvrhy-ng.B222/public/html/predmety/54/67/p5467506.html| Rozvrh NIN 2023]] ====== Zkouška | Exam ====== The first date will be on Wednesday 7.6.2023 from 13:00-15.00h. The next date is Wednesday 21.6.2023 from 14.00-16.00. The room is my office G202, we will eventually move to G205. The oral exam will last 30 minutes, will consist of 3 questions, one question for about 10 minutes, total 40 points (Q1:13 points,Q2:13 points, Q3:14 points). List of questions: {{ :courses:bam33nin:exam_neuroinformatics_2023_en.pdf |}}. /* Zkouška proběhne distanční formou na tomto odkazu: [[https://meet.google.com/ehc-shyf-aic|Ústní zkouška]]. */ ====== Přednášky | Lectures ====== - 22.2: Úvod do neuroinformatiky, organizace předmětu, model membrány | //Introduction// {{{{:courses:bam33nin:lec1.pdf|Přednáška 1}}, [[https://drive.google.com/drive/u/1/folders/0BwkJlam0ZsYwfi1QSzEySk4teHh5M0xkNVJkWHBpU3NhZFQtbmhQeHg3YXVGQlk3bFJSeFU|recorded lecture]] - 1.3.: Modely neuronů: iontové kanály, synapse, Hodgkin-Huxley, Wilsonův model | //Neuron models// {{:courses:bam33nin:lec2.pdf|Přednáška 2}}, [[ https://drive.google.com/file/d/1zM_84EfrQHTPIMidmPedfVbM4apyMWjG/view|recorded lecture]] - 8.3.: Hodgkin-Huxley + šíření AP | //HH model + AP propagation// {{:courses:bam33nin:lec3.pdf|Přednáška 3}}, [[https://drive.google.com/file/d/1pLqcaV3_6EqljMOlIc2u17Sz4tyUtHXF/view|recorded lecture]] - 15.3: Brain vascularisation (David Kala) | //Brain vascularisation// {{:courses:bam33nin:lec8.pdf?nocache|Přednáška 4}}, [[https://drive.google.com/file/d/1Qh_078G5LUz4adHR1DYz6DzsWOB8Wpu1/view|recorded lecture ]], [[https://drive.google.com/file/d/1xEGwxf8I5qXQDkQclwHutE5_YmgC3mIz/view|discussion]] - 22.3: LIF neuron, poissonův proces, variabilita pálení neuronu | //LIF model, Poisson process// /{{:courses:bam33nin:lec4.pdf|Přednáška 5}} , [[https://drive.google.com/file/d/1SXZjb_hSn3JZjUsLRlclq2Uq632Un9td/view|recorded lecture ]] - 29.3: Případová studie - Parkinsonova nemoc | //Case study: Parkinson's disease// (Eduard Bakštein){{ :courses:bam33nin:slidesparkinson2023.pdf |Přednáška 6}} - 5.4.: Cortex modelling | //Cortex// {{:courses:bam33nin:lec7.pdf|Přednáška 7}}, [[https://drive.google.com/file/d/1XJ0ZkMT_tnB4UkBsKkUpe-h_vWcqIs8h/view|recorded lecture 2021]],[[https://drive.google.com/file/d/1NMCeWr1axbaaeKcssMEwMtOmgtzpXwAy/view|recorded lecture 2020]] - 12.4: Random networks ex vivo {{:courses:bam33nin:lec7.pdf|Přednáška 8}},[[https://drive.google.com/file/d/1mIZpaoj7QRVQOsZbrzbjcCzYlJEf6EkV/view|recorded lecture 2021]], [[https://drive.google.com/file/d/1LuAWPgDfbrv5Qu8LTgSAsDIOp4NRfd9T/view|recorded lecture 2020]] - 19.4: Synaptická plasticita | //Plasticity// {{:courses:bam33nin:lec6.pdf ?nocache|Přednáška 9}}, [[https://drive.google.com/file/d/1Je0rzBmYcHA1C5MzZ0Pya-csGSlUg4Rh/view|recorded lecture]] - 26.4: Vědomí, pozornost, emoce, paměť | Consciousness, attention, emotions, memory ([[https://kognice.wixsite.com/vavrecka|Michal Vavrecka]]) {{:courses:bam33nin:lec10michal.pdf?nocache|Přednáška 10}} [[https://drive.google.com/file/d/1nkjRPPypYTbRKi-YgyTa5HMUKvtag8-W/view| rec