Selected topics in cognitive science and biomodeling


"Selected topics in cognitive science and biomodeling" is a course given by Prof. Włodzisław Duch (cognitive science part) and prof. Wiesław Nowak (biomodeling part) in Fall 2022 semester at the Nicolaus Copernicus University. USOS info is here.

This is an introductory course that presents broad perspective on how brains create their minds. Starting with brief history of basic concepts and philosophical approaches that have been used to characterize mental life, evolutionary perspective is introduced, explaining why specific brain functions have developed. Brains process information increasing their chances of survival. Mental functions are based on the brain hardware. Brains have developed specific structures and control of behavior due to the evolutionary pressures.
General information about basic neuroanatomy and the simplest theories of brain functions, core ideas in neuroscience, are presented. The course should lay the foundations on the general system level for understanding of information processing that makes brains so successful as universal controllers of behavior. The brain stem controls basic homeostatic functions, the midbrain contributes to drives and motivations, and the limbic system controls emotions and fast reactions. Cortex processes details of sensory information, and controls movements. Higher cognitive functions – decisions, goals, motivation, language, thinking, intuition, creativity and consciousness, require cooperation of the whole brain structures.
This course should be a good starting point to more specialized courses in cognitive computational neuroscience that are usually focused on neural circuitry. It should also be a good starting point for students planning experiments in usability studies, human-computer interaction, human factors, and learning sciences, where general understanding of brain functions is necessary.
The molecular and cellular levels of cognitive mechanisms are treated in the second part.

Below I have linked my own lecture notes on the CSBio/cognitive science. For people who are interested in running computational experiments I have also included laboratory notes based on the Computational Explorations in Cognitive Neuroscience Understanding the Mind by Simulating the Brain Randall C. O'Reilly and Yuko Munakata, Cambridge, MA: MIT Press. New version of this book is here, and the Emergent simulation software is here.
Tutorials based on this software are here. We do not have time for discussing these experiments but there is a lot of information in the web for self-exploration.

Structure: the first lecture will be given on 11.10.2022, general introduction, one hour bio, one hour neuro. Then 7xbio, and 7xneuro, mixed. Below a sketch of the topics is given, links will be opened during the semester.

Bio-modeling slides:
Molecular foundations of neurocognitive science (password protected), all slides
Sensor neurocognitive science (password protected), all slides

List of lectures and Cognitive Neuroscience slides

  1. B1/N1 Brains, Minds and Cognition, general intro. 11.10.2022

  2. B2. Molecular foundations of neurocognitive science. DNA. RNA and Genetic Code.

  3. N2/N3 Emergence of brain research and Phenomics and brain networks. 8/15.11.2022.

  4. B3. Cells. Information transfer. Neurons and action potential. Synapses. Neurotransmiters.

  5. B4. Vision. Signal Transduction.

  6. B5. Touch and Hearing. Methods of AFM and SMD, Modeling of neuronal proteins.

  7. B6. Molecular foundations of memory.

  8. B7. Smell and Taste.

  9. N4/N5. Brain structures and Large Scale Brain Networks. 7.12.2022

  10. B8. Modeling of brain functions – computational approaches. 14.12.2022

  11. N6/N7. Information flow in brains and Homeostasis. Functional brain networks, brain stem and neurotransmiters regulating emotions. 11.01.2023

  12. N8/N9. Perception and Motor and auditory. Sensory input coding, cortex functions, coding sensory information, somatosensory perception, population coding, sound and music perception. 18.01.2023

  13. N10/N11. Vision and Memory. Visual pathways, hierarchical streams, memory types, memory in the brain. 25.01.2023

  14. N12/N13. Vision and Language. Learning mechanisms, language, concept representation. 1.02.2023

  15. N14/N15. Will and decisions. Complex cognition, consciousness and reading brain states, 8.02.2023

    Exam 15.02.2023?



    This is a short course and our knowledge about the brain is quite extensive. Nevertheless, I hope that it will help you to understand basic principles of how your brains work.
    After the last lecture we plan to run a short quiz/examination.

    Old lab notes (for WD lectures at NTU Singapore) for those who would like to experiment with computer simulations are available upon request.

    Many talks on cognitive science, brain and artificial intelligence are on this page.


    Włodzisław Duch