Hierarchical Re-estimation of Topic Models for Measuring Topical Diversity

A high degree of topical diversity is often considered to be an important characteristic of interesting text documents. A recent proposal for measuring topical diversity identifies three elements for assessing diversity: words, topics, and documents as collections of words. Topic models play a central role in this approach. Using standard topic models for measuring diversity of documents is suboptimal due to generality and impurity. General topics only include common information from a background corpus and are assigned to most of the documents in the collection. Impure topics contain words that are not related to the topic; impurity lowers the interpretability of topic models and impure topics are likely to get assigned to documents erroneously. We propose a hierarchical re-estimation approach for topic models to combat generality and impurity; the proposed approach operates at three levels: words, topics, and documents. Our re-estimation approach for measuring documents' topical diversity outperforms the state of the art on PubMed dataset which is commonly used for diversity experiments.Comment: Proceedings of the 39th European Conference on Information Retrieval (ECIR2017

Generalized triangle groups, expanders, and a problem of Agol and Wise

Answering a question asked by Agol and Wise, we show that a desired stronger form of Wise's malnormal special quotient theorem does not hold. The counterexamples are generalizations of triangle groups, built using the Ramanujan graphs constructed by Lubotzky--Phillips--Sarnak

Association between genotypic diversity and biofilm production in group B Streptococcus

Background: Group B Streptococcus (GBS) is a leading cause of sepsis and meningitis and an important factor in premature and stillbirths. Biofilm production has been suggested to be important for GBS pathogenesis alongside many other elements, including phylogenetic lineage and virulence factors, such as pili and capsule type. A complete understanding of the confluence of these components, however, is lacking. To identify associations between biofilm phenotype, pilus profile and lineage, 293 strains from asymptomatic carriers, invasive disease cases, and bovine mastitis cases, were assessed for biofilm production using an in vitro assay. Results: Multilocus sequence type (ST) profile, pilus island profile, and isolate source were associated with biofilm production. Strains from invasive disease cases and/or belonging to the ST-17 and ST-19 lineages were significantly more likely to form weak biofilms, whereas strains producing strong biofilms were recovered more frequently from individuals with asymptomatic colonization. Conclusions: These data suggest that biofilm production is a lineage-specific trait in GBS and may promote colonization of strains representing lineages other than STs 17 and 19. The findings herein also demonstrate that biofilms must be considered in the treatment of pregnant women, particularly for women with heavy GBS colonization

Scaling and Universality in the Counterion-Condensation Transition at Charged Cylinders

We address the critical and universal aspects of counterion-condensation transition at a single charged cylinder in both two and three spatial dimensions using numerical and analytical methods. By introducing a novel Monte-Carlo sampling method in logarithmic radial scale, we are able to numerically simulate the critical limit of infinite system size (corresponding to infinite-dilution limit) within tractable equilibration times. The critical exponents are determined for the inverse moments of the counterionic density profile (which play the role of the order parameters and represent the inverse localization length of counterions) both within mean-field theory and within Monte-Carlo simulations. In three dimensions (3D), correlation effects (neglected within mean-field theory) lead to an excessive accumulation of counterions near the charged cylinder below the critical temperature (condensation phase), while surprisingly, the critical region exhibits universal critical exponents in accord with the mean-field theory. In two dimensions (2D), we demonstrate, using both numerical and analytical approaches, that the mean-field theory becomes exact at all temperatures (Manning parameters), when number of counterions tends to infinity. For finite particle number, however, the 2D problem displays a series of peculiar singular points (with diverging heat capacity), which reflect successive de-localization events of individual counterions from the central cylinder. In both 2D and 3D, the heat capacity shows a universal jump at the critical point, and the energy develops a pronounced peak. The asymptotic behavior of the energy peak location is used to locate the critical temperature, which is also found to be universal and in accordance with the mean-field prediction.Comment: 31 pages, 16 figure

Superfluid Friction and Late-time Thermal Evolution of Neutron Stars

The recent temperature measurements of the two older isolated neutron stars PSR 1929+10 and PSR 0950+08 (ages of $3\times 10^6$ and $2\times 10^7$ yr, respectively) indicate that these objects are heated. A promising candidate heat source is friction between the neutron star crust and the superfluid it is thought to contain. We study the effects of superfluid friction on the long-term thermal and rotational evolution of a neutron star. Differential rotation velocities between the superfluid and the crust (averaged over the inner crust moment of inertia) of $\bar\omega\sim 0.6$ rad s$^{-1}$ for PSR 1929+10 and $\sim 0.02$ rad s$^{-1}$ for PSR 0950+08 would account for their observed temperatures. These differential velocities could be sustained by pinning of superfluid vortices to the inner crust lattice with strengths of $\sim$ 1 MeV per nucleus. Pinned vortices can creep outward through thermal fluctuations or quantum tunneling. For thermally-activated creep, the coupling between the superfluid and crust is highly sensitive to temperature. If pinning maintains large differential rotation ($\sim 10$ rad s$^{-1}$), a feedback instability could occur in stars younger than $\sim 10^5$ yr causing oscillations of the temperature and spin-down rate over a period of $\sim 0.3 t_{\rm age}$. For stars older than $\sim 10^6$ yr, however, vortex creep occurs through quantum tunneling, and the creep velocity is too insensitive to temperature for a thermal-rotational instability to occur. These older stars could be heated through a steady process of superfluid friction.Comment: 26 pages, 1 figure, submitted to Ap

