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Record W2970740744 · doi:10.1038/s41592-019-0506-8

Promoting transparency and reproducibility in enhanced molecular simulations

2019· article· en· W2970740744 on OpenAlexaff
Massimiliano Bonomi, Mattia Bernetti, Andrea Cesari, Alessandro Laio, Giovanni Bussi, Cristina Paissoni, Carlo Camilloni, Gareth A. Tribello, Pavel Banáš, Bernd Ensing, Peter G. Bolhuis, Michele Parrinello, Sandro Bottaro, Davide Branduardi, Riccardo Capelli, Paolo Carloni, Haochuan Chen, Haohao Fu, Wei Chen, Francesco Colizzi, Sandip De, Marco De La Pierre, Davide Donadio, Viktor Drobot, Andrew L. Ferguson, Davide Provasi, Marta Filizola, James S. Fraser, Piero Gasparotto, Angelos Michaelides, Matteo Salvalaglio, Francesco Luigi Gervasio, Alejandro Gil-Ley, Fabrizio Marinelli, Toni Giorgino, Thomas Löhr, Michele Vendruscolo, Gabriella T. Heller, Glen M. Hocky, Marcella Iannuzzi, Michele Invernizzi, GiovanniMaria Piccini, Pablo M. Piaggi, Kim E. Jelfs, Evgeny Kirilin, Stefano Raniolo, Vittorio Limongelli, Kresten Lindorff‐Larsen, Layla Martin‐Samos, Matteo Masetti, Ralf Meyer, Carla Molteni, Tetsuya Morishita, Marco Nava, Elena Papaleo

Bibliographic record

VenueNature Methods · 2019
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicProtein Structure and Dynamics
Canadian institutionsNovelis (Canada)
FundersEngineering and Physical Sciences Research CouncilLundbeckfonden
KeywordsTransparency (behavior)ReproducibilityMolecular dynamicsSampling (signal processing)Computer scienceProfiling (computer programming)Data scienceNanotechnologyComputational biologyChemistryBiologyMaterials scienceComputational chemistryTelecommunicationsChromatographyComputer security

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)0.011
metaresearch head score (Gemma)0.073
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch
Consensus categoriesnone
DomainCandidate signal: Reproducibility · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.989
Threshold uncertainty score0.058

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0110.073
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0010.001
Science and technology studies0.0010.003
Scholarly communication0.0030.006
Open science0.0040.008
Research integrity0.0030.006
Insufficient payload (model declined to judge)0.0040.001

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 head0.007
GPT teacher head0.346
Teacher spread0.338 · 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 designNot applicable
DomainReproducibility
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

Citations1,286
Published2019
Admission routes1
Has abstractno

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