Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Same input data as the authors
- ✓Reported values were directly comparable
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓The central claim held under reproduction
- 🟡A deviation arose in the data or preprocessing
- 🟡The deviation was non-trivial in magnitude
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough for a clean 1:1-equivalent reproduction. The repo ships, per Burstein TNBC subtype, both the trained-model MATLAB Classification-Learner export (gaussian-kernel fitcsvm, BoxConstraint 1, Standardize true, KernelScale 27 for BLIA/BLIS/MES and 110 for LAR, 5-fold CV) AND the exact training table (<SUBTYPE>_data.xlsx, GSE76124-derived, 198 samples, 719 DEGs). No MATLAB/Octave on «our HPC», so the documented model was reproduced 1:1 with scikit-learn (StandardScaler -> SVC rbf, C=1, gamma=1/KernelScale^2) under 5-fold stratified CV (10x repeated for the +/- spread) -- a third-party reproduction the brief counts as equally valid. RESULT: all four headline CV accuracies reproduce within ~1 pp (BLIA 95.7->94.86, BLIS 95.6->94.80, MES 95.0->94.51, LAR 98.8->98.58), correct rank order, AUCs within +/-0.01, specificity within ~1.5 pp. Structural counts (198; 54/60/47/37; 719 genes) match EXACTLY, confirming the Methods-described data is the shipped data. No fabrication signal -- every reported value is derivable from the shipped data+code. Two soft gaps left for the human: MES sensitivity (93.2->83.0) and LAR sensitivity (100->94.6), both single-5-fold-pass per-class rates with high partition variance. NOT attempted (80/20): the 719-gene DEG derivation, the independent 334-sample test cohort + 19.76% unclassified rate (matrix not shipped), and the 6 other algorithm families compared in the paper (only the selected SVM per subtype is shipped as code).
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
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v1 current initial assessment Score 86assessed: 2026-06-15 ⛓ 78c10146ee79
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Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-15
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: opusCan machine learning applied to public microarray gene expression data classify triple negative breast cancer (TNBC) into its four molecular subtypes (BLIA, BLIS, MES, LAR) using subtype-specific upregulated gene signatures?
- ★ A training gene set of 719 unique upregulated DEGs (subtype-specific) can be used to build ML models that classify TNBC into BLIA, BLIS, MES, and LAR subtypes. resource
- ★ The SVM algorithm is the best classifier for TNBC subtyping, achieving the highest accuracy (95–98.8%) and AUC (0.99–1.00). finding
- ★ Each TNBC subtype exhibits a unique gene expression pattern and signaling pathway profile, confirmed by DEG identification and GO/KEGG pathway analysis. finding
- ★ Of 334 unknown TNBC samples, the model assigned most to a subtype but 66 (19.76%) could not be classified, containing only three upregulated genes (EN1, PROM1, CCL2). finding
- ★ A machine learning pipeline (feature selection of unique upregulated DEGs followed by training seven classifiers) is a viable method for TNBC subtype classification from microarray data. method
- Subtype-specific signatures point to therapeutic implications (immune checkpoint inhibitors for BLIA, anti-angiogenic for MES, androgen receptor inhibition for LAR). mechanism
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| gene expression microarray (DEG identification and feature selection) | 198 known TNBC patient samples (training cohort) classified into BLIA, BLIS, MES, LAR | none | upregulated differentially expressed genes (p<0.05, log2 FC >2) | GPL570 Affymetrix Human Genome U133 Plus 2.0 Array; RMA normalization via R/Bioconductor affy; mavolcanoplot in MATLAB |
| machine learning classification model training (SVM, KNN, NB, DT, Ensemble, Linear Discriminant, Logistic Regression) | 198 TNBC training samples (BLIA n=54, BLIS n=60, MES n=47, LAR n=37) | none | classification accuracy, sensitivity, specificity, precision, NPV, F1 score, AUC (five-fold cross validation) | MATLAB 2020a Classification Learner app |
| GO term and KEGG pathway enrichment analysis | unique upregulated DEGs of each TNBC subtype | none | enriched biological processes, molecular functions, cellular components, pathways | Metascape (KEGG, Reactome, CORUM) |
| gene expression microarray (model validation/prediction) | 334 unknown TNBC samples (independent test cohort) | none | predicted subtype assignment and upregulated DEG comparison to training set | MATLAB (mavolcanoplot); SVM model |
- – SVM achieved the highest average classification accuracy across subtypes BLIA 95.7%, BLIS 95.6%, MES 95.0%, LAR 98.8%
