Search results for: graph coloring

Authors: Angela U. Makolo, Temitayo A. Olagunju

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The knowledge of signaling pathways is central to understanding the biological mechanisms of organisms since it has been identified that in eukaryotic organisms, the number of signaling pathways determines the number of ways the organism will react to external stimuli. Signaling pathways are studied using protein interaction networks constructed from protein-protein interaction data obtained using high throughput experimental procedures. However, these high throughput methods are known to produce very high rates of false positive and negative interactions. In order to construct a useful protein interaction network from this noisy data, computational methods are applied to validate the protein-protein interactions. In this study, a computational technique to identify signaling pathways from a protein interaction network constructed using validated protein-protein interaction data was designed. A weighted interaction graph of the Saccharomyces cerevisiae (Baker’s Yeast) organism using the proteins as the nodes and interactions between them as edges was constructed. The weights were obtained using Bayesian probabilistic network to estimate the posterior probability of interaction between two proteins given the gene expression measurement as biological evidence. Only interactions above a threshold were accepted for the network model. A pathway was formalized as a simple path in the interaction network from a starting protein and an ending protein of interest. We were able to identify some pathway segments, one of which is a segment of the pathway that signals the start of the process of meiosis in S. cerevisiae.

Keywords: Bayesian networks, protein interaction networks, Saccharomyces cerevisiae, signalling pathways

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Authors: Mina Samizadeh

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In the past few decades, there has been an explosion in the amount of available data produced from various sources with different topics. The availability of this enormous data necessitates us to adopt effective computational tools to explore the data. This leads to an intense growing interest in the research community to develop computational methods focused on processing this text data. A line of study focused on condensing the text so that we are able to get a higher level of understanding in a shorter time. The two important tasks to do this are keyword extraction and text summarization. In keyword extraction, we are interested in finding the key important words from a text. This makes us familiar with the general topic of a text. In text summarization, we are interested in producing a short-length text which includes important information about the document. The TextRank algorithm, an unsupervised learning method that is an extension of the PageRank (algorithm which is the base algorithm of Google search engine for searching pages and ranking them), has shown its efficacy in large-scale text mining, especially for text summarization and keyword extraction. This algorithm can automatically extract the important parts of a text (keywords or sentences) and declare them as a result. However, this algorithm neglects the semantic similarity between the different parts. In this work, we improved the results of the TextRank algorithm by incorporating the semantic similarity between parts of the text. Aside from keyword extraction and text summarization, we develop a topic clustering algorithm based on our framework, which can be used individually or as a part of generating the summary to overcome coverage problems.

Keywords: keyword extraction, n-gram extraction, text summarization, topic clustering, semantic analysis

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Authors: Xinyuan Zou, Qihui Tang, Shujian Wang, Yulin Huang, Jie Gui, Xiangping Liu, Gang Liu, Yanqiang Tao

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Childhood trauma can have a long-lasting influence on individuals and contribute to mental disorders, including depression and anxiety. The current study aimed to explore the symptomatic and developmental patterns of depression, anxiety, and stress among adolescents who have suffered from childhood trauma. A total of 3,598 college students (female = 1,617 (44.94%), Mean Age = 19.68, SD Age = 1.35) in China completed the Childhood Trauma Questionnaire (CTQ) and the Depression, Anxiety, and Stress Scales (DASS-21), and 2,337 participants met the selection standard based on the cut-off scores of the CTQ. The symptomatic network and directed acyclic graph (DAG) network approaches were used. The results revealed that males reported experiencing significantly more physical abuse, physical neglect, emotional neglect, and sexual abuse compared to females. However, females scored significantly higher than males on all items of DASS-21, except for “Worthless”. No significant difference between the two genders was observed in the network structure and global strength. Meanwhile, among all participants, “Down-hearted” and “Agitated” appeared to be the most interconnected symptoms, the bridge symptoms in the symptom network, as well as the most vital symptoms in the DAG network. Apart from that, “No-relax” also served as the most prominent symptom in the DAG network. The results suggested that intervention targeted at assisting adolescents in developing more adaptive coping strategies with stress and regulating emotion could benefit the alleviation of comorbid depression, anxiety, and stress.

Keywords: symptom network, childhood trauma, depression, anxiety, stress

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Authors: Richard Molyneux, Christopher Parrott, Kirill Horoshenkov

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This paper aims to demonstrate how various algorithms can be implemented within swarms of autonomous robots to provide continuous inspection within underground pipeline networks. Current methods of fault detection within pipes are costly, time consuming and inefficient. As such, solutions tend toward a more reactive approach, repairing faults, as opposed to proactively seeking leaks and blockages. The paper presents an efficient inspection method, showing that autonomous swarm robotics is a viable way of monitoring underground infrastructure. Tailored adaptations of various Vehicle Routing Problems (VRP) and path-planning algorithms provide a customised inspection procedure for complicated networks of underground pipes. The performance of multiple algorithms is compared to determine their effectiveness and feasibility. Notable inspirations come from ant colonies and stigmergy, graph theory, the k-Chinese Postman Problem ( -CPP) and traffic theory. Unlike most swarm behaviours which rely on fast communication between agents, underground pipe networks are a highly challenging communication environment with extremely limited communication ranges. This is due to the extreme variability in the pipe conditions and relatively high attenuation of acoustic and radio waves with which robots would usually communicate. This paper illustrates how to optimise the inspection process and how to increase the frequency with which the robots pass each other, without compromising the routes they are able to take to cover the whole network.

