2197213
Reconstruction of ancestral gene order after segmental duplication and gene loss
As gene order evolves through a variety of chromosomal rearrangements, conserved segments provide important insight into evolutionary relationships and functional roles of genes. However, gene loss within otherwise conserved segments, as typically occurs following large-scale genome duplication, has received limited algorithmic study. This has been a major impediment to comparative genomics in certain taxa, such as plants and fish. We propose a heuristic algorithm/or the inference of ancestral gene order in a set of related genomes that have undergone large-scale duplication and gene loss. First, approximately conserved (i.e. homologous) segments are identified using pairwise local genome alignment. Second, homologous segments are iteratively clustered under the control of two parameters, (1) the minimal required number of shared genes between two clusters and (2) the maximal allowed number of rearrangement breakpoints along the lineage leading to each descendant segment. Finally, we compute an estimated ancestral gene order for each cluster that is optimal in some sense. We evaluate the performance of this algorithm on simulated data that models a genome evolving by large-scale duplication, duplicate gene loss, transposition, translocation, and inversion. The results suggest that long segments of ancestral gene order may be reconstructed following moderate levels of rearrangement with only minor loss of accuracy.
5788516
Efficient genome ancestry inference in complex pedigrees with inbreeding
Motivation: High-density SNP data of model animal resources provides opportunities for fine-resolution genetic variation studies. These genetic resources are generated through a variety of breeding schemes that involve multiple generations of matings derived from a set of founder animals. In this article, we investigate the problem of inferring the most probable ancestry of resulting genotypes, given a set of founder genotypes. Due to computational difficulty, existing methods either handle only small pedigree data or disregard the pedigree structure. However, large pedigrees of model animal resources often contain repetitive substructures that can be utilized in accelerating computation. Results: We present an accurate and efficient method that can accept complex pedigrees with inbreeding in inferring genome ancestry. Inbreeding is a commonly used process in generating genetically diverse and reproducible animals. It is often carried out for many generations and can account for most of the computational complexity in real-world model animal pedigrees. Our method builds a hidden Markov model that derives the ancestry probabilities through inbreeding process without explicit modeling in every generation. The ancestry inference is accurate and fast, independent of the number of generations, for model animal resources such as the Collaborative Cross (CC). Experiments on both simulated and real CC data demonstrate that our method offers comparable accuracy to those methods that build an explicit model of the entire pedigree, but much better scalability with respect to the pedigree size. Contact: weiwang@cs.unc.edu
62615149
Mining Asynchronous Periodic Patterns in Time Series Data
Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min/spl I.bar/rep and max/spl I.bar/dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space efficiency.
7408751
Quantitative Association Analysis Using Tree Hierarchies
Association analysis arises in many important applications such as bioinformatics and business intelligence. Given a large collection of measurements over a set of samples, association analysis aims to find dependencies of target variables to subsets of measurements. Most previous algorithms adopt a two-stage approach; they first group samples based on the similarity in the subset of measurements, and then they examine the association between these groups and the specified target variables without considering the inter-group similarities or alternative groupings. This can lead to cases where the strength of association depends significantly on arbitrary clustering choices. In this paper, we propose a tree-based method for quantitative association analysis. Tree hierarchies derived from sample similarities represent many possible sample groupings. They also provide a natural way to incorporate domain knowledge such as ontologies and to identify and remove outliers. Given a tree hierarchy, our association analysis evaluates all possible groupings and selects the one with strongest association to the target variable. We introduce an efficient algorithm, TreeQA, to systematically explore the search-space of all possible groupings in a set of input trees, with integrated permutation tests. Experimental results show that TreeQA is able to handlelarge-scale association analysis very efficiently and is more effective and robust in association analysis than previous methods.
2548187
Mining asynchronous periodic patterns in time series data
Periodicy detection in time series data is a challenging problem of great importance in many applications. Most previous work focused on mining synchronous periodic patterns and did not recognize the misaligned presence of a pattern due to the intervention of random noise. In this paper, we propose a more flexible model of asynchronous periodic pattern that may be present only within a subsequence and whose occurrences may be shifted due to disturbance. Two parameters min rep and max dis are employed to specify the minimum number of repetitions that is required within each segment of nondisrupted pattern occurrences and the maximum allowed disturbance between any two successive valid segments. Upon satisfying these two requirements, the longest valid subsequence of a pattern is returned. A two-phase algorithm is devised to first generate potential periods by distance-based pruning followed by an iterative procedure to derive and validate candidate patterns and locate the longest valid subsequence. We also show that this algorithm cannot only provide linear time complexity with respect to the length of the sequence but also achieve space
14969897
Dynamic adaptive file management in a local area network
In light of advances in processor and networking technology, especially the emergence of network attached disks, the traditional client-server architecture of file systems has become suboptimal for many computation/data intensive applications. We introduce a revised architecture for file management employing network attached storage: the dynamic file server environment (Dynamo). Dynamo introduces two main architectural innovations: to provide high scalability, the file management functions are mainly performed cooperatively by the clients in the system. Furthermore, data is transferred directly to the client's cache from network-attached disks, thus avoiding copies from a disk to the server buffer and then over the network to the client. Secondly, Dynamo uses a cooperative cache management which employs a decentralized lottery-based page replacement strategy. We show via performance benchmarks run on the Dynamo system and simulation results how this architecture increases the system's adaptability, scalability and cost performance.
