Journal of Computational Science最新文献

{"title":"Applications of Text Mining techniques to extract meaningful information from gastroenterology medical reports","authors":"Rosarina Vallelunga ,&nbsp;Ileana Scarpino ,&nbsp;Maria Chiara Martinis ,&nbsp;Francesco Luzza ,&nbsp;Chiara Zucco","doi":"10.1016/j.jocs.2024.102458","DOIUrl":"10.1016/j.jocs.2024.102458","url":null,"abstract":"<div><div>Text mining techniques, particularly topic modeling, can be used for the automatic extraction of information from medical reports. The ability to autonomously analyze texts and identify topics within them can provide meaningful clinical insights that support physicians in diagnostic settings and enhance the characterization of intestinal diseases, leading to more efficient and automated systems.</div><div>This study evaluates the effectiveness of Latent Dirichlet Allocation (LDA) and BERTopic in modeling topics from colonoscopy reports related to Crohn’s Disease, Ulcerative Colitis, and Polyps. We compared these models in terms of their ability to identify clinically relevant topics, their influence on the performance of machine learning classifiers trained on the derived topic features, and their scalability.</div><div>Our analysis, based on average results across five iterations of train-test splits, showed that BERTopic generally outperformed LDA in clustering metrics, achieving Adjusted Rand Index (ARI), Normalized Mutual Information (NMI), and Purity scores of 0.5637, 0.5953, and 0.8447, respectively, compared to LDA’s scores of 0.5349, 0.5254, and 0.8149. Additionally, classifiers trained on BERTopic-derived features exhibited improved predictive accuracy and F1-scores, with Logistic Regression reaching a mean accuracy of 0.8464 and a mean F1-score of 0.8507, compared to 0.8319 and 0.8351 for LDA-based features. Despite BERTopic’s overall superior performance, LDA demonstrated greater stability and interpretability, making it a viable option in scenarios where computational efficiency is a priority.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102458"},"PeriodicalIF":3.1,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142663590","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hypoxia-driven hybrid phenotypes in Ewing sarcoma: Insights from computational epithelial-mesenchymal transition modeling","authors":"Daner A. Silveira ,&nbsp;Shantanu Gupta ,&nbsp;André T. Brunetto ,&nbsp;José Carlos Merino Mombach ,&nbsp;Marialva Sinigaglia","doi":"10.1016/j.jocs.2024.102464","DOIUrl":"10.1016/j.jocs.2024.102464","url":null,"abstract":"<div><div>Ewing sarcoma (ES) is an extremely aggressive pediatric tumor primarily propelled by the EWS::FLI1 fusion protein. This fusion protein plays a pivotal role in various biological processes within ES, including hypoxia and epithelial-mesenchymal transition (EMT). Hypoxia has been documented to trigger EMT, a process that can stabilize a hybrid cell state, enhancing metastatic potential and resistance to drugs. However, the precise mechanisms that sustain this hybrid phenotype during hypoxia in ES have remained enigmatic. Our study introduces a logical model for EMT in ES, underscoring the potential significance of the EWS::FLI1/miR-145 circuit in inducing hybrid states during hypoxia. Furthermore, our findings underscore the necessity for downregulating EWS::FLI1 to fully activate EMT under hypoxic conditions. This model aligns well with results derived from existing literature. These insights underscore the crucial role of EWS::FLI1 in inducing the hybrid state in ES during hypoxia.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102464"},"PeriodicalIF":3.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142593795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An information fusion approach based on weight correction and evidence theory","authors":"Xugang Xi ,&nbsp;Yaqing Nie ,&nbsp;Yu Zhou ,&nbsp;Yun-Bo Zhao ,&nbsp;Ting Wang ,&nbsp;Yahong Chen ,&nbsp;Lihua Li ,&nbsp;Jian Yang","doi":"10.1016/j.jocs.2024.102456","DOIUrl":"10.1016/j.jocs.2024.102456","url":null,"abstract":"<div><div>The combination rules of the Dempster-Shafer evidence theory can lead to illogical results for highly conflicting evidence from different information sources. We propose a general formula for conflict degree calculation from the perspective of modifying evidence sources as a weighted sum of conflict coefficients and Jousselme distance, and the new metric of focal element dispersion is defined by adaptively adjusting the ratio of these two metrics: if the focal element dispersion is too high, the impact of conflict coefficients is increased, and vice versa. We then define the concept of preference consistency and propose a formula for calculating this metric that redistributes the weights of individual pieces of evidence based on the preferences of all evidence. Finally, typical examples show that the proposed rules can manage conflicting evidence with better convergence and interference resistance.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102456"},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572830","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"2D scale-3 fractional Euler wavelets optimization algorithm for fractional-order differential equations","authors":"Fengying Zhou,&nbsp;Jiakun Zhang","doi":"10.1016/j.jocs.2024.102459","DOIUrl":"10.1016/j.jocs.2024.102459","url":null,"abstract":"<div><div>A numerical scheme combining particle swarm optimization(PSO) optimization algorithm for solving fractional-order differential equations is developed by using 2D scale-3 fractional Euler wavelets, which are constructed via orthogonal Euler polynomials. The fractional integration formulas for scale-3 fractional Euler wavelets are derived under Riemann–Liouville fractional integral. The error estimation is given through the generalized fractional-order Taylor expansion and the convergence analysis of 2D scale-3 fractional Euler wavelets expansion is studied. According to the fractional integration formulas, together with the collocation method, a numerical technique is created by discretizing the fractional-order differential equation into a system of equations. Some linear and nonlinear problems are provided and PSO algorithm is applied to the numerical scheme. The numerical results are analyzed and compared with existing findings. This not only confirms the feasibility and effectuality of the proposed method but also demonstrates that PSO algorithm can enhance the numerical scheme’s performance.