Connectivity Network Feature Sharing in Single-Cell RNA Sequencing Data Identifies Rare Cells.

Single-cell RNA sequencing is a valuable technique for identifying diverse cell subtypes. A key challenge in this process is that the detection of rare cells is often missed by conventional methods due to low abundance and subtle features of these cells. To overcome this, we developed SCLCNF (Local Connectivity Network Feature Sharing in Single-Cell RNA sequencing), a novel approach that identifies rare cells by analyzing features uniquely expressed in these cells.

MOSGAT: Uniting Specificity-Aware GATs and Cross Modal-Attention to Integrate Multi-Omics Data for Disease Diagnosis.

With the advancement of sequencing methodologies, the acquisition of vast amounts of multi-omics data presents a significant opportunity for comprehending the intricate biological mechanisms underlying diseases and achieving precise diagnosis and treatment for complex disorders. However, as diverse omics data are integrated, extracting sample-specific features within each omics modality and exploring potential correlations among different modalities while avoiding mutual interference becomes a critical challenge in multi-omics data integration research. In the context of this study, we proposed a framework that unites specificity-aware GATs and cross-modal attention to integrate different omics data (MOSGAT).

Heterogeneous graph inference with range constrainted L-collaborative matrix factorization for small molecule-miRNA association prediction.

MicroRNAs (miRNAs) play a vital role in regulating gene expression and various biological processes. As a result, they have been identified as effective targets for small molecule (SM) drugs in disease treatment. Heterogeneous graph inference stands as a classical approach for predicting SM-miRNA associations, showcasing commendable convergence accuracy and speed.

CHL-DTI: A Novel High-Low Order Information Convergence Framework for Effective Drug-Target Interaction Prediction.

Recognizing drug-target interactions (DTI) stands as a pivotal element in the expansive field of drug discovery. Traditional biological wet experiments, although valuable, are time-consuming and costly as methods. Recently, computational methods grounded in network learning have demonstrated great advantages by effective topological feature extraction and attracted extensive research attention.

scSID: A lightweight algorithm for identifying rare cell types by capturing differential expression from single-cell sequencing data.

Single-cell RNA sequencing (scRNA-seq) is currently an important technology for identifying cell types and studying diseases at the genetic level. Identifying rare cell types is biologically important as one of the downstream data analyses of single-cell RNA sequencing. Although rare cell identification methods have been developed, most of these suffer from insufficient mining of intercellular similarities, low scalability, and being time-consuming.

Identifying potential small molecule-miRNA associations via Robust PCA based on γ-norm regularization.

Dysregulation of microRNAs (miRNAs) is closely associated with refractory human diseases, and the identification of potential associations between small molecule (SM) drugs and miRNAs can provide valuable insights for clinical treatment. Existing computational techniques for inferring potential associations suffer from limitations in terms of accuracy and efficiency. To address these challenges, we devise a novel predictive model called RPCA$\Gamma $NR, in which we propose a new Robust principal component analysis (PCA) framework based on $\gamma $-norm and $l_{2,1}$-norm regularization and design an Augmented Lagrange Multiplier method to optimize it, thereby deriving the association scores.

Cross-domain policy adaptation with dynamics alignment.

The implementation of robotic reinforcement learning is hampered by problems such as an unspecified reward function and high training costs. Many previous works have used cross-domain policy transfer to obtain the policy of the problem domain. However, these researches require paired and aligned dynamics trajectories or other interactions with the environment.

Generative Adversarial Matrix Completion Network based on Multi-Source Data Fusion for miRNA-Disease Associations Prediction.

Numerous biological studies have shown that considering disease-associated micro RNAs (miRNAs) as potential biomarkers or therapeutic targets offers new avenues for the diagnosis of complex diseases. Computational methods have gradually been introduced to reveal disease-related miRNAs. Considering that previous models have not fused sufficiently diverse similarities, that their inappropriate fusion methods may lead to poor quality of the comprehensive similarity network and that their results are often limited by insufficiently known associations, we propose a computational model called Generative Adversarial Matrix Completion Network based on Multi-source Data Fusion (GAMCNMDF) for miRNA-disease association prediction.

Predicting potential small molecule-miRNA associations utilizing truncated schatten p-norm.

MicroRNAs (miRNAs) have significant implications in diverse human diseases and have proven to be effectively targeted by small molecules (SMs) for therapeutic interventions. However, current SM-miRNA association prediction models do not adequately capture SM/miRNA similarity. Matrix completion is an effective method for association prediction, but existing models use nuclear norm instead of rank function, which has some drawbacks.

scASGC: An adaptive simplified graph convolution model for clustering single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) is now a successful technique for identifying cellular heterogeneity, revealing novel cell subpopulations, and forecasting developmental trajectories. A crucial component of the processing of scRNA-seq data is the precise identification of cell subpopulations. Although many unsupervised clustering methods have been developed to cluster cell subpopulations, the performance of these methods is vulnerable to dropouts and high dimensionality.

DETHACDA: A Dual-View Edge and Topology Hybrid Attention Model for CircRNA-Disease Associations Prediction.

There exists growing evidence that circRNAs are concerned with many complex diseases physiological processes and pathogenesis and may serve as critical therapeutic targets. Identifying disease-associated circRNAs through biological experiments is time-consuming, and designing an intelligent, precise calculation model is essential. Recently, many models based on graph technology have been proposed to predict circRNA-disease association.

AMCSMMA: Predicting Small Molecule-miRNA Potential Associations Based on Accurate Matrix Completion.

Exploring potential associations between small molecule drugs (SMs) and microRNAs (miRNAs) is significant for drug development and disease treatment. Since biological experiments are expensive and time-consuming, we propose a computational model based on accurate matrix completion for predicting potential SM-miRNA associations (AMCSMMA). Initially, a heterogeneous SM-miRNA network is constructed, and its adjacency matrix is taken as the target matrix.

