8448018
Efficient Frequent Pattern Mining on Web Logs
Mining frequent patterns from Web logs is an important data mining task. Candidate-generation-and-test and pattern-growth are two representative frequent pattern mining approaches. We have conducted extensive experiments on real world Web log data to analyse the characteristics of Web logs and the behaviours of these two approaches on Web logs. To improve the performance of current algorithms on mining Web logs, we propose a new algorithm – Combined Frequent Pattern Mining (CFPM) to cater for Web log data specifically. We use heuristics to prune search space and reduce costs in mining so that better efficiency is achieved. Experimental results show that CFPM significantly improves the performance of the pattern-growth approach by 1.2–7.8 times on mining frequent patterns from Web logs.
30931074
A Distributed Object Database's Basic Design Issues
35361263
Reducing Overfitting in Predicting Intrinsically Unstructured Proteins
Intrinsically unstructured or disordered proteins are proteins that lack fixed 3-D structure globally or contain long disordered regions. Predicting disordered regions has attracted significant research recently. In developing a decision tree based disordered region predictor, we note that many previous predictors applying 20 amino acid compositions as training parameter tend to overfit the data. In this paper we propose to alleviate overfitting in prediction of intrinsically unstructured proteins by reducing input parameters. We also compare this approach with the random forest model, which is inherently tolerant to overfitting. Our experiments suggest that reducing 20 amino acid compositions into 4 groups according to amino acid property can reduce the overfitting in decision tree model. Alternatively, ensemble-learning techniques like random forest is inherently more tolerant to this kind of overfitting and can be a promising candidate in disordered region prediction.
717712
Efficient Computation of Iceberg Cubes by Bounding Aggregate Functions
The iceberg cubing problem is to compute the multidimensional group-by partitions that satisfy given aggregation constraints. Pruning unproductive computation for iceberg cubing when nonantimonotone constraints are present is a great challenge because the aggregate functions do not increase or decrease monotonically along the subset relationship between partitions. In this paper, we propose a novel bound prune cubing (BP-Cubing) approach for iceberg cubing with nonantimonotone aggregation constraints. Given a cube over n dimensions, an aggregate for any group-by partition can be computed from aggregates for the most specific n--dimensional partitions (MSPs). The largest and smallest aggregate values computed this way become the bounds for all partitions in the cube. We provide efficient methods to compute tight bounds for base aggregate functions and, more interestingly, arithmetic expressions thereof, from bounds of aggregates over the MSPs. Our methods produce tighter bounds than those obtained by previous approaches. We present iceberg cubing algorithms that combine bounding with efficient aggregation strategies. Our experiments on real-world and artificial benchmark data sets demonstrate that BP-Cubing algorithms achieve more effective pruning and are several times faster than state-of-the-art iceberg cubing algorithms and that BP-Cubing achieves the best performance with the top-down cubing approach.
29730920
Translating update operations from relational to object-oriented databases
Abstract In migrating a legacy relational database system to the object-oriented (OO) platform, when database migration completes, application modules are to be migrated, where embedded relational database operations are mapped into their OO correspondents. In this paper we study mapping relational update operations to their OO equivalents, which include UPDATE 1 , INSERT and DELETE operations. Relational update operation translation from relational to OO faces the touchy problem of transformation from a value-based relationship model to a reference-based model and maintaining the relational integrity constraints. Moreover, with a relational database where inheritance is expressed as attribute value subset relationship, changing of some attribute values may lead to the change of the position of an object in the class inheritance hierarchy, which we call object migration. Considering all these aspects, algorithms are given mapping relational UPDATE, INSERT and DELETE operations to their OO correspondents. Our work emphasize in examining the differences in the representation of the source schema's semantics resulting from the translation process, as well as differences in the inherent semantics of the two models.
8280671
Information-Based Classification by Aggregating Emerging Patterns
Emerging patterns (EPs) are knowledge patterns capturing contrasts between data classes. In this paper, we propose an information-based approach for classification by aggregating emerging patterns. The constraint-based EP mining algorithm enables the system to learn from large-volume and high-dimensional data; the new approach for selecting representative EPs and efficient algorithm for finding the EPs renders the system high predictive accuracy and short classification time. Experiments on many benchmark datasets show that the resulting classifiers have good overall predictive accuracy, and are often also superior to other state-of-the-art classification systems such as C4.5, CBA and LB.
