1,721,152 research outputs found
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots
No full textWe present HotKnots, a new heuristic algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea of iteratively forming stable stems, our algorithm explores many alternative secondary structures, using a free energy minimization algorithm for pseudoknot free secondary structures to identify promising candidate stems. In an empirical evaluation of the algorithm with 43 sequences taken from the Pseudobase database and from the literature on pseudoknotted structures, we found that overall, in terms of the sensitivity and specificity of predictions, HotKnots outperforms the well-known Pseudoknots algorithm of Rivas and Eddy and the NUPACK algorithm of Dirks and Pierce, both based on dynamic programming approaches for limited classes of pseudoknotted structures. It also outperforms the heuristic Iterated Loop Matching algorithm of Ruan and colleagues, and in many cases gives better results than the genetic algorithm from the STAR package of van Batenburg and colleagues and the recent pknotsRG-mfe algorithm of Reeder and Giegerich. The HotKnots algorithm has been implemented in C/C++ and is available from http://www.cs.ubc.ca/labs/beta/Software/HotKnots
Performance robustness of AI planners in the 2014 International Planning Competition
Full text link. Solver competitions have been used in many areas of AI to assess the current state of the art and guide future research and development. AI planning is no exception, and the International Planning Competition (IPC) has been frequently run for nearly two decades. Due to the organisational and computational burden involved in running these competitions, solvers are generally compared using a single homogeneous hardware and software environment for all competitors. To what extent does the specific choice of hardware and software environment have an effect on solver performance, and is that effect distributed equally across the competing solvers?In this work, we use the competing planners and benchmark instance sets from the 2014 IPC to investigate these two questions. We recreate the 2014 IPC Optimal and Agile tracks on two distinct hardware environments and eight distinct software environments. We show that solver performance varies significantly based on the hardware and software environment, and that this variation is not equal for all planners. Furthermore, the observed variation is sufficient to change the competition rankings, including the top-ranked planners for some tracks
Generating Fast Domain-Specific Planners by Automatically Configuring a Generic Parameterised Planner
No full textWhen designing state-of-the-art, domain-independent planning systems, many decisions have to be made with respect to the domain analysis or compilation performed during preprocessing, the heuristic functions used during search, and other
features of the search algorithm. These design decisions can have a large impact on the performance of the resulting planner. By providing many alternatives for these choices and exposing them as parameters, planning systems can in principle be configured to work well on different domains. However, usually planners are used in default configurations that have been chosen because of their good average performance over a set of benchmark domains, with limited experimentation of the potentially huge range of possible configurations.
In this work, we propose a general framework for automatically configuring a parameterised planner, showing that substantial performance gains can be achieved. We apply the framework to the well-known LPG planner, which has 62 parameters and over 6.5 × 10^17 possible configurations. We demonstrate that by using this highly parameterised planning system in combination with the off-the-shelf, state-of-the-art automatic algorithm configuration procedure ParamILS, substantial performance improvements on specific planning domains can be obtained
Automatic Generation of Efficient Domain-Optimized Planners from Generic Parametrized Planners
No full textWhen designing state-of-the-art, domain-independent planning systems, many decisions have to be made with respect to the domain analysis or
compilation performed during preprocessing, the heuristic functions used during search, and other features of the search algorithm. These design decisions can have a large impact on the performance of the resulting planner. By providing
many alternatives for these choices and exposing them as parameters, planning systems can in principle be configured to work well on different domains. However, usually planners are used in default configurations that have been chosen because of their good average performance over a set of benchmark domains, with limited experimentation of the potentially huge range of possible configurations.
In this work, we propose a general framework for automatically configuring a parameterized planner, showing that substantial performance gains can be achieved. We apply the framework to the well-known LPG planner, which has 62 parame-
ters and over 6.5 × 10^17 possible configurations. We demonstrate that by using
this highly parameterized planning system in combination with the off-the-shelf, state-of-the-art automatic algorithm configuration procedure ParamILS, the planner can be specialized obtaining significantly improved performance
Portfolio Methods for Optimal Planning: an Empirical Analysis
Full text linkCombining the complementary strengths of several algorithms through portfolio approaches has been demonstrated to be effective in solving a wide range of AI problems. Notably, portfolio techniques have been prominently applied to suboptimal (satisficing) AI planning. Here, we consider the construction of sequential planner portfolios for (domain- independent) optimal planning. Specifically, we introduce four techniques (three of which are dynamic) for per-instance planner schedule generation using problem instance features, and investigate the usefulness of a range of static and dynamic techniques for combining planners. Our extensive experimental analysis demonstrates the benefits of using static and dynamic sequential portfolios for optimal planning, and provides insights on the most suitable conditions for their fruitful exploitation
Static and Dynamic Portfolio Methods for Optimal Planning: An Empirical Analysis
Full text linkCombining the complementary strengths of several algorithms through portfolio approaches has been demonstrated to be effective in solving a wide range of AI problems. Notably, portfolio techniques have been prominently applied to suboptimal (satisficing) AI planning.
Here, we consider the construction of sequential planner portfolios for domainindependent optimal planning. Specifically, we introduce four techniques (three of which are dynamic) for per-instance planner schedule generation using problem instance features, and investigate the usefulness of a range of static and dynamic techniques for combining planners. Our extensive empirical analysis demonstrates the benefits of using static and dynamic sequential portfolios for optimal planning, and provides insights on the most suitable conditions for their fruitful exploitation
Automated configuration of negotiation strategies
No full textBidding and acceptance strategies have a substantial impact on the outcome of negotiations in scenarios with linear additive and nonlinear utility functions. Over the years, it has become clear that there is no single best strategy for all negotiation settings, yet many fixed strategies are still being developed. We envision a shift in the strategy design question from: What is a good strategy?, towards: What could be a good strategy? For this purpose, we developed a method leveraging automated algorithm configuration to find the best strategies for a specific set of negotiation settings. By empowering automated negotiating agents using automated algorithm configuration, we obtain a flexible negotiation agent that can be configured automatically for a rich space of opponents and negotiation scenarios. To critically assess our approach, the agent was tested in an ANAC-like bilateral automated negotiation tournament setting against past competitors. We show that our automatically configured agent outperforms all other agents, with a 5.1% increase in negotiation payoff compared to the next-best agent. We note that without our agent in the tournament, the top-ranked agent wins by a margin of only 0.01%.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Interactive Intelligenc
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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