A novel integrative computational framework for breast cancer radiogenomic biomarker discovery
Bibliographic record
Abstract
In precise medicine, it is with great value to develop computational frameworks for identifying prognostic biomarkers which can capture both multi-genomic and phenotypic heterogeneity of breast cancer (BC). Radiogenomics is a field where medical images and genomic measurements are integrated and mined to solve challenging clinical problems. Previous radiogenomic studies suffered from data incompleteness, feature subjectivity and low interpretability. For example, the majority of the radiogenomic studies miss one or two of medical imaging data, genomic data, and clinical outcome data, which results in the data incomplete issue. Feature subjectivity issue comes from the extraction of imaging features with significant human involvement. Thus, there is an urgent need to address above-mentioned limitations so that fully automatic and transparent radiogenomic prognostic biomarkers could be identified for BC. We proposed a novel framework for BC prognostic radiogenomic biomarker identification. This framework involves an explainable DL model for image feature extraction, a Bayesian tensor factorization (BTF) processing for multi-genomic feature extraction, a leverage strategy to utilize unpaired imaging, genomic, and survival outcome data, and a mediation analysis to provide further interpretation for identified biomarkers. This work provided a new perspective for conducting a comprehensive radiogenomic study when only limited resources are given. Compared with baseline traditional radiogenomic biomarkers, the 23 biomarkers identified by the proposed framework performed better in indicating patients' survival outcome. And their interpretability is guaranteed by different levels of build-in and follow-up analyses.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot 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.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.000 |
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.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
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".