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102459"},"PeriodicalIF":3.1,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553933","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"BPMT: A hybrid model for secure and effective electronic medical record management system","authors":"Mehar Nasreen,&nbsp;Sunil Kumar Singh","doi":"10.1016/j.jocs.2024.102457","DOIUrl":"10.1016/j.jocs.2024.102457","url":null,"abstract":"<div><div>Designing an efficient distributed blockchain system to store and access rising electronic medical records (EMR) is still challenging. Although many techniques have been designed to utilize EMRs proficiently, they still suffer from accessing time, storage time, and throughput. In this work, we have proposed a Merkle and B+ tree-based hybrid model to improve the performance of the blockchain system. B+ tree has improved the system's performance because of its practical layout and balanced structure. At the same time, Merkle Tree has ensured the integrity and security of the information. The proposed (B+ Merkle tree) BPMT model has reduced the storage time of records, improved the system's throughput, and significantly reduced memory use. These enhancements are supported by a thorough complexity analysis and testing on several datasets, which validate the efficacy and scalability of the model. The outcomes validate the performance improvements of the model and lay the groundwork for further developments in blockchain-based EMR management.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102457"},"PeriodicalIF":3.1,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142572829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced heat transfer in ternary tangent hyperbolic nanofluids through non-darcy porous media","authors":"Lim Yeou Jiann ,&nbsp;Sharena Mohamad isa ,&nbsp;Noraihan Afiqah Rawi ,&nbsp;Sharidan Shafie ,&nbsp;Ahmad Qushairi Mohamad ,&nbsp;Dennis Ling Chaun Ching ,&nbsp;Nur Azlina Mat Noor","doi":"10.1016/j.jocs.2024.102462","DOIUrl":"10.1016/j.jocs.2024.102462","url":null,"abstract":"<div><div>The effectiveness of heat transfer fluids (HTFs) is pivotal in maximizing the efficiency and longevity of various devices, from small-scale applications to large industrial systems. A comprehensive understanding of the properties of innovative ternary heat transfer nanofluids (TNFs) is essential, particularly when utilized over a Darcy-Forchheimer porous medium. This study explores tangent hyperbolic thermal nanofluids (TNFs) made up of nanoparticles such as graphene, zirconium oxide and magnesium oxide and, suspended in an ethylene glycol base fluid, within a non-Darcy porous medium. Similarity variables are used to streamline the mathematical representation of fluid flow and heat transmission in TNFs. Then, semi-analytical solutions to the reduced governing equations are obtained using the homotopy analysis method. The influence of tri-nanoparticles, porosity, and the Forchheimer parameter on skin friction, fluid flow dynamics, heat transfer rates, and the Nusselt number is investigated. The Forchheimer parameter lowers the Nusselt number by 27.80 % for TNFs, 21.27 % for the hybrid nanofluid, and 21.08 % for the nanofluid. As a result, the temperature within TNFs is more evenly distributed. TNFs can transfer more heat by raising the medium’s porosity and the tri-nanoparticle volume fraction. These results unveil groundbreaking insights into enhancing the efficiency of heat transfer fluids. The introduction of a porous medium emerges as an alternate strategy to boost the performance of TNFs.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102462"},"PeriodicalIF":3.1,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142553932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling and simulation of Fuzzy-rule based WBAN using multi-level fuzzy colored petri-nets and reinforcement learning","authors":"Negar Majma ,&nbsp;Seyed Morteza Babamir","doi":"10.1016/j.jocs.2024.102455","DOIUrl":"10.1016/j.jocs.2024.102455","url":null,"abstract":"<div><div>By developing IoTs (Internet of Things), a new concept is arising in WBANs (Wireless Body Area Networks), called IoBs (Internet of Bodies). WBANs are the safety-critical devices that use rule-based knowledge with fuzzy variables for monitoring patients. There are two issues with the knowledgebase: (1) appropriate knowledge representation and inference and (2) handling the situations for which there is no rule in the knowledgebase. In this paper, for the first issue we present MFCPN (Multi-level Fuzzy Colored Petri-nets) and for the second one we present a RL (Reinforcement Learning) mechanism for decision making based on the past device’s feedback to the environment. Through a few scenarios and two datasets, the proposed approach has been applied to pacemakers to show the approach's effectiveness. The comparison between decision making by our approach and two real datasets indicates the proposed approach has 79.3 % accuracy.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102455"},"PeriodicalIF":3.