水体透射光谱结合主成分分析(PCA )改进化学需氧量(COD)含量估算研究

化学需氧量（Chemical Oxygen Demand,COD）是水体有机污染的一项重要指标,化学需氧量越高,表示水污染程度越严重。 为了解决传统的COD测量方法耗时较长,不利于快速、实时地获取水体中COD的信息等问题。本文提出了基于透射光谱测量结合主成分分析(Principal Component Analysis, PCA)改进水体COD含量估算模型。具体的,采集100组COD水体光谱信息,分别使用3种不同的高光谱数据预处理方法对光谱数据进行预处理,分析不同预处理方法对模型精度的影响,并基于不同的预处理方法分别建立高斯过程回归模型(Gaussian Process Regression, GPR)和BP神经网络模型,分析不同预处理方法对模型精度的影响;并对各模型结合PCA数据降维方法进行模型的改进,通过比较模型的精度选择最优模型进行水体COD含量的检测。结果显示,相比于原始光谱数据建立的GPR模型和BP神经网络模型,数据预处理后的模型精度明显提升;且结合PCA对预处理后的数据进一步降维处理后,模型精度得到了进一步的提升。其中,基于标准正态变量变换特征结合PCA改进BP神经网络模型基于PCA改进的BP神经网络模型R^2高达0.9940,均方根误差RMSE为0.022540。证明了基于PCA改进的BP神经网络数据降维方法对预处理后的光谱数据进行降维处理,有利于去除光谱中的冗余信息,提取特征信息,可以实现高光谱检测方法可以实现COD含量估算模型的优化,从而为传统COD测量方法存在的问题提出了一种新的解决思路。     

An Extensive Assessment of Network Embedding in PPI Network Alignment

Network alignment is a fundamental task in network analysis. In the biological field, where the protein–protein interaction (PPI) is represented as a graph, network alignment allowed the discovery of underlying biological knowledge such as conserved evolutionary pathways and functionally conserved proteins throughout different species. A recent trend in network science concerns network embedding, i.e., the modelling of nodes in a network as a low-dimensional feature vector. In this survey, we present an overview of current PPI network embedding alignment methods, a comparison among them, and a comparison to classical PPI network alignment algorithms. The results of this comparison highlight that: (i) only five network embeddings for network alignment algorithms have been applied in the biological context, whereas the literature presents several classical network alignment algorithms; (ii) there is a need for developing an evaluation framework that may enable a unified comparison between different algorithms; (iii) the majority of the proposed algorithms perform network embedding through matrix factorization-based techniques; (iv) three out of five algorithms leverage external biological resources, while the remaining two are designed for domain agnostic network alignment and tested on PPI networks; (v) two algorithms out of three are stated to perform multi-network alignment, while the remaining perform pairwise network alignment.     

Space-Air-Ground Integrated Mobile Crowdsensing for Partially Observable Data Collection by Multi-Scale Convolutional Graph Reinforcement Learning

Mobile crowdsensing (MCS) is attracting considerable attention in the past few years as a new paradigm for large-scale information sensing. Unmanned aerial vehicles (UAVs) have played a significant role in MCS tasks and served as crucial nodes in the newly-proposed space-air-ground integrated network (SAGIN). In this paper, we incorporate SAGIN into MCS task and present a Space-Air-Ground integrated Mobile CrowdSensing (SAG-MCS) problem. Based on multi-source observations from embedded sensors and satellites, an aerial UAV swarm is required to carry out energy-efficient data collection and recharging tasks. Up to date, few studies have explored such multi-task MCS problem with the cooperation of UAV swarm and satellites. To address this multi-agent problem, we propose a novel deep reinforcement learning (DRL) based method called Multi-Scale Soft Deep Recurrent Graph Network (ms-SDRGN). Our ms-SDRGN approach incorporates a multi-scale convolutional encoder to process multi-source raw observations for better feature exploitation. We also use a graph attention mechanism to model inter-UAV communications and aggregate extra neighboring information, and utilize a gated recurrent unit for long-term performance. In addition, a stochastic policy can be learned through a maximum-entropy method with an adjustable temperature parameter. Specifically, we design a heuristic reward function to encourage the agents to achieve global cooperation under partial observability. We train the model to convergence and conduct a series of case studies. Evaluation results show statistical significance and that ms-SDRGN outperforms three state-of-the-art DRL baselines in SAG-MCS. Compared with the best-performing baseline, ms-SDRGN improves 29.0% reward and 3.8% CFE score. We also investigate the scalability and robustness of ms-SDRGN towards DRL environments with diverse observation scales or demanding communication conditions.     

