Search results for: corpus based approach
34149 An Unbiased Profiling of Immune Repertoire via Sequencing and Analyzing T-Cell Receptor Genes
Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu
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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment
Procedia PDF Downloads 19434148 Social Capital in Housing Reconstruction Post Disaster Case of Yogyakarta Post Earthquake
Authors: Ikaputra
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This paper will focus on the concept of social capital for especially housing reconstruction Post Disaster. The context of the study is Indonesia and Yogyakarta Post Earthquake 2006 as a case, but it is expected that the concept can be adopted in general post disaster reconstruction. The discussion will begin by addressing issues on House Reconstruction Post Disaster in Indonesia and Yogyakarta; defining Social Capital as a concept for effective management capacity based on community; Social Capital Post Java Earthquake utilizing Gotong Royong—community mutual self-help, and Approach and Strategy towards Community-based Reconstruction.Keywords: community empowerment, Gotong Royong, post disaster, reconstruction, social capital, Yogyakarta-Indonesia
Procedia PDF Downloads 32534147 A Machine Learning Approach to Detecting Evasive PDF Malware
Authors: Vareesha Masood, Ammara Gul, Nabeeha Areej, Muhammad Asif Masood, Hamna Imran
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The universal use of PDF files has prompted hackers to use them for malicious intent by hiding malicious codes in their victim’s PDF machines. Machine learning has proven to be the most efficient in identifying benign files and detecting files with PDF malware. This paper has proposed an approach using a decision tree classifier with parameters. A modern, inclusive dataset CIC-Evasive-PDFMal2022, produced by Lockheed Martin’s Cyber Security wing is used. It is one of the most reliable datasets to use in this field. We designed a PDF malware detection system that achieved 99.2%. Comparing the suggested model to other cutting-edge models in the same study field, it has a great performance in detecting PDF malware. Accordingly, we provide the fastest, most reliable, and most efficient PDF Malware detection approach in this paper.Keywords: PDF, PDF malware, decision tree classifier, random forest classifier
Procedia PDF Downloads 9234146 Modeling of Coupled Mechanical State and Diffusion in Composites with Impermeable Fibers
Authors: D. Gueribiz, F. Jacquemin, S. Fréour
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During their service life, composite materials are submitted to humid environments. The moisture absorbed by their matrix polymer induced internal stresses which can lead to multi-scale damage and may reduce the lifetime of composite structures. The estimation of internal stresses is based at a first on realistic evaluation of the diffusive behavior of composite materials. Generally, the modeling and simulation of the diffusive behavior of composite materials are extensively investigated through decoupled models based on the assumption of Fickien behavior. For these approaches, the concentration and the deformation (or stresses), the two state variables of the problem considered are governed by independent equations which are solved separately. In this study, a model coupling diffusive behavior with stresses state for a polymer matrix composite reinforced with impermeable fibers is proposed, the investigation of diffusive behavior is based on a more general thermodynamic approach which introduces a dependence of diffusive behavior on internal stresses state. The coupled diffusive behavior modeling was established in first for homogeneous and isotropic matrix and it is, thereafter, extended to impermeable unidirectional composites.Keywords: composites materials, moisture diffusion, effective moisture diffusivity, coupled moisture diffusion
Procedia PDF Downloads 30834145 Assessing Artificial Neural Network Models on Forecasting the Return of Stock Market Index
Authors: Hamid Rostami Jaz, Kamran Ameri Siahooei
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Up to now different methods have been used to forecast the index returns and the index rate. Artificial intelligence and artificial neural networks have been one of the methods of index returns forecasting. This study attempts to carry out a comparative study on the performance of different Radial Base Neural Network and Feed-Forward Perceptron Neural Network to forecast investment returns on the index. To achieve this goal, the return on investment in Tehran Stock Exchange index is evaluated and the performance of Radial Base Neural Network and Feed-Forward Perceptron Neural Network are compared. Neural networks performance test is applied based on the least square error in two approaches of in-sample and out-of-sample. The research results show the superiority of the radial base neural network in the in-sample approach and the superiority of perceptron neural network in the out-of-sample approach.Keywords: exchange index, forecasting, perceptron neural network, Tehran stock exchange
Procedia PDF Downloads 46434144 Potentials and Challenges of Implementing Participatory Irrigation Management, Tanzania
Authors: Pilly Joseph Kagosi
