Jiuyong Li

Bio: Jiuyong Li is an academic researcher from University of South Australia. The author has contributed to research in topics: Computer science & Association rule learning. The author has an hindex of 38, co-authored 285 publications receiving 5280 citations. Previous affiliations of Jiuyong Li include Kunming University of Science and Technology & Griffith University.

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

Abstract: 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

Abstract: 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.

CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization.

Abstract: Summary Identifying molecular cancer subtypes from multi-omics data is an important step in the personalized medicine. We introduce CancerSubtypes, an R package for identifying cancer subtypes using multi-omics data, including gene expression, miRNA expression and DNA methylation data. CancerSubtypes integrates four main computational methods which are highly cited for cancer subtype identification and provides a standardized framework for data pre-processing, feature selection, and result follow-up analyses, including results computing, biology validation and visualization. The input and output of each step in the framework are packaged in the same data format, making it convenience to compare different methods. The package is useful for inferring cancer subtypes from an input genomic dataset, comparing the predictions from different well-known methods and testing new subtype discovery methods, as shown with different application scenarios in the Supplementary Material. Availability and implementation The package is implemented in R and available under GPL-2 license from the Bioconductor website (http://bioconductor.org/packages/CancerSubtypes/). Contact thuc.le@unisa.edu.au or jiuyong.li@unisa.edu.au. Supplementary information Supplementary data are available at Bioinformatics online.

Discover Dependencies from Data—A Review

Abstract: 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.

Kernel Discriminant Learning for Ordinal Regression

Abstract: 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.

Machine learning

Abstract: Machine Learning is the study of methods for programming computers to learn. Computers are applied to a wide range of tasks, and for most of these it is relatively easy for programmers to design and implement the necessary software. However, there are many tasks for which this is difficult or impossible. These can be divided into four general categories. First, there are problems for which there exist no human experts. For example, in modern automated manufacturing facilities, there is a need to predict machine failures before they occur by analyzing sensor readings. Because the machines are new, there are no human experts who can be interviewed by a programmer to provide the knowledge necessary to build a computer system. A machine learning system can study recorded data and subsequent machine failures and learn prediction rules. Second, there are problems where human experts exist, but where they are unable to explain their expertise. This is the case in many perceptual tasks, such as speech recognition, hand-writing recognition, and natural language understanding. Virtually all humans exhibit expert-level abilities on these tasks, but none of them can describe the detailed steps that they follow as they perform them. Fortunately, humans can provide machines with examples of the inputs and correct outputs for these tasks, so machine learning algorithms can learn to map the inputs to the outputs. Third, there are problems where phenomena are changing rapidly. In finance, for example, people would like to predict the future behavior of the stock market, of consumer purchases, or of exchange rates. These behaviors change frequently, so that even if a programmer could construct a good predictive computer program, it would need to be rewritten frequently. A learning program can relieve the programmer of this burden by constantly modifying and tuning a set of learned prediction rules. Fourth, there are applications that need to be customized for each computer user separately. Consider, for example, a program to filter unwanted electronic mail messages. Different users will need different filters. It is unreasonable to expect each user to program his or her own rules, and it is infeasible to provide every user with a software engineer to keep the rules up-to-date. A machine learning system can learn which mail messages the user rejects and maintain the filtering rules automatically. Machine learning addresses many of the same research questions as the fields of statistics, data mining, and psychology, but with differences of emphasis. Statistics focuses on understanding the phenomena that have generated the data, often with the goal of testing different hypotheses about those phenomena. Data mining seeks to find patterns in the data that are understandable by people. Psychological studies of human learning aspire to understand the mechanisms underlying the various learning behaviors exhibited by people (concept learning, skill acquisition, strategy change, etc.).

“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

The somatic genomic landscape of glioblastoma

Abstract: We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors (GBMs). We identify several novel mutated genes as well as complex rearrangements of signature receptors, including EGFR and PDGFRA. TERT promoter mutations are shown to correlate with elevated mRNA expression, supporting a role in telomerase reactivation. Correlative analyses confirm that the survival advantage of the proneural subtype is conferred by the G-CIMP phenotype, and MGMT DNA methylation may be a predictive biomarker for treatment response only in classical subtype GBM. Integrative analysis of genomic and proteomic profiles challenges the notion of therapeutic inhibition of a pathway as an alternative to inhibition of the target itself. These data will facilitate the discovery of therapeutic and diagnostic target candidates, the validation of research and clinical observations and the generation of unanticipated hypotheses that can advance our molecular understanding of this lethal cancer.