A Comparative Study of Reservoir Computing for Temporal Signal Processing

Reservoir computing (RC) is a novel approach to time series prediction using recurrent neural networks. In RC, an input signal perturbs the intrinsic dynamics of a medium called a reservoir. A readout layer is then trained to reconstruct a target output from the reservoir's state. The multitude of RC architectures and evaluation metrics poses a challenge to both practitioners and theorists who study the task-solving performance and computational power of RC. In addition, in contrast to traditional computation models, the reservoir is a dynamical system in which computation and memory are inseparable, and therefore hard to analyze. Here, we compare echo state networks (ESN), a popular RC architecture, with tapped-delay lines (DL) and nonlinear autoregressive exogenous (NARX) networks, which we use to model systems with limited computation and limited memory respectively. We compare the performance of the three systems while computing three common benchmark time series: H{\'e}non Map, NARMA10, and NARMA20. We find that the role of the reservoir in the reservoir computing paradigm goes beyond providing a memory of the past inputs. The DL and the NARX network have higher memorization capability, but fall short of the generalization power of the ESN

First evidence for a latitudinal body mass effect in extant Crocodylia and the relationships of their reproductive characters

Relationships between distribution patterns and body size have been documented in many endothermic taxa. However, the evidence for these trends in ectotherms generally is equivocal, and there have been no studies of effects in crocodylians specifically. Here, we examine the relationship between latitudinal distribution and body mass in 20 extant species of crocodylians, as well as the relationships between seven important reproductive variables. Using phylogenetically independent contrasts to inform generalized linear models, we provide the first evidence of a latitudinal effect on adult female body mass in crocodylians. In addition, we explore the relationships between reproductive variables including egg mass, hatchling mass and clutch size. We report no correlation between egg mass and clutch size, upholding previously reported within-species trends. We also find no evidence of a correlation between measures of latitudinal range and incubation temperature, contrasting with the trends found in turtles

Evolution and dispersal of snakes across the Cretaceous-Paleogene mass extinction.

Mass extinctions have repeatedly shaped global biodiversity. The Cretaceous-Paleogene (K-Pg) mass extinction caused the demise of numerous vertebrate groups, and its aftermath saw the rapid diversification of surviving mammals, birds, frogs, and teleost fishes. However, the effects of the K-Pg extinction on the evolution of snakes-a major clade of predators comprising over 3,700 living species-remains poorly understood. Here, we combine an extensive molecular dataset with phylogenetically and stratigraphically constrained fossil calibrations to infer an evolutionary timescale for Serpentes. We reveal a potential diversification among crown snakes associated with the K-Pg mass extinction, led by the successful colonisation of Asia by the major extant clade Afrophidia. Vertebral morphometrics suggest increasing morphological specialisation among marine snakes through the Paleogene. The dispersal patterns of snakes following the K-Pg underscore the importance of this mass extinction event in shaping Earth's extant vertebrate faunas

Design and analysis of DNA strand displacement devices using probabilistic model checking

Designing correct, robust DNA devices is difficult because of the many possibilities for unwanted interference between molecules in the system. DNA strand displacement has been proposed as a design paradigm for DNA devices, and the DNA strand displacement (DSD) programming language has been developed as a means of formally programming and analysing these devices to check for unwanted interference. We demonstrate, for the first time, the use of probabilistic verification techniques to analyse the correctness, reliability and performance of DNA devices during the design phase. We use the probabilistic model checker prism, in combination with the DSD language, to design and debug DNA strand displacement components and to investigate their kinetics. We show how our techniques can be used to identify design flaws and to evaluate the merits of contrasting design decisions, even on devices comprising relatively few inputs. We then demonstrate the use of these components to construct a DNA strand displacement device for approximate majority voting. Finally, we discuss some of the challenges and possible directions for applying these methods to more complex designs

