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Liver cancer is the main malignancy in terms of mortality rate, accurate diagnosis can help the treatment outcome of liver cancer. Patient similarity network is an important information which helps in cancer diagnosis. However, recent works rarely take patient similarity into consideration. To address this issue, we constructed patient similarity network using three liver cancer omics data, and proposed a novel liver cancer diagnosis method consisted of similarity network fusion, denoising autoencoder and dense graph convolutional neural network to capitalize on patient similarity network and multi omics data. We compared our proposed method with other state-of-the-art methods and machine learning methods on TCGA-LIHC dataset to evaluate its performance. The results confirmed that our proposed method surpasses these comparison methods in terms of all the metrics. Especially, our proposed method has attained an accuracy up to 0.9857.

Accurate identification of topologically associated domains (TADs), the basic units of 3D genomes, is crucial for deciphering gene regulatory mechanisms. Existing methods rely mostly on Hi-C pairwise contact signals, and struggle to extract synergistic interactions among multiple loci, limiting boundary accuracy. In contrast, multiway chromatin interaction data can overcome the limitations of binary interactions by directly capturing high-order interactions that occur simultaneously across multiple regions, thereby providing critical data support for a more comprehensive analysis of three-dimensional chromatin organization.This study proposes HyperDeepTAD: which involves constructing hypergraphs from multiway chromatin interaction data to retain high-order information, inputting transition probability matrices into dynamic convolutional networks to capture local features, obtaining candidate boundaries via BiGRU and residual connections, screening with hypergraph clustering coefficients and using cosine similarity to obtain hierarchical TADs. Experiments show it that outperforms Hi-C-based methods in metrics such as boundary enrichment. The source code is available from https://github.com/liukaihua0213-source/HyperDeepTAD .

Due to the presence of irrelevant or redundant data in microarray datasets, capturing potential patterns accurately and directly via existing models is difficult. Feature selection (FS) has become a necessary strategy to identify and screen out the most relevant attributes. However, the high dimensionality of microarray datasets poses a serious challenge to most existing FS algorithms. For this purpose, we propose a novel feature selection strategy in this paper, called IG-MBKH. A pre-screening method of feature ranking which is based on information gain (IG) and an improved binary krill herd (MBKH) algorithm are integrated in this strategy. When searching for feature subsets using MBKH, a hyperbolic tangent function, an adaptive transfer factor, and a chaos memory weight factor are introduced to facilitate a better searching the possible feature subsets. The results indicates that the IG-MBKH algorithm can achieve improvement in convergence, the number of features and classification accuracy when compared to the BKH, MBKH, and several newest algorithms. Furthermore, we evaluate the impact of different classifiers on the performance of the strategy we propose.

Background Chromatin loops are critical for the three-dimensional organization of the genome and gene regulation. Accurate identification of chromatin loops is essential for understanding the regulatory mechanisms in disease. However, current mainstream detection methods rely primarily on single-source data, such as Hi-C, which limits these methods’ ability to capture the diverse features of chromatin loop structures. In contrast, multi-source data integration and deep learning approaches, though not yet widely applied, hold significant potential. Results In this study, we developed a method called DconnLoop to integrate Hi-C, ChIP-seq, and ATAC-seq data to predict chromatin loops. This method achieves feature extraction and fusion of multi-source data by integrating residual mechanisms, directional connectivity excitation modules, and interactive feature space decoders. Finally, we apply density estimation and density clustering to the genome-wide prediction results to identify more representative loops. The code is available from https://github.com/kuikui-C/DconnLoop . Conclusions The results demonstrate that DconnLoop outperforms existing methods in both precision and recall. In various experiments, including Aggregate Peak Analysis and peak enrichment comparisons, DconnLoop consistently shows advantages. Extensive ablation studies and validation across different sequencing depths further confirm DconnLoop’s robustness and generalizability.

Background Obtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins and drugs still need to be further analyzed. Recently, deep learning has been successfully used in many fields. Hence, designing a more effective deep learning method for predicting DTA remains attractive. Results Dynamic graph DTA (DGDTA), which uses a dynamic graph attention network combined with a bidirectional long short-term memory (Bi-LSTM) network to predict DTA is proposed in this paper. DGDTA adopts drug compound as input according to its corresponding simplified molecular input line entry system (SMILES) and protein amino acid sequence. First, each drug is considered a graph of interactions between atoms and edges, and dynamic attention scores are used to consider which atoms and edges in the drug are most important for predicting DTA. Then, Bi-LSTM is used to better extract the contextual information features of protein amino acid sequences. Finally, after combining the obtained drug and protein feature vectors, the DTA is predicted by a fully connected layer. The source code is available from GitHub at https://github.com/luojunwei/DGDTA . Conclusions The experimental results show that DGDTA can predict DTA more accurately than some other methods.

