scholarly journals Colony Fingerprint-Based Discrimination of Staphylococcus species with Machine Learning Approaches

Sensors ◽  
2018 ◽  
Vol 18 (9) ◽  
pp. 2789 ◽  
Author(s):  
Yoshiaki Maeda ◽  
Yui Sugiyama ◽  
Atsushi Kogiso ◽  
Tae-Kyu Lim ◽  
Manabu Harada ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Imaging System ◽  
Bacterial Species ◽  
Support Vector ◽  
Learning Approaches ◽  
Wide Range ◽  
Central Regions ◽  
Species Specific ◽  
Staphylococcus Spp

Detection and discrimination of bacteria are crucial in a wide range of industries, including clinical testing, and food and beverage production. Staphylococcus species cause various diseases, and are frequently detected in clinical specimens and food products. In particular, S. aureus is well known to be the most pathogenic species. Conventional phenotypic and genotypic methods for discrimination of Staphylococcus spp. are time-consuming and labor-intensive. To address this issue, in the present study, we applied a novel discrimination methodology called colony fingerprinting. Colony fingerprinting discriminates bacterial species based on the multivariate analysis of the images of microcolonies (referred to as colony fingerprints) with a size of up to 250 μm in diameter. The colony fingerprints were obtained via a lens-less imaging system. Profiling of the colony fingerprints of five Staphylococcus spp. (S. aureus, S. epidermidis, S. haemolyticus, S. saprophyticus, and S. simulans) revealed that the central regions of the colony fingerprints showed species-specific patterns. We developed 14 discriminative parameters, some of which highlight the features of the central regions, and analyzed them by several machine learning approaches. As a result, artificial neural network (ANN), support vector machine (SVM), and random forest (RF) showed high performance for discrimination of theses bacteria. Bacterial discrimination by colony fingerprinting can be performed within 11 h, on average, and therefore can cut discrimination time in half compared to conventional methods. Moreover, we also successfully demonstrated discrimination of S. aureus in a mixed culture with Pseudomonas aeruginosa. These results suggest that colony fingerprinting is useful for discrimination of Staphylococcus spp.

Evaluation of Machine Learning Approaches for Automated Diagnosis of COVID-19 using X-Ray images (Preprint)

2020 ◽  
Author(s):  
Mazin Mohammed ◽  
Karrar Hameed Abdulkareem ◽  
Mashael S. Maashi ◽  
Salama A. Mostafa A. Mostafa ◽  
Abdullah Baz ◽  
...  
Keyword(s):  
Machine Learning ◽  
Computational Method ◽  
Learning Performance ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Approaches ◽  
Data Set ◽  
X Ray ◽  
Wide Range ◽  
Artificial Neural Network Ann

BACKGROUND In most recent times, global concern has been caused by a coronavirus (COVID19), which is considered a global health threat due to its rapid spread across the globe. Machine learning (ML) is a computational method that can be used to automatically learn from experience and improve the accuracy of predictions. OBJECTIVE In this study, the use of machine learning has been applied to Coronavirus dataset of 50 X-ray images to enable the development of directions and detection modalities with risk causes.The dataset contains a wide range of samples of COVID-19 cases alongside SARS, MERS, and ARDS. The experiment was carried out using a total of 50 X-ray images, out of which 25 images were that of positive COVIDE-19 cases, while the other 25 were normal cases. METHODS An orange tool has been used for data manipulation. To be able to classify patients as carriers of Coronavirus and non-Coronavirus carriers, this tool has been employed in developing and analysing seven types of predictive models. Models such as , artificial neural network (ANN), support vector machine (SVM), linear kernel and radial basis function (RBF), k-nearest neighbour (k-NN), Decision Tree (DT), and CN2 rule inducer were used in this study.Furthermore, the standard InceptionV3 model has been used for feature extraction target. RESULTS The various machine learning techniques that have been trained on coronavirus disease 2019 (COVID-19) dataset with improved ML techniques parameters. The data set was divided into two parts, which are training and testing. The model was trained using 70% of the dataset, while the remaining 30% was used to test the model. The results show that the improved SVM achieved a F1 of 97% and an accuracy of 98%. CONCLUSIONS :. In this study, seven models have been developed to aid the detection of coronavirus. In such cases, the learning performance can be improved through knowledge transfer, whereby time-consuming data labelling efforts are not required.the evaluations of all the models are done in terms of different parameters. it can be concluded that all the models performed well, but the SVM demonstrated the best result for accuracy metric. Future work will compare classical approaches with deep learning ones and try to obtain better results. CLINICALTRIAL None

scholarly journals Outdoor Plant Segmentation With Deep Learning for High-Throughput Field Phenotyping on a Diverse Wheat Dataset

2022 ◽  
Vol 12 ◽  
Author(s):  
Radek Zenkl ◽  
Radu Timofte ◽  
Norbert Kirchgessner ◽  
Lukas Roth ◽  
Andreas Hund ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
High Throughput ◽  
Developmental Stages ◽  
Agricultural Practices ◽  
Support Vector ◽  
Learning Approaches ◽  
Support Vector Classifier ◽  
Wide Range ◽  
Field Phenotyping

Robust and automated segmentation of leaves and other backgrounds is a core prerequisite of most approaches in high-throughput field phenotyping. So far, the possibilities of deep learning approaches for this purpose have not been explored adequately, partly due to a lack of publicly available, appropriate datasets. This study presents a workflow based on DeepLab v3+ and on a diverse annotated dataset of 190 RGB (350 x 350 pixels) images. Images of winter wheat plants of 76 different genotypes and developmental stages have been acquired throughout multiple years at high resolution in outdoor conditions using nadir view, encompassing a wide range of imaging conditions. Inconsistencies of human annotators in complex images have been quantified, and metadata information of camera settings has been included. The proposed approach achieves an intersection over union (IoU) of 0.77 and 0.90 for plants and soil, respectively. This outperforms the benchmarked machine learning methods which use Support Vector Classifier and/or Random Forrest. The results show that a small but carefully chosen and annotated set of images can provide a good basis for a powerful segmentation pipeline. Compared to earlier methods based on machine learning, the proposed method achieves better performance on the selected dataset in spite of using a deep learning approach with limited data. Increasing the amount of publicly available data with high human agreement on annotations and further development of deep neural network architectures will provide high potential for robust field-based plant segmentation in the near future. This, in turn, will be a cornerstone of data-driven improvement in crop breeding and agricultural practices of global benefit.

Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs

2019 ◽  
Vol 20 (5) ◽  
pp. 488-500 ◽  
Author(s):  
Yan Hu ◽  
Yi Lu ◽  
Shuo Wang ◽  
Mengying Zhang ◽  
Xiaosheng Qu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Design ◽  
Anticancer Drugs ◽  
Nearest Neighbor ◽  
Cost Effective ◽  
Support Vector ◽  
Learning Approaches ◽  
K Nearest Neighbor ◽  
Activity Prediction ◽  
Linear Discriminant

Background: Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world&#039;s highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. </P><P> Objective: In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. </P><P> Results: Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. </P><P> Conclusion: This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.

scholarly journals Use of Machine Learning to Investigate the Quantitative Checklist for Autism in Toddlers (Q-CHAT) towards Early Autism Screening

Diagnostics ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 574
Author(s):  
Gennaro Tartarisco ◽  
Giovanni Cicceri ◽  
Davide Di Pietro ◽  
Elisa Leonardi ◽  
Stefania Aiello ◽  
...  
Keyword(s):  
Machine Learning ◽  
High Performance ◽  
Behavioral Science ◽  
Autistic Traits ◽  
Classification Performance ◽  
Recursive Feature Elimination ◽  
Diagnostic Tools ◽  
Support Vector ◽  
K Nearest Neighbors ◽  
Autism Screening

