Spatom: a graph neural network for structure-based protein-protein interaction site prediction.

Accurate identification of protein-protein interaction (PPI) sites remains a computational challenge. We propose Spatom, a novel framework for PPI site prediction. This framework first defines a weighted digraph for a protein structure to precisely characterize the spatial contacts of residues, then performs a weighted digraph convolution to aggregate both spatial local and global information and finally adds an improved graph attention layer to drive the predicted sites to form more continuous region(s). Spatom was tested on a diverse set of challenging protein-protein complexes and demonstrated the best performance among all the compared methods. Furthermore, when tested on multiple popular proteins in a case study, Spatom clearly identifies the interaction interfaces and captures the majority of hotspots. Spatom is expected to contribute to the understanding of protein interactions and drug designs targeting protein binding.

Survey on the research direction of EEG-based signal processing.

Electroencephalography (EEG) is increasingly important in Brain-Computer Interface (BCI) systems due to its portability and simplicity. In this paper, we provide a comprehensive review of research on EEG signal processing techniques since 2021, with a focus on preprocessing, feature extraction, and classification methods. We analyzed 61 research articles retrieved from academic search engines, including CNKI, PubMed, Nature, IEEE Xplore, and Science Direct. For preprocessing, we focus on innovatively proposed preprocessing methods, channel selection, and data augmentation. Data augmentation is classified into conventional methods (sliding windows, segmentation and recombination, and noise injection) and deep learning methods [Generative Adversarial Networks (GAN) and Variation AutoEncoder (VAE)]. We also pay attention to the application of deep learning, and multi-method fusion approaches, including both conventional algorithm fusion and fusion between conventional algorithms and deep learning. Our analysis identifies 35 (57.4%), 18 (29.5%), and 37 (60.7%) studies in the directions of preprocessing, feature extraction, and classification, respectively. We find that preprocessing methods have become widely used in EEG classification (96.7% of reviewed papers) and comparative experiments have been conducted in some studies to validate preprocessing. We also discussed the adoption of channel selection and data augmentation and concluded several mentionable matters about data augmentation. Furthermore, deep learning methods have shown great promise in EEG classification, with Convolutional Neural Networks (CNNs) being the main structure of deep neural networks (92.3% of deep learning papers). We summarize and analyze several innovative neural networks, including CNNs and multi-structure fusion. However, we also identified several problems and limitations of current deep learning techniques in EEG classification, including inappropriate input, low cross-subject accuracy, unbalanced between parameters and time costs, and a lack of interpretability. Finally, we highlight the emerging trend of multi-method fusion approaches (49.2% of reviewed papers) and analyze the data and some examples. We also provide insights into some challenges of multi-method fusion. Our review lays a foundation for future studies to improve EEG classification performance.

TriNet: A tri-fusion neural network for the prediction of anticancer and antimicrobial peptides.

The accurate identification of anticancer peptides (ACPs) and antimicrobial peptides (AMPs) remains a computational challenge. We propose a tri-fusion neural network termed TriNet for the accurate prediction of both ACPs and AMPs. The framework first defines three kinds of features to capture the peptide information contained in serial fingerprints, sequence evolutions, and physicochemical properties, which are then fed into three parallel modules: a convolutional neural network module enhanced by channel attention, a bidirectional long short-term memory module, and an encoder module for training and final classification. To achieve a better training effect, TriNet is trained via a training approach using iterative interactions between the samples in the training and validation datasets. TriNet is tested on multiple challenging ACP and AMP datasets and exhibits significant improvements over various state-of-the-art methods. The web server and source code of TriNet are respectively available at http://liulab.top/TriNet/server and https://github.com/wanyunzh/TriNet.

Consensus-based clustering of single cells by reconstructing cell-to-cell dissimilarity.

The development of single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) technology has led to great opportunities for the identification of heterogeneous cell types in complex tissues. Clustering algorithms are of great importance to effectively identify different cell types. In addition, the definition of the distance between each two cells is a critical step for most clustering algorithms. In this study, we found that different distance measures have considerably different effects on clustering algorithms. Moreover, there is no specific distance measure that is applicable to all datasets. In this study, we introduce a new single-cell clustering method called SD-h, which generates an applicable distance measure for different kinds of datasets by optimally synthesizing commonly used distance measures. Then, hierarchical clustering is performed based on the new distance measure for more accurate cell-type clustering. SD-h was tested on nine frequently used scRNA-seq datasets and it showed great superiority over almost all the compared leading single-cell clustering algorithms.

Predictors of Undiagnosed Diabetes among Middle-Aged and Seniors in China: Application of Andersen's Behavioral Model.

Undiagnosed diabetes is a threat to public health. This study aims to identify potential variables related to undiagnosed diabetes using Andersen's behavioral model. Baseline data including blood test data from the China Health and Retirement Longitudinal Study (CHARLS) were adopted. First, we constructed health service related variables based on Andersen model. Second, univariate analysis and multiple logistic regression were used to analyze the relations of variables to undiagnosed diabetes. The strength of relationships was presented by odds ratios (ORs) and 95% confidence intervals (CIs). Finally, the prediction of multiple logistic regression model was assessed using the Receiver Operating Characteristic (ROC) curve and the area under the ROC curve (AUC). According to diagnosis standards, 1234 respondents had diabetes, among which 560 were undiagnosed and 674 were previously diagnosed. Further analysis showed that the following variables were significantly associated with undiagnosed diabetes: age as the predisposing factor; medical insurance, residential places and geographical regions as enabling factors; having other chronic diseases and self-perceived health status as need factors. Moreover, the prediction of regression model was assessed well in the form of ROC and AUC. Andersen model provided a theoretical framework for detecting variables of health service utilization, which may not only explain the undiagnosed reasons but also provide clues for policy-makers to balance health services among diverse social groups in China.