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.
5173411
Email data cleaning
Addressed in this paper is the issue of 'email data cleaning' for text mining. Many text mining applications need take emails as input. Email data is usually noisy and thus it is necessary to clean it before mining. Several products offer email cleaning features, however, the types of noises that can be eliminated are restricted. Despite the importance of the problem, email cleaning has received little attention in the research community. A thorough and systematic investigation on the issue is thus needed. In this paper, email cleaning is formalized as a problem of non-text filtering and text normalization. In this way, email cleaning becomes independent from any specific text mining processing. A cascaded approach is proposed, which cleans up an email in four passes including non-text filtering, paragraph normalization, sentence normalization, and word normalization. As far as we know, non-text filtering and paragraph normalization have not been investigated previously. Methods for performing the tasks on the basis of Support Vector Machines (SVM) have also been proposed in this paper. Features in the models have been defined. Experimental results indicate that the proposed SVM based methods can significantly outperform the baseline methods for email cleaning. The proposed method has been applied to term extraction, a typical text mining processing. Experimental results show that the accuracy of term extraction can be significantly improved by using the data cleaning method.
207188648
Reliable Ad Hoc Routing Based on Mobility Prediction
Reliability is a very important issue in Mobile Ad hoc NETworks (MANETs). Shortest paths are usually used to route packets in MANETs. However, a shortest path may fail quickly, because some of the wireless links along a shortest path may be broken shortly after the path is established due to mobility of mobile nodes. Rediscovering routes may result in substantial data loss and message exchange overhead. In this paper, we study reliable ad hoc routing in the urban environment. Specifically, we formulate and study two optimization problems. In the minimum Cost Duration-bounded Path (CDP) routing problem, we seek a minimum cost source to destination path with duration no less than a given threshold. In the maximum Duration Cost-bounded Path (DCP) routing problem, we seek a maximum duration source to destination path with cost no greater than a given threshold. We use a waypoint graph to model the working area of a MANET and present an offline algorithm to compute a duration prediction table for the given waypoint graph. An entry in the duration prediction table contains the guaranteed worst-case duration of the corresponding wireless link. We then present an efficient algorithm which computes a minimum cost duration-bounded path, using the information provided in the duration prediction table. We also present a heuristic algorithm for the DCP routing problem. In addition, we show that the proposed prediction and routing schemes can be easily applied for designing reliable ad hoc routing protocols. Simulation results show that our mobility prediction based routing algorithms lead to higher network throughput and longer average path duration, compared with the shortest path routing.
1649407
Rhythm modeling, visualizations and applications
People use their awareness of others' temporal patterns to plan work activities and communication. This paper presents algorithms for programatically detecting and modeling temporal patterns from a record of online presence data. We describe analytic and end-user visualizations of rhythmic patterns and the tradeoffs between them. We conducted a design study that explored the accuracy of the derived rhythm models compared to user perceptions, user preference among the visualization alternatives, and users' privacy preferences. We also present a prototype application based on the rhythm model that detects when a person is "away" for an extended period and predicts their return. We discuss the implications of this technology on the design of computer-mediated communication.
6797006
Exploring web browser history comparisons
This work explores how comparing web navigation histories between two people and presenting the results to them might allow them to gain insight about each other. We developed a prototype that presents web matches sorted according to frequency, recency, and web site. Interviews with users of the prototype suggest that common interests and preferences can be inferred from these comparisons.
4332072
A Component Retrieval Method Based on Facet-Weight Self-learning
Component-based development method has been a new software development paradigm. How to get the needed components quickly and accurately is one of the basic problems about reusing software component automatically. In this paper, an intelligent component retrieval model – FWRM. is proposed. Facet presentation is used to model query and component. Multiple types of facets are defined which extends traditional keyword-based facet presentation. Genetic algorithm based facet weight self-learning algorithm can change the facet weight dynamically in order to improve retrieval accuracy. Corresponding similarity functions are defined also. In addition, risk minimization-based component sampling method is used to solve the insufficiency of training data. All these algorithms and methods are integrated into FWRM’s three main implementation parts: Facet-Weight Optimize System, Component Retrieve System and Resource. The experimental results prove that this method is feasible and can improve component retrieval effectively.