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The study aims at assessing challenges observed during implementation of participatory irrigation management (PIM) approach for food security in semi-arid areas of Tanzania. Data were collected through questionnaire, PRA tools, key informants discussion, Focus Group Discussion (FGD), participant observation and literature review. Data collected from questionnaire was analyzed using SPSS while PRA data was analyzed with the help of local communities during PRA exercise. Data from other methods were analyzed using content analysis. The study revealed that PIM approach has contribution in improved food security at household level due to involvement of communities in water management activities and decision making which enhanced availability of water for irrigation and increased crop production. However there were challenges observed during implementation of the approach including; minimum participation of beneficiaries in decision making during planning and designing stages, meaning inadequate devolution of power among scheme owners; Inadequate and lack of transparency on income expenditure in Water Utilization Associations’ (WUAs), water conflict among WUAs members, conflict between farmers and livestock keepers and conflict between WUAs leaders and village government regarding training opportunities and status; WUAs rules and regulation are not legally recognized by the National court and few farmers involved in planting trees around water sources. However it was realized that some of the mentioned challenges were rectified by farmers themselves facilitated by government officials. The study recommends that, the identified challenges need to be rectified for farmers to realize impotence of PIM approach as it was realized by other Asian countries.Keywords: potentials of implementing participatory approach, challenges of participatory approach, irrigation management, Tanzania
Procedia PDF Downloads 30634143 Classification Based on Deep Neural Cellular Automata Model
Authors: Yasser F. Hassan
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Deep learning structure is a branch of machine learning science and greet achievement in research and applications. Cellular neural networks are regarded as array of nonlinear analog processors called cells connected in a way allowing parallel computations. The paper discusses how to use deep learning structure for representing neural cellular automata model. The proposed learning technique in cellular automata model will be examined from structure of deep learning. A deep automata neural cellular system modifies each neuron based on the behavior of the individual and its decision as a result of multi-level deep structure learning. The paper will present the architecture of the model and the results of simulation of approach are given. Results from the implementation enrich deep neural cellular automata system and shed a light on concept formulation of the model and the learning in it.Keywords: cellular automata, neural cellular automata, deep learning, classification
Procedia PDF Downloads 19834142 Shifted Window Based Self-Attention via Swin Transformer for Zero-Shot Learning
Authors: Yasaswi Palagummi, Sareh Rowlands
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Generalised Zero-Shot Learning, often known as GZSL, is an advanced variant of zero-shot learning in which the samples in the unseen category may be either seen or unseen. GZSL methods typically have a bias towards the seen classes because they learn a model to perform recognition for both the seen and unseen classes using data samples from the seen classes. This frequently leads to the misclassification of data from the unseen classes into the seen classes, making the task of GZSL more challenging. In this work of ours, to solve the GZSL problem, we propose an approach leveraging the Shifted Window based Self-Attention in the Swin Transformer (Swin-GZSL) to work in the inductive GSZL problem setting. We run experiments on three popular benchmark datasets: CUB, SUN, and AWA2, which are specifically used for ZSL and its other variants. The results show that our model based on Swin Transformer has achieved state-of-the-art harmonic mean for two datasets -AWA2 and SUN and near-state-of-the-art for the other dataset - CUB. More importantly, this technique has a linear computational complexity, which reduces training time significantly. We have also observed less bias than most of the existing GZSL models.Keywords: generalised, zero-shot learning, inductive learning, shifted-window attention, Swin transformer, vision transformer
Procedia PDF Downloads 7134141 Application of Deep Learning in Top Pair and Single Top Quark Production at the Large Hadron Collider
Authors: Ijaz Ahmed, Anwar Zada, Muhammad Waqas, M. U. Ashraf
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We demonstrate the performance of a very efficient tagger applies on hadronically decaying top quark pairs as signal based on deep neural network algorithms and compares with the QCD multi-jet background events. A significant enhancement of performance in boosted top quark events is observed with our limited computing resources. We also compare modern machine learning approaches and perform a multivariate analysis of boosted top-pair as well as single top quark production through weak interaction at √s = 14 TeV proton-proton Collider. The most relevant known background processes are incorporated. Through the techniques of Boosted Decision Tree (BDT), likelihood and Multlayer Perceptron (MLP) the analysis is trained to observe the performance in comparison with the conventional cut based and count approachKeywords: top tagger, multivariate, deep learning, LHC, single top