Keywords: autonomous inspection, buried pipes, stigmergy, swarm intelligence, vehicle routing problem

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Authors: Ali Essam El Shazly

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The slum survey of 'Sequina' area in Alexandria details the building rooms of twenty-building samples according to the integral measure of space syntax. The essence of room organization sets the most integrative 'visitor' domain between the 'inhabitant' wings of less integrated 'parent' than the 'children' structure with visual ring of 'balcony' space. Despite the collective real relative asymmetry of 'pheno-type' aggregation, the relative asymmetry of individual layouts reveals 'geno-type' structure of spatial diversity. The multifunction of rooms optimizes the integral structure of graph and visibility merge, which contrasts with the deep tailing structure of distinctive social domains. The most integrative layout inverts the geno-type into freed rooms of shallow 'inhabitant' domain against the off-centered 'visitor' space, while the most segregated layout further restricts the pheno-type through isolated 'visitor' from 'inhabitant' domains across the 'staircase' public domain. The catalyst 'kitchen & living' spaces demonstrate multi-structural dimensions among the various social domains. The former ranges from most exposed central integrity to the most hidden 'motherhood' territories. The latter, however, mostly integrates at centrality or at the further ringy 'childern' domain. The study concludes social structure of spatial integrity for redevelopment, which is determined through the micro-level survey of rooms with integral dimensions.

Keywords: Alexandria, Sequina slum, spatial integration, space syntax

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Authors: Anahit Hakobjanyan, Zdenka Navratilova, Gabriela Strakova, Martin Petrek

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Aging has a suppressive influence on human immune cells. Apoptosis may play important role in age-dependent immunosuppression and lymphopenia. Prevention of apoptosis may be promoted by BCL2-dependent and BCL2-independent manner. BCL2 is an antiapoptotic factor that has an antioxidative role by locating the glutathione at mitochondria and repressing oxidative stress. STAT3 may suppress apoptosis in BCL2-independent manner and promote cell survival blocking cytochrome-c release and reducing ROS production. The aim of our study was to estimate the influence of aging on BCL2-dependent and BCL2-independent prevention of apoptosis via measurement of BCL2 and STAT3 mRNAs expressions. The study was done on Armenian population (2 groups: 37 healthy young (mean age±SE; min/max age, male/female: 37.6±1.1; 20/54, 15/22), 28 healthy aged (66.7±1.5; 57/85, 12/16)). mRNA expression in peripheral blood leukocytes (PBL) was determined by RT-PCR using PSMB2 as the reference gene. Statistical analysis was done with Graph-Pad Prism 5; P < 0.05 considered as significant. The expression of BCL2 mRNA was lower in aged group (0.199) compared with young ones (0.643)(p < 0.01). Decrease expression was also recorded for female and male subgroups (p < 0.01). The expression level of STAT3 mRNA was increased (young, 0.228; aged, 0.428) (p < 0.05) during aging (in the whole age group and male/female subgroups). Decreased level of BCL2 mRNA may indicate about the suppression of BCL2-dependent prevention of apoptosis during aging in peripheral blood leukocytes. At the same time increased the level of STAT3 may suggest about activation of BCL2-independent prevention of apoptosis during aging.

Keywords: BCL2, STAT3, aging, apoptosis

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Authors: Shanshan Zhu, Mohammad Nasim

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Financial fraud continues to be a major threat to financial institutions across the world, causing colossal money losses and undermining public trust. Fraud prevention techniques, based on hard rules, have become ineffective due to evolving patterns of fraud in recent times. Against such a background, the present study probes into distinct methodologies that exploit emergent AI-driven techniques to further strengthen fraud detection. We would like to compare the performance of generative adversarial networks and graph neural networks with other popular techniques, like gradient boosting, random forests, and neural networks. To this end, we would recommend integrating all these state-of-the-art models into one robust, flexible, and smart system for real-time anomaly and fraud detection. To overcome the challenge, we designed synthetic data and then conducted pattern recognition and unsupervised and supervised learning analyses on the transaction data to identify which activities were fishy. With the use of actual financial statistics, we compare the performance of our model in accuracy, speed, and adaptability versus conventional models. The results of this study illustrate a strong signal and need to integrate state-of-the-art, AI-driven fraud detection solutions into frameworks that are highly relevant to the financial domain. It alerts one to the great urgency that banks and related financial institutions must rapidly implement these most advanced technologies to continue to have a high level of security.

Keywords: AI-driven fraud detection, financial security, machine learning, anomaly detection, real-time fraud detection

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Authors: Sawitree Wongkittirungrueang

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The objectives of this research were: 1) to study the effect of social stories on social interaction of students with autism. The sample was Pratomsuksa level 5 student with autism, Khon Kaen University Demonstration School, who was diagnosed by the Physician as High Functioning Autism since he was able to read, write, calculate and was studying in inclusive classroom. However, he still had disability in social interaction to participate in social activity group and communication. He could not learn how to develop friendship or create relationship. He had inappropriate behavior in social context. He did not understand complex social situations. In addition, he did seemed not know time and place. He was not able to understand feeling of oneself as well as the others. Consequently, he could not express his emotion appropriately. He did not understand or express his non-verbal language for communicating with friends. He lacked of common interest or emotion with nearby persons. He greeted inappropriately or was not interested in greeting. In addition, he did not have eye contact. He used inadequate language etc. He was elected by Purposive Sampling. His parents were willing to allow them to participate in this study. The research instruments were the lesson plan of social stories, and the picture book of social stories. The instruments used for data collection, were the social interaction evaluation of autistic students. This research was Quasi Experimental Research as One Group Pre-test, Post-test Design. For the Pre-test, the experiment was conducted by social stories. Then, the Post-test was implemented. The statistic used for data analysis, included the Mean, and Standard Deviation. The research findings were shown by Graph. The findings revealed hat the autistic students taught by social stories indicated better social interaction after being taught by social stories.