lecture I]] , [[https://drive.google.com/file/d/1sPZtBSjvMv0yvfcJDOUtEt0hiO3Q0qWD/view|rec lecture II]] - 3.5: Modelovani vizualniho kortexu|Visual cortex modelling ([[http://antolik.net|Jan Antolik]]) {{:courses:bam33nin:cvut_talk.pdf|Přednáška 11}} , [[https://drive.google.com/file/d/1Pj0vzTi_XeeEUiMMtwW1EV2vMa0FmDti/view|recorded lecture]], [[https://drive.google.com/file/d/1k21BHhTrHlyWAp_20z6EX2h1gNEyNpgW/view|discussion]] - 10.5. Rektorský den /* Kódování, dekódování informace | //Information coding// {{:courses:bam33nin:lec13.pdf?nocache|Přednáška 13}}, [[https://drive.google.com/file/d/1kjkxr-FDgJ9sJH3nXmVG9Caj5WUe83LU/view|recorded lecture]] */ - 17.5: Rozhraní mozek-počítač | //Brain-computer interfaces // ([[https://www.researchgate.net/profile/Jiri-Hammer-3|Jiří Hammer]]) - 24.5: Kognitivní modelování | //Cognitive modelling// ([[http://karlastepanova.cz(|Karla Štěpánová]]) /*{{:{{:courses:a6m33nin:lectures:pres_test.pdf|Přednáška 14}} */ [[ https://drive.google.com/open?id=1oZrEiTlaiAI4pPJUCCN4WifDy5tg6SmE|recorded lecture]], [[https://drive.google.com/file/d/1yUI8IHXT3sexwfMecfyYZAM9yy7Ozs3z/view|discussion ]] /* Samo-organizující se sítě {{:courses:bam33nin:lec12.pdf?nocache|Přednáška 12}}, recorded lecture: https://drive.google.com/file/d/1xLI4x1VwlcCXDMJ9xQmd2QdD3c-cF5hI/view, recorder lecture 2021: https://drive.google.com/open?id=1vs7kHA2C5gJ_i5Ff2ybVy0RHsJqvJBVJ */ /* - 31.5: Případová studie: epilepsie | //Case study:epilepsy// (tbd: Jiří Hammer) {{ :courses:bam33nin:lectures:klement.pdf |BONUS od Dana Klementa: Prostorová navigace u zvířat}} */ /* Materiály k přednáškám lze stáhnout [[https://147.32.84.236/teach/nin/doc/|zde]]. Přihlašovací údaje byly sděleny na přednáškách. - 25.3: Prostorová navigace u zvířat | //Spatial orientation in animals// (Daniel Klement) {{:courses:a6m33nin:lectures:klement.pdf ?nocache|Přednáška 6}}*/ ====== Cvičení | Lab exercises ====== **{{ :courses:bam33nin:a6m33ninlabs2021en.pdf ||Instruction for lab exercises}}** (update 15.2.2023) **System for assignment hand-in: https://cw.felk.cvut.cz/brute/** **Labs: in person, room KN:E230** /* ** Google meet link labs: https://meet.google.com/oyg-xukw-nnm (NEW as of 10.3.2021)** */ **Assignments:** All assignments are to be submitted through the brute system (link above). Upload your assignment as a zip archive with all necessary codes with a short pdf report, briefly summarizing the task and showing the results of the simulations. **Deadlines and penalties:** 1 week for completion at full grade, two weeks 50% penalty, 2+ weeks 100% penalty (0 points). All exercises have to be completed and handed in order to obtain assessment. Please be patient with potential mis-configurations and possible technical issues with the system. In case of technical issues, no penalty will be applied, especially during the first weeks. **Doporučená literatura / //Recommended literature// ** Available from the dept. of Cybernetics' library - contact Dr Petr Novak (novakpe@fel.cvut.cz) [1] Thomas Trappenberg. Fundamentals of