Multi-omics data integration is crucial for understanding complex diseases, yet limited sample sizes, noise, and heterogeneity often reduce predictive power. To address these challenges, we introduce Omics-GAN, a Generative Adversarial Network (GAN)-based framework designed to generate high-quality synthetic multi-omics profiles while preserving biological relationships. We evaluated Omics-GAN on three omics types (mRNA, miRNA, and DNA methylation) using the ROSMAP cohort for Alzheimer's disease (AD) and TCGA datasets for colon and liver cancer. A support vector machine (SVM) classifier with repeated 5-fold cross-validation demonstrated that synthetic datasets consistently improved prediction accuracy compared to original omics profiles. The AUC of SVM for mRNA improved from 0.72 to 0.74 in AD, and from 0.68 to 0.72 in liver cancer. Synthetic miRNA enhanced classification in colon cancer from 0.59 to 0.69, while synthetic methylation data improved performance in liver cancer from 0.64 to 0.71. Boxplot analyses confirmed that synthetic data preserved statistical distributions while reducing noise and outliers. Feature selection identified significant genes overlapping with original datasets and revealed additional candidates validated by GO and KEGG enrichment analyses. Finally, molecular docking highlighted potential drug repurposing candidates, including Nilotinib for AD, Atovaquone for liver cancer, and Tecovirimat for colon cancer. Omics-GAN enhances disease prediction, preserves biological fidelity, and accelerates biomarker and drug discovery, offering a scalable strategy for precision medicine applications.

Liver cancer is a leading cause of cancer-related mortality worldwide, with its high genetic heterogeneity complicating diagnosis and treatment. This study introduces DLSOM, a deep learning framework utilizing stacked autoencoders to analyze the complete somatic mutation landscape of 1,139 liver cancer samples, covering 20,356 protein-coding genes. By transforming high-dimensional mutation data into three low-dimensional features, DLSOM enables robust clustering and identifies five distinct liver cancer subtypes with unique mutational, functional, and biological profiles. Subtypes SC1 and SC2 exhibit higher mutational loads, while SC3 has the lowest, reflecting mutational heterogeneity. Novel and COSMIC-associated mutational signatures reveal subtype-specific molecular mechanisms, including links to hypermutation and chemotherapy resistance. Functional analyses further highlight the biological relevance of each subtype. This comprehensive framework advances precision medicine in liver cancer by enabling the development of subtype-specific diagnostics, biomarkers, and therapies, showcasing the potential of deep learning in addressing cancer complexity.

Background: Liver cancer ranks as the fifth most common malignant tumor and the second most fatal in our country. Early diagnosis is crucial, necessitating that physicians identify liver cancer in patients at the earliest possible stage. However, the diagnostic process is complex and demanding. Physicians must analyze a broad spectrum of patient data, encompassing physical condition, symptoms, medical history, and results from various examinations and tests, recorded in both structured and unstructured medical formats. This results in a significant workload for healthcare professionals. In response, integrating knowledge graph technology to develop a liver cancer knowledge graph-assisted diagnosis and treatment system aligns with national efforts toward smart healthcare. Such a system promises to mitigate the challenges faced by physicians in diagnosing and treating liver cancer. Methods: This paper addresses the major challenges in building a knowledge graph for hepatocellular carcinoma diagnosis, such as the discrepancy between public data sources and real electronic medical records, the effective integration of which remains a key issue. The knowledge graph construction process consists of six steps: conceptual layer design, data preprocessing, entity identification, entity normalization, knowledge fusion, and graph visualization. A novel Dynamic Entity Replacement and Masking Strategy (DERM) for named entity recognition is proposed. Results: A knowledge graph for liver cancer was established, including 7 entity types such as disease, symptom, and constitution, containing 1495 entities. The recognition accuracy of the model was 93.23%, the recall was 94.69%, and the F1 score was 93.96%.

The diagnosis of primary liver cancers (PLCs) can be challenging, especially on biopsies and for combined hepatocellular-cholangiocarcinoma (cHCC-CCA). We automatically classified PLCs on routine-stained biopsies using a weakly supervised learning method. Weak tumour/non-tumour annotations served as labels for training a Resnet18 neural network, and the network's last convolutional layer was used to extract new tumour tile features. Without knowledge of the precise labels of the malignancies, we then applied an unsupervised clustering algorithm. Our model identified specific features of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA). Despite no specific features of cHCC-CCA being recognized, the identification of HCC and iCCA tiles within a slide could facilitate the diagnosis of primary liver cancers, particularly cHCC-CCA. Method and results: 166 PLC biopsies were divided into training, internal and external validation sets: 90, 29 and 47 samples. Two liver pathologists reviewed each whole-slide hematein eosin saffron (HES)-stained image (WSI). After annotating the tumour/non-tumour areas, 256x256 pixel tiles were extracted from the WSIs and used to train a ResNet18. The network was used to extract new tile features. An unsupervised clustering algorithm was then applied to the new tile features. In a two-cluster model, Clusters 0 and 1 contained mainly HCC and iCCA histological features. The diagnostic agreement between the pathological diagnosis and the model predictions in the internal and external validation sets was 100% (11/11) and 96% (25/26) for HCC and 78% (7/9) and 87% (13/15) for iCCA, respectively. For cHCC-CCA, we observed a highly variable proportion of tiles from each cluster (Cluster 0: 5-97%; Cluster 1: 2-94%).

