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Record W3084380855 · doi:10.1101/2020.09.08.287573

KuLGaP: A Selective Measure for Assessing Therapy Response in Patient-Derived Xenografts

2020· preprint· en· W3084380855 on OpenAlexafffund
Janosch Ortmann, Ladislav Rampášek, Elijah Tai, Arvind Singh Mer, Ruoshi Shi, Erin Stewart, Céline Mascaux, Aline Fusco Fares, Nhu‐An Pham, Gangesh Beri, Christopher Eeles, Denis Tkachuk, Chantal Ho, Shingo Sakashita, Jessica Weiss, Xiaoqian Jiang, Geoffrey Liu, David W. Cescon, Catherine O′Brien, Sheng Guo, Ming‐Sound Tsao, Benjamin Haibe‐Kains, Anna Goldenberg

Bibliographic record

VenuebioRxiv (Cold Spring Harbor Laboratory) · 2020
Typepreprint
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicSingle-cell and spatial transcriptomics
Canadian institutionsOntario Institute for Cancer ResearchPrincess Margaret Cancer CentreCanadian Institute for Advanced ResearchVector InstituteHospital for Sick ChildrenToronto General HospitalUniversity Health NetworkUniversity of TorontoUniversité de MontréalGroup for Research in Decision AnalysisUniversité du Québec à Montréal
FundersCanadian Institutes of Health ResearchConcordia UniversityCanadian Cancer Society Research InstituteTerry Fox FoundationOntario Institute for Cancer ResearchTerry Fox Research InstituteCalifornia HIV/AIDS Research ProgramCanadian Institute for Advanced ResearchPrincess Margaret Cancer FoundationStand Up To CancerEntertainment Industry FoundationGovernment of OntarioAmerican Association for Cancer Research
KeywordsMeasure (data warehouse)Task (project management)Translation (biology)Computer scienceVariation (astronomy)Clinical PracticeMedicineArtificial intelligenceOncologyMachine learningData miningBiologyFamily medicine

Abstract

fetched live from OpenAlex

Abstract Quantifying response to drug treatment in mouse models of human cancer is important for treatment development and assignment, and yet remains a challenging task. A preferred measure to quantify this response should take into account as much of the experimental data as possible, i.e. both tumor size over time and the variation among replicates. We propose a theoretically grounded measure, KuLGaP, to compute the difference between the treatment and control arms. KuLGaP is more selective than currently existing measures, reduces the risk of false positive calls and improves translation of the lab results to clinical practice.

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 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)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow)
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 score0.031
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0010.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0010.001
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 head0.024
GPT teacher head0.240
Teacher spread0.216 · 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.

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

Citations5
Published2020
Admission routes2
Has abstractyes

Explore more

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