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Article ; Online: Clustgrams

Luosto Panu / Kontkanen Petri

Open Computer Science, Vol 1, Iss 4, Pp 466-

an extension to histogram densities based on the minimum description length principle

2011 Volume 481

Keywords	density estimation ; minimum description length (mdl) principle ; clustering ; histograms ; Electronic computers. Computer science ; QA75.5-76.95
Language	English
Publishing date	2011-12-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: NML computation algorithms for tree-structured multinomial Bayesian networks.

Kontkanen, Petri / Wettig, Hannes / Myllymäki, Petri

EURASIP journal on bioinformatics & systems biology

2008 , Page(s) 90947

Abstract: Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data. The minimum description length (MDL) ... ...

Abstract	Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data. The minimum description length (MDL) principle is a theoretically well-founded, general framework for performing statistical inference. The mathematical formalization of MDL is based on the normalized maximum likelihood (NML) distribution, which has several desirable theoretical properties. In the case of discrete data, straightforward computation of the NML distribution requires exponential time with respect to the sample size, since the definition involves a sum over all the possible data samples of a fixed size. In this paper, we first review some existing algorithms for efficient NML computation in the case of multinomial and naive Bayes model families. Then we proceed by extending these algorithms to more complex, tree-structured Bayesian networks.
Language	English
Publishing date	2008-04-02
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2233385-X
ISSN	1687-4153 ; 1687-4145
ISSN (online)	1687-4153
ISSN	1687-4145
DOI	10.1155/2007/90947
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks

Petri Myllymäki / Hannes Wettig / Petri Kontkanen

EURASIP Journal on Bioinformatics and Systems Biology, Vol

2008 Volume 2007

Abstract	Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data. The minimum description length (MDL) principle is a theoretically well-founded, general framework for performing statistical inference. The mathematical formalization of MDL is based on the normalized maximum likelihood (NML) distribution, which has several desirable theoretical properties. In the case of discrete data, straightforward computation of the NML distribution requires exponential time with respect to the sample size, since the definition involves a sum over all the possible data samples of a fixed size. In this paper, we first review some existing algorithms for efficient NML computation in the case of multinomial and naive Bayes model families. Then we proceed by extending these algorithms to more complex, tree-structured Bayesian networks.
Keywords	Electrical engineering. Electronics. Nuclear engineering ; TK1-9971 ; Technology ; T ; DOAJ:Electrical and Nuclear Engineering ; DOAJ:Technology and Engineering ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences
Subject code	006
Language	English
Publishing date	2008-01-01T00:00:00Z
Publisher	Springer
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: NML Computation Algorithms for Tree-Structured Multinomial Bayesian Networks

Kontkanen Petri / Wettig Hannes / Myllymäki Petri

EURASIP Journal on Bioinformatics and Systems Biology, Vol 2007, Iss 1, p

2007 Volume 90947

Abstract	Typical problems in bioinformatics involve large discrete datasets. Therefore, in order to apply statistical methods in such domains, it is important to develop efficient algorithms suitable for discrete data. The minimum description length (MDL) principle is a theoretically well-founded, general framework for performing statistical inference. The mathematical formalization of MDL is based on the normalized maximum likelihood (NML) distribution, which has several desirable theoretical properties. In the case of discrete data, straightforward computation of the NML distribution requires exponential time with respect to the sample size, since the definition involves a sum over all the possible data samples of a fixed size. In this paper, we first review some existing algorithms for efficient NML computation in the case of multinomial and naive Bayes model families. Then we proceed by extending these algorithms to more complex, tree-structured Bayesian networks.
Keywords	Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
Subject code	006
Language	English
Publishing date	2007-01-01T00:00:00Z
Publisher	Springer
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Antipsychotic drug treatment induces differential gene expression in the rat cortex.

