MersV1, Main, Exploration, bibRecord, 000649

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.

Identifieur interne : 000649 ( Main/Exploration ); précédent : 000648; suivant : 000650

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.

Auteurs : Romain Menegaux [France] ; Jean-Philippe Vert [France]

Source :

Journal of computational biology : a journal of computational molecular cell biology [ 1557-8666 ] ; 2019.

RBID : pubmed:30785347

Abstract

We propose a new model for fast classification of DNA sequences output by next-generation sequencing machines. The model, which we call fastDNA, embeds DNA sequences in a vector space by learning continuous low-dimensional representations of thek-mers it contains. We show on metagenomics benchmarks that it outperforms the state-of-the-art methods in terms of accuracy and scalability.

DOI: 10.1089/cmb.2018.0174
PubMed: 30785347

Affiliations:

Le document en format XML

<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.</title>
<author><name sortKey="Menegaux, Romain" sort="Menegaux, Romain" uniqKey="Menegaux R" first="Romain" last="Menegaux">Romain Menegaux</name>
<affiliation wicri:level="3"><nlm:affiliation>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Vert, Jean Philippe" sort="Vert, Jean Philippe" uniqKey="Vert J" first="Jean-Philippe" last="Vert">Jean-Philippe Vert</name>
<affiliation wicri:level="3"><nlm:affiliation>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2019">2019</date>
<idno type="RBID">pubmed:30785347</idno>
<idno type="pmid">30785347</idno>
<idno type="doi">10.1089/cmb.2018.0174</idno>
<idno type="wicri:Area/PubMed/Corpus">000639</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000639</idno>
<idno type="wicri:Area/PubMed/Curation">000639</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000639</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000625</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000625</idno>
<idno type="wicri:Area/Ncbi/Merge">002116</idno>
<idno type="wicri:Area/Ncbi/Curation">002116</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">002116</idno>
<idno type="wicri:Area/Main/Merge">000652</idno>
<idno type="wicri:Area/Main/Curation">000649</idno>
<idno type="wicri:Area/Main/Exploration">000649</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.</title>
<author><name sortKey="Menegaux, Romain" sort="Menegaux, Romain" uniqKey="Menegaux R" first="Romain" last="Menegaux">Romain Menegaux</name>
<affiliation wicri:level="3"><nlm:affiliation>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
<author><name sortKey="Vert, Jean Philippe" sort="Vert, Jean Philippe" uniqKey="Vert J" first="Jean-Philippe" last="Vert">Jean-Philippe Vert</name>
<affiliation wicri:level="3"><nlm:affiliation>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>1 MINES ParisTech, PSL Research University, CBIO-Centre for Computational Biology, Paris</wicri:regionArea>
<placeName><region type="region">Île-de-France</region>
<region type="old region">Île-de-France</region>
<settlement type="city">Paris</settlement>
</placeName>
</affiliation>
</author>
</analytic>
<series><title level="j">Journal of computational biology : a journal of computational molecular cell biology</title>
<idno type="eISSN">1557-8666</idno>
<imprint><date when="2019" type="published">2019</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><b>We propose a new model for fast classification of DNA sequences output by next-generation sequencing machines. The model, which we call fastDNA, embeds DNA sequences in a vector space by learning continuous low-dimensional representations of the</b>
<i>k</i>
<b>-mers it contains. We show on metagenomics benchmarks that it outperforms the state-of-the-art methods in terms of accuracy and scalability.</b>
</div>
</front>
</TEI>
<affiliations><list><country><li>France</li>
</country>
<region><li>Île-de-France</li>
</region>
<settlement><li>Paris</li>
</settlement>
</list>
<tree><country name="France"><region name="Île-de-France"><name sortKey="Menegaux, Romain" sort="Menegaux, Romain" uniqKey="Menegaux R" first="Romain" last="Menegaux">Romain Menegaux</name>
</region>
<name sortKey="Vert, Jean Philippe" sort="Vert, Jean Philippe" uniqKey="Vert J" first="Jean-Philippe" last="Vert">Jean-Philippe Vert</name>
</country>
</tree>
</affiliations>
</record>

Pour manipuler ce document sous Unix (Dilib)

EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration

HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000649 | SxmlIndent | more

HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000649 | SxmlIndent | more

Pour mettre un lien sur cette page dans le réseau Wicri

{{Explor lien
   |wiki=    Sante
   |area=    MersV1
   |flux=    Main
   |étape=   Exploration
   |type=    RBID
   |clé=     pubmed:30785347
   |texte=   Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.
}}

Pour générer des pages wiki

HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i   -Sk "pubmed:30785347" \
       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MersV1

This area was generated with Dilib version V0.6.33.
Data generation: Mon Apr 20 23:26:43 2020. Site generation: Sat Mar 27 09:06:09 2021

Serveur d'exploration MERS

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.

Continuous Embeddings of DNA Sequencing Reads and Application to Metagenomics.

Source :

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

	Serveur d'exploration MERS
	Attention, ce site est en cours de développement ! Attention, site généré par des moyens informatiques à partir de corpus bruts. Les informations ne sont donc pas validées.