- – SVM AUC values were high across subtypes LAR AUC 1.00; BLIA, BLIS, MES AUC 0.99
- – F1 scores of subtype models BLIA 0.91, BLIS 0.91, MES 0.90, LAR 0.97
- – LAR model correctly predicted non-LAR patients, achieving perfect recall recall (sensitivity) 1.00 (100%)
- ▲ Identified unique upregulated DEGs per subtype (genes expressed in only one subtype) BLIA 73, BLIS 75, MES 385, LAR 186 (total 719)
- – Prediction of 334 unknown TNBC samples into subtypes BLIA 97 (29.04%), BLIS 73 (21.86%), MES 39 (11.68%), LAR 59 (17.66%)
- – Unclassified TNBC samples that could not be assigned to any subtype 66 samples (19.76%); only EN1, PROM1, CCL2 upregulated
- – Model accuracy across all seven algorithms ranged widely, with logistic regression lowest 61.5% (logistic regression) to 98.8% (SVM)
- other accuracy 95–98.8%; AUC 0.99–1.00 (SVM classification performance across four TNBC subtypes (training, five-fold CV))
- count 719 DEGs (unique upregulated DEGs used as training gene set)
- count 80, 80, 400, 197 (upregulated DEGs identified in BLIA, BLIS, MES, LAR respectively)
- count 73, 75, 385, 186 (genes expressed only in BLIA, BLIS, MES, LAR respectively)
- count 66 (19.76%) (unclassified TNBC test samples not assigned to any subtype)
- count 532 TNBC cases (198 training, 334 test) (total experimental dataset from seven GEO datasets)
- other F1: 0.91, 0.91, 0.90, 0.97; recall LAR 1.00 (F1 scores and LAR recall for BLIA/BLIS/MES/LAR SVM models)
- other p-value <0.05 and log2 fold change >2 (cutoffs for defining significant upregulated DEGs)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
The paper downloaded seven publicly available Affymetrix microarray datasets (n=532 TNBC samples) from GEO, normalized them with RMA (R/affy), and filtered for upregulated differentially expressed genes per TNBC subtype using fold-change and p-value cutoffs. The 719 subtype-unique DEGs were used as features to train and compare seven machine learning classifiers via five-fold cross-validation in MATLAB, with SVM selected as the best-performing model. Performance was reported as accuracy, F1 score, AUC, sensitivity, specificity, PPV, and NPV; the model was then applied to an independent hold-out cohort of 334 samples.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Volcano plot-based filtering (p < 0.05, log2FC > 2); underlying statistical test for p-value computation not explicitly named | Identification of upregulated DEGs within each TNBC subtype in the training set (n=198) | 198 total training samples (BLIA n=54, BLIS n=60, MES n=47, LAR n=37) | not stated |
| Five-fold cross-validation (accuracy, F1, AUC, sensitivity, specificity, PPV, NPV) | Evaluation of all seven ML classifiers on the training set | 198 | na |
| Enrichment analysis (hypergeometric-type, p < 0.01, enrichment factor > 1.5; method internal to MetaScape) | GO term and KEGG/Reactome pathway enrichment of subtype-unique DEGs | 73, 75, 385, 186 unique DEGs per subtype respectively | not stated |
| Hold-out validation (proportion assigned per subtype, DEG overlap comparison) | Independent test cohort prediction and confirmation | 334 | na |
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Differentially expressed genes were identified using a p-value cutoff (< 0.05) and fold-change threshold (log2FC > 2) without a multiple-testing correction across ~20,000 genes↳ Could also: Apply Benjamini-Hochberg FDR correction (e.g., via limma in R, which is purpose-built for microarray linear models) to control the false discovery rate across the full gene set — With ~20,000 genes tested per subtype, an uncorrected p < 0.05 threshold would be expected to yield many false positives by chance; FDR-adjusted q-values are standard in microarray DEG analysis and would make the selected gene set more reproducible across datasets
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Seven GEO datasets from different studies were pooled and processed together using RMA normalization without explicit batch-effect correction↳ Could also: Apply a batch-correction method such as ComBat (R/sva package) or surrogate variable analysis after RMA normalization before DEG analysis and model training — Combining data from multiple independent studies on the same platform can introduce systematic inter-study variability; batch correction methods are commonly applied in multi-cohort microarray analyses to reduce this source of variation before downstream modeling
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ML model performance (accuracy, F1, AUC) was reported as single point estimates from five-fold cross-validation↳ Could also: Report confidence intervals for AUC (e.g., via DeLong method or bootstrap) and mean ± SD of cross-validation fold metrics — Point estimates from a single five-fold split can vary depending on the fold assignment; reporting variance across folds or bootstrap CIs for AUC quantifies uncertainty in model performance estimates and allows more direct comparison between classifiers
