Browsing by Author "Pal, NR"

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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.