Computational Neuroscience. Oxford University Press, USA, June 2010. [2] David Fitzpatrick William C. Hall Anthony-Samuel LaMantia Leonard E. White Dale Purves, George J. Augustine. Neuroscience. Sinauer Associates, Inc., 5th. edition edition, 2011. [3] Michael L. Hines Nicholas T. Carnevale. The Neuron Book. Cambridge University Press, 2006. [4] Werner M. Kistler Wulfram Gerstner. Spiking Neuron Models: Single Neurons, Populations, Plas- ticity. Cambridge University Press, 2002. /* //Lab materials are published continuously during the semester in the list below. The PDF instructions will be continuously updated as well (remember to refresh the pdf page - F5!)// Materiály ke cvičením budou průběžně zveřejňovány v seznamu cvičení, stejnětak PDF instrukce budou průběžně doplňovány (pokud zobrazujete stránku s pdf v prohlížeči, nezapomeňte ji obnovit - F5). [[courses:a3b33kui:plagiaty|Co je a není plagiát?]] */ =====Program cvičení | Exercise materials===== - ** Numerical integration - Euler's method | //Matematický aparát: numerické metody řešení dif. rovnic// ** * 22.2.2023 * //Assignment: Exercise 0.1// * [[https://drive.google.com/file/d/18-zx62y6aBHc7_BLfrrVLveFpwEXu0Vc/view|Ex 0.1 - numerical integration video tutorial (EN)]] (25 min) /*[[https://drive.google.com/file/d/16iQlUNcleLZ6bRWZ83BNUpZtrieGGWJ5/view|Záznam CV1 LS 2021]]*/ * {{:courses:a6m33nin:tutorials:matlab_intro.m|}} * + bezpečnost práce /* * {{:courses:a6m33nin:cv:cv1_numint_base.m| zakladni reseni v matlabu}} (//basic solution in matlab//) */ - ** Neuron models: RC model| //Modelování neuronů I - RC a EPSP model// ** * 1.3.2023 * //Assignment: Exercise 1.1//https://cw.fel.cvut.cz/wiki/lib/images/wrap.gif * [[https://drive.google.com/file/d/1lxg8DOz-MG6pnTnau9_R5mnkMtnbNzg6/view|Ex 1.1 - RC video tutorial (EN)]] (22 min) /*,[[https://drive.google.com/file/d/1cFAgcV6gIgOid7iV0pKtVAQA8vOwxs0I/view | Záznam CV2 LS 2021]] */ - ** Hodgkin-Huxley model | //Modelování neuronů II - Hodgkin-Huxley // ** * 8.3.2023 * //Assignment: Exercise 1.3// * [[https://drive.google.com/file/d/1cIWyYmAzt0xLn2FFe-9DxLEXZ-m-oCFq/view?usp=sharing| Ex. 1.3 - Hodgkin Huxley video tutorial (EN)]] (36 min) /* [[https://drive.google.com/file/d/1147YdB3yBGWsjkbAs_2X0YnNKchWiJUP/view|Záznam CV4 LS 2021]] */ * {{ :courses:a6m33nin:tutorials:cv3_hh.m |cv3_hh.m}} - ** RC model continued and EPSP | //Modelování neuronů II - RC a EPSP model// ** * 15.3.2023 * **The in-person lab will be called off. Please, watch the video tutorial and work on the Ex. 1.2** * //Assignment: No asignment// * [[https://drive.google.com/file/d/1UfqXKxd1Aeo7RXXEh6KO3L0ISnsOSJgX/view|Ex. 1.2 - EPSP video tutorial (EN)]] (23 min) /*[[https://drive.google.com/file/d/1QuFoD4mxDig27rX45cjuVMeCqEpjYs4e/view?usp=sharing |Záznam CV3 LS 2021]] */ * {{:courses:a6m33nin:tutorials:cv2_2_epsp.m|cv2_epsp.m}} - ** Poisson spiketrain | //Poissonovský spiketrain (+ LIF model)// ** * 22.3.2023 * //Assignment: Exercise 1.4// * [[https://drive.google.com/file/d/1Rv4-YiN3GVjXrIbSH25-AOmUihQITGoL/view|Ex. 1.4 - LIF video tutorial]] (31 