scholarly journals Effectiveness, Explainability and Reliability of Machine Meta-Learning Methods for Predicting Mortality in Patients with COVID-19: Results of the Brazilian COVID-19 Registry

2021 ◽  
Author(s):  
Bruno Barbosa Miranda de Paiva ◽  
Polianna Delfino Pereira ◽  
Claudio Moises Valiense de Andrade ◽  
Virginia Mara Reis Gomes ◽  
Maria Clara Pontello Barbosa Lima ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
State Of The Art ◽  
Laboratory Data ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
Learning Models ◽  
Learning Methods ◽  
Meta Learning ◽  
Machine Learning Models

Objective: To provide a thorough comparative study among state ofthe art machine learning methods and statistical methods for determining in-hospital mortality in COVID 19 patients using data upon hospital admission; to study the reliability of the predictions of the most effective methods by correlating the probability of the outcome and the accuracy of the methods; to investigate how explainable are the predictions produced by the most effective methods. Materials and Methods: De-identified data were obtained from COVID 19 positive patients in 36 participating hospitals, from March 1 to September 30, 2020. Demographic, comorbidity, clinical presentation and laboratory data were used as training data to develop COVID 19 mortality prediction models. Multiple machine learning and traditional statistics models were trained on this prediction task using a folded cross validation procedure, from which we assessed performance and interpretability metrics. Results: The Stacking of machine learning models improved over the previous state of the art results by more than 26% in predicting the class of interest (death), achieving 87.1% of AUROC and macroF1 of 73.9%. We also show that some machine learning models can be very interpretable and reliable, yielding more accurate predictions while providing a good explanation for the why. Conclusion: The best results were obtained using the meta learning ensemble model Stacking. State of the art explainability techniques such as SHAP values can be used to draw useful insights into the patterns learned by machine-learning algorithms. Machine learning models can be more explainable than traditional statistics models while also yielding highly reliable predictions. Key words: COVID-19; prognosis; prediction model; machine learning

scholarly journals Assessing Continuous Operator Workload With a Hybrid Scaffolded Neuroergonomic Modeling Approach

2017 ◽  
Vol 59 (1) ◽  
pp. 134-146 ◽  
Author(s):  
Brett J. Borghetti ◽  
Joseph J. Giametta ◽  
Christina F. Rusnock
Keyword(s):  
Machine Learning ◽  
Adaptive Systems ◽  
Model Performance ◽  
Machine Learning Algorithms ◽  
Training Data ◽  
State Assessments ◽  
Learning Models ◽  
Dynamic Task ◽  
Operator Workload ◽  
Machine Learning Models

Objective: We aimed to predict operator workload from neurological data using statistical learning methods to fit neurological-to-state-assessment models. Background: Adaptive systems require real-time mental workload assessment to perform dynamic task allocations or operator augmentation as workload issues arise. Neuroergonomic measures have great potential for informing adaptive systems, and we combine these measures with models of task demand as well as information about critical events and performance to clarify the inherent ambiguity of interpretation. Method: We use machine learning algorithms on electroencephalogram (EEG) input to infer operator workload based upon Improved Performance Research Integration Tool workload model estimates. Results: Cross-participant models predict workload of other participants, statistically distinguishing between 62% of the workload changes. Machine learning models trained from Monte Carlo resampled workload profiles can be used in place of deterministic workload profiles for cross-participant modeling without incurring a significant decrease in machine learning model performance, suggesting that stochastic models can be used when limited training data are available. Conclusion: We employed a novel temporary scaffold of simulation-generated workload profile truth data during the model-fitting process. A continuous workload profile serves as the target to train our statistical machine learning models. Once trained, the workload profile scaffolding is removed and the trained model is used directly on neurophysiological data in future operator state assessments. Application: These modeling techniques demonstrate how to use neuroergonomic methods to develop operator state assessments, which can be employed in adaptive systems.

scholarly journals Design and Manufacture of a Multiband Rectangular Spiral-Shaped Microstrip Antenna Using EM-Driven and Machine Learning

2021 ◽  
Vol 27 (1) ◽  
pp. 29-40
Author(s):  
Ashrf Aoad
Keyword(s):  
Machine Learning ◽  
Microstrip Antenna ◽  
Machine Learning Algorithms ◽  
Mobile Systems ◽  
Training Data ◽  
Learning Models ◽  
Prediction Ability ◽  
Antenna Structure ◽  
Wide Range ◽  
Machine Learning Models

