scholarly journals Application of Improved Three-Dimensional Kernel Approach to Prediction of Protein Structural Class

2013 ◽  
Vol 2013 ◽  
pp. 1-8
Author(s):  
Xu Liu ◽  
Yuchao Zhang ◽  
Hua Yang ◽  
Lisheng Wang ◽  
Shuaibing Liu
Keyword(s):  
Support Vector Machines ◽  
Three Dimensional ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Structural Class ◽  
Protein Structural Class ◽  
Complementary Role ◽  
Vector Machines ◽  
Kernel Approach ◽  
Leave One Out

Kernel methods, such as kernel PCA, kernel PLS, and support vector machines, are widely known machine learning techniques in biology, medicine, chemistry, and material science. Based on nonlinear mapping and Coulomb function, two 3D kernel approaches were improved and applied to predictions of the four protein tertiary structural classes of domains (all-α, all-β,α/β, andα + β) and five membrane protein types with satisfactory results. In a benchmark test, the performances of improved 3D kernel approach were compared with those of neural networks, support vector machines, and ensemble algorithm. Demonstration through leave-one-out cross-validation on working datasets constructed by investigators indicated that new kernel approaches outperformed other predictors. It has not escaped our notice that 3D kernel approaches may hold a high potential for improving the quality in predicting the other protein features as well. Or at the very least, it will play a complementary role to many of the existing algorithms in this regard.

Gaussian Processes for Classification: Mean-Field Algorithms

2000 ◽  
Vol 12 (11) ◽  
pp. 2655-2684 ◽  
Author(s):  
Manfred Opper ◽  
Ole Winther
Keyword(s):  
Support Vector Machines ◽  
Gaussian Processes ◽  
Disordered Systems ◽  
Binary Classification ◽  
Computational Cost ◽  
Mean Field ◽  
Strong Support ◽  
Support Vector ◽  
Vector Machines ◽  
Leave One Out

We derive a mean-field algorithm for binary classification with gaussian processes that is based on the TAP approach originally proposed in statistical physics of disordered systems. The theory also yields an approximate leave-one-out estimator for the generalization error, which is computed with no extra computational cost. We show that from the TAP approach, it is possible to derive both a simpler “naive” mean-field theory and support vector machines (SVMs) as limiting cases. For both mean-field algorithms and support vector machines, simulation results for three small benchmark data sets are presented. They show that one may get state-of-the-art performance by using the leave-one-out estimator for model selection and the built-in leave-one-out estimators are extremely precise when compared to the exact leave-one-out estimate. The second result is taken as strong support for the internal consistency of the mean-field approach.

Cow behaviour pattern recognition using a three-dimensional accelerometer and support vector machines

2009 ◽  
Vol 119 (1-2) ◽  
pp. 32-38 ◽  
Author(s):  
Paula Martiskainen ◽  
Mikko Järvinen ◽  
Jukka-Pekka Skön ◽  
Jarkko Tiirikainen ◽  
Mikko Kolehmainen ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Support Vector Machines ◽  
Three Dimensional ◽  
Behaviour Pattern ◽  
Support Vector ◽  
Vector Machines

scholarly journals Protein structural class prediction using predicted secondary structure and hydropathy profile

2021 ◽  
Author(s):  
Syeda Nadia Firdaus
Keyword(s):  
Secondary Structure ◽  
Classification Problem ◽  
Support Vector ◽  
Prediction Problem ◽  
Class Prediction ◽  
Structural Class ◽  
Protein Structural Class ◽  
Vector Machines ◽  
Structural Classes ◽  
New Strategies

This thesis explores machine learning models based on various feature sets to solve the protein structural class prediction problem which is a significant classification problem in bioinformatics. Knowledge of protein structural classes contributes to an understanding of protein folding patterns, and this has made structural class prediction research a major topic of interest. In this thesis, features are extracted from predicted secondary structure and hydropathy sequence using new strategies to classify proteins into one of the four major structural classes: all-α, all-β, α/β, and α+β. The prediction accuracy using these features compares favourably with some existing successful methods. We use Support Vector Machines (SVM), since this learning method has well-known efficiency in solving this classification problem. On a standard dataset (25PDB), the proposed system has an overall accuracy of 89% with as few as 22 features, whereas the previous best performing method had an accuracy of 88% using 2510 features.

