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The accurate prediction of drug–target binding affinity (DTA) is an essential step in drug discovery and drug repositioning. Although deep learning methods have been widely adopted for DTA prediction, the complexity of extracting drug and target protein features hampers the accuracy of these predictions. In this study, we propose a novel model for DTA prediction named MSGNN-DTA, which leverages a fused multi-scale topological feature approach based on graph neural networks (GNNs). To address the challenge of accurately extracting drug and target protein features, we introduce a gated skip-connection mechanism during the feature learning process to fuse multi-scale topological features, resulting in information-rich representations of drugs and proteins. Our approach constructs drug atom graphs, motif graphs, and weighted protein graphs to fully extract topological information and provide a comprehensive understanding of underlying molecular interactions from multiple perspectives. Experimental results on two benchmark datasets demonstrate that MSGNN-DTA outperforms the state-of-the-art models in all evaluation metrics, showcasing the effectiveness of the proposed approach. Moreover, the study conducts a case study based on already FDA-approved drugs in the DrugBank dataset to highlight the potential of the MSGNN-DTA framework in identifying drug candidates for specific targets, which could accelerate the process of virtual screening and drug repositioning. [ABSTRACT FROM AUTHOR]

Exploring potential associations between small molecule drugs (SMs) and microRNAs (miRNAs) is significant for drug development and disease treatment. Since biological experiments are expensive and time-consuming, we propose a computational model based on accurate matrix completion for predicting potential SM–miRNA associations (AMCSMMA). Initially, a heterogeneous SM–miRNA network is constructed, and its adjacency matrix is taken as the target matrix. An optimization framework is then proposed to recover the target matrix with the missing values by minimizing its truncated nuclear norm, an accurate, robust, and efficient approximation to the rank function. Finally, we design an effective two-step iterative algorithm to solve the optimization problem and obtain the prediction scores. After determining the optimal parameters, we conduct four kinds of cross-validation experiments based on two datasets, and the results demonstrate that AMCSMMA is superior to the state-of-the-art methods. In addition, we implement another validation experiment, in which more evaluation metrics in addition to the AUC are introduced and finally achieve great results. In two types of case studies, a large number of SM–miRNA pairs with high predictive scores are confirmed by the published experimental literature. In summary, AMCSMMA has superior performance in predicting potential SM–miRNA associations, which can provide guidance for biological experiments and accelerate the discovery of new SM–miRNA associations. [ABSTRACT FROM AUTHOR]

Cancer is a highly heterogeneous disease, which leads to the fact that even the same cancer can be further classified into different subtypes according to its pathology. With the multi-omics data widely used in cancer subtypes identification, effective feature selection is essential for accurately identifying cancer subtypes. However, the feature selection in the existing cancer subtypes identification methods has the problem that the most helpful features cannot be selected from a biomolecular perspective, and the relationship between the selected features cannot be reflected. To solve this problem, we propose a method for feature selection to identify cancer subtypes based on the heterogeneity score of a single gene: HSSG. In the proposed method, the sample-similarity network of a single gene is constructed, and pseudo-F statistics calculates the heterogeneity score for cancer subtypes identification of each gene. Finally, we construct gene-gene networks using genes with higher heterogeneity scores and mine essential genes from the networks. From the seven TCGA data sets for three experiments, including cancer subtypes identification in single-omics data, the performance in feature selection of multi-omics data, and the effectiveness and stability of the selected features, HSSG achieves good performance in all. This indicates that HSSG can effectively select features for subtypes identification. [ABSTRACT FROM AUTHOR]

