Presentation Based User Interface

A prototype presentation system base is described. It offers mechanisms, tools, and ready-made parts for building user interfaces. A general user interface model underlies the base, organized around the concept of a presentation: a visible text or graphic for conveying information. Te base and model emphasize domain independence and style independence, to apply to the widest possible range of interfaces. The primitive presentation system model treats the interface as a system of processes maintaining a semantic relation between an application data base and a presentation data base, the symbolic screen description containing presentations. A presenter continually updates the presentation data base from the application data base. The user manipulates presentations with a presentation editor. A recognizer translates the user's presentation manipulation into application data base commands. The primitive presentation system can be extended to model more complex systems by attaching additional presentation systems. In order to illustrate the model's generality and descriptive capabilities, extended model structures for several existing user interfaces are discussed. The base provides support for building the application and presentation data bases, linked together into a single, uniform network, including descriptions of classes of objects as we as the objects themselves. The base provides an initial presentation data base network graphics to continually display it, and editing functions. A variety of tools and mechanisms help create and control presenters and recognizers. To demonstrate the base's utility, three interfaces to an operating system were constructed, embodying different styles: icons, menu, and graphical annotation.

Mecanismos virais no Cancro da Próstata

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

A randomized solution to BGP divergence

The Border Gateway Protocol (BGP) is an interdomain routing protocol that allows each Autonomous System (AS) to define its own routing policies independently and use them to select the best routes. By means of policies, ASes are able to prevent some traffic from accessing their resources, or direct their traffic to a preferred route. However, this flexibility comes at the expense of a possibility of divergence behavior because of mutually conflicting policies. Since BGP is not guaranteed to converge even in the absence of network topology changes, it is not safe. In this paper, we propose a randomized approach to providing safety in BGP. The proposed algorithm dynamically detects policy conflicts, and tries to eliminate the conflict by changing the local preference of the paths involved. Both the detection and elimination of policy conflicts are performed locally, i.e. by using only local information. Randomization is introduced to prevent synchronous updates of the local preferences of the paths involved in the same conflict.

Deterministic Computations Whose History Is Independent of the Order of Asynchronous Updating

Consider a network of processors (sites) in which each site x has a finite set N(x) of neighbors. There is a transition function f that for each site x computes the next state ξ(x) from the states in N(x). But these transitions (updates) are applied in arbitrary order, one or many at a time. If the state of site x at time t is η(x; t) then let us define the sequence ζ(x; 0); ζ(x; 1), ... by taking the sequence η(x; 0),η(x; 1), ... , and deleting each repetition, i.e. each element equal to the preceding one. The function f is said to have invariant histories if the sequence ζ(x; i), (while it lasts, in case it is finite) depends only on the initial configuration, not on the order of updates. This paper shows that though the invariant history property is typically undecidable, there is a useful simple sufficient condition, called commutativity: For any configuration, for any pair x; y of neighbors, if the updating would change both ξ(x) and ξ(y) then the result of updating first x and then y is the same as the result of doing this in the reverse order. This fact is derivable from known results on the confluence of term-rewriting systems but the self-contained proof given here may be justifiable.

Client-based Logging: A New Paradigm of Distributed Transaction Management

The proliferation of inexpensive workstations and networks has created a new era in distributed computing. At the same time, non-traditional applications such as computer-aided design (CAD), computer-aided software engineering (CASE), geographic-information systems (GIS), and office-information systems (OIS) have placed increased demands for high-performance transaction processing on database systems. The combination of these factors gives rise to significant challenges in the design of modern database systems. In this thesis, we propose novel techniques whose aim is to improve the performance and scalability of these new database systems. These techniques exploit client resources through client-based transaction management. Client-based transaction management is realized by providing logging facilities locally even when data is shared in a global environment. This thesis presents several recovery algorithms which utilize client disks for storing recovery related information (i.e., log records). Our algorithms work with both coarse and fine-granularity locking and they do not require the merging of client logs at any time. Moreover, our algorithms support fine-granularity locking with multiple clients permitted to concurrently update different portions of the same database page. The database state is recovered correctly when there is a complex crash as well as when the updates performed by different clients on a page are not present on the disk version of the page, even though some of the updating transactions have committed. This thesis also presents the implementation of the proposed algorithms in a memory-mapped storage manager as well as a detailed performance study of these algorithms using the OO1 database benchmark. The performance results show that client-based logging is superior to traditional server-based logging. This is because client-based logging is an effective way to reduce dependencies on server CPU and disk resources and, thus, prevents the server from becoming a performance bottleneck as quickly when the number of clients accessing the database increases.

