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Record W4281862187 · doi:10.1038/s43018-022-00379-w

A community approach to the cancer-variant-interpretation bottleneck

2022· article· en· W4281862187 on OpenAlexaff
Kilannin Krysiak, Arpad Danos, Susanna Kiwala, Joshua F. McMichael, Adam Coffman, Erica K. Barnell, Lana Sheta, Jason Saliba, Cameron J. Grisdale, Lynzey Kujan, Shahil Pema, Jake Lever, Nicholas C. Spies, Andreea Chiorean, Damian Rieke, Kaitlin A. Clark, Payal Jani, Hideaki Takahashi, Peter Horak, Deborah Ritter, Xin Zhou, Benjamin J. Ainscough, Sean DeLong, Mario Lamping, Alexander Marr, Brian V Li, Wan‐Hsin Lin, Panieh Terraf, Yasser Salama, Katie M. Campbell, Kirsten M. Farncombe, Jianling Ji, Xinjie Xu, Rashmi Kanagal‐Shamanna, Kelsy C. Cotto, Zachary L. Skidmore, Jason Walker, Jinghui Zhang, Aleksandar Milosavljevic, Ronak Y. Patel, Rachel H. Giles, Raymond H. Kim, Lynn M. Schriml, Elaine R. Mardis, Steven J.M. Jones, Gordana Raca, Shruti Rao, Subha Madhavan, Alex H. Wagner, Obi L. Griffith, Malachi Griffith

Bibliographic record

VenueNature Cancer · 2022
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGenomics and Rare Diseases
Canadian institutionsToronto General HospitalYork UniversityUniversity Health NetworkPrincess Margaret Cancer CentreCanada's Michael Smith Genome Sciences Centre
FundersNational Cancer InstituteNational Center for Advancing Translational SciencesNational Human Genome Research Institute
KeywordsInterpretation (philosophy)BottleneckDomain (mathematical analysis)CancerComputer scienceData scienceBiologyGeneticsMathematics

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)0.064
metaresearch head score (Gemma)0.211
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: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.064
Threshold uncertainty score0.339

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0640.211
Meta-epidemiology (narrow)0.0020.002
Meta-epidemiology (broad)0.0030.002
Bibliometrics0.0060.004
Science and technology studies0.0050.007
Scholarly communication0.0080.013
Open science0.0090.019
Research integrity0.0070.009
Insufficient payload (model declined to judge)0.0150.003

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 head0.008
GPT teacher head0.271
Teacher spread0.263 · 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
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

Citations15
Published2022
Admission routes1
Has abstractno

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