Search results for: graph matching

Authors: Hanlin Liu, Hua Li, Yintan AI

Abstract:

Network performance prediction (NPP) is essential for the management and optimization of software-defined networking (SDN) and contributes to improving the quality of service (QoS) in SDN to meet the requirements of users. Although current deep learning-based methods can achieve high effectiveness, they still suffer from some problems, such as difficulty in capturing global information of the network, inefficiency in modeling end-to-end network performance, and inadequate graph feature extraction. To cope with these issues, our proposed Graphormer-based architecture for NPP leverages the powerful graph representation ability of Graphormer to effectively model the graph structure data, and a node-edge transformation algorithm is designed to transfer the feature extraction object from nodes to edges, thereby effectively extracting the end-to-end performance characteristics of the network. Moreover, routing oriented centrality measure coefficient for nodes and edges is proposed respectively to assess their importance and influence within the graph. Based on this coefficient, an enhanced feature extraction method and an advanced centrality encoding strategy are derived to fully extract the structural information of the graph. Experimental results on three public datasets demonstrate that the proposed GraphNPP architecture can achieve state-of-the-art results compared to current NPP methods.

Keywords: software-defined networking, network performance prediction, Graphormer, graph neural network

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Authors: Xinghang Lv, Tao Peng, Jia Chen, Junping Liu, Xinrong Hu, Ruhan He, Minghua Jiang, Wenli Cao

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As one of the most dangerous vulnerabilities, effective detection of buffer overflow vulnerabilities is extremely necessary. Traditional detection methods are not accurate enough and consume more resources to meet complex and enormous code environment at present. In order to resolve the above problems, we propose the method for Buffer overflow detection based on Abstract syntax tree, Control flow graph, and Data dependency graph (BodeACD) in C/C++ programs with source code. Firstly, BodeACD constructs the function samples of buffer overflow that are available on Github, then represents them as code representation sequences, which fuse control flow, data dependency, and syntax structure of source code to reduce information loss during code representation. Finally, BodeACD learns vulnerability patterns for vulnerability detection through deep learning. The results of the experiments show that BodeACD has increased the precision and recall by 6.3% and 8.5% respectively compared with the latest methods, which can effectively improve vulnerability detection and reduce False-positive rate and False-negative rate.

Keywords: vulnerability detection, abstract syntax tree, control flow graph, data dependency graph, code representation, deep learning

Procedia PDF Downloads 144

Authors: Mansir Abubakar, Hazlina Hamdan, Norwati Mustapha, Teh Noranis Mohd Aris

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In order to build a matching pattern for each class correspondences of ontology, it is required to specify a set of attribute correspondences across two corresponding classes by clustering. Clustering reduces the size of potential attribute correspondences considered in the matching activity, which will significantly reduce the computation workload; otherwise, all attributes of a class should be compared with all attributes of the corresponding class. Most existing ontology matching approaches lack scalable attributes discovery methods, such as cluster-based attribute searching. This problem makes ontology matching activity computationally expensive. It is therefore vital in ontology matching to design a scalable element or attribute correspondence discovery method that would reduce the size of potential elements correspondences during mapping thereby reduce the computational workload in a matching process as a whole. The objective of this work is 1) to design a clustering method for discovering similar attributes correspondences and relationships between ontologies, 2) to discover element correspondences by classifying elements of each class based on element’s value features using K-medoids clustering technique. Discovering attribute correspondence is highly required for comparing instances when matching two ontologies. During the matching process, any two instances across two different data sets should be compared to their attribute values, so that they can be regarded to be the same or not. Intuitively, any two instances that come from classes across which there is a class correspondence are likely to be identical to each other. Besides, any two instances that hold more similar attribute values are more likely to be matched than the ones with less similar attribute values. Most of the time, similar attribute values exist in the two instances across which there is an attribute correspondence. This work will present how to classify attributes of each class with K-medoids clustering, then, clustered groups to be mapped by their statistical value features. We will also show how to map attributes of a clustered group to attributes of the mapped clustered group, generating a set of potential attribute correspondences that would be applied to generate a matching pattern. The K-medoids clustering phase would largely reduce the number of attribute pairs that are not corresponding for comparing instances as only the coverage probability of attributes pairs that reaches 100% and attributes above the specified threshold can be considered as potential attributes for a matching. Using clustering will reduce the size of potential elements correspondences to be considered during mapping activity, which will in turn reduce the computational workload significantly. Otherwise, all element of the class in source ontology have to be compared with all elements of the corresponding classes in target ontology. K-medoids can ably cluster attributes of each class, so that a proportion of attribute pairs that are not corresponding would not be considered when constructing the matching pattern.