Accurate detection of tropical cyclones (TCs) is important to prevent and mitigate natural disasters associated with TCs. Deep transfer learning methods have advantages in detection tasks, because they can further improve the stability and accuracy of the detection model. Therefore, on the basis of deep transfer learning, we propose a new detection framework of tropical cyclones (NDFTC) from meteorological satellite images by combining the deep convolutional generative adversarial networks (DCGAN) and You Only Look Once (YOLO) v3 model. The algorithm process of NDFTC consists of three major steps: data augmentation, a pre-training phase, and transfer learning. First, to improve the utilization of finite data, DCGAN is used as the data augmentation method to generate images simulated to TCs. Second, to extract the salient characteristics of TCs, the generated images obtained from DCGAN are inputted into the detection model YOLOv3 in the pre-training phase. Furthermore, based on the network-based deep transfer learning method, we train the detection model with real images of TCs and its initial weights are transferred from the YOLOv3 trained with generated images. Training with real images helps to extract universal characteristics of TCs and using transferred weights as initial weights can improve the stability and accuracy of the model. The experimental results show that the NDFTC has a better performance, with an accuracy (ACC) of 97.78% and average precision (AP) of 81.39%, in comparison to the YOLOv3, with an ACC of 93.96% and AP of 80.64%. [ABSTRACT FROM AUTHOR]

The alarms of the program-semantic defect-detection report based on static analysis include defects and false positives. The repair of defects and the elimination of false positives are time-consuming and laborious, and new defects may be introduced in the process. To solve these problems, the safe constraints interval of related variables and methods are proposed for the semantic defects in the program, and proposes a functionally equivalent no-side-effect program-semantic defect repair and false-positive elimination strategy based on the test-equivalence theory. This paper realizes the automatic repair of the typical semantic defects of Java programs and the automatic elimination of false positives by adding safe constraint patches. After the repair, the program functions are equivalent and the status of each program point is within the safety range, so that the functions before and after the defect repair are consistent, and the functions and semantics before and after the false positives are eliminated. We have evaluated our approach by repairing 5 projects; our results show that the repair strategy does not require manual confirmation of alarms, automated repair of the program effectively, shortened the repair time greatly, and ensured the correctness of the program after the repair. [ABSTRACT FROM AUTHOR]

Anthropometric dimensions can be acquired in 2D images by landmarks. Body shape variance causes low accuracy and bad robustness of landmarks extracted, and it is difficult to determine the position of axis division point when dimensions are calculated by the ellipse model. In this paper, landmarks are extracted from images by convolutional neural network instead of the gradient of body outline. A general multi-ellipse model is proposed, the anthropometric dimensions are obtained from the length of different elliptical segments and the position of axis division point is determined by thickness–width ratio of body parts. Finally, an evaluation is completed based on 87 subjects, in which it turns out that the average accuracy of our method for identifying landmarks is 96.6%, when the number of rotation angles is 2, the three main dimensional errors calculated by our model are smaller than existing method, and the errors of other dimensions are also within the margin of error for garment measuring. [ABSTRACT FROM AUTHOR]

Recently, software, especially CPS and Internet of Things (IoT), increasingly have high requirements for quality, while program defects exist inevitably duo to the high complexity. Program defect repair faces serious challenges in that such repairs require considerable manpower, and the existing automatic repair approaches have difficulty generating correct patches efficiently. This paper proposes an automatic method for repairing semantic defects in Java programs based on restricted sets which refer to the interval domains of related variables that can trigger program semantic defects. Our work introduces a repair mechanism symmetrically combining defect patterns and repair templates. First, the program semantic defects are summarized into defect patterns according to their grammar and semantic features. A repair template for each type of defect pattern is predefined based on a restricted-set. Then, for each specific defect, a patch statement is automatically synthesized according to the repair template, and the detected defect information is reported by the static detection tool (DTSJava). Next, the patch location is determined by the def-use chain of defect-related variables. Finally, we evaluate the patches generated by our method using DTSJava. We implemented the method in the defect automatic repair prototype tool DTSFix to verify the effect of repairing the semantic defects detected by DTSJava in 6 Java open-source projects. The experimental results showed that 109 of 129 program semantic defects were repaired. [ABSTRACT FROM AUTHOR]