Background Many studies have shown that structural variations (SVs) strongly impact human disease. As a common type of SV, insertions are usually associated with genetic diseases. Therefore, accurately detecting insertions is of great significance. Although many methods for detecting insertions have been proposed, these methods often generate some errors and miss some variants. Hence, accurately detecting insertions remains a challenging task. Results In this paper, we propose a method named INSnet to detect insertions using a deep learning network. First, INSnet divides the reference genome into continuous sub-regions and takes five features for each locus through alignments between long reads and the reference genome. Next, INSnet uses a depthwise separable convolutional network. The convolution operation extracts informative features through spatial information and channel information. INSnet uses two attention mechanisms, the convolutional block attention module (CBAM) and efficient channel attention (ECA) to extract key alignment features in each sub-region. In order to capture the relationship between adjacent subregions, INSnet uses a gated recurrent unit (GRU) network to further extract more important SV signatures. After predicting whether a sub-region contains an insertion through the previous steps, INSnet determines the precise site and length of the insertion. The source code is available from GitHub at https://github.com/eioyuou/INSnet . Conclusion Experimental results show that INSnet can achieve better performance than other methods in terms of F1 score on real datasets.

Animal pose estimation is crucial for animal health assessment, species protection, and behavior analysis. It is an inevitable and unstoppable trend to apply deep learning to animal pose estimation. In many practical application scenarios, pose estimation models must be deployed on edge devices with limited resource. Therefore, it is essential to strike a balance between model complexity and accuracy. To address this issue, we propose a lightweight network model, i.e., MPE-HRNet.[sup.L], by improving Lite-HRNet. The improvements are threefold. Firstly, we improve Spatial Pyramid Pooling-Fast and apply it and the improved version to different branches. Secondly, we construct a feature extraction module based on a mixed pooling module and a dual spatial and channel attention mechanism, and take the feature extraction module as the basic module of MPE-HRNet.[sup.L]. Thirdly, we introduce a feature enhancement stage to enhance important features. The experimental results on the AP-10K dataset and the Animal Pose dataset verify the effectiveness and efficiency of MPE-HRNet.[sup.L].

Remote sensing image scene classification holds significant application value and has long been a research hotspot in remote sensing. However, remote sensing images contain diverse objects and complex backgrounds. Reducing background interference while focusing on key target regions in the images remains a challenge, which limits the potential improvement of classification accuracy. In this paper, a local image generation module (LIGM) is proposed to generate weights for the original images. The resulting local images, generated by weighting the original images, effectively focus on key target regions while suppressing background regions. Based on the LIGM, a two-stream architecture with self-distillation and local streams (SDLS) is proposed. The self-distillation stream extracts features from the original images using a convolutional neural network (CNN) and two MobileNetV2 networks. Furthermore, a multiplex-guided attention (MGA) module is introduced into this stream to facilitate cross-network attention-guided learning between the CNN and MobileNetV2 features. In the local stream, a MobileNetV2 network is employed to extract features from the local images. The classification logits produced by the two streams are fused, resulting in the final SDLS classification score. Experimental results demonstrate that SDLS achieves competitive performance on multiple datasets.

Background The utilization of long reads for single nucleotide polymorphism (SNP) phasing has become popular, providing substantial support for research on human diseases and genetic studies in animals and plants. However, due to the complexity of the linkage relationships between SNP loci and sequencing errors in the reads, the recent methods still cannot yield satisfactory results. Results In this study, we present a graph-based algorithm, GCphase, which utilizes the minimum cut algorithm to perform phasing. First, based on alignment between long reads and the reference genome, GCphase filters out ambiguous SNP sites and useless read information. Second, GCphase constructs a graph in which a vertex represents alleles of an SNP locus and each edge represents the presence of read support; moreover, GCphase adopts a graph minimum-cut algorithm to phase the SNPs. Next, GCpahse uses two error correction steps to refine the phasing results obtained from the previous step, effectively reducing the error rate. Finally, GCphase obtains the phase block. GCphase was compared to three other methods, WhatsHap, HapCUT2, and LongPhase, on the Nanopore and PacBio long-read datasets. The code is available from https://github.com/baimawjy/GCphase . Conclusions Experimental results show that GCphase under different sequencing depths of different data has the least number of switch errors and the highest accuracy compared with other methods.

Motivation Studies have shown that classifying cancer subtypes can provide valuable information for a range of cancer research, from aetiology and tumour biology to prognosis and personalized treatment. Current methods usually adopt gene expression data to perform cancer subtype classification. However, cancer samples are scarce, and the high-dimensional features of their gene expression data are too sparse to allow most methods to achieve desirable classification results. Results In this paper, we propose a deep learning approach by combining a convolutional neural network (CNN) and bidirectional gated recurrent unit (BiGRU): our approach, DCGN, aims to achieve nonlinear dimensionality reduction and learn features to eliminate irrelevant factors in gene expression data. Specifically, DCGN first uses the synthetic minority oversampling technique algorithm to equalize data. The CNN can handle high-dimensional data without stress and extract important local features, and the BiGRU can analyse deep features and retain their important information; the DCGN captures key features by combining both neural networks to overcome the challenges of small sample sizes and sparse, high-dimensional features. In the experiments, we compared the DCGN to seven other cancer subtype classification methods using breast and bladder cancer gene expression datasets. The experimental results show that the DCGN performs better than the other seven methods and can provide more satisfactory classification results.