Keywords: attribute correspondence, clustering, computational workload, k-medoids clustering, ontology matching

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Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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A simple adaptive voice activity detector (VAD) is implemented using Gabor and gammatone atomic decomposition of speech for high Gaussian noise environments. Matching pursuit is used for atomic decomposition, and is shown to achieve optimal speech detection capability at high data compression rates for low signal to noise ratios. The most active dictionary elements found by matching pursuit are used for the signal reconstruction so that the algorithm adapts to the individual speakers dominant time-frequency characteristics. Speech has a high peak to average ratio enabling matching pursuit greedy heuristic of highest inner products to isolate high energy speech components in high noise environments. Gabor and gammatone atoms are both investigated with identical logarithmically spaced center frequencies, and similar bandwidths. The algorithm performs equally well for both Gabor and gammatone atoms with no significant statistical differences. The algorithm achieves 70% accuracy at a 0 dB SNR, 90% accuracy at a 5 dB SNR and 98% accuracy at a 20dB SNR using 30dB SNR as a reference for voice activity.

Keywords: atomic decomposition, gabor, gammatone, matching pursuit, voice activity detection

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Authors: Ying Wang, Haiyan Xie, Aoming Zhang

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The degree distance of a graph is a graph invariant that is more sensitive than the Wiener index. In this paper, we calculate the vertex degree distances of one vertex union of the cycle and the star, and the degree distance of one vertex union of the cycle and the star. These results lay a foundation for further study on the extreme value of the vertex degree distances, and the distribution of the vertices with the extreme value in one vertex union of the cycle and the star.

Keywords: degree distance, vertex-degree-distance, one vertex union of a cycle and a star, graph

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Authors: N. M. G. Al-Saidi, K. A. Kadhim, N. A. Rajab

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Over the past decades, computer networks and data communication system has been developing fast, so, the necessity to protect a transmitted data is a challenging issue, and data security becomes a serious problem nowadays. A secret sharing scheme is a method which allows a master key to be distributed among a finite set of participants, in such a way that only certain authorized subsets of participants to reconstruct the original master key. To create a secret sharing scheme, many mathematical structures have been used; the most widely used structure is the one that is based on graph theory (graph access structure). Subsequently, many researchers tried to find efficient schemes based on graph access structures. In this paper, we propose a novel efficient construction of a perfect secret sharing scheme for uniform access structure. The dominating set of vertices in a regular graph is used for this construction in the following way; each vertex represents a participant and each minimum independent dominating subset represents a minimal qualified subset. Some relations between dominating set, graph order and regularity are achieved, and can be used to demonstrate the possibility of using dominating set to construct a secret sharing scheme. The information rate that is used as a measure for the efficiency of such systems is calculated to show that the proposed method has some improved values.

Keywords: secret sharing scheme, dominating set, information rate, access structure, rank

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Authors: Attallah Bilal, Hendel Fatiha

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This paper proposes the bimodal biometrics system for identity verification iris and fingerprint, at matching score level architecture using weighted sum of score technique. The features are extracted from the pre processed images of iris and fingerprint. These features of a query image are compared with those of a database image to obtain matching scores. The individual scores generated after matching are passed to the fusion module. This module consists of three major steps i.e., normalization, generation of similarity score and fusion of weighted scores. The final score is then used to declare the person as genuine or an impostor. The system is tested on CASIA database and gives an overall accuracy of 91.04% with FAR of 2.58% and FRR of 8.34%.

