The discovery of protein-protein interaction sites (PPIs) is vital for exploring the principle of PPI and understanding the nature of life activities. Developing computational approaches to predict PPIs can effectivel...
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ISBN:
(数字)9781665468190
ISBN:
(纸本)9781665468206
The discovery of protein-protein interaction sites (PPIs) is vital for exploring the principle of PPI and understanding the nature of life activities. Developing computational approaches to predict PPIs can effectively compensate for the shortcomings of biological experiments, which are mostly time-consuming and vulnerable to noise. In recent years, deep learning has been used to develop PPIs prediction models. Most of them consider the contextual information of the target amino acid residues and use a local protein sequence to represent the targets. However, the traditional deep-learning techniques, e.g., deep neural networks (DNNs) and convolutional neural networks (CNNs), disregard the important spatial hierarchies contained in the features of protein sequences, leading to their failure to effectively distinguish the interaction sites from different residue regions. In this work, we design MSE-CapsPPISP, a new deep-learning model to address the PPIs prediction with spatial hierarchies. The key idea of MSE-CapsPPISP is to take into account the hierarchical relationships between the features of protein sequences. We characterize the hierarchical relationships by designing a tailored Capsule Network (CapsNet) model, which is a novel type of neural network with vector neurons. Moreover, to make the network representation more robust, MSE-CapsPPISP uses multi-scale CNNs to extract multi-scale features of protein sequences and Squeeze-and-Excitation blocks to recalibrate the features. The validation results show that our MSE-CapsPPISP outperforms the baseline CNNs-based architecture DeepPPISP and other competing schemes in the PPIs prediction task.
Java Virtual Machine (JVM) is the fundamental software system that supports the interpretation and execution of Java bytecode. To support the surging performance demands for the increasingly complex and large-scale Ja...
Java Virtual Machine (JVM) is the fundamental software system that supports the interpretation and execution of Java bytecode. To support the surging performance demands for the increasingly complex and large-scale Java programs, Just-In-Time (JIT) compiler was proposed to perform sophisticated runtime optimization. However, this inevitably induces various bugs, which are becoming more pervasive over the decades and can often cause significant consequences. To facilitate the design of effective and efficient testing techniques to detect JIT compiler bugs. This study first performs a preliminary study aiming to understand the characteristics of JIT compiler bugs and the corresponding triggering test cases. Inspired by the empirical findings, we propose JOpFuzzer, a new JVM testing approach with a specific focus on JIT compiler bugs. The main novelty of JOpFuzzer is embodied in three aspects. First, besides generating new seeds, JOpFuzzer also searches for diverse configurations along the new dimension of optimization options. Second, JOpFuzzer learns the correlations between various code features and different optimization options to guide the process of seed mutation and option exploration. Third, it leverages the profile data, which can reveal the program execution information, to guide the fuzzing process. Such nov-elties enable JOpFuzzer to effectively and efficiently explore the two-dimensional input spaces. Extensive evaluation shows that JOpFuzzer outperforms the state-of-the-art approaches in terms of the achieved code coverages. More importantly, it has detected 41 bugs in OpenJDK, and 25 of them have already been confirmed or fixed by the corresponding developers.
The recent emergence of time series contrastive clustering methods can be broadly categorized into two classes. The first class uses contrastive learning to learn universal representations for time series. Though they...
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Compared with rasterization rendering, ray tracing rendering can improve the image’s visual effect and make the image look more realistic. Real-time ray tracing requires very high computing power of graphics processi...
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Human facial action units (AUs) are mutually related in a hierarchical manner, as not only they are associated with each other in both spatial and temporal domains but also AUs located in the same/close facial regions...
