With the continuous development of digital agriculture and intelligent forestry, the demand for three-dimensional modeling of trees or plants using agricultural robots is also increasing. Laser radar technology has gradually become an important technical means for agricultural robots to obtain three-dimensional information about trees. When using laser radar to scan trees, incomplete point cloud data are often obtained due to leaf occlusion, visual angle limitation, or operation error, which leads to quality degradation of the subsequent 3D modeling and quantitative analysis of trees. At present, a lot of research work has been carried out in the direction of point cloud completion, in which the deep learning model is the mainstream solution. However, the existing deep learning models have mainly been applied to urban scene completion or the point cloud completion of indoor regularized objects, and the research objects generally have obvious continuity and symmetry characteristics. There has been no relevant research on the point cloud completion method for objects with obvious individual morphological differences, such as trees. Therefore, this paper proposes a single-tree point cloud completion method based on feature fusion. This method uses PointNet, based on point structure, to extract the global features of trees, and EdgeConv, based on graph structure, to extract the local features of trees. After integrating global and local features, FoldingNet is used to realize the generation of a complete point cloud. Compared to other deep learning methods on the open source data set, the CD index using this method increased by 21.772% on average, and the EMD index increased by 15.672% on average, which proves the effectiveness of the method in this paper and provides a new solution for agricultural robots to obtain three-dimensional information about trees.

A growing number of studies have shown that aberrant microRNA (miRNA) expression is closely associated with the evolution and development of various complex human diseases. These key biomarkers’ identification and observation are significant for gaining a deeper understanding of disease pathogenesis and therapeutic mechanisms. Consequently, pinpointing potential miRNA–disease associations (MDA) has become a prominent bioinformatics subject, encouraging several new computational methods given the advances in graph neural networks (GNN). Nevertheless, these existing methods commonly fail to exploit the network nodes’ global feature information, leaving the generation of high-quality embedding representations using graph properties as a critical unsolved issue. Addressing these challenges, we introduce the DAEMDA, a computational method designed to optimize the current models’ efficacy. First, we construct similarity and heterogeneous networks involving miRNAs and diseases, relying on experimentally corroborated miRNA–disease association data and analogous information. Then, a newly-fashioned parallel dual-channel feature encoder, designed to better comprehend the global information within the heterogeneous network and generate varying embedding representations, follows this. Ultimately, employing a neural network classifier, we merge the dual-channel embedding representations and undertake association predictions between miRNA and disease nodes. The experimental results of five-fold cross-validation and case studies of major diseases based on the HMDD v3.2 database show that this method can generate high-quality embedded representations and effectively improve the accuracy of MDA prediction.

In recent times, airborne and terrestrial laser scanning have been utilized to collect point cloud data for forest resource surveys, aiding in the estimation of tree and stand attributes over hectare-scale plots. In this study, an automated approach was devised to estimate the diameter at breast height (DBH) and tree height across the entire sample area, utilizing information acquired from terrestrial laser scanning (TLS) and airborne laser scanning (ULS). Centered around a meticulously managed artificial forest in Northern China, where Mongolian oak and Chinese Scots pine are the predominant species, both TLS and ULS operations were conducted concurrently on each plot. Subsequent to data collection, a detailed processing of the point cloud data was carried out, introducing an innovative algorithm to facilitate the matching of individual tree point clouds from ULS and TLS sources. To enhance the accuracy of DBH estimation, a weighted regression correction equation based on TLS data was introduced. The estimations obtained for the Chinese Scots pine plots showed a correlation of R2 = 0.789 and a root mean square error (RMSE) of 3.2 cm, while for the Mongolian oak plots, an improved correlation of R2 = 0.761 and a RMSE of 3.1 cm was observed between predicted and measured values. This research significantly augments the potential for non-destructive estimations of tree structural parameters on a hectare scale by integrating TLS and ULS technologies. The advancements hold paramount importance in the domain of large-scale forest surveys, particularly in the calibration and validation of aboveground biomass (AGB) estimations.

