Fundamental constraints to the logic of living systems.

It has been argued that the historical nature of evolution makes it a highly path-dependent process. Under this view, the outcome of evolutionary dynamics could have resulted in organisms with different forms and functions. At the same time, there is ample evidence that convergence and constraints strongly limit the domain of the potential design principles that evolution can achieve.

Thermodynamic dissipation does not bound replicator growth and decay rates.

In a well-known paper, Jeremy England derived a bound on the free energy dissipated by a self-replicating system [J. L. England, "Statistical physics of self-replication," J.

Partial Information Decomposition: Redundancy as Information Bottleneck.

The partial information decomposition (PID) aims to quantify the amount of redundant information that a set of sources provides about a target. Here, we show that this goal can be formulated as a type of information bottleneck (IB) problem, termed the "redundancy bottleneck" (RB). The RB formalizes a tradeoff between prediction and compression: it extracts information from the sources that best predict the target, without revealing which source provided the 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 to a single output y. In prior work, Zurek proposed that this cost was given by K(x|y), the conditional Kolmogorov complexity of x given y (up to an additive constant that 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).

Thermodynamic Bound on the Asymmetry of Cross-Correlations.

The principle of microscopic reversibility says that, in equilibrium, two-time cross-correlations are symmetric under the exchange of observables. Thus, the asymmetry of cross-correlations is a fundamental, measurable, and often-used statistical signature of deviation from equilibrium. Here we find a simple and universal inequality that bounds the magnitude of asymmetry by the cycle affinity, i.

Computational capacity of LRC, memristive, and hybrid reservoirs.

Reservoir computing is a machine learning paradigm that uses a high-dimensional dynamical system, or reservoir, to approximate and predict time series data. The scale, speed, and power usage of reservoir computers could be enhanced by constructing reservoirs out of electronic circuits, and several experimental studies have demonstrated promise in this direction. However, designing quality reservoirs requires a precise understanding of how such circuits process and store information.

A Novel Approach to the Partial Information Decomposition.

We consider the "partial information decomposition" (PID) problem, which aims to decompose the information that a set of source random variables provide about a target random variable into separate redundant, synergistic, union, and unique components. In the first part of this paper, we propose a general framework for constructing a multivariate PID. Our framework is defined in terms of a formal analogy with intersection and union from set theory, along with an ordering relation which specifies when one information source is more informative than another.

Dependence of integrated, instantaneous, and fluctuating entropy production on the initial state in quantum and classical processes.

We consider the additional entropy production (EP) incurred by a fixed quantum or classical process on some initial state ρ, above the minimum EP incurred by the same process on any initial state. We show that this additional EP, which we term the "mismatch cost of ρ," has a universal information-theoretic form: it is given by the contraction of the relative entropy between ρ and the least-dissipative initial state φ over time. We derive versions of this result for integrated EP incurred over the course of a process, for trajectory-level fluctuating EP, and for instantaneous EP rate.

Entropy production given constraints on the energy functions.

We consider the problem of driving a finite-state classical system from some initial distribution p to some final distribution p^{'} with vanishing entropy production (EP), under the constraint that the driving protocols can only use some limited set of energy functions E. Assuming no other constraints on the driving protocol, we derive a simple condition that guarantees that such a transformation can be carried out, which is stated in terms of the smallest probabilities in {p,p^{'}} and a graph-theoretic property defined in terms of E. Our results imply that a surprisingly small amount of control over the energy function is sufficient (in particular, any transformation p→p^{'} can be carried out as soon as one can control some one-dimensional parameter of the energy function, e.

Decomposing information into copying versus transformation.

In many real-world systems, information can be transmitted in two qualitatively different ways: by or by . occurs when messages are transmitted without modification, e.g.

Dynamics of beneficial epidemics.

Pathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models.

Publisher Correction: A space-time tradeoff for implementing a function with master equation dynamics.

The original version of the Supplementary Information associated with this Article contained an error throughout in which all inline references to Theorems, Definitions and Lemmas given in the main Article were incorrectly given as '??'. The HTML has been updated to include a corrected version of the Supplementary Information.

A space-time tradeoff for implementing a function with master equation dynamics.

Master equations are commonly used to model the dynamics of physical systems, including systems that implement single-valued functions like a computer's update step. However, many such functions cannot be implemented by any master equation, even approximately, which raises the question of how they can occur in the real world. Here we show how any function over some "visible" states can be implemented with master equation dynamics-if the dynamics exploits additional, "hidden" states at intermediate times.

A spectrum of routing strategies for brain networks.

Communication of signals among nodes in a complex network poses fundamental problems of efficiency and cost. Routing of messages along shortest paths requires global information about the topology, while spreading by diffusion, which operates according to local topological features, is informationally "cheap" but inefficient. We introduce a stochastic model for network communication that combines local and global information about the network topology to generate biased random walks on the network.

Semantic information, autonomous agency and non-equilibrium statistical physics.

Shannon information theory provides various measures of so-called syntactic information, which reflect the amount of statistical correlation between systems. By contrast, the concept of 'semantic information' refers to those correlations which carry significance or 'meaning' for a given system. Semantic information plays an important role in many fields, including biology, cognitive science and philosophy, and there has been a long-standing interest in formulating a broadly applicable and formal theory of semantic information.

The Minor fall, the Major lift: inferring emotional valence of musical chords through lyrics.

We investigate the association between musical chords and lyrics by analysing a large dataset of user-contributed guitar tablatures. Motivated by the idea that the emotional content of chords is reflected in the words used in corresponding lyrics, we analyse associations between lyrics and chord categories. We also examine the usage patterns of chords and lyrics in different musical genres, historical eras and geographical regions.

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).

Extraction of pharmacokinetic evidence of drug-drug interactions from the literature.

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from published literature and clinical databases. Though DDI is investigated in domains ranging in scale from intracellular biochemistry to human populations, literature mining has not been used to extract specific types of experimental evidence, which are reported differently for distinct experimental goals.

Multi-scale integration and predictability in resting state brain activity.

The human brain displays heterogeneous organization in both structure and function. Here we develop a method to characterize brain regions and networks in terms of information-theoretic measures. We look at how these measures scale when larger spatial regions as well as larger connectome sub-networks are considered.

Neural correlates of apparent motion perception of impoverished facial stimuli: a comparison of ERP and ERSP activity.

Our brains readily decode human movements, as shown by neural responses to face and body motion. N170 event-related potentials (ERPs) are earlier and larger to mouth opening movements relative to closing in both line-drawn and natural faces, and gaze aversions relative to direct gaze in natural faces (Puce and Perrett, 2003; Puce et al., 2000).

Classification of protein-protein interaction full-text documents using text and citation network features.

We participated (as Team 9) in the Article Classification Task of the Biocreative II.5 Challenge: binary classification of full-text documents relevant for protein-protein interaction. We used two distinct classifiers for the online and offline challenges: 1) the lightweight Variable Trigonometric Threshold (VTT) linear classifier we successfully introduced in BioCreative 2 for binary classification of abstracts and 2) a novel Naive Bayes classifier using features from the citation network of the relevant literature.