Keywords: social story, autism spectrum disorder (ASD), autism, social interaction

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Authors: Hounyèmè Romuald, Mama Daouda, Argillier Christine

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The present study focused on the use of benthic macrofauna to define the reference state of an anthropized lagoon (Nokoué-Benin) from the responses of relevant metrics to proxies. The approach used is a combination of a joint species distribution model and Bayesian networks. The joint species distribution model was used to select the relevant metrics and generate posterior probabilities that were then converted into posterior response probabilities for each of the quality classes (pressure levels), which will constitute the conditional probability tables allowing the establishment of the probabilistic graph representing the different causal relationships between metrics and pressure proxies. For the definition of the reference thresholds, the predicted responses for low-pressure levels were read via probability density diagrams. Observations collected during high and low water periods spanning 03 consecutive years (2004-2006), sampling 33 macroinvertebrate taxa present at all seasons and sampling points, and measurements of 14 environmental parameters were used as application data. The study demonstrated reliable inferences, selection of 07 relevant metrics and definition of quality thresholds for each environmental parameter. The relevance of the metrics as well as the reference thresholds for ecological assessment despite the small sample size, suggests the potential for wider applicability of the approach for aquatic ecosystem monitoring and assessment programs in developing countries generally characterized by a lack of monitoring data.

Keywords: pressure proxies, bayesian inference, bioindicators, acadjas, functional traits

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Authors: Zuhal Kurt, Meral Kurt, Bilge T. Bal, Kemal Ozkan

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Shade matching and reproduction is the most important element of success in prosthetic dentistry. Until recently, shade matching procedure was implemented by dentists visual perception with the help of shade guides. Since many factors influence visual perception; tooth shade matching using visual devices (shade guides) is highly subjective and inconsistent. Subjective nature of this process has lead to the development of instrumental devices. Nowadays, colorimeters, spectrophotometers, spectroradiometers and digital image analysing systems are used for instrumental shade selection. Instrumental devices have advantages that readings are quantifiable, can obtain more rapidly and simply, objectively and precisely. However, these devices have noticeable drawbacks. For example, translucent structure and irregular surfaces of teeth lead to defects on measurement with these devices. Also between the results acquired by devices with different measurement principles may make inconsistencies. So, its obligatory to search for new methods for dental shade matching process. A computer-aided system device; digital camera has developed rapidly upon today. Currently, advances in image processing and computing have resulted in the extensive use of digital cameras for color imaging. This procedure has a much cheaper process than the use of traditional contact-type color measurement devices. Digital cameras can be taken by the place of contact-type instruments for shade selection and overcome their disadvantages. Images taken from teeth show morphology and color texture of teeth. In last decades, a new method was recommended to compare the color of shade tabs taken by a digital camera using color features. This method showed that visual and computer-aided shade matching systems should be used as concatenated. Recently using methods of feature extraction techniques are based on shape description and not used color information. However, color is mostly experienced as an essential property in depicting and extracting features from objects in the world around us. When local feature descriptors with color information are extended by concatenating color descriptor with the shape descriptor, that descriptor will be effective on visual object recognition and classification task. Therefore, the color descriptor is to be used in combination with a shape descriptor it does not need to contain any spatial information, which leads us to use local histograms. This local color histogram method is remain reliable under variation of photometric changes, geometrical changes and variation of image quality. So, coloring local feature extraction methods are used to extract features, and also the Scale Invariant Feature Transform (SIFT) descriptor used to for shape description in the proposed method. After the combination of these descriptors, the state-of-art descriptor named by Color-SIFT will be used in this study. Finally, the image feature vectors obtained from quantization algorithm are fed to classifiers such as Nearest Neighbor (KNN), Naive Bayes or Support Vector Machines (SVM) to determine label(s) of the visual object category or matching. In this study, SVM are used as classifiers for color determination and shade matching. Finally, experimental results of this method will be compared with other recent studies. It is concluded from the study that the proposed method is remarkable development on computer aided tooth shade determination system.

Keywords: classifiers, color determination, computer-aided system, tooth shade matching, feature extraction

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Authors: Tulsi Ram Bhusal

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Global climate change is known to have a huge impact on agriculture due to changing in rainfall pattern and elevated air temperature that lead to drought and/or flooding. This systematic study has focused on agriculture in Nepal. The study has shown that the trend of current climatic change is affecting rice production, while the farmers with technological access have tried to adapt to the changing conditions at their level. There is insufficient intervention from the government side in terms of policies and schemes. The lack of sufficient funds is one of the significant reasons in terms of governance. The climatic trends and the way it is affecting the annual riceyieldinNepal has been discussed in this study thoroughly. This study has reviewed published studies and ferred important points regarding the Nepal’s status on rice production. Mainly due to the increasing graph of average temperature and other physical conditions needed for the proper cultivation of ricearechanging due to which there is significant dropofannual rice production. Although from corners of the country, many farmers have attempted to adapt the methods of cultivation to the changing climatic conditions, lack of access to technologies, and fund allocation from the governmental level, it is difficult for the mtobringchanges in rice production by the crown without any institutional help. This systematic study effectively presents the magnitude of the impact on rice cultivation due to climatic changes inrecenttimesinNepal. This review aims to bring the current scenarioofNepal’sricefarming, and it impacts due to changing climate, which can subsequently contribute in devising plans for proper governance, formulating policies, and allocation of funds for the betterment.

Keywords: rice, climate change, rice production, nepal, agriculture

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Authors: Songul Cinaroglu

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Regional planning in health has gained speed for developing countries in recent years. In Turkey, 89 different Public Hospital Unions (PHUs) were conducted based on provincial levels. In this study technical efficiencies of 89 PHUs were examined by using Data Envelopment Analysis (DEA) and machine learning techniques by dividing them into two clusters in terms of similarities of input and output indicators. Number of beds, physicians and nurses determined as input variables and number of outpatients, inpatients and surgical operations determined as output indicators. Before performing DEA, PHUs were grouped into two clusters. It is seen that the first cluster represents PHUs which have higher population, demand and service density than the others. The difference between clusters was statistically significant in terms of all study variables (p ˂ 0.001). After clustering, DEA was performed for general and for two clusters separately. It was found that 11% of PHUs were efficient in general, additionally 21% and 17% of them were efficient for the first and second clusters respectively. It is seen that PHUs, which are representing urban parts of the country and have higher population and service density, are more efficient than others. Random forest decision tree graph shows that number of inpatients is a determinative factor of efficiency of PHUs, which is a measure of service density. It is advisable for public health policy makers to use statistical learning methods in resource planning decisions to improve efficiency in health care.

