What determines the specificity of conflict adaptation? A review, critical analysis, and proposed synthesis

Over the past decade, many cognitive control researchers have studied to what extent adaptations to conflict are domain-general or rather specific, mostly by testing whether or not the congruency sequence effect (CSE) transfers across different conditions (e.g., conflict type, task sets, contexts, et cetera). The CSE refers to the observation that congruency effects in conflict tasks tend to be reduced following incongruent relative to following congruent trials, and is considered a prime measure of cognitive control. By investigating the transfer of this CSE across different conflict types, tasks, or contexts, researchers made several inferences about the scope of cognitive control. This method gained popularity during the last few years, spawning an interesting, yet seemingly inconsistent set of results. Consequently, these observations gave rise to a number of equally divergent theories about the determinants and scope of conflict adaptation. In this review, we offer a systematic overview of these past studies, as well as an evaluation of the theories that have been put forward to account for the results. Finally, we propose an integration of these various theoretical views in a unifying framework that centers on the role of context (dis)similarity. This framework allows us to generate new predictions about the relation between task or context similarity and the scope of cognitive control. Specifically, while most theories imply that increasing contextual differences will result in reduced transfer of the CSE, we propose that context similarity and across-context control follow a U-shaped function instead

Online Discrimination of Nonlinear Dynamics with Switching Differential Equations

How to recognise whether an observed person walks or runs? We consider a dynamic environment where observations (e.g. the posture of a person) are caused by different dynamic processes (walking or running) which are active one at a time and which may transition from one to another at any time. For this setup, switching dynamic models have been suggested previously, mostly, for linear and nonlinear dynamics in discrete time. Motivated by basic principles of computations in the brain (dynamic, internal models) we suggest a model for switching nonlinear differential equations. The switching process in the model is implemented by a Hopfield network and we use parametric dynamic movement primitives to represent arbitrary rhythmic motions. The model generates observed dynamics by linearly interpolating the primitives weighted by the switching variables and it is constructed such that standard filtering algorithms can be applied. In two experiments with synthetic planar motion and a human motion capture data set we show that inference with the unscented Kalman filter can successfully discriminate several dynamic processes online

Learning hard quantum distributions with variational autoencoders

Studying general quantum many-body systems is one of the major challenges in modern physics because it requires an amount of computational resources that scales exponentially with the size of the system.Simulating the evolution of a state, or even storing its description, rapidly becomes intractable for exact classical algorithms. Recently, machine learning techniques, in the form of restricted Boltzmann machines, have been proposed as a way to efficiently represent certain quantum states with applications in state tomography and ground state estimation. Here, we introduce a new representation of states based on variational autoencoders. Variational autoencoders are a type of generative model in the form of a neural network. We probe the power of this representation by encoding probability distributions associated with states from different classes. Our simulations show that deep networks give a better representation for states that are hard to sample from, while providing no benefit for random states. This suggests that the probability distributions associated to hard quantum states might have a compositional structure that can be exploited by layered neural networks. Specifically, we consider the learnability of a class of quantum states introduced by Fefferman and Umans. Such states are provably hard to sample for classical computers, but not for quantum ones, under plausible computational complexity assumptions. The good level of compression achieved for hard states suggests these methods can be suitable for characterising states of the size expected in first generation quantum hardware.Comment: v2: 9 pages, 3 figures, journal version with major edits with respect to v1 (rewriting of section "hard and easy quantum states", extended discussion on comparison with tensor networks

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog