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Descriptions of S-114 Courses |
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28 + 28 (2 + 2) autumn
Teacher: Mika Ala-Korpela, docent, Ph.D.
Contents: Basics of computational mathematical modelling for natural
sciences and engineering; for example, quantum mechanical modelling,
electron structures and force fields, spectroscopic data analysis,
simulation methods, Lattice-Boltzmann modelling, analyses of genes and
proteins, complex interaction networks. Important methods and
algorithms; for example, interpolation and extrapolation, integration
and optimisation, solution of linear algebraic equations, modelling of
data, nonlinear models, statistical description of data, Fourier
transform and its applications, Monte Carlo modelling, molecular
dynamics. Computer exercises.
Requirements: Examination and mathematical exercises.
Literature: Lecture material and given articles / references. Books:
Numerical mathematics and computing, 4th edition, W. Cheney, D.
Kincaid, Brooks/Cole (1999) and Numerical Recipes (in C++ / Fortran),
The Art of Scientific Computing. W. H. Press, S. A. Teukolsky, W. T.
Vetterling, B. P. Flannery, Cambridge University Press, Second Edition
(1992, 2002).
Prerequisites: Basic math courses S1-S3. The student should also be
familiar with programming (preferably C or Fortran).
Note: This course replaces course S-114.100.
I-II
Teacher: M.Sc. Janne Ojanen
Contents: The objective of this course is to give understanding about
the basic priciples of modeling, emphasizing on statistical modeling.
Also information theory and its applications in statistical modeling
are discussed. Practical solutions are given to model class selection,
model complexity and parameter selection.
Requirements: Exam and project work.
Literature: T.M Cover and J.A. Thomas: Elements of Information Theory.
Y. Sakamoto, M. Ishiguro Statistical Inquiry and other literature
announced.
Prerequisites: Basics of statistics and probability calculus.
Note: This course replaces course S-114.310.
(4 + 4) III-IV
Teacher: Prof Jukka Tulkki and Prof Ilkka Tittonen
Contents: Introduction to the quantum physics of matter and
electromagnetic radiation. De Broglie wave length, Planc’s
photon hypothesis, Schrödinger equation, hydrogen atom,
electron spin, Pauli’s exclusion princeiple, quantum
statistics, black body radiation, electronic structure of molecules and
solids, conductivity, phonons.
Requirements: Examination and participation in the exercise sessions.
Literature: P. Tipler&Llewellyn: Modern physics (Freeman)
Note: Replaces S-114.325/326 and S-114.425/426
with S-114.1427.
Language: Finnish
(2 + 4) III-IV
Teacher: Prof Jukka Tulkki and Prof Ilkka Tittonen
Contents: Dynamics of electron wave packets, Ehrenfest theorem,
introduction to the formal quantum theory, postulates of quantum
mechanics, computational methods of electron states in molecules and
solids, electronic states in metallic and semiconducting quantum
structures, transport in electron wave
Requirements: Participation in the exercise sessions and approved
project work.
Literature: P. Tipler&Llewellyn: Modern physics (Freeman)
Prerequisites: S-114.1327
Note: S-114.1327 and S-114.1427 together replaces S-114.425
and S-114.426.
Language: Finnish
Teacher: ma. prof. Iiro Jääskeläinen
Contents: The course is an introduction to cognitive processes
(attention, memory, perception, executive functions, and emotions) and
their neural basis. The neuron as an elementary processing unit of the
brain, neurotransmitter systems, plasticity, research methods and
applications of systemic neuroscience.
Assessment: Examination and practicals.
Literature: Gazzaniga, Ivry and Mangun (2002): Cognitive Neuroscience,
The Biology of the Mind (2nd edition) and material distributed during
the course.
Note: This course replaces courses S-114.790
and S-114.101.
III-IV
Teacher: dos Mika Ala-Korpela
Contents: The objective of the seminar is to give exercise in preparing
and presenting a seminar speech, and giving criticism of the
presentations. Topics of the seminar are announced at the begining of
the course.