Procedia PDF Downloads 11134140 Penetrating Neck Injury: No Zone Approach
Authors: Abhishek Sharma, Amit Gupta, Manish Singhal
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Background: The management of patients with penetrating neck injuries in the prehospital setting and in the emergency department has evolved with regard to the use of multidetector computed tomographic (MDCT) imaging. Hence, there is a shift in the management of neck injuries from mandatory exploration in certain anatomic areas to more conservative approach using imaging and so-called “no zone approach”. Objective: To study the no zone approach in the management of penetrating neck injury using routine imaging in all stable patients. Methods: 137 patients with penetrating neck injury attending emergency department of level 1 trauma centre at AIIMS between 2008–2014 were retrospectively analysed. All hemodynamically stable patients were evaluated using CT scanning. Results: Stab injury is most common (55.91%) mode of pni in civilian population followed by gunshot(18.33%). The majority of patients could be managed with imaging and close observation. 39 patients (28.46%) required operative intervention. The most common indication for operative intervention was vascular followed by airway injury manifesting as hemodynamic destabilisation.There was no statistical difference between the zonal distribution of injuries in patients managed conservatively and those taken to OR. Conclusions: Study shows that patients with penetrating neck trauma who are haemodynamically stable and exhibit no “hard signs” of vascular injury or airway injury may be evaluated initially by MDCT imaging even when platysma violation is present. “No Zone” policy may be superior to traditional zone wise management.Keywords: penetrating neck injury, zone approach, CT scanning, multidetector computed tomographic (MDCT)
Procedia PDF Downloads 40334139 A Digital Twin Approach for Sustainable Territories Planning: A Case Study on District Heating
Authors: Ahmed Amrani, Oussama Allali, Amira Ben Hamida, Felix Defrance, Stephanie Morland, Eva Pineau, Thomas Lacroix
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The energy planning process is a very complex task that involves several stakeholders and requires the consideration of several local and global factors and constraints. In order to optimize and simplify this process, we propose a tool-based iterative approach applied to district heating planning. We build our tool with the collaboration of a French territory using actual district data and implementing the European incentives. We set up an iterative process including data visualization and analysis, identification and extraction of information related to the area concerned by the operation, design of sustainable planning scenarios leveraging local renewable and recoverable energy sources, and finally, the evaluation of scenarios. The last step is performed by a dynamic digital twin replica of the city. Territory’s energy experts confirm that the tool provides them with valuable support towards sustainable energy planning.Keywords: climate change, data management, decision support, digital twin, district heating, energy planning, renewables, smart city
Procedia PDF Downloads 17234138 Improvement of Direct Torque and Flux Control of Dual Stator Induction Motor Drive Using Intelligent Techniques
Authors: Kouzi Katia
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This paper proposes a Direct Torque Control (DTC) algorithm of dual Stator Induction Motor (DSIM) drive using two approach intelligent techniques: Artificial Neural Network (ANN) approach replaces the switching table selector block of conventional DTC and Mamdani Fuzzy Logic controller (FLC) is used for stator resistance estimation. The fuzzy estimation method is based on an online stator resistance correction through the variations of stator current estimation error and its variation. The fuzzy logic controller gives the future stator resistance increment at the output. The main advantage of suggested algorithm control is to reduce the hardware complexity of conventional selectors, to avoid the drive instability that may occur in certain situation and ensure the tracking of the actual of the stator resistance. The effectiveness of the technique and the improvement of the whole system performance are proved by results.Keywords: artificial neural network, direct torque control, dual stator induction motor, fuzzy logic estimator, switching table
Procedia PDF Downloads 34534137 Identification of Thermally Critical Zones Based on Inter Seasonal Variation in Temperature
Authors: Sakti Mandal
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Varying distribution of land surface temperature in an urbanized environment is a globally addressed phenomenon. Usually has been noticed that criticality of surface temperature increases from the periphery to the urban centre. As the centre experiences maximum severity of heat throughout the year, it also represents most critical zone in terms of thermal condition. In this present study, an attempt has been taken to propose a quantitative approach of thermal critical zonation (TCZ) on the basis of seasonal temperature variation. Here the zonation is done by calculating thermal critical value (TCV). From the Landsat 8 thermal digital data of summer and winter seasons for the year 2014, the land surface temperature maps and thermally critical zonation has been prepared, and corresponding dataset has been computed to conduct the overall study of that particular study area. It is shown that TCZ can be clearly identified and analyzed by the help of inter-seasonal temperature range. The results of this study can be utilized effectively in future urban development and planning projects as well as a framework for implementing rules and regulations by the authorities for a sustainable urban development through an environmentally affable approach.Keywords: thermal critical values (TCV), thermally critical zonation (TCZ), land surface temperature (LST), Landsat 8, Kolkata Municipal Corporation (KMC)
