scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning.

Cell type annotation is a critical step in analyzing single-cell RNA sequencing (scRNA-seq) data. A large number of deep learning (DL)-based methods have been proposed to annotate cell types of scRNA-seq data and have achieved impressive results. However, there are several limitations to these methods.

AER-Net: Attention-Enhanced Residual Refinement Network for Nuclei Segmentation and Classification in Histology Images.

The acurate segmentation and classification of nuclei in histological images are crucial for the diagnosis and treatment of colorectal cancer. However, the aggregation of nuclei and intra-class variability in histology images present significant challenges for nuclei segmentation and classification. In addition, the imbalance of various nuclei classes exacerbates the difficulty of nuclei classification and segmentation using deep learning models.

DGNMDA: Dual Heterogeneous Graph Neural Network Encoder for miRNA-Disease Association Prediction.

In recent years, numerous studies have highlighted the pivotal importance of miRNAs in personalized healthcare, showcasing broad application prospects. miRNAs hold significant potential in disease diagnosis, prognosis assessment, and therapeutic target discovery, making them an integral part of precision medicine. They are expected to enable precise disease subtyping and risk prediction, thereby advancing the development of precision medicine.

iAmyP: A Multi-view Learning for Amyloidogenic Hexapeptides Identification Based on Sequence Least Squares Programming.

The development of peptide drug is hindered by the risk of amyloidogenic aggregation; if peptides tend to aggregate in this manner, they may be unsuitable for drug design. Computational methods aimed at predicting amyloidogenic sequences often face challenges in extracting high-quality features, and their predictive performance can be enchanced. To surmount these challenges, iAmyP was introduced as a specialized computational tool designed for predicting amyloidogenic hexapeptides.

Enhancing Spatial Domain Identification in Spatially Resolved Transcriptomics Using Graph Convolutional Networks with Adaptively Feature-Spatial Balance and Contrastive Learning.

Recent advancements in spatially transcriptomics (ST) technologies have enabled the comprehensive measurement of gene expression profiles while preserving the spatial information of cells. Combining gene expression profiles and spatial information has been the most commonly used method to identify spatial functional domains and genes. However, most existing spatial domain decipherer methods are more focused on spatially neighboring structures and fail to take into account balancing the self-characteristics and the spatial structure dependency of spots.

MLRR-ATV: A Robust Manifold Nonnegative LowRank Representation with Adaptive Total-Variation Regularization for scRNA-seq Data Clustering.

Since genomics was proposed, the exploration of genes has been the focus of research. The emergence of single-cell RNA sequencing (scRNA-seq) technology makes it possible to explore gene expression at the single-cell level. Due to the limitations of sequencing technology, the data contains a lot of noise.

Adaptive Space Search-based Molecular Evolution Optimization Algorithm.

Motivation: In drug development process, a significant portion of budget and research time are dedicated to the lead compound optimization procedure in order to identify potential drugs. This procedure focuses on enhancing the pharmacological and bioactive properties of compounds by optimizing their local substructures. However, due to the vast and discrete chemical structure space and the unpredictable element combinations within this space, the optimization process is inherently complex.

MEFFGRN: Matrix enhancement and feature fusion-based method for reconstructing the gene regulatory network of epithelioma papulosum cyprini cells by spring viremia of carp virus infection.

Gene regulatory networks (GRNs) are crucial for understanding organismal molecular mechanisms and processes. Construction of GRN in the epithelioma papulosum cyprini (EPC) cells of cyprinid fish by spring viremia of carp virus (SVCV) infection helps understand the immune regulatory mechanisms that enhance the survival capabilities of cyprinid fish. Although many computational methods have been used to infer GRNs, specialized approaches for predicting the GRN of EPC cells following SVCV infection are lacking.

Inference of gene regulatory networks based on directed graph convolutional networks.