In situ measurement of atmospheric krypton and xenon on Mars with Mars Science Laboratory

Mars Science Laboratory's Sample Analysis at Mars (SAM) investigation has measured all of the stable isotopes of the heavy noble gases krypton and xenon in the martian atmosphere, in situ, from the Curiosity Rover at Gale Crater, Mars. Previous knowledge of martian atmospheric krypton and xenon isotope ratios has been based upon a combination of the Viking mission's krypton and xenon detections and measurements of noble gas isotope ratios in martian meteorites. However, the meteorite measurements reveal an impure mixture of atmospheric, mantle, and spallation contributions. The xenon and krypton isotopic measurements reported here include the complete set of stable isotopes, unmeasured by Viking. The new results generally agree with Mars meteorite measurements but also provide a unique opportunity to identify various non-atmospheric heavy noble gas components in the meteorites. Kr isotopic measurements define a solar-like atmospheric composition, but deviating from the solar wind pattern at 80Kr and 82Kr in a manner consistent with contributions originating from neutron capture in Br. The Xe measurements suggest an intriguing possibility that isotopes lighter than 132Xe have been enriched to varying degrees by spallation and neutron capture products degassed to the atmosphere from the regolith, and a model is constructed to explore this possibility. Such a spallation component, however, is not apparent in atmospheric Xe trapped in the glassy phases of martian meteorites

Photon collection from a trapped ion--cavity system

We present the design and implementation of a trapped ion cavity QED system. A single ytterbium ion is confined by a micron-scale ion trap inside a 2 mm optical cavity. The ion is coherently pumped by near resonant laser light while the cavity output is monitored as a function of pump intensity and cavity detuning. We observe a Purcell enhancement of scattered light into the solid angle subtended by the optical cavity, as well as a three-peak structure arising from strongly driving the atom. This system can be integrated into existing atom{photon quantum network protocols and is a pathway towards an efficient atom{photon quantum interface

Word Embeddings for Entity-annotated Texts

Learned vector representations of words are useful tools for many information retrieval and natural language processing tasks due to their ability to capture lexical semantics. However, while many such tasks involve or even rely on named entities as central components, popular word embedding models have so far failed to include entities as first-class citizens. While it seems intuitive that annotating named entities in the training corpus should result in more intelligent word features for downstream tasks, performance issues arise when popular embedding approaches are naively applied to entity annotated corpora. Not only are the resulting entity embeddings less useful than expected, but one also finds that the performance of the non-entity word embeddings degrades in comparison to those trained on the raw, unannotated corpus. In this paper, we investigate approaches to jointly train word and entity embeddings on a large corpus with automatically annotated and linked entities. We discuss two distinct approaches to the generation of such embeddings, namely the training of state-of-the-art embeddings on raw-text and annotated versions of the corpus, as well as node embeddings of a co-occurrence graph representation of the annotated corpus. We compare the performance of annotated embeddings and classical word embeddings on a variety of word similarity, analogy, and clustering evaluation tasks, and investigate their performance in entity-specific tasks. Our findings show that it takes more than training popular word embedding models on an annotated corpus to create entity embeddings with acceptable performance on common test cases. Based on these results, we discuss how and when node embeddings of the co-occurrence graph representation of the text can restore the performance.Comment: This paper is accepted in 41st European Conference on Information Retrieva

Bounds on the diameter of Cayley graphs of the symmetric group

In this paper we are concerned with the conjecture that, for any set of generators S of the symmetric group of degree n, the word length in terms of S of every permutation is bounded above by a polynomial of n. We prove this conjecture for sets of generators containing a permutation fixing at least 37% of the points.Comment: 17 pages, 6 table

Pilus distribution among lineages of group b <i>streptococcus</i>: an evolutionary and clinical perspective

&lt;b&gt;Background&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Group B Streptococcus (GBS) is an opportunistic pathogen in both humans and bovines. Epidemiological and phylogenetic analyses have found strains belonging to certain phylogenetic lineages to be more frequently associated with invasive newborn disease, asymptomatic maternal colonization, and subclinical bovine mastitis. Pilus structures in GBS facilitate colonization and invasion of host tissues and play a role in biofilm formation, though few large-scale studies have estimated the frequency and diversity of the three pilus islands (PIs) across diverse genotypes. Here, we examined the distribution of pilus islands (PI) 1, 2a and 2b among 295 GBS strains representing 73 multilocus sequence types (STs) belonging to eight clonal complexes. PCR-based RFLP was also used to evaluate variation in the genes encoding pilus backbone proteins of PI-2a and PI-2b.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Results&lt;/b&gt;&lt;p&gt;&lt;/p&gt; All 295 strains harbored one of the PI-2 variants and most human-derived strains contained PI-1. Bovine-derived strains lacked PI-1 and possessed a unique PI-2b backbone protein allele. Neonatal strains more frequently had PI-1 and a PI-2 variant than maternal colonizing strains, and most CC-17 strains had PI-1 and PI-2b with a distinct backbone protein allele. Furthermore, we present evidence for the frequent gain and loss of genes encoding certain pilus types.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions&lt;/b&gt;&lt;p&gt;&lt;/p&gt; These data suggest that pilus combinations impact host specificity and disease presentation and that diversification often involves the loss or acquisition of PIs. Such findings have implications for the development of GBS vaccines that target the three pilus islands