Procedia PDF Downloads 19734136 Ontological Modeling Approach for Statistical Databases Publication in Linked Open Data
Authors: Bourama Mane, Ibrahima Fall, Mamadou Samba Camara, Alassane Bah
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At the level of the National Statistical Institutes, there is a large volume of data which is generally in a format which conditions the method of publication of the information they contain. Each household or business data collection project includes a dissemination platform for its implementation. Thus, these dissemination methods previously used, do not promote rapid access to information and especially does not offer the option of being able to link data for in-depth processing. In this paper, we present an approach to modeling these data to publish them in a format intended for the Semantic Web. Our objective is to be able to publish all this data in a single platform and offer the option to link with other external data sources. An application of the approach will be made on data from major national surveys such as the one on employment, poverty, child labor and the general census of the population of Senegal.Keywords: Semantic Web, linked open data, database, statistic
Procedia PDF Downloads 17534135 A Study on Bilingual Semantic Processing: Category Effects and Age Effects
Authors: Lai Yi-Hsiu
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The present study addressed the nature of bilingual semantic processing in Mandarin Chinese and Southern Min and examined category effects and age effects. Nineteen bilingual adults of Mandarin Chinese and Southern Min, nine monolingual seniors of Mandarin Chinese, and ten monolingual seniors of Southern Min in Taiwan individually completed two semantic tasks: Picture naming and category fluency tasks. The instruments for the naming task were sixty black-and-white pictures, including thirty-five object pictures and twenty-five action pictures. The category fluency task also consisted of two semantic categories – objects (or nouns) and actions (or verbs). The reaction time for each picture/question was additionally calculated and analyzed. Oral productions in Mandarin Chinese and in Southern Min were compared and discussed to examine the category effects and age effects. The results of the category fluency task indicated that the content of information of these seniors was comparatively deteriorated, and thus they produced a smaller number of semantic-lexical items. Significant group differences were also found in the reaction time results. Category effects were significant for both adults and seniors in the semantic fluency task. The findings of the present study will help characterize the nature of the bilingual semantic processing of adults and seniors, and contribute to the fields of contrastive and corpus linguistics.Keywords: bilingual semantic processing, aging, Mandarin Chinese, Southern Min
Procedia PDF Downloads 57134134 Metagenomics-Based Molecular Epidemiology of Viral Diseases
Authors: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov
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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis
Procedia PDF Downloads 28134133 A Methodological Approach to Development of Mental Script for Mental Practice of Micro Suturing
Authors: Vaikunthan Rajaratnam
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Intro: Motor imagery (MI) and mental practice (MP) can be an alternative to acquire mastery of surgical skills. One component of using this technique is the use of a mental script. The aim of this study was to design and develop a mental script for basic micro suturing training for skill acquisition using a low-fidelity rubber glove model and to describe the detailed methodology for this process. Methods: This study was based on a design and development research framework. The mental script was developed with 5 expert surgeons performing a cognitive walkthrough of the repair of a vertical opening in a rubber glove model using 8/0 nylon. This was followed by a hierarchal task analysis. A draft script was created, and face and content validity assessed with a checking-back process. The final script was validated with the recruitment of 28 participants, assessed using the Mental Imagery Questionnaire (MIQ). Results: The creation of the mental script is detailed in the full text. After assessment by the expert panel, the mental script had good face and content validity. The average overall MIQ score was 5.2 ± 1.1, demonstrating the validity of generating mental imagery from the mental script developed in this study for micro suturing in the rubber glove model. Conclusion: The methodological approach described in this study is based on an instructional design framework to teach surgical skills. This MP model is inexpensive and easily accessible, addressing the challenge of reduced opportunities to practice surgical skills. However, while motor skills are important, other non-technical expertise required by the surgeon is not addressed with this model. Thus, this model should act a surgical training augment, but not replace it.Keywords: mental script, motor imagery, cognitive walkthrough, verbal protocol analysis, hierarchical task analysis
