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Record W2763540102 · doi:10.1038/nbt.3960

Towards standards for human fecal sample processing in metagenomic studies

2017· article· en· W2763540102 on OpenAlexaff
Paul Igor Costea, Georg Zeller, Shinichi Sunagawa, Éric Pelletier, Adriana Alberti, Florence Levenez, Melanie Tramontano, Marja Driessen, Rajna Hercog, Ferris Jung, Jens Roat Kultima, Matthew R. Hayward, Luís Pedro Coelho, Emma Allen‐Vercoe, Laurie Bertrand, Michaël Blaut, Jillian R. Brown, Thomas Carton, Stéphanie Cools-Portier, Michelle C. Daigneault, Muriel Derrien, Anne Druesne, Willem M. de Vos, B. Brett Finlay, Harry J. Flint, Francisco Guarner, Masahira Hattori, Hans G. H. J. Heilig, Ruth Ann Luna, Johan van Hylckama Vlieg, Jana Junick, Ingeborg Klymiuk, Philippe Langella, Emmanuelle Le Chatelier, Volker Mai, Chaysavanh Manichanh, Jennifer C. Martin, Clémentine Mery, Hidetoshi Morita, Paul W. O’Toole, Céline Orvain, Kiran Raosaheb Patil, John Penders, Søren Persson, Nicolas Pons, Milena Popova, Anne Salonen, Delphine Saulnier, Karen P. Scott, Bhagirath Singh, Kathleen Slezak, Patrick Veiga, James Versalovic, Liping Zhao, Erwin G. Zoetendal, S. Dusko Ehrlich, Joël Doré, Peer Bork

Bibliographic record

VenueNature Biotechnology · 2017
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGut microbiota and health
Canadian institutionsWestern UniversityCanada's Michael Smith Genome Sciences CentreUniversity of British ColumbiaUniversity of Guelph
FundersAgence Nationale de la Recherche
KeywordsMetagenomicsMicrobiomeComparabilityDNA extractionBiologyHuman microbiomeFecesTransferabilityComputational biologyComputer scienceBioinformaticsMicrobiologyGeneticsPolymerase chain reactionMathematicsGeneMachine learning

Abstract

fetched live from OpenAlex
No abstract in any covered source. Its absence is recorded, not treated as a negative.

No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.095
metaresearch head score (Gemma)0.111
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch
Consensus categoriesnone
DomainCandidate signal: Methods · Consensus signal: none
Study designCandidate signal: Theoretical or conceptual · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.905
Threshold uncertainty score0.504

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0950.111
Meta-epidemiology (narrow)0.0020.002
Meta-epidemiology (broad)0.0030.002
Bibliometrics0.0060.004
Science and technology studies0.0030.007
Scholarly communication0.0080.004
Open science0.0060.008
Research integrity0.0080.009
Insufficient payload (model declined to judge)0.0030.005

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.028
GPT teacher head0.405
Teacher spread0.377 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designTheoretical or conceptual
DomainMethods
GenreMethods

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations904
Published2017
Admission routes1
Has abstractno

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