With the ongoing advancements in science and technology and the increasing research focus on cancer-related issues, there has been a proliferation of omics-related resources for in-depth analysis and exploration. This burgeoning volume and complexity of biological data have fostered the integration of machine-learning techniques into biology. As a result, numerous machine-learning strategies have been established to identify driver mutations. Yet, many of these strategies produce complex models, complicating comprehension and thereby clouding the impact of input features on the resulting predictions. Our analysis presented the CIXG framework, which integrates a driver gene prediction module using XGBoost with a causality interpretation module anchored on CXPlain. This architecture enables quantifying each input feature’s contribution to the prediction outcome and ensures precise predictions of driver genes. When benchmarked against the state-of-the-art (SOTA) method, CIXG demonstrated superior accuracy in pinpointing driver genes across pan-cancer studies and within the 32 specific cancer types. Importantly, our results underscored that mutation features chiefly influence CIXG’s predictive prowess, with additional support from other omics features.

Advancements in single-cell multi-omics sequencing technologies have dramatically transformed the analysis of cellular states at single-cell resolution. Cluster analyses leveraging single-cell transcriptome and epigenome data have enabled the characterization of cellular states and the delineation of transcriptomic regulatory programs associated with cellular heterogeneity. However, the high dimensionality, sparsity, and heterogeneity inherent to multi-omics data present significant challenges to their clustering analysis. In this study, we introduced single-cell Multi-Omics Generative Adversarial Networks (scMOGAN), an unsupervised clustering model specifically tailored for single-cell transcriptome and epigenome data. scMOGAN accomplishes this by efficaciously modeling the omics data and mining potential features through neural networks, ultimately utilizing Gaussian mixture models for cell type identification. To validate and scrutinize the performance of scMOGAN, we performed analyses on two actual multi-omics datasets and one simulated dataset. The results demonstrate that scMOGAN surpasses other existing methods in terms of clustering performance, underscoring its efficacy in navigating the complexities of multi-omics data.

Genomic variants, which can disrupt cellular functions, present a challenge in distinguishing deleterious from benign instances. While assessing genome-wide functional impacts, many current algorithms neglect protein tertiary structure of coding region variants due to limitations in protein structural prediction. This study introduces PMMVar, an advanced multimodal deep convolutional network, which adeptly integrates protein tertiary structures with conservation properties from ESM-2, supplemented by other protein structural sequences. PMMVar achieves outstanding performance on the latest clinical variant datasets, NCBI ClinVar (2023), and the Mendelian variant dataset, surpassing existing benchmarks. Ablation analyses validate the significance of protein multi-level structures in enhancing the model’s accuracy. Overall, our findings spotlight the essential role of multi-level protein structures in pathogenicity predictions and their potential to discern deleterious genomic variants effectively.

Hepatocellular Carcinoma (HCC) holds a record of high incidence and severe global harm. In tasks of liver cancer segmentation based on 3D medical images, the majority of methods have endeavored to enhance the 3D U-net by integrating the latest modules from the field of Computer Vision (such as the transformer), often overlooking the distinct characteristics of liver components. We introduced a novel deep learning architecture, Modif-SegUnet, to circumvent this limitation. This architecture extends the U-net model by incorporating a 3D-modifiable attention module, thereby fostering a heightened focus on distinguishing between normal liver sections and lesions. Furthermore, Modif-SegUnet ingeniously amalgamates the 3D-modifiable attention module with the Modif-transformer block, enabling efficient capture of relevant and valuable full-text information in CT images that contain liver or tumor regions. We subjected the proposed Modif-SegUnet to evaluation on the Liver Tumor Segmentation benchmark dataset. Experimental outcomes indicate that our methodology surpasses state-of-the-art approaches in liver tumor segmentation, suggesting potential pathways for advancing the diagnosis and treatment of liver cancer.

The COVID-19 pandemic has had a profound impact on human society. It has highlighted the need for faster diagnostic methods. Research has shown that combining semantic segmentation with traditional medical approaches can significantly accelerate the process. To address this, leveraging COVID-19 CT images, our team designs a revolutionary semantic segmentation model called Level of Detail Enhancement U-Net (LDE-UNet), which shows the lesion area on CT images. By introducing the LDE block, the model has the unique advantage of overcoming the loss of data details during the downsampling process by emphasizing and transmitting details at the same level. Our SOTA model outperforms the second-best model by at least 0.7% in the most critical indicator precision. Compared with other models, LDE-UNet’s strong reliability determines its ability to be used in the medical field to accelerate the localization and division of lesion areas on CT images by professional doctors, thus completing patient diagnosis faster. In addition, we also propose a standardized method for processing medical images.

Cancer survival prediction is pivotal in tailoring individualized treatment strategies and guiding clinician decision-making. Yet, existing methodologies grapple with efficiently harnessing the intricate distribution of medical data spanning various modalities. In response, we present SAMMS, an advanced multi-omics multimodal deep learning framework tailored for survival prediction. SAMMS leverages the robust image segmentation model, "Segment Anything" to adeptly characterize pathological images. This prowess is further enhanced by integrating multi-omics data and clinical insights, facilitating holistic modeling across a diverse modal spectrum. The framework weaves a modality-specific subnetwork with a cross-modality common subnetwork, meticulously capturing intra-modality nuances and inter-modality correlations. SAMMS eclipsed its contemporaries by delivering remarkable performance on TCGA’s LGG and KIRC tumor datasets. A battery of analyses underscored SAMMS’s unparalleled capability to distill multifaceted insights from multimodal datasets, yielding richer and more integrative multimodal representations. Such strides promise significant advancements in cancer survival analytics, bolstering the precision and efficacy of patient-centric treatments, disease oversight, and clinical decision processes.

The grim situation of novel coronavirus pneumonia 2019 (COVID-19) and its terrible spreading speed have already constituted a severe risk to human life, so it is ultimately essential to rapidly and accurately diagnose for COVID-19 pneumonia. Based on this study’s 746 lung CT images, we propose Multi-MedVit, a novel auxiliary COVID-19 diagnosis framework based on the multi-input Transformer. We compare Multi-MedVit with state-of-the-art deep learning methods, such as CNN, VGG16, and ResNet50. Multi-MedVit outperformed the other methods on the benchmark dataset and proved that multiscale data input for data augmentation helped enhance model stability. Based on an interpretable analysis of the input and output of Multi-MedVit, we found that with the support of the training set data, the model has been possible to accurately focus on the lesion area for diagnosis of COVID-19 without expert annotations, which can provide initial references containing more potential information to doctors more precisely and fleetly.