Computational Biology eJournal最新文献

{"title":"Transfer Learning-Based Plant Disease Detection","authors":"G. Sumalatha, Dr S. Krishna Rao, Dr. Jhansi Rani Singothu","doi":"10.48047/ijiemr/v10/i03/99","DOIUrl":"https://doi.org/10.48047/ijiemr/v10/i03/99","url":null,"abstract":"Deep Neural Networks in the field of Machine Learning (ML) are broadly used for deep learning. Among many of DNN structures, the Convolutional Neural Networks (CNN) are currently the main tool used for the image analysis and classification problems. Deep neural networks have been highly successful in image classification problems. In this paper, we have shown the use of deep neural networks for plant disease detection, through image classification. This study provides a transfer learning-based solution for detecting multiple diseases in several plant varieties using simple leaf images of healthy and diseased plants taken from PlantVillage dataset. We have addressed a multi-class classification problem in which the models were trained, validated and tested using 11,333 images from 10 different classes containing 2 crop species and 8 diseases. Six different CNN architectures VGG16, InceptionV3, Xception, Resnet50, MobileNet, and DenseNet121 are compared. We found that DenseNet121 achieves best accuracy of 95.48 on test data.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"70 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127470133","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"AIRR Data Under the E.U. Trade Secrets Directive: Aligning Scientific Practices with Commercial Realities","authors":"Jacob S. Sherkow, T. Minssen","doi":"10.2139/ssrn.3249498","DOIUrl":"https://doi.org/10.2139/ssrn.3249498","url":null,"abstract":"Whether the E.U. Trade Secrets Directive sufficiently and appropriately covers cutting-edge complex technologies is of critical interest to policy-makers, scientists, and commercial developers alike. One such technology — adaptive immune receptor repertoire sequencing, or AIRR-seq — raises difficult questions concerning what information is and should be protected under the new Directive, and how to best align scientific practices with commercial realities. The ‘raw’ form AIRR-seq data — massive genetic datasets of hundreds of millions of individuals’ immune cells — tends to be freely shared among academic researchers, thus typically destroying the protectability of the underlying information. But follow-on data — essentially, information interpreting that data — is nonetheless protectable under the Directive because it is both economically valuable and not readily available from an examination of the raw data itself. Protecting this follow-on information while encouraging the free sharing of AIRR-seq data best accords the purpose of the Trade Secrets Directive. Lessons from the case of AIRR-seq data also sheds light on other puzzles concerning the tensions between disclosure and various forms of legal protections, such as the mutual exclusivity of patents and trade secrets, the sharing of clinical trial data, and protecting genetic diagnostics.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-07-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129184914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulation Study on Effect of Lockdown and Recovery Time on Spread of COVID-19 in High and Low-Density Areas","authors":"Moses J. Kartha, H. Pathan","doi":"10.2139/ssrn.3572697","DOIUrl":"https://doi.org/10.2139/ssrn.3572697","url":null,"abstract":"We have carried out a Monte-Carlo simulation study of diffusion of healthy and infected disks for low and high density to understand the spread of COVID-19. Each disk has a fixed size and consists of an infecting region and is allowed to move in any random direction. When a healthy disk enters into the infecting region of the other disk, it also turns to an infected one mimicking the spread of COVID-19. Once infected it become again healthy after a fixed recovery time, τ. We show that when the density disk is low, for the low value of τ, the infected cases can be brought down to zero even without lockdown. When the lockdown is not applied, for higher values of τ, the infected cases reaches a saturation value, Ns which shows a power-law behavior, Ns ~ τβ, where β = 0.58. When the density of the system is high, the number of infected cases goes to zero only for a complete lockdown and the saturation value of infected case Ns is found independent of recovery time.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130379677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Capítulo de Estudio: Farmacocinética. Taller de Farmacocinética II (Study Chapter: Pharmacokinetics. Pharmacokinetic Workshop II)","authors":"Elisa Pedraza Vázquez, J.R. García Martínez, Miguel Ángel Trejo-Rodríguez","doi":"10.2139/ssrn.3556296","DOIUrl":"https://doi.org/10.2139/ssrn.3556296","url":null,"abstract":"Spanish Abstract: Este documento representa una revision de conceptos de los modelos farmacocineticos y forma parte de la serie de un capitulo de estudio sobre la farmacocinetica. Esta disenado como complemento para que se utilice como material para introducir al estudio de la Farmacologia. Se utilizan las ecuaciones que explican de manera sencilla el comportamiento del farmaco a traves del organismo determinados por los factores fisiologicos y de esta forma se podra cuantificar las concentraciones de farmaco en funcion del tiempo contribuyendo a la explicacion del efecto posible a observar. \u0000 \u0000English Abstract: This document represents a review of the concepts of pharmacokinetic models and is part of the series of a study chapter on pharmacokinetics. It is designed as a complement to be used as a material to introduce to the study of Pharmacology. The equations that explain in a simple way the behavior of the drug throughout the body determined by the physiological factors are used and in this way the concentrations of the drug can be quantified as a function of time, contributing to the explanation of the possible effect to be observed.