Procedia PDF Downloads 10334132 Automatic Calibration of Agent-Based Models Using Deep Neural Networks
Authors: Sima Najafzadehkhoei, George Vega Yon
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This paper presents an approach for calibrating Agent-Based Models (ABMs) efficiently, utilizing Convolutional Neural Networks (CNNs) and Long Short-Term Memory (LSTM) networks. These machine learning techniques are applied to Susceptible-Infected-Recovered (SIR) models, which are a core framework in the study of epidemiology. Our method replicates parameter values from observed trajectory curves, enhancing the accuracy of predictions when compared to traditional calibration techniques. Through the use of simulated data, we train the models to predict epidemiological parameters more accurately. Two primary approaches were explored: one where the number of susceptible, infected, and recovered individuals is fully known, and another using only the number of infected individuals. Our method shows promise for application in other ABMs where calibration is computationally intensive and expensive.Keywords: ABM, calibration, CNN, LSTM, epidemiology
Procedia PDF Downloads 2434131 Endocardial Ultrasound Segmentation using Level Set method
Authors: Daoudi Abdelaziz, Mahmoudi Saïd, Chikh Mohamed Amine
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This paper presents a fully automatic segmentation method of the left ventricle at End Systolic (ES) and End Diastolic (ED) in the ultrasound images by means of an implicit deformable model (level set) based on Geodesic Active Contour model. A pre-processing Gaussian smoothing stage is applied to the image, which is essential for a good segmentation. Before the segmentation phase, we locate automatically the area of the left ventricle by using a detection approach based on the Hough Transform method. Consequently, the result obtained is used to automate the initialization of the level set model. This initial curve (zero level set) deforms to search the Endocardial border in the image. On the other hand, quantitative evaluation was performed on a data set composed of 15 subjects with a comparison to ground truth (manual segmentation).Keywords: level set method, transform Hough, Gaussian smoothing, left ventricle, ultrasound images.
Procedia PDF Downloads 46534130 Engagement Analysis Using DAiSEE Dataset
Authors: Naman Solanki, Souraj Mondal
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With the world moving towards online communication, the video datastore has exploded in the past few years. Consequently, it has become crucial to analyse participant’s engagement levels in online communication videos. Engagement prediction of people in videos can be useful in many domains, like education, client meetings, dating, etc. Video-level or frame-level prediction of engagement for a user involves the development of robust models that can capture facial micro-emotions efficiently. For the development of an engagement prediction model, it is necessary to have a widely-accepted standard dataset for engagement analysis. DAiSEE is one of the datasets which consist of in-the-wild data and has a gold standard annotation for engagement prediction. Earlier research done using the DAiSEE dataset involved training and testing standard models like CNN-based models, but the results were not satisfactory according to industry standards. In this paper, a multi-level classification approach has been introduced to create a more robust model for engagement analysis using the DAiSEE dataset. This approach has recorded testing accuracies of 0.638, 0.7728, 0.8195, and 0.866 for predicting boredom level, engagement level, confusion level, and frustration level, respectively.Keywords: computer vision, engagement prediction, deep learning, multi-level classification
Procedia PDF Downloads 11434129 Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach
Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini
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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing
Procedia PDF Downloads 16734128 Phenotype Prediction of DNA Sequence Data: A Machine and Statistical Learning Approach
Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini
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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanismsKeywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing
Procedia PDF Downloads 15934127 Model of Optimal Centroids Approach for Multivariate Data Classification
Authors: Pham Van Nha, Le Cam Binh
