scholarly journals Comparison of Machine Learning Approaches to Improve Diagnosis of Optic Neuropathy Using Photopic Negative Response Measured Using a Handheld Device

2021 ◽  
Vol 8 ◽  
Author(s):  
Tina Diao ◽  
Fareshta Kushzad ◽  
Megh D. Patel ◽  
Megha P. Bindiganavale ◽  
Munam Wasi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Optic Neuropathy ◽  
Negative Response ◽  
Photopic Negative Response ◽  
Learning Approaches ◽  
Data Set ◽  
Full Field ◽  
Handheld Device ◽  
Technical Requirements

The photopic negative response of the full-field electroretinogram (ERG) is reduced in optic neuropathies. However, technical requirements for measurement and poor classification performance have limited widespread clinical application. Recent advances in hardware facilitate efficient clinic-based recording of the full-field ERG. Time series classification, a machine learning approach, may improve classification by using the entire ERG waveform as the input. In this study, full-field ERGs were recorded in 217 eyes (109 optic neuropathy and 108 controls) of 155 subjects. User-defined ERG features including photopic negative response were reduced in optic neuropathy eyes (p < 0.0005, generalized estimating equation models accounting for age). However, classification of optic neuropathy based on user-defined features was only fair with receiver operating characteristic area under the curve ranging between 0.62 and 0.68 and F1 score at the optimal cutoff ranging between 0.30 and 0.33. In comparison, machine learning classifiers using a variety of time series analysis approaches had F1 scores of 0.58–0.76 on a test data set. Time series classifications are promising for improving optic neuropathy diagnosis using ERG waveforms. Larger sample sizes will be important to refine the models.

Machine learning identifies an immunological pattern associated with multiple juvenile idiopathic arthritis subtypes

2019 ◽  
Vol 78 (5) ◽  
pp. 617-628 ◽  
Author(s):  
Erika Van Nieuwenhove ◽  
Vasiliki Lagou ◽  
Lien Van Eyck ◽  
James Dooley ◽  
Ulrich Bodenhofer ◽  
...  
Keyword(s):  
Machine Learning ◽  
Juvenile Idiopathic Arthritis ◽  
Large Scale ◽  
Inflammatory Diseases ◽  
Adaptive Immune System ◽  
Healthy Children ◽  
Learning Approaches ◽  
Data Set ◽  
Immune Signature ◽  
Systemic Jia

ObjectivesJuvenile idiopathic arthritis (JIA) is the most common class of childhood rheumatic diseases, with distinct disease subsets that may have diverging pathophysiological origins. Both adaptive and innate immune processes have been proposed as primary drivers, which may account for the observed clinical heterogeneity, but few high-depth studies have been performed.MethodsHere we profiled the adaptive immune system of 85 patients with JIA and 43 age-matched controls with indepth flow cytometry and machine learning approaches.ResultsImmune profiling identified immunological changes in patients with JIA. This immune signature was shared across a broad spectrum of childhood inflammatory diseases. The immune signature was identified in clinically distinct subsets of JIA, but was accentuated in patients with systemic JIA and those patients with active disease. Despite the extensive overlap in the immunological spectrum exhibited by healthy children and patients with JIA, machine learning analysis of the data set proved capable of discriminating patients with JIA from healthy controls with ~90% accuracy.ConclusionsThese results pave the way for large-scale immune phenotyping longitudinal studies of JIA. The ability to discriminate between patients with JIA and healthy individuals provides proof of principle for the use of machine learning to identify immune signatures that are predictive to treatment response group.

scholarly journals Comparison of Photopic Negative Response of Full-Field and Focal Electroretinograms in Detecting Glaucomatous Eyes

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Shigeki Machida ◽  
Kunifusa Tamada ◽  
Taku Oikawa ◽  
Yasutaka Gotoh ◽  
Tomoharu Nishimura ◽  
...  
Keyword(s):  
Receiver Operating Characteristic ◽  
Operating Characteristic ◽  
Negative Response ◽  
Photopic Negative Response ◽  
Diagnostic Ability ◽  
Full Field ◽  
Receiver Operating Characteristic Curves ◽  
Advanced Glaucoma ◽  
Blue Background ◽  
Higher Sensitivity

Purpose. To compare the photopic negative response (PhNR) of the full-field electroretinogram (ERG) to the PhNR of the focal ERGs in detecting glaucoma.Methods. One hundred and three eyes with glaucoma and 42 normal eyes were studied. Full-field ERGs were elicited by red stimuli on a blue background. The focal ERGs were elicited by a15∘white stimulus spot centered on the macula, the superotemporal or the inferotemporal areas of the macula.Results. In early glaucoma, the areas under the receiver operating characteristic curves (AUCs) were significantly larger for the focal PhNR (0.863–0.924) than those for the full-field PhNR (0.666–0.748) (P<.05). The sensitivity was significantly higher for the focal PhNR than for the full-field PhNR in early (P<.01) and intermediate glaucoma (P<.05). In advanced glaucoma, there was no difference in the AUCs and sensitivities between the focal and full-field PhNRs.Conclusions. The focal ERG has the diagnostic ability with higher sensitivity in detecting early and intermediate glaucoma than the full-field ERG.

Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning Techniques

2012 ◽  
pp. 155-165
Author(s):  
S. Prasanthi ◽  
S.Durga Bhavani ◽  
T. Sobha Rani ◽  
Raju S. Bapi
Keyword(s):  
Machine Learning ◽  
Decision Tree ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Classification Problem ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Decision Tree Classifier ◽  
Data Set ◽  
Learning Techniques

Vast majority of successful drugs or inhibitors achieve their activity by binding to, and modifying the activity of a protein leading to the concept of druggability. A target protein is druggable if it has the potential to bind the drug-like molecules. Hence kinase inhibitors need to be studied to understand the specificity of a kinase inhibitor in choosing a particular kinase target. In this paper we focus on human kinase drug target sequences since kinases are known to be potential drug targets. Also we do a preliminary analysis of kinase inhibitors in order to study the problem in the protein-ligand space in future. The identification of druggable kinases is treated as a classification problem in which druggable kinases are taken as positive data set and non-druggable kinases are chosen as negative data set. The classification problem is addressed using machine learning techniques like support vector machine (SVM) and decision tree (DT) and using sequence-specific features. One of the challenges of this classification problem is due to the unbalanced data with only 48 druggable kinases available against 509 non-drugggable kinases present at Uniprot. The accuracy of the decision tree classifier obtained is 57.65 which is not satisfactory. A two-tier architecture of decision trees is carefully designed such that recognition on the non-druggable dataset also gets improved. Thus the overall model is shown to achieve a final performance accuracy of 88.37. To the best of our knowledge, kinase druggability prediction using machine learning approaches has not been reported in literature.

scholarly journals To use or not to use: Feature selection for sentiment analysis of highly imbalanced data

2017 ◽  
Vol 24 (1) ◽  
pp. 3-37 ◽  
Author(s):  
SANDRA KÜBLER ◽  
CAN LIU ◽  
ZEESHAN ALI SAYYED
Keyword(s):  
Machine Learning ◽  
Feature Selection ◽  
Sentiment Analysis ◽  
Information Gain ◽  
Binary Classification ◽  
Small Subset ◽  
Large Set ◽  
Learning Approaches ◽  
Selection Methods ◽  
Data Set

AbstractWe investigate feature selection methods for machine learning approaches in sentiment analysis. More specifically, we use data from the cooking platform Epicurious and attempt to predict ratings for recipes based on user reviews. In machine learning approaches to such tasks, it is a common approach to use word or part-of-speech n-grams. This results in a large set of features, out of which only a small subset may be good indicators for the sentiment. One of the questions we investigate concerns the extension of feature selection methods from a binary classification setting to a multi-class problem. We show that an inherently multi-class approach, multi-class information gain, outperforms ensembles of binary methods. We also investigate how to mitigate the effects of extreme skewing in our data set by making our features more robust and by using review and recipe sampling. We show that over-sampling is the best method for boosting performance on the minority classes, but it also results in a severe drop in overall accuracy of at least 6 per cent points.

scholarly journals MITRE: predicting host status from microbiota time-series data

2018 ◽  
Author(s):  
Elijah Bogart ◽  
Richard Creswell ◽  
Georg K. Gerber
Keyword(s):  
Machine Learning ◽  
Time Series ◽  
Time Series Data ◽  
Synthetic Data ◽  
Black Box ◽  
Series Data ◽  
Learning Approaches ◽  
Rule Engine ◽  
Microbiome Composition ◽  
Host Status

AbstractLongitudinal studies are crucial for discovering casual relationships between the microbiome and human disease. We present Microbiome Interpretable Temporal Rule Engine (MITRE), the first machine learning method specifically designed for predicting host status from microbiome time-series data. Our method maintains interpretability by learning predictive rules over automatically inferred time-periods and phylogenetically related microbes. We validate MITRE’s performance on semi-synthetic data, and five real datasets measuring microbiome composition over time in infant and adult cohorts. Our results demonstrate that MITRE performs on par or outperforms “black box” machine learning approaches, providing a powerful new tool enabling discovery of biologically interpretable relationships between microbiome and human host.

scholarly journals Machine learning forecasting of CR and PRC balance of trade

2020 ◽  
Vol 73 ◽  
pp. 01004
Author(s):  
Tomàš Brabenec ◽  
Petr Šuleř
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Time Series ◽  
Data Set ◽  
Republic Of China ◽  
The People ◽  
The Future ◽  
Balance Of Trade ◽  
Political Economic ◽  
Social Importance

International trade is an important factor of economic growth. While foreign trade has existed throughout the history, its political, economic and social importance has grown significantly in the last centuries. The objective of the contribution is to use machine learning forecasting for predicting the balance of trade of the Czech Republic (CR) and the People´s Republic of China (PRC) through analysing and machine learning forecasting of the CR import from the PRC and the CR export to the PRC. The data set includes monthly trade balance intervals from January 2000 to June 2019. The contribution investigates and subsequently smooths two time series: the CR import from the PRC; the CR export to the PRC. The balance of trade of both countries in the entire monitored period is negative from the perspective of the CR. A total of 10,000 neural networks are generated. 5 neural structures with the best characteristics are retained. Neural networks are able to capture both the trend of the entire time series and its seasonal fluctuations, but it is necessary to work with time series lag. The CR import from the PRC is growing and it is expected to grow in the future. The CR export to the PRC is growing and it is expected to grow in the future, but its increase in absolute values will be slower than the increase of the CR import from the PRC.

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