Keywords: public hospital unions, efficiency, data envelopment analysis, random forest

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Authors: Somayeh Komeylian

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The direction of arrival (DoA) estimation is the crucial aspect of the radar technologies for detecting and dividing several signal sources. In this scenario, the antenna array output modeling involves numerous parameters including noise samples, signal waveform, signal directions, signal number, and signal to noise ratio (SNR), and thereby the methods of the DoA estimation rely heavily on the generalization characteristic for establishing a large number of the training data sets. Hence, we have analogously represented the two different optimization models of the DoA estimation; (1) the implementation of the decision directed acyclic graph (DDAG) for the multiclass least-squares support vector machine (LS-SVM), and (2) the optimization method of the deep neural network (DNN) radial basis function (RBF). We have rigorously verified that the LS-SVM DDAG algorithm is capable of accurately classifying DoAs for the three classes. However, the accuracy and robustness of the DoA estimation are still highly sensitive to technological imperfections of the antenna arrays such as non-ideal array design and manufacture, array implementation, mutual coupling effect, and background radiation and thereby the method may fail in representing high precision for the DoA estimation. Therefore, this work has a further contribution on developing the DNN-RBF model for the DoA estimation for overcoming the limitations of the non-parametric and data-driven methods in terms of array imperfection and generalization. The numerical results of implementing the DNN-RBF model have confirmed the better performance of the DoA estimation compared with the LS-SVM algorithm. Consequently, we have analogously evaluated the performance of utilizing the two aforementioned optimization methods for the DoA estimation using the concept of the mean squared error (MSE).

Keywords: DoA estimation, Adaptive antenna array, Deep Neural Network, LS-SVM optimization model, Radial basis function, and MSE

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Authors: H. Khanfari, M. Johari Fard

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Dealing with carbonate reservoirs can be mind-boggling for the reservoir engineers due to various digenetic processes that cause a variety of properties through the reservoir. A good estimation of the reservoir heterogeneity which is defined as the quality of variation in rock properties with location in a reservoir or formation, can better help modeling the reservoir and thus can offer better understanding of the behavior of that reservoir. Most of reservoirs are heterogeneous formations whose mineralogy, organic content, natural fractures, and other properties vary from place to place. Over years, reservoir engineers have tried to establish methods to describe the heterogeneity, because heterogeneity is important in modeling the reservoir flow and in well testing. Geological methods are used to describe the variations in the rock properties because of the similarities of environments in which different beds have deposited in. To illustrate the heterogeneity of a reservoir vertically, two methods are generally used in petroleum work: Dykstra-Parsons permeability variations (V) and Lorenz coefficient (L) that are reviewed briefly in this paper. The concept of Lorenz is based on statistics and has been used in petroleum from that point of view. In this paper, we correlated the statistical-based Lorenz method to a petroleum concept, i.e. Kozeny-Carman equation and derived the straight line plot of Lorenz graph for a homogeneous system. Finally, we applied the two methods on a heterogeneous field in South Iran and discussed each, separately, with numbers and figures. As expected, these methods show great departure from homogeneity. Therefore, for future investment, the reservoir needs to be treated carefully.

Keywords: carbonate reservoirs, heterogeneity, homogeneous system, Dykstra-Parsons permeability variations (V), Lorenz coefficient (L)

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Authors: Meng Su

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High-dimensional data analysis often presents challenges in capturing the complex, nonlinear relationships and manifold structures inherent to the data. This article presents a novel approach that leverages the strengths of two powerful techniques, Diffusion Maps and Diffusion Probabilistic Models (DPMs), to address these challenges. By integrating the dimensionality reduction capability of Diffusion Maps with the data modeling ability of DPMs, the proposed method aims to provide a comprehensive solution for analyzing and generating high-dimensional data. The Diffusion Map technique preserves the nonlinear relationships and manifold structure of the data by mapping it to a lower-dimensional space using the eigenvectors of the graph Laplacian matrix. Meanwhile, DPMs capture the dependencies within the data, enabling effective modeling and generation of new data points in the low-dimensional space. The generated data points can then be mapped back to the original high-dimensional space, ensuring consistency with the underlying manifold structure. Through a detailed example implementation, the article demonstrates the potential of the proposed hybrid approach to achieve more accurate and effective modeling and generation of complex, high-dimensional data. Furthermore, it discusses possible applications in various domains, such as image synthesis, time-series forecasting, and anomaly detection, and outlines future research directions for enhancing the scalability, performance, and integration with other machine learning techniques. By combining the strengths of Diffusion Maps and DPMs, this work paves the way for more advanced and robust data analysis methods.

Keywords: diffusion maps, diffusion probabilistic models (DPMs), manifold learning, high-dimensional data analysis

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Authors: Martin H¨ausl, Maximilian Auch, Johannes Forster, Peter Mandl, Alexander Schill

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In order to survive on the market, companies must constantly develop improved and new products. These products are designed to serve the needs of their customers in the best possible way. The creation of new products is also called innovation and is primarily driven by a company’s internal research and development department. However, a new approach has been taking place for some years now, involving external knowledge in the innovation process. This approach is called open innovation and identifies customer knowledge as the most important source in the innovation process. This paper presents a concept of using social media posts as an external source to support the open innovation approach in its initial phase, the Ideation phase. For this purpose, the social media posts are semantically structured with the help of an ontology and the authors are evaluated using graph-theoretical metrics such as density. For the structuring and evaluation of relevant social media posts, we also use the findings of Natural Language Processing, e. g. Named Entity Recognition, specific dictionaries, Triple Tagger and Part-of-Speech-Tagger. The selection and evaluation of the tools used are discussed in this paper. Using our ontology and metrics to structure social media posts enables users to semantically search these posts for new product ideas and thus gain an improved insight into the external sources such as customer needs.

