scholarly journals A Machine Learning Approach Towards Standardizing Microscopic Agglutination Test for Diagnosis of Leptospirosis

2020 ◽  
Author(s):  
Yuji Oyamada ◽  
Ryo Ozuru ◽  
Toshiyuki Masuzawa ◽  
Satoshi Miyahara ◽  
Yasuhiko Nikaido ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dark Field ◽  
Classification Performance ◽  
Agglutination Test ◽  
Microscopic Agglutination Test ◽  
Support Vector ◽  
Automatic Identification ◽  
Identification Algorithm ◽  
Negative Images ◽  
Antibody Titers

AbstractLeptospirosis is a zoonosis caused by the pathogenic bacterium Leptospira. The Microscopic Agglutination Test (MAT) is widely used as the gold standard for diagnosis of leptospirosis. In this method, diluted patient serum is mixed with serotype-determined Leptospiras, and the presence or absence of aggregation is determined under a dark-field microscope to calculate the antibody titer. Problems of the current MAT method are 1) a requirement of examining many specimens per sample, and 2) a need of distinguishing contaminants from true aggregates to accurately identify positivity. Therefore, increasing efficiency and accuracy are the key to refine MAT. It is possible to achieve efficiency and standardize accuracy at the same time by automating the decision making process. In this study, we built an automatic identification algorithm of MAT using a machine learning method to determine aggregation within microscopic images. The machine learned the features from 316 positive and 230 negative MAT images created with sera of Leptospira-infected (positive) and non-infected (negative) hamsters, respectively. In addition to the acquired original images, wavelet-transformed images were also considered as features. We utilized a support vector machine (SVM) as a proposed decision method. We validated the trained SVMs with 210 positive and 154 negative images. When the features were obtained from original or wavelet-transformed images, all negative images were misjudged as positive, and the classification performance was very low with sensitivity of 1 and specificity of 0. In contrast, when the histograms of wavelet coefficients were used as features, the performance was greatly improved with sensitivity of 0.99 and specificity of 0.99. We confirmed that the current algorithm judges the positive or negative of agglutinations in MAT images, that it gave the further possibility of making a much suitable algorithm by adding more indices (e.g., antibody titers and bacterial counts) in the future.

scholarly journals A machine learning model of microscopic agglutination test for diagnosis of leptospirosis

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259907
Author(s):  
Yuji Oyamada ◽  
Ryo Ozuru ◽  
Toshiyuki Masuzawa ◽  
Satoshi Miyahara ◽  
Yasuhiko Nikaido ◽  
...  
Keyword(s):  
Machine Learning ◽  
Dark Field ◽  
Classification Performance ◽  
Agglutination Test ◽  
Microscopic Agglutination Test ◽  
Support Vector ◽  
Automatic Identification ◽  
Identification Algorithm ◽  
Machine Learning Model ◽  
Negative Images

Leptospirosis is a zoonosis caused by the pathogenic bacterium Leptospira. The Microscopic Agglutination Test (MAT) is widely used as the gold standard for diagnosis of leptospirosis. In this method, diluted patient serum is mixed with serotype-determined Leptospires, and the presence or absence of aggregation is determined under a dark-field microscope to calculate the antibody titer. Problems of the current MAT method are 1) a requirement of examining many specimens per sample, and 2) a need of distinguishing contaminants from true aggregates to accurately identify positivity. Therefore, increasing efficiency and accuracy are the key to refine MAT. It is possible to achieve efficiency and standardize accuracy at the same time by automating the decision-making process. In this study, we built an automatic identification algorithm of MAT using a machine learning method to determine agglutination within microscopic images. The machine learned the features from 316 positive and 230 negative MAT images created with sera of Leptospira-infected (positive) and non-infected (negative) hamsters, respectively. In addition to the acquired original images, wavelet-transformed images were also considered as features. We utilized a support vector machine (SVM) as a proposed decision method. We validated the trained SVMs with 210 positive and 154 negative images. When the features were obtained from original or wavelet-transformed images, all negative images were misjudged as positive, and the classification performance was very low with sensitivity of 1 and specificity of 0. In contrast, when the histograms of wavelet coefficients were used as features, the performance was greatly improved with sensitivity of 0.99 and specificity of 0.99. We confirmed that the current algorithm judges the positive or negative of agglutinations in MAT images and gives the further possibility of automatizing MAT procedure.

