OmniLatent-TCGA-BRCA-model

Year: 2025–Present
License: MIT
Author: Sepideh Moafi

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OmniLatent — Deep Representation Learning for TCGA-BRCA Transcriptomic Data

Model Description

OmniLatent is a deep autoencoder framework for learning compact, biologically meaningful latent representations from high-dimensional transcriptomic data.

The model was developed as part of the OmniLatent research project, which explores nonlinear representation learning for cancer genomics and precision medicine.

The model compresses genome-wide gene-expression profiles into a low-dimensional latent space, enabling downstream analysis such as clustering, visualization, and pattern discovery.

Model Details

• Model type: Stacked autoencoder
• Framework: PyTorch
• Latent dimension: 128
• Input dimension: 23,375 gene-expression features
• Dimensionality reduction: 99.5%
• Test reconstruction loss: 0.3129
• Format: PyTorch (best_model.pt)
• License: MIT

Intended Use

The model is intended for:

• Representation learning on bulk RNA-seq data
• Dimensionality reduction of transcriptomic profiles
• Clustering and visualization of cancer transcriptomes
• Research on cancer genomics and precision medicine
• Reproducible computational biology experiments

The model is not intended for clinical diagnosis, treatment decisions, or direct clinical use.

Training Data

• Dataset: TCGA-BRCA RNA-seq
• Samples: 1,231
• Genes: 23,375

Training

The model was trained as part of the OmniLatent research workflow. The associated project includes:

• End-to-end reproducible transcriptomic pipeline (data acquisition, preprocessing, gene filtering, normalization, QC)
• Stacked autoencoder architecture
• Latent space characterized via PCA, UMAP, and clustering
• Reproducible implementation and released research artifacts

Evaluation

Evaluation should be interpreted as research-model evaluation rather than clinical validation.

• Test reconstruction loss: 0.3129
• Latent space: 128-dimensional (99.5% reduction)

Performance depends on the downstream task and dataset. The model should be independently evaluated before use in downstream research applications.

Limitations

• Trained specifically on TCGA-BRCA data; may not generalize to other cancer types or datasets without retraining.
• Not validated for clinical decision-making.
• Latent representations should be interpreted with domain knowledge.
• Biological patterns identified in the latent space should be independently verified.

Ethical and Safety Considerations

This model is released for research and educational purposes. It should not be used as a substitute for professional medical or clinical expertise.

For applications involving human health data, outputs should be reviewed and independently verified by qualified researchers.

Reproducibility

Related resources:

• Model: Sepideh2027/OmniLatent-TCGA-BRCA-model
• Dataset: Sepideh2027/biolatent-brca-tcga

Citation

If you use this model in research, please cite the associated OmniLatent research output.

Contact

Sepideh Moafi
GitHub: AIResearcher20
Hugging Face: Sepideh2027