Comparative Analysis of Multi-Omics Integration Using Advanced Graph Neural Networks for Cancer Classification

Multi-omics data is increasingly being utilized to advance computational methods for cancer classification. However, multi-omics data integration poses significant challenges due to the high dimensionality, data complexity, and distinct characteristics of various omics types. This study addresses these challenges and evaluates three graph neural network architectures for multi-omics (MO) integration based on graph-convolutional networks (GCN), graph-attention networks (GAT), and graph-transformer networks (GTN) for classifying 31 cancer types and normal tissues. To address the high-dimensionality of multi-omics data, we employed LASSO (Least Absolute Shrinkage and Selection Operator) regression for feature selection, leading to the creation of LASSO-MOGCN, LASSO-MOGAT, and LASSO-MOTGN models. Graph structures for the networks were constructed using gene correlation matrices and protein-protein interaction networks for multi-omics integration of messenger-RNA, micro-RNA, and DNA methylation data. Such data integration enables the networks to dynamically focus on important relationships between biological entities, improving both model performance and interpretability. Among the models, LASSO-MOGAT with a correlation-based graph structure achieved state-of-the-art accuracy (95.9%) and outperformed the LASSO-MOGCN and LASSO-MOTGN models in terms of precision, recall, and F1-score. Our findings demonstrate that integrating multi-omics data in graph-based architectures enhances cancer classification performance by uncovering distinct molecular patterns that contribute to a better understanding of cancer biology and potential biomarkers for disease progression.

LASSO-MOGAT: A Multi-Omics Graph Attention Framework for Cancer Classification

The application of machine learning methods to analyze changes in gene expression patterns has recently emerged as a powerful approach in cancer research, enhancing our understanding of the molecular mechanisms underpinning cancer development and progression. Combining gene expression data with other types of omics data has been reported by numerous works to improve cancer classification outcomes. Despite these advances, effectively integrating high-dimensional multi-omics data and capturing the complex relationships across different biological layers remains challenging. This paper introduces LASSO-MOGAT (LASSO-Multi-Omics Gated ATtention), a novel graph-based deep learning framework that integrates messenger RNA, microRNA, and DNA methylation data to classify 31 cancer types. Utilizing differential expression analysis with LIMMA and LASSO regression for feature selection, and leveraging Graph Attention Networks (GATs) to incorporate protein-protein interaction (PPI) networks, LASSO-MOGAT effectively captures intricate relationships within multi-omics data. Experimental validation using five-fold cross-validation demonstrates the method's precision, reliability, and capacity for providing comprehensive insights into cancer molecular mechanisms. The computation of attention coefficients for the edges in the graph by the proposed graph-attention architecture based on protein-protein interactions proved beneficial for identifying synergies in multi-omics data for cancer classification.

A2DMN: Anatomy-Aware Dilated Multiscale Network for Breast Ultrasound Semantic Segmentation

In recent years, convolutional neural networks for semantic segmentation of breast ultrasound (BUS) images have shown great success; however, two major challenges still exist. 1) Most current approaches inherently lack the ability to utilize tissue anatomy, resulting in misclassified image regions. 2) They struggle to produce accurate boundaries due to the repeated down-sampling operations. To address these issues, we propose a novel breast anatomy-aware network for capturing fine image details and a new smoothness term that encodes breast anatomy. It incorporates context information across multiple spatial scales to generate more accurate semantic boundaries. Extensive experiments are conducted to compare the proposed method and eight state-of-the-art approaches using a BUS dataset with 325 images. The results demonstrate the proposed method significantly improves the segmentation of the muscle, mammary, and tumor classes and produces more accurate fine details of tissue boundaries.

Uncertainty Quantification in Multivariable Regression for Material Property Prediction with Bayesian Neural Networks

With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including the multi-scale and multi-physics nature of advanced materials, intricate interactions between numerous factors, limited availability of large curated datasets for model training, etc. Recently, Bayesian Neural Networks (BNNs) have emerged as a promising approach for UQ, offering a probabilistic framework for capturing uncertainties within neural networks. In this work, we introduce an approach for UQ within physics-informed BNNs, which integrates knowledge from governing laws in material modeling to guide the models toward physically consistent predictions. To evaluate the effectiveness of this approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of collected measurements from creep tests demonstrates the ability of BNNs to produce accurate point and uncertainty estimates that are competitive or exceed the performance of the conventional method of Gaussian Process Regression. Similarly, we evaluated the suitability of BNNs for UQ in an active learning application and reported competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs. The codes are available at: https://github.com/avakanski/Creep-uncertainty-quantification.

Review of Machine Learning Methods for Additive Manufacturing of Functionally Graded Materials

Additive manufacturing has revolutionized the manufacturing of complex parts by enabling direct material joining and offers several advantages such as cost-effective manufacturing of complex parts, reducing manufacturing waste, and opening new possibilities for manufacturing automation. One group of materials for which additive manufacturing holds great potential for enhancing component performance and properties is Functionally Graded Materials (FGMs). FGMs are advanced composite materials that exhibit smoothly varying properties making them desirable for applications in aerospace, automobile, biomedical, and defense industries. Such composition differs from traditional composite materials, since the location-dependent composition changes gradually in FGMs, leading to enhanced properties. Recently, machine learning techniques have emerged as a promising means for fabrication of FGMs through optimizing processing parameters, improving product quality, and detecting manufacturing defects. This paper first provides a brief literature review of works related to FGM fabrication, followed by reviewing works on employing machine learning in additive manufacturing, Afterward, we provide an overview of published works in the literature related to the application of machine learning methods in Directed Energy Deposition and for fabrication of FGMs.

