Jiuyong Li

(α, k)-anonymity: an enhanced k-anonymity model for privacy preserving data publishing

Privacy preservation is an important issue in the release of data for mining purposes. The k-anonymity model has been introduced for protecting individual identification. Recent studies show that a more sophisticated model is necessary to protect the association of individuals to sensitive information. In this paper, we propose an (α, k)-anonymity model to protect both identifications and relationships to sensitive information in data. We discuss the properties of (α, k)-anonymity model. We prove that the optimal (α, k)-anonymity problem is NP-hard. We first presentan optimal global-recoding method for the (α, k)-anonymity problem. Next we propose a local-recoding algorithm which is more scalable and result in less data distortion. The effectiveness and efficiency are shown by experiments. We also describe how the model can be extended to more general case.

Identifying miRNAs, targets and functions

microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology.

Kernel Discriminant Learning for Ordinal Regression

Ordinal regression has wide applications in many domains where the human evaluation plays a major role. Most current ordinal regression methods are based on Support Vector Machines (SVM) and suffer from the problems of ignoring the global information of the data and the high computational complexity. Linear Discriminant Analysis (LDA) and its kernel version, Kernel Discriminant Analysis (KDA), take into consideration the global information of the data together with the distribution of the classes for classification, but they have not been utilized for ordinal regression yet. In this paper, we propose a novel regression method by extending the Kernel Discriminant Learning using a rank constraint. The proposed algorithm is very efficient since the computational complexity is significantly lower than other ordinal regression methods. We demonstrate experimentally that the proposed method is capable of preserving the rank of data classes in a projected data space. In comparison to other benchmark ordinal regression methods, the proposed method is competitive in accuracy.

On optimal rule discovery

In machine learning and data mining, heuristic and association rules are two dominant schemes for rule discovery. Heuristic rule discovery usually produces a small set of accurate rules, but fails to find many globally optimal rules. Association rule discovery generates all rules satisfying some constraints, but yields too many rules and is infeasible when the minimum support is small. Here, we present a unified framework for the discovery of a family of optimal rule sets and characterize the relationships with other rule-discovery schemes such as nonredundant association rule discovery. We theoretically and empirically show that optimal rule discovery is significantly more efficient than association rule discovery independent of data structure and implementation. Optimal rule discovery is an efficient alternative to association rule discovery, especially when the minimum support is low.

Identifying functional miRNA–mRNA regulatory modules with correspondence latent dirichlet allocation

MOTIVATION MicroRNAs (miRNAs) are small non-coding RNAs that cause mRNA degradation and translational inhibition. They are important regulators of development and cellular homeostasis through their control of diverse processes. Recently, great efforts have been made to elucidate their regulatory mechanism, but the functions of most miRNAs and their precise regulatory mechanisms remain elusive. With more and more matched expression profiles of miRNAs and mRNAs having been made available, it is of great interest to utilize both expression profiles to discover the functional regulatory networks of miRNAs and their target mRNAs for potential biological processes that they may participate in. RESULTS We present a probabilistic graphical model to discover functional miRNA regulatory modules at potential biological levels by integrating heterogeneous datasets, including expression profiles of miRNAs and mRNAs, with or without the prior target binding information. We applied this model to a mouse mammary dataset. It effectively captured several biological process specific modules involving miRNAs and their target mRNAs. Furthermore, without using prior target binding information, the identified miRNAs and mRNAs in each module show a large proportion of overlap with predicted miRNA target relationships, suggesting that expression profiles are crucial for both target identification and discovery of regulatory modules.

Achieving k -anonymity by clustering in attribute hierarchical structures

Individual privacy will be at risk if a published data set is not properly de-identified. k-anonymity is a major technique to de-identify a data set. A more general view of k-anonymity is clustering with a constraint of the minimum number of objects in every cluster. Most existing approaches to achieving k-anonymity by clustering are for numerical (or ordinal) attributes. In this paper, we study achieving k-anonymity by clustering in attribute hierarchical structures. We define generalisation distances between tuples to characterise distortions by generalisations and discuss the properties of the distances. We conclude that the generalisation distance is a metric distance. We propose an efficient clustering-based algorithm for k-anonymisation. We experimentally show that the proposed method is more scalable and causes significantly less distortions than an optimal global recoding k-anonymity method.

Mining risk patterns in medical data

In this paper, we discuss a problem of finding risk patterns in medical data. We define risk patterns by a statistical metric, relative risk, which has been widely used in epidemiological research. We characterise the problem of mining risk patterns as an optimal rule discovery problem. We study an anti-monotone property for mining optimal risk pattern sets and present an algorithm to make use of the property in risk pattern discovery. The method has been applied to a real world data set to find patterns associated with an allergic event for ACE inhibitors. The algorithm has generated some useful results for medical researchers.

Discover Dependencies from Data—A Review

Functional and inclusion dependency discovery is important to knowledge discovery, database semantics analysis, database design, and data quality assessment. Motivated by the importance of dependency discovery, this paper reviews the methods for functional dependency, conditional functional dependency, approximate functional dependency, and inclusion dependency discovery in relational databases and a method for discovering XML functional dependencies.

Privacy preserving serial data publishing by role composition

Previous works about privacy preserving serial data publishing on dynamic databases have relied on unrealistic assumptions of the nature of dynamic databases. In many applications, some sensitive values changes freely while others never change. For example, in medical applications, the disease attribute changes with time when patients recover from one disease and develop another disease. However, patients do not recover from some diseases such as HIV. We call such diseases permanent sensitive values. To the best of our knowledge, none of the existing solutions handle these realistic issues. We propose a novel anonymization approach called HD-composition to solve the above problems. Extensive experiments with real data confirm our theoretical results.

Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy

BackgroundmicroRNAs (miRNAs) regulate target gene expression by controlling their mRNAs post-transcriptionally. Increasing evidence demonstrates that miRNAs play important roles in various biological processes. However, the functions and precise regulatory mechanisms of most miRNAs remain elusive. Current research suggests that miRNA regulatory modules are complicated, including up-, down-, and mix-regulation for different physiological conditions. Previous computational approaches for discovering miRNA-mRNA interactions focus only on down-regulatory modules. In this work, we present a method to capture complex miRNA-mRNA interactions including all regulatory types between miRNAs and mRNAs.ResultsWe present a method to capture complex miRNA-mRNA interactions using Bayesian network structure learning with splitting-averaging strategy. It is designed to explore all possible miRNA-mRNA interactions by integrating miRNA-targeting information, expression profiles of miRNAs and mRNAs, and sample categories. We also present an analysis of data sets for epithelial and mesenchymal transition (EMT). Our results show that the proposed method identified all possible types of miRNA-mRNA interactions from the data. Many interactions are of tremendous biological significance. Some discoveries have been validated by previous research, for example, the miR-200 family negatively regulates ZEB1 and ZEB2 for EMT. Some are consistent with the literature, such as LOX has wide interactions with the miR-200 family members for EMT. Furthermore, many novel interactions are statistically significant and worthy of validation in the near future.ConclusionsThis paper presents a new method to explore the complex miRNA-mRNA interactions for different physiological conditions using Bayesian network structure learning with splitting-averaging strategy. The method makes use of heterogeneous data including miRNA-targeting information, expression profiles of miRNAs and mRNAs, and sample categories. Results on EMT data sets show that the proposed method uncovers many known miRNA targets as well as new potentially promising miRNA-mRNA interactions. These interactions could not be achieved by the normal Bayesian network structure learning.