15076919
Serving queries to multi-resolution datasets on disk-based storage clusters
This paper is concerned with efficient querying of very large multi-resolution datasets on storage and compute clusters. We present a suite of services that support storage, indexing, and data processing (data sampling and data aggregation) on datasets that consist of a collection of multi-resolution Grids. We empirically evaluate the performance impact of different data declustering, indexing, and query processing strategies. The experimental evaluation is carried out using a data server implemented to serve multi-terabyte multi-resolution volumetric datasets to remote visualization clients and a one-terabyte multi-resolution volumetric dataset on a PC cluster with distributed disk space.
17933107
Safety analysis of usage control authorization models
The usage control (UCON) model was introduced as a unified approach to capture a number of extensions for traditional access control models. While the policy specification flexibility and expressive power of this model have been studied in previous work, as a related and fundamental problem, the safety analysis of UCON has not been explored. This paper presents two fundamental safety results for UCONA, a sub-model of UCON only considering authorizations. In UCONA, an access control decision is based on the subject and/or the object attributes, which can be changed as the side-effects of using the access right, resulting in possible changes to future access control decisions. Hence the safety question in UCONA is all the more pressing since every access can potentially enable additional permissions due to the mutability of attributes in UCON. In this paper, first we show that the safety problem is in general undecidable. Then, we show that a restricted form of UCONA with finite attribute value domains and acyclic attribute creation relation has a decidable safety property. The decidable model maintains good expressive power as shown by specifying an RBAC system with a specific user-role assignment scheme and a DRM application with consumable rights.
8353152
An Efficient Algorithm for Mining Coherent Patterns from Heterogeneous Microarrays
DNA microarray techniques present a novel way for geneticists to monitor interactions among tens of thousands of genes simultaneously, and have become standard lab routines in gene discovery, disease diagnosis, and drug design. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. This implies that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data, which is shown effective for revealing truthful patterns and reducing spurious ones. We also develop an efficient and scalable hybrid approach that combines gene-pair based and sample-pair based pruning to generate F-clusters from multiple gene expression matrices simultaneously. The experimental results demonstrate that our model can discover significant clusters that may not be identified by previous models.
2396831
Mining coherent patterns from heterogeneous microarray data
Microarray technology is a powerful tool for geneticists to monitor interactions among tens of thousands of genes simultaneously. There has been extensive research on coherent subspace clustering of gene expressions measured under consistent experimental settings. However, these methods assume that all experiments are run using the same batch of microarray chips with similar characteristics of noise. Algorithms developed under this assumption may not be applicable for analyzing data collected from heterogeneous settings, where the set of genes being monitored may be different and expression levels may be not directly comparable even for the same gene. In this paper, we propose a model, F-cluster, for mining subspace coherent patterns from heterogeneous gene expression data. We compare our model with previously proposed models. We analyze the search space of the problem and give a naïve solution for it.
14773046
Predicting methylation status of CpG islands in the human brain
MOTIVATION
Over 50% of human genes contain CpG islands in their 5'-regions. Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulation. Mis-epigenetic silencing associated with aberrant CpG island methylation is one mechanism leading to the loss of tumor suppressor functions in cancer cells. Large-scale experimental detection of DNA methylation is still both labor-intensive and time-consuming. Therefore, it is necessary to develop in silico approaches for predicting methylation status of CpG islands.


RESULTS
Based on a recent genome-scale dataset of DNA methylation in human brain tissues, we developed a classifier called MethCGI for predicting methylation status of CpG islands using a support vector machine (SVM). Nucleotide sequence contents as well as transcription factor binding sites (TFBSs) are used as features for the classification. The method achieves specificity of 84.65% and sensitivity of 84.32% on the brain data, and can also correctly predict about two-third of the data from other tissues reported in the MethDB database.


AVAILABILITY
An online predictor based on MethCGI is available at http://166.111.201.7/MethCGI.html


CONTACT
mzhang@cshl.edu


SUPPLEMENTARY INFORMATION
Supplementary data available at Bioinformatics online and http://166.111.201.7/help.html.