Support Vector Machine Classification applied on Weaning Trials Patients

2008 ◽  
pp. 1277-1282
Author(s):  
B.F. Giraldo ◽  
A. Garde ◽  
C. Arizmendi ◽  
R. Jané ◽  
I. Diaz ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Support Vector Machine ◽  
Support Vector Machines ◽  
Work Of Breathing ◽  
Selection Procedure ◽  
Respiratory Pattern ◽  
Support Vector ◽  
Vector Machines ◽  
Leave One Out ◽  
Pattern Variability

The most common reason for instituting mechanical ventilation is to decrease a patient’s work of breathing. Many attempts have been made to increase the effectiveness on the evaluation of the respiratory pattern by means of respiratory signal analysis. This work suggests a method of studying the lying differences in respiratory pattern variability between patients on weaning trials. The core of the proposed method is the use of support vector machines to classify patients into two groups, taking into account 35 features of each one, previously extracted from the respiratory flow. 146 patients from mechanical ventilation were studied: Group S of 79 patients with Successful trials, and Group F of 67 patients that Failed on the attempt to maintain spontaneous breathing and had to be reconnected. Applying a feature selection procedure based on the use of the support vector machine with leave-one-out cross-validation, it was obtained 86.67% of well classified patients into the Group S and 73.34% into Group F, using only eight of the 35 features. Therefore, support vector machines can be an interesting classification method in the study of the respiratory pattern variability.

Twitter sentiment analysis for the estimation of voting intention in the 2017 Chilean elections

2020 ◽  
Vol 24 (5) ◽  
pp. 1141-1160
Author(s):  
Tomás Alegre Sepúlveda ◽  
Brian Keith Norambuena
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Sentiment Analysis ◽  
Classification Model ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Traditional Methods ◽  
Actual Result ◽  
Learning Techniques ◽  
Vector Machines

In this paper, we apply sentiment analysis methods in the context of the first round of the 2017 Chilean elections. The purpose of this work is to estimate the voting intention associated with each candidate in order to contrast this with the results from classical methods (e.g., polls and surveys). The data are collected from Twitter, because of its high usage in Chile and in the sentiment analysis literature. We obtained tweets associated with the three main candidates: Sebastián Piñera (SP), Alejandro Guillier (AG) and Beatriz Sánchez (BS). For each candidate, we estimated the voting intention and compared it to the traditional methods. To do this, we first acquired the data and labeled the tweets as positive or negative. Afterward, we built a model using machine learning techniques. The classification model had an accuracy of 76.45% using support vector machines, which yielded the best model for our case. Finally, we use a formula to estimate the voting intention from the number of positive and negative tweets for each candidate. For the last period, we obtained a voting intention of 35.84% for SP, compared to a range of 34–44% according to traditional polls and 36% in the actual elections. For AG we obtained an estimate of 37%, compared with a range of 15.40% to 30.00% for traditional polls and 20.27% in the elections. For BS we obtained an estimate of 27.77%, compared with the range of 8.50% to 11.00% given by traditional polls and an actual result of 22.70% in the elections. These results are promising, in some cases providing an estimate closer to reality than traditional polls. Some differences can be explained due to the fact that some candidates have been omitted, even though they held a significant number of votes.

Detection of Loss Zones while Drilling Using Different Machine Learning Techniques

2021 ◽  
pp. 1-29
Author(s):  
Ahmed Alsaihati ◽  
Mahmoud Abughaban ◽  
Salaheldin Elkatatny ◽  
Abdulazeez Abdulraheem
Keyword(s):  
Machine Learning ◽  
Support Vector Machines ◽  
Random Forests ◽  
Nearest Neighbors ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
K Nearest Neighbors ◽  
Learning Techniques ◽  
Vector Machines ◽  
Testing Set

Abstract Fluid loss into formations is a common operational issue that is frequently encountered when drilling across naturally or induced fractured formations. This could pose significant operational risks, such as well-control, stuck pipe, and wellbore instability, which, in turn, lead to an increase of well time and cost. This research aims to use and evaluate different machine learning techniques, namely: support vector machines, random forests, and K-nearest neighbors in detecting loss circulation occurrences while drilling using solely drilling surface parameters. Actual field data of seven wells, which had suffered partial or severe loss circulation, were used to build predictive models, while Well-8 was used to compare the performance of the developed models. Different performance metrics were used to evaluate the performance of the developed models. Recall, precision, and F1-score measures were used to evaluate the ability of the developed model to detect loss circulation occurrences. The results showed the K-nearest neighbors classifier achieved a high F1-score of 0.912 in detecting loss circulation occurrence in the testing set, while the random forests was the second-best classifier with almost the same F1-score of 0.910. The support vector machines achieved an F1-score of 0.83 in predicting the loss circulation occurrence in the testing set. The K-nearest neighbors outperformed other models in detecting the loss circulation occurrences in Well-8 with an F1-score of 0.80. The main contribution of this research as compared to previous studies is that it identifies losses events based on real-time measurements of the active pit volume.

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