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Particle swarm optimization (PSO) is a population-based stochastic optimization algorithm. PSO was inspired by the natural behavior of birds and fish in migration and foraging for food. PSO is considered as a multidisciplinary optimization model that can be applied in various optimization problems. PSO’s ideas are simple and easy to understand but PSO is only applied in simple model problems. We think that in order to expand the applicability of PSO in complex problems, PSO should be described more explicitly in the form of a mathematical model. In this paper, we represent PSO in a mathematical model and apply in the multivariate data classification. First, PSOs general mathematical model (MPSO) is analyzed as a universal optimization model. Then, Model of Optimal Centroids (MOC) is proposed for the multivariate data classification. Experiments were conducted on some benchmark data sets to prove the effectiveness of MOC compared with several proposed schemes.Keywords: analysis of optimization, artificial intelligence based optimization, optimization for learning and data analysis, global optimization
Procedia PDF Downloads 20834126 Constructivism and Situational Analysis as Background for Researching Complex Phenomena: Example of Inclusion
Authors: Radim Sip, Denisa Denglerova
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It’s impossible to capture complex phenomena, such as inclusion, with reductionism. The most common form of reductionism is the objectivist approach, where processes and relationships are reduced to entities and clearly outlined phases, with a consequent search for relationships between them. Constructivism as a paradigm and situational analysis as a methodological research portfolio represent a way to avoid the dominant objectivist approach. They work with a situation, i.e. with the essential blending of actors and their environment. Primary transactions are taking place between actors and their surroundings. Researchers create constructs based on their need to solve a problem. Concepts therefore do not describe reality, but rather a complex of real needs in relation to the available options how such needs can be met. For examination of a complex problem, corresponding methodological tools and overall design of the research are necessary. Using an original research on inclusion in the Czech Republic as an example, this contribution demonstrates that inclusion is not a substance easily described, but rather a relationship field changing its forms in response to its actors’ behaviour and current circumstances. Inclusion consists of dynamic relationship between an ideal, real circumstances and ways to achieve such ideal under the given circumstances. Such achievement has many shapes and thus cannot be captured by description of objects. It can be expressed in relationships in the situation defined by time and space. Situational analysis offers tools to examine such phenomena. It understands a situation as a complex of dynamically changing aspects and prefers relationships and positions in the given situation over a clear and final definition of actors, entities, etc. Situational analysis assumes creation of constructs as a tool for solving a problem at hand. It emphasizes the meanings that arise in the process of coordinating human actions, and the discourses through which these meanings are negotiated. Finally, it offers “cartographic tools” (situational maps, socials worlds / arenas maps, positional maps) that are able to capture the complexity in other than linear-analytical ways. This approach allows for inclusion to be described as a complex of phenomena taking place with a certain historical preference, a complex that can be overlooked if analyzed with a more traditional approach.Keywords: constructivism, situational analysis, objective realism, reductionism, inclusion
Procedia PDF Downloads 14934125 A Framework Based Blockchain for the Development of a Social Economy Platform
Authors: Hasna Elalaoui Elabdallaoui, Abdelaziz Elfazziki, Mohamed Sadgal
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Outlines: The social economy is a moral approach to solidarity applied to the projects’ development. To reconcile economic activity and social equity, crowdfunding is as an alternative means of financing social projects. Several collaborative blockchain platforms exist. It eliminates the need for a central authority or an inconsiderate middleman. Also, the costs for a successful crowdfunding campaign are reduced, since there is no commission to be paid to the intermediary. It improves the transparency of record keeping and delegates authority to authorities who may be prone to corruption. Objectives: The objectives are: to define a software infrastructure for projects’ participatory financing within a social and solidarity economy, allowing transparent, secure, and fair management and to have a financial mechanism that improves financial inclusion. Methodology: The proposed methodology is: crowdfunding platforms literature review, financing mechanisms literature review, requirements analysis and project definition, a business plan, Platform development process and implementation technology, and testing an MVP. Contributions: The solution consists of proposing a new approach to crowdfunding based on Islamic financing, which is the principle of Mousharaka inspired by Islamic financing, which presents a financial innovation that integrates ethics and the social dimension into contemporary banking practices. Conclusion: Crowdfunding platforms need to secure projects and allow only quality projects but also offer a wide range of options to funders. Thus, a framework based on blockchain technology and Islamic financing is proposed to manage this arbitration between quality and quantity of options. The proposed financing system, "Musharaka", is a mode of financing that prohibits interests and uncertainties. The implementation is offered on the secure Ethereum platform as investors sign and initiate transactions for contributions using their digital signature wallet managed by a cryptography algorithm and smart contracts. Our proposal is illustrated by a crop irrigation project in the Marrakech region.Keywords: social economy, Musharaka, blockchain, smart contract, crowdfunding