MSGNN-DTA: Multi-Scale Topological Feature Fusion Based on Graph Neural Networks for Drug-Target Binding Affinity Prediction.

The accurate prediction of drug-target binding affinity (DTA) is an essential step in drug discovery and drug repositioning. Although deep learning methods have been widely adopted for DTA prediction, the complexity of extracting drug and target protein features hampers the accuracy of these predictions. In this study, we propose a novel model for DTA prediction named MSGNN-DTA, which leverages a fused multi-scale topological feature approach based on graph neural networks (GNNs).

SPReCHD: Four-Chamber Semantic Parsing Network for Recognizing Fetal Congenital Heart Disease in Medical Metaverse.

Echocardiography is essential for evaluating cardiac anatomy and function during early recognition and screening for congenital heart disease (CHD), a widespread and complex congenital malformation. However, fetal CHD recognition still faces many difficulties due to instinctive fetal movements, artifacts in ultrasound images, and distinctive fetal cardiac structures. These factors hinder capturing robust and discriminative representations from ultrasound images, resulting in CHD's low prenatal detection rate.

HSSG: Identification of Cancer Subtypes Based on Heterogeneity Score of A Single Gene.

Cancer is a highly heterogeneous disease, which leads to the fact that even the same cancer can be further classified into different subtypes according to its pathology. With the multi-omics data widely used in cancer subtypes identification, effective feature selection is essential for accurately identifying cancer subtypes. However, the feature selection in the existing cancer subtypes identification methods has the problem that the most helpful features cannot be selected from a biomolecular perspective, and the relationship between the selected features cannot be reflected.

MSHGANMDA: Meta-Subgraphs Heterogeneous Graph Attention Network for miRNA-Disease Association Prediction.

MicroRNAs (miRNAs) influence several biological processes involved in human disease. Biological experiments for verifying the association between miRNA and disease are always costly in terms of both money and time. Although numerous biological experiments have identified multi-types of associations between miRNAs and diseases, existing computational methods are unable to sufficiently mine the knowledge in these associations to predict unknown associations.

A Pseudo-Siamese Feature Fusion Generative Adversarial Network for Synthesizing High-Quality Fetal Four-Chamber Views.

Four-chamber (FC) views are the primary ultrasound(US) images that cardiologists diagnose whether the fetus has congenital heart disease (CHD) in prenatal diagnosis and screening. FC views intuitively depict the developmental morphology of the fetal heart. Early diagnosis of fetal CHD has always been the focus and difficulty of prenatal screening.

AMDE: a novel attention-mechanism-based multidimensional feature encoder for drug-drug interaction prediction.

The properties of the drug may be altered by the combination, which may cause unexpected drug-drug interactions (DDIs). Prediction of DDIs provides combination strategies of drugs for systematic and effective treatment. In most of deep learning-based methods for predicting DDI, encoded information about the drugs is insufficient in some extent, which limits the performances of DDIs prediction.

EOESGC: predicting miRNA-disease associations based on embedding of embedding and simplified graph convolutional network.

Background: A large number of biological studies have shown that miRNAs are inextricably linked to many complex diseases. Studying the miRNA-disease associations could provide us a root cause understanding of the underlying pathogenesis in which promotes the progress of drug development. However, traditional biological experiments are very time-consuming and costly.

FLDS: An Intelligent Feature Learning Detection System for Visualizing Medical Images Supporting Fetal Four-Chamber Views.

Fetal congenital heart disease (CHD) is the most common type of fatal congenital malformation. Fetal four-chamber (FC) view is a significant and easily accessible ultrasound (US) image among fetal echocardiography images. Automatic detection of four fetal heart chambers considerably contributes to the early diagnosis of fetal CHD.

PESM: A novel approach of tumor purity estimation based on sample specific methylation sites.

Tumor purity is of great significance for the study of tumor genotyping and the prediction of recurrence, which is significantly affected by tumor heterogeneity. Tumor heterogeneity is the basis of drug resistance in various cancer treatments, and DNA methylation plays a core role in the generation of tumor heterogeneity. Almost all types of cancer cells are associated with abnormal DNA methylation in certain regions of the genome.

PEIS: a novel approach of tumor purity estimation by identifying information sites through integrating signal based on DNA methylation data.

Background: Tumor purity plays an important role in understanding the pathogenic mechanism of tumors. The purity of tumor samples is highly sensitive to tumor heterogeneity. Due to Intratumoral heterogeneity of genetic and epigenetic data, it is suitable to study the purity of tumors.

An artificial intelligent diagnostic system on mobile Android terminals for cholelithiasis by lightweight convolutional neural network.

Artificial intelligence (AI) tools have been applied to diagnose or predict disease risk from medical images with recent data disclosure actions, but few of them are designed for mobile terminals due to the limited computational power and storage capacity of mobile devices. In this work, a novel AI diagnostic system is proposed for cholelithiasis recognition on mobile devices with Android platform. To this aim, a data set of CT images of cholelithiasis is firstly collected from The Third Hospital of Shandong Province, China, and then we technically use histogram equalization to preprocess these CT images.

A novel YOLOv3-arch model for identifying cholelithiasis and classifying gallstones on CT images.

Locating diseases precisely from medical images, like ultrasonic and CT images, have been one of the most challenging problems in medical image analysis. In recent years, the vigorous development of deep learning models have greatly improved the accuracy in disease location on medical images. However, there are few artificial intelligent methods for identifying cholelithiasis and classifying gallstones on CT images, since no open source CT images dataset of cholelithiasis and gallstones is available for training the models and verifying their performance.