Phase Transitions Induced by Top-Priority of Randomization

We study the characteristics of phase transition to take the top-priority of randomization in the rules of NaSch model (i.e.noise-first model) into account via computing the relaxation time and the order parameter.The scaling exponents of the relaxation time and the scaling relation of order parameter,respectively,axe obtained.     

KEADA: Identifying Key Classes in Software Systems Using Dynamic Analysis and Entropy-Based Metrics

Software maintenance is indispensable in the software development process. Developers need to spend a lot of time and energy to understand the software when maintaining the software, which increases the difficulty of software maintenance. It is a feasible method to understand the software through the key classes of the software. Identifying the key classes of the software can help developers understand the software more quickly. Existing techniques on key class identification mainly use static analysis techniques to extract software structure information. Such structure information may contain redundant relationships that may not exist when the software runs and ignores the actual interaction times between classes. In this paper, we propose an approach based on dynamic analysis and entropy-based metrics to identify key classes in the Java GUI software system, called KEADA (identifying KEy clAsses based on Dynamic Analysis and entropy-based metrics). First, KEADA extracts software structure information by recording the calling relationship between classes during the software running process; such structure information takes into account the actual interaction of classes. Second, KEADA represents the structure information as a weighted directed network and further calculates the importance of each node using an entropy-based metric OSE (One-order Structural Entropy). Third, KEADA ranks classes in descending order according to their OSE values and selects a small number of classes as the key class candidates. In order to verify the effectiveness of our approach, we conducted experiments on three Java GUI software systems and compared them with seven state-of-the-art approaches. We used the Friedman test to evaluate all approaches, and the results demonstrate that our approach performs best in all software systems.     

Investigation Driven by Network Pharmacology on Potential Components and Mechanism of DGS,a Natural Vasoprotective Combination,for the Phytotherapy of Coronary Artery Disease

Phytotherapy offers obvious advantages in the intervention of Coronary Artery Disease (CAD), but it is difficult to clarify the working mechanisms of the medicinal materials it uses. DGS is a natural vasoprotective combination that was screened out in our previous research, yet its potential components and mechanisms are unknown. Therefore, in this study, HPLC-MS and network pharmacology were employed to identify the active components and key signaling pathways of DGS. Transgenic zebrafish and HUVECs cell assays were used to evaluate the effectiveness of DGS. A total of 37 potentially active compounds were identified that interacted with 112 potential targets of CAD. Furthermore, PI3K-Akt, MAPK, relaxin, VEGF, and other signal pathways were determined to be the most promising DGS-mediated pathways. NO kit, ELISA, and Western blot results showed that DGS significantly promoted NO and VEGFA secretion via the upregulation of VEGFR2 expression and the phosphorylation of Akt, Erk1/2, and eNOS to cause angiogenesis and vasodilation. The result of dynamics molecular docking indicated that Salvianolic acid C may be a key active component of DGS in the treatment of CAD. In conclusion, this study has shed light on the network molecular mechanism of DGS for the intervention of CAD using a network pharmacology-driven strategy for the first time to aid in the intervention of CAD.     

