With the rising incidence of breast cancer among women, Neoadjuvant Chemotherapy (NAC) is becoming increasingly crucial as a preoperative treatment modality, enabling tumor downstaging and volume reduction. However, its efficacy varies significantly among patients, underscoring the importance of predicting Pathological Complete Response (pCR) following NAC. Early research relied on statistical methods to integrate clinical data for predicting treatment outcomes. With the advent of artificial intelligence (AI), traditional machine learning approaches were subsequently employed for efficacy prediction. Deep learning emerged to dominate this field, and demonstrated the capability to automatically extract imaging features and integrate multimodal data for pCR prediction. This review comprehensively examined the applications and limitations of these three methodologies in predicting breast cancer pCR. Future efforts must prioritize the development of superior predictive models to achieve precise predictions, integrate them into clinical workflows, enhance patient care, and ultimately improve therapeutic outcomes and quality of life.
O6-carboxymethyl guanine(O6-CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant Mycobacterium smegmatis porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machine learning technology has been widely used in the analysis of nanopore sequencing data. But the machine learning always need a large number of data labels that have brought extra work burden to researchers, which greatly affects its practicability. Accordingly, this paper proposes a nano-Unsupervised-Deep-Learning method (nano-UDL) based on an unsupervised clustering algorithm to identify methylation events in nanopore data automatically. Specially, nano-UDL first uses the deep AutoEncoder to extract features from the nanopore dataset and then applies the MeanShift clustering algorithm to classify data. Besides, nano-UDL can extract the optimal features for clustering by joint optimizing the clustering loss and reconstruction loss. Experimental results demonstrate that nano-UDL has relatively accurate recognition accuracy on the O6-CMG dataset and can accurately identify all sequence segments containing O6-CMG. In order to further verify the robustness of nano-UDL, hyperparameter sensitivity verification and ablation experiments were carried out in this paper. Using machine learning to analyze nanopore data can effectively reduce the additional cost of manual data analysis, which is significant for many biological studies, including genome sequencing.