Keywords: iris, fingerprint, sum rule, fusion

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Authors: Arun Prabhakar

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Threat modeling is an important activity carried out in the initial stages of the development lifecycle that helps in building proactive security measures in the product. Though there are many techniques and tools available today, one of the common challenges with the traditional methods is the lack of a systematic approach in identifying security threats. The proposed solution describes an organized model by defining ontologies that help in building patterns to enumerate threats. The concepts of graph theory are applied to build the pattern for discovering threats for any given scenario. This graph-based solution also brings in other benefits, making it a customizable and scalable model.

Keywords: directed acyclic graph, ontology, patterns, threat identification, threat modeling

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Authors: Giselle Maggie Fer Castañeda, Diego Iván González

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The objective of this work was to study the autoshaped choice behavior in the Donahoe, Burgos and Palmer (DBP) neural network model and analyze it under the matching law. Autoshaped choice can be viewed as a form of economic behavior defined as the preference between alternatives according to their relative outcomes. The Donahoe, Burgos and Palmer (DBP) model is a connectionist proposal that unifies operant and Pavlovian conditioning. This model has been used for more than three decades as a neurobehavioral explanation of conditioning phenomena, as well as a generator of predictions suitable for experimental testing with non-human animals and humans. The study consisted of different simulations in which, in each one, a ratio of reinforcement was established for two alternatives, and the responses (i.e., activations) in each of them were measured. Choice studies with animals have demonstrated that the data generally conform closely to the generalized matching law equation, which states that the response ratio equals proportionally to the reinforcement ratio; therefore, it was expected to find similar results with the neural networks of the Donahoe, Burgos and Palmer (DBP) model since these networks have simulated and predicted various conditioning phenomena. The results were analyzed by the generalized matching law equation, and it was observed that under some contingencies, the data from the networks adjusted approximately to what was established by the equation. Implications and limitations are discussed.

Keywords: matching law, neural networks, computational models, behavioral sciences

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Authors: Jung-Min Yang

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A method of tolerating input faults for input/state asynchronous sequential machines is proposed. A corrective controller is placed in front of the considered asynchronous machine to realize model matching with a reference model. The value of the external input transmitted to the closed-loop system may change by fault. We address the existence condition for the controller that can counteract adverse effects of any input fault while maintaining the objective of model matching. A design procedure for constructing the controller is outlined. The proposed reachability condition for the controller design is validated in an illustrative example.

Keywords: asynchronous sequential machines, corrective control, fault tolerance, input faults, model matching

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Authors: Pedro M. A. Vitoriano, Tito. G. Amaral

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Automated Optical Inspection (AOI) Systems are commonly used on Printed Circuit Boards (PCB) manufacturing. The use of this technology has been proven as highly efficient for process improvements and quality achievements. The correct extraction of the component for posterior analysis is a critical step of the AOI process. Nowadays, the Pattern Matching Algorithm is commonly used, although this algorithm requires extensive calculations and is time consuming. This paper will present an improved algorithm for the component localization process, with the capability of implementation in a parallel execution system.

Keywords: AOI, automated optical inspection, SMD, surface mounting devices, pattern matching, parallel execution

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Authors: Yihao Kuang, Bowen Ding

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With the increasing scale and complexity of knowledge graph, modern knowledge graph contains more and more types of entity, relationship, and attribute information. Therefore, in recent years, it has been a trend for knowledge graph inference to use reinforcement learning to deal with large-scale, incomplete, and noisy knowledge graphs and improve the inference effect and interpretability. The Proximal Policy Optimization (PPO) algorithm utilizes a near-end strategy optimization approach. This allows for more extensive updates of policy parameters while constraining the update extent to maintain training stability. This characteristic enables PPOs to converge to improved strategies more rapidly, often demonstrating enhanced performance early in the training process. Furthermore, PPO has the advantage of offline learning, effectively utilizing historical experience data for training and enhancing sample utilization. This means that even with limited resources, PPOs can efficiently train for reinforcement learning tasks. Based on these characteristics, this paper aims to obtain a better and more efficient inference effect by introducing PPO into knowledge inference technology.