Kontkanen, Outi / Törönen, Petri / Lakso, Merja / Wong, Garry / Castrén, Eero

Journal of neurochemistry

2002 Volume 83, Issue 5, Page(s) 1043–1053

Abstract: Antipsychotic drug treatment is known to modulate gene expression in experimental animals. In this study, candidate target genes for antipsychotic drug action were searched using microarrays after acute clozapine treatment (1, 6 and 24 h) in the rat ... ...

Abstract	Antipsychotic drug treatment is known to modulate gene expression in experimental animals. In this study, candidate target genes for antipsychotic drug action were searched using microarrays after acute clozapine treatment (1, 6 and 24 h) in the rat prefrontal cortex. Microarray data clustering with a self-organizing map algorithm revealed differential expression of genes involved in presynaptic function following acute clozapine treatment. The differential expression of 35 genes most profoundly regulated in expression arrays was further examined using in situ hybridization following acute clozapine, and chronic clozapine and haloperidol treatments. Acute administration of clozapine regulated the expression of chromogranin A, synaptotagmin V and calcineurin A mRNAs in the cortex. Chronic clozapine treatment induced differential cortical expression of chromogranin A, son of sevenless (SoS) and Sec-1. Chronic treatment with haloperidol regulated the mRNA expression of inhibitor of DNA-binding 2 (ID-2) and Rab-12. Furthermore, the expression of visinin-like proteins-1, -2 and -3 was regulated by chronic drug treatments in various brain regions. Our data suggest that acute and chronic treatments with haloperidol and clozapine modulate the expression of genes involved in synaptic function and in regulation of intracellular Ca2+ in cortex.
MeSH term(s)	Animals ; Antipsychotic Agents/pharmacology ; Calcineurin/genetics ; Calcineurin/metabolism ; Calcium-Binding Proteins/genetics ; Calcium-Binding Proteins/metabolism ; Cerebral Cortex/chemistry ; Cerebral Cortex/drug effects ; Cerebral Cortex/metabolism ; Chromogranin A ; Chromogranins/genetics ; Chromogranins/metabolism ; Clozapine/pharmacology ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Gene Expression Profiling ; Gene Expression Regulation/drug effects ; Gene Expression Regulation/physiology ; Haloperidol/pharmacology ; In Situ Hybridization ; Inhibitor of Differentiation Protein 2 ; Male ; Membrane Glycoproteins/genetics ; Membrane Glycoproteins/metabolism ; Munc18 Proteins ; Nerve Tissue Proteins/genetics ; Nerve Tissue Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; RNA, Messenger/metabolism ; Rats ; Rats, Wistar ; Repressor Proteins ; Son of Sevenless Proteins/genetics ; Son of Sevenless Proteins/metabolism ; Synaptotagmins ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism ; rab GTP-Binding Proteins/genetics ; rab GTP-Binding Proteins/metabolism
Chemical Substances	Antipsychotic Agents ; Calcium-Binding Proteins ; Chromogranin A ; Chromogranins ; DNA-Binding Proteins ; Id2 protein, rat ; Inhibitor of Differentiation Protein 2 ; Membrane Glycoproteins ; Munc18 Proteins ; Nerve Tissue Proteins ; RNA, Messenger ; Repressor Proteins ; Son of Sevenless Proteins ; Syt5 protein, rat ; Transcription Factors ; Vesicular Transport Proteins ; Synaptotagmins (134193-27-4) ; Calcineurin (EC 3.1.3.16) ; rab GTP-Binding Proteins (EC 3.6.5.2) ; Clozapine (J60AR2IKIC) ; Haloperidol (J6292F8L3D)
Language	English
Publishing date	2002-08-23
Publishing country	England
Document type	Journal Article
ZDB-ID	80158-6
ISSN	1471-4159 ; 0022-3042 ; 1474-1644
ISSN (online)	1471-4159
ISSN	0022-3042 ; 1474-1644
DOI	10.1046/j.1471-4159.2002.01213.x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The effect of acid-base clustering and ions on the growth of atmospheric nano-particles.

