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

In this paper we present an assume-guarantee specification theory (aka interface theory from [14]) for modular synthesis and verification of real-time systems with critical timing constraints. It is a further step of our earlier work [10] which achieved an elegant algebraic specification theory for real-time systems endowed with the capability to freeze time. In this paper we relinquish such (unrealisable) capability and target more realistic systems without the ability to stop time. 
Our theory, in a combined process-algebraic and reactive-synthesis style, provides the operations of parallel composition for system integration, logical conjunction/disjunction for viewpoint fusion and independent development, and quotient for incremental synthesis. 
We show that a substitutive refinement preorder, which is a coarsening of the pre-congruence in [10], constitutes the weakest pre-congruence preserving freedom of incompatibility errors. The coarsening requires a shift in the focus of our theory to a more game-theoretical treatment, where the coarsening constitutes a reactive synthesis game named normalisation and is efficiently implementable by a novel local bot-backpropagation algorithm. 
Previously, timed concurrent games have been studied in [1,14,13], where one of the key concern is the removal of time-blocking strategies by applying blame assignment [13]. Our timed games also have the issue of time-blocking strategies, which may arise through the composition of specifications. However, due to our distinctively different formulation of timed games, we have discovered another elegant solution to the problem without blame assignment. Our solution utilises a second reactive synthesis game called realisation, which is dual to normalisation and implementable by the dual local top-backpropagation algorithm.

Revisiting Timed Specification Theory II : Realisability

Neuro-symbolic artificial intelligence is an emerging area that combines traditional symbolic techniques with neural networks. In this paper, we consider its application to sequential decision making under uncertainty. We introduce neuro-symbolic partially observable Markov decision processes (NS-POMDPs), which model an agent that perceives a continuous-state environment using a neural network and makes decisions symbolically, and study the problem of optimising discounted cumulative rewards. This requires functions over continuous-state beliefs, for which we propose a novel piecewise linear and convex representation (P-PWLC) in terms of polyhedra covering the continuous-state space and value vectors, and extend Bellman backups to this representation. We prove the convexity and continuity of value functions and present two value iteration algorithms that ensure finite representability by exploiting the underlying structure of the continuous-state model and the neural perception mechanism. The first is a classical (exact) value iteration algorithm extending $\alpha$-functions of Porta et al (2006) to the P-PWLC representation for continuous-state spaces. The second is a point-based (approximate) method called NS-HSVI, which uses the P-PWLC representation and belief-value induced functions to approximate value functions from below and above for two types of beliefs, particle-based and region-based. Using a prototype implementation, we show the practical applicability of our approach on two case studies that employ (trained) ReLU neural networks as perception functions, dynamic car parking and an aircraft collision avoidance system, by synthesising (approximately) optimal strategies. An experimental comparison with the finite-state POMDP solver SARSOP demonstrates that NS-HSVI is more robust to particle disturbances.

Point-based Value Iteration for Neuro-Symbolic POMDPs

Distributional assumptions have been shown to be necessary for the robust learnability of concept classes when considering the exact-in-the-ball robust risk and access to random examples by Gourdeau et al. (2019). In this paper, we study learning models where the learner is given more power through the use of local queries, and give the first distribution-free algorithms that perform robust empirical risk minimization (ERM) for this notion of robustness. The first learning model we consider uses local membership queries (LMQ), where the learner can query the label of points near the training sample. We show that, under the uniform distribution, LMQs do not increase the robustness threshold of conjunctions and any superclass, e.g., decision lists and halfspaces. Faced with this negative result, we introduce the local equivalence query ($\mathsf{LEQ}$) oracle, which returns whether the hypothesis and target concept agree in the perturbation region around a point in the training sample, as well as a counterexample if it exists. We show a separation result: on the one hand, if the query radius $\lambda$ is strictly smaller than the adversary's perturbation budget $\rho$, then distribution-free robust learning is impossible for a wide variety of concept classes; on the other hand, the setting $\lambda=\rho$ allows us to develop robust ERM algorithms. We then bound the query complexity of these algorithms based on online learning guarantees and further improve these bounds for the special case of conjunctions. We finish by giving robust learning algorithms for halfspaces on $\{0,1\}^n$ and then obtaining robustness guarantees for halfspaces in $\mathbb{R}^n$ against precision-bounded adversaries.

pdf/when-are-local-queries-useful-for-robust-learning-kbrjaplo.pdf

When are Local Queries Useful for Robust Learning?

This paper presents an assume-guarantee specification theory (aka interface theory from [11]) for modular synthesis and verification of real-time processes with critical timing constraints. Four operations, i.e. conjunction, disjunction, parallel and quotient, are defined over specifications, drawing inspirations from classic specification theories like refinement calculus [4, 19]. We show that a congruence (or pre-congruence) characterised by a trace-based semantics [14] captures exactly the notion of substitutivity (or refinement) between specifications.

A Specification Theory of Real-Time Processes

Unsupervised representation learning leverages large unlabeled datasets and is competitive with supervised learning. But non-robust encoders may affect downstream task robustness. Recently, robust representation encoders have become of interest. Still, all prior work evaluates robustness using a downstream classiﬁcation task. Instead, we propose a family of unsupervised robustness measures, which are model-and task-agnostic and label-free. We benchmark state-of-the-art representation encoders and show that none dominates the rest. We offer unsupervised extensions to the FGSM and PGD attacks. When used in adversarial training, they improve most unsupervised robustness measures, including certiﬁed robustness. We validate our results against a linear probe and show that, for MOCOv2, adversarial training results in 3 times higher certiﬁed accuracy, a 2-fold decrease in impersonation attack success rate and considerable improvements in certiﬁed robustness.

R obustness of u nsupervised r epresentation l earning without l abels

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