scholarly journals A Novel Method of Predicting Protein Disordered Regions Based on Sequence Features

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Tong-Hui Zhao ◽  
Min Jiang ◽  
Tao Huang ◽  
Bi-Qing Li ◽  
Ning Zhang ◽  
...  
Keyword(s):  
Conservation Score ◽  
Query Sequence ◽  
Disordered Proteins ◽  
Training Set ◽  
Disordered Structures ◽  
Feature List ◽  
Novel Method ◽  
Scoring Matrix ◽  
Fold Cross Validation ◽  
Disordered Regions

With a large number of disordered proteins and their important functions discovered, it is highly desired to develop effective methods to computationally predict protein disordered regions. In this study, based on Random Forest (RF), Maximum Relevancy Minimum Redundancy (mRMR), and Incremental Feature Selection (IFS), we developed a new method to predict disordered regions in proteins. The mRMR criterion was used to rank the importance of all candidate features. Finally, top 128 features were selected from the ranked feature list to build the optimal model, including 92 Position Specific Scoring Matrix (PSSM) conservation score features and 36 secondary structure features. As a result, Matthews correlation coefficient (MCC) of 0.3895 was achieved on the training set by 10-fold cross-validation. On the basis of predicting results for each query sequence by using the method, we used the scanning and modification strategy to improve the performance. The accuracy (ACC) and MCC were increased by 4% and almost 0.2%, respectively, compared with other three popular predictors: DISOPRED, DISOclust, and OnD-CRF. The selected features may shed some light on the understanding of the formation mechanism of disordered structures, providing guidelines for experimental validation.

NUMERICAL SIMULATION AND VALIDITY OF A NOVEL METHOD FOR THE PREDICTION OF ARTERY STENOSIS VIA INPUT IMPEDANCE AND SUPPORT VECTOR MACHINE

2014 ◽  
Vol 26 (01) ◽  
pp. 1450002 ◽  
Author(s):  
Hanguang Xiao
Keyword(s):  
Support Vector Machine ◽  
Input Impedance ◽  
Recursive Algorithm ◽  
Artery Stenosis ◽  
Support Vector ◽  
Arterial Tree ◽  
Novel Method ◽  
The Mean ◽  
Fold Cross Validation ◽  
Systemic Arterial Tree

The early detection and intervention of artery stenosis is very important to reduce the mortality of cardiovascular disease. A novel method for predicting artery stenosis was proposed by using the input impedance of the systemic arterial tree and support vector machine (SVM). Based on the built transmission line model of a 55-segment systemic arterial tree, the input impedance of the arterial tree was calculated by using a recursive algorithm. A sample database of the input impedance was established by specifying the different positions and degrees of artery stenosis. A SVM prediction model was trained by using the sample database. 10-fold cross-validation was used to evaluate the performance of the SVM. The effects of stenosis position and degree on the accuracy of the prediction were discussed. The results showed that the mean specificity, sensitivity and overall accuracy of the SVM are 80.2%, 98.2% and 89.2%, respectively, for the 50% threshold of stenosis degree. Increasing the threshold of the stenosis degree from 10% to 90% increases the overall accuracy from 82.2% to 97.4%. Increasing the distance of the stenosis artery from the heart gradually decreases the overall accuracy from 97.1% to 58%. The deterioration of the stenosis degree to 90% increases the prediction accuracy of the SVM to more than 90% for the stenosis of peripheral artery. The simulation demonstrated theoretically the feasibility of the proposed method for predicting artery stenosis via the input impedance of the systemic arterial tree and SVM.

A Novel Method for Gender and Age Detection Based on EEG Brain Signals

2021 ◽  
Vol 18 (5) ◽  
Author(s):  
Haitham Issa ◽  
Sali Issa ◽  
Wahab Shah
Keyword(s):  
Cross Validation ◽  
Image Feature ◽  
Emotional States ◽  
Time Frequency ◽  
Brain Signals ◽  
Average Accuracy ◽  
Gender And Age ◽  
Novel Method ◽  
Fold Cross Validation ◽  
Validation Strategy

This paper presents a new gender and age classification system based on Electroencephalography (EEG) brain signals. First, Continuous Wavelet Transform (CWT) technique is used to get the time-frequency information of only one EEG electrode for eight distinct emotional states instead of the ordinary neutral or relax states. Then, sequential steps are implemented to extract the improved grayscale image feature. For system evaluation, a three-fold-cross validation strategy is applied to construct four different classifiers. The experimental test shows that the proposed extracted feature with Convolutional Neural Network (CNN) classifier improves the performance of both gender and age classification, and achieves an average accuracy of 96.3% and 89% for gender and age classification, respectively. Moreover, the ability to predict human gender and age during the mood of different emotional states is practically approved.

scholarly journals Embedding Undersampling Rotation Forest for Imbalanced Problem

2018 ◽  
Vol 2018 ◽  
pp. 1-15 ◽  
Author(s):  
Huaping Guo ◽  
Xiaoyu Diao ◽  
Hongbing Liu
Keyword(s):  
Imbalanced Data ◽  
Feature Space ◽  
Original Data ◽  
Training Set ◽  
Data Set ◽  
Minority Class ◽  
Rotation Forest ◽  
Novel Method ◽  
Individual Classifier ◽  
The Cost

Rotation Forest is an ensemble learning approach achieving better performance comparing to Bagging and Boosting through building accurate and diverse classifiers using rotated feature space. However, like other conventional classifiers, Rotation Forest does not work well on the imbalanced data which are characterized as having much less examples of one class (minority class) than the other (majority class), and the cost of misclassifying minority class examples is often much more expensive than the contrary cases. This paper proposes a novel method called Embedding Undersampling Rotation Forest (EURF) to handle this problem (1) sampling subsets from the majority class and learning a projection matrix from each subset and (2) obtaining training sets by projecting re-undersampling subsets of the original data set to new spaces defined by the matrices and constructing an individual classifier from each training set. For the first method, undersampling is to force the rotation matrix to better capture the features of the minority class without harming the diversity between individual classifiers. With respect to the second method, the undersampling technique aims to improve the performance of individual classifiers on the minority class. The experimental results show that EURF achieves significantly better performance comparing to other state-of-the-art methods.

scholarly journals Sistem Informasi Posyandu Ibu Hamil dengan Penerapan Klasifikasi Resiko Kehamilan Menggunakan Metode Naïve Bayes

2018 ◽  
Vol 6 (1) ◽  
pp. 1
Author(s):  
Qomariyatul Hasanah ◽  
Anang Andrianto ◽  
Muhammad Arief Hidayat
Keyword(s):  
Cross Validation ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
Training Set ◽  
Test Set ◽  
Fold Cross Validation

Sistem informasi posyandu ibu hamil dapat mengelola data kesehatan ibu hamil yang berkaitan dengan faktor resiko kehamilan. Faktor resiko kehamilan berdasarkan ketentuan Kartu Skor Poedji Rochyati (KSPR) digunakan bidan untuk menentukan resiko kehamilan dengan memberikan skor pada masing-masing parameter. KSPR memiliki kelemahan tidak dapat memberikan skor pada parameter yang belum pasti sehingga jika belum diketahui dengan pasti maka dianggap tidak terjadi. Konsep membaca pola data yang diadopsi dari teknik datamining menggunakan metode klasifikasi naive bayes dapat menjadi alternatif untuk kelemahan KSPR tersebut yaitu dengan mengklasifikasikan resiko kehamilan. Metode naïve bayes menghitung probabilitas parameter tertentu berdasarkan data pada periode sebelumnya yang telah ditentukan sebagai data training, berdasarkan hasil perhitungan tersebut dapat diketahui resiko kehamilan secara tepat sesuai parameter yang telah diketahui. Metode naïve bayes dipilih karena memiliki tingkat akurasi yang cukup tinggi daripada metode klasifikasi lainnya. Sistem informasi ini dibangun berbasis website agar dapat diakses secara mudah oleh beberapa posyandu yang berbeda tempat. Sistem dibangun mengadopsi dari model Waterfall. Sistem informasi posyandu ibu hamil dirancang dan dibangun dengan tiga (3) hak akses yaitu admin, bidan dan kader dengan masing-masing fitur yang dapat memudahkan penggunanya. Hasil dari penelitian ini adalah sistem informasi posyandu ibu hamil dengan penerapan klasifikasi resiko kehamilan menggunakan metode naïve bayes, dengan tingkat akurasi ketika menggunakan 17 atribut didapatkan 53.913%, 19 atribut didapatkan 54.348%, , 21 atribut didapatkan 54.783%, dan 22 atribut didapatkan 56.957%. Tingkat akurasi klasifikasi diperoleh menggunakan metode pengujian menggunakan Ten-Fold Cross Validation dimana training set dibagi menjadi 10 kelompok, jika kelompok 1 dijadikan test set maka kelompok 2 hingga 10 menjadi training set. Kata Kunci: Posyandu, Resiko Kehamilan, Waterfall, Datamining, Klasifikasi, Naïve bayes

