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Record W6930949167 · doi:10.5281/zenodo.15832651

Distributed Biomarker Discovery Pipeline

2025· preprint· en· W6930949167 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueZenodo (CERN European Organization for Nuclear Research) · 2025
Typepreprint
Languageen
FieldMathematics
TopicStatistical Methods and Applications
Canadian institutionsPrincess Margaret Cancer Centre
Fundersnot available
KeywordsPipeline (software)SPARK (programming language)Multivariable calculusPipeline transportBig dataKey (lock)Predictive modelling

Abstract

fetched live from OpenAlex

This dataset supports a distributed framework for predictive modeling of Immuno-Oncology (IO) response using pre-treatment RNA-seq data across multiple cohorts. It includes both univariable and multivariable pipelines designed for privacy-preserving, center-specific analysis without sharing patient-level data. Univariable modeling applies gene signature scoring and meta-analysis across centers. Multivariable modeling trains local XGBoost models using Apache Spark and aggregates them into a global predictor, validated across private datasets. Note: Private validation cohorts were used in this study but cannot be publicly shared. Access to these datasets may require collaboration agreements or institutional permissions.

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.

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)0.005
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesMeta-epidemiology (narrow), Insufficient payload (model declined to judge)
Consensus categoriesInsufficient payload (model declined to judge)
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: Not applicable
GenreCandidate signal: Methods · Consensus signal: Methods
Teacher disagreement score0.427
Threshold uncertainty score1.000

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.005
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0010.000
Scholarly communication0.0010.000
Open science0.0010.004
Research integrity0.0000.001
Insufficient payload (model declined to judge)0.0050.001

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 head0.132
GPT teacher head0.374
Teacher spread0.242 · 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