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Filip Piękniewski PhD

Scientist (computational neuroscientist)

Brain Corporation
5665 Morehouse Drive
San Diego, CA, 92121 USA
Building: QRC
Office: 224N

e-mail: email

Assistant Professor

Faculty of Mathematics and Computer Science
Nicolaus Copernicus University,
Ul. Chopina 12/18, Toruń
POLAND

e-mail: email

GPG key*: gpg public key
skype*:

Bright stars die young

Tomasz Schreiber, my scientific advisor, collaborator, coauthor, friend. We started working together in 2003, at that time he was already a rising star of polish mathematics. Working with him was always a pleasure. Tomek was a kind of man who had been giving the best, never asking for anything in exchange. Always smiling, full of energy, full of faith in people. He was incredibly bright, with a great sense of humor. He could play with mathematical symbols so cleverly that it sometimes took a few days to understand what he achieved in seconds. When a few years ago Tomek was mourning his advisor, Alexander Nagaev who died in a tragic accident I could not imagine that I'll be mourning him so soon. In recent years he has been fighting with a fatal disease. But the disease was never an excuse for him. Instead it was something that motivated him to an even harder work. He died on first of December 2010. He was 35. He left his wife, loving family, great students and friends, tens of unfinished mathematical ideas. I will always remember him smiling.

My personal interests

Computer Science in general
Computational Intelligence
Neural networks
Random graphs and small world networks
Hopfield networks, phase diagrams
Spiking Neural Networks

Computer Networking
Texture analysis
Dynamic systems and fractals
Information theory
Computer modeling/GPU programming
UNIX/Linux/MacOSX administration

Recent research activities

Creating large scale neural simulation, spike based computing
Analysis of network topologies emerging from spiking neural models and other simplified computational models

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Teaching/Lectures View/Hide

Mathematical Foundations of Neuroscience - winter semester 2009/2010. Preliminary program. Any supplemental material will be published here.
Lecture presentations:

Lecture 1 - Basic facts about the brain and its analysis, Sample questions
Lecture 2 - Electrophysiology of neurons, Sample questions
Lecture 3 - Electrophysiology of neurons (continued), Sample questions
Lecture 4 - 1d systems, Sample questions
Lecture 5 - 2d systems, Sample questions
Lecture 6 - Bifurcations in 2d systems, Sample questions
Lecture 7 - Bifurcations II, Sample questions
Lecture 8 - Classes of excitability, Sample questions
Lecture 9 - Simple models of neurons and synapses, Sample questions
Lecture 10 - Bursting, Sample questions
Lecture 11 - Bursting continued Sample questions
Lecture 12 - Synchronization Sample questions
Lecture 13 - Coupled Oscillators Sample questions
Lecture 14 - Synchronization of neurons and synaptic plasticity Sample questions
Lecture 15 - Building large models step by step Sample questions

Programs/scripts/animations:

DTI tracking with Slicer 3d - a QuickTime animation
Slicer3d program webpage - an opensource medical visualization software. Also check the tutorials which include the nescessary data files.
Numerical stability demo - Matlab/Octave script
Saddle node bifurcation of a 1d system - Matlab/Octave script
Quadratic integrate and fire neuron - Matlab/Octave script
Saddle-node bifurcation in 1d system - a QuickTime animation
Saddle-node on invariant cicrle bifurcation in the Na-p-K model - a QuickTime animation
Phase portrait plot - Matlab/Octave script and sample fields to plot: sample field (pdf image), sample field 2 (pdf image), sample field 3 (pdf image), sample field 4 (pdf image)
Fold Cycle bifurcation in the canonical model - a QuickTime animation
Saddle Homoclinic Orbit bifurcation in the Na-p-K model - a QuickTime animation
Supercritical Andronov-Hopf bifurcation in the Na-p-K model - a QuickTime animation
Subcritical Andronov-Hopf bifurcation in the Na-p-K model - a QuickTime animation
Saddle node bifurcation in the Na-p-K model - a QuickTime animation
Dynamic regimes near Bogdanov-Takens bifurcation - a QuickTime animation
A script simulating an array of coupled neurons - good student project seed - Matlab/Octave script
Lecture notes of Georgi Medvedev, useful supplementary material
Publications of Eugene Izhikevich, useful supplementary material
A script simulating a piece of an axon with the cable equation - good student project seed - Matlab/Octave script
An animation of an action potential propagating spatialy along the fiber - a QuickTime animation
Spiking Neuron Models Single Neurons, Populations, Plasticity a book by Wulfram Gerstner and Werner M. Kistler - useful supplementary material
A script simulating a piece of an axon with the cable equation (FitzHugh-Nagumo) - good student project seed - Matlab/Octave script
A spiking network with CUDA - A project by Jayram Moorkanikara Nageswaran et.al
Hysteresis loop - a QuickTime animation
Hysteresis loop - Matlab/Octave script
INa-IK-IK(M) burster - Matlab/Octave script
An animation of an action potential propagating spatialy along the fiber in a bursting model (fold/homoclinic bursting) - a QuickTime animation
An animation of an action potential propagating spatialy along the fiber in a bursting model (circle/circle bursting) - a QuickTime animation
INa-IK-IK(M) circle/circle burster spatial solution - Matlab/Octave script
A mesh resembling a neuron in 3d - Blender file
Another mesh resembling a neuron in 3d - Blender file
INa-IK-IK(M) Fold/Homoclinic burster spatial solution - Matlab/Octave script
Propagating Waves in Neocortical Slices Research results of JIAN-YOUNG WU, PH.D.
Some more movies of Jian-Young Wu
Okinawa computational neuroscience course - a very good summer school, I encourage my students to apply!
Neuron - software for neuron simulations
Web page of Bard Ermentrout an author of XPP and many publications on mathematical neuroscience
Solution of a bursting neuron in 2d - note the artifacts related to the second order derrivative mask
Solution of a bursting neuron in 2d (source) - Matlab/Octave script
Rotating waves in a grid of coupled oscillators - a QuickTime animation
Spiral waves in a grid of coupled oscillators - a QuickTime animation
2d grid of coupled oscillators (source) - Matlab/Octave script
Computing PRC - Matlab/Octave script
Poincare phase map - Matlab/Octave script

Selected student projects:

Multi compartment neuron model Rafal Malkowski
NiC (Neurons in CUDA) Michal Matuszak
3D Neuron Model Bartosz Paprzycki
Persistent sodium and potassium neuron model Jaroslaw Piersa
Neurotest Andrzej Rutkowski
Neurons in flash Bartosz Zielinski
The Hodgkin-Huxley model - action potential Marcin Duchinski

Publications View/Hide

2010 - Persistent activation blobs in spiking neural networks with mexican hat connectivity - accepted to ICAISC 2010. Supplemental matlab script and movie 1, movie 2.
2010 - Spectra of the Spike Flow Graphs of Recurrent Neural Networks - presentation for the ICANN conference.
2010 - Theoretical model for mesoscopic-level scale-free self-organization of functional brain networks, preprint submitted to IEEE TNN (BiBTeX)
2009 - Spectra of the Spike Flow Graphs of Recurrent Neural Networks preprint submitted to ICANN (BiBTeX)
2009 - Robustness of Power Laws in Degree Distributions for Spiking Neural Networks preprint submitted to IJCNN 2009. BiBTeX
2008 - PhD thesis - defended on April 1st 2009 at Warsaw University.
2008 - Spontaneous Scale-free Structure of Spike Flow Graphs in Recurrent Neural Networks, preprint submitted to Neural Networks (BiBTeX)
2007 - Emergence of Scale-Free Graphs in Dynamical Spiking Neural Networks, a poster presented at 2007 International Joint Conference on Neural Networks, Orlando 2007 (BiBTeX)
2007 - Emergence of Scale-Free Graphs in Dynamical Spiking Neural Networks, 2007 International Joint Conference on Neural Networks, Orlando 2007 (BiBTeX)
2007 - Emergence of Scale-Free Spike Flow Graphs in Recurrent Neural Networks, 2007 IEEE Symposium on Foundations of Computational Intelligence, Honolulu Hawai 1-5 April 2007 (BiBTeX)
2006 - Mesoscopic Approach to Locally Hopfield Neural Networks in Presence of Correlated Patterns, 2006 International Joint Conference on Neural Networks, Vancouver, BC, Canada July 16-21, 2006, pp 5899 (BiBTeX)
2005 - Phase diagrams for locally Hopfield neural networks in presence of correlated patterns,Proceedings of International Joint Conference on Neural Networks, Montreal, Canada, July 31 - August 4, 2005, pp 776 (BiBTeX)
2004 - Visualizing and Analyzing Multidimensional Output from MLP Networks via Barycentric Projections, Springer-Verlag, Lecture Notes on Artificial Inteligence vol 3070 (BiBTeX)
2004 - Visual comparison of performance for different activation functions in MLP networks, Proceedings of Internartional Joint Conference on Neural Networks, Budapest, Hungary 2004, pp 2947-2953. (BiBTeX)

