Recently, low-rank tensor recovery methods based on subspace representation have received increased attention in the field of hyperspectral image (HSI) denoising. Unfortunately, those methods usually analyze the prior structural information within different dimensions indiscriminately, ignoring the differences between modes, leaving substantial room for improvement. In this article, we first consider the low-rank properties in the subspace and prove that the structure correlation across the nonlocal self-similarity mode is much stronger than in the spatial sparsity and spectral correlation modes. On that basis, we introduce a new multidirectional low-rank regularization, in which each mode is assigned a different weight to characterize its contribution to estimating the tensor rank. After that, integrating the proposed regularization with the subspace-based tensor recovery framework, an optimization model for HSI mixed noise removal is developed. The proposed model can be addressed efficiently via the alternating minimization algorithm. Extensive experiments implemented with synthetic and real data demonstrate that the proposed method significantly outperforms other state-of-the-art HSI denoising methods, which clearly indicates the effectiveness of the proposed approach in HSI denoising.

Path-planning for uninhabited combat air vehicles (UCAV) is a typically complicated global optimization problem. It seeks a superior flight path in a complex battlefield environment, taking into various constraints. Many swarm intelligence (SI) algorithms have recently gained remarkable attention due to their capability to address complex optimization problems. However, different SI algorithms present various performances for UCAV path-planning since each algorithm has its own strengths and weaknesses. Therefore, this study provides an overview of different SI algorithms for UCAV path-planning research. In the experiment, twelve algorithms that published in major journals and conference proceedings are surveyed and then applied to UCAV path-planning. Moreover, to demonstrate the performance of different algorithms in further, we design different scales of problem cases for those comparative algorithms. The experimental results show that UCAV can find the safe path to avoid the threats efficiently based on most SI algorithms. In particular, the Spider Monkey Optimization is more effective and robust than other algorithms in handling the UCAV path-planning problem. The analysis from different perspectives contributes to highlight trends and open issues in the field of UCAVs.

Single-cell ATAC-seq technology advances our understanding of single-cell heterogeneity in gene regulation by enabling exploration of epigenetic landscapes and regulatory elements. However, low sequencing depth per cell leads to data sparsity and high dimensionality, limiting the characterization of gene regulatory elements. Here, we develop scAGDE, a single-cell chromatin accessibility model-based deep graph representation learning method that simultaneously learns representation and clustering through explicit modeling of data generation. Our evaluations demonstrated that scAGDE outperforms existing methods in cell segregation, key marker identification, and visualization across diverse datasets while mitigating dropout events and unveiling hidden chromatin-accessible regions. We find that scAGDE preferentially identifies enhancer-like regions and elucidates complex regulatory landscapes, pinpointing putative enhancers regulating the constitutive expression of CTLA4 and the transcriptional dynamics of CD8A in immune cells. When applied to human brain tissue, scAGDE successfully annotated cis-regulatory element-specified cell types and revealed functional diversity and regulatory mechanisms of glutamatergic neurons.

Proteins and nucleic-acids are essential components of living organisms that interact in critical cellular processes. Accurate prediction of nucleic acid-binding residues in proteins can contribute to a better understanding of protein function. However, the discrepancy between protein sequence information and obtained structural and functional data renders most current computational models ineffective. Therefore, it is vital to design computational models based on protein sequence information to identify nucleic acid binding sites in proteins. Here, we implement an ensemble deep learning model-based nucleic-acid-binding residues on proteins identification method, called SOFB, which characterizes protein sequences by learning the semantics of biological dynamics contexts, and then develop an ensemble deep learning-based sequence network to learn feature representation and classification by explicitly modeling dynamic semantic information. Among them, the language learning model, which is constructed from natural language to biological language, captures the underlying relationships of protein sequences, and the ensemble deep learning-based sequence network consisting of different convolutional layers together with Bi-LSTM refines various features for optimal performance. Meanwhile, to address the imbalanced issue, we adopt ensemble learning to train multiple models and then incorporate them. Our experimental results on several DNA/RNA nucleic-acid-binding residue datasets demonstrate that our proposed model outperforms other state-of-the-art methods. In addition, we conduct an interpretability analysis of the identified nucleic acid binding residue sequences based on the attention weights of the language learning model, revealing novel insights into the dynamic semantic information that supports the identified nucleic acid binding residues. SOFB is available at https://github.com/Encryptional/SOFB and https://figshare.com/articles/online_resource/SOFB_figshare_rar/25499452.

Motivation: Predicting RNA-binding proteins (RBPs) is central to understanding post-transcriptional regulatory mechanisms. Here, we introduce EnrichRBP, an automated and interpretable computational platform specifically designed for the comprehensive analysis of RBP interactions with RNA. Results: EnrichRBP is a web service that enables researchers to develop original deep learning and machine learning architectures to explore the complex dynamics of RBPs. The platform supports 70 deep learning algorithms, covering feature representation, selection, model training, comparison, optimization, and evaluation, all integrated within an automated pipeline. EnrichRBP is adept at providing comprehensive visualizations, enhancing model interpretability, and facilitating the discovery of functionally significant sequence regions crucial for RBP interactions. In addition, EnrichRBP supports base-level functional annotation tasks, offering explanations and graphical visualizations that confirm the reliability of the predicted RNA-binding sites. Leveraging high-performance computing, EnrichRBP provides ultra-fast predictions ranging from seconds to hours, applicable to both pre-trained and custom model scenarios, thus proving its utility in real-world applications. Case studies highlight that EnrichRBP provides robust and interpretable predictions, demonstrating the power of deep learning in the functional analysis of RBP interactions. Finally, EnrichRBP aims to enhance the reproducibility of computational method analyses for RBP sequences, as well as reduce the programming and hardware requirements for biologists, thereby offering meaningful functional insights. Availability and implementation: EnrichRBP is available at https://airbp.aibio-lab.com/. The source code is available at https://github.com/wangyb97/EnrichRBP, and detailed online documentation can be found at https://enrichrbp.readthedocs.io/en/latest/.