scholarly journals Leptospirosis of the dogs in Kyiv in 2016-2018, serological monitoring and analysis of the ethioological structure

2018 ◽  
pp. 20-27
Author(s):  
S. Babyuk ◽  
O. Piskun ◽  
V. Ukhovskyi ◽  
A. Piskun ◽  
L. Korniienko ◽  
...  
Keyword(s):  
Blood Serum ◽  
Dark Field ◽  
Agglutination Test ◽  
Microscopic Agglutination Test ◽  
Minor Role ◽  
National Academy Of Sciences ◽  
Dark Field Microscopy ◽  
Antibody Titers ◽  
A Minor ◽  
Academy Of Sciences

Leptospirosis – common to humans and animals is a dangerous infectious disease that is caused by microbes - leptospires. The disease is accompanied by fever, kidney damage, liver, cardiovascular and nervous system. Leptospirosis in dogs is considered one of the most common diseases. Particularly difficult is the breed with a faulty type of body structure, such as: Neapolitan Mastino, Bulmastiff, English Bulldog, French Bulldog, Boxer, Bologna, Bloodhound, Basset Hound. The disease is most often diagnosed in dogs of hunting breeds, as a result of frequent contact with standing water, as well as in courtyard and stray dogs. Young animals and puppies get sick more often, as they do not have a stable immunity, the hemorrhagic form is more often diagnosed in older dogs. The subject was to study the distribution of leptospirosis among dogs, to establish the seropositivity level and to determine the seroprevalence of the most common of Leptospira serotypes that circulate among this species of animals. For research, an extensive diagnostic series of L. interrogans which includes 20 serovars, and blood serum from dogs that were selected in veterinary clinics in the city of Kyiv, were used as antigen and were transferred to the laboratory of leptospirosis in agricultural animals from the Museum of Microorganisms of the Institute of Veterinary Medicine of the National Academy of Sciences of Ukraine. Studies of blood serum were performed by the microagglutination test (MAT) followed by dark-field microscopy. PMA was placed in 4 dilutions: 1:50, 1: 100, 1: 500 and 1: 2500. According to numerous publications of scientists from different countries of the world, the seroprevalence level of leptospirosis infection among the dogs varies from 39% to 95%. A total of 1831 samples of blood serum were studied in the microscopic agglutination test. As a result of the serological study, 873 animals reacted positively, which is 47.7% of the total number of investigated ones. Analyzing the registered antibody titers, which is most often found titer 1: 100, which is 50.4% of the total number of positive reactions. This indicates the presence of a disease in dogs. Serrogroup Icterohaemorrhagiae is recorded in almost 50% of all positive reactions to leptospirosis and plays a major role in the etiology of the disease. It can be assumed that these dogs had contact with rats or their urine. In turn, the leading for these animals serogroup Canicola was detected in only a third of cases. Other serological groups played a minor role in the etiological structure. Summing up the aforesaid, according to the results of our work, serological prevalence of the pathogenesis of leptospirosis among dogs was determined to be 47.7%. Was detected the circulation of Leptospira`s antibodies in blood serum of these animals. The analysis of the etiological structure of leptospirosis showed that the dominant serogroups were Icterohaemorrhagiae and Canicola. Seven serogroups (Pomona, Sejroe, Grippotyphosa, Australis, Autumnalis, Celledoni, Ballum) were recorded in the range of 1% to 4%. Other serogroups do not have a significant effect on the morbidity of dogs. Keywords: leptospirosis, dogs, etiological structure, serological monitoring, antibody, microscopic agglutination test.

