Efficient Trace Encodings of Bounded Synthesis for Asynchronous Distributed Systems

The manual implementation of distributed systems is an error-prone task because of the asynchronous interplay of components and the environment. Bounded synthesis automatically generates an implementation for the specification of the distributed system if one exists. So far, bounded synthesis for distributed systems does not utilize their asynchronous nature. Instead, concurrent behavior of components is encoded by all interleavings and only then checked against the specification. We close this gap by identifying true concurrency in synthesis of asynchronous distributed systems represented as Petri games. This defines when several interleavings can be subsumed by one true concurrent trace. Thereby, fewer and shorter verification problems have to be solved in each iteration of the bounded synthesis algorithm. For Petri games, experimental results show that our implementation using true concurrency outperforms the implementation based on checking all interleavings

Second-Order Hyperproperties

We introduce Hyper$^2$LTL, a temporal logic for the specification of hyperproperties that allows for second-order quantification over sets of traces. Unlike first-order temporal logics for hyperproperties, such as HyperLTL, Hyper$^2$LTL can express complex epistemic properties like common knowledge, Mazurkiewicz trace theory, and asynchronous hyperproperties. The model checking problem of Hyper$^2$LTL is, in general, undecidable. For the expressive fragment where second-order quantification is restricted to smallest and largest sets, we present an approximate model-checking algorithm that computes increasingly precise under- and overapproximations of the quantified sets, based on fixpoint iteration and automata learning. We report on encouraging experimental results with our model-checking algorithm, which we implemented in the tool~\texttt{HySO}

Leonardo's rule, self-similarity and wind-induced stresses in trees

Examining botanical trees, Leonardo da Vinci noted that the total cross-section of branches is conserved across branching nodes. In this Letter, it is proposed that this rule is a consequence of the tree skeleton having a self-similar structure and the branch diameters being adjusted to resist wind-induced loads

Live synthesis

Synthesis automatically constructs an implementation that satisfies a given logical specification. In this paper, we study the live synthesis problem, where the synthesized implementation replaces an already running system. In addition to satisfying its own specification, the synthesized implementation must guarantee a sound transition from the previous implementation. This version of the synthesis problem is highly relevant in “always-on” applications, where updates happen while the system is running. To specify the correct handover between the old and new implementation, we introduce an extension of linear-time temporal logic (LTL) called LiveLTL. A LiveLTL specification defines separate requirements on the two implementations and ensures that the new implementation satisfies, in addition to its own requirements, any obligations left unfinished by the old implementation. For specifications in LiveLTL, we show that the live synthesis problem can be solved within the same complexity bound as standard reactive synthesis, i.e., in 2EXPTIME. Our experiments show the necessity of live synthesis for LiveLTL specifications created from benchmarks of SYNTCOMP and robot control

Information Flow Guided Synthesis

Compositional synthesis relies on the discovery of assumptions, i.e., restrictions on the behavior of the remainder of the system that allow a component to realize its specification. In order to avoid losing valid solutions, these assumptions should be necessary conditions for realizability. However, because there are typically many different behaviors that realize the same specification, necessary behavioral restrictions often do not exist. In this paper, we introduce a new class of assumptions for compositional synthesis, which we call information flow assumptions. Such assumptions capture an essential aspect of distributed computing, because components often need to act upon information that is available only in other components. The presence of a certain flow of information is therefore often a necessary requirement, while the actual behavior that establishes the information flow is unconstrained. In contrast to behavioral assumptions, which are properties of individual computation traces, information flow assumptions are hyperproperties, i.e., properties of sets of traces. We present a method for the automatic derivation of information-flow assumptions from a temporal logic specification of the system. We then provide a technique for the automatic synthesis of component implementations based on information flow assumptions. This provides a new compositional approach to the synthesis of distributed systems. We report on encouraging first experiments with the approach, carried out with the BoSyHyper synthesis tool

Second-Order Hyperproperties

We introduce Hyper^2LTL, a temporal logic for the specification of hyperproperties that allows for second-order quantification over sets of traces. Unlike first-order temporal logics for hyperproperties, such as HyperLTL, Hyper^2LTL can express complex epistemic properties like common knowledge, Mazurkiewicz trace theory, and asynchronous hyperproperties. The model checking problem of Hyper^2LTL is, in general, undecidable. For the expressive fragment where second-order quantification is restricted to smallest and largest sets, we present an approximate model-checking algorithm that computes increasingly precise under- and overapproximations of the quantified sets, based on fixpoint iteration and automata learning. We report on encouraging experimental results with our model-checking algorithm, which we implemented in the tool HySO

Explaining Hyperproperty Violations

Hyperproperties relate multiple computation traces to each other. Model checkers for hyperproperties thus return, in case a system model violates the specification, a set of traces as a counterexample. Fixing the erroneous relations between traces in the system that led to the counterexample is a difficult manual effort that highly benefits from additional explanations. In this paper, we present an explanation method for counterexamples to hyperproperties described in the specification logic HyperLTL. We extend Halpern and Pearl's definition of actual causality to sets of traces witnessing the violation of a HyperLTL formula, which allows us to identify the events that caused the violation. We report on the implementation of our method and show that it significantly improves on previous approaches for analyzing counterexamples returned by HyperLTL model checkers

Visual Analysis of Hyperproperties for Understanding Model Checking Results

Model checkers provide algorithms for proving that a mathematical model of a system satisfies a given specification. In case of a violation, a counterexample that shows the erroneous behavior is returned. Understanding these counterexamples is challenging, especially for hyperproperty specifications, i.e., specifications that relate multiple executions of a system to each other. We aim to facilitate the visual analysis of such counterexamples through our HYPERVIS tool, which provides interactive visualizations of the given model, specification, and counterexample. Within an iterative and interdisciplinary design process, we developed visualization solutions that can effectively communicate the core aspects of the model checking result. Specifically, we introduce graphical representations of binary values for improving pattern recognition, color encoding for better indicating related aspects, visually enhanced textual descriptions, as well as extensive cross-view highlighting mechanisms. Further, through an underlying causal analysis of the counterexample, we are also able to identify values that contributed to the violation and use this knowledge for both improved encoding and highlighting. Finally, the analyst can modify both the specification of the hyperproperty and the system directly within HYPERVIS and initiate the model checking of the new version. In combination, these features notably support the analyst in understanding the error leading to the counterexample as well as iterating the provided system and specification. We ran multiple case studies with HYPERVIS and tested it with domain experts in qualitative feedback sessions. The participants’ positive feedback confirms the considerable improvement over the manual, text-based status quo and the value of the tool for explaining hyperproperties

The evolution of seeds

The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the \u27how\u27 question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long \u27distance\u27 time travel. Answering the \u27why\u27 question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of research describing the comparative biology of seeds is discussed. The review will be divided into sections dealing with: (1) the development and anatomy of seeds; (2) the endosperm; (3) dormancy; (4) early seed-like structures and the transition to seeds; and (5) the evolution of seed size (mass). In many cases, a special distinction is made between angiosperm and gymnosperm seeds. Finally, we make some recommendations for future research in seed biology

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe