Open-Category Classification by Adversarial Sample Generation

In real-world classification tasks, it is difficult to collect training samples from all possible categories of the environment. Therefore, when an instance of an unseen class appears in the prediction stage, a robust classifier should be able to tell that it is from an unseen class, instead of classifying it to be any known category. In this paper, adopting the idea of adversarial learning, we propose the ASG framework for open-category classification. ASG generates positive and negative samples of seen categories in the unsupervised manner via an adversarial learning strategy. With the generated samples, ASG then learns to tell seen from unseen in the supervised manner. Experiments performed on several datasets show the effectiveness of ASG.Comment: Published in IJCAI 201

De novo assembly of the cattle reference genome with single-molecule sequencing.

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species

Asymmetric Quantum Rabi Models for Light-Matter Interaction

The quantum Rabi model (QRM), describing a two-level system coupled to a quantum harmonic oscillator, is one of the simplest and most ubiquitous interaction models in quantum mechanics. Despite its simplicity, the QRM has found applications in various fields of physics. The most exciting realization of the QRM nowadays is arguably the circuit quantum electrodynamics (QED) system, where an on-chip artificial atom (or a qubit) is coupled to a transmission line or a waveguide. The qubits in circuit QED systems contain a bias term, which breaks the Z_2 symmetry in the QRM. Therefore, the precise model realized in circuit QED systems is referred to as the asymmetric quantum Rabi model (AQRM). This thesis explores theoretical methods to treat the AQRM and develops a complete approach to describe its energy landscape. The hidden symmetry of the AQRM is investigated in detail, and seen to be a rather general phenomenon in light-matter interaction models. The equivalence between the generalised Poschl-Teller potential and the spectrum of the AQRM is also established. Chapter 1 is dedicated to reviewing the analytic solutions and conventional approximations to the QRM/AQRM. Regarding the analytic solutions, the analytic results in terms of the transcendental functions determining the eigenspectrum of the AQRM are collected. Special emphasis is placed on the isolated closed-form exceptional solutions to the AQRM. Due to the lack of simple closed-form expressions for the general eigenvalues, some well-known approximations are considered. In Chapter 2, a generalised adiabatic approximation (GAA) is developed to calculate the eigenvalues of the excited states of the QRM and apply it to the AQRM. The GAA is based on the similarity between the exact exceptional solutions and the Laguerre polynomials. By construction, the GAA always has exact exceptional energy and approximates the regular spectrum with rather good agreement in a large parameter regime. Furthermore, the GAA is applied to the AQRM and shown to correctly recover the conical intersections in the energy landscape. The geometric phases around these conical intersections are calculated analytically as an illustrative example. In Chapter 3, a physically motivated variational wave function is presented for the ground state of the AQRM. The wave function is a weighted superposition of squeezed coherent states entangled with non-orthogonal qubit states and relies only on three variational parameters in the regimes of interest. The variational expansion describes the ground state remarkably well in almost all parameter regimes, especially with arbitrary bias. The results show that the variational expansion is a significant improvement over the existing approximations for the AQRM. In Chapter 4, the hidden symmetry and tunnelling dynamics in the AQRM and several related models are analysed in detail. The AQRM has a broken Z_2 symmetry, with generally a non-degenerate eigenvalue spectrum. In some special cases of the related models, stable level crossings typical of the Z_2-symmetric quantum Rabi model are recovered. It is thus shown that this hidden symmetry is not limited to the AQRM, but exists in various related light-matter interaction models. In Chapter 5, starting with the Gaudin-like Bethe ansatz equations associated with the quasi-exactly solved (QES) exceptional points of the AQRM, a spectral equivalence is established with QES hyperbolic Schrodinger potentials. This leads to particular QES Poschl-Teller potentials. The complete spectral equivalence is then established between the AQRM and generalised Poschl-Teller potentials. Conclusions and future directions are presented in the final Chapter 6

Noncovalent Interactions-Driven Self-Assembly of Polyanionic Additive for Long Anti-Calendar Aging and High-Rate Zinc Metal Batteries

