RAVAR: a curated repository for rare variant-trait associations.

Rare variants contribute significantly to the genetic causes of complex traits, as they can have much larger effects than common variants and account for much of the missing heritability in genome-wide association studies. The emergence of UK Biobank scale datasets and accurate gene-level rare variant-trait association testing methods have dramatically increased the number of rare variant associations that have been detected. However, no systematic collection of these associations has been carried out to date, especially at the gene level. To address the issue, we present the Rare Variant Association Repository (RAVAR), a comprehensive collection of rare variant associations. RAVAR includes 95 047 high-quality rare variant associations (76186 gene-level and 18 861 variant-level associations) for 4429 reported traits which are manually curated from 245 publications. RAVAR is the first resource to collect and curate published rare variant associations in an interactive web interface with integrated visualization, search, and download features. Detailed gene and SNP information are provided for each association, and users can conveniently search for related studies by exploring the EFO tree structure and interactive Manhattan plots. RAVAR could vastly improve the accessibility of rare variant studies. RAVAR is freely available for all users without login requirement at http://www.ravar.bio.

A novel method for drug-target interaction prediction based on graph transformers model.

BACKGROUND: Drug-target interactions (DTIs) prediction becomes more and more important for accelerating drug research and drug repositioning. Drug-target interaction network is a typical model for DTIs prediction. As many different types of relationships exist between drug and target, drug-target interaction network can be used for modeling drug-target interaction relationship. Recent works on drug-target interaction network are mostly concentrate on drug node or target node and neglecting the relationships between drug-target. RESULTS: We propose a novel prediction method for modeling the relationship between drug and target independently. Firstly, we use different level relationships of drugs and targets to construct feature of drug-target interaction. Then, we use line graph to model drug-target interaction. After that, we introduce graph transformer network to predict drug-target interaction. CONCLUSIONS: This method introduces a line graph to model the relationship between drug and target. After transforming drug-target interactions from links to nodes, a graph transformer network is used to accomplish the task of predicting drug-target interactions.

An Interval Iteration Based Multilevel Thresholding Algorithm for Brain MR Image Segmentation.

In this paper, we propose an interval iteration multilevel thresholding method (IIMT). This approach is based on the Otsu method but iteratively searches for sub-regions of the image to achieve segmentation, rather than processing the full image as a whole region. Then, a novel multilevel thresholding framework based on IIMT for brain MR image segmentation is proposed. In this framework, the original image is first decomposed using a hybrid L1 - L0 layer decomposition method to obtain the base layer. Second, we use IIMT to segment both the original image and its base layer. Finally, the two segmentation results are integrated by a fusion scheme to obtain a more refined and accurate segmentation result. Experimental results showed that our proposed algorithm is effective, and outperforms the standard Otsu-based and other optimization-based segmentation methods.

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments.

The assignment of secondary structure elements in proteins is a key step in the analysis of their structures and functions. We have developed an algorithm, SACF (secondary structure assignment based on Cα fragments), for secondary structure element (SSE) assignment based on the alignment of Cα backbone fragments with central poses derived by clustering known SSE fragments. The assignment algorithm consists of three steps: First, the outlier fragments on known SSEs are detected. Next, the remaining fragments are clustered to obtain the central fragments for each cluster. Finally, the central fragments are used as a template to make assignments. Following a large-scale comparison of 11 secondary structure assignment methods, SACF, KAKSI and PROSS are found to have similar agreement with DSSP, while PCASSO agrees with DSSP best. SACF and PCASSO show preference to reducing residues in N and C cap regions, whereas KAKSI, P-SEA and SEGNO tend to add residues to the terminals when DSSP assignment is taken as standard. Moreover, our algorithm is able to assign subtle helices (310-helix, π-helix and left-handed helix) and make uniform assignments, as well as to detect rare SSEs in ß-sheets or long helices as outlier fragments from other programs. The structural uniformity should be useful for protein structure classification and prediction, while outlier fragments underlie the structure-function relationship.

EHR-HGCN: An Enhanced Hybrid Approach for Text Classification Using Heterogeneous Graph Convolutional Networks in Electronic Health Records.

Text classification is a central part of natural language processing, with important applications in understanding the knowledge behind biomedical texts including electronic health records (EHR). In this article, we propose a novel heterogeneous graph convolutional network method for classifying EHR texts. Our method, called EHR-HGCN, is able to combine context-sensitive word and sentence embeddings with structural sentence-level and word-level relation information to perform text classification. EHR-HGCN reframes EHR text classification as a graph classification task to better capture structural information about the document using a heterogeneous graph. To mine contextual information from a document, EHR-HGCN first applies a bidirectional recurrent neural network (BiRNN) on word embeddings obtained via Global Vectors for word representation (GloVe) to obtain context-sensitive word-level and sentence-level embeddings. To mine structural relationships from the document, EHR-HGCN then constructs a heterogeneous graph over the word and sentence embeddings, where sentence-word and word-word relationships are represented by graph edges. Finally, a heterogeneous graph convolutional neural network is used to classify documents by their graph representation. We evaluate EHR-HGCN on a variety of standard text classification benchmarks and find that EHR-HGCN has higher accuracy and F1-score than other representative machine learning and deep learning methods. We also apply EHR-HGCN to the MedLit benchmark and find it performs with high accuracy and F1-score on the task of section classification in EHR texts. Our ablation experiments show that the heterogeneous graph construction and heterogeneous graph convolutional network are critical to the performance of EHR-HGCN.

