Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Weak force detection with superposed coherent states

We investigate the utility of non classical states of simple harmonic oscillators, particularly a superposition of coherent states, for sensitive force detection. We find that like squeezed states a superposition of coherent states allows displacement measurements at the Heisenberg limit. Entangling many superpositions of coherent states offers a significant advantage over a single mode superposition states with the same mean photon number.Comment: 6 pages, no figures: New section added on entangled resources. Changes to discussions and conclusio

Bures Metrics for Certain High-Dimensional Quantum Systems

Hubner's formula for the Bures (statistical distance) metric is applied to both a one-parameter and a two-parameter series (n=2,...,7) of sets of 2^n x 2^n density matrices. In the doubly-parameterized series, the sets are comprised of the n-fold tensor products --- corresponding to n independent, identical quantum systems --- of the 2 x 2 density matrices with real entries. The Gaussian curvatures of the corresponding Bures metrics are found to be constants (4/n). In the second series of 2^n x 2^n density matrices studied, the singly-parameterized sets are formed --- following a study of Krattenthaler and Slater --- by averaging with respect to a certain Gibbs distribution, the n-fold tensor products of the 2 x 2 density matrices with complex entries. For n = 100, we are also able to compute the Bures distance between two arbitrary (not necessarily neighboring) density matrices in this particular series, making use of the eigenvalue formulas of Krattenthaler and Slater, together with the knowledge that the 2^n x 2^n density matrices in this series commute.Comment: 8 pages, LaTeX, 4 postscript figures, minor changes, to appear in Physics Letters

Quantum teleportation with squeezed vacuum states

We show how the partial entanglement inherent in a two mode squeezed vacuum state admits two different teleportation protocols. These two protocols refer to the different kinds of joint measurements that may be made by the sender. One protocol is the recently implemented quadrature phase approach of Braunstein and Kimble[Phys. Rev. Lett.{\bf 80}, 869 (1998)]. The other is based on recognising that a two mode squeezed vacuum state is also entangled with respect to photon number difference and phase sum. We show that this protocol can also realise teleportation, however limitations can arise due to the fact that the photon number spectrum is bounded from below by zero. Our examples show that a given entanglement resource may admit more than a single teleportation protocol and the question then arises as to what is the optimum protocol in the general case

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

A Bayesian Variable Selection Approach to Major League Baseball Hitting Metrics

Numerous statistics have been proposed for the measure of offensive ability in major league baseball. While some of these measures may offer moderate predictive power in certain situations, it is unclear which simple offensive metrics are the most reliable or consistent. We address this issue with a Bayesian hierarchical model for variable selection to capture which offensive metrics are most predictive within players across time. Our sophisticated methodology allows for full estimation of the posterior distributions for our parameters and automatically adjusts for multiple testing, providing a distinct advantage over alternative approaches. We implement our model on a set of 50 different offensive metrics and discuss our results in the context of comparison to other variable selection techniques. We find that 33/50 metrics demonstrate signal. However, these metrics are highly correlated with one another and related to traditional notions of performance (e.g., plate discipline, power, and ability to make contact)

Bures distance between two displaced thermal states

The Bures distance between two displaced thermal states and the corresponding geometric quantities (statistical metric, volume element, scalar curvature) are computed. Under nonunitary (dissipative) dynamics, the statistical distance shows the same general features previously reported in the literature by Braunstein and Milburn for two--state systems. The scalar curvature turns out to have new interesting properties when compared to the curvature associated with squeezed thermal states.Comment: 3 pages, RevTeX, no figure

Gene-network inference by message passing

The inference of gene-regulatory processes from gene-expression data belongs to the major challenges of computational systems biology. Here we address the problem from a statistical-physics perspective and develop a message-passing algorithm which is able to infer sparse, directed and combinatorial regulatory mechanisms. Using the replica technique, the algorithmic performance can be characterized analytically for artificially generated data. The algorithm is applied to genome-wide expression data of baker's yeast under various environmental conditions. We find clear cases of combinatorial control, and enrichment in common functional annotations of regulated genes and their regulators.Comment: Proc. of International Workshop on Statistical-Mechanical Informatics 2007, Kyot

Qubit metrology and decoherence

Quantum properties of the probes used to estimate a classical parameter can be used to attain accuracies that beat the standard quantum limit. When qubits are used to construct a quantum probe, it is known that initializing $n$ qubits in an entangled "cat state," rather than in a separable state, can improve the measurement uncertainty by a factor of $1/\sqrt{n}$. We investigate how the measurement uncertainty is affected when the individual qubits in a probe are subjected to decoherence. In the face of such decoherence, we regard the rate $R$ at which qubits can be generated and the total duration $\tau$ of a measurement as fixed resources, and we determine the optimal use of entanglement among the qubits and the resulting optimal measurement uncertainty as functions of $R$ and $\tau$.Comment: 24 Pages, 3 Figure

Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems

We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above the critical value d_c=z, kinetics are always mean field (MF). Below d_c, the density n_t initially follows MF decay, n_0 - n_t ~ n_0^2 Q t. A 2-body diffusion-controlled regime follows for strongly reactive systems (Q>Qstar ~ n_0^{(z-d)/d}) with n_0 - n_t ~ n_0^2 x_t^d. For Q<Qstar, MF kinetics persist, with n_t ~ 1/Qt. In all cases n_t ~ 1/x_t^d at the longest times. Our analysis avoids decoupling approximations by instead postulating weak physically motivated bounds on correlation functions.Comment: 10 pages, 1 figure, uses bulk2.sty, minor changes, submitted to Europhysics Letter