An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors

Cancer progression is linked to aberrant protein glycosylation due to the overexpression of several glycosylation enzymes. These enzymes are underexploited as potential anticancer drug targets and the development of rapid-screening methods and identification of glycosylation inhibitors are highly sought. An integrated bioinformatics and mass spectrometry-based glycomics-driven glycoproteomics analysis pipeline was performed to identify an N-glycan inhibitor against lung cancer cells. Combined network pharmacology and in silico screening approaches were used to identify a potential inhibitor, pictilisib, against several glycosylation-related proteins, such as Alpha1-6FucT, GlcNAcT-V, and Alpha2,6-ST-I. A glycomics assay of lung cancer cells treated with pictilisib showed a significant reduction in the fucosylation and sialylation of N-glycans, with an increase in high mannose-type glycans. Proteomics analysis and in vitro assays also showed significant upregulation of the proteins involved in apoptosis and cell adhesion, and the downregulation of proteins involved in cell cycle regulation, mRNA processing, and protein translation. Site-specific glycoproteomics analysis further showed that glycoproteins with reduced fucosylation and sialylation were involved in apoptosis, cell adhesion, DNA damage repair, and chemical response processes. To determine how the alterations in N-glycosylation impact glycoprotein dynamics, modeling of changes in glycan interactions of the ITGA5–ITGB1 (Integrin alpha 5-Integrin beta-1) complex revealed specific glycosites at the interface of these proteins that, when highly fucosylated and sialylated, such as in untreated A549 cells, form greater hydrogen bonding interactions compared to the high mannose-types in pictilisib-treated A549 cells. This study highlights the use of mass spectrometry to identify a potential glycosylation inhibitor and assessment of its impact on cell surface glycoprotein abundance and protein–protein interaction.     

Prisoner’s Dilemma Game with Cooperation-Defection Dominance Strategies on Correlational Multilayer Networks

As multilayer networks are widely applied in modern society, numerous studies have shown the impact of a multilayer network structure and the network nature on the proportion of cooperators in the network. In this paper, we use Barabási–Albert scale-free networks (BA) and Watts and Strogatz networks (WS) to build a multilayer network structure, and we propose a new strategy-updating rule called “cooperation-defection dominance”, which can be likened to dominant and recessive traits in biogenetics. With the newly constructed multilayer network structure and the strategy-updating rules, based on the simulation results, we find that in the BA-BA network, the cooperation dominance strategy can make the networks with different rs show a cooperative trend, while the defection dominance strategy only has an obvious effect on the network cooperation with a larger r. When the BA network is connected to the WS network, we find that the effect of strategy on the proportion of cooperators in the network decreases, and the main influencing factor is the structure of the network. In the three-layer network, the cooperation dominance strategy has a greater impact on the BA network, and the proportion of the cooperators is enhanced more than under the natural evolution strategy, but the promotion effect is still smaller than that of the two-layer BA network because of the WS network. Under the defection dominance strategy, the WS layer appears different from the first two strategies, and we conclude through simulation that when the payoff parameter is at the middle level, its cooperator proportion will be suppressed, and we deduce that the proportion of cooperators and defectors, as well as the payoff, play an important role.     

Adversarial Data Hiding in Digital Images

In recent studies of generative adversarial networks (GAN), researchers have attempted to combine adversarial perturbation with data hiding in order to protect the privacy and authenticity of the host image simultaneously. However, most of the studied approaches can only achieve adversarial perturbation through a visible watermark; the quality of the host image is low, and the concealment of data hiding cannot be achieved. In this work, we propose a true data hiding method with adversarial effect for generating high-quality covers. Based on GAN, the data hiding area is selected precisely by limiting the modification strength in order to preserve the fidelity of the image. We devise a genetic algorithm that can explore decision boundaries in an artificially constrained search space to improve the attack effect as well as construct aggressive covert adversarial samples by detecting “sensitive pixels” in ordinary samples to place discontinuous perturbations. The results reveal that the stego-image has good visual quality and attack effect. To the best of our knowledge, this is the first attempt to use covert data hiding to generate adversarial samples based on GAN.     

Conserved Control Path in Multilayer Networks

The determination of directed control paths in complex networks is important because control paths indicate the structure of the propagation of control signals through edges. A challenging problem is to identify them in complex networked systems characterized by different types of interactions that form multilayer networks. In this study, we describe a graph pattern called the conserved control path, which allows us to model a common control structure among different types of relations. We present a practical conserved control path detection method (CoPath), which is based on a maximum-weighted matching, to determine the paths that play the most consistent roles in controlling signal transmission in multilayer networks. As a pragmatic application, we demonstrate that the control paths detected in a multilayered pan-cancer network are statistically more consistent. Additionally, they lead to the effective identification of drug targets, thereby demonstrating their power in predicting key pathways that influence multiple cancers.