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Record W1938354469 · doi:10.1016/j.ebiom.2015.07.010

Rethinking the Antibiotic Discovery Paradigm

2015· letter· en· W1938354469 on OpenAlexafffundabout
Robert E. W. Hancock

Bibliographic record

VenueEBioMedicine · 2015
Typeletter
Languageen
FieldImmunology and Microbiology
TopicAntimicrobial Peptides and Activities
Canadian institutionsUniversity of British Columbia
FundersNational Institute of Allergy and Infectious DiseasesCanadian Institutes of Health ResearchCanada Research ChairsNational Institutes of HealthCystic Fibrosis Foundation
KeywordsAntibioticsDrug discoveryComputational biologyMedicineData scienceIntensive care medicineBioinformaticsBiologyComputer scienceMicrobiology

Abstract

fetched live from OpenAlex

Experience is a valuable asset in scientific discovery. It enables the researcher to understand what has and has not worked in the past, and the way that problems can or should be addressed. However sometimes experience becomes enmired in dogma, and we must become careful as scientists not to think that what has been done previously is the only meaningful route forward. A strong object lesson is provided by the antibiotic discovery paradigm. With few exceptions, since the very first investigations we have considered that the gold standard for discovery of a useful antibiotic is its ability to kill or prevent the growth of serious bacterial pathogens using standard laboratory protocols that have been enshrined as the Clinical and Laboratory Standards Institute (CLSI) guidelines (Wiegand et al, 2008).

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 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)0.114
metaresearch head score (Gemma)0.056
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Theoretical or conceptual · Consensus signal: Theoretical or conceptual
GenreCandidate signal: Commentary · Consensus signal: Commentary
Teacher disagreement score0.114
Threshold uncertainty score0.601

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.1140.056
Meta-epidemiology (narrow)0.0020.001
Meta-epidemiology (broad)0.0040.003
Bibliometrics0.0080.004
Science and technology studies0.0080.071
Scholarly communication0.0290.065
Open science0.0100.021
Research integrity0.0180.048
Insufficient payload (model declined to judge)0.0050.004

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 head0.025
GPT teacher head0.242
Teacher spread0.217 · 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 designTheoretical or conceptual
Domainnot available
GenreCommentary

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

Citations25
Published2015
Admission routes3
Has abstractyes

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