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Record W2905158219 · doi:10.1186/s13059-018-1600-4

We simply cannot go on being so vague about ‘function’

2018· letter· en· W2905158219 on OpenAlexafffund
W. Ford Doolittle

Bibliographic record

VenueGenome biology · 2018
Typeletter
Languageen
FieldMedicine
TopicLipid metabolism and disorders
Canadian institutionsDalhousie University
FundersNatural Sciences and Engineering Research Council of Canada
KeywordsBiologyGenome BiologyHuman geneticsEvolutionary biologyComputational genomicsFunction (biology)Computational biologyGenomicsGeneticsGenomeGene

Abstract

fetched live from OpenAlex

Function is an onerous concept, as the recent study by Steven Salzberg and colleagues demonstrates. We should be careful and always specific in using the 'F-word'.

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)0.011
metaresearch head score (Gemma)0.044
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Commentary · Consensus signal: Commentary
Teacher disagreement score0.053
Threshold uncertainty score0.057

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0110.044
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0030.002
Bibliometrics0.0010.001
Science and technology studies0.0050.017
Scholarly communication0.0060.015
Open science0.0040.004
Research integrity0.0530.116
Insufficient payload (model declined to judge)0.0080.013

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 head0.017
GPT teacher head0.262
Teacher spread0.245 · 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.

The models applied no category: nothing in the taxonomy fit this work.
Study designNot applicable
Domainnot available
GenreCommentary

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

Citations28
Published2018
Admission routes2
Has abstractyes

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