scholarly journals IdentPMP: identification of moonlighting proteins in plants using sequence-based learning models

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11900
Author(s):  
Xinyi Liu ◽  
Yueyue Shen ◽  
Youhua Zhang ◽  
Fei Liu ◽  
Zhiyu Ma ◽  
...  
Keyword(s):  
Machine Learning ◽  
Plant Protein ◽  
Prediction Tool ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods ◽  
Benchmark Data ◽  
Moonlighting Protein ◽  
Protein Prediction ◽  
Moonlighting Proteins

Background A moonlighting protein refers to a protein that can perform two or more functions. Since the current moonlighting protein prediction tools mainly focus on the proteins in animals and microorganisms, and there are differences in the cells and proteins between animals and plants, these may cause the existing tools to predict plant moonlighting proteins inaccurately. Hence, the availability of a benchmark data set and a prediction tool specific for plant moonlighting protein are necessary. Methods This study used some protein feature classes from the data set constructed in house to develop a web-based prediction tool. In the beginning, we built a data set about plant protein and reduced redundant sequences. We then performed feature selection, feature normalization and feature dimensionality reduction on the training data. Next, machine learning methods for preliminary modeling were used to select feature classes that performed best in plant moonlighting protein prediction. This selected feature was incorporated into the final plant protein prediction tool. After that, we compared five machine learning methods and used grid searching to optimize parameters, and the most suitable method was chosen as the final model. Results The prediction results indicated that the eXtreme Gradient Boosting (XGBoost) performed best, which was used as the algorithm to construct the prediction tool, called IdentPMP (Identification of Plant Moonlighting Proteins). The results of the independent test set shows that the area under the precision-recall curve (AUPRC) and the area under the receiver operating characteristic curve (AUC) of IdentPMP is 0.43 and 0.68, which are 19.44% (0.43 vs. 0.36) and 13.33% (0.68 vs. 0.60) higher than state-of-the-art non-plant specific methods, respectively. This further demonstrated that a benchmark data set and a plant-specific prediction tool was required for plant moonlighting protein studies. Finally, we implemented the tool into a web version, and users can use it freely through the URL: http://identpmp.aielab.net/.

scholarly journals Automatic Misinformation Detection About COVID-19 in Brazilian Portuguese WhatsApp Messages

2021 ◽  
Author(s):  
Antônio Diogo Forte Martins ◽  
José Maria Monteiro ◽  
Javam Machado
Keyword(s):  
Machine Learning ◽  
Social Networks ◽  
Brazilian Portuguese ◽  
Primary Sources ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods

During the coronavirus pandemic, the problem of misinformation arose once again, quite intensely, through social networks. In Brazil, one of the primary sources of misinformation is the messaging application WhatsApp. However, due to WhatsApp's private messaging nature, there still few methods of misinformation detection developed specifically for this platform. In this context, the automatic misinformation detection (MID) about COVID-19 in Brazilian Portuguese WhatsApp messages becomes a crucial challenge. In this work, we present the COVID-19.BR, a data set of WhatsApp messages about coronavirus in Brazilian Portuguese, collected from Brazilian public groups and manually labeled. Then, we are investigating different machine learning methods in order to build an efficient MID for WhatsApp messages. So far, our best result achieved an F1 score of 0.774 due to the predominance of short texts. However, when texts with less than 50 words are filtered, the F1 score rises to 0.85.

scholarly journals Comparison of machine learning methods for crack localization

2019 ◽  
Vol 23 (1) ◽  
pp. 125-142
Author(s):  
Helle Hein ◽  
Ljubov Jaanuska
Keyword(s):  
Machine Learning ◽  
Random Forests ◽  
Crack Depth ◽  
Haar Wavelet ◽  
Extensive Investigation ◽  
Learning Methods ◽  
Data Set ◽  
Crack Location ◽  
Machine Learning Methods ◽  
Discrete Transform

In this paper, the Haar wavelet discrete transform, the artificial neural networks (ANNs), and the random forests (RFs) are applied to predict the location and severity of a crack in an Euler–Bernoulli cantilever subjected to the transverse free vibration. An extensive investigation into two data collection sets and machine learning methods showed that the depth of a crack is more difficult to predict than its location. The data set of eight natural frequency parameters produces more accurate predictions on the crack depth; meanwhile, the data set of eight Haar wavelet coefficients produces more precise predictions on the crack location. Furthermore, the analysis of the results showed that the ensemble of 50 ANN trained by Bayesian regularization and Levenberg–Marquardt algorithms slightly outperforms RF.