Requirements: Seminar presentation and written report. No exam.
Note: This course replaces course S-114.240.
I-II
Teacher: Peter Engelhardt docent and visiting experts
Contents: The course gives basic knowledge to biosystems of the cell
concentrating on genomics (genes, DNA and RNA) and proteomics (protein
synthesis, structure and interactions), cell metabolism and signalling.
Requirements: Examination.
Literature: Alberts et al, Molecular Biology of The Cell, 4th Ed.,
Garlands Science 2002, chapters 4-8.
Additional: Replaces S-114.500.
Language: Finnish
I-II, III-IV
Teacher: N.N.
Contents: Seminar focuses on timely research topics on Bioinformation
technology.
Requirements: Preparation of oral presentation on a given topic. Active
participation and acting as opponent.
Literature:: Ilmoitetaan seminaarin alussa.
Note: This course replaces course S-114.502.
I-II, III-IV
Teacher: Mika Ala-Korpela docent
Contents: Seminar deals with preparing a research plan and a research
report. It is recommended a preliminary exercise before starting
Master’s thesis.
Requirements: Active participation, preparation of research plan and
giving intermediate reports on Master’s thesis.
Additional: Replaces S-114.503
Language: Finnish and English
I-II, III-IV
Teacher: Mika Ala-Korpela docent
Contents: Seminar deals with preparing a research plan and a research
report. It is recommended a preliminary exercise before starting
Master’s thesis.
Requirements: Active participation, preparation of research plan and
giving intermediate reports on Master’s thesis.
Language: Finnish and English
III-IV
Teacher: Jukka Heikkonen docent
Contents: The course introduces the most important computational
methods used in gene mapping, DNA and RNA sequence and microarray
analysis (genomics) and protein structure (proteomics).
Requirements: Examination and special project.
Literature: Joao Setubal: Introduction to Biological Computing.
Prerequisites: S-114.2500
Additional: Replaces S-114.510
Language: Finnish
I-II
Teacher: Docent, Dr.Tech. Aki Vehtari
Contents: Bayesian probability theory and Bayesian inference. Bayesian
models and their analysis. Computational methods, Markov chain Monte
Carlo.
Requirements: Exam and exercises.
Literature: Gelman, Carlin, Stern & Rubin: Bayesian Data
Analysis,
Second edition and other material announced on lectures.
Prerequisites: Basics in statistical mathematics and probability
calculus.
Additional: Replaces S-114.601
Language: Finnish and English
Teacher: doc., PhD Kaisa Tiippana
Contents: Mechanisms and phenomena related to visual and auditory
perception, multisensory perception, and motor actions. Basic
principles of research methods.
Assessment: Examination and practicals.
Literature: E. Bruce Goldstein (1999): Sensation and Perception (5th or
later edition), New York: Brooks Cole Publishing, and material
distributed during the course.
Additional: Replaces S-114.780. See also
Language: Finnish and English
III
Teacher: FT Jari Kätsyri, DI Mikko Viinikainen, tekn.yo. Katri
Koskentalo
Contents: The course deals with human emotions, mechanisms of
socio-emotional communication, and the utilisation of this information
in human-computer interfaces. Practicals include laboratory experiments
on emotions and social communication, the results of which will be
analysed and discussed.
Requirements: Examination, practicals.
Literature: K.Oatley & J.M. Jenkins: Understanding emotions.
Cambridge MA: Blackwell Publishers, 1996 or later ed. and material to
be announced during the course.
Additional: Replaces S-114.760
Language: Finnish and English
period IV
Teacher: Riikka Möttönen Ph.D.
Contents: The course deals with neurocognitive mechanisms of speech,
and speech technology. Practicals include laboratory experiments on
speech, the results of which will be analysed.
Requirements: Examination, practicals.
Literature: To be announced.
Additional: Replaces S-114.710.
Language: Finnish and English
IV
Teacher: N.N.
Contents: Human memory systems and the underlying neural mechanisms.
Sensory memory, working memory, attention, and
long-term memory. Episodic and semantic memory. Disorders of memory.
Neural and neural network models of the memory.
Requirements: Agreed separately with the teacher.
Additional: Replaces S-114.771
Language: Finnish and English
I or II or III or IV
Teacher: N.N.
Contents: Introduction to neuroinformatics. Utilization of information
technology in neurosciences. Statistical modelling in
neuroinformatics. Databases and interoperability in neuroinformatics.
Applications of neuroinformatics. The course will be given either as a
series of lectures or as a seminar.
Literature: Material will be distributed during the course.
Additional: Replaces S-114.801
Language: Finnish
III
Teacher: Dr.Tech, Ph.D KTT Juuso Töyli
Contents: The business game gives participants an overall view of a
company's various functions and their interdependencies, and provides
an opportunity to practice the management of strategic and operative
administration and growth. It enables one's administrative skills to be
tested without having to pay dearly for unwanted consequences, and
creates a suitable environment for practicing teamwork skills under
time pressure.
Course method: Companies, made up of four students, compete against one
another in the same game. Decisions are made in computer classrooms
during guided game sessions. The attendance of all team members is
necessary in all sessions. To complete course requirements, each team
must submit a written initial and final report about their particular
case.
Literature: A description of the virtual game world is distributed in
the opening lecture.
NOTE: This course replaces course S-114.155/TU-22.164.
I-II
Teacher: prof. Jouko Lampinen
Contents: The course introduces nonlinear statistical modelling
methods. Main topics of the course include methods based on neural
networks, and their relation to other statistical modelling methods.
Objective of the course is to give students both theoretical and
practical capabilities to design and analyse neural network models.
Requirements: Exam and project work.
Literature: Collection of articles announced during the course, and C.
Bishop, Neural networks for pattern recognition, Oxford Press, 1995
Prerequisites: T-61.261 recommended.
NOTE: This course replaces course S-114.200.
I-IV
Teachers: prof. Kimmo Kaski, prof. Jouko Lampinen, prof. Mikko Sams,
prof. Jukka Tulkki
Contents: Project work in computational engineering.
Requirements: Planning and implementation of the project under guidance
of the supervisor, final report.
Literature: Work instructions
NOTE: This course replaces course S-114.215.
IV
Teacher: Mikko Karttunen Ph.D.
Contents: The aim of this course is to provide the student with an
understanding of the advantages and limitations of various
computer simulation methods commonly used in physics and engineering.
Requirements: Homework proband Englishlems, project work.
Literature: D.W. Heerman: Computer Simulation Methods in Theoretical
Physics. K. Binderand D.W. Heerman: Monte Carlo Simulation in
Statistical Physics. D. Frenkel, B. Smit: Understanding Molecular
Simulation: From Algorithms to Applications. A. Kersh, W.J. Mokoroff:
Transport Simulation in Microelectronics, Springer Verlag 1995.
Prerequisites: Basic statistical physics.
Additional: Replaces S-114.250.
Language: Finnish and English
III-IV (odd years)
Teacher: Prof Jukka Tulkki, N.N.
Contents: The course deals with electronic and optical properties of
semiconductors and their heterostructures. The goal of
the course is to provide knowledge of basic physical properties course
is to provide knowledge of basic physical properties needed for
understanding the working principles of electronic and photonic devices.
Requirements: Examination, exercises and project work.
Additional: Replaces S-114.401
Language: English
III-IV
Teacher: Jukka Heikkonen docent, Peter Engelhardt docent,
Academy Prof Kimmo Kaski
Contents: The course contains a special project related to
computational systems biology.
Literature: Manuals
Additional: Replaces S-114.520
Language: Finnish and English
III-IV
Teacher: Mika Ala-Korpela docent
Contents: Structure, function and interaction of living organisms and
machines, human anatomy, physiology and nervous
system, human and machine intelligence, implants and artificial organs,
basics of system biology, basics of molecular biotechnology, stem cells
and new medical treatments, future user interfaces, robots, learning
and intelligent systems in consumer products, new scientific
achievements - e.g. mind control and artificial eye, discussion about
business opportunities, movies, future visions and ethics in the area
Requirements: Examination and written exercise.