Procedia PDF Downloads 7734124 Fuzzy-Genetic Algorithm Multi-Objective Optimization Methodology for Cylindrical Stiffened Tanks Conceptual Design
Authors: H. Naseh, M. Mirshams, M. Mirdamadian, H. R. Fazeley
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This paper presents an extension of fuzzy-genetic algorithm multi-objective optimization methodology that could effectively be used to find the overall satisfaction of objective functions (selecting the design variables) in the early stages of design process. The coupling of objective functions due to design variables in an engineering design process will result in difficulties in design optimization problems. In many cases, decision making on design variables conflicts with more than one discipline in system design. In space launch system conceptual design, decision making on some design variable (e.g. oxidizer to fuel mass flow rate O/F) in early stages of the design process is related to objective of liquid propellant engine (specific impulse) and Tanks (structure weight). Then, the primary application of this methodology is the design of a liquid propellant engine with the maximum specific impulse and cylindrical stiffened tank with the minimum weight. To this end, the design problem is established the fuzzy rule set based on designer's expert knowledge with a holistic approach. The independent design variables in this model are oxidizer to fuel mass flow rate, thickness of stringers, thickness of rings, shell thickness. To handle the mentioned problems, a fuzzy-genetic algorithm multi-objective optimization methodology is developed based on Pareto optimal set. Consequently, this methodology is modeled with the one stage of space launch system to illustrate accuracy and efficiency of proposed methodology.Keywords: cylindrical stiffened tanks, multi-objective, genetic algorithm, fuzzy approach
Procedia PDF Downloads 65534123 Logistic Model Tree and Expectation-Maximization for Pollen Recognition and Grouping
Authors: Endrick Barnacin, Jean-Luc Henry, Jack Molinié, Jimmy Nagau, Hélène Delatte, Gérard Lebreton
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Palynology is a field of interest for many disciplines. It has multiple applications such as chronological dating, climatology, allergy treatment, and even honey characterization. Unfortunately, the analysis of a pollen slide is a complicated and time-consuming task that requires the intervention of experts in the field, which is becoming increasingly rare due to economic and social conditions. So, the automation of this task is a necessity. Pollen slides analysis is mainly a visual process as it is carried out with the naked eye. That is the reason why a primary method to automate palynology is the use of digital image processing. This method presents the lowest cost and has relatively good accuracy in pollen retrieval. In this work, we propose a system combining recognition and grouping of pollen. It consists of using a Logistic Model Tree to classify pollen already known by the proposed system while detecting any unknown species. Then, the unknown pollen species are divided using a cluster-based approach. Success rates for the recognition of known species have been achieved, and automated clustering seems to be a promising approach.Keywords: pollen recognition, logistic model tree, expectation-maximization, local binary pattern
Procedia PDF Downloads 18234122 Deep Learning Based Text to Image Synthesis for Accurate Facial Composites in Criminal Investigations
Authors: Zhao Gao, Eran Edirisinghe
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The production of an accurate sketch of a suspect based on a verbal description obtained from a witness is an essential task for most criminal investigations. The criminal investigation system employs specifically trained professional artists to manually draw a facial image of the suspect according to the descriptions of an eyewitness for subsequent identification. Within the advancement of Deep Learning, Recurrent Neural Networks (RNN) have shown great promise in Natural Language Processing (NLP) tasks. Additionally, Generative Adversarial Networks (GAN) have also proven to be very effective in image generation. In this study, a trained GAN conditioned on textual features such as keywords automatically encoded from a verbal description of a human face using an RNN is used to generate photo-realistic facial images for criminal investigations. The intention of the proposed system is to map corresponding features into text generated from verbal descriptions. With this, it becomes possible to generate many reasonably accurate alternatives to which the witness can use to hopefully identify a suspect from. This reduces subjectivity in decision making both by the eyewitness and the artist while giving an opportunity for the witness to evaluate and reconsider decisions. Furthermore, the proposed approach benefits law enforcement agencies by reducing the time taken to physically draw each potential sketch, thus increasing response times and mitigating potentially malicious human intervention. With publically available 'CelebFaces Attributes Dataset' (CelebA) and additionally providing verbal description as training data, the