Course conditions / Podmínky předmětu 2025

Rozvrh / Timetable NIN 2024/2025

The first date will be on Wednesday 28.5.2025 from 11:00-13.00h. The next date is Wednesday 11.6.2025 from 11.00-13.00.

The exam will take place in room G205.

It will be divided into two parts:

• Part 1: A written section with 3 questions, lasting a total of 30 minutes.
• Part 2: An in-person review and correction of the test.

Student can receive total 40 points (Q1:13 points,Q2:13 points, Q3:14 points).

The questions will be selected from this list List of questions.

1. 19.2: Úvod do neuroinformatiky, organizace předmětu, model membrány | Introduction Přednáška 1, recorded lecture
2. 26.2: Případová studie - Parkinsonova nemoc a jednotková aktivita | Case study: Parkinson's disease and real data processing (Eduard Bakštein)Lecture 2
3. 5.3.: Modely neuronů: iontové kanály, synapse, Hodgkin-Huxley, Wilsonův model | Neuron models Přednáška 3, recorded lecture
4. 12.3.: Hodgkin-Huxley + šíření AP | HH model + AP propagation Přednáška 4, recorded lecture
5. 19.3: LIF neuron, poissonův proces, variabilita pálení neuronu | LIF model, Poisson process /Přednáška 5 , recorded lecture
6. 26.3: Synaptická plasticita | Plasticity Přednáška 6, recorded lecture
7. 2.4: Brain vascularisation (David Kala) | Brain vascularisation Přednáška 7, recorded lecture , discussion
8. 9.4.: Cortex modelling | Cortex Přednáška 8, recorded lecture 2021,recorded lecture 2020
9. 16.4: Random networks ex vivo Přednáška 9,recorded lecture 2021, recorded lecture 2020
10. 23.4: Bioinspired and neuromorphic algorithms to model visual attention Přednáška 10 (Giulia D Angelo), Tutorials
11. 30.4: Modelovani vizualniho kortexu|Visual cortex modelling (Jan Antolik) Přednáška 11 , recorded lecture, discussion
12. 7.5: Kognitivní modelování | Cognitive modelling (Karla Štěpánová) recorded lecture, discussion
13. 14.5. Rektorský den
14. 21.5: Rozhraní mozek-počítač | Brain-computer interfaces (Jiří Hammer)

Instruction for lab exercises (update 5.5.2025)

BRUTE System for assignment hand-in: https://cw.felk.cvut.cz/brute/

Labs: in person, room KN:E230

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 - See https://cyber.felk.cvut.cz/department/library/

[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.

1. Numerical integration - Euler's method | Matematický aparát: numerické metody řešení dif. rovnic
   • 19.2.2025
   • Assignment: Exercise 0.1
   • Ex 0.1 - numerical integration video tutorial (EN) (25 min)
   • matlab_intro.m
   • + bezpečnost práce
2. Neuron models: RC model| Modelování neuronů I - RC a EPSP model
   • 26.2.2025
   • Assignment: Exercise 1.1
   • Ex 1.1 - RC video tutorial (EN) (22 min)
3. EPSP - post-synaptic potential | Modelování neuronů II - EPSP post-synaptic potential model
   • 5.3.2025
   • Assignment: No asignment
   • Ex. 1.2 - EPSP video tutorial (EN) (23 min)
   • cv2_epsp.m
   • epsp.ipynb
4. Hodgkin-Huxley model | Modelování neuronů II - Hodgkin-Huxley
   • 12.3.2025
   • Assignment: Exercise 1.3
   • Ex. 1.3 - Hodgkin Huxley video tutorial (EN) (36 min)
   • cv3_hh.m
   • 1_3_hh.ipynb
5. Poisson spiketrain | Poissonovský spiketrain (+ LIF model)
   • 19.3.2025
   • Assignment: Exercise 1.4
   • Ex. 1.4 - LIF video tutorial (31 min)
   • cv4_lif.m
   • 1_4_lif.ipynb
6. Generation of artificial uEEG, LIF model | Vytváření simulovaného uEEG signálu, LIF model
   • 26.3.2025
   • Assignment: Exercise 2.1
   • Video tutorial Ex. 2.1 (21 min) Extra tutorial note: matrix reshaping in matlab and common errors (18 min)
7. Comparison of real and simulated data | Porovnání simulovaných dat s reálnými s reálnými
   • 2.4.2025
   • Assignment: Exercise 2.2
   • Ex. 2.2 - video tutorial (35 min),
   • Spike templates: cv6_spikeset.matcv6_spikeset.csv
   • Real micro-EEG data: cv6_realmeeg.mat cv6_drealmeeg.csv(fs=24kHz)
8. Real data analysis - spike sorting | Analýza reálných dat - Spike sorting
   • 9.4.2025
   • Assignment: Exercise 2.3
   • Ex. 2.3 - video tutorial (43 min)
   • cv7_spikesorting_data.mat
   • cv7_amp_detect.m
9. Real data analysis - eye movements | Analýza reálných dat - okohybné pohyby
   • 16.4.2025
   • Assignment: Exercise 2.4
   • Ex. 2.4 - video tutorial (11 min)
   • cv8_eogdata.mat
10. Hebbian learning | Hebbovské učení
    • 23.4.2025
    • Assignment: Exercise 3.1
    • Ex. 3.1 - video tutorial (26 min)
11. Spiking networks | Spontánní aktivita neuronových sítí
    • 30.4.2025
    • Assignment: Exercise 3.2
    • Ex. 3.2 - video tutorial (4 min)
12. Spiking networks in neuromorphic applications Giulia D'Angelo) | Neuromorphic computing
    • 7.5.2025
    • Assignment: Exercise 3.3
    • Lab materials: https://github.com/GiuliaDAngelo/CTU-EDNeuromorphic/tree/main
    • This time, you hand in no report. Just fill your answers in the Answer form. Only answers to Tutorial 1,2, and 5 are required, others are voluntary
13. Rector's day, lab cancelled | Rektorské volno, cvičení odpadá
    • 14.5.2025
14. Self-organizing maps | Samoorganizující mapy
    • Assignment: No assignment. Exercise 3.4 will be done within the lab
    • 21.5.2025
    • Ex. 3.3 - video tutorial (32 min)
    • vowel data mirror

Přednášející | Lecturer: Daniel Novák

Cvičící | Labs TAs: Eduard Bakštein

Konzultace po individuální e-mailové domluvě s cvičícím / Consultations possible upon email request to the TAs

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