Binary Spectrum Feature for Improved Classifier Performance

2020 ◽  
Author(s):  
Nalika Ulapane ◽  
Karthick Thiyagarajan ◽  
sarath kodagoda
Keyword(s):  
Machine Learning ◽  
Classification Performance ◽  
Feature Reduction ◽  
Sensor Data ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Svm Classifier ◽  
Monitoring Task ◽  
Classifier Performance ◽  
Spectrum Feature

<div>Classification has become a vital task in modern machine learning and Artificial Intelligence applications, including smart sensing. Numerous machine learning techniques are available to perform classification. Similarly, numerous practices, such as feature selection (i.e., selection of a subset of descriptor variables that optimally describe the output), are available to improve classifier performance. In this paper, we consider the case of a given supervised learning classification task that has to be performed making use of continuous-valued features. It is assumed that an optimal subset of features has already been selected. Therefore, no further feature reduction, or feature addition, is to be carried out. Then, we attempt to improve the classification performance by passing the given feature set through a transformation that produces a new feature set which we have named the “Binary Spectrum”. Via a case study example done on some Pulsed Eddy Current sensor data captured from an infrastructure monitoring task, we demonstrate how the classification accuracy of a Support Vector Machine (SVM) classifier increases through the use of this Binary Spectrum feature, indicating the feature transformation’s potential for broader usage.</div><div><br></div>

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 Phybrata Sensors and Machine Learning for Enhanced Neurophysiological Diagnosis and Treatment

Sensors ◽  
2021 ◽  
Vol 21 (21) ◽  
pp. 7417
Author(s):  
Alex J. Hope ◽  
Utkarsh Vashisth ◽  
Matthew J. Parker ◽  
Andreas B. Ralston ◽  
Joshua M. Roper ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Random Forest ◽  
Binary Classification ◽  
Classification Performance ◽  
Support Vector ◽  
Use Case ◽  
Signal Features ◽  
Test Population

Concussion injuries remain a significant public health challenge. A significant unmet clinical need remains for tools that allow related physiological impairments and longer-term health risks to be identified earlier, better quantified, and more easily monitored over time. We address this challenge by combining a head-mounted wearable inertial motion unit (IMU)-based physiological vibration acceleration (“phybrata”) sensor and several candidate machine learning (ML) models. The performance of this solution is assessed for both binary classification of concussion patients and multiclass predictions of specific concussion-related neurophysiological impairments. Results are compared with previously reported approaches to ML-based concussion diagnostics. Using phybrata data from a previously reported concussion study population, four different machine learning models (Support Vector Machine, Random Forest Classifier, Extreme Gradient Boost, and Convolutional Neural Network) are first investigated for binary classification of the test population as healthy vs. concussion (Use Case 1). Results are compared for two different data preprocessing pipelines, Time-Series Averaging (TSA) and Non-Time-Series Feature Extraction (NTS). Next, the three best-performing NTS models are compared in terms of their multiclass prediction performance for specific concussion-related impairments: vestibular, neurological, both (Use Case 2). For Use Case 1, the NTS model approach outperformed the TSA approach, with the two best algorithms achieving an F1 score of 0.94. For Use Case 2, the NTS Random Forest model achieved the best performance in the testing set, with an F1 score of 0.90, and identified a wider range of relevant phybrata signal features that contributed to impairment classification compared with manual feature inspection and statistical data analysis. The overall classification performance achieved in the present work exceeds previously reported approaches to ML-based concussion diagnostics using other data sources and ML models. This study also demonstrates the first combination of a wearable IMU-based sensor and ML model that enables both binary classification of concussion patients and multiclass predictions of specific concussion-related neurophysiological impairments.

scholarly journals Automatic recognition of self-acknowledged limitations in clinical research literature

2018 ◽  
Vol 25 (7) ◽  
pp. 855-861 ◽  
Author(s):  
Halil Kilicoglu ◽  
Graciela Rosemblat ◽  
Mario Malički ◽  
Gerben ter Riet
Keyword(s):  
Machine Learning ◽  
Clinical Research ◽  
Binary Classification ◽  
Classification Performance ◽  
Research Literature ◽  
Machine Learning Algorithms ◽  
Supervised Machine Learning ◽  
Support Vector ◽  
Rule Based ◽  
Research Transparency