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"6 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2020-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114205645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Third Order Cybernetics of Eric Schwarz","authors":"E. Schwarz, M. Yolles","doi":"10.2139/ssrn.3427683","DOIUrl":"https://doi.org/10.2139/ssrn.3427683","url":null,"abstract":"There have been many discussions in the area of cybernetics that highlights the importance of second order cybernetics, with its implied notions of autopoiesis, and its capacity to represent the social as a living system (e.g., Yolles, 2018; Yolles, 2018a). \u0000 \u0000Eric Schwarz was a professor emeritus from 1999 at the Institute of Physics of the Faculty of Science at the University of Neuchâte, Switzerland, where he was honorary research director, and former head of the Interdisciplinary Centre for Systemic Studies of the University of Neucâtel (CIES) founded in 1988. He produced the first explicitly third order cybernetic model at his cybernetic unit in 1988 in collaboration with the other members of CIES. He has written 21 papers on the development of his paradigm, but most of his many publications have been through conferences, and they have been lost or are not easily accessible, and access to existing papers appears to be continually reducing. Those papers lost cannot be regained easily since he passed away in March 2015 at the age of 81 after declining ill-health. It is for this reason that I have put together this collection of his papers that I have available.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133546926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of Policies for Biodiversity Informatics in Central Africa: Case Studies of the Democratic Republic of Congo (DRC) and Gabon","authors":"Pamela Y. Abbott, A. Tsinda, R. Mugisha","doi":"10.2139/ssrn.3098716","DOIUrl":"https://doi.org/10.2139/ssrn.3098716","url":null,"abstract":"Biodiversity informatics is an emerging discipline which deals with the collection, collation, analysis, prediction, and dissemination of data and information related to the earth’s biotic resources. This article is a review of the policy and legislation instruments relevant to biodiversity informatics, grouped in four categories, (i) mobilizing biodiversity data, (ii) standards, protocols, and tools, (iii) informatics infrastructure-building initiatives, and (iv) capacity-building, outreach and open access initiatives. A meta-analysis of 705 documents on policies, legislations and papers about biodiversity data management in Central Africa (Case studies of DRC and Gabon) was conducted. A number of search engines were used to find policies, legislation and articles relevant to this review. Results showed that although significant efforts have been invested in developing policies, the enactment of biodiversity-related legislation and establishing institutions is still weak. Successful implementation and enforcement of policies is greatly impeded by several factors which, in turn, constitute challenges to biodiversity data management. Weaknesses in institutional frameworks are characterized, among other factors, by poor coordination, inadequate funding of biodiversity protection, corruption and jurisdictional conflicts. Findings from this review suggest that the governments of DRC and Gabon need to take urgent action to reform flawed biodiversity-related policy and legal instruments, ensure their effective enforcement and strengthen the institutions in charge of biodiversity conservation.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"60 2‐3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"120838490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Introducing the HFTE Model: A Multi-Species Predator Prey Ecosystem for High Frequency Quantitative Financial Strategies","authors":"Babak Mahdavi-Damghani","doi":"10.2139/ssrn.2946436","DOIUrl":"https://doi.org/10.2139/ssrn.2946436","url":null,"abstract":"In this paper we take a new approach to studying electronic trading & systemic risk by introducing the HFTE model. We specify an approach in which agents interact through a topological structure designed to address the complexity demands of most common high frequency strategies but designed randomly at inception. The primitive strategy ecosystem is then studied through a simplified genetic algorithm. The results open up intriguing social and regulatory implications with the helping doors of Mathematical Biology & Game Theory which specific mirror points have been summarized for the sake of illustrating the puzzling findings.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"30 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122079754","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Promoting Ethical and Professional Responsibility in Biomedical Informatics Education","authors":"B. Kaplan, T. Liaw, V. Subbian, K. Courtney, H. Hochheiser, K. Goodman","doi":"10.2139/SSRN.3099251","DOIUrl":"https://doi.org/10.2139/SSRN.3099251","url":null,"abstract":"Increasing use of information technologies in clinical care; concerns over the role of algorithmic decision-making in everyday life; collection of vast amounts of physical, social, and personal heath data through devices, social media, and the Internet of Things; and highly-visible, informatics-driven efforts such as the Precision Medicine Initiative, make calls for responsible technology use more important than ever. This rapidly-changing landscape challenges informaticians to understand the ethical, legal, and social (ELSI) implications of these developments and informatics educators to develop approaches for incorporating them into already-crowded