Inferring gene regulatory network (GRN) is one of the important challenges in systems biology, and many outstanding computational methods have been proposed; however there remains some challenges especially in real datasets. In this study, we propose Directed Graph Convolutional neural network-based method for GRN inference (DGCGRN). To better understand and process the directed graph structure data of GRN, a directed graph convolutional neural network is conducted which retains the structural information of the directed graph while also making full use of neighbor node features.

Evolutionary Multiobjective Molecule Optimization in an Implicit Chemical Space.

Optimization techniques play a pivotal role in advancing drug development, serving as the foundation of numerous generative methods tailored to efficiently design optimized molecules derived from existing lead compounds. However, existing methods often encounter difficulties in generating diverse, novel, and high-property molecules that simultaneously optimize multiple drug properties. To overcome this bottleneck, we propose a multiobjective molecule optimization framework (MOMO).

Dissecting Spatiotemporal Structures in Spatial Transcriptomics via Diffusion-Based Adversarial Learning.

Recent advancements in spatial transcriptomics (ST) technologies offer unprecedented opportunities to unveil the spatial heterogeneity of gene expression and cell states within tissues. Despite these capabilities of the ST data, accurately dissecting spatiotemporal structures (e.g.

A Novel Skip-Connection Strategy by Fusing Spatial and Channel Wise Features for Multi-Region Medical Image Segmentation.

Recent methods often introduce attention mechanisms into the skip connections of U-shaped networks to capture features. However, these methods usually overlook spatial information extraction in skip connections and exhibit inefficiency in capturing spatial and channel information. This issue prompts us to reevaluate the design of the skip-connection mechanism and propose a new deep-learning network called the Fusing Spatial and Channel Attention Network, abbreviated as FSCA-Net.

scVSC: Deep Variational Subspace Clustering for Single-Cell Transcriptome Data.

Single-cell RNA sequencing (scRNA-seq) is a potent advancement for analyzing gene expression at the individual cell level, allowing for the identification of cellular heterogeneity and subpopulations. However, it suffers from technical limitations that result in sparse and heterogeneous data. Here, we propose scVSC, an unsupervised clustering algorithm built on deep representation neural networks.

DMA-HPCNet: Dual Multi-Level Attention Hybrid Pyramid Convolution Neural Network for Alzheimer's Disease Classification.

Computer-aided diagnosis (CAD) plays a crucial role in the clinical application of Alzheimer's disease (AD). In particular, convolutional neural network (CNN)-based methods are highly sensitive to subtle changes caused by brain atrophy in medical images (e.g.

UsIL-6: An unbalanced learning strategy for identifying IL-6 inducing peptides by undersampling technique.

Background And Objective: Interleukin-6 (IL-6) is the critical factor of early warning, monitoring, and prognosis in the inflammatory storm of COVID-19 cases. IL-6 inducing peptides, which can induce cytokine IL-6 production, are very important for the development of diagnosis and immunotherapy. Although the existing methods have some success in predicting IL-6 inducing peptides, there is still room for improvement in the performance of these models in practical application.

AMPFLDAP: Adaptive Message Passing and Feature Fusion on Heterogeneous Network for LncRNA-Disease Associations Prediction.

Exploration of the intricate connections between long noncoding RNA (lncRNA) and diseases, referred to as lncRNA-disease associations (LDAs), plays a pivotal and indispensable role in unraveling the underlying molecular mechanisms of diseases and devising practical treatment approaches. It is imperative to employ computational methods for predicting lncRNA-disease associations to circumvent the need for superfluous experimental endeavors. Graph-based learning models have gained substantial popularity in predicting these associations, primarily because of their capacity to leverage node attributes and relationships within the network.

DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding.

The inference of gene regulatory networks (GRNs) from gene expression profiles has been a key issue in systems biology, prompting many researchers to develop diverse computational methods. However, most of these methods do not reconstruct directed GRNs with regulatory types because of the lack of benchmark datasets or defects in the computational methods. Here, we collect benchmark datasets and propose a deep learning-based model, DeepFGRN, for reconstructing fine gene regulatory networks (FGRNs) with both regulation types and directions.