14433108
Using amino acid patterns to accurately predict translation initiation sites
The translation initiation site (TIS) prediction problem is about how to correctly identify TIS in mRNA, cDNA, or other types of genomic sequences. High prediction accuracy can be helpful in a better understanding of protein coding from nucleotide sequences. This is an important step in genomic analysis to determine protein coding from nucleotide sequences. In this paper, we present an in silico method to predict translation initiation sites in vertebrate cDNA or mRNA sequences. This method consists of three sequential steps as follows. In the first step, candidate features are generated using k-gram amino acid patterns. In the second step, a small number of top-ranked features are selected by an entropy-based algorithm. In the third step, a classification model is built to recognize true TISs by applying support vector machines or ensembles of decision trees to the selected features. We have tested our method on several independent data sets, including two public ones and our own extracted sequences. The experimental results achieved are better than those reported previously using the same data sets. Our high accuracy not only demonstrates the feasibility of our method, but also indicates that there might be "amino acid" patterns around TIS in cDNA and mRNA sequences.
9642703
Discovering typical structures of documents: a road map approach
The structure of a document refers to the role and hierarchy of subdocument references. Many online documents are similarly structured, though not identically structured. We study the problem of discovering “typical” structures of a collection of such documents, where the user specifies the minimum frequency of a typical structure. We will consider structural features of subdocument references such as labeling, nesting, ordering, cyclicity, and wild-card references, like those found on the Web and digital libraries. Typical structures can be used to serve the following purposes. (a) The “table-ofcontent” for gaining the general information of a source. (b) A road map for browsing and querying a source. (c) A basis for clustering documents. (d) Partial schemas for building structured layers to provide standard database access methods. (e) User/customer’s interests and browsing patterns. We present a solution to the discovery problem.
29257622
Use of Built-in Features in the Interpretation of High-dimensional Cancer Diagnosis Data
Cancer diagnosis data, for example microarray gene expression profiling data and proteomic profiling data, are often described by thousands of features. To computationally make a diagnosis for new samples, these data are usually input to a learning algorithm, the algorithm then induces a classifier, the classifier then predicts a class label for any test sample. As the data is so high-dimensional, most of the resulting classifiers are very complicated particularly those based on kernel-functions such as support vector machines---the interpretation of the decision results must need all the features to be involved. In this paper, we discuss built-in features and use them to concisely characterize the data and to easily interpret the decisions. Built-in features are features that are used only in the classifiers, and that are only a small subset of the original features, e.g., the features in a decision tree. So, the notion of built-in features is different from input features and also from original features. As there is a significant reduction from the huge size of original features to a small number of relevant features, the complexity of the interpretation can be much eased. The use of built-in features also provides much potential for elucidating the translation between raw data and clinically useful knowledge. In this paper, we also report that the performance of classifiers using built-in features tends to remain stable even input feature space changes, but other types of classifiers fluctuate their performance. So, once again, we promote the use of classifiers that use built-in features since the algorithms can avoid the existing hard problem of selecting best number of features for learning.
15390292
Selection of patient samples and genes for outcome prediction
Gene expression profiles with clinical outcome data enable monitoring of disease progression and prediction of patient survival at the molecular level. We present a new computational method for outcome prediction. Our idea is to use an informative subset of original training samples. This subset consists of only short-term survivors who died within a short period and long-term survivors who were still alive after a long follow-up time. These extreme training samples yield a clear platform to identify genes whose expression is related to survival. To find relevant genes, we combine two feature selection methods - entropy measure and Wilcoxon rank sum test - so that a set of sharp discriminating features are identified. The selected training samples and genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a survival/relapse risk score for drawing Kaplan-Meier survival curves. We apply this method to two data sets: diffuse large-B-cell lymphoma (DLBCL) and primary lung adenocarcinoma. In both cases, patients in high and low risk groups stratified by our risk scores are clearly distinguishable. We also compare our risk scores to some clinical factors, such as International Prognostic Index score for DLBCL analysis and tumor stage information for lung adenocarcinoma. Our results indicate that gene expression profiles combined with carefully chosen learning algorithms can predict patient survival for certain diseases.
13995613
DNAFSMiner: a web-based software toolbox to recognize two types of functional sites in DNA sequences
UNLABELLED
DNAFSMiner (DNA Functional Sites Miner) is a web-based software toolbox to recognize functional sites in nucleic acid sequences. Currently in this toolbox, we provide two software: TIS Miner and Poly(A) Signal Miner. The TIS Miner can be used to predict translation initiation sites in vertebrate DNA/mRNA/cDNA sequences, and the Poly(A) Signal Miner can be used to predict polyadenylation [poly(A)] signals in human DNA sequences. The prediction results are better than those by literature methods on two benchmark applications. This good performance is mainly attributable to our unique learning method. DNAFSMiner is available free of charge for academic and non-profit organizations.