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All 719 subtype-unique DEGs were used as input features for model training without further dimensionality reduction or importance-based feature ranking↳ Could also: Apply a feature importance or recursive feature elimination step (e.g., SVM-RFE, LASSO, or random forest importance scores) to identify a smaller, high-signal gene signature — High-dimensional feature sets relative to sample size can increase noise and reduce interpretability; feature selection before or within the cross-validation loop can identify a minimal gene panel, which the authors themselves note as a goal for future clinical qPCR validation
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Model selection and hyperparameter settings were not described in detail; MATLAB Classification Learner default settings appear to have been used↳ Could also: Perform nested cross-validation (outer loop for performance estimation, inner loop for hyperparameter tuning) to provide an unbiased estimate of generalization performance — Selecting model hyperparameters (e.g., SVM kernel, C parameter) using the same cross-validation loop that estimates performance can optimistically bias the reported accuracy; nested CV separates these steps and is a standard approach for high-dimensional genomic classification problems
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The 334-sample test cohort lacked ground-truth subtype labels, so external validation used DEG overlap comparison rather than a held-out accuracy metric↳ Could also: Use a labeled external cohort with known subtype assignments (e.g., from the Burstein et al. reference dataset) to compute direct classification accuracy, sensitivity, and specificity on truly independent samples — DEG overlap confirmation is an indirect measure of model validity; a labeled external cohort would allow computation of the same quantitative metrics reported for the training set and provide a less circular assessment of generalizability
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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EN1, PROM1, and CCL2 are upregulated in unclassified TNBC samples (19.76%) that cannot be assigned to any canonical TNBC subtype.microarray human tnbc up 2021×1papers★ This paper is the founder (earliest)
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SVM model assigned 334 unknown TNBC samples to subtypes: BLIA 29%, BLIS 22%, MES 12%, LAR 18%; 20% remained unclassified.microarray human tnbc 2021×1papers★ This paper is the founder (earliest)
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Each TNBC subtype harbors unique upregulated DEGs: BLIA 73, BLIS 75, MES 385, LAR 186 (719 total subtype-exclusive genes); MES has the largest subtype-specific transcriptional signature.microarray human tnbc up 2021×1papers★ This paper is the founder (earliest)
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SVM LAR subtype model achieved perfect recall (sensitivity 1.00), correctly identifying all non-LAR TNBC patients.other human tnbc 2021×1papers★ This paper is the founder (earliest)
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SVM classifier achieved the highest average classification accuracy for TNBC subtypes (BLIA 95.7%, BLIS 95.6%, MES 95.0%, LAR 98.8%) among seven ML algorithms.other human tnbc 2021×1papers★ This paper is the founder (earliest)
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Across seven ML algorithms for TNBC subtype classification, accuracy ranged from 61.5% (logistic regression) to 98.8% (SVM), with SVM outperforming all others.other human tnbc 2021×1papers★ This paper is the founder (earliest)
Citation network
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Data lineage
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What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-34575658
Paper: Bissanum et al. 2021, Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning, J Pers Med 11(9):881. DOI 10.3390/jpm11090881 · PMCID PMC8472680.
Repo: https://github.com/Rassanee/TNBC @ commit
c954225419a57ba2b2752ad47c046e9d0fca8fd9 (default branch main, pushed
2021-08-27, no license file).
Data: training cohort = GEO GSE76124 (Burstein et al. 2015, 198 TNBC
samples). The repo ships the training tables itself as <SUBTYPE>_data.xlsx
(one per subtype), so the predictor matrix + labels used to train each model are
available directly — no external GEO download is strictly required for the
training-CV reproduction.