Lehtipalo, Katrianne / Rondo, Linda / Kontkanen, Jenni / Schobesberger, Siegfried / Jokinen, Tuija / Sarnela, Nina / Kürten, Andreas / Ehrhart, Sebastian / Franchin, Alessandro / Nieminen, Tuomo / Riccobono, Francesco / Sipilä, Mikko / Yli-Juuti, Taina / Duplissy, Jonathan / Adamov, Alexey / Ahlm, Lars / Almeida, João / Amorim, Antonio / Bianchi, Federico /

Breitenlechner, Martin / Dommen, Josef / Downard, Andrew J / Dunne, Eimear M / Flagan, Richard C / Guida, Roberto / Hakala, Jani / Hansel, Armin / Jud, Werner / Kangasluoma, Juha / Kerminen, Veli-Matti / Keskinen, Helmi / Kim, Jaeseok / Kirkby, Jasper / Kupc, Agnieszka / Kupiainen-Määttä, Oona / Laaksonen, Ari / Lawler, Michael J / Leiminger, Markus / Mathot, Serge / Olenius, Tinja / Ortega, Ismael K / Onnela, Antti / Petäjä, Tuukka / Praplan, Arnaud / Rissanen, Matti P / Ruuskanen, Taina / Santos, Filipe D / Schallhart, Simon / Schnitzhofer, Ralf / Simon, Mario / Smith, James N / Tröstl, Jasmin / Tsagkogeorgas, Georgios / Tomé, António / Vaattovaara, Petri / Vehkamäki, Hanna / Vrtala, Aron E / Wagner, Paul E / Williamson, Christina / Wimmer, Daniela / Winkler, Paul M / Virtanen, Annele / Donahue, Neil M / Carslaw, Kenneth S / Baltensperger, Urs / Riipinen, Ilona / Curtius, Joachim / Worsnop, Douglas R / Kulmala, Markku

Nature communications

2016 Volume 7, Page(s) 11594

Abstract: The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound ... ...

Abstract	The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere.
Language	English
Publishing date	2016-05-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/ncomms11594
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The effect of acid-base clustering and ions on the growth of atmospheric nano-particles

Lehtipalo, Katrianne / Rondo, Linda / Kontkanen, Jenni / Schobesberger, Siegfried / Jokinen, Tuija / Sarnela, Nina / Kürten, Andreas / Ehrhart, Sebastian / Franchin, Alessandro / Nieminen, Tuomo / Kulmala, Markku / Riccobono, Francesco / Sipila, Mikko / Yli-Juuti, Taina / Duplissy, Jonathan / Adamov, Alexey / Ahlm, Lars / Almeida, Joa˜o / Amorim, Antonio /

Bianchi, Federico / Breitenlechner, Martin / Dommen, Josef / Downard, Andrew J. / Dunne, Eimear M. / Flagan, Richard C. / Guida, Roberto / Hakala, Jani / Hansel, Armin / Jud, Werner / Kangasluoma, Juha / Kerminen, Veli-Matti / Keskinen, Helmi / Kim, Jaeseok / Kirkby, Jasper / Kupc, Agnieszka / Kupiainen-Määttä, Oona / Laaksonen, Ari / Lawler, Michael J. / Leiminger, Markus / Mathot, Serge / Olenius, Tinja / Ortega, Ismael K. / Onnela, Antti / Petäjä, Tuukka / Praplan, Arnaud / Rissanen, Matti P. / Ruuskanen, Taina / Santos, Filipe D. / Schallhart, Simon / Schnitzhofer, Ralf / Simon, Mario / Smith, James N. / Tröstl, Jasmin / Tsagkogeorgas, Georgios / Tomé, António / Vaattovaara, Petri / Vehkamäki, Hanna / Vrtala, Aron E. / Wagner, Paul E. / Williamson, Christina / Wimmer, Daniela / Winkler, Paul M. / Virtanen, Annele / Donahue, Neil M. / Carslaw, Kenneth S. / Baltensperger, Urs / Riipinen, Ilona / Curtius, Joachim / Worsnop, Douglas R.

