Personal Record
Name:         Konstantin Tretyakov
Location:     University of Tartu, Estonia
Affiliations: Bioinformatics Group,
              Institute of Computer Science,
              Software Technology and Competence Centre.
Occupation:   PhD Student, Researcher
Contact:      kt at ut dot ee
Mind scans:
* Machine Learning (Spring 2012) (Spring 2013) (Spring 2014)
                   (Spring 2015)
* Computer Graphics (Fall 2005) (Fall 2013)
* Advanced Algorithmics (Spring 2011)
* Bioinformatics (Fall 2010) (Fall 2011)
* Data Mining (Fall 2009)
* Introduction to Informatics (Spring 2009) (Fall 2009)
* Mathematics of Sound and Music (Spring 2007)
* Software Engineering (Fall 2006)
* Pattern Analysis (Fall 2006)
* Neural Networks (Spring 2005)
Stray Presentations
* 5-6.08.2015  - Introduction to Machine Learning    (AACIMP 2015 summer school)
* 1-2.08.2014  - Introduction to Data Management     (AACIMP 2014 summer school)
* 24.06.2014   - Machine Learning with Python        (IFI Summer School 2014)
* 1-17.08.2013 - Elements of Robotics                (AACIMP 2013 summer school)
* 3-16.08.2012 - Introduction to Machine Learning    (AACIMP 2012 summer school)
* 27.04.2011   - Machine Learning                    (, in Russian)
* 04.12.2010   - Analysis of Gene Expression [1,2,3] (SpbSU SABA, in Russian)
* 2004--       - EIO Training Sessions               (in Estonian)
Publications, Theses & Reports
* Age-related profiling of DNA methylation in CD8+ T cells reveals changes in
  immune response and transcriptional regulator genes.
    Liina Tserel, Raivo Kolde, Maia Limbach, Konstantin Tretyakov, Silva Kasela,
    Kai Kisand, Mario Saare, Jaak Vilo, Andres Metspalu, Lili Milani and Pärt Peterson.
    Scientific Reports 5, 13107 (2015). 
    doi:doi:10.1038/srep13107 [bib] [pdf]
* Memory-efficient fast shortest path estimation in large social networks.
    Volodymyr Floreskul, Konstantin Tretyakov and Marlon Dumas.
    Proceedings of ICWSM 2014, Ann Arbor, USA. [bib] [pdf] [poster pdf]
* Summary of talks and papers at ISCB-Asia/SCCG 2012.
    Konstantin Tretyakov, Tatyana Goldberg, Victor X Jin and Paul Horton.
    BMC Genomics 2013, 14(Suppl 2):I1. doi:10.1186/1471-2164-14-S2-I1 [bib] [pdf]
* Probabilistic file fingerprinting for big data.
    Konstantin Tretyakov, Sven Laur, Geert Smant, Jaak Vilo and Pjotr Prins.
    BMC Genomics 2013, 14(Suppl 2):S8. doi:10.1186/1471-2164-14-S2-S8 [bib] [pdf]
* Fraud Detection: Methods of Analysis for Hypergraph Data.
    Anna Leontjeva, Konstantin Tretyakov, Jaak Vilo, and Taavi Tamkivi.
    Proceedings of IEEE/ACM CSOSN 2012, Istanbul, Turkey. [bib] [pdf]
* Fast fully dynamic landmark-based estimation of shortest path distances in
  very large graphs.
    Konstantin Tretyakov, Abel Armas-Cervantes, Luciano García-Bañuelos, Jaak Vilo,
    Marlon Dumas.
    Proceedings of CIKM 2011. doi:10.1145/2063576.2063834 [bib] [pdf]
* G=MAT: Linking Transcription Factor Expression and DNA Binding Data.
    Konstantin Tretyakov, Sven Laur, Jaak Vilo.
    PLoS ONE 6(1): e14559. doi:10.1371/journal.pone.0014559 [bib] [pdf]
* Comprehensive transcriptome analysis of mouse embryonic
  stem cell adipogenesis unravels new processes of adipocyte development.
    Nathalie Billon, Raivo Kolde, Juri Reimand, Miguel C Monteiro, Meelis Kull, 
    Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski,
    Jaak Vilo and Christian Dani.
    Genome Biology (2010), 11:R80 [bib] [pdf]
* An Evolutionary Model of DNA Substring Distribution. 
    Meelis Kull, Konstantin Tretyakov and Jaak Vilo.
