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Record W2171324524 · doi:10.1186/jbiol104

'Validation' in genome-scale research

2008· article· en· W2171324524 on OpenAlexaff
Timothy R. Hughes

Bibliographic record

VenueJournal of Biology · 2008
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicBioinformatics and Genomic Networks
Canadian institutionsUniversity of Toronto
Fundersnot available
KeywordsComputational biologyGenomeScale (ratio)BiologyGeneticsGeographyGene

Abstract

fetched live from OpenAlex

The individual 'validation' experiments typically included in papers reporting genome-scale studies often do not reflect the overall merits of the work.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

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)0.600
metaresearch head score (Gemma)0.710
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesMetaresearch
Consensus categoriesMetaresearch
DomainCandidate signal: Methods · Consensus signal: Methods
Study designCandidate signal: Theoretical or conceptual · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.400
Threshold uncertainty score0.494

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.6000.710
Meta-epidemiology (narrow)0.0030.002
Meta-epidemiology (broad)0.0050.004
Bibliometrics0.0090.014
Science and technology studies0.0070.020
Scholarly communication0.0170.016
Open science0.0090.015
Research integrity0.0120.010
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 head0.036
GPT teacher head0.318
Teacher spread0.282 · 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; the direct Gemma label and the distilled Codex classifier agree on what is shown here.

Study designTheoretical or conceptual
DomainMethods
GenreEmpirical

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

Citations33
Published2008
Admission routes1
Has abstractyes

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