How biased are maximum entropy models?

Maximum entropy models have become popular statistical models in neuroscience and other areas in biology, and can be useful tools for obtaining estimates of mutual information in biological systems. However, maximum entropy models fit to small data sets can be subject to sampling bias; i.e. the true entropy of the data can be severely underestimated. Here we study the sampling properties of estimates of the entropy obtained from maximum entropy models. We show that if the data is generated by a distribution that lies in the model class, the bias is equal to the number of parameters divided by twice the number of observations. However, in practice, the true distribution is usually outside the model class, and we show here that this misspecification can lead to much larger bias. We provide a perturbative approximation of the maximally expected bias when the true model is out of model class, and we illustrate our results using numerical simulations of an Ising model; i.e. the second-order maximum entropy distribution on binary data.

CCharPPI web server: computational characterization of protein–protein interactions from structure

The atomic structures of protein–protein interactions are central to understanding their role in biological systems, and a wide variety of biophysical functions and potentials have been developed for their characterization and the construction of predictive models. These tools are scattered across a multitude of stand-alone programs, and are often available only as model parameters requiring reimplementation. This acts as a significant barrier to their widespread adoption. CCharPPI integrates many of these tools into a single web server. It calculates up to 108 parameters, including models of electrostatics, desolvation and hydrogen bonding, as well as interface packing and complementarity scores, empirical potentials at various resolutions, docking potentials and composite scoring functions.The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Unions Seventh Framework Programme (FP7/2007- 2013) under REA grant agreement PIEF-GA-2012-327899 and grant BIO2013-48213-R from Spanish Ministry of Economy and Competitiveness.Peer ReviewedPostprint (published version

Hard Matching for Boosted Tops at Two Loops

Cross sections for top quarks provide very interesting physics opportunities, being both sensitive to new physics and also perturbatively tractable due to the large top quark mass. Rigorous factorization theorems for top cross sections can be derived in several kinematic scenarios, including the boosted regime in the peak region that we consider here. In the context of the corresponding factorization theorem for $e^+e^-$ collisions we extract the last missing ingredient that is needed to evaluate the cross section differential in the jet-mass at two-loop order, namely the matching coefficient at the scale $\mu\simeq m_t$. Our extraction also yields the final ingredients needed to carry out logarithmic resummation at next-to-next-to-leading logarithmic order (or N$^3$LL if we ignore the missing 4-loop cusp anomalous dimension). This coefficient exhibits an amplitude level rapidity logarithm starting at $\mathcal{O}(\alpha_s^2)$ due to virtual top quark loops, which we treat using rapidity renormalization group (RG) evolution. Interestingly, this rapidity RG evolution appears in the matching coefficient between two effective theories around the heavy quark mass scale $\mu\simeq m_t$.Comment: 35 pages, 3 figures, v2: added extraction of 3-loop anon. dimension, journal versio

Open-Loop Spatial Multiplexing and Diversity Communications in Ad Hoc Networks

This paper investigates the performance of open-loop multi-antenna point-to-point links in ad hoc networks with slotted ALOHA medium access control (MAC). We consider spatial multiplexing transmission with linear maximum ratio combining and zero forcing receivers, as well as orthogonal space time block coded transmission. New closed-form expressions are derived for the outage probability, throughput and transmission capacity. Our results demonstrate that both the best performing scheme and the optimum number of transmit antennas depend on different network parameters, such as the node intensity and the signal-to-interference-and-noise ratio operating value. We then compare the performance to a network consisting of single-antenna devices and an idealized fully centrally coordinated MAC. These results show that multi-antenna schemes with a simple decentralized slotted ALOHA MAC can outperform even idealized single-antenna networks in various practical scenarios.Comment: 51 pages, 19 figures, submitted to IEEE Transactions on Information Theor

Factorization Approach for Top Mass Reconstruction at High Energies

Using effective theories for jets and heavy quarks it is possible to prove that the double differential top-antitop invariant mass distribution for the process $e^+e^-\to t\bar t$ in the resonance region for c.m. energies $Q$ much larger than the top mass can factorized into perturbatively computable hard coefficients and jet functions and a non-perturbative soft function. For invariant mass prescriptions based on hemispheres defined with respect to the thrust axis the soft function can be extracted from massless jet event shape distributions. This approach allows in principle for top mass determinations without uncertainties from hadronization using the reconstruction method and to quantify the top mass scheme dependence of the measured top quark mass value.Comment: Talk given at 2007 International Linear Collider Workshop (LCWS07 and ILC07), Hamburg, Germany, 30 May - 3 Jun 2007, 7 pages, 4 figures, title modifie

Infrared Renormalization Group Flow for Heavy Quark Masses

A short-distance heavy quark mass depends on two parameters, the renormalization scale mu controlling the absorption of ultraviolet fluctuations into the mass, and a scale R controlling the absorption of infrared fluctuations. 1/R can be thought of as the radius for perturbative corrections that build up the mass beyond its point-like definition in the pole scheme. Treating R as a variable gives a renormalization group equation. We argue that the sign of this anomalous dimension is universal: increasing R to add IR modes decreases m(R). The flow improves the stability of conversions between mass schemes, allowing us to avoid large logs and the renormalon. The flow in R can be used to study IR renormalons without using bubble chains, and we use it to determine the coefficient of the LambdaQCD renormalon ambiguity of the pole mass with a convergent sum-rule.Comment: 4 pages, 2 figures, Added explicit result for the top MSbar mass with uncertaintie

Laterally-Coupled Dual-Grating Distributed Feedback Lasers for Generating Mode-Beat Terahertz Signals

We present a laterally-coupled AlGaInAs/InP DFB laser emitting two longitudinal modes simultaneously within the same cavity and integrated with EAM. A stable 0.82 THz beating signal was observed over a wide range of bias parameters