8476755
Succinct Text Indexes on Large Alphabet
In this paper, we first consider some properties of strings who have the same suffix array. Next, we design a data structure to support rank and select operations on an alphabet Σ using nlog|Σ| + (nlog|Σ|) bits in O(log|Σ|) time for a text of length n. It also supports an extended rank, namely rank≤, such that rank$^{\rm \leq}_{\alpha}$(T,i) returns the number of letters which are smaller than α in string T, plus the number of αs up to position i. Also, it runs in O(log|Σ|) time. By this structure, we implement the DAWG succinctly. The main structure only takes nlog|Σ| + o(nlog|Σ|) bits and supports basic operations of DAWG efficiently.
14427891
Phylogenetic reconstruction from arbitrary gene-order data
Phylogenetic reconstruction from gene-order data has attracted attention from both biologists and computer scientists over the last few years. So far, our software suite GRAPPA is the most accurate approach, but it requires that all genomes have identical gene content, with each gene appearing exactly once in each genome. Some progress has been made in handling genomes with unequal gene content, both in terms of computing pair-wise genomic distances and in terms of reconstruction. In this paper, we present a new approach for computing the median of three arbitrary genomes and apply it to the reconstruction of phylogenies from arbitrary gene-order data. We implemented these methods within GRAPPA and tested them on simulated datasets under various conditions as well as on a real dataset of chloroplast genomes; we report the results of our simulations and our analysis of the real dataset and compare them to reconstructions made by using neighbor-joining and using the original GRAPPA on the same genomes with equalized gene contents. Our new approach is remarkably accurate both in simulations and on the real dataset, in contrast to the distance-based approaches and to reconstructions using the original GRAPPA applied to equalized gene contents.
1746627
Inversion Medians Outperform Breakpoint Medians in Phylogeny Reconstruction from Gene-Order Data
Phylogeny reconstruction from gene-order data has attracted much attention over the last few years. The two software packages used for that purpose, BPAnalysis and GRAPPA, both use so-called breakpoint medians in their computations. Some of our past results indicate that using inversion scores rather than breakpoint scores in evaluating trees leads to the selection of better trees. On that basis, we conjectured that phylogeny reconstructions could be improved by using inversion medians, which minimize evolutionary distance under an inversions-only model of genome rearrangement. Recent algorithmic developments have made it possible to compute inversion medians for problems of realistic size.Our experimental studies unequivocally show that inversion medians are strongly preferable to breakpoint medians in the context of phylogenetic reconstruction from gene-order data. Improvements are most pronounced in the reconstruction of ancestral genomes, but are also evident in the topological accuracy of the reconstruction as well as, surprisingly, in the overall running time. Improvements are strongest for small average distances along tree edges and for evolutionary scenarios with a preponderance of inversion events, but occur in all cases, including evolutionary scenarios with high proportions of transpositions.All of our tests were run using our GRAPPA package, available (under GPL) at www.cs.unm.edu/~moret/GRAPPA; the next release will include the inversion median software we used in this study. The software used includes RevMed, developed by the authors and available at www.cs.unm.edu/~acs, and A. Caprara's inversion median code, generously made available for testing.
1484935
Improving genome rearrangement phylogeny using sequence-style parsimony
The study of genome rearrangements, the evolutionary events that change the order and strandedness of genes within genomes, presents new opportunities for discoveries about deep evolutionary events. The best software so far, GRAPPA, solves breakpoint and inversion phylogenies by scoring each tree topology through iterative improvements of internal node gene orders. We find that the greedy hill-climbing approach means the accuracy is limited because of multiple local optima. To address this problem, we propose integration GRAPPA with MPME, a string encoding of gene adjacency relationships whose optimal internal node assignments can be determined globally in polynomial time, to provide better initializations for GRAPPA. In simulation studies, the new algorithm yields shorter tree lengths and better accuracy in phylogeny reconstruction.
