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Proteins, as the material basis of life, are the ultimate controller and direct performer of life activities. Most proteins perform their biological functions by binding to other proteins to form complexes. The identification of protein complexes can help people to better understand the organization and functions of the complexes, as well as the mechanisms of cells. At present, the rapid development of high-throughput experimental technology has led to huge amounts of protein-protein interaction (PPI) data. Many methods for computationally predicting protein complexes based on PPI data have been proposed. Different methods have their own characteristics and advantages, and they also have inherent drawbacks. Firstly, this paper classifies and comprehensively analyzes and reviews the existing protein complex prediction methods. Then, it introduces the commonly used evaluation indicators and main data sets in complex prediction, compares and analyzes the prediction performance of several representative methods. Finally, it summarizes state-of-the-art complex prediction methods, highlights future research directions, and puts forward several issues to be resolved in the future. It is hoped that through the analysis and comparison of various methods, this paper can provide some valuable guidance and future directions for users and researchers on using the existing methods and developing new methods of protein complex prediction.

Multivariate Time Series Anomaly Detection (MTS-AD) is crucial for the effective management and maintenance of devices in complex systems, such as server clusters, spacecrafts, and financial systems, and so on. However, upgrade or cross-platform deployment of these devices will introduce the issue of cross-domain distribution shift, which leads to the prototypical problem of domain adaptation for MTS-AD. Compared with general domain adaptation problems, MTS-AD domain adaptation presents two peculiar challenges: (1) the dimensions of data from the source domain and the target domain are usually different, so alignment without losing any information is necessary; and (2) the association between different variates plays a vital role in the MTS-AD task, which is overlooked by traditional domain adaptation approaches. Aiming at addressing the above issues, we propose a Variate Associated Domain Adaptation Method Combined with a Graph Deviation Network (VANDA) for MTS-AD, which includes two major contributions. First, we characterize the intra-domain variate associations of the source domain by a graph deviation network (GDN), which can share parameters across domains without dimension alignment. Second, we propose a sliding similarity to measure the inter-domain variate associations and perform joint training by minimizing the optimal transport distance between source and target data for transferring variate associations across domains. VANDA achieves domain adaptation by transferring both variate associations and GDN parameters from the source domain to the target domain. We construct two pairs of MTS-AD datasets from existing MTS-AD data and combine three domain adaptation strategies with six MTS-AD backbones as the benchmark methods for experimental evaluation and comparison. Extensive experiments demonstrate the effectiveness of our approach, which outperforms the benchmark methods, and significantly improves the AD performance of the target domain by effectively utilizing the source domain knowledge. [ABSTRACT FROM AUTHOR]

With the rapid growth of the data scale in data centers, the high reliability of storage is facing various challenges. Specifically, hardware failures such as disk faults occur frequently, causing serious system availability issues. In this context, hardware fault prediction based on AI and big data technologies has become a research hotspot, aiming to guide operation and maintenance personnel to implement preventive replacement through accurate prediction to reduce hardware failure rates. However, existing methods still have weaknesses in terms of accuracy due to the impacts of data quality issues such as the sample imbalance. This article proposes a disk fault prediction method based on classification intensity resampling, which fills the gap between the degree of data imbalance and the actual classification intensity of the task by introducing a base classifier to calculate the classification intensity, thus better preserving the data features of the original dataset. In addition, using ensemble learning methods such as random forests, combined with resampling, an integrated classifier for imbalanced data is developed to further improve the prediction accuracy. Experimental verification shows that compared with traditional methods, the F1-score of disk fault prediction is improved by 6%, and the model training time is also greatly reduced. The fault prediction method proposed in this paper has been applied to approximately 80 disk drives and nearly 40,000 disks in the production environment of a large bank's data center to guide preventive replacements. Compared to traditional methods, the number of preventive replacements based on our method has decreased by approximately 21%, while the overall disk failure rate remains unchanged, thus demonstrating the effectiveness of our method. [ABSTRACT FROM AUTHOR]

Under a distributed information system, the scale of various operational components such as applications, operating systems, databases, servers, and networks is immense, with intricate access relationships. The silo effect of each professional is prominent, and the linkage mechanism is insufficient, making it difficult to locate the infrastructure components that cause exceptions under a particular application. Current research only plays a role in local scenarios, and its accuracy and generalization are still very limited. This paper proposes a novel fault location method based on dynamic operation maps and alarm common point analysis. During the fault period, various alarm entities are associated with dynamic operation maps, and alarm common points are obtained based on graph search addressing methods, covering deployment relationship common points, connection common points (physical and logical), and access flow common points. This method, compared with knowledge graph approaches, eliminates the complex process of knowledge graph construction, making it more concise and efficient. Furthermore, in contrast to indicator correlation analysis methods, this approach supplements with configuration correlation information, resulting in more precise positioning. Through practical validation, its fault hit rate exceeds 82%, which is significantly better than the existing main methods. [ABSTRACT FROM AUTHOR]