This paper presents a multiband rectangular microstrip antenna using spiral-shaped configurations. The antenna has been designed by combining two configurations of microstrip and spiral with consideration of careful selection of the substrate material, the dimension of the rectangular microstrip, the distance between the turned spiral, and the number of turns of the spiral. The efficiency and accuracy have been improved using machine learning algorithms as well. Machine learning has been studied to model the proposed antenna based on the performance requirements, which requires a sufficient training data to improve the accuracy. Three different machine learning models are applied to improve the accuracy and generalization performance and compared to simulation and measurement results. Simulation, measurement, and machine learning results confirm that the proposed antenna is a new electrically small and operating over a wide range of high-frequency bands between 1 GHz–4 GHz. Machine learning models have the best prediction ability with a mean square error (MSE) of 0.03, and 0.05. The antenna structure and size are compatible and suitable for several multi-band wireless mobile systems operating in L-band and S-band. The results, such as directivity, Half-Power Beamwidth, Voltage Standing Wave Ratio (VSWR), and S-parameter curves, are analysed and compared with the numerical formulation for both spiral and microstrip antennas.

Field Development Optimization Using Machine Learning Methods to Identify the Optimal Water Flooding Regime

2021 ◽  
Author(s):  
Alexey Vasilievich Timonov ◽  
Arturas Rimo Shabonas ◽  
Sergey Alexandrovich Schmidt
Keyword(s):  
Machine Learning ◽  
Optimization Algorithms ◽  
Machine Learning Algorithms ◽  
Water Flooding ◽  
Learning Models ◽  
Learning Methods ◽  
Injection Wells ◽  
Field Development ◽  
Machine Learning Methods ◽  
Machine Learning Models

Abstract The main technology used to optimize field development is hydrodynamic modeling, which is very costly in terms of computing resources and expert time to configure the model. And in the case of brownfields, the complexity increases exponentially. The paper describes the stages of developing a hybrid geological-physical-mathematical proxy model using machine learning methods, which allows performing multivariate calculations and predicting production including various injection well operating regimes. Based on the calculations, we search for the optimal ratio of injection volume distribution to injection wells under given infrastructural constraints. The approach implemented in this work takes into account many factors (some features of the geological structure, history of field development, mutual influence of wells, etc.) and can offer optimal options for distribution of injection volumes of injection wells without performing full-scale or sector hydrodynamic simulation. To predict production, we use machine learning methods (based on decision trees and neural networks) and methods for optimizing the target functions. As a result of this research, a unified algorithm for data verification and preprocessing has been developed for feature extraction tasks and the use of deep machine learning models as input data. Various machine learning algorithms were tested and it was determined that the highest prediction accuracy is achieved by building machine learning models based on Temporal Convolutional Networks (TCN) and gradient boosting. Developed and tested an algorithm for finding the optimal allocation of injection volumes, taking into account the existing infrastructure constraints. Different optimization algorithms are tested. It is determined that the choice and setting of boundary conditions is critical for optimization algorithms in this problem. An integrated approach was tested on terrigenous formations of the West Siberian field, where the developed algorithm showed effectiveness.

scholarly journals Survey of Public Assay Data: Opportunities and Challenges to Understanding Antimicrobial Resistance

2019 ◽  
Author(s):  
Akshay Agarwal ◽  
Gowri Nayar ◽  
James Kaufman
Keyword(s):  
Machine Learning ◽  
Antimicrobial Resistance ◽  
Pathogen Detection ◽  
Ground Truth ◽  
Training Data ◽  
Learning Models ◽  
Learning Methods ◽  
Ground Truth Data ◽  
Specificity And Sensitivity ◽  
Machine Learning Models

