- Kostic  Aleksandar D., Gevers  Dirk, Siljander  Heli, Vatanen  Tommi, Hyötyläinen  Tuulia, Hämäläinen  Anu-Maaria, Peet  Aleksandr, Tillmann  Vallo, Poho  Päivi, Mattila  Ismo, Lähdesmäki  Harri, Franzosa  Eric A., Vaarala  Outi, de Goffay  Marcus, Harmsen  Hermie, Ilonen  Jorma, Virtanen  Suvi M., Clish  Clary B., Oresic  Matej, Huttenhower  Curtis, Knip  Mikael, Xavier  Ramnik J.. The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes. Cell Host & Microbe, 17(2):260-273, 2015. [More info] [BibTeX]  
@article{
    chm2015,
    author = {Kostic, Aleksandar D. and Gevers, Dirk and Siljander, Heli and Vatanen, Tommi and Hy{\"o}tyl\"ainen, Tuulia and H\"am\"al\"ainen, Anu-Maaria and Peet, Aleksandr and Tillmann, Vallo and P\"oh\"o, P\"aivi and Mattila, Ismo and L\"ahdesm\"aki, Harri and Franzosa, Eric A. and Vaarala, Outi and de Goffay, Marcus and Harmsen, Hermie and Ilonen, Jorma and Virtanen, Suvi M. and Clish, Clary B. and Oresic, Matej and Huttenhower, Curtis and Knip, Mikael and Xavier, Ramnik J.},
    responsibleauthor = "Vatanen, Tommi",
    doi = "http://dx.doi.org/10.1016/j.chom.2015.01.001",
    language = "eng",
    title = "The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes",
    url = "http://www.sciencedirect.com/science/article/pii/S1931312815000219",
    journal = "Cell Host & Microbe",
    issn = "1931-3128",
    number = "2",
    volume = "17",
    juforank = "1",
    flags = "CSB puclic",
    il = "yes",
    year = "2015",
    unitcode = "T306-100",
    kay = "A,C",
    impactfactor = "A1",
    pages = "260-273"
}
 
- Vatanen  Tommi, Osmala  Maria, Raiko  Tapani, Lagus  Krista, Sysi-Aho  Marko, Oresic  Matej, Honkela  Timo, Lähdesmäki  Harri. Self-organization and missing values in SOM and GTM. Neurocomputing, 147(1):60-70, 2015. [More info] [BibTeX]  
@article{
    neurocomputing2015,
    author = {Vatanen, Tommi and Osmala, Maria and Raiko, Tapani and Lagus, Krista and Sysi-Aho, Marko and Oresic, Matej and Honkela, Timo and L\"{a}hdesm\"{a}ki, Harri},
    note = "Advances in Self-Organizing Maps Subtitle of the special issue: Selected Papers from the Workshop on Self-Organizing Maps 2012 (WSOM 2012)",
    doi = "http://dx.doi.org/10.1016/j.neucom.2014.02.061",
    responsibleauthor = "Vatanen, Tommi",
    language = "eng",
    title = "Self-organization and missing values in SOM and GTM",
    url = "http://www.sciencedirect.com/science/article/pii/S0925231214007127",
    country = "Netherlands",
    journal = "Neurocomputing",
    issn = "0925-2312",
    number = "1",
    volume = "147",
    juforank = "1",
    flags = "CSB public TRITON",
    il = "yes",
    year = "2015",
    unitcode = "T306-100",
    kay = "C",
    impactfactor = "A1",
    pages = "60-70"
}
 