Keywords: idea ontology, innovation management, semantic search, open information extraction

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Authors: Kanika S. Raheja, A. Pandey, Shaila Bahl, Pratik Kumar, S. P. Lochab

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The subject of undertaking for this paper is the study of BaSO4 nanophosphor doped with Europium in which mainly the concentration of the rare earth impurity Eu (0.05, 0.1, 0.2, 0.5, and 1 mol %) has been varied. A comparative study of the thermoluminescence(TL) properties of the given nanophosphor has also been done using a well-known standard dosimetry material i.e. TLD-100.Firstly, a number of samples were prepared successfully by the chemical co-precipitation method. The whole lot was then compared to a well established standard material (TLD-100) for its TL sensitivity property. BaSO4:Eu ( 0.2 mol%) showed the highest sensitivity out of the lot. It was also found that when compared to the standard TLD-100, BaSo4:Eu (0.2mol%) showed surprisingly high sensitivity for a large range of doses. The TL response curve for all prepared samples has also been studied over a wide range of doses i.e 10Gy to 2kGy for gamma radiation. Almost all the samples of BaSO4:Eu showed a remarkable linearity for a broad range of doses, which is a characteristic feature of a fine TL dosimeter. The graph remained linear even beyond 1kGy for gamma radiation. Thus, the given nanophosphor has been successfully optimised for the concentration of the dopant material to achieve its highest TL sensitivity. Further, the comparative study with the standard material revealed that the current optimised sample shows an astonishingly better TL sensitivity and a phenomenal linear response curve for an incredibly wide range of doses for gamma radiation (Co-60) as compared to the standard TLD-100, which makes the current optimised BaSo4:Eu quite promising as an efficient gamma radiation dosimeter. Lastly, the present phosphor has been optimised for its annealing temperature to acquire the best results while also studying its fading and reusability properties.

Keywords: gamma radiation, nanoparticles, radiation dosimetry, thermoluminescence

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Authors: Jacob Green, Cecilia Cabrera, Maximilian Jakobs, Andrea Dimitracopoulos, Mark van der Wilk, Ryan Greenhalgh

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Predicting drug properties is key in drug discovery to enable de-risking of assets before expensive clinical trials and to find highly active compounds faster. Interest from the machine learning community has led to the release of a variety of benchmark datasets and proposed methods. However, it remains unclear for practitioners which method or approach is most suitable, as different papers benchmark on different datasets and methods, leading to varying conclusions that are not easily compared. Our large-scale empirical study links together numerous earlier works on different datasets and methods, thus offering a comprehensive overview of the existing property classes, datasets, and their interactions with different methods. We emphasise the importance of uncertainty quantification and the time and, therefore, cost of applying these methods in the drug development decision-making cycle. To the best of the author's knowledge, it has been observed that the optimal approach varies depending on the dataset and that engineered features with classical machine learning methods often outperform deep learning. Specifically, QSAR datasets are typically best analysed with classical methods such as Gaussian Processes, while ADMET datasets are sometimes better described by Trees or deep learning methods such as Graph Neural Networks or language models. Our work highlights that practitioners do not yet have a straightforward, black-box procedure to rely on and sets a precedent for creating practitioner-relevant benchmarks. Deep learning approaches must be proven on these benchmarks to become the practical method of choice in drug property prediction.

Keywords: activity (QSAR), ADMET, classical methods, drug property prediction, empirical study, machine learning

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Authors: Po-Ting Chen, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang

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Classical molecular dynamics (CMD) simulations are highly efficient for material simulations but have limited accuracy. In contrast, ab initio molecular dynamics (AIMD) provides high precision by solving the Kohn–Sham equations yet requires significant computational resources, restricting the size of systems and time scales that can be simulated. To address these challenges, we employed NequIP, a machine learning model based on an E(3)-equivariant graph neural network, to accelerate molecular dynamics simulations of a 1M LiPF6 in EC/EMC (v/v 3:7) for Li battery applications. AIMD calculations were initially conducted using the Vienna Ab initio Simulation Package (VASP) to generate highly accurate atomic positions, forces, and energies. This data was then used to train the NequIP model, which efficiently learns from the provided data. NequIP achieved AIMD-level accuracy with significantly less training data. After training, NequIP was integrated into the LAMMPS software to enable molecular dynamics simulations of larger systems over longer time scales. This method overcomes the computational limitations of AIMD while improving the accuracy limitations of CMD, providing an efficient and precise computational framework. This study showcases NequIP’s applicability to electrolyte systems, particularly for simulating the dynamics of LiPF6 ionic mixtures. The results demonstrate substantial improvements in both computational efficiency and simulation accuracy, highlighting the potential of machine learning models to enhance molecular dynamics simulations.

Keywords: lithium-ion batteries, electrolyte simulation, molecular dynamics, neural network

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Authors: Chang Qin, Daham Mustafa, Abderrahmane Khiat, Pierre Bienert, Paulo Zanini

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Nowadays, companies are facing lots of challenges in the process of digital transformation, which can be a complex and costly undertaking. Digital transformation involves the collection and analysis of large amounts of data, which can create challenges around data management and governance. Furthermore, it is also challenged to integrate data from multiple systems and technologies. Although with these pains, companies are still pursuing digitalization because by embracing advanced technologies, companies can improve efficiency, quality, decision-making, and customer experience while also creating different business models and revenue streams. In this paper, the issue that data is stored in data silos with different schema and structures is focused. The conventional approaches to addressing this issue involve utilizing data warehousing, data integration tools, data standardization, and business intelligence tools. However, these approaches primarily focus on the grammar and structure of the data and neglect the importance of semantic modeling and semantic standardization, which are essential for achieving data interoperability. In this session, the challenge of data silos in Industry 4.0 is addressed by developing a semantic modeling approach compliant with Asset Administration Shell (AAS) models as an efficient standard for communication in Industry 4.0. The paper highlights how our approach can facilitate the data mapping process and semantic lifting according to existing industry standards such as ECLASS and other industrial dictionaries. It also incorporates the Asset Administration Shell technology to model and map the company’s data and utilize a knowledge graph for data storage and exploration.