Assessing Replicability of Machine Learning Results: An Introduction to Methods on Predictive Accuracy in Social Sciences

2019 ◽  
pp. 089443931988844
Author(s):  
Ranjith Vijayakumar ◽  
Mike W.-L. Cheung
Keyword(s):  
Machine Learning ◽  
Empirical Data ◽  
Fixed Effects ◽  
Predictive Accuracy ◽  
Support Vector ◽  
Learning Methods ◽  
Data Set ◽  
Replication Studies ◽  
Machine Learning Methods ◽  
Accuracy Measure

Machine learning methods have become very popular in diverse fields due to their focus on predictive accuracy, but little work has been conducted on how to assess the replicability of their findings. We introduce and adapt replication methods advocated in psychology to the aims and procedural needs of machine learning research. In Study 1, we illustrate these methods with the use of an empirical data set, assessing the replication success of a predictive accuracy measure, namely, R 2 on the cross-validated and test sets of the samples. We introduce three replication aims. First, tests of inconsistency examine whether single replications have successfully rejected the original study. Rejection will be supported if the 95% confidence interval (CI) of R 2 difference estimates between replication and original does not contain zero. Second, tests of consistency help support claims of successful replication. We can decide apriori on a region of equivalence, where population values of the difference estimates are considered equivalent for substantive reasons. The 90% CI of a different estimate lying fully within this region supports replication. Third, we show how to combine replications to construct meta-analytic intervals for better precision of predictive accuracy measures. In Study 2, R 2 is reduced from the original in a subset of replication studies to examine the ability of the replication procedures to distinguish true replications from nonreplications. We find that when combining studies sampled from same population to form meta-analytic intervals, random-effects methods perform best for cross-validated measures while fixed-effects methods work best for test measures. Among machine learning methods, regression was comparable to many complex methods, while support vector machine performed most reliably across a variety of scenarios. Social scientists who use machine learning to model empirical data can use these methods to enhance the reliability of their findings.

scholarly journals Prediction of Collapsibility of Loess of Construction Sites in Xining Based on Machine Learning Methods

2021 ◽  
Author(s):  
Qifei Zhao ◽  
Xiaojun Li ◽  
Yunning Cao ◽  
Zhikun Li ◽  
Jixin Fan
Keyword(s):  
Machine Learning ◽  
Support Vector Machine ◽  
Training Data ◽  
Support Vector ◽  
Engineering Practice ◽  
Burial Depth ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods ◽  
North East

Abstract Collapsibility of loess is a significant factor affecting engineering construction in loess area, and testing the collapsibility of loess is costly. In this study, A total of 4,256 loess samples are collected from the north, east, west and middle regions of Xining. 70% of the samples are used to generate training data set, and the rest are used to generate verification data set, so as to construct and validate the machine learning models. The most important six factors are selected from thirteen factors by using Grey Relational analysis and multicollinearity analysis: burial depth、water content、specific gravity of soil particles、void rate、geostatic stress and plasticity limit. In order to predict the collapsibility of loess, four machine learning methods: Support Vector Machine (SVM), Random Subspace Based Support Vector Machine (RSSVM), Random Forest (RF) and Naïve Bayes Tree (NBTree), are studied and compared. The receiver operating characteristic (ROC) curve indicators, standard error (SD) and 95% confidence interval (CI) are used to verify and compare the models in different research areas. The results show that: RF model is the most efficient in predicting the collapsibility of loess in Xining, and its AUC average is above 80%, which can be used in engineering practice.

scholarly journals Natural language processing systems for data extraction and mapping on the basis of unstructured text blocks

2020 ◽  
Vol 26 (3) ◽  
pp. 53-61
Author(s):  
Pavel Kikin ◽  
Alexey Kolesnikov ◽  
Alexey Portnov ◽  
Denis Grischenko
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Mathematical Models ◽  
Optimal Algorithm ◽  
The State ◽  
Gradient Boosting ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods ◽  
Spatio Temporal

The state of ecological systems, along with their general characteristics, is almost always described by indicators that vary in space and time, which leads to a significant complication of constructing mathematical models for predicting the state of such systems. One of the ways to simplify and automate the construction of mathematical models for predicting the state of such systems is the use of machine learning methods. The article provides a comparison of traditional and based on neural networks, algorithms and machine learning methods for predicting spatio-temporal series representing ecosystem data. Analysis and comparison were carried out among the following algorithms and methods: logistic regression, random forest, gradient boosting on decision trees, SARIMAX, neural networks of long-term short-term memory (LSTM) and controlled recurrent blocks (GRU). To conduct the study, data sets were selected that have both spatial and temporal components: the values of the number of mosquitoes, the number of dengue infections, the physical condition of tropical grove trees, and the water level in the river. The article discusses the necessary steps for preliminary data processing, depending on the algorithm used. Also, Kolmogorov complexity was calculated as one of the parameters that can help formalize the choice of the most optimal algorithm when constructing mathematical models of spatio-temporal data for the sets used. Based on the results of the analysis, recommendations are given on the application of certain methods and specific technical solutions, depending on the characteristics of the data set that describes a particular ecosystem

scholarly journals Comparison of Soil Total Nitrogen Content Prediction Models Based on Vis-NIR Spectroscopy