Keywords: reinforcement learning, PPO, knowledge inference

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Authors: G. Balakrishnan

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Stereo Correspondence plays a major role in estimation of distance of an object from the stereo camera pair for various applications. In this paper, a stereo correspondence algorithm based on block-matching technique is presented. Initially, an energy matrix is calculated for every disparity obtained using modified Sum of Absolute Difference (SAD). Higher energy matrix errors are removed by using threshold value in order to reduce the mismatch errors. A smoothening filter is applied to eliminate unreliable disparity estimate across the object boundaries. The purpose is to improve the reliability of calculation of disparity map. The experimental results obtained shows that the final depth map produce better results and can be used to all the applications using stereo cameras.

Keywords: stereo matching, filters, energy matrix, disparity

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Authors: Hoda Ghavamipoor, S. Alireza Hashemi Golpayegani

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An approach to model the customer interaction with e-commerce websites is presented. Considering the service quality level as a predictive feature, we offer an improved method based on the Customer Behavior Model Graph (CBMG), a state-transition graph model. To derive the Quality of Service sensitive-CBMG (QoS-CBMG) model, process-mining techniques is applied to pre-processed website server logs which are categorized as ‘buy’ or ‘visit’. Experimental results on an e-commerce website data confirmed that the proposed method outperforms CBMG based method.

Keywords: customer behavior model, electronic commerce, quality of service, customer behavior model graph, process mining

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Authors: Benny Benyamin Nasution, Rahmat Widia Sembiring, Abdul Rahman Dalimunthe, Nursiah Mustari, Nisfan Bahri, Berta br Ginting, Riadil Akhir Lubis, Rita Tavip Megawati, Indri Dithisari

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The earth coordinate system is an important part of an attempt for earthquake forecasting, such as the one using Single Layer Hierarchical Graph Neuron (SLHGN). However, there are a number of problems that need to be worked out before the coordinate system can be utilized for the forecaster. One example of those is that SLHGN requires that the focused area of an earthquake must be constructed in a grid-like form. In fact, within the current earth coordinate system, the same longitude-difference would produce different distances. This can be observed at the distance on the Equator compared to distance at both poles. To deal with such a problem, a coordinate system has been developed, so that it can be used to support the ongoing earthquake forecasting using SLHGN. Two important issues have been developed in this system: 1) each location is not represented through two-value (longitude and latitude), but only a single value, 2) the conversion of the earth coordinate system to the x-y cartesian system requires no angular formulas, which is therefore fast. The accuracy and the performance have not been measured yet, since earthquake data is difficult to obtain. However, the characteristics of the SLHGN results show a very promising answer.

Keywords: hierarchical graph neuron, multidimensional hierarchical graph neuron, single layer hierarchical graph neuron, natural disaster forecasting, earthquake forecasting, earth coordinate system

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Authors: Lin Cheng, Zijiang Yang

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Program synthesis is the task to automatically generate programs based on user specification. In this paper, we present a framework that synthesizes programs from flow charts that serve as accurate and intuitive specification. In order doing so, we propose a deep neural network called GRCNN that recognizes graph structure from its image. GRCNN is trained end-to-end, which can predict edge and node information of the flow chart simultaneously. Experiments show that the accuracy rate to synthesize a program is 66.4%, and the accuracy rates to recognize edge and node are 94.1% and 67.9%, respectively. On average, it takes about 60 milliseconds to synthesize a program.

Keywords: program synthesis, flow chart, specification, graph recognition, CNN

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Authors: B. Roopa Sri, Y Lakshmi Naidu

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Chemical Graph Theory (CGT) is the branch of mathematical chemistry in which molecules are modeled to study their physicochemical properties using molecular descriptors. Amongst these descriptors, topological indices play a vital role in predicting the properties by defining the graph topology of the molecule. Recently, the bond-additive topological index known as the Mostar index has been proposed. In this paper, we compute the Mostar-type indices of octane isomers and use the data obtained to perform QSPR analysis. Furthermore, we show the correlation between the Mostar type indices and the properties.