Motivation Molecular property prediction (MPP) is a fundamental but challenging task in the computer-aided drug discovery process. More and more recent works employ different graph-based models for MPP, which have achieved considerable progress in improving prediction performance. However, current models often ignore relationships between molecules, which could be also helpful for MPP. Results For this sake, in this article we propose a graph structure learning (GSL) based MPP approach, called GSL-MPP. Specifically, we first apply graph neural network (GNN) over molecular graphs to extract molecular representations. Then, with molecular fingerprints, we construct a molecule similarity graph (MSG). Following that, we conduct GSL on the MSG, i.e. molecule-level GSL, to get the final molecular embeddings, which are the results of fuzing both GNN encoded molecular representations and the relationships among molecules. That is, combining both intra-molecule and inter-molecule information. Finally, we use these molecular embeddings to perform MPP. Extensive experiments on 10 various benchmark datasets show that our method could achieve state-of-the-art performance in most cases, especially on classification tasks. Further visualization studies also demonstrate the good molecular representations of our method. Availability and implementation Source code is available at https://github.com/zby961104/GSL-MPP. [ABSTRACT FROM AUTHOR]

Background: The rapid devolvement of single cell RNA sequencing (scRNA-seq) technology leads to huge amounts of scRNA-seq data, which greatly advance the research of many biomedical fields involving tissue heterogeneity, pathogenesis of disease and drug resistance etc. One major task in scRNA-seq data analysis is to cluster cells in terms of their expression characteristics. Up to now, a number of methods have been proposed to infer cell clusters, yet there is still much space to improve their performance. Results: In this paper, we develop a new two-step clustering approach to effectively cluster scRNA-seq data, which is called TSC — the abbreviation of Two-Step Clustering. Particularly, by dividing all cells into two types: core cells (those possibly lying around the centers of clusters) and non-core cells (those locating in the boundary areas of clusters), we first clusters the core cells by hierarchical clustering (the first step) and then assigns the non-core cells to the corresponding nearest clusters (the second step). Extensive experiments on 12 real scRNA-seq datasets show that TSC outperforms the state of the art methods. Conclusion: TSC is an effective clustering method due to its two-steps clustering strategy, and it is a useful tool for scRNA-seq data analysis. [ABSTRACT FROM AUTHOR]

Simple Summary: Both the lack of bird object detection datasets and the scarcity of technical references for evaluating the performance of object detection models and model lightweighting present challenges in the application of bird object detection technology. In this study, we have not only constructed the largest known bird object detection dataset, but also compared the performance of eight mainstream detection models on bird object detection tasks and proposed a feasible approach for model lightweighting in bird object detection. Our research results not only provide more accurate and comprehensive data for the field of bird detection, but also serve as a technical reference for users in selecting appropriate object detection models. The application of object detection technology has a positive auxiliary role in advancing the intelligence of bird recognition and enhancing the convenience of bird field surveys. However, challenges arise due to the absence of dedicated bird datasets and evaluation benchmarks. To address this, we have not only constructed the largest known bird object detection dataset, but also compared the performances of eight mainstream detection models on bird object detection tasks and proposed feasible approaches for model lightweighting in bird object detection. Our constructed bird detection dataset of GBDD1433-2023, includes 1433 globally common bird species and 148,000 manually annotated bird images. Based on this dataset, two-stage detection models like Faster R-CNN and Cascade R-CNN demonstrated superior performances, achieving a Mean Average Precision (mAP) of 73.7% compared to one-stage models. In addition, compared to one-stage object detection models, two-stage object detection models have a stronger robustness to variations in foreground image scaling and background interference in bird images. On bird counting tasks, the accuracy ranged between 60.8% to 77.2% for up to five birds in an image, but this decreased sharply beyond that count, suggesting limitations of object detection models in multi-bird counting tasks. Finally, we proposed an adaptive localization distillation method for one-stage lightweight object detection models that are suitable for offline deployment, which improved the performance of the relevant models. Overall, our work furnishes an enriched dataset and practice guidelines for selecting suitable bird detection models. [ABSTRACT FROM AUTHOR]