79892
Resource Allocation and Quality of Service Evaluation for Wireless Communication Systems Using Fluid Models
Wireless systems offer a unique mixture of connectivity, flexibility, and freedom. It is therefore not surprising that wireless technology is being embraced with increasing vigor. For real-time applications, user satisfaction is closely linked to quantities such as queue length, packet loss probability, and delay. System performance is therefore related to, not only Shannon capacity, but also quality of service (QoS) requirements. This work studies the problem of resource allocation in the context of stringent QoS constraints. The joint impact of spectral bandwidth, power, and code rate is considered. Analytical expressions for the probability of buffer overflow, its associated exponential decay rate, and the effective capacity are obtained. Fundamental performance limits for Markov wireless channel models are identified. It is found that, even with an unlimited power and spectral bandwidth budget, only a finite arrival rate can be supported for a QoS constraint defined in terms of exponential decay rate
10355154
Supporting distributed groups with a Montage of lightweight interactions
The Montage prototype provides lightweight audio-video glances among distributed collaborators and integrates other applications for coordinating future contact. We studied a distributed group across three conditions: before installing Montage, with Montage, and after removing Montage. We collected quantitative measures of usage as well as video-tape and user perception data. We found that the group used Montage glances for short, lightweight interactions that were like face-to-face conversations in many respects. Yet like the phone, Montage offered convenient access to other people without leaving the office. Most glances revealed that the person was not available, so it was important to integrate other tools for coordinating future interaction. Montage did not appear to displace the use of e-mail, voice-mail, or scheduled meetings.
4300632
Keyword Extraction Using Support Vector Machine
This paper is concerned with keyword extraction. By keyword extraction, we mean extracting a subset of words/phrases from a document that can describe the ‘meaning' of the document. Keywords are of benefit to many text mining applications. However, a large number of documents do not have keywords and thus it is necessary to assign keywords before enjoying the benefit from it. Several research efforts have been done on keyword extraction. These methods make use of the ‘global context information', which makes the performance of extraction restricted. A thorough and systematic investigation on the issue is thus needed. In this paper, we propose to make use of not only ‘global context information', but also ‘local context information' for extracting keywords from documents. As far as we know, utilizing both ‘global context information' and ‘local context information' in keyword extraction has not been sufficiently investigated previously. Methods for performing the tasks on the basis of Support Vector Machines have also been proposed in this paper. Features in the model have been defined. Experimental results indicate that the proposed SVM based method can significantly outperform the baseline methods for keyword extraction. The proposed method has been applied to document classification, a typical text mining processing. Experimental results show that the accuracy of document classification can be significantly improved by using the keyword extraction method.
14586033
Dynamic Data-Driven Fault Diagnosis of Wind Turbine Systems
In this multi-university collaborative research, we will develop a framework for the dynamic data-driven fault diagnosis of wind turbines which aims at making the wind energy a competitive alternative in the energy market. This new methodology is fundamentally different from the current practice whose performance is limited due to the non-dynamic and non-robust nature in the modeling approaches and in the data collection and processing strategies. The new methodology consists of robust data pre-processing modules, interrelated, multi-level models that describe different details of the system behaviors, and a dynamic strategy that allows for measurements to be adaptively taken according to specific physical conditions and the associated risk level. This paper summarizes the latest progresses in the research.
13492639
Relay node placement in large scale wireless sensor networks
Scalability and extended lifetime are two critical design goals of any large scale wireless sensor network. A two-tiered network model has been proposed recently for this purpose. This is a cluster-based network model composed of relay and sensor nodes. Relay nodes are placed in the playing field to serve as cluster heads and to form a connected network topology for information dissemination at the higher tier. The relay nodes are capable of aggregating data packets from the sensor nodes in their clusters and transmitting them to the sink node via wireless multi-hop paths. In this paper, we study the relay node placement problem in large scale wireless sensor networks. Our objective is to place the fewest number of relay nodes in the playing field of a sensor network such that (1) each sensor node can communicate with at least one relay node and (2) the network of relay nodes is connected. However, placement strategies realizing goals (1) and (2) do not provide any fault-tolerance as the network may lose functionality after failure of some of the relay nodes. In order to incorporate fault-tolerance in such a network, we ensure that every sensor node is able to communicate with at least two relay nodes and the induced network topology is 2-connected. This strategy will ensure survivability of the network in the event of single fault, in lieu of higher relay node placement cost. We formulate the relay node placement in wireless sensor networks as two optimization problems: (i) Connected Relay Node Single Cover (CRNSC) problem and (ii) 2-Connected Relay Node Double Cover (2CRNDC) problem. We present two polynomial time approximation algorithms to solve the CRNSC problem. We prove that the ratio of the number of relay nodes needed by the approximation algorithm to the number of relay nodes needed by the optimal algorithm is bounded by 8 for the first algorithm and 4.5 for the second. In addition, for the 2CRNDC problem we provide two approximation algorithms with performance bounds 6 and 4.5, respectively.