Dependence of dissipation on the initial distribution over states

We analyze how the amount of work dissipated by a fixed nonequilibrium process depends on the initial distribution over states. Specifically, we compare the amount of dissipation when the process is used with some specified initial distribution to the minimal amount of dissipation possible for any initial distribution. We show that the difference between those two amounts of dissipation is given by a simple information-theoretic function that depends only on the initial and final state distributions. Crucially, this difference is independent of the details of the process relating those distributions. We then consider how dissipation depends on the initial distribution for a 'computer', i.e., a nonequilibrium process whose dynamics over coarse-grained macrostates implement some desired input-output map. We show that our results still apply when stated in terms of distributions over the computer's coarse-grained macrostates. This can be viewed as a novel thermodynamic cost of computation, reflecting changes in the distribution over inputs rather than the logical dynamics of the computation

Estimating Mixture Entropy with Pairwise Distances

Mixture distributions arise in many parametric and non-parametric settings -- for example, in Gaussian mixture models and in non-parametric estimation. It is often necessary to compute the entropy of a mixture, but, in most cases, this quantity has no closed-form expression, making some form of approximation necessary. We propose a family of estimators based on a pairwise distance function between mixture components, and show that this estimator class has many attractive properties. For many distributions of interest, the proposed estimators are efficient to compute, differentiable in the mixture parameters, and become exact when the mixture components are clustered. We prove this family includes lower and upper bounds on the mixture entropy. The Chernoff $\alpha$-divergence gives a lower bound when chosen as the distance function, with the Bhattacharyya distance providing the tightest lower bound for components that are symmetric and members of a location family. The Kullback-Leibler divergence gives an upper bound when used as the distance function. We provide closed-form expressions of these bounds for mixtures of Gaussians, and discuss their applications to the estimation of mutual information. We then demonstrate that our bounds are significantly tighter than well-known existing bounds using numeric simulations. This estimator class is very useful in optimization problems involving maximization/minimization of entropy and mutual information, such as MaxEnt and rate distortion problems.Comment: Corrects several errata in published version, in particular in Section V (bounds on mutual information

Generalized Zurek's bound on the cost of an individual classical or quantum computation

We consider the minimal thermodynamic cost of an individual computation, where a single input $x$ is mapped into a single output $y$. In prior work, Zurek proposed that this cost was given by $K(x\vert y)$, the conditional Kolmogorov complexity of $x$ given $y$ (up to an additive constant which does not depend on $x$ or $y$). However, this result was derived from an informal argument, applied only to deterministic computations, and had an arbitrary dependence on the choice of protocol (via the additive constant). Here we use stochastic thermodynamics to derive a generalized version of Zurek's bound from a rigorous Hamiltonian formulation. Our bound applies to all quantum and classical processes, whether noisy or deterministic, and it explicitly captures the dependence on the protocol. We show that $K(x\vert y)$ is a minimal cost of mapping $x$ to $y$ that must be paid using some combination of heat, noise, and protocol complexity, implying a tradeoff between these three resources. Our result is a kind of ``algorithmic fluctuation theorem'' with implications for the relationship between the Second Law and the Physical Church-Turing thesis

Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries. Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.Comment: Pacific Symposium on Biocomputing, 201

Caveats for information bottleneck in deterministic scenarios

Information bottleneck (IB) is a method for extracting information from one random variable $X$ that is relevant for predicting another random variable $Y$. To do so, IB identifies an intermediate "bottleneck" variable $T$ that has low mutual information $I(X;T)$ and high mutual information $I(Y;T)$. The "IB curve" characterizes the set of bottleneck variables that achieve maximal $I(Y;T)$ for a given $I(X;T)$, and is typically explored by maximizing the "IB Lagrangian", $I(Y;T) - \beta I(X;T)$. In some cases, $Y$ is a deterministic function of $X$, including many classification problems in supervised learning where the output class $Y$ is a deterministic function of the input $X$. We demonstrate three caveats when using IB in any situation where $Y$ is a deterministic function of $X$: (1) the IB curve cannot be recovered by maximizing the IB Lagrangian for different values of $\beta$; (2) there are "uninteresting" trivial solutions at all points of the IB curve; and (3) for multi-layer classifiers that achieve low prediction error, different layers cannot exhibit a strict trade-off between compression and prediction, contrary to a recent proposal. We also show that when $Y$ is a small perturbation away from being a deterministic function of $X$, these three caveats arise in an approximate way. To address problem (1), we propose a functional that, unlike the IB Lagrangian, can recover the IB curve in all cases. We demonstrate the three caveats on the MNIST dataset

Nonlinear Information Bottleneck

Information bottleneck (IB) is a technique for extracting information in one random variable $X$ that is relevant for predicting another random variable $Y$. IB works by encoding $X$ in a compressed "bottleneck" random variable $M$ from which $Y$ can be accurately decoded. However, finding the optimal bottleneck variable involves a difficult optimization problem, which until recently has been considered for only two limited cases: discrete $X$ and $Y$ with small state spaces, and continuous $X$ and $Y$ with a Gaussian joint distribution (in which case optimal encoding and decoding maps are linear). We propose a method for performing IB on arbitrarily-distributed discrete and/or continuous $X$ and $Y$, while allowing for nonlinear encoding and decoding maps. Our approach relies on a novel non-parametric upper bound for mutual information. We describe how to implement our method using neural networks. We then show that it achieves better performance than the recently-proposed "variational IB" method on several real-world datasets

Modularity and the spread of perturbations in complex dynamical systems

We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize 'perturbation modularity', defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the 'Markov stability' method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., 'relevance networks' or 'functional networks'). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously-coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems

The Revival of the Russian Literary Avantgarde

This study is devoted to the authors who initiated the revival of the Russian avantgarde tradition, which had been brutally suppressed by the Soviet authorities in the mid- 1930s. The revival of this tradition took place in the literary underground, where writers who endeavored to fulfil this challenging task largely remained until the collapse of the Soviet regime. Most of them emerged from obscurity only at the beginning of the 1990s, which explains why their dramatic and fascinating history has been so little examined by scholars. Although the situation has changed significantly in the last decade, during which some insightful studies have appeared in both Russia and the West, the subject obviously requires more thorough and systematic exploration. This book aims to narrow important gaps in the scholarship on the Russian literary avantgarde during its least investigated period