Protein secondary structure prediction (PSSP) plays a crucial role in resolving protein functions and properties. Significant progress has been made in this field in recent years, and the use of a variety of protein-related features, including amino acid sequences, position-specific score matrices (PSSM), amino acid properties, and secondary structure trend factors, to improve prediction accuracy is an important technical route for it. However, a comprehensive evaluation of the impact of these factor features in secondary structure prediction is lacking in the current work. This study quantitatively analyzes the impact of several major factors on secondary structure prediction models using a more explanatory four-class machine learning approach. The applicability of each factor in the different types of methods, the extent to which the different methods work on each factor, and the evaluation of the effect of multi-factor combinations are explored in detail. Through experiments and analyses, it was found that PSSM performs best in methods with strong high-dimensional features and complex feature extraction capabilities, while amino acid sequences, although performing poorly overall, perform relatively well in methods with strong linear processing capabilities. Also, the combination of amino acid properties and trend factors significantly improved the prediction performance. This study provides empirical evidence for future researchers to optimize multi-factor feature combinations and apply them to protein secondary structure prediction models, which is beneficial in further optimizing the use of these factors to enhance the performance of protein secondary structure prediction models.

Background: Protein secondary structure prediction (PSSP) is a critical task in computational biology, pivotal for understanding protein function and advancing medical diagnostics. Recently, approaches that integrate multiple amino acid sequence features have gained significant attention in PSSP research. Objectives: We aim to automatically extract additional features represented by evolutionary information from a large number of sequences while simultaneously incorporating positional information for more comprehensive sequence features. Additionally, we consider the interdependence between secondary structures during the prediction stage. Methods: To this end, we propose a deep neural network model, ILMCNet, which utilizes a language model and Conditional Random Field (CRF). Protein language models (PLMs) pre-trained on sequences from multiple large databases can provide sequence features that incorporate evolutionary information. ILMCNet uses positional encoding to ensure that the input features include positional information. To better utilize these features, we propose a hybrid network architecture that employs a Transformer Encoder to enhance features and integrates a feature extraction module combining a Convolutional Neural Network (CNN) with a Bidirectional Long Short-Term Memory Network (BiLSTM). This design enables deep extraction of localized features while capturing global bidirectional information. In the prediction stage, ILMCNet employs CRF to capture the interdependencies between secondary structures. Results: Experimental results on benchmark datasets such as CB513, TS115, NEW364, CASP11, and CASP12 demonstrate that the prediction performance of our method surpasses that of comparable approaches. Conclusions: This study proposes a new approach to PSSP research and is expected to play an important role in other protein-related research fields, such as protein tertiary structure prediction.

Peptide binders, serving as a critical drug modality bridging small-molecule compounds and protein macromolecules, can effectively mimic the secondary structural elements of natural proteins. Peptides exhibit unique physicochemical advantages when targeting protein protein interaction (PPI) interfaces, which are typically characterized by flat surfaces and extensive contact areas. Recently, diffusion models represented by RFdiffusion have established a new computational paradigm for protein backbone generation by defining a denoising process over the rigid-body transformation group. However, in the de novo design of binders targeting “undruggable” PPI targets, this general paradigm encounters significant adaptability bottlenecks. First, its underlying rigid-body assumption struggles to accurately describe the dynamic induced-fit process of peptides at the binding interface. Second, it lacks sufficient robustness to the experimental resolution heterogeneity inherent in training data. Furthermore, the decoupled two-stage generation of sequence and structure severs the synergy of physicochemical properties, leading to backbones with idealized, singular secondary structures that lack authentic spatial binding capacity and reasonable side-chain physicochemical features. To address these challenges, this study proposes PPI-Diff, a novel generative framework. While preserving the generative capability of diffusion models, PPI-Diff introduces three core mechanisms: (1) a resolution-aware constraint mechanism that maps the measurement precision of experimental data into explicit contextual constraints to dynamically suppress geometric noise from low-resolution samples; (2) an internal-coordinate-driven manifold diffusion model that performs conformational evolution on a Riemannian manifold constructed by dihedral angles, balancing local stereochemical validity with the precise capture of flexible peptide conformations; and (3) a geometry-semantic synergistic modeling mechanism that leverages the evolutionary embeddings of a pre-trained protein language model (ESM-2) as latent variables to align structure generation with biophysical functions. Systematic benchmarking demonstrates that, on a strictly non-homologous test set, the binders generated by PPI-Diff significantly outperform existing baseline models in terms of interface contact density, stereochemical validity, and sequence novelty.