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Record W4391187567 · doi:10.21203/rs.3.rs-3864137/v1

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

2024· preprint· en· W4391187567 on OpenAlexaff
Catherine L. Lawson, Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Vincent Chen, Paul Emsley, Alberto Gobbi, A. Joachimiak, Sigrid Noreng, Michael Prisant, Randy J. Read, Jane S. Richardson, Alexis Rohou, Bohdan Schneider, Benjamin Sellers, Chenghua Chao, Elizabeth Sourial, Chris Williams, Christopher J. Williams, Ying Yang, Venkat Abbaraju, Pavel V. Afonine, Matthew L. Baker, Paul S. Bond, Tom L. Blundell, Tom Burnley, Arthur J. Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kevin Cowtan, Frank DiMaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F. Hryc, Carola Hunte, Maxim Igaev, Agnel Praveen Joseph, Wei‐Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W. Moriarty, Andrew Muenks, Garib N. Murshudov, Robert A. Nicholls, Mateusz Olek, Colin M. Palmer, Alberto Pérez, Emmi Pohjolainen, Karunakar R. Pothula, Christopher N. Rowley, Daipayan Sarkar, Luisa Schäfer, Christopher J. Schlicksup, G.F. Schroeder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V. Sobolev, Genki Terashi, Andrea C. Vaiana, Sundeep Chaitanya Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F. Schmid, Helen M. Berman, Wah Chiu

Bibliographic record

VenueResearch Square · 2024
Typepreprint
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicAdvanced Electron Microscopy Techniques and Applications
Canadian institutionsCarleton University
FundersDivision of ChemistryNational Institute of General Medical SciencesDepartment of Biochemistry, University of CambridgeBiotechnology and Biological Sciences Research CouncilAkademie Věd České RepublikyMedical Research CouncilNational Institutes of HealthDirectorate for Biological SciencesU.S. Department of EnergyAmerican Leprosy MissionsWellcome TrustDeutsche ForschungsgemeinschaftScience and Engineering Research BoardNational Science Foundation
KeywordsComputer science

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 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: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.105
Threshold uncertainty score0.563

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 science0.0010.003
Research integrity0.0000.001
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 head0.044
GPT teacher head0.433
Teacher spread0.389 · 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 designBench or experimental
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

Citations2
Published2024
Admission routes1
Has abstractno

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