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ISBN:
(数字)9798350353006
ISBN:
(纸本)9798350353013
Human facial action units (AUs) are mutually related in a hierarchical manner, as not only they are associated with each other in both spatial and temporal domains but also AUs located in the same/close facial regions show stronger relationships than those of different facial regions. While none of existing approach thoroughly model such hi-erarchical inter-dependencies among AUs, this paper proposes to comprehensively model multi-scale AU-related dynamic and hierarchical spatiotemporal relationship among AUs for their occurrences recognition. Specifically, we first propose a novel multi-scale temporal differencing network with an adaptive weighting block to explicitly capture facial dynamics across frames at different spatial scales, which specifically considers the heterogeneity of range and mag-nitude in different AUs' activation. Then, a two-stage strategy is introduced to hierarchically model the relationship among AUs based on their spatial distribution (i.e., local and cross-region AU relationship modelling). Experimental results achieved on BP4D and DISFA show that our approach is the new state-of-the-art in the field of AU occurrence recognition. Our code is publicly available at https://***/CVI-SZU/MDHR.
Existing smart contract vulnerability identification approaches mainly focus on complete program detection. Consequently, lots of known potentially vulnerable locations need manual verification, which is energy-exhaus...
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Real-world data often have a long-tailed and open-ended distribution. A reliable practical machine learning system need to learn from the majority classes and also generalize to minority *** achieve this, acknowledge ...
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The analysis of Cardiotocography (CTG) signals is often hindered by challenges such as limited data availability and label imbalance, which can undermine the performance of deep learning models. To address these issue...
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ISBN:
(数字)9798350368741
ISBN:
(纸本)9798350368758
The analysis of Cardiotocography (CTG) signals is often hindered by challenges such as limited data availability and label imbalance, which can undermine the performance of deep learning models. To address these issues, we present CTGDiff, a novel conditional diffusion model designed for generating synthetic Fetal Heart Rate (FHR) and Uterine Contraction (UC) signals. CTGDiff leverages both Phase-Rectified Signal Averaging (PRSA) spectrograms and UC as conditioning inputs for FHR, and integrates time encoding, condition generation from PRSA features, and residual blocks with dilated convolutions to capture both temporal dynamics and long-range dependencies. Extensive experiments, both qualitative and quantitative, demonstrate the model’s ability to synthesize high-quality CTG signals. In comparison with GANs and image-based diffusion models, CTGDiff achieves superior signal fidelity and distribution similarity for FHR, as indicated by metrics such as a 0.004 maximum mean deviation (MMD), 0.646 percent root mean square difference (PRD), 3.951 relative entropy (RE), and 0.291 Frechet distance (FD). Expert evaluations confirm that the model can generate both normal and abnormal CTG signals with high accuracy, conditioned on specific input data. These results underscore the potential of diffusion models for a wide range of applications in biomedical time series analysis, including signal synthesis, imputation, and noise reduction.
Deep Forest, a powerful alternative to deep neural networks, has gained much attention due to its advantages, such as low complexity, minimal hyperparameter requirements, and strong application performance. In the cur...
Deep Forest, a powerful alternative to deep neural networks, has gained much attention due to its advantages, such as low complexity, minimal hyperparameter requirements, and strong application performance. In the current bigdata environment, where data volumes and model complexities are growing rapidly, distributed computing is needed to increase computational efficiency. Recently, a distributed deep forest approach, called BLB-gcForest (Bag of Little Bootstraps-gcForest), has been successful in reducing training instances within cascade forests, combining BLB and granularity segmentation, thus improving the computational efficiency and scalability of distributed deep forests. However, it still transmits the entire data set between layers and requires double sampling with BLB, limiting the amount of data and the scalability of resource utilization. This paper introduces a novel algorithm, RSP-gcForest, based on Random Sample Partition (RSP) to improve distributed deep forests computational efficiency and scalability. RSP-gcForest uses block-level samples that replace the full dataset, significantly reducing interlayer instance transmission and prediction within cascade forests. Additionally, RSP blocks are integrated with the segmentation granularity of cascade forests for ensemble learning, effectively addressing computational efficiency and resource constraints. We conducted experiments on four extensive datasets using Spark and evaluated performance across five key metrics. The results clearly show that RSP-gcForest, while maintaining high classification quality, surpasses state-of-the-art methods in terms of computational efficiency and resource utilization. Furthermore, it achieves superior load balancing, demonstrating its potential as a powerful tool in bigdata and distributed computing.
Existing privacy-preserving approaches are generally designed to provide privacy guarantee for individual data in a database, which reduces the utility of the database for data analysis. In this paper, we propose a no...
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