Nature Communications, Volume 7

2016

Abstract	The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere.
Keywords	Atmospheric chemistry ; Physical chemistry ; 550
Subject code	540
Language	English
Publisher	London : Nature Publishing Group
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The effect of acid-base clustering and ions on the growth of atmospheric nano-particles

Lehtipalo, Katrianne / Rondo, Linda / Kontkanen, Jenni / Schobesberger, Siegfried / Jokinen, Tuija / Sarnela, Nina / Kürten, Andreas / Ehrhart, Sebastian / Franchin, Alessandro / Nieminen, Tuomo / Kulmala, Markku / Riccobono, Francesco / Sipila, Mikko / Yli-Juuti, Taina / Duplissy, Jonathan / Adamov, Alexey / Ahlm, Lars / Almeida, Joa˜o / Amorim, Antonio /

Nature Communications, Volume 7

2016

Abstract	The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere. publishedVersion
Keywords	Atmospheric chemistry ; Physical chemistry ; 550
Subject code	540
Language	English
Publisher	London : Nature Publishing Group
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: The effect of acid-base clustering and ions on the growth of atmospheric nano-particles

Lehtipalo, Katrianne / Rondo, Linda / Kontkanen, Jenni / Schobesberger, Siegfried / Jokinen, Tuija / Sarnela, Nina / Kürten, Andreas / Ehrhart, Sebastian / Franchin, Alessandro / Nieminen, Tuomo / Kulmala, Markku / Riccobono, Francesco / Sipila, Mikko / Yli-Juuti, Taina / Duplissy, Jonathan / Adamov, Alexey / Ahlm, Lars / Almeida, Joa˜o / Amorim, Antonio /

Nature Communications, Volume 7

2016

Abstract	The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere. publishedVersion
Keywords	Atmospheric chemistry ; Physical chemistry ; 550
Subject code	540
Language	English
Publisher	London : Nature Publishing Group
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: The effect of acid-base clustering and ions on the growth of atmospheric nano-particles

Lehtipalo, Katrianne / Rondo, Linda / Kontkanen, Jenni / Schobesberger, Siegfried / Jokinen, Tuija / Sarnela, Nina / Kürten, Andreas / Ehrhart, Sebastian / Franchin, Alessandro / Nieminen, Tuomo / Kulmala, Markku / Riccobono, Francesco / Sipila, Mikko / Yli-Juuti, Taina / Duplissy, Jonathan / Adamov, Alexey / Ahlm, Lars / Almeida, Joa˜o / Amorim, Antonio /

Nature Communications, Volume 7

2016

Abstract	The growth of freshly formed aerosol particles can be the bottleneck in their survival to cloud condensation nuclei. It is therefore crucial to understand how particles grow in the atmosphere. Insufficient experimental data has impeded a profound understanding of nano-particle growth under atmospheric conditions. Here we study nano-particle growth in the CLOUD (Cosmics Leaving OUtdoors Droplets) chamber, starting from the formation of molecular clusters. We present measured growth rates at sub-3 nm sizes with different atmospherically relevant concentrations of sulphuric acid, water, ammonia and dimethylamine. We find that atmospheric ions and small acid-base clusters, which are not generally accounted for in the measurement of sulphuric acid vapour, can participate in the growth process, leading to enhanced growth rates. The availability of compounds capable of stabilizing sulphuric acid clusters governs the magnitude of these effects and thus the exact growth mechanism. We bring these observations into a coherent framework and discuss their significance in the atmosphere. publishedVersion
Keywords	Atmospheric chemistry ; Physical chemistry ; 550
Subject code	540
Language	English
Publisher	London : Nature Publishing Group
Publishing country	de
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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