curricula. \u0000This workshop will promote discussion of approaches to incorporating ELSI competencies in biomedical informatics education, research, and practice, including: \u0000(1) a survey of foundations and competencies, \u0000(2) current approaches for teaching ELSI concepts, and \u0000(3) experiences, lessons learned, and novel proposals for ELSI instruction in biomedical informatics curricula. \u0000AMIA’s core competencies include fundamental knowledge in “ethical, legal, social issues: for example, human subjects, HIPAA, informed consent, secondary use of data, confidentiality, privacy.” How should these competencies be included and evaluated in a course of study? Are they sufficient for socially responsible and ethical use of technology in biomedicine and health care? The paucity of such topics in biomedical informatics courses and curricula provides an opportunity to elicit diverse opinions and approaches about these questions. Presenters and audience will address them from varying perspectives and educational experiences. \u0000In addition to their expertise in biomedical informatics research and teaching, presenters will draw on their different disciplinary backgrounds (engineering, history, information systems, bioethics, law, social studies of science, computer science, philosophy, human factors, nursing, anthropology, medicine, public health) and country perspectives (US, Canada, Australia) to explore ways to promote ethical and professional responsibility in biomedical informatics.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126452932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Compartmental Models Simulating a Dichotomy of Action Potential Backpropagation in Ca1 Pyramidal Neuron Dendrites","authors":"W. Kath, Nace L. Golding, N. Spruston","doi":"10.1152/JN.2001.86.6.2998","DOIUrl":"https://doi.org/10.1152/JN.2001.86.6.2998","url":null,"abstract":"In hippocampal CA1 pyramidal neurons, action potentials are typically initiated in the axon and backpropagate into the dendrites, shaping the integration of synaptic activity and influencing the induction of synaptic plasticity. Despite previous reports describing action-potential propagation in the proximal apical dendrites, the extent to which action potentials invade the distal dendrites of CA1 pyramidal neurons remains controversial. Using paired somatic and dendritic whole cell recordings, we find that in the dendrites proximal to 280 microm from the soma, single backpropagating action potentials exhibit <50% attenuation from their amplitude in the soma. However, in dendritic recordings distal to 300 microm from the soma, action potentials in most cells backpropagated either strongly (26-42% attenuation; n = 9/20) or weakly (71-87% attenuation; n = 10/20) with only one cell exhibiting an intermediate value (45% attenuation). In experiments combining dual somatic and dendritic whole cell recordings with calcium imaging, the amount of calcium influx triggered by backpropagating action potentials was correlated with the extent of action-potential invasion of the distal dendrites. Quantitative morphometric analyses revealed that the dichotomy in action-potential backpropagation occurred in the presence of only subtle differences in either the diameter of the primary apical dendrite or branching pattern. In addition, action-potential backpropagation was not dependent on a number of electrophysiological parameters (input resistance, resting potential, voltage sensitivity of dendritic spike amplitude). There was, however, a striking correlation of the shape of the action potential at the soma with its amplitude in the dendrite; larger, faster-rising, and narrower somatic action potentials exhibited more attenuation in the distal dendrites (300-410 microm from the soma). Simple compartmental models of CA1 pyramidal neurons revealed that a dichotomy in action-potential backpropagation could be generated in response to subtle manipulations of the distribution of either sodium or potassium channels in the dendrites. Backpropagation efficacy could also be influenced by local alterations in dendritic side branches, but these effects were highly sensitive to model parameters. Based on these findings, we hypothesize that the observed dichotomy in dendritic action-potential amplitude is conferred primarily by differences in the distribution, density, or modulatory state of voltage-gated channels along the somatodendritic axis.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"48 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2001-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127330227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine Learning-Assisted Intelligent Fibers for Remote Control","authors":"Shengshun Duan, Yucheng Lin, Yinghui Li, Di Zhu, Binghao Wang, Jun Wu, W. Lei","doi":"10.2139/ssrn.3873471","DOIUrl":"https://doi.org/10.2139/ssrn.3873471","url":null,"abstract":"Under the impact of Covid-19 virus, remote control is of value in non-contact systems. Glove-based wearable systems are promising for precise and low-cost hand gesture recognition. Yet, preparing stable intelligent fibers using facile techniques for reliable machine learning is still challenging. Here, we propose a stable intelligent fiber via layer-by-layer assemble for reliable machine learning, which exhibits a gauge factor of 4. The adoption of PVA and PU film can improve adherence of CNTs and stability of intelligent fiber during cyclic deformations, thus improving electrical performances and service time. Besides, integrating a flexible hybrid electronic system, we demonstrate remote control of robots using our fabricated glove and a shallow neural network.","PeriodicalId":141051,"journal":{"name":"Computational Biology eJournal","volume":"135 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"115301770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}