Abstract Objective To automatically recognize self-acknowledged limitations in clinical research publications to support efforts in improving research transparency. Methods To develop our recognition methods, we used a set of 8431 sentences from 1197 PubMed Central articles. A subset of these sentences was manually annotated for training/testing, and inter-annotator agreement was calculated. We cast the recognition problem as a binary classification task, in which we determine whether a given sentence from a publication discusses self-acknowledged limitations or not. We experimented with three methods: a rule-based approach based on document structure, supervised machine learning, and a semi-supervised method that uses self-training to expand the training set in order to improve classification performance. The machine learning algorithms used were logistic regression (LR) and support vector machines (SVM). Results Annotators had good agreement in labeling limitation sentences (Krippendorff’s α = 0.781). Of the three methods used, the rule-based method yielded the best performance with 91.5% accuracy (95% CI [90.1-92.9]), while self-training with SVM led to a small improvement over fully supervised learning (89.9%, 95% CI [88.4-91.4] vs 89.6%, 95% CI [88.1-91.1]). Conclusions The approach presented can be incorporated into the workflows of stakeholders focusing on research transparency to improve reporting of limitations in clinical studies.

scholarly journals Automatic identification of bird targets with radar via patterns produced by wing flapping

2008 ◽  
Vol 5 (26) ◽  
pp. 1041-1053 ◽  
Author(s):  
Serge Zaugg ◽  
Gilbert Saporta ◽  
Emiel van Loon ◽  
Heiko Schmaljohann ◽  
Felix Liechti
Keyword(s):  
Bird Migration ◽  
Wind Farms ◽  
Classification Performance ◽  
Future Research ◽  
Support Vector ◽  
Automatic Identification ◽  
Radar Meteorology ◽  
Ground Clutter ◽  
Environmental Impact Assessments ◽  
Radar Signals

Bird identification with radar is important for bird migration research, environmental impact assessments (e.g. wind farms), aircraft security and radar meteorology. In a study on bird migration, radar signals from birds, insects and ground clutter were recorded. Signals from birds show a typical pattern due to wing flapping. The data were labelled by experts into the four classes BIRD, INSECT, CLUTTER and UFO (unidentifiable signals). We present a classification algorithm aimed at automatic recognition of bird targets. Variables related to signal intensity and wing flapping pattern were extracted (via continuous wavelet transform). We used support vector classifiers to build predictive models. We estimated classification performance via cross validation on four datasets. When data from the same dataset were used for training and testing the classifier, the classification performance was extremely to moderately high. When data from one dataset were used for training and the three remaining datasets were used as test sets, the performance was lower but still extremely to moderately high. This shows that the method generalizes well across different locations or times. Our method provides a substantial gain of time when birds must be identified in large collections of radar signals and it represents the first substantial step in developing a real time bird identification radar system. We provide some guidelines and ideas for future research.

Quantitative Assessment of Ataxia in Multiple Sclerosis Patients using Spatiotemporal Parameters: A Relief-Based Machine Learning Analysis

2021 ◽  
Author(s):  
Furkan Bilek ◽  
Ferhat Balgetir ◽  
Caner Feyzi Demir ◽  
Gökhan Alkan ◽  
Seda Arslan-Tuncer
Keyword(s):  
Machine Learning ◽  
Multiple Sclerosis ◽  
Sensitivity And Specificity ◽  
Classification Performance ◽  
Support Vector ◽  
Learning Methods ◽  
K Nearest Neighbors ◽  
Machine Learning Methods ◽  
Spatiotemporal Parameters ◽  
Multiple Sclerosis Patients

Abstract Background and Objective Multiple sclerosis (MS) is a chronic, progressive, and autoimmune disease of the central nervous system (CNS) characterized by inflammation, demyelination, and axonal injury. In patients with newly diagnosed MS (ndMS), ataxia can present either as mild or severe and can be difficult to diagnose in the absence of clinical disability. Such difficulties can be eliminated by using decision support systems supported by machine learning methods. The present study aimed to achieve early diagnosis of ataxia in ndMS patients by using machine learning methods with spatiotemporal parameters. Materials and Methods The prospective study included 32 ndMS patients with an Expanded Disability Status Scale (EDSS) score of≤2.0 and 32 healthy volunteers. A total of 14 parameters were elicited by using a Win-Track platform. The ndMS patients were differentiated from healthy individuals using multiple classifiers including Artificial Neural Network (ANN), Support Vector Machine (SVM), the k-nearest neighbors (K-NN) algorithm, and Decision Tree Learning (DTL). To improve the performance of the classification, a Relief-based feature selection algorithm was applied to select the subset that best represented the whole dataset. Performance evaluation was achieved based on several criteria such as Accuracy (ACC), Sensitivity (SN), Specificity (SP), and Precision (PREC). Results ANN had a higher classification performance compared to other classifiers, whereby it provided an accuracy, sensitivity, and specificity of 89, 87.8, 90.3% with the use of all parameters and provided the values of 93.7, 96.6%, and 91.1% with the use of parameters selected by the Relief algorithm, respectively. Significance To our knowledge, this is the first study of its kind in the literature to investigate the diagnosis of ataxia in ndMS patients by using machine learning methods with spatiotemporal parameters. The proposed method, i. e. Relief-based ANN method, successfully diagnosed ataxia by using a lower number of parameters compared to the numbers of parameters reported in clinical studies, thereby reducing the costs and increasing the performance of the diagnosis. The method also provided higher rates of accuracy, sensitivity, and specificity in the diagnosis of ataxia in ndMS patients compared to other methods. Taken together, these findings indicate that the proposed method could be helpful in the diagnosis of ataxia in minimally impaired ndMS patients and could be a pathfinder for future studies.