AVAILABILITY
http://research.i2r.a-star.edu.sg/DNAFSMiner/


CONTACT
huiqing@i2r.a-star.edu.sg.
10722883
Use of extreme patient samples for outcome prediction from gene expression data
MOTIVATION
Patient outcome prediction using microarray technologies is an important application in bioinformatics. Based on patients' genotypic microarray data, predictions are made to estimate patients' survival time and their risk of tumor metastasis or recurrence. So, accurate prediction can potentially help to provide better treatment for patients.


RESULTS
We present a new computational method for patient outcome prediction. In the training phase of this method, we make use of two types of extreme patient samples: short-term survivors who got an unfavorable outcome within a short period and long-term survivors who were maintaining a favorable outcome after a long follow-up time. These extreme training samples yield a clear platform for us to identify relevant genes whose expression is closely related to the outcome. The selected extreme samples and the relevant genes are then integrated by a support vector machine to build a prediction model, by which each validation sample is assigned a risk score that falls into one of the special pre-defined risk groups. We apply this method to several public datasets. In most cases, patients in high and low risk groups stratified by our method have clearly distinguishable outcome status as seen in their Kaplan-Meier curves. We also show that the idea of selecting only extreme patient samples for training is effective for improving the prediction accuracy when different gene selection methods are used.
5882174
Active learning for detecting a spectrally variable subject in color infrared imagery
To classify Egeria densa, Brazilian waterweed, in scan-digitized color infrared aerial photographs, we are developing an interactive computer system based on data-mining techniques with active learning capabilities. Key components of the system are: feature extraction, automatic classification, active learning, and experimental evaluation.
2528293
Rule mining with prior knowledge - a belief networks approach
Some existing data mining methods, such as classification trees, neural networks and association rules, have the drawbacks that the user's prior knowledge cannot be easily specified and incorporated into the knowledge discovery process, and the rules mined from databases lack quantitative analyses. In this paper, we propose a belief networks method for rule mining, which takes the advantage of belief networks as the directed acyclic graph language and their function for numerical representation of probabilistic dependencies among the variables in the database, so that it can overcome the drawbacks. Since belief networks provide a natural representation for capturing causal relationship among a set of variables, our proposed method can mine more general correlation rules which can capture the relationship of more than two attribute variables. The potential application of the proposed method is demonstrated through the detailed case studies on benchmark databases.
9357291
A Balanced Ensemble Approach to Weighting Classifiers for Text Classification
This paper studies the problem of constructing an effective heterogeneous ensemble classifier for text classification. One major challenge of this problem is to formulate a good combination function, which combines the decisions of the individual classifiers in the ensemble. We show that the classification performance is affected by three weight components and they should be included in deriving an effective combination function. They are: (1) Global effectiveness, which measures the effectiveness of a member classifier in classifying a set of unseen documents; (2) Local effectiveness, which measures the effectiveness of a member classifier in classifying the particular domain of an unseen document; and (3) Decision confidence, which describes how confident a classifier is when making a decision when classifying a specific unseen document. We propose a new balanced combination function, called dynamic classifier weighting (DCW), that incorporates the aforementioned three components. The empirical study demonstrates that the new combination function is highly effective for text classification.
46834678
Efficient Search of Reliable Exceptions
Finding patterns from data sets is a fundamental task of data mining. If we categorize all patterns into strong, weak, and random, conventional data mining techniques are designed only to find strong patterns, which hold for numerous objects and are usually consistent with the expectations of experts. While such strong patterns are helpful in prediction, the unexpectedness and contradiction exhibited by weak patterns are also very useful although they represent a relatively small number of objects. In this paper, we address the problem of finding weak patterns (i.e., reliable exceptions) from databases. A simple and efficient approach is proposed which uses deviation analysis to identify interesting exceptions and explore reliable ones. Besides, it is flexible in handling both subjective and objective exceptions. We demonstrate the effectiveness of the proposed approach through a set of real-life data sets, and present interesting findings.
7205040
Effective Data Mining Using Neural Networks
Classification is one of the data mining problems receiving great attention recently in the database community. The paper presents an approach to discover symbolic classification rules using neural networks. Neural networks have not been thought suited for data mining because how the classifications were made is not explicitly stated as symbolic rules that are suitable for verification or interpretation by humans. With the proposed approach, concise symbolic rules with high accuracy can be extracted from a neural network. The network is first trained to achieve the required accuracy rate. Redundant connections of the network are then removed by a network pruning algorithm. The activation values of the hidden units in the network are analyzed, and classification rules are generated using the result of this analysis. The effectiveness of the proposed approach is clearly demonstrated by the experimental results on a set of standard data mining test problems.