Real-Time Mutable Broadcast Disks

There is an increased interest in using broadcast disks to support mobile access to real-time databases. However, previous work has only considered the design of real-time immutable broadcast disks, the contents of which do not change over time. This paper considers the design of programs for real-time mutable broadcast disks - broadcast disks whose contents are occasionally updated. Recent scheduling-theoretic results relating to pinwheel scheduling and pfair scheduling are used to design algorithms for the efficient generation of real-time mutable broadcast disk programs.

Principles of Safe Policy Routing Dynamics

We introduce the Dynamic Policy Routing (DPR) model that captures the propagation of route updates under arbitrary changes in topology or path preferences. DPR introduces the notion of causation chains where the route flap at one node causes a flap at the next node along the chain. Using DPR, we model the Gao-Rexford (economic) guidelines that guarantee the safety (i.e., convergence) of policy routing. We establish three principles of safe policy routing dynamics. The non-interference principle provides insight into which ASes can directly induce route changes in one another. The single cycle principle and the multi-tiered cycle principle provide insight into how cycles of routing updates can manifest in any network. We develop INTERFERENCEBEAT, a distributed algorithm that propagates a small token along causation chains to check adherence to these principles. To enhance the diagnosis power of INTERFERENCEBEAT, we model four violations of the Gao-Rexford guidelines (e.g., transiting between peers) and characterize the resulting dynamics.

Authenticated Index Structures for Aggregation Queries in Outsourced Databases

In an outsourced database system the data owner publishes information through a number of remote, untrusted servers with the goal of enabling clients to access and query the data more efficiently. As clients cannot trust servers, query authentication is an essential component in any outsourced database system. Clients should be given the capability to verify that the answers provided by the servers are correct with respect to the actual data published by the owner. While existing work provides authentication techniques for selection and projection queries, there is a lack of techniques for authenticating aggregation queries. This article introduces the first known authenticated index structures for aggregation queries. First, we design an index that features good performance characteristics for static environments, where few or no updates occur to the data. Then, we extend these ideas and propose more involved structures for the dynamic case, where the database owner is allowed to update the data arbitrarily. Our structures feature excellent average case performance for authenticating queries with multiple aggregate attributes and multiple selection predicates. We also implement working prototypes of the proposed techniques and experimentally validate the correctness of our ideas.

Sequential anomaly detection in the presence of noise and limited feedback

This paper describes a methodology for detecting anomalies from sequentially observed and potentially noisy data. The proposed approach consists of two main elements: 1) filtering, or assigning a belief or likelihood to each successive measurement based upon our ability to predict it from previous noisy observations and 2) hedging, or flagging potential anomalies by comparing the current belief against a time-varying and data-adaptive threshold. The threshold is adjusted based on the available feedback from an end user. Our algorithms, which combine universal prediction with recent work on online convex programming, do not require computing posterior distributions given all current observations and involve simple primal-dual parameter updates. At the heart of the proposed approach lie exponential-family models which can be used in a wide variety of contexts and applications, and which yield methods that achieve sublinear per-round regret against both static and slowly varying product distributions with marginals drawn from the same exponential family. Moreover, the regret against static distributions coincides with the minimax value of the corresponding online strongly convex game. We also prove bounds on the number of mistakes made during the hedging step relative to the best offline choice of the threshold with access to all estimated beliefs and feedback signals. We validate the theory on synthetic data drawn from a time-varying distribution over binary vectors of high dimensionality, as well as on the Enron email dataset. © 1963-2012 IEEE.

The distribution of sales revenues from pharmaceutical innovation.