In the past two decades, several screening instruments were developed to detect toddlers who may be autistic both in clinical and unselected samples. Among others, the Quantitative CHecklist for Autism in Toddlers (Q-CHAT) is a quantitative and normally distributed measure of autistic traits that demonstrates good psychometric properties in different settings and cultures. Recently, machine learning (ML) has been applied to behavioral science to improve the classification performance of autism screening and diagnostic tools, but mainly in children, adolescents, and adults. In this study, we used ML to investigate the accuracy and reliability of the Q-CHAT in discriminating young autistic children from those without. Five different ML algorithms (random forest (RF), naïve Bayes (NB), support vector machine (SVM), logistic regression (LR), and K-nearest neighbors (KNN)) were applied to investigate the complete set of Q-CHAT items. Our results showed that ML achieved an overall accuracy of 90%, and the SVM was the most effective, being able to classify autism with 95% accuracy. Furthermore, using the SVM–recursive feature elimination (RFE) approach, we selected a subset of 14 items ensuring 91% accuracy, while 83% accuracy was obtained from the 3 best discriminating items in common to ours and the previously reported Q-CHAT-10. This evidence confirms the high performance and cross-cultural validity of the Q-CHAT, and supports the application of ML to create shorter and faster versions of the instrument, maintaining high classification accuracy, to be used as a quick, easy, and high-performance tool in primary-care settings.

scholarly journals Machine Learning Methods Applied to the Prediction of Pseudo-nitzschia spp. Blooms in the Galician Rias Baixas (NW Spain)

2021 ◽  
Vol 10 (4) ◽  
pp. 199
Author(s):  
Francisco M. Bellas Aláez ◽  
Jesus M. Torres Palenzuela ◽  
Evangelos Spyrakos ◽  
Luis González Vilas
Keyword(s):  
Machine Learning ◽  
Performance Metrics ◽  
Prediction Models ◽  
Support Vector ◽  
False Alarms ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Rías Baixas ◽  
New Algorithms

This work presents new prediction models based on recent developments in machine learning methods, such as Random Forest (RF) and AdaBoost, and compares them with more classical approaches, i.e., support vector machines (SVMs) and neural networks (NNs). The models predict Pseudo-nitzschia spp. blooms in the Galician Rias Baixas. This work builds on a previous study by the authors (doi.org/10.1016/j.pocean.2014.03.003) but uses an extended database (from 2002 to 2012) and new algorithms. Our results show that RF and AdaBoost provide better prediction results compared to SVMs and NNs, as they show improved performance metrics and a better balance between sensitivity and specificity. Classical machine learning approaches show higher sensitivities, but at a cost of lower specificity and higher percentages of false alarms (lower precision). These results seem to indicate a greater adaptation of new algorithms (RF and AdaBoost) to unbalanced datasets. Our models could be operationally implemented to establish a short-term prediction system.

scholarly journals Practical CO2—WAG Field Operational Designs Using Hybrid Numerical-Machine-Learning Approaches

Energies ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1055
Author(s):  
Qian Sun ◽  
William Ampomah ◽  
Junyu You ◽  
Martha Cather ◽  
Robert Balch
Keyword(s):  
Machine Learning ◽  
Oil Recovery ◽  
History Matching ◽  
Optimization Problems ◽  
Learning Technologies ◽  
Petroleum Engineering ◽  
Support Vector ◽  
Learning Approaches ◽  
Field Development ◽  
Proxy Models

