"In this paper we use the Birkhoff–von Neumann decomposition of the diffusion kernel to compute a polytopal measure of graph complexity. We decompose the diffusion kernel into a series of weighted Birkhoff combinations and compute the entropy associated with the weighting proportions (polytopal complexity). The maximum entropy Birkhoff combination can be expressed in terms of matrix permanents. This allows us to introduce a phase-transition principle that links our definition of polytopal complexity to the heat flowing through the network at a given diffusion time. The result is an efficiently computed complexity measure, which we refer to as flow complexity. Moreover, the flow complexity measure allows us to analyze graphs and networks in terms of the thermodynamic depth. We compare our method with three alternative methods described in the literature (Estrada's heterogeneity index, the Laplacian energy, and the von Neumann entropy). Our study is based on 217 protein-protein interaction (PPI) networks including histidine kinases from several species of bacteria. We find a correlation between structural complexity and phylogeny (more evolved species have statistically more complex PPIs). Although our methods outperform the alternatives, we find similarities with Estrada's heterogeneity index in terms of network size independence and predictive power."

"A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an (implicit) model of the environmental variables. The system's state retains information about past environmental fluctuations, and a fraction of this information is predictive of future ones. The remaining nonpredictive information reflects model complexity that does not improve predictive power, and represents the ineffectiveness of the model. We expose the fundamental equivalence between this model inefficiency and thermodynamic inefficiency, measured by the energy dissipated during the interaction between system and environment. Our results hold arbitrarily far from thermodynamic equilibrium and are applicable to a wide range of systems, including biomolecular machines. They highlight a profound connection between the effective use of information and efficient thermodynamic operation: any system constructed to keep memory about its environment and to operate energetically efficiently has to be predictive."

--- Hrmph, time to send some copies of old papers.

"Effective complexity measures the information content of the regularities of an object. It has been introduced by M. Gell-Mann and S. Lloyd to avoid some of the disadvantages of Kolmogorov complexity, also known as algorithmic information content. In this paper, we give a precise formal definition of effective complexity and rigorous proofs of its basic properties. In particular, we show that incompressible binary strings are effectively simple, and we prove the existence of strings that have effective complexity close to their lengths. Furthermore, we show that effective complexity is related to Bennett's logical depth: If the effective complexity of a string $x$ exceeds a certain explicit threshold then that string must have astronomically large depth; otherwise, the depth can be arbitrarily small."

"We study two measures of the complexity of heterogeneous extended systems, taking random Boolean networks as prototypical cases. A measure defined by Shalizi et al. for cellular automata, based on a criterion for optimal statistical prediction [1], does not distinguish between the spatial inhomogeneity of the ordered phase and the dynamical inhomogeneity of the disordered phase. A modification in which complexities of individual nodes are calculated yields vanishing complexity values for networks in the ordered and critical regimes and for highly disordered networks, peaking somewhere in the disordered regime. Individual nodes with high complexity are the ones that pass the most information from the past to the future, a quantity that depends in a nontrivial way on both the Boolean function of a given node and its location within the network."

"We treat observable operator models (OOM) and their non-commutative generalisation, which we call NC-OOMs. A natural characteristic of a stochastic process in the context of classical OOM theory is the process dimension. We investigate its properties within the more general formulation, which allows to consider process dimension as a measure of complexity of non-commutative processes: We prove lower semi-continuity, and derive an ergodic decomposition formula. Further, we obtain results on the close relationship between the canonical OOM and the concept of causal states which underlies the definition of statistical complexity. In particular, the topological statistical complexity, i.e. the logarithm of the number of causal states, turns out to be an upper bound to the logarithm of process dimension."

Unless this has changed drastically from the version Karoline showed me in Bristol in October.

"We introduce an information theoretic measure of statistical structure, called 'binding information', for sets of random variables, and compare it with several previously proposed measures including excess entropy, Bialek et al.'s predictive information, and the multi-information. We derive some of the properties of the binding information, particularly in relation to the multi-information, and show that, for finite sets of binary random variables, the processes which maximises binding information are the 'parity' processes. Finally we discuss some of the implications this has for the use of the binding information as a measure of complexity."

"We evaluate new complexity measures on the symbolic dynamics of coupled tent maps and cellular automata. These measures quantify complexity in terms of $k$-th order statistical dependencies that cannot be reduced to interactions between $k-1$ units. We demonstrate that these measures are able to identify complex dynamical regimes."

My reaction to this must, I imagine, be a little bit like how a proud parent feels when they hear from someone else about their child doing something worthwhile.

"We evaluate information-theoretic quantities that quantify complexity in terms of kth-order statistical dependences that cannot be reduced to interactions among k−1 random variables. Using symbolic dynamics of coupled maps and cellular automata as model systems, we demonstrate that these measures are able to identify complex dynamical regimes."

The abstract makes this sound closely akin to good old-fashioned Lloyd-Pagels thermodynamic depth.

*dramatic sigh* Shalizi and Moore (2003) *dramatic sigh*

How much information (in the Fisher sense) does the present state of a recurrent dynamical network retain about the history of its inputs? All, or almost all, done for linear-Gaussian systems, but numerical results for nonlinear, non-Gaussian systems would be straightforward in principle.

"We obtain an index of the complexity of a random sequence by allowing the role of the measure in classical probability theory to be played by a function we call the generating mechanism. Typically, this generating mechanism will be a finite automata. We generate a set of biased sequences by applying a finite state automata with a specified number, $m$, of states to the set of all binary sequences. Thus we can index the complexity of our random sequence by the number of states of the automata. We detail optimal algorithms to predict sequences generated in this way."