Integrating deep learning for accurate gastrointestinal cancer classification: a comprehensive analysis of MSI and MSS patterns using histopathology data

Abstract

AbstractEarly detection of microsatellite instability (MSI) and microsatellite stability (MSS) is crucial in the fight against gastrointestinal (GI) cancer. MSI is a sign of genetic instability often associated with DNA repair mechanism deficiencies, which can cause (GI) cancers. On the other hand, MSS signifies genomic stability in microsatellite regions. Differentiating between these two states is pivotal in clinical decision-making as it provides prognostic and predictive information and treatment strategies. Rapid identification of MSI and MSS enables oncologists to tailor therapies more accurately, potentially saving patients from unnecessary treatments and guiding them toward regimens with the highest likelihood of success. Detecting these microsatellite status markers at an initial stage can improve patient outcomes and quality of life in GI cancer management. Our research paper introduces a cutting-edge method for detecting early GI cancer using deep learning (DL). Our goal is to identify the optimal model for GI cancer detection that surpasses previous works. Our proposed model comprises four stages: data acquisition, image processing, feature extraction, and classification. We use histopathology images from the Cancer Genome Atlas (TCGA) and Kaggle website with some modifications for data acquisition. In the image processing stage, we apply various operations such as color transformation, resizing, normalization, and labeling to prepare the input image for enrollment in our DL models. We present five different DL models, including convolutional neural networks (CNNs), a hybrid of CNNs-simple RNN (recurrent neural network), a hybrid of CNNs with long short-term memory (LSTM) (CNNs-LSTM), a hybrid of CNNs with gated recurrent unit (GRU) (CNNs-GRU), and a hybrid of CNNs-SimpleRNN-LSTM-GRU. Our empirical results demonstrate that CNNs-SimpleRNN-LSTM-GRU outperforms other models in accuracy, specificity, recall, precision, AUC, and F1, achieving an accuracy of 99.90%. Our proposed methodology offers significant improvements in GI cancer detection compared to recent techniques, highlighting the potential of DL-based approaches for histopathology data. We expect our findings to inspire future research in DL-based GI cancer detection.