Partition function approach to non-Gaussian likelihoods: macrocanonical partitions and replicating Markov-chains

Monte-Carlo techniques are standard numerical tools for exploring non-Gaussian and multivariate likelihoods. Many variants of the original Metropolis-Hastings algorithm have been proposed to increase the sampling efficiency. Motivated by Ensemble Monte Carlo we allow the number of Markov chains to vary by exchanging particles with a reservoir, controlled by a parameter analogous to a chemical potential $\mu$, which effectively establishes a random process that samples microstates from a macrocanonical instead of a canonical ensemble. In this paper, we develop the theory of macrocanonical sampling for statistical inference on the basis of Bayesian macrocanonical partition functions, thereby bringing to light the relations between information-theoretical quantities and thermodynamic properties. Furthermore, we propose an algorithm for macrocanonical sampling, $\texttt{Avalanche Sampling}$, and apply it to various toy problems as well as the likelihood on the cosmological parameters $\Omega_m$ and $w$ on the basis of data from the supernova distance redshift relation.Comment: 13 pages, 9 figure

LocTree3 prediction of localization

The prediction of protein sub-cellular localization is an important step toward elucidating protein function. For each query protein sequence, LocTree2 applies machine learning (profile kernel SVM) to predict the native sub-cellular localization in 18 classes for eukaryotes, in six for bacteria and in three for archaea. The method outputs a score that reflects the reliability of each prediction. LocTree2 has performed on par with or better than any other state-of-the-art method. Here, we report the availability of LocTree3 as a public web server. The server includes the machine learning-based LocTree2 and improves over it through the addition of homology-based inference. Assessed on sequence-unique data, LocTree3 reached an 18-state accuracy Q18 = 80 ± 3% for eukaryotes and a six-state accuracy Q6 = 89 ± 4% for bacteria. The server accepts submissions ranging from single protein sequences to entire proteomes. Response time of the unloaded server is about 90 s for a 300-residue eukaryotic protein and a few hours for an entire eukaryotic proteome not considering the generation of the alignments. For over 1000 entirely sequenced organisms, the predictions are directly available as downloads. The web server is available at http://www.rostlab.org/services/loctree3

The potential value of hybrid positron emission tomography/dual-source computed tomography imaging in coronary bypass surgery

Background: We evaluated how comprehensive assessment of coronary artery lesions and their hemodynamic relevance by means of hybrid positron emission tomography (PET) and computed tomography (CT) imaging would affect decision-making in coronary artery bypass surgery (CABG), compared with using invasive coronary angiography (ICA) alone.Methods: After undergoing ICA, 27 patients (21 men and 6 women; mean SD age, 66 ± 10 years) planned for cardiac surgery were scheduled for myocardial perfusion stress/rest evaluation with [13N]ammonia PET and CT coronary angiography. Only ICA was available to the surgeon. Postoperatively, the performed CABG was compared with the hypothetical strategy based on hybrid PET/CT findings (regional coronary flow reserve [CFR], myocardial perfusion defects). Procedures included CABG (n = 18) alone, CABG combined with valve replacement (n = 6), and CABG combined with isolated valve replacement (n = 3). A total of 56 bypass grafts (28 venous and 28 arterial) and 66 distal anastomoses were placed.Results: CT evaluation showed 93% concordance (66/71) with ICA regarding significant stenoses, with sensitivity, specificity, positive predictive value, and negative predictive value of 93.1%, 98.7%, 94.4%, and 98.4%, respectively. In the PET scan, 16 patients had 1 ischemic region, and 12 patients had 1 scar region, including 5 patients who presented with mixed conditions (scar and ischemia). One patient had a completely normal myocardium. Compared with the performed surgery, PET/CT fusion evaluation showed that of the performed anastomoses, 48% had documented ischemia (with a CFR <2 in 86%), 38% were nonischemic (although a CFR value <2 was found in 78%), and 14% had scar tissue (fixed perfusion defect).Conclusions: Although <50% of bypasses were placed to areas with myocardial ischemia, the CFR was low in the majority of nonischemic regions, a finding that may have important prognostic relevance. PET/CT fusion imaging could potentially influence planning for CABG and provide incremental prognostic information