There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality.

Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

I and i

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

UNLABELLED: The multiplex capability and high yield of current day DNA-sequencing instruments has made bacterial whole genome sequencing a routine affair. The subsequent de novo assembly of reads into contigs has been well addressed. The final step of annotating all relevant genomic features on those contigs can be achieved slowly using existing web- and email-based systems, but these are not applicable for sensitive data or integrating into computational pipelines. Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers. AVAILABILITY AND IMPLEMENTATION: Prokka is implemented in Perl and is freely available under an open source GPLv2 license from http://vicbioinformatics.com/.

/pdf/prokka-rapid-prokaryotic-genome-annotation-4t1evn8spy.pdf

Prokka: Rapid Prokaryotic Genome Annotation

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

Neural networks provide state-of-the-art results for most machine learning tasks. Unfortunately, neural networks are vulnerable to adversarial examples: given an input x and any target classification t, it is possible to find a new input x' that is similar to x but classified as t. This makes it difficult to apply neural networks in security-critical areas. Defensive distillation is a recently proposed approach that can take an arbitrary neural network, and increase its robustness, reducing the success rate of current attacks' ability to find adversarial examples from 95% to 0.5%.In this paper, we demonstrate that defensive distillation does not significantly increase the robustness of neural networks by introducing three new attack algorithms that are successful on both distilled and undistilled neural networks with 100% probability. Our attacks are tailored to three distance metrics used previously in the literature, and when compared to previous adversarial example generation algorithms, our attacks are often much more effective (and never worse). Furthermore, we propose using high-confidence adversarial examples in a simple transferability test we show can also be used to break defensive distillation. We hope our attacks will be used as a benchmark in future defense attempts to create neural networks that resist adversarial examples.

/pdf/towards-evaluating-the-robustness-of-neural-networks-40dfcinzm4.pdf

Towards Evaluating the Robustness of Neural Networks

Power-aware computing aims either to maximise the performance of a system under certain constraints on its power consumption and dissipation or, dually, to reduce power consumption in order to meet desired performance or throughput targets. This area is currently gaining importance due to the increasing usage of portable, mobile and hand-held electronic devices. In this paper we illustrate the applicability of probabilistic model checking, a formal verification technique for the analysis of systems which exhibit stochastic behaviour, to the field of power-aware computing. We use the probabilistic model checking tool PRISM on two case studies in this application domain: dynamic power management and dynamic voltage scaling.

/pdf/probabilistic-model-checking-and-power-aware-computing-46foibn48k.pdf

Probabilistic Model Checking and Power-Aware Computing

Interoperability of heterogeneous networked systems has yet to reach the maturity required by ubiquitous computing due to the technology-dependent nature of solutions. The CONNECT Integrated Project attempts to develop a novel network infrastructure to allow heterogeneous networked systems to freely communicate with one another by synthesising the required connectors on-the-fly. A key objective of CONNECT is to build a comprehensive theory of composable connectors, by devising an algebra for rigorously characterising complex interaction protocols in order to support automated reasoning. With this aim in mind, we formalise a high-level algebra for reasoning about protocol mismatches. Basic mismatches can be solved by suitably defined primitives, while complex mismatches can be settled by composition operators that build connectors out of simpler ones. The semantics of the algebra is given in terms of Interface Automata, and an example in the domain of instant messaging is used to illustrate how the algebra can characterise the interaction behaviour of a connector for mediating protocols.

/pdf/towards-a-connector-algebra-bzqgfizmnj.pdf

Towards a connector algebra

Neural network NLP models are vulnerable to small modifications of the input that maintain the original meaning but result in a different prediction. In this paper, we focus on robustness of text classification against word substitutions, aiming to provide guarantees that the model prediction does not change if a word is replaced with a plausible alternative, such as a synonym. As a measure of robustness, we adopt the notion of the maximal safe radius for a given input text, which is the minimum distance in the embedding space to the decision boundary. Since computing the exact maximal safe radius is not feasible in practice, we instead approximate it by computing a lower and upper bound. For the upper bound computation, we employ Monte Carlo Tree Search in conjunction with syntactic filtering to analyse the effect of single and multiple word substitutions. The lower bound computation is achieved through an adaptation of the linear bounding techniques implemented in tools CNN-Cert and POPQORN, respectively for convolutional and recurrent network models. We evaluate the methods on sentiment analysis and news classification models for four datasets (IMDB, SST, AG News and NEWS) and a range of embeddings, and provide an analysis of robustness trends. We also apply our framework to interpretability analysis and compare it with LIME.

/pdf/assessing-robustness-of-text-classification-through-maximal-2l5wbgl7nz.pdf

Assessing Robustness of Text Classification through Maximal Safe Radius Computation

We consider Bayesian classification with Gaussian processes (GPs) and define robustness of a classifier in terms of the worst-case difference in the classification probabilities with respect to input perturbations. For a subset of the input space $T\subseteq \mathbb{R}^m$ such properties reduce to computing the infimum and supremum of the classification probabilities for all points in $T$. Unfortunately, computing the above values is very challenging, as the classification probabilities cannot be expressed analytically. Nevertheless, using the theory of Gaussian processes, we develop a framework that, for a given dataset $\mathcal{D}$, a compact set of input points $T\subseteq \mathbb{R}^m$ and an error threshold $\epsilon>0$, computes lower and upper bounds of the classification probabilities by over-approximating the exact range with an error bounded by $\epsilon$. We provide experimental comparison of several approximate inference methods for classification on tasks associated to MNIST and SPAM datasets showing that our results enable quantification of uncertainty in adversarial classification settings.

Robustness Quantification for Classification with Gaussian Processes.

In an expected reachability-time game (ERTG) two players, Min and Max, move a token along the transitions of a probabilistic timed automaton, so as to minimise and maximise, respectively, the expected time to reach a target. These games are concurrent since at each step of the game both players choose a timed move (a time delay and action under their control), and the transition of the game is determined by the timed move of the player who proposes the shorter delay. A game is turn-based if at any step of the game, all available actions are under the control of precisely one player. We show that while concurrent ERTGs are not always determined, turn-based ERTGs are positionally determined. Using the boundary region graph abstraction, and a generalisation of Asarin and Maler's simple function, we show that the decision problems related to computing the upper/lower values of concurrent ERTGs, and computing the value of turn-based ERTGs are decidable and their complexity is in NEXPTIME ∩ co-NEXPTIME.

/pdf/expected-reachability-time-games-1zfsqtrse4.pdf

Expected Reachability-Time Games

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