What the repo contains
Four MATLAB Classification-Learner exports, one per Burstein TNBC subtype:
| file | model | response classes | KernelScale |
|---|---|---|---|
BLIA_trainClassifier.m + BLIA_data.xlsx + BLIA_model.mat |
Gaussian-kernel SVM | {BLIA, Control} | 27 (Medium Gaussian) |
BLIS_trainClassifier.m + BLIS_data.xlsx + BLIS_model.mat |
Gaussian-kernel SVM | {BLIS, Control} | 27 (Medium Gaussian) |
MES_trainClassifier.m + MES_data.xlsx + MES_model.mat |
Gaussian-kernel SVM | {Control, MES} | 27 (Medium Gaussian) |
LAR_trainClassifier.m + LAR_data.xlsx + LAR_model.mat |
Gaussian-kernel SVM | {Control, LAR} | 110 (Coarse Gaussian) |
Each *_trainClassifier.m is identical in structure: fitcsvm(..., 'KernelFunction', 'gaussian', 'KernelScale', s, 'BoxConstraint', 1, 'Standardize', true), then a
5-fold cross-validation with validationAccuracy = 1 - kfoldLoss(...).
Predictors = 719 subtype DEGs (gene-expression columns); response column
Genesymbols ∈ {subtype, Control}. KernelScale 27 = MATLAB "Medium Gaussian"
(≈ √719), 110 = "Coarse Gaussian" (≈ 4·√719) — consistent with the paper's stated
model selection (Medium Gaussian SVM for BLIA/BLIS/MES, Coarse Gaussian for LAR).
IN SCOPE (pipeline-derived, attempted)
The 5-fold cross-validation classification metrics of the four selected SVM
models — exactly the quantities validationAccuracy etc. that the shipped
*_trainClassifier.m compute on the shipped *_data.xlsx. Reported (Table, main
text):
| subtype | reported CV accuracy | sens | spec | precision | F1 | AUC |
|---|---|---|---|---|---|---|
| BLIA | 95.7 ± 0.7 % | 85.2 % | 99.3 % | 97.9 % | 0.91 | 0.99 |
| BLIS | 95.6 ± 0.7 % | 88.3 % | 97.1 % | 93.0 % | 0.91 | 0.99 |
| MES | 95.0 ± 0.3 % | 93.2 % | 96.1 % | 87.2 % | 0.90 | 0.99 |
| LAR | 98.8 ± 0.2 % | 100.0 % | 98.8 % | 94.6 % | 0.97 | 1.00 |
Pipeline: supervised ML — Gaussian-kernel SVM (fitcsvm), per-feature
standardization, BoxConstraint 1, 5-fold stratified CV. Reproduced with a
faithful re-implementation of that exact model in scikit-learn (StandardScaler
→ SVC(kernel='rbf', C=1, gamma=1/KernelScale²)), which the brief permits as an
equally-valid third-party reproduction. MATLAB/Octave are not available on the
«our HPC» modules, so a bit-exact fitcsvm rerun is not attempted; the sklearn RBF
SVM is the documented mathematical equivalent (MATLAB gaussian kernel
exp(−‖x−z‖²) on x/KernelScale ⇒ sklearn gamma = 1/KernelScale²).
OUT OF SCOPE (not attempted, why)
- DEG selection / the 719-gene signature derivation (limma-style DE across 7 GEO datasets → up-regulated subtype-specific genes). The shipped xlsx already encode the final 719-gene predictor set, so the feature-selection upstream is not re-derived. Out of scope as upstream-of-the-shipped-artifact.
- Independent test cohort (334 samples) predictions & the 19.76 % "unclassified" rate. The test-cohort expression matrix is not shipped in the repo; would require re-assembling 6 additional GEO series + re-normalization (the hard ~20 %). Skipped per the 80/20 rule.
- The other 6 algorithm families (KNN, DT, LDA, logistic, naïve Bayes, ensembles) compared in the paper — only the selected SVM per subtyp
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
Clean, near-1:1 reproduction on the authors' side. The repo ships the exact GSE76124-derived training tables and the fitcsvm model spec; structural counts (198; 54/60/47/37; 719 genes) reproduce exactly and all four headline accuracies land within ~1 pp with correct rank order and AUCs within 0.01 — no fabrication signal, every value derivable from shipped data+code. The only non-trivial deviations are two high-variance single-split per-class sensitivities (MES 93.2→83.0, LAR 100→94.6), which sit on our side (a scikit-learn re-implementation of the MATLAB models plus stochastic fold partitions), not the authors'. Central conclusion fully holds; graded solid-with-explainable-deviations rather than flawless because of the sensitivity gaps and the unattempted DEG derivation / 334-sample test cohort / 6 other algorithms.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.