scholarly journals Lifelong Zero-Shot Learning

2020 ◽  
Author(s):  
Kun Wei ◽  
Cheng Deng ◽  
Xu Yang
Keyword(s):  
Fine Tuning ◽  
Training Set ◽  
Continuous Training ◽  
Evaluation Protocol ◽  
Multiple Datasets ◽  
Real World Applications ◽  
Knowledge Distillation ◽  
Novel Method ◽  
Previous Training ◽  
Current Stage

Zero-Shot Learning (ZSL) handles the problem that some testing classes never appear in training set. Existing ZSL methods are designed for learning from a fixed training set, which do not have the ability to capture and accumulate the knowledge of multiple training sets, causing them infeasible to many real-world applications. In this paper, we propose a new ZSL setting, named as Lifelong Zero-Shot Learning (LZSL), which aims to accumulate the knowledge during the learning from multiple datasets and recognize unseen classes of all trained datasets. Besides, a novel method is conducted to realize LZSL, which effectively alleviates the Catastrophic Forgetting in the continuous training process. Specifically, considering those datasets containing different semantic embeddings, we utilize Variational Auto-Encoder to obtain unified semantic representations. Then, we leverage selective retraining strategy to preserve the trained weights of previous tasks and avoid negative transfer when fine-tuning the entire model. Finally, knowledge distillation is employed to transfer knowledge from previous training stages to current stage. We also design the LZSL evaluation protocol and the challenging benchmarks. Extensive experiments on these benchmarks indicate that our method tackles LZSL problem effectively, while existing ZSL methods fail.

scholarly journals Intrinsically disordered proteins identified in the aggregate proteome serve as biomarkers of neurodegeneration

2021 ◽  
Author(s):  
Srinivas Ayyadevara ◽  
Akshatha Ganne ◽  
Meenakshisundaram Balasubramaniam ◽  
Robert J. Shmookler Reis
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Protein Complexes ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Physiological Processes ◽  
Protein Partners ◽  
And Function ◽  
Computational Analyses ◽  
Disordered Regions

AbstractA protein’s structure is determined by its amino acid sequence and post-translational modifications, and provides the basis for its physiological functions. Across all organisms, roughly a third of the proteome comprises proteins that contain highly unstructured or intrinsically disordered regions. Proteins comprising or containing extensive unstructured regions are referred to as intrinsically disordered proteins (IDPs). IDPs are believed to participate in complex physiological processes through refolding of IDP regions, dependent on their binding to a diverse array of potential protein partners. They thus play critical roles in the assembly and function of protein complexes. Recent advances in experimental and computational analyses predicted multiple interacting partners for the disordered regions of proteins, implying critical roles in signal transduction and regulation of biological processes. Numerous disordered proteins are sequestered into aggregates in neurodegenerative diseases such as Alzheimer’s disease (AD) where they are enriched even in serum, making them good candidates for serum biomarkers to enable early detection of AD.

scholarly journals The Distinct Properties of the Consecutive Disordered Regions Inside or Outside Protein Domains and Their Functional Significance