Post-Hoc Explainability of BI-RADS Descriptors in a Multi-task Framework for Breast Cancer Detection and Segmentation

Despite recent medical advancements, breast cancer remains one of the most prevalent and deadly diseases among women. Although machine learning-based Computer-Aided Diagnosis (CAD) systems have shown potential to assist radiologists in analyzing medical images, the opaque nature of the best-performing CAD systems has raised concerns about their trustworthiness and interpretability. This paper proposes MT-BI-RADS, a novel explainable deep learning approach for tumor detection in Breast Ultrasound (BUS) images. The approach offers three levels of explanations to enable radiologists to comprehend the decision-making process in predicting tumor malignancy. Firstly, the proposed model outputs the BI-RADS categories used for BUS image analysis by radiologists. Secondly, the model employs multi-task learning to concurrently segment regions in images that correspond to tumors. Thirdly, the proposed approach outputs quantified contributions of each BI-RADS descriptor toward predicting the benign or malignant class using post-hoc explanations with Shapley Values.

Breast Ultrasound Tumor Classification Using a Hybrid Multitask CNN-Transformer Network

Capturing global contextual information plays a critical role in breast ultrasound (BUS) image classification. Although convolutional neural networks (CNNs) have demonstrated reliable performance in tumor classification, they have inherent limitations for modeling global and long-range dependencies due to the localized nature of convolution operations. Vision Transformers have an improved capability of capturing global contextual information but may distort the local image patterns due to the tokenization operations. In this study, we proposed a hybrid multitask deep neural network called Hybrid-MT-ESTAN, designed to perform BUS tumor classification and segmentation using a hybrid architecture composed of CNNs and Swin Transformer components. The proposed approach was compared to nine BUS classification methods and evaluated using seven quantitative metrics on a dataset of 3,320 BUS images. The results indicate that Hybrid-MT-ESTAN achieved the highest accuracy, sensitivity, and F1 score of 82.7%, 86.4%, and 86.0%, respectively.

Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review

Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early detection of cancer, as it is indicative of the biochemical processes in tissue and cells, as well as the genetic characteristics of an organism. Deoxyribonucleic Acid (DNA) microarrays and Ribonucleic Acid (RNA)- sequencing methods for gene expression data allow quantifying the expression levels of genes and produce valuable data for computational analysis. This study reviews recent progress in gene expression analysis for cancer classification using machine learning methods. Both conventional and deep learning-based approaches are reviewed, with an emphasis on the ap-plication of deep learning models due to their comparative advantages for identifying gene patterns that are distinctive for various types of cancers. Relevant works that employ the most commonly used deep neural network architectures are covered, including multi-layer perceptrons, convolutional, recurrent, graph, and transformer networks. This survey also presents an overview of the data collection methods for gene expression analysis and lists important datasets that are commonly used for supervised machine learning for this task. Furthermore, reviewed are pertinent techniques for feature engineering and data preprocessing that are typically used to handle the high dimensionality of gene expression data, caused by a large number of genes present in data samples. The paper concludes with a discussion of future research directions for machine learning-based gene expression analysis for cancer classification.

Enhanced Sharp-GAN For Histopathology Image Synthesis

Histopathology image synthesis aims to address the data shortage issue in training deep learning approaches for accurate cancer detection. However, existing methods struggle to produce realistic images that have accurate nuclei boundaries and less artifacts, which limits the application in downstream tasks. To address the challenges, we propose a novel approach that enhances the quality of synthetic images by using nuclei topology and contour regularization. The proposed approach uses the skeleton map of nuclei to integrate nuclei topology and separate touching nuclei. In the loss function, we propose two new contour regularization terms that enhance the contrast between contour and non-contour pixels and increase the similarity between contour pixels. We evaluate the proposed approach on the two datasets using image quality metrics and a downstream task (nuclei segmentation). The proposed approach outperforms Sharp-GAN in all four image quality metrics on two datasets. By integrating 6k synthetic images from the proposed approach into training, a nuclei segmentation model achieves the state-of-the-art segmentation performance on TNBC dataset and its detection quality (DQ), segmentation quality (SQ), panoptic quality (PQ), and aggregated Jaccard index (AJI) is 0.855, 0.863, 0.691, and 0.683, respectively.

SIAN: Style-Guided Instance-Adaptive Normalization for Multi-Organ Histopathology Image Synthesis

Existing deep networks for histopathology image synthesis cannot generate accurate boundaries for clustered nuclei and cannot output image styles that align with different organs. To address these issues, we propose a style-guided instance-adaptive normalization (SIAN) to synthesize realistic color distributions and textures for different organs. SIAN contains four phases, semantization, stylization, instantiation, and modulation. The four phases work together and are integrated into a generative network to embed image semantics, style, and instance-level boundaries. Experimental results demonstrate the effectiveness of all components in SIAN, and show that the proposed method outperforms the state-of-the-art conditional GANs for histopathology image synthesis using the Frechet Inception Distance (FID), structural similarity Index (SSIM), detection quality(DQ), segmentation quality(SQ), and panoptic quality(PQ). Furthermore, the performance of a segmentation network could be significantly improved by incorporating synthetic images generated using SIAN.