Keywords: chemical graph theory, mostar type indices, octane isomers, qspr analysis, topological index

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Authors: Rashini Maduka, C. R. Wijesinghe, A. R. Weerasinghe

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Drug-drug interactions (DDIs) can happen when two or more drugs are taken together. Today DDIs have become a serious health issue due to adverse drug effects. In vivo and in vitro methods for identifying DDIs are time-consuming and costly. Therefore, in-silico-based approaches are preferred in DDI identification. Most machine learning models for DDI prediction are used chemical and biological drug properties as features. However, some drug features are not available and costly to extract. Therefore, it is better to make automatic feature engineering. Furthermore, people who have diabetes already suffer from other diseases and take more than one medicine together. Then adverse drug effects may happen to diabetic patients and cause unpleasant reactions in the body. In this study, we present a model with a graph convolutional autoencoder and a graph decoder using a dataset from DrugBank version 5.1.3. The main objective of the model is to identify unknown interactions between antidiabetic drugs and the drugs taken by diabetic patients for other diseases. We considered automatic feature engineering and used Known DDIs only as the input for the model. Our model has achieved 0.86 in AUC and 0.86 in AP.

Keywords: drug-drug interaction prediction, graph embedding, graph convolutional networks, adverse drug effects

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Authors: H. Nabaei, M. Joghataie

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In this article, we study the design methods of matched filter with commercial software including CST Studio and ADS in specific frequency: 900 MHz. At first, we select two amounts of impedance for studying matching of them. Then, using by matched filter utility tool in ADS software, we simulate and deviate the elements of matched filters. In the following, we implement matched filter in CST STUDIO software. The simulated results show the great conformity in this field. Also, we peruse scattering and Impedance parameters in the Derivative structure. Finally, the layout of matched filter is obtained by the schematic tool of CST STUDIO. In fact, here, we present the design process of matched filters in the specific frequency.

Keywords: impedance matching, lumped element, transmission line, maximum power transmission, 3D layout

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Authors: Masoumeh Ali Pouri, Hamid Haj Seyyed Javadi

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Nowadays, cloud processing is one of the important issues in information technology. Since scheduling of tasks graph is an NP-hard problem, considering approaches based on undeterminisitic methods such as evolutionary processing, mostly genetic and cuckoo algorithms, will be effective. Therefore, an efficient algorithm has been proposed for scheduling of tasks graph to obtain an appropriate scheduling with minimum time. In this algorithm, the new approach is based on making the length of the critical path shorter and reducing the cost of communication. Finally, the results obtained from the implementation of the presented method show that this algorithm acts the same as other algorithms when it faces graphs without communication cost. It performs quicker and better than some algorithms like DSC and MCP algorithms when it faces the graphs involving communication cost.

Keywords: cloud computing, scheduling, tasks graph, chakoos algorithm

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Authors: Israa Sh. Tawfic, Sema Koc Kayhan

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Given a large sparse signal, great wishes are to reconstruct the signal precisely and accurately from lease number of measurements as possible as it could. Although this seems possible by theory, the difficulty is in built an algorithm to perform the accuracy and efficiency of reconstructing. This paper proposes a new proved method to reconstruct sparse signal depend on using new method called Least Support Matching Pursuit (LS-OMP) merge it with the theory of Partial Knowing Support (PSK) given new method called Partially Knowing of Least Support Orthogonal Matching Pursuit (PKLS-OMP). The new methods depend on the greedy algorithm to compute the support which depends on the number of iterations. So to make it faster, the PKLS-OMP adds the idea of partial knowing support of its algorithm. It shows the efficiency, simplicity, and accuracy to get back the original signal if the sampling matrix satisfies the Restricted Isometry Property (RIP). Simulation results also show that it outperforms many algorithms especially for compressible signals.

Keywords: compressed sensing, lest support orthogonal matching pursuit, partial knowing support, restricted isometry property, signal reconstruction