    In Algorithms and Applications, 2010. Springer, LNCS vol. 6060. [bib] [pdf]
* G=MAT: Linking Transcription Factor Expression with DNA Binding. 
    Master's Thesis (2008). [bib] [pdf]
* Text mining for automatic annotation of microarray experiment clusters. 
    Aleksandr Tkachenko, Konstantin Tretjakov, Priit Adler and Jaak Vilo.
    8th International Baltic Conference on Databases and Information Systems (2008).
* Example-Based Machine Translation of Short Phrases Using the 
  Context-Equivalence Principle.
    Tech.Report (2005).
* A Linear Model of Genetic Transcription Regulation that Combines Microarray 
  and Genome Sequence Data.
    Bachelor's Thesis (2005).
* Machine Learning Techniques in Spam Filtering.
    Tech.Report (2004). Published as a chapter in Combating Spam.
* Computer Graphics Learning Materials.
    Raimond-Hendrik Tunnel, M.Tech (2015) [pdf]
* Memory-Efficient Fast Shortest Path Distance Estimation in Large Graphs.
    Volodymyr Floreskul, M.Tech (2013)
* Adaptive Interactive Learning: a Novel Approach to Training 
  Brain-Computer Interface Systems.
    Ilya Kuzovkin, M.Tech (2013) [pdf]
* Fast Approximate Max-correlation Queries.
    Dmytro Fishman, M.Tech (2013) [pdf]
* Probabilistic Localization of a Soccer Robot.
    Priit Kallas, M.Tech (2013) [pdf]
* Procedural Tree Generation.
    Raimond-Hendrik Tunnel, B.Tech (2012) [pdf]
* Automatic Data-driven Generation of Database Schemas.
    Joel Edenberg, M.Tech (2012) [pdf]
* Predicting Paid Service Adoption in a Large Social Network.
    Dmitri Melnikov, M.Tech (2012)
* Shortest Path Approximation in Very Large Graphs.
    Abel Armas Cervantes, M.Tech (2011)
* Automatic Personalized Playlist Generation.
    Anastasia Semyonova, M.Tech (2011) [pdf]
* Automatic Musical Key Detection.
    Anna Alyanaki, M.Tech (2011) [pdf]
* Pattern Recognition for Non-invasive EEG-based BCI.
    Ilya Kuzovkin, B.Tech (2011) [pdf]
* Named Entity Recognition for the Estonian Language.
    Aleksandr Tkachenko, M.Tech (2010) [pdf]
* Statistical Analysis of Hypergraph Data with Application to Fraud Detection.
    Anna Leontyeva, M.Tech (2010)
* Detecting Influential Transcription Factors Using Linear Models.
    Nikita Shipilov, M.Tech (2010) [pdf]
* Managing Rapidly Changing Dimensions in Data Warehouses.
    Juta Vaks, B.Tech (2010) [pdf]
* Clustering Web Sessions Based on User Navigation. 
    Riivo Kikas, B.Tech (2009) [pdf]
* Music Genre Detection using the Naive Bayes Classifier.
    Anastasia Semyonova, B.Tech (2009) [pdf]
* Text Mining for Automatic Annotation of Microarray Experiment Clusters. 
    Alexandr Tkachenko, B.Tech (2008)
* Genetic Algorithm for the Improved Discovery of DNA Regulatory Elements. 
    Anton Stalnuhhin, B.Tech (2007) [pdf]
* The Blog
* The Github
* The Garage and other short projects with a webpage
  - (Aug 2010) [+]
  - (Feb 2011)
  - (Apr 2011, hibernated)
  - (Aug 2011, hibernated)
  - (Sep-Nov 2011, Robotex 2011)
  - (Mar 2012, alpha prototype - updates still pending)
  - E-garantii (Oct 2012, proof of concept, + bonus easter-egg)
  - pypi://matplotlib-venn [post]
  - (Oct 2012, hibernated)
  - pypi://pyliftover [post]
  - pypi://pyopossum3
  - pypi://ucscgenome
  - (Mar 2013)
  - (Feb 2014, proof of concept)
  - pypi://python_boilerplate_template [+] [post]
  - pypi://PyIntervalTree
  - pypi://intervaltree_bio
  - pypi://PyENCODE
  - pypi://skype-chatsync-reader [post]
  - (Mar 2015) [post]
  - Flask-Boilerplate [post]
  - (Apr 2015) [+] [tv]
* The Homework
* Travel (in Russian)
Important Information
A hedgehog is properly combed, if all his needles are tangential to the body. 
Only an even-dimensional hedgehog can be properly combed.