GeNetFormer: Transformer-Based Framework for Gene Expression Prediction in Breast Cancer
Bibliographic record
Abstract
Background: Histopathological images are often used to diagnose breast cancer and have shown high accuracy in classifying cancer subtypes. Prediction of gene expression from whole-slide images and spatial transcriptomics data is important for cancer treatment in general and breast cancer in particular. This topic has been a challenge in numerous studies. Method: In this study, we present a deep learning framework called GeNetFormer. We evaluated eight advanced transformer models including EfficientFormer, FasterViT, BEiT v2, and Swin Transformer v2, and tested their performance in predicting gene expression using the STNet dataset. This dataset contains 68 H&E-stained histology images and transcriptomics data from different types of breast cancer. We followed a detailed process to prepare the data, including filtering genes and spots, normalizing stain colors, and creating smaller image patches for training. The models were trained to predict the expression of 250 genes using different image sizes and loss functions. GeNetFormer achieved the best performance using the MSELoss function and a resolution of 256 × 256 while integrating EfficientFormer. Results: It predicted nine out of the top ten genes with a higher Pearson Correlation Coefficient (PCC) compared to the retrained ST-Net method. For cancer biomarker genes such as DDX5 and XBP1, the PCC values were 0.7450 and 0.7203, respectively, outperforming ST-Net, which scored 0.6713 and 0.7320, respectively. In addition, our method gave better predictions for other genes such as FASN (0.7018 vs. 0.6968) and ERBB2 (0.6241 vs. 0.6211). Conclusions: Our results show that GeNetFormer provides improvements over other models such as ST-Net and show how transformer architectures are capable of analyzing spatial transcriptomics data to advance cancer research.
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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 | 0.001 |
| 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 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
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.
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".