Browsing by Author "Huang, CD"

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Hierarchical learning architecture with automatic feature selection for multiclass protein fold classification
(2003-12-01)
Huang, CD
;
Lin, CT
;
Pal, NR
;
電控工程研究所
;
Institute of Electrical and Control Engineering
The structure classification of proteins plays a very important role in bioinformatics, since the relationships and characteristics among those known proteins can be exploited to predict the structure of new proteins. The success of a classification system depends heavily on two things: the tools being used and the features considered. For the bioinformatics applications, the role of appropriate features has not been paid adequate importance. In this investigation we use three novel ideas for multiclass protein fold classification. First, we use the gating neural network, where each input node is associated with a gate. This network can select important features in an online manner when the learning goes on. At the beginning of the training, all gates are almost closed, i.e., no feature is allowed to enter the network. Through the training, gates corresponding to good features are completely opened while gates corresponding to bad features are closed more tightly, and some gates may be partially open. The second novel idea is to use a hierarchical learning architecture (HLA). The classifier in the first level of HLA classifies the protein features into four major classes: all alpha, all beta, alpha + beta, and alpha/beta. And in the next level we have another set of classifiers, which further classifies the protein features into 27 folds. The third novel idea is to induce the indirect coding features from the amino-acid composition sequence of proteins based on the N-gram concept. This provides us with more representative and discriminative new local features of protein sequences for multiclass protein fold classification. The proposed HLA with new indirect coding features increases the protein fold classification accuracy by about 12%. Moreover, the gating neural network is found to reduce the number of features drastically. Using only half of the original features selected by the gating neural network can reach comparable test accuracy as that using all the original features. The gating mechanism also helps us to get a better insight into the folding process of proteins. For example, tracking the evolution of different gates we can find which characteristics (features) of the data are more important for the folding process. And, of course, it also reduces the computation time.
Machine learning for multi-class protein fold classification based on neural networks with feature gating
(2003)
Huang, CD
;
Chung, IF
;
Pal, NR
;
Lin, CT
;
電控工程研究所
The success of a classification system depends heavily on two things: the tools being used and the features considered. For the bioinformatics applications the role of appropriate features has not been paid adequate importance. In this investigation we use two novel ideas. First, we use neural networks where each input node is associated with a gate. At the beginning of the training all gates are almost closed, i.e., no feature is allowed to enter the network. During the training, depending on the requirements, gates are either opened or closed. At the end of the training, gates corresponding to good features are completely opened while gates corresponding to bad features are closed more tightly. And of course, some gates may be partially open. So the network can not only select features in an online manner when the learning goes on, it also does some feature extraction. The second novel idea is to use a hierarchical machine learning architecture. Where at the first level the network classifies the data into four major folds : all alpha, all beta, alpha + beta and alpha/beta. And in the next level we have another set of networks, which further classifies the data into twenty seven folds. This approach helps us to achieve the following. The gating network is found to reduce the number of features drastically. It is interesting to observe that for the first level using just 50 features selected by the gating network we can get a comparable test accuracy as that using 125 features using neural classifiers. The process also helps us to get a better insight into the folding process. For example, tracking the evolution of different gates we can find which characteristics (features) of the data are more important for the folding process. And, of course, it reduces the computation time. The use of the hierarchical architecture helps us to get a better performance also.
Machine learning with automatic feature selection for multi-class protein fold classification
(2005-07-01)
Huang, CD
;
Liang, SF
;
Lin, CT
;
Wu, RC
;
電控工程研究所
In machine learning, both the properly used networks and the selected features are important factors which should be considered carefully. These two factors will influence the result, whether for better or worse. In bioinformatics, the amount of features may be very large to make machine learning possible. In this study we introduce the idea of feature selection in the problem of bioinformatics. We use neural networks to complete our task where each input node is associated with a gate. At the beginning of the training, all gates are almost closed, and, at this time, no features are allowed to enter the network. During the training phase, gates are either opened or closed, depending oil the requirements. After the selection training phase has completed, gates corresponding to the helpful features are completely opened while gates Corresponding to the useless features are closed more tightly. Some gates may be partially open, depending oil the importance of the corresponding features. So, the network can not only select features in an online manner during learning, but it also does some feature extraction. We combine feature selection with our novel hierarchical machine learning architecture and apply it to multi-class protein fold classification. At the first level the network classifies the data into four major folds: all alpha, all beta, alpha + beta and alpha/beta. In the next level, we have another set of networks which further classifies the data into twenty-seven folds. This approach helps achieve the following. The gating network is found to reduce the number of features drastically. It is interesting to observe that, for the first level using just 50 features selected by the gating network, we can get a test accuracy comparable to that using 125 features in neural classifiers. The process also helps us get a better insight into the folding process. For example, tracking the evolution of different gates, we call find which characteristics (features) of the data are more important for the folding process. Eventually, it reduces the computation time. The use of the hierarchical architecture helps LIS get a better performance also.
Protein metal binding residue prediction based on neural networks
(2005-02-01)
Lin, CT
;
Lin, KL
;
Yang, CH
;
Chung, IF
;
Huang, CD
Over one-third of protein structures contain metal ions, which are the necessary elements in life systems. Traditionally, structural biologists were used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpreting the function formation and reaction mechanism of enzyme by their structures and observations from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict the protein metal-binding amino acid residues from its sequence information only by neural networks with sliding window-based feature extraction and biological feature encoding techniques. In four major bulk elements (Calcium, Potassium, Magnesium, and Sodium), the metal-binding residues are identified by the proposed method with higher than 90% sensitivity and very good accuracy under 5-fold cross validation. With such promising results, it can be extended and used as a powerful methodology for metal-binding characterization from rapidly increasing protein sequences in the future.
Protein metal binding residue prediction based on neural networks
(2004)
Lin, CT
;
Lin, KL
;
Yang, CH
;
Chung, IF
;
Huang, CD
It is known that over one-third of protein structures contain metal ions, and they are the necessary elements in life system. Traditionally, structural biologists used to investigate properties of metalloproteins (proteins which bind with metal ions) by physical means and interpret the function formation and reaction mechanism of enzyme by their structures and observation from experiments in vitro. Most of proteins have primary structures (amino acid sequence information) only; however, the 3-dimension structures are not always available. In this paper, a direct analysis method is proposed to predict protein metalbinding amino acid residues only from its sequence information by neural network with sliding window-based feature extraction and biological feature encoding techniques and it can successfully detect 15 binding elements in protein, and 6 binding elements in enzyme.
Recognition of structure classification of protein folding by NN and SVM hierarchical learning architecture
(2003)
Chung, IF
;
Huang, CD
;
Shen, YH
;
Lin, CT
;
電控工程研究所
Classifying the structure of protein is a very important task in biological data. By means of the classification, the relationships and characteristics among known proteins can be exploited to predict the structure of new proteins. The study of the protein structures is based on the sequences and their similarity. It is a difficult task. Recently, due to the ability of machine learning techniques, many researchers have applied them to probe into this protein classification problem. We also apply here machine learning methods for multi-class protein fold recognition problem by proposing a novel hierarchical learning architecture. This novel hierarchical learning architecture can be formed by NN (neural networks) or SVM (support vector machine) as basic building blocks. Our results show that both of them can perform well. We use this new architecture to attack the multi-class protein fold recognition problem as proposed by Dubchak and Ding in 2001. With the same set of features our method can not only obtain better prediction accuracy and lower computation time, but also can avoid the use of the stochastic voting process in the original approach.