Application of rough set-based analysis to extract spatial relationship indicator rules: An example of land use in Pearl River Delta

Spatial relations, reflecting the complex association between geographical phenomena and environments, are very important in the solution of geographical issues. Different spatial relations can be expressed by indicators which are useful for the analysis of geographical issues. Urbanization, an important geographical issue, is considered in this paper. The spatial relationship indicators concerning urbanization are expressed with a decision table. Thereafter, the spatial relationship indicator rules are extracted based on the application of rough set theory. The extraction process of spatial relationship indicator rules is illustrated with data from the urban and rural areas of Shenzhen and Hong Kong, located in the Pearl River Delta. Land use vector data of 1995 and 2000 are used. The extracted spatial relationship indicator rules of 1995 are used to identify the urban and rural areas in Zhongshan, Zhuhai and Macao. The identification accuracy is approximately 96.3%. Similar procedures are used to extract the spatial relationship indicator rules of 2000 for the urban and rural areas in Zhongshan, Zhuhai and Macao. An identification accuracy of about 83.6% is obtained.

Uncovering the rules for protein-protein interactions from yeast genomic data

Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated.

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.