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Record W3040460291 · doi:10.1371/journal.pcbi.1009803

Ten quick tips for deep learning in biology

2022· article· en· W3040460291 on OpenAlexaff
Benjamin D. Lee, Anthony Gitter, Casey S. Greene, Sebastian Raschka, Finlay Maguire, Alexander Titus, Michael D. Kessler, Alexandra Lee, Marc G. Chevrette, Paul A. Stewart, Thiago Britto‐Borges, Evan M. Cofer, Kun‐Hsing Yu, Juan J. Carmona, Elana J. Fertig, Alexandr A. Kalinin, Beth Signal, Benjamin J. Lengerich, Timothy J. Triche, Simina M. Boca

Bibliographic record

VenuePLoS Computational Biology · 2022
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenetics, Bioinformatics, and Biomedical Research
Canadian institutionsDalhousie University
FundersNational Institute of Dental and Craniofacial ResearchNational Institute of Allergy and Infectious DiseasesNational Institute of General Medical SciencesNational Cancer InstituteNational Institutes of HealthNational Institute of Food and AgricultureNational Heart, Lung, and Blood InstituteAllegheny Health NetworkNational Science Foundation of Sri LankaMoffitt Cancer CenterLustgarten FoundationGrand Rapids Community FoundationGordon and Betty Moore FoundationNational Human Genome Research InstituteHope FoundationU.S. Department of AgricultureNational Science Foundation
KeywordsArtificial intelligenceDeep learningMachine learningComputer scienceContext (archaeology)Active learning (machine learning)Task (project management)Instance-based learningSet (abstract data type)Data scienceEngineering

Abstract

fetched live from OpenAlex

applications of algorithms that

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 distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.633
Threshold uncertainty score0.503

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0000.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

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 head0.024
GPT teacher head0.308
Teacher spread0.284 · 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 teacher head, not a consensus.

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

Citations0
Published2022
Admission routes1
Has abstractyes

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