507681
A Novel Approach to Model Generation for Heterogeneous Data Classification
Ensemble methods such as bagging and boosting have been successfully applied to classification problems. Two important issues associated with an ensemble approach are: how to generate models to construct an ensemble, and how to combine them for classification. In this paper, we focus on the problem of model generation for heterogeneous data classification. If we could partition heterogeneous data into a number of homogeneous partitions, we will likely generate reliable and accurate classification models over the homogeneous partitions. We examine different ways of forming homogeneous subsets and propose a novel method that allows a data point to be assigned multiple times in order to generate homogeneous partitions for ensemble learning. We present the details of the new algorithm and empirical studies over the UCI benchmark datasets and datasets of image classification, and show that the proposed approach is effective for heterogeneous data classification.
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.
46794790
Analysis of Hidden Representations by Greedy Clustering
The hidden layer of backpropagation neural networks (NNs) holds the key to the networks' success in solving pattern classification problems. The units in the hidden layer encapsulate the network's internal representations of the outside world described by the input data. this paper, the hidden representations of trained networks are investigated by means simple greedy clustering algorithm. This clustering algorithm is applied to networks have been trained to solve well-known problems: the monks problems, the 5-bit problem and the contiguity problem. The results from applying the algorithm to problems with known concepts provide us with a better understanding of NN learning. These also explain why NNs achieve higher predictive accuracy than that of decision-tree methods. The results of this study can be readily applied to rule extraction from Production rules are extracted for the parity and the monks problems, as well as benchmark data set: Pima Indian diabetes diagnosis. The extracted rules from the Indi...
16386059
A Monotonic Measure for Optimal Feature Selection
Feature selection is a problem of choosing a subset of relevant features. In general, only exhaustive search can bring about the optimal subset. With a monotonic measure, exhaustive search can be avoided without sacrificing optimality. Unfortunately, most error- or distancebased measures are not monotonic. A new measure is employed in this work that is monotonic and fast to compute. The search for relevant features according to this measure is guaranteed to be complete but not exhaustive. Experiments are conducted for verification.
8367210
Sensor Sequence Modeling for Driving
Intelligent systems in automobiles need to be aware of the driving and driver context. Available sensor data stream has to be modeled and monitored in order to do so. Currently there exist no building blocks for hierarchical modeling of driving. By semi-supervised segmentation such building blocks can be discovered. We call them drivemes in analogy to phonemes. More parsimonious modeling of driving becomes now possible.
14543078
Resource description framework: metadata and its applications
Universality, the property of the Web that makes it the largest data and information source in the world, is also the property behind the lack of a uniform organization scheme that would allow easy access to data and information. A semantic web, wherein different applications and Web sites can exchange information and hence exploit Web data and information to their full potential, requires the information about Web resources to be represented in a detailed and structured manner. Resource Description Framework (RDF), an effort in this direction supported by the World Wide Web Consortium, provides a means for the description of metadata which is a necessity for the next generation of interoperable Web applications. The success of RDF and the semantic web will depend on (1) the development of applications that prove the applicability of the concept, (2) the availability of application interfaces which enable the development of such applications, and (3) databases and inference systems that exploit RDF to identify and locate most relevant Web resources. In addition, many practical issues, such as security, ease of use, and compatibility, will be crucial in the success of RDF. This survey aims at providing a glimpse at the past, present, and future of this upcoming technology and highlights why we believe that the next generation of the Web will be more organized, informative, searchable, accessible, and, most importantly, useful. It is expected that knowledge discovery and data mining can benefit from RDF and the Semantic Web.
17890414
Identifying significant genes from microarray data
Microarray technology is a recent development in experimental molecular biology which can produce quantitative expression measurements for thousands of genes in a single, cellular mRNA sample. These many gene expression measurements form a composite profile of the sample, which can be used to differentiate samples from different classes such as tissue types or treatments. However, for the gene expression profile data obtained in a specific comparison, most likely only some of the genes will, be differentially expressed between the classes, while many other genes have similar expression levels. Selecting a list of informative differential genes from these data is important for microarray data analysis. In this paper, we describe a framework for selecting informative genes, called ranking and combination analysis (RAC), which combines various existing informative gene selection methods. We conducted experiments using three data sets and six existing feature selection methods. The results show that the RAC framework is a robust and efficient approach to identify informative gene for microarray data. The combination approach on two selecting methods almost always performed better than the less efficient individual, and in many cases, better than both. More significantly, when considering all three data sets together, the combination approach, on average, outperforms each individual feature selection method. All of these indicate that RCA might be a viable and feasible approach for the microarray gene expression analysis.
34797702
Implicit Runge–Kutta methods based on Lobatto quadrature formula
Using W-transformation of Hairre and Wanner, high-order implicit Runge–Kutta (RK) methods based on Lobatto quadrature are studied. Methods constructed and presented include and extend the existing Lobatto III type RK methods. Two to four stages general Lobatto III methods with three parameters α, β, γ are constructed, and a particular one-parameter family Lobatto III C(γ) method is also presented.
7448673
Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients
MOTIVATIONS AND RESULTS
For classifying gene expression profiles or other types of medical data, simple rules are preferable to non-linear distance or kernel functions. This is because rules may help us understand more about the application in addition to performing an accurate classification. In this paper, we discover novel rules that describe the gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients. We also introduce a new classifier, named PCL, to make effective use of the rules. PCL is accurate and can handle multiple parallel classifications. We evaluate this method by classifying 327 heterogeneous ALL samples. Our test error rate is competitive to that of support vector machines, and it is 71% better than C4.5, 50% better than Naive Bayes, and 43% better than k-nearest neighbour. Experimental results on another independent data sets are also presented to show the strength of our method.