Keywords: data interoperability in industry 4.0, digital integration, industrial dictionary, semantic modeling

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Authors: Luiz G. Véras, Felipe L. Medeiros, Lamartine F. Guimarães

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This work approaches the automatic planning of paths for Unmanned Aerial Vehicles (UAVs) through the application of the Rapidly Exploring Random Tree Star-Smart (RRT*-Smart) algorithm. RRT*-Smart is a sampling process of positions of a navigation environment through a tree-type graph. The algorithm consists of randomly expanding a tree from an initial position (root node) until one of its branches reaches the final position of the path to be planned. The algorithm ensures the planning of the shortest path, considering the number of iterations tending to infinity. When a new node is inserted into the tree, each neighbor node of the new node is connected to it, if and only if the extension of the path between the root node and that neighbor node, with this new connection, is less than the current extension of the path between those two nodes. RRT*-smart uses an intelligent sampling strategy to plan less extensive routes by spending a smaller number of iterations. This strategy is based on the creation of samples/nodes near to the convex vertices of the navigation environment obstacles. The planned paths are smoothed through the application of the method called quintic pythagorean hodograph curves. The smoothing process converts a route into a dynamically-viable one based on the kinematic constraints of the vehicle. This smoothing method models the hodograph components of a curve with polynomials that obey the Pythagorean Theorem. Its advantage is that the obtained structure allows computation of the curve length in an exact way, without the need for quadratural techniques for the resolution of integrals.

Keywords: path planning, path smoothing, Pythagorean hodograph curve, RRT*-Smart

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Authors: Williams A. Adu, Cynthia A. Danquah, Paul P. S. Ossei, Selase Ativui, Michael Ofori, James Asenso, George Owusu

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Background Silicosis is an occupational disease of the lung that is caused by chronic exposure to silica dust. There is a higher frequency of co-existence of silicosis with tuberculosis (TB), ultimately resulting in lung fibrosis and respiratory failure. Chronic intake of synthetic drugs has resulted in undesirable side effects. Diosgenin is a steroidal saponin that has been shown to exert a therapeutic effect on lung injury. Therefore, we investigated the ability of diosgenin to reduce the susceptibility of silica-induced TB in rats. Method Silicosis was induced by intratracheal instillation of 50 mg/kg crystalline silica in Sprague Dawley rats. Different doses of diosgenin (1, 10, and 100 mg/kg), Mycobacterium smegmatis and saline were administered for 30 days. Afterwards, 5 of the rats from each group were sacrificed, and the 5 remaining rats in each group, except the control, received Mycobacterium smegmatis. Treatment of diosgenin continued until the 50th day, and the rats were sacrificed at the end of the experiment. The result was analysed using a one-way analysis of variance (ANOVA) with a Graph-pad prism Result At a half-maximal inhibition concentration of 48.27 µM, diosgenin inhibited the growth of Mycobacterium smegmatis. There was a marked decline in the levels of immune cell infiltration and cytokines production. Lactate dehydrogenase and total protein levels were significantly reduced compared to control. There was an increase in the survival rate of the treatment group compared to the control. Conclusion Diosgenin ameliorated silica-induced pulmonary tuberculosis by declining the levels of inflammatory and pro-inflammatory cytokines and, in effect, significantly reduced the susceptibility of rats to pulmonary TB.

Keywords: silicosis, tuberculosis, diosgenin, fibrosis, crystalline silica

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Authors: M. Mohan, J. P. Roise, G. P. Catts

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Despite living in an era where conservation zones are de-facto the central element in any sustainable wildlife management strategy, we still find ourselves grappling with several pareto-optimal situations regarding resource allocation and area distribution for the same. In this paper, a multi-objective decision making (MODM) model is presented to answer the question of whether or not we can establish mutual relationships between these contradicting objectives. For our study, we considered a Red-cockaded woodpecker (Picoides borealis) habitat conservation scenario in the coastal plain of North Carolina, USA. Red-cockaded woodpecker (RCW) is a non-migratory territorial bird that excavates cavities in living pine trees for roosting and nesting. The RCW groups nest in an aggregation of cavity trees called ‘cluster’ and for our model we use the number of clusters to be established as a measure of evaluating the size of conservation zone required. The case study is formulated as a linear programming problem and the objective function optimises the Red-cockaded woodpecker clusters, carbon retention rate, biofuel, public safety and Net Present Value (NPV) of the forest. We studied the variation of individual objectives with respect to the amount of area available and plotted a two dimensional dynamic graph after establishing interrelations between the objectives. We further explore the concept of interdependency by integrating the MODM model with GIS, and derive a raster file representing carbon distribution from the existing forest dataset. Model results demonstrate the applicability of interdependency from both linear and spatial perspectives, and suggest that this approach holds immense potential for enhancing environmental investment decision making in future.