Stochastic Simulation of Process Calculi for Biology

Biological systems typically involve large numbers of components with complex, highly parallel interactions and intrinsic stochasticity. To model this complexity, numerous programming languages based on process calculi have been developed, many of which are expressive enough to generate unbounded numbers of molecular species and reactions. As a result of this expressiveness, such calculi cannot rely on standard reaction-based simulation methods, which require fixed numbers of species and reactions. Rather than implementing custom stochastic simulation algorithms for each process calculus, we propose to use a generic abstract machine that can be instantiated to a range of process calculi and a range of reaction-based simulation algorithms. The abstract machine functions as a just-in-time compiler, which dynamically updates the set of possible reactions and chooses the next reaction in an iterative cycle. In this short paper we give a brief summary of the generic abstract machine, and show how it can be instantiated with the stochastic simulation algorithm known as Gillespie's Direct Method. We also discuss the wider implications of such an abstract machine, and outline how it can be used to simulate multiple calculi simultaneously within a common framework.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Is automatic imitation a specialized form of stimulus–response compatibility? Dissociating imitative and spatial compatibilities

In recent years research on automatic imitation has received considerable attention because it represents an experimental platform for investigating a number of inter-related theories suggesting that the perception of action automatically activates corresponding motor programs. A key debate within this research centers on whether automatic imitation is any different than other long-term S-R associations, such as spatial stimulus-response compatibility. One approach to resolving this issue is to examine whether automatic imitation shows similar response characteristics as other classes of stimulus-response compatibility. This hypothesis was tested by comparing imitative and spatial compatibility effects with a two alternative forced-choice stimulus-response compatibility paradigm and two tasks: one that involved selecting a response to the stimulus (S-R) and one that involved selecting a response to the opposite stimulus (OS-R), i.e., the one not presented. The stimulus for both tasks was a left or right hand with either the index or middle finger tapping down. Speeded responses were performed with the index or middle finger of the right hand in response to the finger identity or the left-right spatial position of the fingers. Based on previous research and a connectionist model, we predicted standard compatibility effects for both spatial and imitative compatibility in the S-R task, and a reverse compatibility effect for spatial compatibility but not for imitative compatibility in the OS-R task. The results from the mean response times, mean percentage of errors, and response time distributions all converged to support these predictions. A second noteworthy result was that the recoding of the finger identity in the OS-R task required significantly more time than the recoding of the left-right spatial position, but the encoding time for the two stimuli in the S-R task was equivalent. In sum, this evidence suggests that the processing of spatial and imitative compatibility is dissociable with regard to two different processes in dual processing models of stimulus-response compatibility

Building a community to engineer synthetic cells and organelles from the bottom-up

Employing concepts from physics, chemistry and bioengineering, 'learning-by-building' approaches are becoming increasingly popular in the life sciences, especially with researchers who are attempting to engineer cellular life from scratch. The SynCell2020/21 conference brought together researchers from different disciplines to highlight progress in this field, including areas where synthetic cells are having socioeconomic and technological impact. Conference participants also identified the challenges involved in designing, manipulating and creating synthetic cells with hierarchical organization and function. A key conclusion is the need to build an international and interdisciplinary research community through enhanced communication, resource-sharing, and educational initiatives

Constraint solving in non-permutative nominal abstract syntax

Nominal abstract syntax is a popular first-order technique for encoding, and reasoning about, abstract syntax involving binders. Many of its applications involve constraint solving. The most commonly used constraint solving algorithm over nominal abstract syntax is the Urban-Pitts-Gabbay nominal unification algorithm, which is well-behaved, has a well-developed theory and is applicable in many cases. However, certain problems require a constraint solver which respects the equivariance property of nominal logic, such as Cheney's equivariant unification algorithm. This is more powerful but is more complicated and computationally hard. In this paper we present a novel algorithm for solving constraints over a simple variant of nominal abstract syntax which we call non-permutative. This constraint problem has similar complexity to equivariant unification but without many of the additional complications of the equivariant unification term language. We prove our algorithm correct, paying particular attention to issues of termination, and present an explicit translation of name-name equivariant unification problems into non-permutative constraints