EMGP-Net: A Hybrid Deep Learning Architecture for Breast Cancer Gene Expression Prediction
Bibliographic record
Abstract
Background: The accurate prediction of gene expression is essential in breast cancer research. However, spatial transcriptomics technologies are usually too expensive. Recent studies have used whole-slide images combined with spatial transcriptomics data to predict breast cancer gene expression. To this end, we present EMGP-Net, a novel hybrid deep learning architecture developed by combining two state-of-the-art models, MambaVision and EfficientFormer. Method: EMGP-Net was first trained on the HER2+ dataset, containing data from eight patients using a leave-one-patient-out approach. To ensure generalizability, we conducted external validation and alternately trained EMGP-Net on the HER2+ dataset and tested it on the STNet dataset, containing data from 23 patients, and vice versa. We evaluated EMGP-Net’s ability to predict the expression of 250 selected genes. EMGP-Net mixes features from both models, and uses attention mechanisms followed by fully connected layers. Results: Our model outperformed both EfficientFormer and MambaVision, which were trained separately on the HER2+ dataset, achieving the highest PCC of 0.7903 for the PTMA gene, with the top 14 genes having PCCs greater than 0.7, including other important breast cancer biomarkers such as GNAS and B2M. The external validation showed that it also outperformed models that were retrained with our approach. Conclusions: The results of EMGP-Net were better than those of existing models, showing that the combination of advanced models is an effective strategy to improve performance in this task.
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 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 | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 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".