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142531421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Generative model-based framework for parameter estimation and uncertainty quantification applied to a compartmental model in epidemiology","authors":"Vinicius L.S. Silva ,&nbsp;Claire E. Heaney ,&nbsp;Nenko Nenov ,&nbsp;Christopher C. Pain","doi":"10.1016/j.jocs.2024.102451","DOIUrl":"10.1016/j.jocs.2024.102451","url":null,"abstract":"<div><div>We propose a new method in which a generative network (GN) set within a reduced-order model (ROM) framework is used to solve inverse problems for partial differential equations (PDE). The aim is to match available measurements and estimate the corresponding uncertainties associated with the states and parameters of a numerical physical simulation. We train the GN using only unconditional simulations of the discretized PDE model. A GN is used here to exploit the ability of these methods to generate realistic outputs from complex probability distributions, such as the ones that represent the possible states and parameters of a physical problem. We compare the proposed method with the gold standard Markov chain Monte Carlo (MCMC). Additionally, we suggest the use of a novel type of time-stepping regularization to improve the representativeness of the physical solution, and we present a new way of evaluating the GN training, taking advantage of the real/generated sample structure. We apply the proposed approaches to a spatio-temporal compartmental model in epidemiology. The results show that the proposed GN-based ROM can efficiently quantify uncertainty and accurately match the measurements and the gold standard. This is achieved using only a limited number of unconditional simulations from the full-order numerical PDE model (40 simulations). The GN-based ROM operates 60 times faster than the gold standard (MCMC), while producing uncertainties that closely match those generated by the MCMC approach. The proposed method is a general framework for quantifying uncertainties in numerical physical simulations and is not restricted to the specific physics of this application.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102451"},"PeriodicalIF":3.1,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142531422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the theory of quantum and towards practical computation: A review","authors":"Robert Kudelić","doi":"10.1016/j.jocs.2024.102454","DOIUrl":"10.1016/j.jocs.2024.102454","url":null,"abstract":"<div><div>Quantum computing exposes the brilliance of quantum mechanics through computer science (in theory and otherwise), giving oneself a marvelous and exhilarating journey to go through. This review article leads along that journey with a historical and current outlook on quantum computation that is geared toward computer experts (via algorithmics) but also to experts from other disciplines as well. It is an article that will open an entering wedge through which one will be able to bring himself up to speed on quantum computation and challenges/limitations thereof. We are indeed in luck to be living in an age where computing is being reinvented, and not only seeing history in the making firsthand but, in fact, having the opportunity to be the ones who are reinventing—and that is quite a thought.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102454"},"PeriodicalIF":3.1,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142445580","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A numerical framework for modeling evaporation and combustion of isolated, spherically-symmetric, multi-component fuel droplets","authors":"Alberto Cuoci ,&nbsp;Edoardo Cipriano ,&nbsp;Abd Essamade Saufi ,&nbsp;Alessio Frassoldati","doi":"10.1016/j.jocs.2024.102453","DOIUrl":"10.1016/j.jocs.2024.102453","url":null,"abstract":"<div><div>This paper presents a comprehensive numerical framework for simulating the evaporation and combustion of isolated, spherically-symmetric, multi-component fuel droplets. The framework incorporates a detailed description of chemical reactions in the gaseous phase and is capable of modeling pure evaporation, autoignition, and hot-wire ignition scenarios.</div><div>The transport equations for mass, species, and energy are solved in both the liquid (droplet) and gaseous (surrounding atmosphere) phases. Diffusion in the liquid phase is described using the Stefan–Maxwell theory, while in the gaseous phase, both molecular and thermal diffusion are considered. The model also includes the thermophoretic effect for carbonaceous particles and accounts for gas radiation through various models, ranging from optically-thin approximations to more complex methods like the P1 and discrete ordinate methods. Non-gray radiative effects are handled using the Weighted-Sum-of-Gray-Gases Model (WSGGM). Liquid/gas interface conditions are evaluated by imposing flux continuity of mass and energy, along with thermodynamic equilibrium for species. Deviations from ideal thermodynamic behavior in the liquid droplet are managed by incorporating a suitable activity coefficient or by using a proper cubic equation of state. Additionally, the presence of supporting fibers is modeled using a simplified one-dimensional approach. The transport equations are solved using the method of lines, with spatial discretization performed via the finite difference method on a body-fitted grid. The resulting system of Differential–Algebraic Equations (DAEs) is then solved using a fully-coupled approach.</div><div>Thanks to its generality in terms of kinetic and thermodynamic descriptions and the reduced computational time, the proposed framework offers significant potential for advancing our understanding of the complex combustion processes of multi-component liquid fuels and for enhancing the planning and execution of experiments involving isolated fuel droplets.</div></div>","PeriodicalId":48907,"journal":{"name":"Journal of Computational Science","volume":"83 ","pages":"Article 102453"},"PeriodicalIF":3.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142433345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}