Machine-learning technologies have exhibited robust competences in solving many petroleum engineering problems. The accurate predictivity and fast computational speed enable a large volume of time-consuming engineering processes such as history-matching and field development optimization. The Southwest Regional Partnership on Carbon Sequestration (SWP) project desires rigorous history-matching and multi-objective optimization processes, which fits the superiorities of the machine-learning approaches. Although the machine-learning proxy models are trained and validated before imposing to solve practical problems, the error margin would essentially introduce uncertainties to the results. In this paper, a hybrid numerical machine-learning workflow solving various optimization problems is presented. By coupling the expert machine-learning proxies with a global optimizer, the workflow successfully solves the history-matching and CO2 water alternative gas (WAG) design problem with low computational overheads. The history-matching work considers the heterogeneities of multiphase relative characteristics, and the CO2-WAG injection design takes multiple techno-economic objective functions into accounts. This work trained an expert response surface, a support vector machine, and a multi-layer neural network as proxy models to effectively learn the high-dimensional nonlinear data structure. The proposed workflow suggests revisiting the high-fidelity numerical simulator for validation purposes. The experience gained from this work would provide valuable guiding insights to similar CO2 enhanced oil recovery (EOR) projects.

scholarly journals Detection of Malicious Software by Analyzing Distinct Artifacts Using Machine Learning and Deep Learning Algorithms

Electronics ◽  
2021 ◽  
Vol 10 (14) ◽  
pp. 1694
Author(s):  
Mathew Ashik ◽  
A. Jyothish ◽  
S. Anandaram ◽  
P. Vinod ◽  
Francesco Mercaldo ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Support Vector ◽  
Malware Analysis ◽  
Learning Approaches ◽  
Dynamic Features ◽  
System Calls ◽  
Prevention Methods ◽  
Structural Aspects

Malware is one of the most significant threats in today’s computing world since the number of websites distributing malware is increasing at a rapid rate. Malware analysis and prevention methods are increasingly becoming necessary for computer systems connected to the Internet. This software exploits the system’s vulnerabilities to steal valuable information without the user’s knowledge, and stealthily send it to remote servers controlled by attackers. Traditionally, anti-malware products use signatures for detecting known malware. However, the signature-based method does not scale in detecting obfuscated and packed malware. Considering that the cause of a problem is often best understood by studying the structural aspects of a program like the mnemonics, instruction opcode, API Call, etc. In this paper, we investigate the relevance of the features of unpacked malicious and benign executables like mnemonics, instruction opcodes, and API to identify a feature that classifies the executable. Prominent features are extracted using Minimum Redundancy and Maximum Relevance (mRMR) and Analysis of Variance (ANOVA). Experiments were conducted on four datasets using machine learning and deep learning approaches such as Support Vector Machine (SVM), Naïve Bayes, J48, Random Forest (RF), and XGBoost. In addition, we also evaluate the performance of the collection of deep neural networks like Deep Dense network, One-Dimensional Convolutional Neural Network (1D-CNN), and CNN-LSTM in classifying unknown samples, and we observed promising results using APIs and system calls. On combining APIs/system calls with static features, a marginal performance improvement was attained comparing models trained only on dynamic features. Moreover, to improve accuracy, we implemented our solution using distinct deep learning methods and demonstrated a fine-tuned deep neural network that resulted in an F1-score of 99.1% and 98.48% on Dataset-2 and Dataset-3, respectively.

scholarly journals Analysis of the Nosema Cells Identification for Microscopic Images

Sensors ◽  
2021 ◽  
Vol 21 (9) ◽  
pp. 3068
Author(s):  
Soumaya Dghim ◽  
Carlos M. Travieso-González ◽  
Radim Burget
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Image Processing ◽  
Deep Learning ◽  
The Other ◽  
Support Vector ◽  
Learning Approaches ◽  
Microscopic Images ◽  
Trained Neural Network ◽  
Nosema Disease

The use of image processing tools, machine learning, and deep learning approaches has become very useful and robust in recent years. This paper introduces the detection of the Nosema disease, which is considered to be one of the most economically significant diseases today. This work shows a solution for recognizing and identifying Nosema cells between the other existing objects in the microscopic image. Two main strategies are examined. The first strategy uses image processing tools to extract the most valuable information and features from the dataset of microscopic images. Then, machine learning methods are applied, such as a neural network (ANN) and support vector machine (SVM) for detecting and classifying the Nosema disease cells. The second strategy explores deep learning and transfers learning. Several approaches were examined, including a convolutional neural network (CNN) classifier and several methods of transfer learning (AlexNet, VGG-16 and VGG-19), which were fine-tuned and applied to the object sub-images in order to identify the Nosema images from the other object images. The best accuracy was reached by the VGG-16 pre-trained neural network with 96.25%.