ABSTRACTComputational learning methods allow researchers to make predictions, draw inferences, and automate generation of mathematical models. These models are crucial to solving real world problems, such as antimicrobial resistance, pathogen detection, and protein evolution. Machine learning methods depend upon ground truth data to achieve specificity and sensitivity. Since the data is limited in this case, as we will show during the course of this paper, and as the size of available data increases super-linearly, it is of paramount importance to understand the distribution of ground truth data and the analyses it is suited and where it may have limitations that bias downstream learning methods. In this paper, we focus on training data required to model antimicrobial resistance (AR). We report an analysis of bacterial biochemical assay data associated with whole genome sequencing (WGS) from the National Center for Biotechnology Information (NCBI), and discuss important implications when making use of assay data, utilizing genetic features as training data for machine learning models. Complete discussion of machine learning model implementation is outside the scope of this paper and the subject to a later publication.The antimicrobial assay data was obtained from NCBI BioSample, which contains descriptive information about the physical biological specimen from which experimental data is obtained and the results of those experiments themselves.[1] Assay data includes minimum inhibitory concentrations (MIC) of antibiotics, links to associated microbial WGS data, and treatment of a particular microorganism with antibiotics.We observe that there is minimal microbial data available for many antibiotics and for targeted taxonomic groups. The antibiotics with the highest number of assays have less than 1500 measurements each. Corresponding bias in available assays makes machine learning problematic for some important microbes and for building more advanced models that can work across microbial genera. In this study we focus, therefore, on the antibiotic with most assay data (tetracycline) and the corresponding genus with the most available sequence (Acinetobacter with 14000 measurements across 49 antibiotic compounds). Using this data for training and testing, we observed contradictions in the distribution of assay outcomes and report methods to identify and resolve such conflicts. Per antibiotic, we find that there can be up to 30% of (resolvable) conflicting measurements. As more data becomes available, automated training data curation will be an important part of creating useful machine learning models to predict antibiotic resistance.CCS CONCEPTS• Applied computing → Computational biology; Computational genomics; Bioinformatics;

scholarly journals Quantitative Interpretation Explains Machine Learning Models for Chemical Reaction Prediction and Uncovers Bias

2020 ◽  
Author(s):  
David Peter Kovacs ◽  
William McCorkindale ◽  
Alpha Lee
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Model Performance ◽  
Training Data ◽  
Correct Prediction ◽  
Learning Models ◽  
Reaction Prediction ◽  
Wrong Reason ◽  
Realistic Assessment ◽  
Machine Learning Models

<div><div><div><p>Organic synthesis remains a stumbling block in drug discovery. Although a plethora of machine learning models have been proposed as solutions in the literature, they suffer from being opaque black-boxes. It is neither clear if the models are making correct predictions because they inferred the salient chemistry, nor is it clear which training data they are relying on to reach a prediction. This opaqueness hinders both model developers and users. In this paper, we quantitatively interpret the Molecular Transformer, the state-of-the-art model for reaction prediction. We develop a framework to attribute predicted reaction outcomes both to specific parts of reactants, and to reactions in the training set. Furthermore, we demonstrate how to retrieve evidence for predicted reaction outcomes, and understand counterintuitive predictions by scrutinising the data. Additionally, we identify ”Clever Hans” predictions where the correct prediction is reached for the wrong reason due to dataset bias. We present a new debiased dataset that provides a more realistic assessment of model performance, which we propose as the new standard benchmark for comparing reaction prediction models.</p></div></div></div>

Development of Rainfall Prediction Models Using Machine Learning Approaches for Different Agro-Climatic Zones

2021 ◽  
pp. 72-94
Author(s):  
Diwakar Naidu ◽  
Babita Majhi ◽  
Surendra Kumar Chandniha
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Large Scale ◽  
Prediction Models ◽  
Machine Learning Algorithms ◽  
Learning Approaches ◽  
Learning Models ◽  
Climatic Zones ◽  
Environmental Prediction ◽  
Machine Learning Models

This study focuses on modelling the changes in rainfall patterns in different agro-climatic zones due to climate change through statistical downscaling of large-scale climate variables using machine learning approaches. Potential of three machine learning algorithms, multilayer artificial neural network (MLANN), radial basis function neural network (RBFNN), and least square support vector machine (LS-SVM) have been investigated. The large-scale climate variable are obtained from National Centre for Environmental Prediction (NCEP) reanalysis product and used as predictors for model development. Proposed machine learning models are applied to generate projected time series of rainfall for the period 2021-2050 using the Hadley Centre coupled model (HadCM3) B2 emission scenario data as predictors. An increasing trend in anticipated rainfall is observed during 2021-2050 in all the ACZs of Chhattisgarh State. Among the machine learning models, RBFNN found as more feasible technique for modeling of monthly rainfall in this region.

scholarly journals Quantitative interpretation explains machine learning models for chemical reaction prediction and uncovers bias

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dávid Péter Kovács ◽  
William McCorkindale ◽  
Alpha A. Lee
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Model Performance ◽  
Training Data ◽  
Correct Prediction ◽  
Learning Models ◽  
Reaction Prediction ◽  
Wrong Reason ◽  
Realistic Assessment ◽  
Machine Learning Models

