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Record W4214544930 · doi:10.1038/s41587-021-01186-x

Multiscale PHATE identifies multimodal signatures of COVID-19

2022· article· en· W4214544930 on OpenAlexafffund
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean‐Christophe Grenier, Dennis Shung, Alexander Tong, Carolina Lucas, Jon Klein, Daniel B. Burkhardt, Scott Gigante, Abhinav Godavarthi, Bastian Rieck, Benjamin Israelow, Michael Simonov, Tianyang Mao, Ji Eun Oh, Julio Silva, Takehiro Takahashi, Camila D. Odio, Arnau Casanovas‐Massana, John Fournier, Abeer Obaid, Adam J. Moore, Alice Lu-Culligan, Allison Nelson, Anderson F. Brito, Ángela Núñez, Anjelica Martin, Anne L. Wyllie, Annie Watkins, Annsea Park, Arvind Venkataraman, Bertie Geng, Chaney C. Kalinich, Chantal B. F. Vogels, Christina A. Harden, Codruta Todeasa, Cole Jensen, Daniel Kim, David McDonald, Denise Shepard, Edward Courchaine, Elizabeth B. White, Eric Song, Erin Silva, Eriko Kudo, Giuseppe DeIuliis, Haowei Wang, Harold Rahming, Hong‐Jai Park, Irene Matos, Isabel M. Ott, Jessica Nouws, Jordan Valdez, Joseph R. Fauver, Joseph Lim, Kadi-Ann Rose, Kelly Anastasio, Kristina Brower, Laura Glick, Lokesh Kumar Sharma, Lorenzo R. Sewanan, Lynda Knaggs, Maksym Minasyan, Maria Batsu, Maria Tokuyama, M. Cate Muenker, Mary E. Petrone, Maxine Kuang, Maura Nakahata, Melissa Campbell, Melissa Linehan, Michael H. Askenase, Mikhail Smolgovsky, Nathan D. Grubaugh, Nicole Sonnert, Nida Naushad, Pavithra Vijayakumar, Peiwen Lu, Rebecca Earnest, Rick Martinello, Roy S. Herbst, Rupak Datta, Ryan Handoko, Santos Bermejo, Sarah Lapidus, Sarah Prophet, Sean Bickerton, Sofia Velazquez, Subhasis Mohanty, Tara Alpert, Tyler Rice, Wade L. Schulz, William Khoury-Hanold, Xiaohua Peng, Yexin Yang, Yiyun Cao, Yvette Strong, Shelli Farhadian, Charles S. Dela Cruz, Albert I. Ko, Matthew Hirn, F. Perry Wilson, Julie Hussin, Guy Wolf, Akiko Iwasaki, Smita Krishnaswamy

Bibliographic record

VenueNature Biotechnology · 2022
Typearticle
Languageen
FieldMedicine
TopicCOVID-19 diagnosis using AI
Canadian institutionsMila - Quebec Artificial Intelligence InstituteUniversité de MontréalMontreal Heart Institute
FundersNational Center for Advancing Translational SciencesNational Institute of Diabetes and Digestive and Kidney DiseasesNatural Sciences and Engineering Research Council of CanadaFondation Institut de Cardiologie de MontréalInstitut de Valorisation des DonnéesNational Institute of Allergy and Infectious DiseasesHoward Hughes Medical InstituteInstitut de Cardiologie de MontréalEunice Kennedy Shriver National Institute of Child Health and Human DevelopmentAgency for Healthcare Research and QualityYale UniversityNational Institute of General Medical SciencesNational Institute of Mental HealthCanadian Institute for Advanced ResearchStrong
KeywordsCoronavirus disease 2019 (COVID-19)Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)2019-20 coronavirus outbreakVirologyComputational biologyComputer scienceBiologyMedicineInfectious disease (medical specialty)

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)0.000
metaresearch head score (Gemma)0.001
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: Empirical
Teacher disagreement score0.002
Threshold uncertainty score0.007

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0000.001
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0010.000
Science and technology studies0.0000.000
Scholarly communication0.0010.001
Open science0.0000.001
Research integrity0.0010.001
Insufficient payload (model declined to judge)0.0020.001

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 head0.014
GPT teacher head0.328
Teacher spread0.314 · 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

Citations80
Published2022
Admission routes2
Has abstractno

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