AVAILABILITY
Under http://sdmc.lit.org.sg/GEDatasets/, click on Supplementary Information.
15137899
Ensembles of cascading trees
We introduce a new method, called CS4, to construct committees of decision trees for classification. The method considers different top-ranked features as the root nodes of member trees. This idea is particularly suitable for dealing with high-dimensional bio-medical data as top-ranked features in this type of data usually possess similar merits for classification. To make a decision, the committee combines the power of individual trees in a weighted manner. Unlike Bagging or Boosting which uses bootstrapped training data, our method builds all the member trees of a committee using exactly the same set of training data. We have tested these ideas on UCI data sets as well as recent bio-medical data sets of gene expression or proteomic profiles that are usually described by more than 10,000 features. All the experimental results show that our method is efficient and that the classification performance are superior to C4.5 family algorithms.
3172606
Gene name ambiguity of eukaryotic nomenclatures
MOTIVATION
With more and more scientific literature published online, the effective management and reuse of this knowledge has become problematic. Natural language processing (NLP) may be a potential solution by extracting, structuring and organizing biomedical information in online literature in a timely manner. One essential task is to recognize and identify genomic entities in text. 'Recognition' can be accomplished using pattern matching and machine learning. But for 'identification' these techniques are not adequate. In order to identify genomic entities, NLP needs a comprehensive resource that specifies and classifies genomic entities as they occur in text and that associates them with normalized terms and also unique identifiers so that the extracted entities are well defined. Online organism databases are an excellent resource to create such a lexical resource. However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it.


RESULTS
We obtained gene information from 21 organisms and quantified naming ambiguities within species, across species, with English words and with medical terms. When the case (of letters) was retained, official symbols displayed negligible intra-species ambiguity (0.02%) and modest ambiguities with general English words (0.57%) and medical terms (1.01%). In contrast, the across-species ambiguity was high (14.20%). The inclusion of gene synonyms increased intra-species ambiguity substantially and full names contributed greatly to gene-medical-term ambiguity. A comprehensive lexical resource that covers gene information for the 21 organisms was then created and used to identify gene names by using a straightforward string matching program to process 45,000 abstracts associated with the mouse model organism while ignoring case and gene names that were also English words. We found that 85.1% of correctly retrieved mouse genes were ambiguous with other gene names. When gene names that were also English words were included, 233% additional 'gene' instances were retrieved, most of which were false positives. We also found that authors prefer to use synonyms (74.7%) to official symbols (17.7%) or full names (7.6%) in their publications.


CONTACT
lifeng.chen@dbmi.columbia.edu