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Authors: Benniche Omar

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We are concerned with abstract fully nonlinear differential equations having the form y’(t)=Ay(t)+f(t,y(t)) where A is an m—dissipative operator (possibly multi—valued) defined on a subset D(A) of a Banach space X with values in X and f is a given function defined on I×X with values in X. We consider a graph K in I×X. We recall that K is said to be viable with respect to the above abstract differential equation if for each initial data in K there exists at least one trajectory starting from that initial data and remaining in K at least for a short time. The viability problem has been studied by many authors by using various techniques and frames. If K is closed, it is shown that a tangency condition, which is mainly linked to the dynamic, is crucial for viability. In the case when X is infinite dimensional, compactness and convexity assumptions are needed. In this paper, we are concerned with the notion of near viability for a given graph K with respect to y’(t)=Ay(t)+f(t,y(t)). Roughly speaking, the graph K is said to be near viable with respect to y’(t)=Ay(t)+f(t,y(t)), if for each initial data in K there exists at least one trajectory remaining arbitrary close to K at least for short time. It is interesting to note that the near viability is equivalent to an appropriate tangency condition under mild assumptions on the dynamic. Adding natural convexity and compactness assumptions on the dynamic, we may recover the (exact) viability. Here we investigate near viability for a graph K in I×X with respect to y’(t)=Ay(t)+f(t,y(t)) where A and f are as above. We emphasis that the t—dependence on the perturbation f leads us to introduce a new tangency concept. In the base of a tangency conditions expressed in terms of that tangency concept, we formulate criteria for K to be near viable with respect to y’(t)=Ay(t)+f(t,y(t)). As application, an abstract null—controllability theorem is given.

Keywords: abstract differential equation, graph, tangency condition, viability

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Authors: M. Ghasemi, F. Eskandari, B. Hamzehei, A. R. Arshi

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Bioelectric activity of nervous cells might be changed causing by various factors. This alteration can lead to unforeseen circumstances in other organs of the body. Therefore, the purpose of this study was to model a single neuron and its behavior under an initial stimulation. This study was developed based on cable theory by means of the Bond Graph method. The numerical values of the parameters were derived from empirical studies of cellular electrophysiology experiments. Initial excitation was applied through square current functions, and the resulted action potential was estimated along the neuron. The results revealed that the model was developed in this research adapted with the results of experimental studies and demonstrated the electrical behavior of nervous cells properly.

Keywords: bond graph, stimulation, nervous cells, modeling

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Authors: Benazzouz Djamel, Termeche Adel, Touati Youcef, Alem Said, Ouziala Mahdi

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This paper presents an approach which detect and isolate efficiently a fault in a system. This approach avoids false alarms, non-detections and delays in detecting faults. A study case have been proposed to show the importance of taking into consideration the uncertainties in the decision-making procedure and their effect on the degradation diagnostic performance and advantage of using Bond Graph (BG) for such degradation. The use of BG in the Linear Fractional Transformation (LFT) form allows generating robust Analytical Redundancy Relations (ARR’s), where the uncertain part of ARR’s is used to generate the residuals adaptive thresholds. The study case concerns an electromechanical system composed of a motor, a reducer and an external load. The aim of this application is to show the effectiveness of the BG-LFT approach to robust fault detection.

Keywords: bond graph, LFT, uncertainties, detection and faults isolation, ARR

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Authors: Chia-Yen Lee, Hao-Jen Wang, Jhih-Hao Lai

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In recent years, infrared (IR) imaging has been considered as a potential tool to assess the efficacy of chemotherapy and early detection of breast cancer. Regions of tumor growth with high metabolic rate and angiogenesis phenomenon lead to the high temperatures. Observation of differences between the heat maps in long term is useful to help assess the growth of breast cancer cells and detect breast cancer earlier, wherein the multi-time infrared image alignment technology is a necessary step. Representative feature points detection and matching are essential steps toward the good performance of image registration and quantitative analysis. However, there is no clear boundary on the infrared images and the subject's posture are different for each shot. It cannot adhesive markers on a body surface for a very long period, and it is hard to find anatomic fiducial markers on a body surface. In other words, it’s difficult to detect and match features in an IR sequence images. In this study, automated feature detection and matching algorithms with two type of automatic feature points (i.e., vascular branch points and modified Harris corner) are developed respectively. The preliminary results show that the proposed method could identify the representative feature points on the IR breast images successfully of 98% accuracy and the matching results of 93% accuracy.

