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.
16551486
Feature Extraction for Image Mining
Due to the digitization of data and advances in technology, it has become extremely easy to obtain and store large quantities of data, particularly Multimedia data. Fields ranging from Commercial to Military need to analyze these data in an efficient and fast manner. Presently, tools for mining images are few and require human intervention. Feature selection and extraction is the pre-processing step of Image Mining. Obviously this is a critical step in the entire scenario of Image Mining. Our approach to mine from Images – to extract patterns and derive knowledge from large collections of images, deals mainly with identification and extraction of unique features for a particular domain. Though there are various features available, the aim is to identify the best features and thereby extract relevant information from the images. We have tried various methods for extraction; the features extracted and the techniques used are evaluated for their contribution to solving the problem. Experimental results show that the features used are sufficient to identify the patterns from the Images. The extracted features were evaluated for goodness and tested on test images. An interactive system was developed which allows the user to define new features and to resolve uncertain regions.
5365583
NeuroRule: A Connectionist Approach to Data Mining
Classification, which involves finding rules that partition a given da.ta set into disjoint groups, is one class of data mining problems. Approaches proposed so far for mining classification rules for large databases are mainly decision tree based symbolic learning methods. The connectionist approach based on neura.l networks has been thought not well suited for data mining. One of the major reasons cited is that knowledge generated by neural networks is not explicitly represented in the form of rules suitable for verification or interpretation by humans. This paper examines this issue. With our newly developed algorithms, rules which are similar to, or more concise than those generated by the symbolic methods can be extracted from the neural networks. The data mining process using neural networks with the emphasis on rule extraction is described. ExperimenM results and comparison with previously published works are presented.
207156949
Design and implementation of a single system image operating system for ad hoc networks
In this paper, we describe the design and implementation of a distributed operating system for ad hoc networks. Our system simplifies the programming of ad hoc networks and extends total system lifetime by making the entire network appear as a single virtual machine. It automatically and transparently partitions applications into components and dynamically finds them a placement on nodes within the network to reduce energy consumption and to increase system longevity. This paper describes our programming model, outlines the design and implementation of our system and examines the energy efficiency of our approach through extensive simulations as well as validation of a deployment on a physical testbed. We evaluate practical, power-aware, general-purpose algorithms for component placement and migration, and demonstrate that they can significantly increase system longevity by effectively distributing energy consumption and avoiding hotspots.
3660238
Active Feature Selection Using Classes
Feature selection is frequently used in data pre-processing for data mining. When the training data set is too large, sampling is commonly used to overcome the difficulty. This work investigates the applicability of active sampling in feature selection in a filter model setting. Our objective is to partition data by taking advantage of class information so as to achieve the same or better performance for feature selection with fewer but more relevant instances than random sampling. Two versions of active feature selection that employ class information are proposed and empirically evaluated. In comparison with random sampling, we conduct extensive experiments with benchmark data sets, and analyze reasons why class-based active feature selection works in the way it does. The results will help us deal with large data sets and provide ideas to scale up other feature selection algorithms.
14573187
Feature Selection for Classification
Feature selection has been the focus of interest for quite some time and much work has been done. With the creation of huge databases and the consequent requirements for good machine learning techniques, new problems arise and novel approaches to feature selection are in demand. This survey is a comprehensive overview of many existing methods from the 1970's to the present. It identifies four steps of a typical feature selection method, and categorizes the different existing methods in terms of generation procedures and evaluation functions, and reveals hitherto unattempted combinations of generation procedures and evaluation functions. Representative methods are chosen from each category for detailed explanation and discussion via example. Benchmark datasets with different characteristics are used for comparative study. The strengths and weaknesses of different methods are explained. Guidelines for applying feature selection methods are given based on data types and domain characteristics. This survey identifies the future research areas in feature selection, introduces newcomers to this field, and paves the way for practitioners who search for suitable methods for solving domain-specific real-world applications.