Efficient AUC Optimization for Information Ranking Applications

Adequate evaluation of an information retrieval system to estimate future performance is a crucial task. Area under the ROC curve (AUC) is widely used to evaluate the generalization of a retrieval system. However, the objective function optimized in many retrieval systems is the error rate and not the AUC value. This paper provides an efficient and effective non-linear approach to optimize AUC using additive regression trees, with a special emphasis on the use of multi-class AUC (MAUC) because multiple relevance levels are widely used in many ranking applications. Compared to a conventional linear approach, the performance of the non-linear approach is comparable on binary-relevance benchmark datasets and is better on multi-relevance benchmark datasets.Comment: 12 page

Interferometric mapping of Magnetic fields: G30.79 FIR 10

We present polarization maps of G30.79 FIR 10 (in W43) from thermal dust emission at 1.3 mm and from CO J=$2 \to 1$ line emission. The observations were obtained using the Berkeley-Illinois-Maryland Association array in the period 2002-2004. The G30.79 FIR 10 region shows an ordered polarization pattern in dust emission, which suggests an hourglass shape for the magnetic field. Only marginal detections for line polarization were made from this region. Application of the Chandrashkar-Fermi method yielded $B_{pos} \approx 1.7$ mG and a statistically corrected mass to magnetic flux ratio $\lambda_{C} \approx 0.9$, or essentially critical.Comment: 11 pages, 2 Figures, Published in Ap

Hamiltonization of Nonholonomic Systems and the Inverse Problem of the Calculus of Variations

We introduce a method which allows one to recover the equations of motion of a class of nonholonomic systems by finding instead an unconstrained Hamiltonian system on the full phase space, and to restrict the resulting canonical equations to an appropriate submanifold of phase space. We focus first on the Lagrangian picture of the method and deduce the corresponding Hamiltonian from the Legendre transformation. We illustrate the method with several examples and we discuss its relationship to the Pontryagin maximum principle.Comment: 23 pages, accepted for publication in Rep. Math. Phy

Translational regulation in mycobacteria and its implications for pathogenicity

Protein synthesis is a fundamental requirement of all cells for survival and replication. To date, vast numbers of genetic and biochemical studies have been performed to address the mechanisms of translation and its regulation in Escherichia coli, but only a limited number of studies have investigated these processes in other bacteria, particularly in slow growing bacteria like Mycobacterium tuberculosis, the causative agent of human tuberculosis. In this Review, we highlight important differences in the translational machinery of M. tuberculosis compared with E. coli, specifically the presence of two additional proteins and subunit stabilizing elements such as the B9 bridge. We also consider the role of leaderless translation in the ability of M. tuberculosis to establish latent infection and look at the experimental evidence that translational regulatory mechanisms operate in mycobacteria during stress adaptation, particularly focussing on differences in toxin-antitoxin systems between E. coli and M. tuberculosis and on the role of tuneable translational fidelity in conferring phenotypic antibiotic resistance. Finally, we consider the implications of these differences in the context of the biological adaptation of M. tuberculosis and discuss how these regulatory mechanisms could aid in the development of novel therapeutics for tuberculosis

Hot Core, Outflows and Magnetic Fields in W43-MM1 (G30.79 FIR 10)

We present submillimeter spectral line and dust continuum polarization observations of a remarkable hot core and multiple outflows in the high-mass star-forming region W43-MM1 (G30.79 FIR 10), obtained using the Submillimeter Array (SMA). A temperature of $\sim$ 400 K is estimated for the hot-core using CH$_3$CN (J=19-18) lines, with detections of 11 K-ladder components. The high temperature and the mass estimates for the outflows indicate high-mass star-formation. The continuum polarization pattern shows an ordered distribution, and its orientation over the main outflow appears aligned to the outflow. The derived magnetic field indicates slightly super-critical conditions. While the magnetic and outflow energies are comparable, the B-field orientation appears to have changed from parsec scales to $\sim$ 0.1 pc scales during the core/star-formation process.Comment: accepted, ApJ Letter

A novel chromosome segregation mechanism during female meiosis.

In a wide range of eukaryotes, chromosome segregation occurs through anaphase A, in which chromosomes move toward stationary spindle poles, anaphase B, in which chromosomes move at the same velocity as outwardly moving spindle poles, or both. In contrast, Caenorhabditis elegans female meiotic spindles initially shorten in the pole-to-pole axis such that spindle poles contact the outer kinetochore before the start of anaphase chromosome separation. Once the spindle pole-to-kinetochore contact has been made, the homologues of a 4-μm-long bivalent begin to separate. The spindle shortens an additional 0.5 μm until the chromosomes are embedded in the spindle poles. Chromosomes then separate at the same velocity as the spindle poles in an anaphase B-like movement. We conclude that the majority of meiotic chromosome movement is caused by shortening of the spindle to bring poles in contact with the chromosomes, followed by separation of chromosome-bound poles by outward sliding

A snapshot of translation in Mycobacterium tuberculosis during exponential growth and nutrient starvation revealed by ribosome profiling

Mycobacterium tuberculosis, which causes tuberculosis, can undergo prolonged periods of non-replicating persistence in the host. The mechanisms underlying this are not fully understood, but translational regulation is thought to play a role. A large proportion of mRNA transcripts expressed in M. tuberculosis lack canonical bacterial translation initiation signals, but little is known about the implications of this for fine-tuning of translation. Here, we perform ribosome profiling to characterize the translational landscape of M. tuberculosis under conditions of exponential growth and nutrient starvation. Our data reveal robust, widespread translation of non-canonical transcripts and point toward different translation initiation mechanisms compared to canonical Shine-Dalgarno transcripts. During nutrient starvation, patterns of ribosome recruitment vary, suggesting that regulation of translation in this pathogen is more complex than originally thought. Our data represent a rich resource for others seeking to understand translational regulation in bacterial pathogens

Enhancing Sensitivity Classification with Semantic Features using Word Embeddings

Government documents must be reviewed to identify any sensitive information they may contain, before they can be released to the public. However, traditional paper-based sensitivity review processes are not practical for reviewing born-digital documents. Therefore, there is a timely need for automatic sensitivity classification techniques, to assist the digital sensitivity review process. However, sensitivity is typically a product of the relations between combinations of terms, such as who said what about whom, therefore, automatic sensitivity classification is a difficult task. Vector representations of terms, such as word embeddings, have been shown to be effective at encoding latent term features that preserve semantic relations between terms, which can also be beneficial to sensitivity classification. In this work, we present a thorough evaluation of the effectiveness of semantic word embedding features, along with term and grammatical features, for sensitivity classification. On a test collection of government documents containing real sensitivities, we show that extending text classification with semantic features and additional term n-grams results in significant improvements in classification effectiveness, correctly classifying 9.99% more sensitive documents compared to the text classification baseline

The effect of neural adaptation of population coding accuracy

Most neurons in the primary visual cortex initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. The functional consequences of adaptation are unclear. Typically a reduction of firing rate would reduce single neuron accuracy as less spikes are available for decoding, but it has been suggested that on the population level, adaptation increases coding accuracy. This question requires careful analysis as adaptation not only changes the firing rates of neurons, but also the neural variability and correlations between neurons, which affect coding accuracy as well. We calculate the coding accuracy using a computational model that implements two forms of adaptation: spike frequency adaptation and synaptic adaptation in the form of short-term synaptic plasticity. We find that the net effect of adaptation is subtle and heterogeneous. Depending on adaptation mechanism and test stimulus, adaptation can either increase or decrease coding accuracy. We discuss the neurophysiological and psychophysical implications of the findings and relate it to published experimental data.Comment: 35 pages, 8 figure