Zinc anodes of zinc metal batteries suffer from unsatisfactory plating/striping reversibility due to interfacial parasitic reactions and poor Zn2+ mass transfer kinetics. Herein, methoxy polyethylene glycol-phosphate (mPEG-P) is introduced as an electrolyte additive to achieve long anti-calendar aging and high-rate capabilities. The polyanionic of mPEG-P self-assembles via noncovalent-interactions on electrode surface to form polyether-based cation channels and in situ organic–inorganic hybrid solid electrolyte interface layer, which ensure rapid Zn2+ mass transfer and suppresses interfacial parasitic reactions, realizing outstanding cycling/calendar aging stability. As a result, the Zn//Zn symmetric cells with mPEG-P present long lifespans over 9000 and 2500 cycles at ultrahigh current densities of 120 and 200 mA cm−2, respectively. Besides, the coulombic efficiency (CE) of the Zn//Cu cell with mPEG-P additive (88.21%) is much higher than that of the cell (36.4%) at the initial cycle after the 15-day calendar aging treatment, presenting excellent anti-static corrosion performance. Furthermore, after 20-day aging, the Zn//MnO2 cell exhibits a superior capacity retention of 89% compared with that of the cell without mPEG-P (28%) after 150 cycles. This study provides a promising avenue for boosting the development of high efficiency and durable metallic zinc based stationary energy storage system

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Observation of associated near-side and away-side long-range correlations in √sNN=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δϕ) and pseudorapidity (Δη) are measured in √sNN=5.02  TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1  μb-1 of data as a function of transverse momentum (pT) and the transverse energy (ΣETPb) summed over 3.1<η<4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2<|Δη|<5) “near-side” (Δϕ∼0) correlation that grows rapidly with increasing ΣETPb. A long-range “away-side” (Δϕ∼π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣETPb, is found to match the near-side correlation in magnitude, shape (in Δη and Δϕ) and ΣETPb dependence. The resultant Δϕ correlation is approximately symmetric about π/2, and is consistent with a dominant cos⁡2Δϕ modulation for all ΣETPb ranges and particle pT

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

PAREsnip2: A tool for high-throughput prediction of small RNA targets from degradome sequencing data using configurable targeting rules

Small RNAs (sRNAs) are short, non-coding RNAs that play critical roles in many important biological pathways. They suppress the translation of messenger RNAs (mRNAs) by directing the RNA-induced silencing complex to their sequence-specific mRNA target(s). In plants, this typically results in mRNA cleavage and subsequent degradation of the mRNA. The resulting mRNA fragments, or degradome, provide evidence for these interactions, and thus degradome analysis has become an important tool for sRNA target prediction. Even so, with the continuing advances in sequencing technologies, not only are larger and more complex genomes being sequenced, but also degradome and associated datasets are growing both in number and read count. As a result, existing degradome analysis tools are unable to process the volume of data being produced without imposing huge resource and time requirements. Moreover, these tools use stringent, non-configurable targeting rules, which reduces their flexibility. Here, we present a new and user configurable software tool for degradome analysis, which employs a novel search algorithm and sequence encoding technique to reduce the search space during analysis. The tool significantly reduces the time and resources required to perform degradome analysis, in some cases providing more than two orders of magnitude speed-up over current methods

A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome

Citation: Chapman, J. A., Mascher, M., Buluç, A., Barry, K., Georganas, E., Session, A., . . . Rokhsar, D. S. (2015). A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biology, 16(1). doi:10.1186/s13059-015-0582-8Polyploid species have long been thought to be recalcitrant to whole-genome assembly. By combining high-throughput sequencing, recent developments in parallel computing, and genetic mapping, we derive, de novo, a sequence assembly representing 9.1 Gbp of the highly repetitive 16 Gbp genome of hexaploid wheat, Triticum aestivum, and assign 7.1 Gb of this assembly to chromosomal locations. The genome representation and accuracy of our assembly is comparable or even exceeds that of a chromosome-by-chromosome shotgun assembly. Our assembly and mapping strategy uses only short read sequencing technology and is applicable to any species where it is possible to construct a mapping population. © 2015 Chapman et al. licensee BioMed Central.Additional Authors: Muehlbauer, G. J.;Stein, N.;Rokhsar, D. S