Sea Surface Temperature (SST) prediction is a hot topic that has received tremendous popularity in recent years. Existing methods for SST prediction usually select one sea area of interest and conduct SST prediction by learning the spatial and temporal dependencies and patterns in historical SST data. However, global SST is a unified system of high regionality, and the SST in different sea areas shows different changing patterns due to the influence of various factors, e.g., geographic location, ocean currents and sea depth. Without a good understanding of such regionality of SST, we cannot quantitatively integrate the regionality information of SST into SST prediction models to make them adaptive to different SST patterns around the world and improve the prediction accuracy. To address this issue, we proposed the Multi-Stage Spatio–Temporal Clustering (MuSTC) method to quantitatively identify sea areas with similar SST patterns. First, MuSTC sequentially learns the representation of long-term SST with a deep temporal encoder and calculates the spatial correlation scores between grid ocean regions with self-attention. Then, MuSTC clusters grid ocean regions based on the original SST data, encoded long-term SST representation and spatial correlation scores, respectively, to obtain the sea areas with similar SST patterns from different perspectives. According to the experiments in three ocean areas, i.e., the North Pacific Ocean (NPO), the South Atlantic Ocean (SAO) and the North Atlantic Ocean (NAO), the clustering results generally match the distribution of ocean currents, which demonstrates the effectiveness of our MuSTC method. In addition, we integrate the clustering results into two representative spatio–temporal prediction models, i.e., Spatio–Temporal Graph Convolutional Networks (STGCN) and Adaptive Graph Convolutional Recurrent Network (AGCRN), to conduct SST prediction. According to the results of experiments, the integration of regionality information leads to the reduction of Root Mean Square Error (RMSE) by 1.95%, 1.39% and 1.28% in NPO, SAO and NAO, respectively, using the STGCN model, and the reduction of RMSE by 4.94%, 0.74% and 1.43% by using the AGCRN model. Such results indicate that the integration of regionality information could notably improve the prediction accuracy of SST. [ABSTRACT FROM AUTHOR]

Molecular property prediction (MPP) is a crucial and fundamental task for AI-aided drug discovery (AIDD). Recent studies have shown great promise of applying self-supervised learning (SSL) to producing molecular representations to cope with the widely-concerned data scarcity problem in AIDD. As some specific substructures of molecules play important roles in determining molecular properties, molecular representations learned by deep learning models are expected to attach more importance to such substructures implicitly or explicitly to achieve better predictive performance. However, few SSL pre-trained models for MPP in the literature have ever focused on such substructures. To challenge this situation, this paper presents a C hemistry- A ware F ragmentation for E ffective MPP (CAFE-MPP in short) under the self-supervised contrastive learning framework. First, a novel fragment-based molecular graph (FMG) is designed to represent the topological relationship between chemistry-aware substructures that constitute a molecule. Then, with well-designed hard negative pairs, a is pre-trained on fragment-level by contrastive learning to extract representations for the nodes in FMGs. Finally, a Graphormer model is leveraged to produce molecular representations for MPP based on the embeddings of fragments. Experiments on 11 benchmark datasets show that the proposed CAFE-MPP method achieves state-of-the-art performance on 7 of the 11 datasets and the second-best performance on 3 datasets, compared with six remarkable self-supervised methods. Further investigations also demonstrate that CAFE-MPP can learn to embed molecules into representations implicitly containing the information of fragments highly correlated to molecular properties, and can alleviate the over-smoothing problem of graph neural networks. [ABSTRACT FROM AUTHOR]

Motivation Protein complexes are groups of polypeptide chains linked by non-covalent protein–protein interactions, which play important roles in biological systems and perform numerous functions, including DNA transcription, mRNA translation, and signal transduction. In the past decade, a number of computational methods have been developed to identify protein complexes from protein interaction networks by mining dense subnetworks or subgraphs. Results In this article, different from the existing works, we propose a novel approach for this task based on generative adversarial networks, which is called PCGAN , meaning identifying P rotein C omplexes by GAN. With the help of some real complexes as training samples, our method can learn a model to generate new complexes from a protein interaction network. To effectively support model training and testing, we construct two more comprehensive and reliable protein interaction networks and a larger gold standard complex set by merging existing ones of the same organism (including human and yeast). Extensive comparison studies indicate that our method is superior to existing protein complex identification methods in terms of various performance metrics. Furthermore, functional enrichment analysis shows that the identified complexes are of high biological significance, which indicates that these generated protein complexes are very possibly real complexes. Availability and implementation https://github.com/yul-pan/PCGAN. [ABSTRACT FROM AUTHOR]

Motivation Contrastive learning has been widely used as pretext tasks for self-supervised pre-trained molecular representation learning models in AI-aided drug design and discovery. However, existing methods that generate molecular views by noise-adding operations for contrastive learning may face the semantic inconsistency problem, which leads to false positive pairs and consequently poor prediction performance. Results To address this problem, in this article, we first propose a semantic-invariant view generation method by properly breaking molecular graphs into fragment pairs. Then, we develop a Fragment-based Semantic-Invariant Contrastive Learning (FraSICL) model based on this view generation method for molecular property prediction. The FraSICL model consists of two branches to generate representations of views for contrastive learning, meanwhile a multi-view fusion and an auxiliary similarity loss are introduced to make better use of the information contained in different fragment-pair views. Extensive experiments on various benchmark datasets show that with the least number of pre-training samples, FraSICL can achieve state-of-the-art performance, compared with major existing counterpart models. Availability and implementation The code is publicly available at https://github.com/ZiqiaoZhang/FraSICL. [ABSTRACT FROM AUTHOR]