This paper presents a new approach for classifying 2D histopathology patches using few-shot learning. The method is designed to tackle a significant challenge in histopathology, which is the limited availability of labeled data. By applying a sliding window technique to histopathology slides, we illustrate the practical benefits of transductive learning (i.e., making joint predictions on patches) to achieve consistent and accurate classification. Our approach involves an optimization-based strategy that actively penalizes the prediction of a large number of distinct classes within each window. We conducted experiments on histopathological data to classify tissue classes in digital slides of liver cancer, specifically hepatocellular carcinoma. The initial results show the effectiveness of our method and its potential to enhance the process of automated cancer diagnosis and treatment, all while reducing the time and effort required for expert annotation.

Histopathological images are the gold standard for diagnosing liver cancer. However, the accuracy of fully digital diagnosis in computational pathology needs to be improved. In this paper, in order to solve the problem of multi-label and low classification accuracy of histopathology images, we propose a locally deep convolutional Swim framework (LDCSF) to classify multi-label histopathology images. In order to be able to provide local field of view diagnostic results, we propose the LDCSF model, which consists of a Swin transformer module, a local depth convolution (LDC) module, a feature reconstruction (FR) module, and a ResNet module. The Swin transformer module reduces the amount of computation generated by the attention mechanism by limiting the attention to each window. The LDC then reconstructs the attention map and performs convolution operations in multiple channels, passing the resulting feature map to the next layer. The FR module uses the corresponding weight coefficient vectors obtained from the channels to dot product with the original feature map vector matrix to generate representative feature maps. Finally, the residual network undertakes the final classification task. As a result, the classification accuracy of LDCSF for interstitial area, necrosis, non-tumor and tumor reached 0.9460, 0.9960, 0.9808, 0.9847, respectively. Finally, we use the results of multi-label pathological image classification to calculate the tumor-to-stromal ratio, which lays the foundation for the analysis of the microenvironment of liver cancer histopathological images. Second, we released a multilabel histopathology image of liver cancer, our code and data are available at https://github.com/panliangrui/LSF.

Tissue biomarkers are crucial for cancer diagnosis, prognosis assessment and treatment planning. However, there are few known biomarkers that are robust enough to show true analytical and clinical value. Deep learning (DL)-based computational pathology can be used as a strategy to predict survival, but the limited interpretability and generalizability prevent acceptance in clinical practice. Here we present an interpretable human-centric DL-guided framework called PathFinder (Pathological-biomarker-finder) that can help pathologists to discover new tissue biomarkers from well-performing DL models. By combining sparse multi-class tissue spatial distribution information of whole slide images with attribution methods, PathFinder can achieve localization, characterization and verification of potential biomarkers, while guaranteeing state-of-the-art prognostic performance. Using PathFinder, we discovered that spatial distribution of necrosis in liver cancer, a long-neglected factor, has a strong relationship with patient prognosis. We therefore proposed two clinically independent indicators, including necrosis area fraction and tumour necrosis distribution, for practical prognosis, and verified their potential in clinical prognosis according to criteria derived from the Reporting Recommendations for Tumor Marker Prognostic Studies. Our work demonstrates a successful example of introducing DL into clinical practice in a knowledge discovery way, and the approach may be adopted in identifying biomarkers in various cancer types and modalities. The potential of deep learning in pathological prognosis has been hampered by limited interpretability in clinical applications. Liang and colleagues present a human-centric deep learning framework that supports the discovery of prognostic biomarkers in an interpretable way.

A new study by Cedars-Sinai investigators describes how ChatGPT, an artificial intelligence (AI) chatbot, may help improve health outcomes for patients with cirrhosis and liver cancer by providing easy-to-understand information about basic knowledge, lifestyle and treatments for these conditions. The findings, published in the peer-reviewed journal Clinical and Molecular Hepatology, highlights the AI system's potential to play a role in clinical practice. "Patients with cirrhosis and/or liver cancer and their caregivers often have unmet needs and insufficient knowledge about managing and preventing complications of their disease," said Brennan Spiegel, MD, MSHS, director of Health Services Research at Cedars-Sinai and co-corresponding author of the study. "We found ChatGPT--while it has limitations--can help empower patients and improve health literacy for different populations." Patients diagnosed with liver cancer and cirrhosis, an end-stage liver disease that is also a major risk factor for the most common form of liver cancer, often require extensive treatment that can be complex and challenging to manage.

Artificial intelligence has developed a treatment for an aggressive form of cancer in just 30 days and demonstrated it can predict a patient's survival rate using doctors' notes. The breakthroughs were performed by separate systems, but show how the powerful technology's uses go far beyond the generation of images and text. University of Toronto researchers worked with Insilico Medicine to develop potential treatment for hepatocellular carcinoma (HCC) using an AI drug discovery platform called Pharma. HCC is a form of liver cancer, but the AI discovered a previously unknown treatment pathway and designed a'novel hit molecule' that could bind to that target. The system, which can also predict survival rate, is the invention of scientists from the University of British Columbia and B.C. Cancer, who found the model is 80 percent accurate.

Structure-based drug discovery (SBDD) is a standard method for identifying prospective medications for a target by leveraging its structural information. AlphaFold, a technique for predicting protein structure, has been regarded as a helpful resource for the discovery of therapeutics for new targets with low or no structural knowledge. In this study, the scientists utilized AlphaFold predictions as input for their AI-powered drug discovery engines (PandaOmics and Chemistry42) to efficiently identify a potential drug for CDK20 within 30 days. Understanding the structure of proteins is important in order to figure out their functions and the effect of change in amino acid sequence. The 3D structure of a protein allows us to visualize its functions and how genes and diseases are connected.