- Lagus  Krista, Vatanen  Tommi, Kettunen  Oili, Heikkilä  Antti, Heikkilä  Matti, Pantzar  Mika, Honkela  Timo. Paths of Wellbeing on Self-Organizing Maps.  In Advances in Self-Organizing Maps, pages 345-352, 2013.  [BibTeX]  
@inproceedings{
    lagus2012,
    author = {Lagus, Krista and Vatanen, Tommi and Kettunen, Oili and Heikkil\"{a}, Antti and Heikkil\"{a}, Matti and Pantzar, Mika and Honkela, Timo},
    juforank = "1",
    isbn = "978-3-642-35229-4",
    language = "eng",
    title = "Paths of Wellbeing on Self-Organizing Maps",
    booktitle = "Advances in Self-Organizing Maps",
    responsibleauthor = "Lagus, Krista",
    flags = "COG AIRC public copy",
    il = "no",
    eventdetails = "International Workshop on Self-organizing Map, (WSOM 2012), Santiago, Chile, 12 - 14 December 2012",
    year = "2013",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A4",
    pages = "345-352"
}
 
- Vatanen  Tommi, Nieminen  Ilari T., Honkela  Timo, Raiko  Tapani, Lagus  Krista. Controlling Self-Organization and Handling Missing Values in SOM and GTM.  In Advances in Self-Organizing Maps, pages 55-64, 2013.  [BibTeX]  
@inproceedings{
    wsom2012,
    author = "Vatanen, Tommi and Nieminen, Ilari T. and Honkela, Timo and Raiko, Tapani and Lagus, Krista",
    juforank = "1",
    isbn = "978-3-642-35229-4",
    language = "eng",
    title = "Controlling Self-Organization and Handling Missing Values in SOM and GTM",
    country = "Germany",
    booktitle = "Advances in Self-Organizing Maps",
    responsibleauthor = "Vatanen, Tommi",
    flags = "COG AIRC CSB public",
    il = "no",
    eventdetails = "International Workshop on Self-organizing Map, (WSOM 2012), Santiago, Chile, 12 - 14 December 2012",
    year = "2013",
    unitcode = "T306-100",
    kay = "NA",
    impactfactor = "A4",
    pages = "55-64"
}
 
- Vatanen  Tommi, Raiko  Tapani, Valpola  Harri, LeCun  Yann. Pushing Stochastic Gradient towards Second-Order Methods - Backpropagation Learning with Transformations in Nonlinearities.  In Neural Information Processing , volume 8226 of Lecture Notes in Computer Science, pages 442-449, 2013.  [BibTeX]  
@inproceedings{
    Vatanen13ICONIP,
    author = "Vatanen, Tommi and Raiko, Tapani and Valpola, Harri and LeCun, Yann",
    volume = "8226",
    language = "eng",
    title = "Pushing Stochastic Gradient towards Second-Order Methods - Backpropagation Learning with Transformations in Nonlinearities",
    series = "Lecture Notes in Computer Science",
    booktitle = "Neural Information Processing (ICONIP 2013)",
    year = "2013",
    corerank = "A",
    month = "Nov",
    responsibleauthor = "Tommi Vatanen",
    juforank = "1",
    flags = "CSB COIN public",
    il = "yes",
    address = "Daegu, Korea",
    unitcode = "T306",
    kay = "NA",
    impactfactor = "A4",
    pages = "442--449"
}
 
- Vatanen  Tommi, Raiko  Tapani, Valpola  Harri, LeCun  Yann. Pushing Stochastic Gradient towards Second-Order Methods - Backpropagation Learning with Transformations in Nonlinearities. 2013.  [BibTeX]  
@misc{
    Vatanen13ICLR,
    author = "Vatanen, Tommi and Raiko, Tapani and Valpola, Harri and LeCun, Yann",
    juforank = "-",
    language = "eng",
    title = "Pushing Stochastic Gradient towards Second-Order Methods - Backpropagation Learning with Transformations in Nonlinearities",
    booktitle = "workshop of the International Conference on Learning Representations (ICLR 2013)",
    year = "2013",
    month = "May",
    responsibleauthor = "Tommi Vatanen",
    flags = "COIN copy",
    il = "yes",
    address = "Scottsdale, Arizona",
    unitcode = "T306",
    kay = "NA",
    impactfactor = "B3",
    corerank = "-"
}
 
