Hamiltonian Monte Carlo Without Detailed Balance

We present a method for performing Hamiltonian Monte Carlo that largely eliminates sample rejection for typical hyperparameters. In situations that would normally lead to rejection, instead a longer trajectory is computed until a new state is reached that can be accepted. This is achieved using Markov chain transitions that satisfy the fixed point equation, but do not satisfy detailed balance. The resulting algorithm significantly suppresses the random walk behavior and wasted function evaluations that are typically the consequence of update rejection. We demonstrate a greater than factor of two improvement in mixing time on three test problems. We release the source code as Python and MATLAB packages.Comment: Accepted conference submission to ICML 2014 and also featured in a special edition of JMLR. Since updated to include additional literature citation

Minimum and maximum entropy distributions for binary systems with known means and pairwise correlations

Maximum entropy models are increasingly being used to describe the collective activity of neural populations with measured mean neural activities and pairwise correlations, but the full space of probability distributions consistent with these constraints has not been explored. We provide upper and lower bounds on the entropy for the {\em minimum} entropy distribution over arbitrarily large collections of binary units with any fixed set of mean values and pairwise correlations. We also construct specific low-entropy distributions for several relevant cases. Surprisingly, the minimum entropy solution has entropy scaling logarithmically with system size for any set of first- and second-order statistics consistent with arbitrarily large systems. We further demonstrate that some sets of these low-order statistics can only be realized by small systems. Our results show how only small amounts of randomness are needed to mimic low-order statistical properties of highly entropic distributions, and we discuss some applications for engineered and biological information transmission systems.Comment: 34 pages, 7 figure

The sensory feedback mechanisms enabling couples to walk synchronously: An initial investigation

The inattentive eye often will not notice it, but synchronization among human walking partners is quite common. In this first investigation of this phenomenon, we studied its frequency and the mechanisms that contribute to this form of "entrainment." Specifically, by modifying the available communication links between two walking partners, we isolated the feedback mechanisms that enable couples to synchronize their stepping pattern when they walk side-by-side. Although subjects were unaware of the research aims and were not specifically asked to walk in synchrony, we observed synchronized walking in almost 50% of the walking trials, among couples who do not usually walk together. The strongest in-phase synchrony occurred in the presence of tactile feedback (i.e., handholding), perhaps because of lower and upper extremity coupling driven in part by arm swing. Interestingly, however, even in the absence of visual or auditory communication, couples also frequently walked in synchrony while 180 degrees out-of-phase, likely using different feedback mechanisms. These findings may partially explain how patients with certain gait disorders and disturbed rhythm enhance their gait when they walk with a partner and suggest alternative interventions that might improve the stepping pattern. Further, this preliminary investigation highlights the relatively ubiquitous nature of an interesting phenomenon that has not previously been studied and suggests that further work is needed to better understand the mechanisms that entrain the gait of two walking partners and allows couples to walk in synchrony with minimal or no conscious effort

Type of atrial fibrillation and clinical outcomes in patients with heart failure and reduced ejection fraction

Background: Atrial fibrillation (AF) is common in heart failure (HF), but the outcome by type of AF is largely unknown. Objectives: This study investigated outcomes related to type of AF (paroxysmal, persistent or permanent, or new onset) in 2 recent large trials in patients with HF with reduced ejection fraction. Methods: The study analyzed patients in the PARADIGM-HF (Prospective comparison of ARNI with ACEI to Determine Impact on Global Mortality and morbidity in Heart Failure) and ATMOSPHERE (Aliskiren Trial to Minimize Outcomes in Patients with Heart Failure) trials. Multivariable Cox regression models were used to estimate hazard ratios (HRs) for outcomes related to AF type. Results: Of 15,415 patients, 5,481 (35.6%) had a history of AF at randomization, and of these, 1,645 (30.0%) had paroxysmal AF. Compared with patients without AF, patients with paroxysmal AF at randomization had a higher risk of the primary composite endpoint of cardiovascular death or HF hospitalization (HR: 1.20; 95% confidence interval [CI]: 1.09 to 1.32; p < 0.001), HF hospitalization (HR: 1.34; 95% CI: 1.19 to 1.51; < 0.001), and stroke (HR: 1.34; 95% CI: 1.02 to 1.76; p = 0.037), whereas the corresponding risks in patients with persistent or permanent AF were not elevated. Neither type of AF was associated with higher mortality. New onset AF was associated with the greatest risk of adverse outcomes: primary endpoint (HR: 2.21; 95% CI: 1.80 to 2.71), HF hospitalization (HR: 2.11; 95% CI: 1.58 to 2.81), stroke (HR: 2.20; 95% CI: 1.25 to 3.88), and all-cause mortality (HR: 2.26; 95% CI: 1.86 to 2.74), all p values < 0.001, compared with patients without AF. Anticoagulants were used less often in patients with paroxysmal (53%) and new onset (16%) AF than in patients with persistent or permanent AF (71%). Conclusions: Among HF patients with a history of AF, those with paroxysmal AF were at greater risk of HF hospitalization and stroke than were patients with persistent or permanent AF, underlining the importance of anticoagulant therapy. New onset AF was associated with increased risk of all outcomes. (Prospective comparison of ARNI with ACEI to Determine Impact on Global Mortality and Morbidity in Heart Failure [PARADIGM-HF]; NCT01035255) (Aliskiren Trial to Minimize Outcomes in Patients with Heart Failure [ATMOSPHERE]; NCT00853658

A leaf spot and blight of greenhouse tomato seedlings incited by a Herbaspirillum sp.

A leaf spot and blighting were observed on leaves of tomato transplants from a producer in Florida in 2001 and 2002. A nonfluorescent bacterium was isolated consistently from affected tissue. The typical bacterium was a gram negative, strictly aerobic, slightly curved rod with one or two flagella. Sequence analysis of the 16S rRNA indicated that two representative strains, F1 and SE1, had greater than 99% nucleotide sequence identity with Herbaspirillum huttiense and H. rubrisubalbicans. The cellular fatty acid composition of the total of 16 tomato strains was very similar to H. huttiense and H. rubrisubalbicans. Based on carbon utilization, six of nine strains tested with the Biolog system were identified as Herbaspirillum spp. The tomato strains were oxidase positive and grew at 40 degrees C, but were negative for levan production, pectate hydrolysis, and arginine dihydrolase activity. Based upon this polyphasic analysis, we concluded that the strains were most closely related to H. huttiense, although placement in this species would require further analyses. However, the tomato strains and H. rubrisubalbicans, but not H. huttiense, caused confluent necrosis when infiltrated at high concentrations into tomato leaves and were able to produce leaf spot symptoms on inoculated tomato seedlings in the greenhouse. Using pulsed-field gel electrophoresis, we determined that there was considerable variability between the strains collected in 2001 and 2002