Optimal variable identification for accurate detection of causal expression Quantitative Trait Loci with applications in heart-related diseases.

Gene expression plays a pivotal role in various diseases, contributing significantly to their mechanisms. Most GWAS risk loci are in non-coding regions, potentially affecting disease risk by altering gene expression in specific tissues. This expression is notably tissue-specific, with genetic variants substantially influencing it. However, accurately detecting the expression Quantitative Trait Loci (eQTL) is challenging due to limited heritability in gene expression, extensive linkage disequilibrium (LD), and multiple causal variants. The single variant association approach in eQTL analysis is limited by its susceptibility to capture the combined effects of multiple variants, and a bias towards common variants, underscoring the need for a more robust method to accurately identify causal eQTL variants. To address this, we developed an algorithm, CausalEQTL, which integrates L 0 +L 1 penalized regression with an ensemble approach to localize eQTL, thereby enhancing prediction performance precisely. Our results demonstrate that CausalEQTL outperforms traditional models, including LASSO, Elastic Net, Ridge, in terms of power and overall performance. Furthermore, analysis of heart tissue data from the GTEx project revealed that eQTL sites identified by our algorithm provide deeper insights into heart-related tissue eQTL detection. This advancement in eQTL mapping promises to improve our understanding of the genetic basis of tissue-specific gene expression and its implications in disease. The source code and identified causal eQTLs for CausalEQTL are available on GitHub: https://github.com/zhc-moushang/CausalEQTL.

Attention-aided lightweight networks friendly to smart weeding robot hardware resources for crops and weeds semantic segmentation.

Weed control is a global issue of great concern, and smart weeding robots equipped with advanced vision algorithms can perform efficient and precise weed control. Furthermore, the application of smart weeding robots has great potential for building environmentally friendly agriculture and saving human and material resources. However, most networks used in intelligent weeding robots tend to solely prioritize enhancing segmentation accuracy, disregarding the hardware constraints of embedded devices. Moreover, generalized lightweight networks are unsuitable for crop and weed segmentation tasks. Therefore, we propose an Attention-aided lightweight network for crop and weed semantic segmentation. The proposed network has a parameter count of 0.11M, Floating-point Operations count of 0.24G. Our network is based on an encoder and decoder structure, incorporating attention module to ensures both fast inference speed and accurate segmentation while utilizing fewer hardware resources. The dual attention block is employed to explore the potential relationships within the dataset, providing powerful regularization and enhancing the generalization ability of the attention mechanism, it also facilitates information integration between channels. To enhance the local and global semantic information acquisition and interaction, we utilize the refinement dilated conv block instead of 2D convolution within the deep network. This substitution effectively reduces the number and complexity of network parameters and improves the computation rate. To preserve spatial information, we introduce the spatial connectivity attention block. This block not only acquires more precise spatial information but also utilizes shared weight convolution to handle multi-stage feature maps, thereby further reducing network complexity. The segmentation performance of the proposed network is evaluated on three publicly available datasets: the BoniRob dataset, the Rice Seeding dataset, and the WeedMap dataset. Additionally, we measure the inference time and Frame Per Second on the NVIDIA Jetson Xavier NX embedded system, the results are 18.14 msec and 55.1 FPS. Experimental results demonstrate that our network maintains better inference speed on resource-constrained embedded systems and has competitive segmentation performance.

A Dataset for Forestry Pest Identification.

The identification of forest pests is of great significance to the prevention and control of the forest pests' scale. However, existing datasets mainly focus on common objects, which limits the application of deep learning techniques in specific fields (such as agriculture). In this paper, we collected images of forestry pests and constructed a dataset for forestry pest identification, called Forestry Pest Dataset. The Forestry Pest Dataset contains 31 categories of pests and their different forms. We conduct several mainstream object detection experiments on this dataset. The experimental results show that the dataset achieves good performance on various models. We hope that our Forestry Pest Dataset will help researchers in the field of pest control and pest detection in the future.

Amino Acids in Nine Ligand-Prefer Ramachandran Regions.

Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.

Link Clustering with Extended Link Similarity and EQ Evaluation Division.

Link Clustering (LC) is a relatively new method for detecting overlapping communities in networks. The basic principle of LC is to derive a transform matrix whose elements are composed of the link similarity of neighbor links based on the Jaccard distance calculation; then it applies hierarchical clustering to the transform matrix and uses a measure of partition density on the resulting dendrogram to determine the cut level for best community detection. However, the original link clustering method does not consider the link similarity of non-neighbor links, and the partition density tends to divide the communities into many small communities. In this paper, an Extended Link Clustering method (ELC) for overlapping community detection is proposed. The improved method employs a new link similarity, Extended Link Similarity (ELS), to produce a denser transform matrix, and uses the maximum value of EQ (an extended measure of quality of modularity) as a means to optimally cut the dendrogram for better partitioning of the original network space. Since ELS uses more link information, the resulting transform matrix provides a superior basis for clustering and analysis. Further, using the EQ value to find the best level for the hierarchical clustering dendrogram division, we obtain communities that are more sensible and reasonable than the ones obtained by the partition density evaluation. Experimentation on five real-world networks and artificially-generated networks shows that the ELC method achieves higher EQ and In-group Proportion (IGP) values. Additionally, communities are more realistic than those generated by either of the original LC method or the classical CPM method.