Some of my other work/hobbies View/Hide

Mixed photos from San Diego area, 2010,2011
A movie related to Brain Corporation shown by PBS
Milky Way time lapse movie taken on 14 Dec 2010 on Mt Laguna, some meteors are visible too, mov
Mysterious e a presentation for high school, Swiecie 2009, polish pdf
Scale-free networks a presentation on a seminar, polish pdf
Digital Signal Processing a presentation for high school students, polish pdf
Signal and image processing algorithms a presentation on a seminar, polish pdf
Inside the Menger Sponge a ptviewer 360 panorama inside this exciting shape
Scale free structures in recurrent neural networks a presentation on a seminar, polish pdf
A Beamer theme with my Faculty colors and university logos
Finding roots using binary or interpolation search a demonstration I made in Mathematica for Wolfram Demonstrations Project
Cayley Trees in Mathematica a demonstration I made in Mathematica for Wolfram Demonstrations Project
Map of Computer Science graphical representation of areas in computer science and relations between them, english pdf
Expander graphs and their applications a presentation on a seminar, polish pdf
A couple of pics of Torun in HSIR pictures with V (value) channel replaced by infrared image, nice effect
Magia algorytmów obróbki obrazu a presentation for annual science and art festival about digital photography and image processing (polish, html)
My faculty yard via PTviewer a 360 degree panorama of a yard at my faculty
Fractals with Maple a set of Maple procedures used to plot a number of fractals
My infrared photographs a couple of compositions done with Hoya R72 filter and olympus C7070
2d Lattice of Simplified Dynamical Neurons student project for OCNC 2006 (english, mov)
Losowosc w informatyce a presentation for annual science and art festival in Torun (polish, pdf)
WLAN safety - a presentation that I commited for the eduroam semminar in march 2006 (polish, pdf).
Torun in my lens - a web gallery containing some photos of my hometown that I collected in recent years.
Analiza stabilności i diagramów fazowych dla lokalnie hopfieldowskich sieci neuronowych w obecności wysoce skorelowanych wzorców okresowych - My masters thesis (Polish pdf)
CS in Education 2005 Conference - Arythmetic routines in Pascal and C++ - materials for workshops (polish html)
Samba and LDAP Howto - useful howto on ldap authorization in samba (Polish pdf)
Real Video Streaming Howto - useful howto on real video streaming (Polish pdf)
Fractals - Presentation for science festival about fractals (Polish HTML!!! <- NEW )
Fractals - Presentation for science festival about fractals (Polish pdf)
SIMP documentation - Technical aspects of the project that my team has written, and won departamets team programming contest '2004 (Polish pdf).
Gamma tranformations - Short thesis about gamma transformations of digital images (Polish pdf).
Java project - A small java applet for demonstration of Kohonen Self Organizing Map (neural network method).

Links on the Web that I recommend View/Hide

Eugene M. Izhikevich web page - a mathematician involved into study of brain function and its simulation.
Steve Furber - developer of the ARM chip, involved into the SpiNNaker project (a parallel chip designed to run neurosimulations)
Scholarpedia - a peer reviewed version of wikipedia.
Computational Cognitive Neuroscience Laboratory Indiana University Bloomington
prof. Dante R. Chialvo - author of interesting neuroscience research related to my work
racjonalista.pl - polish site for rational people
slashdot.org - web magazine for those with open minds (well, those that dont mind being a bit America-centric).
meteo.icm.edu.pl - good numeric weather forecast for central Europe
mathworld.woflram.com - online encyclopedia of mathematics
citeseer.com - Scientific literature digital library
Prof. W. Duch webpage - An AI specialist, this page is a gold mine.
Leszek Rybicki - the page of my friend and coauthor of some the projects.
Agata Piekniewska - the page of my wife.
Airbrush studio R if you need a fancy painting on your car!
E. Dyguda page - Nice page of a young researcher who likes Linux.
WMiI - The departament that I study in
PTI - Polish Information Processing Society (Koło Toruńskie Polskiego Towarzystwa Informatycznego), a society that I'm an active member.
www.subaqua.pl - A web page that I've designed for my favourite diving club.
Wysokie progi - Polish/American hiking club in Southern California.
eduroam.umk.pl - Worldwide safe Wifi project, that I participated in 2005r.

Photos from journeys/conferences etc. View/Hide

My calendar View/Hide

(CC) 2004 Filip Piękniewski
This work including my photographs is licensed under a Creative Commons License. Some of the materials however, including papers published in journals are copyrighted. Please contact me for details on licensing before you use any of the materials published on this page in your work.