Probabilistic abductive logic programming using Dirichlet priors

Probabilistic programming is an area of research that aims to develop general inference algorithms for probabilistic models expressed as probabilistic programs whose execution corresponds to inferring the parameters of those models. In this paper, we introduce a probabilistic programming language (PPL) based on abductive logic programming for performing inference in probabilistic models involving categorical distributions with Dirichlet priors. We encode these models as abductive logic programs enriched with probabilistic definitions and queries, and show how to execute and compile them to boolean formulas. Using the latter, we perform generalized inference using one of two proposed Markov Chain Monte Carlo (MCMC) sampling algorithms: an adaptation of uncollapsed Gibbs sampling from related work and a novel collapsed Gibbs sampling (CGS). We show that CGS converges faster than the uncollapsed version on a latent Dirichlet allocation (LDA) task using synthetic data. On similar data, we compare our PPL with LDA-specific algorithms and other PPLs. We find that all methods, except one, perform similarly and that the more expressive the PPL, the slower it is. We illustrate applications of our PPL on real data in two variants of LDA models (Seed and Cluster LDA), and in the repeated insertion model (RIM). In the latter, our PPL yields similar conclusions to inference with EM for Mallows models

The complexity and generality of learning answer set programs

Traditionally most of the work in the field of Inductive Logic Programming (ILP) has addressed the problem of learning Prolog programs. On the other hand, Answer Set Programming is increasingly being used as a powerful language for knowledge representation and reasoning, and is also gaining increasing attention in industry. Consequently, the research activity in ILP has widened to the area of Answer Set Programming, witnessing the proposal of several new learning frameworks that have extended ILP to learning answer set programs. In this paper, we investigate the theoretical properties of these existing frameworks for learning programs under the answer set semantics. Specifically, we present a detailed analysis of the computational complexity of each of these frameworks with respect to the two decision problems of deciding whether a hypothesis is a solution of a learning task and deciding whether a learning task has any solutions. We introduce a new notion of generality of a learning framework, which enables us to define a framework to be more general than another in terms of being able to distinguish one ASP hypothesis solution from a set of incorrect ASP programs. Based on this notion, we formally prove a generality relation over the set of existing frameworks for learning programs under answer set semantics. In particular, we show that our recently proposed framework, Context-dependent Learning from Ordered Answer Sets, is more general than brave induction, induction of stable models, and cautious induction, and maintains the same complexity as cautious induction, which has the highest complexity of these frameworks

Combined use of a femtosecond laser and a microkeratome in obtaining thin grafts for Descemet stripping automated endothelial keratoplasty: an eye bank study

Purpose: To evaluate the use of a femtosecond laser combined with a microkeratome in the preparation of posterior corneal disks for Descemet stripping automated endothelial keratoplasty (DSAEK).
Methods: This experimental study involved ultrathin DSAEK tissue preparation of 22 donor corneas unsuitable for transplantation. The first cut was performed with an Intralase® FS60 laser and the second cut with a Moria CBm 300-µm microkeratome. The thickness of the first cut was modified for each cornea to obtain a final graft thickness of less than 110 µm. Precut and postcut central pachymetry were performed with an ultrasonic pachymeter. Central endothelial cell density (ECD) was calculated before and 24 hours after tissue preparation. 
Results: Final graft thickness was 105.0 ± 26.1 (SD) µm (range 65-117). The mean microkeratome head cut thickness was 324.5 ± 10.9 µm (range 310-345). Precut and postcut ECDs averaged 2250 ± 222 and 2093 ± 286 cells/mm2, respectively, representing 6.9% of cell loss. No corneas were perforated.
Conclusion: Femtosecond FS60 lasers and Moria CBm 300-µm microkeratomes can be used sequentially to prepare consistently thin DSAEK grafts with no irregular cuts or cornea perforations

Mycobacterium tuberculosis ClpP Proteases Are Co-transcribed but Exhibit Different Substrate Specificities

PMCID: PMC3613350This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

The Girgentana Goat Breed: A Zootechnical Overview on Genetics, Nutrition and Dairy Production Aspects

In recent years, there has been a great interest in recovering and preserving local livestock breeds. An interesting situation is represented by the Girgentana goat, an ancient local breed reared in Sicily. Over recent years, this breed has become almost extinct, in part as a consequence of the marked decrease in fresh goat milk consumption. On the basis of these considerations, several studies on its genetic structure and management aspects have been conducted in order to protect the Girgentana goat from the risk of extinction and recover its genetic and economic value. In this context, information on genetics, nutrition and dairy production aspects may have a crucial role in the improvement and management of the breed. Thus, this chapter describes some points of these applications through recent investigations on this goat breed