- Vatanen  Tommi, Heikkilä  Matti, Honkela  Timo, Kettunen  Oili, Lagus  Krista, Pantzar  Mika. Kuntotiedot kartalle - erilaiset hyvä- ja huonokuntoisten ryhmät näkyviin. Liikunta & Tiede, 49(2-3):48-53, 2012.  [BibTeX]  
@article{
    liikuntajatiede,
    author = {Vatanen, Tommi and Heikkil\"{a}, Matti and Honkela, Timo and Kettunen, Oili and Lagus, Krista and Pantzar, Mika},
    volume = "49",
    language = "fin",
    title = {Kuntotiedot kartalle - erilaiset hyv\"{a}- ja huonokuntoisten ryhm\"{a}t n\"{a}kyviin},
    country = "Finland",
    journal = "Liikunta & Tiede",
    issn = "0358-7010",
    number = "2-3",
    responsibleauthor = "Vatanen, Tommi",
    juforank = "1",
    il = "no",
    year = "2012",
    unitcode = "T306-100",
    impactfactor = "B1",
    pages = "48-53",
    flags = "AIRC COG public"
}
 
- Vatanen  Tommi, Kuusela  Mikael, Malmi  Eric, Raiko  Tapani, Aaltonen  Timo, Nagai  Yoshikazu. Semi-Supervised Detection of Collective Anomalies with an Application in High Energy Particle Physics.  In IJCNN 2012, International Joint Conference on Neural Networks, pages 1-8, 2012.  [BibTeX]  
@inproceedings{
    vatanen2012b,
    author = "Vatanen, Tommi and Kuusela, Mikael and Malmi, Eric and Raiko, Tapani and Aaltonen, Timo and Nagai, Yoshikazu",
    juforank = "1",
    eventtime = "June 11-15",
    language = "eng",
    title = "Semi-Supervised Detection of Collective Anomalies with an Application in High Energy Particle Physics",
    eventlocation = "Brisbane, Australia",
    country = "United States",
    booktitle = "IJCNN 2012, International Joint Conference on Neural Networks",
    responsibleauthor = "Vatanen, Tommi",
    flags = "AIRC COG csb public",
    il = "yes",
    year = "2012",
    unitcode = "T306-100",
    impactfactor = "A4",
    pages = "1-8"
}
 
- Vatanen  Tommi. Missing Value Imputation Using Subspace Methods with Applications on Survey Data. 2012.  [BibTeX]  
@mastersthesis{
    vatanen2012a,
    author = "Vatanen, Tommi",
    pdf = "mthesis_vatanen.pdf",
    school = "Aalto University",
    address = "Espoo, Finland",
    year = "2012",
    title = "Missing Value Imputation Using Subspace Methods with Applications on Survey Data"
}
 
- Kuusela  Mikael, Malmi  Eric, Orava  Risto, Vatanen  Tommi. Soft Classification of Diffractive Interactions at the LHC. AIP Conference Proceedings, 1350(1):111-114, 2011. [Pdf] [BibTeX]  
@article{
    Kuusela2010c,
    editor = "Capua, Marcella and Fiore, Roberto and Ivanov, Igor and Papa, Alessandro and Soffer, Jacques and Tassi, Enrico",
    author = "Kuusela, Mikael and Malmi, Eric and Orava, Risto and Vatanen, Tommi",
    publisher = "AIP",
    title = "Soft Classification of Diffractive Interactions at the {LHC}",
    journal = "AIP Conference Proceedings",
    number = "1",
    volume = "1350",
    flags = "AIRC COG public copy",
    year = "2011",
    pdf = "Kuusela2011diff.pdf",
    pages = "111-114"
}
 