Sensors ◽  
2020 ◽  
Vol 20 (24) ◽  
pp. 7078
Author(s):  
Yueting Wang ◽  
Minzan Li ◽  
Ronghua Ji ◽  
Minjuan Wang ◽  
Lihua Zheng
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Prediction Model ◽  
Total Nitrogen ◽  
Nir Spectroscopy ◽  
Learning Method ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods ◽  
Conventional Machine

Visible-near-infrared spectrum (Vis-NIR) spectroscopy technology is one of the most important methods for non-destructive and rapid detection of soil total nitrogen (STN) content. In order to find a practical way to build STN content prediction model, three conventional machine learning methods and one deep learning approach are investigated and their predictive performances are compared and analyzed by using a public dataset called LUCAS Soil (19,019 samples). The three conventional machine learning methods include ordinary least square estimation (OLSE), random forest (RF), and extreme learning machine (ELM), while for the deep learning method, three different structures of convolutional neural network (CNN) incorporated Inception module are constructed and investigated. In order to clarify effectiveness of different pre-treatments on predicting STN content, the three conventional machine learning methods are combined with four pre-processing approaches (including baseline correction, smoothing, dimensional reduction, and feature selection) are investigated, compared, and analyzed. The results indicate that the baseline-corrected and smoothed ELM model reaches practical precision (coefficient of determination (R2) = 0.89, root mean square error of prediction (RMSEP) = 1.60 g/kg, and residual prediction deviation (RPD) = 2.34). While among three different structured CNN models, the one with more 1 × 1 convolutions preforms better (R2 = 0.93; RMSEP = 0.95 g/kg; and RPD = 3.85 in optimal case). In addition, in order to evaluate the influence of data set characteristics on the model, the LUCAS data set was divided into different data subsets according to dataset size, organic carbon (OC) content and countries, and the results show that the deep learning method is more effective and practical than conventional machine learning methods and, on the premise of enough data samples, it can be used to build a robust STN content prediction model with high accuracy for the same type of soil with similar agricultural treatment.

STACKING OF THE SGTM NEURAL-LIKE STRUCTURE WITH RBF LAYER BASED ON GENERATION OF A RANDOM CURTAIN OF ITS HYPERPARAMETERS FOR PREDICTION TASKS

2021 ◽  
Vol 3 (1) ◽  
pp. 49-55
Author(s):  
R. O. Tkachenko ◽  
◽  
I. V. Izonіn ◽  
V. M. Danylyk ◽  
V. Yu. Mykhalevych ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Accuracy ◽  
Experimental Studies ◽  
Real Data ◽  
Optimal Number ◽  
Individual Member ◽  
Optimal Parameters ◽  
Learning Methods ◽  
Data Set ◽  
Machine Learning Methods

Improving prediction accuracy by artificial intelligence tools is an important task in various industries, economics, medicine. Ensemble learning is one of the possible options to solve this task. In particular, the construction of stacking models based on different machine learning methods, or using different parts of the existing data set demonstrates high prediction accuracy of the. However, the need for proper selection of ensemble members, their optimal parameters, etc., necessitates large time costs for the construction of such models. This paper proposes a slightly different approach to building a simple but effective ensemble method. The authors developed a new model of stacking of nonlinear SGTM neural-like structures, which is based on the use of only one type of ANN as an element base of the ensemble and the use of the same training sample for all members of the ensemble. This approach provides a number of advantages over the procedures for building ensembles based on different machine learning methods, at least in the direction of selecting the optimal parameters for each of them. In our case, a tuple of random hyperparameters for each individual member of the ensemble was used as the basis of ensemble. That is, the training of each combined SGTM neural-like structure with an additional RBF layer, as a separate member of the ensemble occurs using different, randomly selected values of RBF centers and centersfof mass. This provides the necessary variety of ensemble elements. Experimental studies on the effectiveness of the developed ensemble were conducted using a real data set. The task is to predict the amount of health insurance costs based on a number of independent attributes. The optimal number of ensemble members is determined experimentally, which provides the highest prediction accuracy. The results of the work of the developed ensemble are compared with the existing methods of this class. The highest prediction accuracy of the developed ensemble at satisfactory duration of procedure of its training is established.

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