Thyroid Cancer Staging Prediction System Based on RNA-seq and Machine Learning

This article introduces a binary classification system for thyroid cancer built using RNA sequencing (RNA-seq) data and machine learning techniques, aiming to achieve automated cancer staging prediction. The system covers key technical steps including data preprocessing, dimensionality reduction, differential gene expression analysis, SMOTE sample balancing, and neural network classification, providing molecular-level support for the precise staging of thyroid cancer.

Thyroid cancer is the most common endocrine system malignancy globally, with an increasing incidence rate, especially ranking among the top in women. Early accurate staging is crucial for treatment plan formulation and prognosis evaluation. Traditional staging relies on pathological and imaging examinations, which have subjectivity and limitations; RNA-seq technology provides a new perspective for cancer molecular typing, enabling the identification of biomarkers related to progression and facilitating precision medicine.

The classification system built in this project integrates bioinformatics and deep learning technologies. Its core modules include: data preprocessing (quality control, standardization, filtering low-expression genes), dimensionality reduction analysis (PCA, t-SNE), differential gene expression analysis, SMOTE sample balancing strategy, and neural network classifier, forming a complete process from raw data to prediction results.

RNA-seq data preprocessing requires standardization (such as TPM, FPKM, or DESeq2 size factor) to eliminate systematic biases, and filtering low-expression genes to reduce noise. In terms of feature processing, key genes related to staging are screened through differential gene expression analysis; PCA is used to retain main variation information, and t-SNE is used to visualize the local structure of samples, alleviating the curse of dimensionality caused by high-dimensional data.

Medical data often has class imbalance (more early-stage samples than late-stage ones), leading the classifier to be biased towards the majority class. The SMOTE algorithm effectively alleviates the imbalance problem and improves the ability to identify late-stage cancer by interpolating and synthesizing minority class samples in the feature space (finding K-nearest neighbors and randomly selecting points along the lines connecting them).

A fully connected neural network is used as the classifier, leveraging its nonlinear modeling ability to learn gene expression patterns. The architecture design considers input dimensions and sample size, introducing Dropout regularization and early stopping to prevent overfitting; ReLU (hidden layers) and Sigmoid (output layer) are selected as activation functions, the loss function is binary cross-entropy, and hyperparameters are optimized through cross-validation.

Challenges and Solutions: Data quality issues (batch effects, noise) are mitigated through quality control and batch correction; model interpretability is addressed by analyzing gene contributions using SHAP values or attention mechanisms; sample size limitations are handled via SMOTE augmentation and regularization. Application Prospects: Assisting pathologists in objective staging and supporting personalized treatment; in the future, it will integrate single-cell sequencing, multi-omics fusion, and federated learning to improve prediction accuracy and data sharing efficiency.