Minimax Structured Normal Means Inference

We provide a unified treatment of a broad class of noisy structure recovery problems, known as structured normal means problems. In this setting, the goal is to identify, from a finite collection of Gaussian distributions with different means, the distribution that produced some observed data. Recent work has studied several special cases including sparse vectors, biclusters, and graph-based structures. We establish nearly matching upper and lower bounds on the minimax probability of error for any structured normal means problem, and we derive an optimality certificate for the maximum likelihood estimator, which can be applied to many instantiations. We also consider an experimental design setting, where we generalize our minimax bounds and derive an algorithm for computing a design strategy with a certain optimality property. We show that our results give tight minimax bounds for many structure recovery problems and consider some consequences for interactive sampling

The stochastic behavior of a molecular switching circuit with feedback

Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists of a kinase and phosphatase acting on multiple sites of a substrate that, contingent on its modification state, catalyzes its own phosphorylation and, in a symmetric scenario, dephosphorylation. The symmetric case is viewed as a cartoon of conflicting feedback that could result from antagonistic pathways impinging on the state of a shared component. Results: Multisite phosphorylation is sufficient for bistable behavior under feedback even when catalysis is linear in substrate concentration, which is the case we consider. We compute the phase diagram, fluctuation spectrum and large-deviation properties related to switch memory within a statistical mechanics framework. Bistability occurs as either a first-order or second-order non-equilibrium phase transition, depending on the network symmetries and the ratio of phosphatase to kinase numbers. In the second-order case, the circuit never leaves the bistable regime upon increasing the number of substrate molecules at constant kinase to phosphatase ratio. Conclusions: The number of substrate molecules is a key parameter controlling both the onset of the bistable regime, fluctuation intensity, and the residence time in a switched state. The relevance of the concept of memory depends on the degree of switch symmetry, as memory presupposes information to be remembered, which is highest for equal residence times in the switched states. Reviewers: This article was reviewed by Artem Novozhilov (nominated by Eugene Koonin), Sergei Maslov, and Ned Wingreen.Comment: Version published in Biology Direct including reviewer comments and author responses, 28 pages, 7 figure

An alternate view of complexity in k-SAT problems

The satisfiability threshold for constraint satisfaction problems is that value of the ratio of constraints (or clauses) to variables, above which the probability that a random instance of the problem has a solution is zero in the large system limit. Two different approaches to obtaining this threshold have been discussed in the literature - using first or second-moment methods which give rigorous bounds or using the non-rigorous but powerful replica-symmetry breaking (RSB) approach, which gives very accurate predictions on random graphs. In this paper, we lay out a different route to obtaining this threshold on a Bethe lattice. We need make no assumptions about the solution-space structure, a key assumption in the RSB approach. Despite this, our expressions and threshold values exactly match the best predictions of the cavity method under the 1-RSB assumption. Our method hence provides alternate interpretations as well as motivations for the key equations in the RSB approach.Comment: 5 pages, 3 figures, typos correcte

An analytical framework for the performance evaluation of proximity-aware structured overlays

In this paper, we present an analytical study of proximity-aware structured peer-to-peer networks under churn. We use a master-equation-based approach, which is used traditionally in non-equilibrium statistical mechanics to describe steady-state or transient phenomena. In earlier work we have demonstrated that this methodology is in fact also well suited to describing structured overlay networks under churn, by showing how we can accurately predict the average number of hops taken by a lookup, for any value of churn, for the Chord system. In this paper, we extend the analysis so as to also be able to predict lookup latency, given an average latency for the links in the network. Our results show that there exists a region in the parameter space of the model, depending on churn, the number of nodes, the maintenance rates and the delays in the network, when the network cannot function as a small world graph anymore, due to the farthest connections of a node always being wrong or dead. We also demonstrate how it is possible to analyse proximity neighbour selection or proximity route selection within this formalism