OBJECTIVE: This report updates our earlier work on the returns to pharmaceutical research and development (R&D) in the US (1980 to 1984), which showed that the returns distributions are highly skewed. It evaluates a more recent cohort of new drug introductions in the US (1988 to 1992) and examines how the returns distribution is emerging for drugs with life cycles concentrated in the 1990s versus the 1980s. DESIGN AND SETTING: Methods were described in detail in our earlier reports. The current sample included 110 new drug entities (including 28 orphan drugs), and sales data were obtained for the period 1988 to 1998, which represented between 7 and 11 years of sales for the drugs included. 20 years was chosen as the expected market life for this cohort, and a 2-step procedure was used to project future sales for the drugs--during the period until patent expiry and then beyond patent expiry until the 20-year time-horizon was completed. Thus, the values in the first half of the life cycle are essentially based on realised sales, while those in the second half are projected using information on patent expiry and other inputs. MAIN OUTCOME MEASURES AND RESULTS: Peak annual sales for the top decile of drugs introduced between 1988 and 1992 in the US amounted to almost $US1.1 billion compared with peak sales of less than $US175 million (1992 values) for the mean compound. In particular, the top decile accounted for 56% of overall sales revenue. Although the sales distributions were skewed in both our earlier and current analysis, the top decile in the later time-period exhibited more rapid rates of growth after launch, a peak that was more than 50% greater in real terms than for the 1980 to 1984 cohort, and a faster rate of expected decline in sales after patent expiry. One factor contributing to the distribution of sales revenues becoming more skewed over time is the orphan drug phenomenon (i.e. most of the orphan drugs are concentrated at the bottom of the distribution). CONCLUSION: The distribution of sales revenues for new drug compounds is highly skewed in nature. In this regard, the top decile of new drugs accounts for more than half of the total sales generated by the 1988 to 1992 cohort analysed. Furthermore, the distribution of sales revenues for this cohort is more skewed than that of the 1980 to 1984 cohort we analysed in previous research.

Lognormal and gamma mixed negative binomial regression

In regression analysis of counts, a lack of simple and efficient algorithms for posterior computation has made Bayesian approaches appear unattractive and thus underdeveloped. We propose a lognormal and gamma mixed negative binomial (NB) regression model for counts, and present efficient closed-form Bayesian inference; unlike conventional Poisson models, the proposed approach has two free parameters to include two different kinds of random effects, and allows the incorporation of prior information, such as sparsity in the regression coefficients. By placing a gamma distribution prior on the NB dispersion parameter r, and connecting a log-normal distribution prior with the logit of the NB probability parameter p, efficient Gibbs sampling and variational Bayes inference are both developed. The closed-form updates are obtained by exploiting conditional conjugacy via both a compound Poisson representation and a Polya-Gamma distribution based data augmentation approach. The proposed Bayesian inference can be implemented routinely, while being easily generalizable to more complex settings involving multivariate dependence structures. The algorithms are illustrated using real examples. Copyright 2012 by the author(s)/owner(s).

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

BACKGROUND: A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and common names, and monophyletic supraspecific taxa that reflect our current understanding of phylogenetic relationships. DESCRIPTION: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically defined taxonomic resource derived from the integration of existing taxonomic compilations, and freely distributed under a Creative Commons Zero (CC0) public domain waiver. The VTO includes both extant and extinct vertebrates and currently contains 106,947 taxonomic terms, 22 taxonomic ranks, 104,736 synonyms, and 162,400 cross-references to other taxonomic resources. Key challenges in constructing the VTO included (1) extracting and merging names, synonyms, and identifiers from heterogeneous sources; (2) structuring hierarchies of terms based on evolutionary relationships and the principle of monophyly; and (3) automating this process as much as possible to accommodate updates in source taxonomies. CONCLUSIONS: The VTO is the primary source of taxonomic information used by the Phenoscape Knowledgebase (http://phenoscape.org/), which integrates genetic and evolutionary phenotype data across both model and non-model vertebrates. The VTO is useful for inferring phenotypic changes on the vertebrate tree of life, which enables queries for candidate genes for various episodes in vertebrate evolution.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

The HITRAN 2008 molecular spectroscopic database

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for the microwave through visible spectra of molecules in the gas phase; absorption cross-sections for molecules having dense spectral features, i.e. spectra in which the individual lines are not resolved; individual line parameters and absorption cross-sections for bands in the ultraviolet; refractive indices of aerosols, tables and files of general properties associated with the database; and database management software. The line-by-line portion of the database contains spectroscopic parameters for 42 molecules including many of their isotopologues. © 2009 Elsevier Ltd.