2021 ◽  
Vol 22 (19) ◽  
pp. 10677
Author(s):  
Huqiang Wang ◽  
Haolin Zhong ◽  
Chao Gao ◽  
Jiayin Zang ◽  
Dong Yang
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Protein Domains ◽  
Comprehensive Analysis ◽  
Disordered Proteins ◽  
Functional Constraints ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Intrinsically Disordered ◽  
And Function ◽  
Disordered Regions

The consecutive disordered regions (CDRs) are the basis for the formation of intrinsically disordered proteins, which contribute to various biological functions and increasing organism complexity. Previous studies have revealed that CDRs may be present inside or outside protein domains, but a comprehensive analysis of the property differences between these two types of CDRs and the proteins containing them is lacking. In this study, we investigated this issue from three viewpoints. Firstly, we found that in-domain CDRs are more hydrophilic and stable but have less stickiness and fewer post-translational modification sites compared with out-domain CDRs. Secondly, at the protein level, we found that proteins with only in-domain CDRs originated late, evolved rapidly, and had weak functional constraints, compared with the other two types of CDR-containing proteins. Proteins with only in-domain CDRs tend to be expressed spatiotemporal specifically, but they tend to have higher abundance and are more stable. Thirdly, we screened the CDR-containing protein domains that have a strong correlation with organism complexity. The CDR-containing domains tend to be evolutionarily young, or they changed from a domain without CDR to a CDR-containing domain during evolution. These results provide valuable new insights about the evolution and function of CDRs and protein domains.

scholarly journals Hierarchical Classification Based on Label Distribution Learning

2019 ◽  
Vol 33 ◽  
pp. 5533-5540 ◽  
Author(s):  
Changdong Xu ◽  
Xin Geng
Keyword(s):  
Hierarchical Classification ◽  
Experimental Results ◽  
Challenging Problem ◽  
Training Set ◽  
True Label ◽  
Major Bottleneck ◽  
Novel Method ◽  
Class Labels ◽  
Label Distribution ◽  
The Given

Hierarchical classification is a challenging problem where the class labels are organized in a predefined hierarchy. One primary challenge in hierarchical classification is the small training set issue of the local module. The local classifiers in the previous hierarchical classification approaches are prone to over-fitting, which becomes a major bottleneck of hierarchical classification. Fortunately, the labels in the local module are correlated, and the siblings of the true label can provide additional supervision information for the instance. This paper proposes a novel method to deal with the small training set issue. The key idea of the method is to represent the correlation among the labels by the label distribution. It generates a label distribution that contains the supervision information of each label for the given instance, and then learns a mapping from the instance to the label distribution. Experimental results on several hierarchical classification datasets show that our method significantly outperforms other state-of-theart hierarchical classification approaches.

scholarly journals North American Hardwoods Identification Using Machine-Learning

Forests ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 298 ◽  
Author(s):  
Dercilio Junior Verly Lopes ◽  
Greg W. Burgreen ◽  
Edward D. Entsminger
Keyword(s):  
Machine Learning ◽  
North American ◽  
Mobile Application ◽  
Cross Validation ◽  
Data Augmentation ◽  
Technical Note ◽  
Machine Learning Method ◽  
Training Set ◽  
Hardwood Species ◽  
Fold Cross Validation

This technical note determines the feasibility of using an InceptionV4_ResNetV2 convolutional neural network (CNN) to correctly identify hardwood species from macroscopic images. The method is composed of a commodity smartphone fitted with a 14× macro lens for photography. The end-grains of ten different North American hardwood species were photographed to create a dataset of 1869 images. The stratified 5-fold cross-validation machine-learning method was used, in which the number of testing samples varied from 341 to 342. Data augmentation was performed on-the-fly for each training set by rotating, zooming, and flipping images. It was found that the CNN could correctly identify hardwood species based on macroscopic images of its end-grain with an adjusted accuracy of 92.60%. With the current growing of machine-learning field, this model can then be readily deployed in a mobile application for field wood identification.

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