Literature: Handout and given articles/references. Marie
O’Mahony: Cyborg - the man-machine, Eero Hyvönen
(toim.): Inhimillinen kone - konemainen ihminen.
Additional: Replaces S-114.530
Language: Finnish or English
S-114.3760 Measurement of electroencephalography (6 cr) P
II period
Teacher: Laura Kauhanen and prof Christina Krause
Contents: Electroencephalography (EEG) and its applications in brain
research. Lectures deal with the origins of the EEG signal in the
brain, and measurement principles, as well as some applied uses of EEG.
The emphasis of this course is on practical measurement and analysis of
EEG signals. The practicals consist of running EEG experiments and
analysing the results in small study groups.
Assessment: Lecture reports, practicals.
Literature: Will be announced in the beginning of the course.
Prerequisites: S-114.1710 Cognitive neuroscience or corresponding
knowledge.
Additional information: Organized jointly with University of Helsinki
Cognitive Science.
S-114.3812 Computational Neuroscience (6 cr)
II (even years)
Teacher: PhD Harri Valpola, PhD Jarmo Hurri (University of Helsinki)
Contents: On this course, the participants learn how to use
computational methods to quantitatively model the activity of neurons,
groups of neurons and neural systems.
Requirements: Exam and project work
Literature: Dayan, P., Abbot, L. F.: Theoretical Neuroscience (MIT
Press, 2001)
Additional: Replaces S-114.3811, S-114.811
Language: English
I-II tai III-IV
Autumn & spring
Teacher: Prof Jouko Lampinen, Academy Prof Kimmo Kaski
Additional: Replaces S-114.150
Language: Finnish
III-IV
Teacher: prof. Jouko Lampinen
Contents: Kurssin sisältö vaihtelee vuosittain.
Kurssin tavoitteena on antaa lisensiaattitasoista opetusta
laskennalliseen tekniikkaan liittyvästä
aihepiiristä. Kurssi voi olla luento- tai seminaarimuotoinen.
Requirements: Suoritustavasta sovitaan erikseen vuosittain.
Literature: Oppikirja tai kokoelma artikkeleita, ilmoitetaan kurssin
alussa.
Note: This course replaces course S-114.202.
Teachers: Prof. Jouko Lampinen, doc. Kaisa Tiippana, doc. Aapo
Hyvärinen (University of Helsinki)
Contents: Mechanisms and modelling of human visual perception are the
topics of the course. The emphasis is on modelling of visual feature
extraction and object recognition.
Assessment: Examination and practical work.
Literature: Will be announced in the beginning of the course.
Prerequisites: Basic knowledge of differential calculus, probability
and linear algebra. Basic knowledge of the human visual system
recommended (e.g. Perception and action or Structure and functioning of
the human brain).
Additional information: Lectured in English. Organized jointly with the
Department of Computer Science, University of Helsinki.
Additional: Replaces S-114.204
Language: English.
I-II, III-IV
Teacher: Prof Jouko Lampinen
Contents: Course with varying content.
Requirements: Seminar presentation, report and active participation.
Additional: Replaces S-114.220
Language: Finnish and English
S-114.4230 Individual Studies on Computational Engineering (1-6 cr) P V
Teacher: prof. Jouko Lampinen, prof. Kimmo Kaski, prof. Jukka
Tulkki, dos. Mika Ala-Korpela; PhD Riku Linna; FT Riikka
Möttönen; TkT Jari Saramäki; dos. Kaisa
Tiippana; TkT, KTT Juuso Töyli; TkT Harri Valpola; dos. Aki
Vehtari.
Contents: The topic and its depth shall be negotiated with one of the
teachers.