proposed architecture is able to effectively produce facial structures from given text. Word Embeddings are learnt by applying the RNN architecture in order to perform semantic parsing, the output of which is fed into the GAN for synthesizing photo-realistic images. Rather than the grid search method, a metaheuristic search based on genetic algorithms is applied to evolve the network with the intent of achieving optimal hyperparameters in a fraction the time of a typical brute force approach. With the exception of the ‘CelebA’ training database, further novel test cases are supplied to the network for evaluation. Witness reports detailing criminals from Interpol or other law enforcement agencies are sampled on the network. Using the descriptions provided, samples are generated and compared with the ground truth images of a criminal in order to calculate the similarities. Two factors are used for performance evaluation: The Structural Similarity Index (SSIM) and the Peak Signal-to-Noise Ratio (PSNR). A high percentile output from this performance matrix should attribute to demonstrating the accuracy, in hope of proving that the proposed approach can be an effective tool for law enforcement agencies. The proposed approach to criminal facial image generation has potential to increase the ratio of criminal cases that can be ultimately resolved using eyewitness information gathering.Keywords: RNN, GAN, NLP, facial composition, criminal investigation
Procedia PDF Downloads 16234121 A Combined Approach Based on Artificial Intelligence and Computer Vision for Qualitative Grading of Rice Grains
Authors: Hemad Zareiforoush, Saeed Minaei, Ahmad Banakar, Mohammad Reza Alizadeh
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The quality inspection of rice (Oryza sativa L.) during its various processing stages is very important. In this research, an artificial intelligence-based model coupled with computer vision techniques was developed as a decision support system for qualitative grading of rice grains. For conducting the experiments, first, 25 samples of rice grains with different levels of percentage of broken kernels (PBK) and degree of milling (DOM) were prepared and their qualitative grade was assessed by experienced experts. Then, the quality parameters of the same samples examined by experts were determined using a machine vision system. A grading model was developed based on fuzzy logic theory in MATLAB software for making a relationship between the qualitative characteristics of the product and its quality. Totally, 25 rules were used for qualitative grading based on AND operator and Mamdani inference system. The fuzzy inference system was consisted of two input linguistic variables namely, DOM and PBK, which were obtained by the machine vision system, and one output variable (quality of the product). The model output was finally defuzzified using Center of Maximum (COM) method. In order to evaluate the developed model, the output of the fuzzy system was compared with experts’ assessments. It was revealed that the developed model can estimate the qualitative grade of the product with an accuracy of 95.74%.Keywords: machine vision, fuzzy logic, rice, quality
Procedia PDF Downloads 41934120 Modelling Patient Condition-Based Demand for Managing Hospital Inventory
Authors: Esha Saha, Pradip Kumar Ray
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A hospital inventory comprises of a large number and great variety of items for the proper treatment and care of patients, such as pharmaceuticals, medical equipment, surgical items, etc. Improper management of these items, i.e. stockouts, may lead to delay in treatment or other fatal consequences, even death of the patient. So, generally the hospitals tend to overstock items to avoid the risk of stockout which leads to unnecessary investment of money, difficulty in storing, more expiration and wastage, etc. Thus, in such challenging environment, it is necessary for hospitals to follow an inventory policy considering the stochasticity of demand in a hospital. Statistical analysis captures the correlation of patient condition based on bed occupancy with the patient demand which changes stochastically. Due to the dependency on bed occupancy, the markov model is developed that helps to map the changes in demand of hospital inventory based on the changes in the patient condition represented by the movements of bed occupancy states (acute care state, rehabilitative state and long-care state) during the length-of-stay of patient in a hospital. An inventory policy is developed for a hospital based on the fulfillment of patient demand with the objective of minimizing the frequency and quantity of placement of orders of inventoried items. The analytical structure of the model based on probability calculation is provided to show the optimal inventory-related decisions. A case-study is illustrated in this paper for the development of hospital inventory model based on patient demand for multiple inpatient pharmaceutical items. A sensitivity analysis is conducted to investigate the impact of inventory-related parameters on the developed optimal inventory policy. Therefore, the developed model and solution approach may help the hospital managers and pharmacists in managing the hospital inventory in case of stochastic demand of inpatient pharmaceutical items.Keywords: bed occupancy, hospital inventory, markov model, patient condition, pharmaceutical items
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