Data Mining - Concepts and Techniques.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

We propose a framework for modeling sequence motifs based on the maximum entropy principle (MEP). We recommend approximating short sequence motif distributions with the maximum entropy distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between nonadjacent as well as adjacent positions. Many maximum entropy models (MEMs) are specified by simply changing the set of constraints. Such models can be utilized to discriminate between signals and decoys. Classification performance using different MEMs gives insight into the relative importance of dependencies between different positions. We apply our framework to large datasets of RNA splicing signals. Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models.

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.

Graph neural network, as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. However, it has not been fully considered in graph neural network for heterogeneous graph which contains different types of nodes and links. The heterogeneity and rich semantic information bring great challenges for designing a graph neural network for heterogeneous graph. Recently, one of the most exciting advancements in deep learning is the attention mechanism, whose great potential has been well demonstrated in various areas. In this paper, we first propose a novel heterogeneous graph neural network based on the hierarchical attention, including node-level and semantic-level attentions. Specifically, the node-level attention aims to learn the importance between a node and its meta-path based neighbors, while the semantic-level attention is able to learn the importance of different meta-paths. With the learned importance from both node-level and semantic-level attention, the importance of node and meta-path can be fully considered. Then the proposed model can generate node embedding by aggregating features from meta-path based neighbors in a hierarchical manner. Extensive experimental results on three real-world heterogeneous graphs not only show the superior performance of our proposed model over the state-of-the-arts, but also demonstrate its potentially good interpretability for graph analysis.

Heterogeneous Graph Attention Network

We propose a framework for modeling sequence motifs based on the Maximum Entropy principle (MEP).We recommend approximating short sequence motif distributions with the Maximum Entropy Distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between non-adjacent as well as adjacent positions.Finally, we suggest mechanistically-motivated ways of comparing models.

Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals

Service providers like Google and Amazon are moving into the SaaS (Software as a Service) business. They turn their huge infrastructure into a cloud-computing environment and aggressively recruit businesses to run applications on their platforms. To enforce security and privacy on such a service model, we need to protect the data running on the platform. Unfortunately, traditional encryption methods that aim at providing "unbreakable" protection are often not adequate because they do not support the execution of applications such as database queries on the encrypted data. In this paper we discuss the general problem of secure computation on an encrypted database and propose a SCONEDB Secure Computation ON an Encrypted DataBase) model, which captures the execution and security requirements. As a case study, we focus on the problem of k-nearest neighbor (kNN) computation on an encrypted database. We develop a new asymmetric scalar-product-preserving encryption (ASPE) that preserves a special type of scalar product. We use APSE to construct two secure schemes that support kNN computation on encrypted data; each of these schemes is shown to resist practical attacks of a different background knowledge level, at a different overhead cost. Extensive performance studies are carried out to evaluate the overhead and the efficiency of the schemes.

/pdf/secure-knn-computation-on-encrypted-databases-uwfgefdq47.pdf

Secure kNN computation on encrypted databases

A more general incremental updating technique is developed for maintaining the association rules discovered in a database in the cases including insertion, deletion, and modijication of transactions in the database. A previously proposed algorithm FUP can only handle the maintenance problem in the case of insertion. The proposed algorithm FUP2 makes use of the previous mining result to cut down the cost of finding the new rules in an updated database. In the insertion only case, FUP2 is equivalent to FUP. In the deletion only case, FUP2 is a complementary algorithm of FUP which is very eficient when the deleted transactions is a small part of the database, which is the most applicable case. In the general case, FUP2 can elqiciently update the discovered rules when new transactions are added to a transaction database, and obsolete transactions are removed from it. The proposed algorithm has been implemented and its performance is studied and compared with the best algorithms for mining association rules studied so far. The study shows that the new incremental algorithm is signijcantly faster than the traditional approach of mining the whole updated database.

/pdf/a-general-incremental-technique-for-maintaining-discovered-2js4h73b1q.pdf

A General Incremental Technique for Maintaining Discovered Association Rules

We study the problem of mining frequent itemsets from uncertain data under a probabilistic framework. We consider transactions whose items are associated with existential probabilities and give a formal definition of frequent patterns under such an uncertain data model. We show that traditional algorithms for mining frequent itemsets are either inapplicable or computationally inefficient under such a model. A data trimming framework is proposed to improve mining efficiency. Through extensive experiments, we show that the data trimming technique can achieve significant savings in both CPU cost and I/O cost.

/pdf/mining-frequent-itemsets-from-uncertain-data-50f9222xl6.pdf

Mining frequent itemsets from uncertain data

In an "uncertain database", an object o is associated with a multi-dimensional probability density function(pdf), which describes the likelihood that o appears at each position in the data space. A fundamental operation is the "probabilistic range search" which, given a value pq and a rectangular area rq, retrieves the objects that appear in rq with probabilities at least pq. In this paper, we propose the U-tree, an access method designed to optimize both the I/O and CPU time of range retrieval on multi-dimensional imprecise data. The new structure is fully dynamic (i.e., objects can be incrementally inserted/deleted in any order), and does not place any constraints on the data pdfs. We verify the query and update efficiency of U-trees with extensive experiments.

/pdf/indexing-multi-dimensional-uncertain-data-with-arbitrary-2tng22rxkd.pdf

Indexing multi-dimensional uncertain data with arbitrary probability density functions

We study the problem of clustering data objects whose locations are uncertain. A data object is represented by an uncertainty region over which a probability density function (pdf) is defined. One method to cluster uncertain objects of this sort is to apply the UK-means algorithm, which is based on the traditional K-means algorithm. In UK-means, an object is assigned to the cluster whose representative has the smallest expected distance to the object. For arbitrary pdf, calculating the expected distance between an object and a cluster representative requires expensive integration computation. We study various pruning methods to avoid such expensive expected distance calculation.

/pdf/efficient-clustering-of-uncertain-data-3jcxdk1n5c.pdf

Ben Kao

Papers

Secure kNN computation on encrypted databases

A General Incremental Technique for Maintaining Discovered Association Rules

Mining frequent itemsets from uncertain data

Indexing multi-dimensional uncertain data with arbitrary probability density functions

Efficient Clustering of Uncertain Data