Additional: Replaces S-114.230
I-IV
Teacher: Prof Lampinen, Academy Prof Sams, Prof Tulkki,
Academy Prof Kaski
Additional: Replaces S-114.245
Language: English
I-II tai III-IV
Teacher: Mikko Karttunen docent
Contents: Basics concepts of molecular modeling, quantum mechanical
models, empirical force fields, review of molecular
dynamics and Monte Carlo, minimization methods in molecular modeling,
conformational analysis, the use of molecular
modeling to discover and design new drugs, future challenges in
molecular modeling.
Requirements: Lectures, exercises and examination: 4 cr. Lectures,
exercises, examination and project work: 6 cr.
Literature: A.R.Leach: Molecular Modeling.
Prerequisites: S-114.3250, computational physics or corresponding.
Basic statistical physics and thermodynamics.
Additional: Replaces S-114.260
Language: Finnish and English
III-IV
Teacher: Riku Linna Ph.D.
Contents: Mathematical/computational modelling and analysis of
processes taking places at cellular level. Topics include molecular
motors, ion pumps, intercellular communication, and various cell
models.
Requirements: Seminar pesentation and small exercise
Literature: C.P. Fall, E.S. Marland, J.M. Wagner & J.J.Tyson:
Computational Cell Biology. Handout.
Prerequisites: Mathematics 1-3, S-114.1100 recommended.
Additional: Replaces S-114.270
Language: English or Finnish
III-IV
Teacher: Docent, Dr.Tech. Aki Vehtari
Contents: Course with varying content. Objective of the course is to
give licentiate level teaching on a topic related to
computational engineering. The course may consist of lectures or
seminars.
Requirements: Agreed separately for each years course.
Literature: Book or collection of articles, announced at the beginning
of the course.
Prerequisites: Basics in Bayesian modeling.
Additional: Replaces S-114.610
Language: Finnish or English
S-114.4612 Special course in Bayesian modeling II (1-8 cr) L V
I tai II tai III tai IV
Teacher: dos. Aki Vehtari
Contents: Course with varying content. Objective of the course is to
give licentiate level teaching on a topic related to computational
engineering. The course may consist of lectures or seminars.
Requirements: Agreed separately for each years course.
Literature: Book or collection of articles, announced at the beginning
of the course.
Prerequisites: Basics in Bayesian modeling.
I or II or III or IV
Teacher: N.N.
Contents: Varying every year and consisting of a current research
problem.
Requirements: Active participation and seminar presentation.
Literature: To be announced
Additional: Replaces S-114.740
Language: Finnish or English
I or II or III or IV
Teacher: N.N.
Contents: Annually changing topic is related to current research
questions. The course can be shared with other laboratories.
Requirements: Active participation, seminar presentations and possibly
practicals.
Literature: To be announced.
Additional: Replaces S-114.720
Language: Finnish or English
I or II or III or IV
Teacher: Academy Prof Sams, Prof
Jääskeläinen, Kaisa Tiippana
Ph.D., Jyrki Tuomainen researcher, Jari Kätsyri researcher
Contents: Special project in the field of cognitive science and
technology.
Requirements: To be agreed with the supervising teacher.
Literature: To be agreed with the supervising teacher.
Additional: Replaces S-114.745
Language: Finnish or English
I or II or III or IV
Teacher: Academy Prof Sams, Academy Prof Kaski, Prof Lampinen, Prof
Tulkki, Prof Jääskeläinen, Jukka Heikkonen
docent,
Kaisa Tiippana Ph.D., Jari Kätsyri Ph.D., Prof Kari-Jouko
Räihä
Contents: The contents and extent of individual studies to be agreed
with the teacher beforehand.
Additional: Replaces S-114.750
Language: Finnish or English
S-114.7220 Memory and learning (3 cr)
Teacher: N.N.
Contents: Human memory systems and the underlying neural mechanisms.
Sensory memory, working memory, attention, and long-term memory.
Episodic and semantic memory. Disorders of memory. Neural and neural
network models of memory.
Assessment: Examination.
Literature: To be announced.