14966701
A Deterministic approach to evaluate path loss exponents in large-scale outdoor 802.11 WLANs
Accurate network planning is critical with deployments of large outdoor wireless networks. Propagation and path loss considerations are key factors in predicting performance of wireless networks. We are currently studying large-scale wireless networks for US railway environments. In this study, both theoretical and measurement based propagation models indicate that the average received signal power decreased logarithmically with distance. The average large-scale path loss is expressed as a function of distance between the transmitter and the receiver by using a path loss exponent n and the close-in reference distance d0. However it is very important to select a suitable space reference distance that is appropriate for a specific propagation environment. In this paper, a deterministic approach is proposed to select an appropriate reference distance for a given propagation environment. Also a Minimum Mean Square Error (MMSE) based method is introduced to compute path loss exponents. Furthermore the comparison between the site specific measurement data collected from our testbed and the estimated values verifies the accuracy of our proposed method.
1912292
Opportunistic Energy-Efficient Contact Probing in Delay-Tolerant Applications
In many delay-tolerant applications, information is opportunistically exchanged between mobile devices that encounter each other. In order to affect such information exchange, mobile devices must have knowledge of other devices in their vicinity. We consider scenarios in which there is no infrastructure and devices must probe their environment to discover other devices. This can be an extremely energy-consuming process and highlights the need for energy-conscious contact-probing mechanisms. If devices probe very infrequently, they might miss many of their contacts. On the other hand, frequent contact probing might be energy inefficient. In this paper, we investigate the tradeoff between the probability of missing a contact and the contact-probing frequency. First, via theoretical analysis, we characterize the tradeoff between the probability of a missed contact and the contact-probing interval for stationary processes. Next, for time-varying contact arrival rates, we provide an optimization framework to compute the optimal contact-probing interval as a function of the arrival rate. We characterize real-world contact patterns via Bluetooth phone contact-logging experiments and show that the contact arrival process is self-similar. We design STAR, a contact-probing algorithm that adapts to the contact arrival process. Instead of using constant probing intervals, STAR dynamically chooses the probing interval using both the short-term contact history and the long-term history based on time of day information. Via trace-driven simulations on our experimental data, we demonstrate that STAR requires three to five times less energy for device discovery than a constant contact-probing interval scheme.
15939515
GraphMiner: a structural pattern-mining system for large disk-based graph databases and its applications
Mining frequent structural patterns from graph databases is an important research problem with broad applications. Recently, we developed an effective index structure, ADI, and efficient algorithms for mining frequent patterns from large, disk-based graph databases [5], as well as constraint-based mining techniques. The techniques have been integrated into a research prototype system--- GraphMiner. In this paper, we describe a demo of GraphMiner which showcases the technical details of the index structure and the mining algorithms including their efficient implementation, the mining performance and the comparison with some state-of-the-art methods, the constraint-based graph-pattern mining techniques and the procedure of constrained graph mining, as well as mining real data sets in novel applications.
19006089
Processing of massive audit data streams for real-time anomaly intrusion detection
Intrusion detection is an important technique in the defense-in-depth network security framework. Most current intrusion detection models lack the ability to process massive audit data streams for real-time anomaly detection. In this paper, we present an effective anomaly intrusion detection model based on Principal Component Analysis (PCA). The model is more suitable for high speed processing of massive data streams in real-time from various data sources by considering the frequency property of audit events than by use of the transition property or the correlation property. It can serve as a general framework that a practical Intrusion Detection Systems (IDS) can be implemented in various computing environments. In this method, a multi-pronged anomaly detection model is used to monitor various computer system and network behaviors. Three sources of data, system call data from the University of New Mexico (lpr) and from KLINNS Lab of Xi'an Jiaotong University (ftp), shell command data from AT&T Research laboratory, and network data from MIT Lincoln Lab, are used to validate the model and the method. The frequencies of individual system calls generated by one process and of individual commands embedded in one command block as well as features extracted in one network connection are transformed into an input data vector. Our method is employed to reduce the high dimensional data vectors and thus the detection is handled in a lower dimension with high efficiency and low use of system resources. The distance between a vector and its reconstruction in the reduced subspace is used for anomaly detection. Empirical results show that our model is promising in terms of detection accuracy and computational efficiency, and thus amenable for real-time intrusion detection.
207162632
Utility-based anonymization for privacy preservation with less information loss
Privacy becomes a more and more serious concern in applications involving microdata. Recently, efficient anonymization has attracted much research work. Most of the previous methods use global recoding, which maps the domains of the quasi-identifier attributes to generalized or changed values. However, global recoding may not always achieve effective anonymization in terms of discernability and query answering accuracy using the anonymized data. Moreover, anonymized data is often used for analysis. As well accepted in many analytical applications, different attributes in a data set may have different utility in the analysis. The utility of attributes has not been considered in the previous methods.
 In this paper, we study the problem of utility-based anonymization. First, we propose a simple framework to specify utility of attributes. The framework covers both numeric and categorical data. Second, we develop two simple yet efficient heuristic local recoding methods for utility-based anonymization. Our extensive performance study using both real data sets and synthetic data sets shows that our methods outperform the state-of-the-art multidimensional global recoding methods in both discernability and query answering accuracy. Furthermore, our utility-based method can boost the quality of analysis using the anonymized data.