min) * {{ :courses:a6m33nin:tutorials:cv4_lif.m |cv4_lif.m}} - ** Generation of artificial uEEG, LIF model | //Vytváření simulovaného uEEG signálu, LIF model //** * 29.3.2023 * //Assignment: Exercise 2.1 // * [[https://drive.google.com/file/d/1_hYLC3Byyho68jFJXVI03UQ7hXOqRELO/view|Video tutorial Ex. 2.1]] (21 min) [[https://drive.google.com/file/d/1glrAcqjgsZlnJVjvzE8Z_d0xapSOoq9U/view| Extra tutorial note: matrix reshaping in matlab and common errors]] (18 min) - ** Comparison of real and simulated data | //Porovnání simulovaných dat s reálnými s reálnými//** * 5.4.2023 * //Assignment: Exercise 2.2// * [[https://drive.google.com/file/d/11CnR34nIAzry3zxf1SfsVJgyp74r9WOY/view|Ex. 2.2 - video tutorial]] (35 min), /*[[https://drive.google.com/file/d/10Wnoxwbb0AwRnKSVLAeHA_fzdUSQiUtf|Záznam Cv. 31.3.2021]] */ * Spike templates: {{ :courses:a6m33nin:tutorials:cv6_spikeset.mat |cv6_spikeset.mat}} * Real micro-EEG data: {{ :courses:a6m33nin:tutorials:cv6_realmeeg.mat |cv6_realmeeg.mat}} (fs=24kHz) - ** Real data analysis - spike sorting | //Analýza reálných dat - Spike sorting// ** * 12.4.2023 * //Assignment: Exercise 2.3// * [[https://drive.google.com/file/d/1bTK7OJaryjUSuPo2uvVWCbSRRuUb60nn/view | Ex. 2.3 - video tutorial]] (43 min) * {{:courses:a6m33nin:tutorials:cv7_spikesorting_data.mat |cv7_spikesorting_data.mat}} * {{:courses:a6m33nin:tutorials:cv7_amp_detect.m |cv7_amp_detect.m}} - ** Real data analysis - eye movements | //Analýza reálných dat - okohybné pohyby//** * 19.4.2023 * //Assignment: Exercise 2.4// * [[https://drive.google.com/file/d/10L70yg9PzrrdRDnPIYCgsUW-al6H9ZWz/view?usp=sharing | Ex. 2.4 - video tutorial]] (11 min) * {{ :courses:a6m33nin:tutorials:cv8_eogdata.mat |cv8_eogdata.mat}} - ** Hebbian learning | //Hebbovské učení // ** * 26.4.2023 * //Assignment: Exercise 3.1// * [[https://drive.google.com/file/d/1IA2k7JzOxl76w3W2q7p-G_pnV-KLEsLP|Ex. 3.1 - video tutorial]] (26 min) - ** Spiking networks | //Spontánní aktivita neuronových sítí//** * 3.5.2023 * //Assignment: Exercise 3.2// * [[https://drive.google.com/file/d/1FsBlQ9sScLmvq8T3WX7AT8r4sJB-OxVO|Ex. 3.2 - video tutorial]] (4 min) - ** Rector's day, lab cancelled | Rektorské volno, cvičení odpadá ** * 10.5.2023 - ** Self-organizing maps | //Samoorganizující mapy// ** * //Assignment: Exercise 3.3// * 17.5.2023 * //[[https://drive.google.com/file/d/12eGurkQEg_EFerC9TDIwl00Hubsb0xg0/view | Ex. 3.3 - video tutorial]] (32 min)// * {{ :courses:bam33nin:tutorials:cv11_vowel_data.zip |vowel data mirror}} - ** Hand-in of remaining assignments, assessment//odevzdání zbývajících úloh, zápočet// ** * 24.5.2023 ====== Kontakty | Contacts ====== Přednášející | //Lecturer//: [[xnovakd1@labe.felk.cvut.cz|Daniel Novák]] /*, [[vavrecka@fel.cvut.cz|Michal Vavrečka]]*/ Cvičící | Labs TAs: [[bakstedu@fel.cvut.cz|Eduard Bakštein]] /* , [[stepakar@fel.cvut.cz|Karla Štěpánová]] ,[[vavrecka@fel.cvut.cz|Michal Vavrečka]] */ Konzultace po individuální e-mailové domluvě s cvičícím / //Consultations possible upon email request to the TAs// [[https://cw.felk.cvut.cz/forum|Fórum]]