scholarly journals Cell morphology-based machine learning models for human cell state classification

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Yi Li ◽  
Chance M. Nowak ◽  
Uyen Pham ◽  
Khai Nguyen ◽  
Leonidas Bleris
Keyword(s):  
Machine Learning ◽  
Flow Cytometry ◽  
Multilayer Perceptron ◽  
Nearest Neighbor ◽  
Annexin V ◽  
Classification Performance ◽  
Training Data ◽  
Support Vector ◽  
Apoptotic Cells ◽  
K Nearest Neighbor

AbstractHerein, we implement and access machine learning architectures to ascertain models that differentiate healthy from apoptotic cells using exclusively forward (FSC) and side (SSC) scatter flow cytometry information. To generate training data, colorectal cancer HCT116 cells were subjected to miR-34a treatment and then classified using a conventional Annexin V/propidium iodide (PI)-staining assay. The apoptotic cells were defined as Annexin V-positive cells, which include early and late apoptotic cells, necrotic cells, as well as other dying or dead cells. In addition to fluorescent signal, we collected cell size and granularity information from the FSC and SSC parameters. Both parameters are subdivided into area, height, and width, thus providing a total of six numerical features that informed and trained our models. A collection of logistical regression, random forest, k-nearest neighbor, multilayer perceptron, and support vector machine was trained and tested for classification performance in predicting cell states using only the six aforementioned numerical features. Out of 1046 candidate models, a multilayer perceptron was chosen with 0.91 live precision, 0.93 live recall, 0.92 live f value and 0.97 live area under the ROC curve when applied on standardized data. We discuss and highlight differences in classifier performance and compare the results to the standard practice of forward and side scatter gating, typically performed to select cells based on size and/or complexity. We demonstrate that our model, a ready-to-use module for any flow cytometry-based analysis, can provide automated, reliable, and stain-free classification of healthy and apoptotic cells using exclusively size and granularity information.

scholarly journals Evaluating machine learning techniques for archaeological lithic sourcing: a case study of flint in Britain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tom Elliot ◽  
Robert Morse ◽  
Duane Smythe ◽  
Ashley Norris
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Random Forest ◽  
Objective Evaluation ◽  
Classification Performance ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Techniques ◽  
Vector Machines

AbstractIt is 50 years since Sieveking et al. published their pioneering research in Nature on the geochemical analysis of artefacts from Neolithic flint mines in southern Britain. In the decades since, geochemical techniques to source stone artefacts have flourished globally, with a renaissance in recent years from new instrumentation, data analysis, and machine learning techniques. Despite the interest over these latter approaches, there has been variation in the quality with which these methods have been applied. Using the case study of flint artefacts and geological samples from England, we present a robust and objective evaluation of three popular techniques, Random Forest, K-Nearest-Neighbour, and Support Vector Machines, and present a pipeline for their appropriate use. When evaluated correctly, the results establish high model classification performance, with Random Forest leading with an average accuracy of 85% (measured through F1 Scores), and with Support Vector Machines following closely. The methodology developed in this paper demonstrates the potential to significantly improve on previous approaches, particularly in removing bias, and providing greater means of evaluation than previously utilised.

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