Performance of the CMS Cathode Strip Chambers with Cosmic Rays

The Cathode Strip Chambers (CSCs) constitute the primary muon tracking device in the CMS endcaps. Their performance has been evaluated using data taken during a cosmic ray run in fall 2008. Measured noise levels are low, with the number of noisy channels well below 1%. Coordinate resolution was measured for all types of chambers, and fall in the range 47 microns to 243 microns. The efficiencies for local charged track triggers, for hit and for segments reconstruction were measured, and are above 99%. The timing resolution per layer is approximately 5 ns

Joy leads to overconfidence, and a simple countermeasure

Overconfidence has been identified as a source of suboptimal decision making in many real-life domains, with often far-reaching consequences. This study identifies a mechanism that can cause overconfidence and demonstrates a simple, effective countermeasure in an incentive-compatible experimental study. We observed that joy induced overconfidence if the reason for joy (an unexpected gift) was u

Discovery of Western European R1b1a2 Y Chromosome Variants in 1000 Genomes Project Data: An Online Community Approach

The authors have used an online community approach, and tools that were readily available via the Internet, to discover genealogically and therefore phylogenetically relevant Y-chromosome polymorphisms within core haplogroup R1b1a2-L11/S127 (rs9786076). Presented here is the analysis of 135 unrelated L11 derived samples from the 1000 Genomes Project. We were able to discover new variants and build a much more complex phylogenetic relationship for L11 sub-clades. Many of the variants were further validated using PCR amplification and Sanger sequencing. The identification of these new variants will help further the understanding of population history including patrilineal migrations in Western and Central Europe where R1b1a2 is the most frequent haplogroup. The fine-grained phylogenetic tree we present here will also help to refine historical genetic dating studies. Our findings demonstrate the power of citizen science for analysis of whole genome sequence data

The semi-classical expansion and resurgence in gauge theories: new perturbative, instanton, bion, and renormalon effects

We study the dynamics of four dimensional gauge theories with adjoint fermions for all gauge groups, both in perturbation theory and non-perturbatively, by using circle compactification with periodic boundary conditions for the fermions. There are new gauge phenomena. We show that, to all orders in perturbation theory, many gauge groups are Higgsed by the gauge holonomy around the circle to a product of both abelian and nonabelian gauge group factors. Non-perturbatively there are monopole-instantons with fermion zero modes and two types of monopole-anti-monopole molecules, called bions. One type are "magnetic bions" which carry net magnetic charge and induce a mass gap for gauge fluctuations. Another type are "neutral bions" which are magnetically neutral, and their understanding requires a generalization of multi-instanton techniques in quantum mechanics - which we refer to as the Bogomolny-Zinn-Justin (BZJ) prescription - to compactified field theory. The BZJ prescription applied to bion-anti-bion topological molecules predicts a singularity on the positive real axis of the Borel plane (i.e., a divergence from summing large orders in peturbation theory) which is of order N times closer to the origin than the leading 4-d BPST instanton-anti-instanton singularity, where N is the rank of the gauge group. The position of the bion--anti-bion singularity is thus qualitatively similar to that of the 4-d IR renormalon singularity, and we conjecture that they are continuously related as the compactification radius is changed. By making use of transseries and Ecalle's resurgence theory we argue that a non-perturbative continuum definition of a class of field theories which admit semi-classical expansions may be possible.Comment: 112 pages, 7 figures; v2: typos corrected, discussion of supersymmetric models added at the end of section 8.1, reference adde

Dental management considerations for the patient with an acquired coagulopathy. Part 1: Coagulopathies from systemic disease

Current teaching suggests that many patients are at risk for prolonged bleeding during and following invasive dental procedures, due to an acquired coagulopathy from systemic disease and/or from medications. However, treatment standards for these patients often are the result of long-standing dogma with little or no scientific basis. The medical history is critical for the identification of patients potentially at risk for prolonged bleeding from dental treatment. Some time-honoured laboratory tests have little or no use in community dental practice. Loss of functioning hepatic, renal, or bone marrow tissue predisposes to acquired coagulopathies through different mechanisms, but the relationship to oral haemostasis is poorly understood. Given the lack of established, science-based standards, proper dental management requires an understanding of certain principles of pathophysiology for these medical conditions and a few standard laboratory tests. Making changes in anticoagulant drug regimens are often unwarranted and/or expensive, and can put patients at far greater risk for morbidity and mortality than the unlikely outcome of postoperative bleeding. It should be recognised that prolonged bleeding is a rare event following invasive dental procedures, and therefore the vast majority of patients with suspected acquired coagulopathies are best managed in the community practice setting