AI, Volume 6, Issue 1 (January 2025) – 2 articles

This study investigates the use of machine learning (ML) models combined with explainable artificial intelligence (XAI) techniques to identify the most influential genes in the classification of five recurrent cancer types in women: breast cancer (BRCA), lung adenocarcinoma (LUAD), thyroid cancer (THCA), ovarian cancer (OV), and colon adenocarcinoma (COAD). Gene expression data from RNA-seq, extracted from The Cancer Genome Atlas (TCGA), were used to train ML models, including decision trees (DTs), random forest (RF), and XGBoost (XGB), which achieved accuracies of 98.69%, 99.82%, and 99.37%, respectively. However, the challenges in this analysis included the high dimensionality of the dataset and the lack of transparency in the ML models. To mitigate these challenges, the SHAP (Shapley Additive Explanations) method was applied to generate a list of features, aiming to understand which characteristics influenced the models’ decision-making processes and, consequently, the prediction results for the five tumor types. The SHAP analysis identified 119, 80, and 10 genes for the RF, XGB, and DT models, respectively, totaling 209 genes, resulting in 172 unique genes. The new list, representing 0.8% of the original input features, is coherent and fully explainable, increasing confidence in the applied models. Additionally, the results suggest that the SHAP method can be effectively used as a feature selector in gene expression data. This approach not only enhances model transparency but also maintains high classification performance, highlighting its potential in identifying biologically relevant features that may serve as biomarkers for cancer diagnostics and treatment planning. Full article

Background: Integrating nonlinear behavior into the architecture of artificial neural networks is regarded as essential requirement to constitute their effectual learning capacity for solving complex tasks. This claim seems to be true for moderate-sized networks, i.e., with a lower double-digit number of layers. However, going deeper with neural networks regularly turns into destructive tendencies of gradual performance degeneration during training. To circumvent this degradation problem, the prominent neural architectures Residual Network and Highway Network establish skip connections with additive identity mappings between layers. Methods: In this work, we unify the mechanics of both architectures into Capsule Networks (CapsNet)s by showing their inherent ability to learn skip connections. As a necessary precondition, we introduce the concept of Adaptive Nonlinearity Gates (ANG)s which dynamically steer and limit the usage of nonlinear processing. We propose practical methods for the realization of ANGs including biased batch normalization, the Doubly-Parametric ReLU (D-PReLU) activation function, and Gated Routing (GR) dedicated to extremely deep CapsNets. Results: Our comprehensive empirical study using MNIST substantiates the effectiveness of our developed methods and delivers valuable insights for the training of very deep nets of any kind. The final experiments on Fashion-MNIST and SVHN demonstrate the potential of pure capsule-driven networks with GR. Full article