Motivation Predicting molecular properties is one of the fundamental problems in drug design and discovery. In recent years, self-supervised learning (SSL) has shown its promising performance in image recognition, natural language processing, and single-cell data analysis. Contrastive learning (CL) is a typical SSL method used to learn the features of data so that the trained model can more effectively distinguish the data. One important issue of CL is how to select positive samples for each training example, which will significantly impact the performance of CL. Results In this article, we propose a new method for molecular property prediction (MPP) by C ontrastive   L earning with   A ttention-guided   P ositive-sample   S election (CLAPS). First, we generate positive samples for each training example based on an attention-guided selection scheme. Second, we employ a Transformer encoder to extract latent feature vectors and compute the contrastive loss aiming to distinguish positive and negative sample pairs. Finally, we use the trained encoder for predicting molecular properties. Experiments on various benchmark datasets show that our approach outperforms the state-of-the-art (SOTA) methods in most cases. Availability and implementation The code is publicly available at https://github.com/wangjx22/CLAPS. [ABSTRACT FROM AUTHOR]

Sea surface temperature (SST) has important impacts on the global ecology, and having a good understanding of the predictability, i.e., the possibility of achieving accurate prediction, of SST can help us monitor the marine environment and climate change, and guide the selection and design of SST prediction methods. However, existing studies for analyzing SST mostly measure the rising or falling trends of SST. To address this issue, we introduce a temporal-correlated entropy to quantify the predictability of SST series from both global coarse-grained and local fine-grained aspects, and make SST prediction with multiple deep learning models to prove the effectiveness of such predictability evaluation method. In addition, we explore the dynamics of SST predictability by dividing the time range of interest into consecutive time periods, evaluating the corresponding predictability of SST for each time period, and analyzing the stability of the predictability of SST over time. According to the experiments, the SST predictability values near the poles and equator are really high. The average SST predictability values of the East China Sea, Bohai Sea, and Antarctic Ocean are 0.719, 0.706, and 0.886, respectively, and the size relationship of the SST predictability in the three local sea areas is consistent with our prediction results using multiple representative SST prediction methods, which corroborates the reliability of the predictability evaluation method. In addition, we found that the SST predictability in the Antarctic Ocean changes more dramatically over time than in the East China Sea and the Bohai Sea. The results of SST predictability and its dynamic analysis indicate that global warming, ocean currents, and human activities all have significant impacts on the predictability of SST. [ABSTRACT FROM AUTHOR]

Marine plankton classification is important for monitoring marine biological populations and understanding marine ecosystems. However, it is difficult to obtain abundant annotated image data of marine plankton to train classification models of high quality. To classify marine plankton with a small number of image samples, a cross‐domain few‐shot learning model (CDFM) is proposed. First, CDFM learns knowledge from existing labelled images and then transfers the knowledge to new images. In this process, there is an issue of domain differences between the new images and the existing datasets due to differences in data acquisition time and locations. To address this issue, the authors pre‐train a model in the source domain and then use fine‐tuning to adapt it to the target domain. Second, the graph neural network is used as a meta‐learning module to learn a feature distance metric for marine plankton classification with limited samples. Extensive experiments on four marine plankton image datasets are conducted, including Kaggle Plankton, miniPPlankton, ZooScan and WHOI, and CDFM outperforms existing methods for marine plankton classification. [ABSTRACT FROM AUTHOR]

Satellite data is of high importance for ocean environment monitoring and protection. However, due to the missing values in satellite data, caused by various force majeure factors such as cloud cover, bad weather and sensor failure, the quality of satellite data is reduced greatly, which hinders the applications of satellite data in practice. Therefore, a variety of methods have been proposed to conduct missing data imputation for satellite data to improve its quality. However, these methods cannot well learn the short-term temporal dependence and dynamic spatial dependence in satellite data, resulting in bad imputation performance when the data missing rate is large. To address this issue, we propose the Spatio-Temporal Attention Generative Adversarial Network (STA-GAN) for missing value imputation in satellite data. First, we develop the Spatio-Temporal Attention (STA) mechanism based on Graph Attention Network (GAT) to learn features for capturing both short-term temporal dependence and dynamic spatial dependence in satellite data. Then, the learned features from STA are fused to enrich the spatio-temporal information for training the generator and discriminator of STA-GAN. Finally, we use the generated imputation data by the trained generator of STA-GAN to fill the missing values in satellite data. Experimental results on real datasets show that STA-GAN largely outperforms the baseline data imputation methods, especially for filling satellite data with large missing rates. [ABSTRACT FROM AUTHOR]