- Vatanen  Tommi, Kuusela  Mikael, Malmi  Eric, Raiko  Tapani, Aaltonen  Timo, Nagai  Yoshikazu. Fixed-Background EM Algorithm for Semi-Supervised Anomaly Detection. Report Aalto University School of Science, 2011. Pdf] [BibTeX]  
@techreport{
    Vatanen2011a,
    author = "Vatanen, Tommi and Kuusela, Mikael and Malmi, Eric and Raiko, Tapani and Aaltonen, Timo and Nagai, Yoshikazu",
    pdf = "Vatanen2011aaltoSci.pdf",
    year = "2011",
    flags = "AIRC COG public",
    institution = "Aalto University School of Science",
    title = "Fixed-Background {EM} Algorithm for Semi-Supervised Anomaly Detection"
}
 
- Kuusela  Mikael, Malmi  Eric, Orava  Risto, Vatanen  Tommi. Soft Classification of Diffractive Interactions at the LHC.  In Proceedings of Diffraction 2010, 2010. American Institute of Physics [Pdf] [BibTeX]  
@inproceedings{
    Kuusela10,
    author = "Kuusela, Mikael and Malmi, Eric and Orava, Risto and Vatanen, Tommi",
    publisher = "American Institute of Physics",
    title = "Soft Classification of Diffractive Interactions at the {LHC}",
    booktitle = "Proceedings of Diffraction 2010",
    flags = "AIRC COG public",
    year = "2010",
    pdf = "kuusela10diffraction.pdf"
}
 
- Kuusela  Mikeal, Malmi  Eric, Vatanen  Tommi, Orava  Risto, Aaltonen  Timo, Nagai  Yoshikazu. Detection of New Physics Using Density Estimation Based Anomaly Search. 2010. [More info] [BibTeX]  
@misc{
    cdfnote,
    author = "Kuusela, Mikeal and Malmi, Eric and Vatanen, Tommi and Orava, Risto and Aaltonen, Timo and Nagai, Yoshikazu",
    note = "CDF Internal Note. CDF/DOC/EXOTIC/CDFR/10227",
    url = "http://www-cdf.fnal.gov/publications/cdf10227_anomaly_search.pdf",
    year = "2010",
    flags = "AIRC COG copy public",
    title = "Detection of New Physics Using Density Estimation Based Anomaly Search"
}
 
- Vatanen  Tommi, Kuusela  Mikael, Malmi  Eric, Orava  Risto. Anomaly Search with Density Estimation and EM algorithm. 2010.  [BibTeX]  
@misc{
    Vatanen2010a,
    author = "Vatanen, Tommi and Kuusela, Mikael and Malmi, Eric and Orava, Risto",
    title = "Anomaly Search with Density Estimation and {EM} algorithm",
    month = "September",
    note = "Poster",
    flags = "AIRC COG public",
    year = "2010",
    howpublished = "6th International Summer School on Pattern Recognition, ISSPR 2010"
}
 
- Vatanen  Tommi, Väyrynen  Jaakko J., Virpioja  Sami. Language identification of short text segments with n-gram models.  In Proceedings of the Seventh conference on International Language Resources and Evaluation , pages 3423-3430, 2010. European Language Resources Association (ELRA) [Pdf] [BibTeX]  
@inproceedings{
    Vatanen10LREC,
    author = {Vatanen, Tommi and V{\"{a}}yrynen, Jaakko J. and Virpioja, Sami},
    publisher = "European Language Resources Association (ELRA)",
    resposibleauthor = "Vatanen, Tommi",
    title = "Language identification of short text segments with n-gram models",
    booktitle = "Proceedings of the Seventh conference on International Language Resources and Evaluation (LREC'10)",
    corerank = "NA",
    pages = "3423--3430",
    flags = "AIRC COG public",
    year = "2010",
    pdf = "vatanen10lrec.pdf",
    impactfactor = "A4",
    opteditor = "Nicoletta Calzolari (Conference Chair) and Khalid Choukri and Bente Maegaard and Joseph Mariani and Jan Odijk and Stelios Piperidis"
}