AbstractOrganic synthesis remains a major challenge in drug discovery. Although a plethora of machine learning models have been proposed as solutions in the literature, they suffer from being opaque black-boxes. It is neither clear if the models are making correct predictions because they inferred the salient chemistry, nor is it clear which training data they are relying on to reach a prediction. This opaqueness hinders both model developers and users. In this paper, we quantitatively interpret the Molecular Transformer, the state-of-the-art model for reaction prediction. We develop a framework to attribute predicted reaction outcomes both to specific parts of reactants, and to reactions in the training set. Furthermore, we demonstrate how to retrieve evidence for predicted reaction outcomes, and understand counterintuitive predictions by scrutinising the data. Additionally, we identify Clever Hans predictions where the correct prediction is reached for the wrong reason due to dataset bias. We present a new debiased dataset that provides a more realistic assessment of model performance, which we propose as the new standard benchmark for comparing reaction prediction models.

scholarly journals Quantitative Interpretation Explains Machine Learning Models for Chemical Reaction Prediction and Uncovers Bias

2020 ◽  
Author(s):  
David Peter Kovacs ◽  
William McCorkindale ◽  
Alpha Lee
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Model Performance ◽  
Training Data ◽  
Correct Prediction ◽  
Learning Models ◽  
Reaction Prediction ◽  
Wrong Reason ◽  
Realistic Assessment ◽  
Machine Learning Models

<div><div><div><p>Organic synthesis remains a stumbling block in drug discovery. Although a plethora of machine learning models have been proposed as solutions in the literature, they suffer from being opaque black-boxes. It is neither clear if the models are making correct predictions because they inferred the salient chemistry, nor is it clear which training data they are relying on to reach a prediction. This opaqueness hinders both model developers and users. In this paper, we quantitatively interpret the Molecular Transformer, the state-of-the-art model for reaction prediction. We develop a framework to attribute predicted reaction outcomes both to specific parts of reactants, and to reactions in the training set. Furthermore, we demonstrate how to retrieve evidence for predicted reaction outcomes, and understand counterintuitive predictions by scrutinising the data. Additionally, we identify ”Clever Hans” predictions where the correct prediction is reached for the wrong reason due to dataset bias. We present a new debiased dataset that provides a more realistic assessment of model performance, which we propose as the new standard benchmark for comparing reaction prediction models.</p></div></div></div>

Prediction of aircraft estimated time of arrival using machine learning methods

2021 ◽  
pp. 1-15
Author(s):  
O. Basturk ◽  
C. Cetek
Keyword(s):  
Machine Learning ◽  
Web Application ◽  
Absolute Error ◽  
Machine Learning Algorithms ◽  
Weather Data ◽  
Time Of Arrival ◽  
Learning Models ◽  
Trajectory Data ◽  
Different Sources ◽  
Machine Learning Models

ABSTRACT In this study, prediction of aircraft Estimated Time of Arrival (ETA) is proposed using machine learning algorithms. Accurate prediction of ETA is important for management of delay and air traffic flow, runway assignment, gate assignment, collaborative decision making (CDM), coordination of ground personnel and equipment, and optimisation of arrival sequence etc. Machine learning is able to learn from experience and make predictions with weak assumptions or no assumptions at all. In the proposed approach, general flight information, trajectory data and weather data were obtained from different sources in various formats. Raw data were converted to tidy data and inserted into a relational database. To obtain the features for training the machine learning models, the data were explored, cleaned and transformed into convenient features. New features were also derived from the available data. Random forests and deep neural networks were used to train the machine learning models. Both models can predict the ETA with a mean absolute error (MAE) less than 6min after departure, and less than 3min after terminal manoeuvring area (TMA) entrance. Additionally, a web application was developed to dynamically predict the ETA using proposed models.

scholarly journals Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 252
Author(s):  
Laura M. Bergner ◽  
Nardus Mollentze ◽  
Richard J. Orton ◽  
Carlos Tello ◽  
Alice Broos ◽  
...  
Keyword(s):  
Machine Learning ◽  
Phylogenetic Analyses ◽  
Human Infection ◽  
Machine Learning Algorithms ◽  
Zoonotic Potential ◽  
Metagenomic Sequencing ◽  
Learning Models ◽  
Sequencing Data ◽  
Vampire Bats ◽  
Machine Learning Models

The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.

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