Forecasting the risk at infractions: an ensemble comparison of machine learning approach

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Lei Li ◽  
Desheng Wu
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Short Term Memory ◽  
Model Performance ◽  
Large Data ◽  
Support Vector ◽  
Learning Approaches ◽  
Content Type ◽  
Day To Day Operations ◽  
Prediction Approach

PurposeThe infraction of securities regulations (ISRs) of listed firms in their day-to-day operations and management has become one of common problems. This paper proposed several machine learning approaches to forecast the risk at infractions of listed corporates to solve financial problems that are not effective and precise in supervision.Design/methodology/approachThe overall proposed research framework designed for forecasting the infractions (ISRs) include data collection and cleaning, feature engineering, data split, prediction approach application and model performance evaluation. We select Logistic Regression, Naïve Bayes, Random Forest, Support Vector Machines, Artificial Neural Network and Long Short-Term Memory Networks (LSTMs) as ISRs prediction models.FindingsThe research results show that prediction performance of proposed models with the prior infractions provides a significant improvement of the ISRs than those without prior, especially for large sample set. The results also indicate when judging whether a company has infractions, we should pay attention to novel artificial intelligence methods, previous infractions of the company, and large data sets.Originality/valueThe findings could be utilized to address the problems of identifying listed corporates' ISRs at hand to a certain degree. Overall, results elucidate the value of the prior infraction of securities regulations (ISRs). This shows the importance of including more data sources when constructing distress models and not only focus on building increasingly more complex models on the same data. This is also beneficial to the regulatory authorities.

scholarly journals Dynamic Detection of Delayed Cerebral Ischemia Using Machine Learning

2020 ◽  
Author(s):  
Murad Megjhani ◽  
Kalijah Terilli ◽  
Ayham Alkhachroum ◽  
David J. Roh ◽  
Sachin Agarwal ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cerebral Ischemia ◽  
Characteristic Curve ◽  
Delayed Cerebral Ischemia ◽  
Risk Scores ◽  
Support Vector ◽  
Model Parameters ◽  
Learning Approaches ◽  
Physiologic Data ◽  
Over Time

AbstractObjectiveTo develop a machine learning based tool, using routine vital signs, to assess delayed cerebral ischemia (DCI) risk over time.MethodsIn this retrospective analysis, physiologic data for 540 consecutive acute subarachnoid hemorrhage patients were collected and annotated as part of a prospective observational cohort study between May 2006 and December 2014. Patients were excluded if (i) no physiologic data was available, (ii) they expired prior to the DCI onset window (< post bleed day 3) or (iii) early angiographic vasospasm was detected on admitting angiogram. DCI was prospectively labeled by consensus of treating physicians. Occurrence of DCI was classified using various machine learning approaches including logistic regression, random forest, support vector machine (linear and kernel), and an ensemble classifier, trained on vitals and subject characteristic features. Hourly risk scores were generated as the posterior probability at time t. We performed five-fold nested cross validation to tune the model parameters and to report the accuracy. All classifiers were evaluated for good discrimination using the area under the receiver operating characteristic curve (AU-ROC) and confusion matrices.ResultsOf 310 patients included in our final analysis, 101 (32.6%) patients developed DCI. We achieved maximal classification of 0.81 [0.75-0.82] AU-ROC. We also predicted 74.7 % of all DCI events 12 hours before typical clinical detection with a ratio of 3 true alerts for every 2 false alerts.ConclusionA data-driven machine learning based detection tool offered hourly assessments of DCI risk and incorporated new physiologic information over time.

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