Keywords: Harris corner, infrared image, feature detection, registration, matching

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Authors: J. Andrade-Garda, A. Anguera, J. Ares-Casal, M. Hidalgo-Lorenzo, J.-A. Lara, D. Lizcano, S. Suárez-Garaboa

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In the current constantly changing economic context, collaborative networks allow partners to undertake projects that would not be possible if attempted by them individually. These projects usually involve the performance of a group of tasks (named roles) that have to be distributed among the partners. Thus, an allocation/matching problem arises that will be referred to as Role-Partner Allocation problem. In real life this situation is addressed by negotiation between partners in order to reach ad hoc agreements. Besides taking a long time and being hard work, both historical evidence and economic analysis show that such approach is not recommended. Instead, the allocation process should be automated by means of a centralized matching scheme. However, as a preliminary step to start the search for such a matching mechanism (or even the development of a new one), the problem and its core components must be specified. To this end, this paper establishes (i) the definition of the problem and its constraints, (ii) the key features of the involved elements (i.e., roles and partners); and (iii) how to create preference lists both for roles and partners. Only this way it will be possible to conduct subsequent methodological research on the solution method.     

Keywords: collaborative network, matching, partner, preference list, role

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Authors: Jake Gonzalez, Tommy Dang

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This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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Authors: Yaw-Ling Lin

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A de Bruijn graph of order k is a graph whose vertices representing all length-k sequences with edges joining pairs of vertices whose sequences have maximum possible overlap (length k−1). Every Hamiltonian cycle of this graph defines a distinct, minimum length de Bruijn sequence containing all k-mers exactly once. A Kautz sequence is the minimal generating sequence so as the sequence of minimal length that produces all possible length-k sequences with the restriction that every two consecutive alphabets in the sequences must be different. A collection of de Bruijn/Kautz sequences are orthogonal if any two sequences are of maximally differ in sequence composition; that is, the maximum length of their common substring is k. In this paper, we discuss how such a collection of (maximal) orthogonal de Bruijn/Kautz sequences can be made and use the algorithm to build up a web application service for the synthesized DNA and other related biomolecular sequences.

Keywords: biomolecular sequence synthesis, de Bruijn sequences, Eulerian cycle, Hamiltonian cycle, Kautz sequences, orthogonal sequences

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Authors: Raghavi C. Janaswamy

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In the healthcare sector, heterogenous data elements such as patients, diagnosis, symptoms, conditions, observation text from physician notes, and prescriptions form the essentials of the Electronic Health Record (EHR). The data in the form of clear text and images are stored or processed in a relational format in most systems. However, the intrinsic structure restrictions and complex joins of relational databases limit the widespread utility. In this regard, the design and development of realistic mapping and deep connections as real-time objects offer unparallel advantages. Herein, a graph neural network-based classification of EHR data has been developed. The patient conditions have been predicted as a node classification task using a graph-based open source EHR data, Synthea Database, stored in Tigergraph. The Synthea DB dataset is leveraged due to its closer representation of the real-time data and being voluminous. The graph model is built from the EHR heterogeneous data using python modules, namely, pyTigerGraph to get nodes and edges from the Tigergraph database, PyTorch to tensorize the nodes and edges, PyTorch-Geometric (PyG) to train the Graph Neural Network (GNN) and adopt the self-supervised learning techniques with the AutoEncoders to generate the node embeddings and eventually perform the node classifications using the node embeddings. The model predicts patient conditions ranging from common to rare situations. The outcome is deemed to open up opportunities for data querying toward better predictions and accuracy.

Keywords: electronic health record, graph neural network, heterogeneous data, prediction

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Authors: Jiajun Wang, Xiaoge Li

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The purpose of the aspect-level sentiment analysis task is to identify the sentiment polarity of aspects in a sentence. Currently, most methods mainly focus on using neural networks and attention mechanisms to model the relationship between aspects and context, but they ignore the dependence of words in different ranges in the sentence, resulting in deviation when assigning relationship weight to other words other than aspect words. To solve these problems, we propose a new aspect-level sentiment analysis model that combines a multi-channel convolutional network and graph convolutional network (GCN). Firstly, the context and the degree of association between words are characterized by Long Short-Term Memory (LSTM) and self-attention mechanism. Besides, a multi-channel convolutional network is used to extract the features of words in different ranges. Finally, a convolutional graph network is used to associate the node information of the dependency tree structure. We conduct experiments on four benchmark datasets. The experimental results are compared with those of other models, which shows that our model is better and more effective.

Keywords: aspect-level sentiment analysis, attention, multi-channel convolution network, graph convolution network, dependency tree

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