The average time between two occurrences of the same event, referred to as its return time (or return period), is a useful statistical concept for practical applications. For instance insurances or public agencies may...
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The average time between two occurrences of the same event, referred to as its return time (or return period), is a useful statistical concept for practical applications. For instance insurances or public agencies may be interested by the return time of a 10 m flood of the Seine river in Paris. However, due to their scarcity, reliably estimating return times for rare events is very dificult using either observational data or direct numerical simulations. For rare events, an estimator for return times can be built from the extrema of the observable on trajectory blocks. Here, we show that this estimator can be improved to remain accurate for return times of the order of the block size. More importantly, we show that this approach can be generalised to estimate return times from numerical algorithms specifically designed to sample rare events. So far those algorithms often compute probabilities, rather than return times. The approach we propose provides a computationally extremely efficient way to estimate numerically the return times of rare events for a dynamical system, gaining several orders of magnitude of computational costs. We illustrate the method on two kinds of observables, instantaneous and time-averaged, using two different rare event algorithms, for a simple stochastic process, the Ornstein-Uhlenbeck process. As an example of realistic applications to complex systems, we finally discuss extreme values of the drag on an object in a turbulent flow.
Decentralized Autonomous Organizations (DAOs) are sovereign digital communities that are owned by their members and that are algorithmically-controlled, usually by encoding their rules of conduct as smart contracts. E...
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ISBN:
(纸本)9781450394321
Decentralized Autonomous Organizations (DAOs) are sovereign digital communities that are owned by their members and that are algorithmically-controlled, usually by encoding their rules of conduct as smart contracts. Even though such communities become more popular and influential, their governance capabilities are still limited and lacking in quality. We argue that the MAS community holds the keys to improving the governance capabilities of DAOs; and that the challenge of DAO governance constitutes an important, new application area for MAS research that has the potential to have both scientific and societal impacts. Concretely, we describe DAOs and their governance needs and highlight gaps between the state of the art of MAS research and the governance needs of DAOs.
Protein–protein interactions play critical roles in essentially every cellular process. These interactions are often mediated by protein interaction domains that enable proteins to recognize their interaction partner...
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Protein–protein interactions play critical roles in essentially every cellular process. These interactions are often mediated by protein interaction domains that enable proteins to recognize their interaction partners, often by binding to short peptide motifs. For example, PDZ domains, which are among the most common protein interaction domains in the human proteome, recognize specific linear peptide sequences that are often at the C-terminus of other proteins. Determining the set of peptide sequences that a protein interaction domain binds, or it’s “peptide specificity,” is crucial for understanding its cellular function, and predicting how mutations impact peptide specificity is important for elucidating the mechanisms underlying human diseases. Moreover, engineering novel cellular functions for synthetic biology applications, such as the biosynthesis of biofuels or drugs, requires the design of protein interaction specificity to avoid crosstalk with native metabolic and signaling pathways. The ability to accurately predict and design protein–peptide interaction specificity is therefore critical for understanding and engineering biological function. One approach that has recently been employed toward accomplishing this goal is computational protein design. This chapter provides an overview of recent methodological advances in computational protein design and highlights examples of how these advances can enable increased accuracy in predicting and designing peptide specificity. less
Knauff and Gazzo Castaneda (2022) object to using the term "new paradigm" to describe recent developments in the psychology of reasoning. This paper concedes that the Kuhnian term "paradigm" may be...
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Knauff and Gazzo Castaneda (2022) object to using the term "new paradigm" to describe recent developments in the psychology of reasoning. This paper concedes that the Kuhnian term "paradigm" may be queried. What cannot is that the work subsumed under this heading is part of a new, progressive movement that spans the brain and cognitive sciences: Bayesian cognitive science. sampling algorithms and Bayes nets used to explain biases in JDM can implement the Bayesian new paradigm approach belying any advantages of mental models theory (MMT) at the algorithmic level. Moreover, this paper argues that new versions of MMT lack a computational level theory and questions the grounds for MMTs much-vaunted generality. The paper then examines common ground on the importance of small-scale models/simulations of the world and the importance of argumentation in the social domain rather than individual reasoning. Finally, the paper concludes that although there may be prospects for moving reasoning research forward in a more collective, collaborative manner, many disagreements remain to be resolved.
There is much interest in the Hierarchical Dirichlet Process Hidden Markov Model (HDP-HMM) as a natural Bayesian nonparametric extension of the ubiquitous Hidden Markov Model for learning from sequential and time-seri...
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There is much interest in the Hierarchical Dirichlet Process Hidden Markov Model (HDP-HMM) as a natural Bayesian nonparametric extension of the ubiquitous Hidden Markov Model for learning from sequential and time-series data. However, in many settings the HDP-HMM's strict Markovian constraints are undesirable, particularly if we wish to learn or encode non-geometric state durations. We can extend the HDP-HMM to capture such structure by drawing upon explicit-duration semi-Markov modeling, which has been developed mainly in the parametric non-Bayesian setting, to allow construction of highly interpretable models that admit natural prior information on state *** this paper we introduce the explicit-duration Hierarchical Dirichlet Process Hidden semi-Markov Model (HDP-HSMM) and develop sampling algorithms for efficient posterior inference. The methods we introduce also provide new methods for sampling inference in the finite Bayesian HSMM. Our modular Gibbs sampling methods can be embedded in samplers for larger hierarchical Bayesian models, adding semi-Markov chain modeling as another tool in the Bayesian inference toolbox. We demonstrate the utility of the HDP-HSMM and our inference methods on both synthetic and real experiments.
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