Keywords: conservation, interdependency, multi-objective decision making, red-cockaded woodpecker

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Authors: Naila Nasreen, Dianchen Lu

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This paper explores the dynamical behavior of the (2+1)-dimensional Boussinesq equation, which is a nonlinear water wave equation and is used to model wave packets in dispersive media with weak nonlinearity. This equation depicts how long wave made in shallow water propagates due to the influence of gravity. The (2+1)- dimensional Boussinesq equation combines the two-way propagation of the classical Boussinesq equation with the dependence on a second spatial variable, as that occurs in the two-dimensional Kadomstev- Petviashvili equation. This equation provides a description of head- on collision of oblique waves and it possesses some interesting properties. The governing model is discussed by the assistance of Ricatti equation mapping method, a relatively integration tool. The solutions have been extracted in different forms the solitary wave solutions as well as hyperbolic and periodic solutions. Moreover, the sensitivity analysis is demonstrated for the designed dynamical structural system’s wave profiles, where the soliton wave velocity and wave number parameters regulate the water wave singularity. In addition to being helpful for elucidating nonlinear partial differential equations, the method in use gives previously extracted solutions and extracts fresh exact solutions. Assuming the right values for the parameters, various graph in different shapes are sketched to provide information about the visual format of the earned results. This paper’s findings support the efficacy of the approach taken in enhancing nonlinear dynamical behavior. We believe this research will be of interest to a wide variety of engineers that work with engineering models. Findings show the effectiveness simplicity, and generalizability of the chosen computational approach, even when applied to complicated systems in a variety of fields, especially in ocean engineering.

Keywords: (2+1)-dimensional Boussinesq equation, solitary wave solutions, Ricatti equation mapping approach, nonlinear phenomena

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Authors: Hongyun Li, Zhibin Jiang

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The travel of passengers in the urban rail transit network is influenced by changes in network structure and operational status, and the response of individual travel preferences to these changes also varies. Firstly, the influence of the suspension of urban rail transit line sections on passenger travel along the line is analyzed. Secondly, passenger travel trajectories containing multi-dimensional semantics are described based on network UD data. Next, passenger panel data based on spatio-temporal sequences is constructed to achieve frequent passenger clustering. Then, the Graph Convolutional Network (GCN) is used to model and identify the changes in travel modes of different types of frequent passengers. Finally, taking Shanghai Metro Line 11 as an example, the travel behavior patterns of frequent passengers after the Huaqiao section shutdown during the COVID-19 epidemic are analyzed. The results showed that after the section shutdown, most passengers would transfer to the nearest Anting station for boarding, while some passengers would transfer to other stations for boarding or cancel their travels directly. Among the passengers who transferred to Anting station for boarding, most of passengers maintained the original normalized travel mode, a small number of passengers waited for a few days before transferring to Anting station for boarding, and only a few number of passengers stopped traveling at Anting station or transferred to other stations after a few days of boarding on Anting station. The results can provide a basis for understanding urban rail transit passenger travel patterns and improving the accuracy of passenger flow prediction in abnormal operation scenarios.

Keywords: urban rail transit, section shutdown, frequent passenger, travel behavior pattern

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Authors: E. Von Cheong, Carol Sinnott, Darren Dahly, Patricia M. Kearney

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Introduction and Aim: Adverse childhood experiences (ACEs) are all too common and have been linked to poorer health and wellbeing across the life course. While the prevention of ACEs is a worthy goal, it is important that we also try to lessen the impact of ACEs for those who do experience them. This study aims to investigate associations between adverse childhood experiences (ACEs) and later-life depressive symptoms; and to explore whether perceived social support (PSS) moderates these. Method: We analysed baseline data from the Mitchelstown (Ireland) 2010-11 cohort involving 2047 men and women aged 50–69 years. Self-reported assessments included ACEs (Centre for Disease Control ACE questionnaire), PSS (Oslo Social Support Scale), and depressive symptoms (CES-D). The primary exposure was self-report of at least one ACE. We also investigated the effects of ACE exposure by the subtypes abuse, neglect, and household dysfunction. Associations between each of these exposures and depressive symptoms were estimated using logistic regression, adjusted for socio-demographic factors that were selected using the Directed Acyclic Graph (DAG) approach. We also tested whether the estimated associations varied across levels of PSS (poor, moderate, and good). Results: 23.7% of participants reported at least one ACE (95% CI: 21.9% to 25.6%). ACE exposures (overall or subtype) were associated with a higher odds of depressive symptoms, but only among individuals with poor PSS. For example, exposure to any ACE (vs. none) was associated with 3 times the odds of depressive symptoms (Adjusted OR 2.97; 95% CI 1.63 to 5.40) among individuals reporting poor PSS, while among those reporting moderate PSS, the adjusted OR was 1.18 (95% CI 0.72 to 1.94). Discussion: ACEs are common among older adults in Ireland and are associated with higher odds of later-life depressive symptoms among those also reporting poor PSS. Interventions that enhance perception of social support following ACE exposure may help reduce the burden of depression in older populations.

Keywords: adverse childhood experiences, depression, later-life, perceived social support

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Authors: Ashish Bhattarai, Bishnu Bhatta, Hem Raj Joshi, Nabin Neupane, Pankaj Yadav

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This report concerns the design, development, and analysis of the combined Darrieus and Savonius wind turbine. Vertical Axis Wind Turbines (VAWT's) are of two type's viz. Darrieus (lift type) and Savonius (drag type). The problem associated with Darrieus is the lack of self-starting while Savonius has low efficiency. There are 3 straight Darrieus blades having the cross-section of NACA(National Advisory Committee of Aeronautics) 0018 placed circumferentially and a helically twisted Savonius blade to get even torque distribution. This unique design allows the use of Savonius as a method of self-starting the wind turbine, which the Darrieus cannot achieve on its own. All the parts of the wind turbine are designed in CAD software, and simulation data were obtained via CFD(Computational Fluid Dynamics) approach. Also, the design was imported to FlashForge Finder to 3D print the wind turbine profile and finally, testing was carried out. The plastic material used for Savonius was ABS(Acrylonitrile Butadiene Styrene) and that for Darrieus was PLA(Polylactic Acid). From the data obtained experimentally, the hybrid VAWT so fabricated has been found to operate at the low cut-in speed of 3 m/s and maximum power output has been found to be 7.5537 watts at the wind speed of 6 m/s. The maximum rpm of the rotor blade is recorded to be 431 rpm(rotation per minute) at the wind velocity of 6 m/s, signifying its potentiality of wind power production. Besides, the data so obtained from both the process when analyzed through graph plots has shown the similar nature slope wise. Also, the difference between the experimental and theoretical data obtained has shown mechanical losses. The objective is to eliminate the need for external motors for self-starting purposes and study the performance of the model. The testing of the model was carried out for different wind velocities.

