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Record W3112662112 · doi:10.1038/s42256-020-00232-8

Integration of mechanistic immunological knowledge into a machine learning pipeline improves predictions

2020· article· en· W3112662112 on OpenAlexafffund
Anthony Culos, Amy S. Tsai, Natalie Stanley, Martin Becker, Mohammad Sajjad Ghaemi, David R. McIlwain, Ramin Fallahzadeh, Athena Tanada, Huda Nassar, Camilo Espinosa, Maria Xenochristou, Edward A. Ganio, Laura S. Peterson, Xiaoyuan Han, Ina A. Stelzer, Kazuo Ando, Dyani Gaudillière, Thanaphong Phongpreecha, Ivana Marić, Alan L. Chang, Gary M. Shaw, David K. Stevenson, Sean C. Bendall, Kara L. Davis, Wendy J. Fantl, Garry P. Nolan, Trevor Hastie, Robert Tibshirani, Martin S. Angst, Brice Gaudillière, Nima Aghaeepour

Bibliographic record

VenueNature Machine Intelligence · 2020
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicSingle-cell and spatial transcriptomics
Canadian institutionsLockheed Martin (Canada)National Research Council Canada
FundersStanford Maternal and Child Health Research InstituteNational Institute of Dental and Craniofacial ResearchNational Institute of Allergy and Infectious DiseasesNational Institute of Neurological Disorders and StrokeNational Institute of General Medical SciencesNational Heart, Lung, and Blood InstituteNational Institute on AgingBurroughs Wellcome FundU.S. Food and Drug AdministrationAmerican Heart AssociationNational Institutes of HealthU.S. Department of Health and Human ServicesMarch of Dimes FoundationHamilton Health Sciences FoundationBill and Melinda Gates FoundationRobertson FoundationDoris Duke Charitable Foundation
KeywordsMass cytometryComputer scienceOverfittingMachine learningArtificial intelligenceProfiling (computer programming)Immune systemImmunologyMedicineArtificial neural networkBiology

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)0.002
metaresearch head score (Gemma)0.005
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Simulation or modeling · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.007
Threshold uncertainty score0.024

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0020.005
Meta-epidemiology (narrow)0.0020.001
Meta-epidemiology (broad)0.0010.002
Bibliometrics0.0020.001
Science and technology studies0.0010.000
Scholarly communication0.0020.003
Open science0.0020.001
Research integrity0.0020.003
Insufficient payload (model declined to judge)0.0070.003

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 head0.014
GPT teacher head0.268
Teacher spread0.254 · 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 designSimulation or modeling
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

Citations84
Published2020
Admission routes2
Has abstractno

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