Keywords: VAWT, Darrieus, Savonius, helical blades, CFD, flash forge finder, ABS, PLA

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Authors: Aniekan Peter, ECS Naidu, Edidiong Akang, U. Offor, R. Kalhapure, A. A. Chuturgoon, T. Govender, O. O. Azu

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Introduction: Nano-drugs are novel innovations in the management of human immunodeficiency virus (HIV) pandemic, especially resistant strains of the virus in their sanctuary sites: testis and the brain. There are safety concerns to be addressed to achieve the full potential of this new drug delivery system. Aim of study: Our study was designed to investigate toxicity profile of Tenofovir Nanoparticle (TDF-N) synthesized by University of Kwazulu-Natal (UKZN) Nano-team for prevention and treatment of HIV infection. Methodology: Ten adult male Sprague-Dawley rats maintained at the Animal House of the Biomedical Resources Unit UKZN were used for the study. The animals were weighed and divided into two groups of 5 animal each. Control animals (A) were administered with normal saline. Therapeutic dose (4.3 mg/kg) of TDF-N was administered to group B. At the end of four weeks, animals were weighed and sacrificed. Liver and kidney were removed fixed in formal saline, processed and stained using H/E, PAS and MT stains for light microscopy. Serum was obtained for renal function test (RFT), liver function test (LFT) and full blood count (FBC) using appropriate analysers. Cellular measurements were done using ImageJ and Leica software 2.0. Data were analysed using graph pad 6, values < 0.05 were significant. Results: We reported no histological alterations in the liver, kidney, FBC, LFT and RFT between the TDF-N animals and saline control. There were no significant differences in weight, organo-somatic index and histological measurements in the treatment group when compared with saline control. Conclusion/recommendations: TDF-N is not toxic to the liver, kidney and blood cells in our study. More studies using human subjects is recommended.

Keywords: tenofovir nanoparticles, liver, kidney, blood cells

Procedia PDF Downloads 183

Authors: Abhimanyu Sharma

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India is known for its cultural heritage. As the country is rich in diversity along its length and breadth, the state of Jammu & Kashmir is world famous for the beautiful tourist destinations in the Kashmir region of the state. However, equally destined destinations are also located in Jammu region of the said state. For most of the time in last 50-60 years, the prime focus of development was centered around Kashmir region. But now due to an ever increase in globalization, the focus is decentralizing throughout the country. Pertinently, the potential of Jammu Region needs to be incorporated into the world tourist map in particular. One such spot in the Jammu region of the state is a place called ‘Mubarak Mandi’ – the palace with the royal residence of the Maharaja of Jammu & Kashmir from the Dogra Dynasty, is located in the heart of Jammu city (the winter capital of the state). Since the place is destined with a heritage importance but yet lack the supporting infrastructure to attract the national tourist in general and worldwide tourist at large. For such places, conservation and restoration of the existing structures are the potential tools to overcome the present limiting nature of the place. The rejuvenation of this place through potential and dynamic conservation techniques is targeted through this paper. This paper deals with developing and restoring the areas within the whole campus with appropriate building materials, conservation techniques, etc. to promote a great number of visitors by developing it into a prioritised tourist attraction point. Major thrust shall be on studying the criteria’s for developing the place considering the psychological effect needed to create a socially interactive environment. Additionally, thrust shall be on the spatial elements that will aid in creating a common platform for all kinds of tourists. Accordingly, different conservation guidelines (or model) shall be targeted through this paper so that this Jammu region shall also be an equally contributor to the tourist graph of the country as the Kashmir part is.

Keywords: conservation, heritage architecture, rejuvenating, restoration

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Authors: N. Alias, W. Z. W. Muhammad, M. N. M. Ibrahim, M. Mohamed, H. F. S. Saipol, U. N. Z. Ariffin, N. A. Zakaria, M. S. Z. Suardi

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This paper presents the performance comparison of some computation software for solving the boundary element method (BEM). BEM formulation is the numerical technique and high potential for solving the advance mathematical modeling to predict the production of oil well in arbitrarily shaped based on multiple leases reservoir. The limitation of data validation for ensuring that a program meets the accuracy of the mathematical modeling is considered as the research motivation of this paper. Thus, based on this limitation, there are three steps involved to validate the accuracy of the oil production simulation process. In the first step, identify the mathematical modeling based on partial differential equation (PDE) with Poisson-elliptic type to perform the BEM discretization. In the second step, implement the simulation of the 2D BEM discretization using COMSOL Multiphysic and MATLAB programming languages. In the last step, analyze the numerical performance indicators for both programming languages by using the validation of Fortran programming. The performance comparisons of numerical analysis are investigated in terms of percentage error, comparison graph and 2D visualization of pressure on oil production of multiple leases reservoir. According to the performance comparison, the structured programming in Fortran programming is the alternative software for implementing the accurate numerical simulation of BEM. As a conclusion, high-level language for numerical computation and numerical performance evaluation are satisfied to prove that Fortran is well suited for capturing the visualization of the production of oil well in arbitrarily shaped.

Keywords: performance comparison, 2D visualization, COMSOL multiphysic, MATLAB, Fortran, modelling and simulation, boundary element method, reservoir pressure

Procedia PDF Downloads 491