SAT Modulo Monotonic Theories

We define the concept of a monotonic theory and show how to build efficient SMT (SAT Modulo Theory) solvers, including effective theory propagation and clause learning, for such theories. We present examples showing that monotonic theories arise from many common problems, e.g., graph properties such as reachability, shortest paths, connected components, minimum spanning tree, and max-flow/min-cut, and then demonstrate our framework by building SMT solvers for each of these theories. We apply these solvers to procedural content generation problems, demonstrating major speed-ups over state-of-the-art approaches based on SAT or Answer Set Programming, and easily solving several instances that were previously impractical to solve

The Configurable SAT Solver Challenge (CSSC)

It is well known that different solution strategies work well for different types of instances of hard combinatorial problems. As a consequence, most solvers for the propositional satisfiability problem (SAT) expose parameters that allow them to be customized to a particular family of instances. In the international SAT competition series, these parameters are ignored: solvers are run using a single default parameter setting (supplied by the authors) for all benchmark instances in a given track. While this competition format rewards solvers with robust default settings, it does not reflect the situation faced by a practitioner who only cares about performance on one particular application and can invest some time into tuning solver parameters for this application. The new Configurable SAT Solver Competition (CSSC) compares solvers in this latter setting, scoring each solver by the performance it achieved after a fully automated configuration step. This article describes the CSSC in more detail, and reports the results obtained in its two instantiations so far, CSSC 2013 and 2014

Reachability analysis for AWS-based networks

Cloud services provide the ability to provision virtual networked infrastructure on demand over the Internet. The rapid growth of these virtually provisioned cloud networks has increased the demand for automated reasoning tools capable of identifying misconfigurations or security vulnerabilities. This type of automation gives customers the assurance they need to deploy sensitive workloads. It can also reduce the cost and time-to-market for regulated customers looking to establish compliance certification for cloud-based applications. In this industrial case-study, we describe a new network reachability reasoning tool, called Tiros, that uses off-the-shelf automated theorem proving tools to fill this need. Tiros is the foundation of a recently introduced network security analysis feature in the Amazon Inspector service now available to millions of customers building applications in the cloud. Tiros is also used within Amazon Web Services (AWS) to automate the checking of compliance certification and adherence to security invariants for many AWS services that build on existing AWS networking features

Plant and prokaryotic TIR domains generate distinct cyclic ADPR NADase products

Toll/interleukin-1 receptor (TIR) domain proteins function in cell death and immunity. In plants and bacteria, TIR domains are often enzymes that produce isomers of cyclic adenosine 5′-diphosphate–ribose (cADPR) as putative immune signaling molecules. The identity and functional conservation of cADPR isomer signals is unclear. A previous report found that a plant TIR could cross-activate the prokaryotic Thoeris TIR–immune system, suggesting the conservation of plant and prokaryotic TIR-immune signals. Here, we generate autoactive Thoeris TIRs and test the converse hypothesis: Do prokaryotic Thoeris TIRs also cross-activate plant TIR immunity? Using in planta and in vitro assays, we find that Thoeris and plant TIRs generate overlapping sets of cADPR isomers and further clarify how plant and Thoeris TIRs activate the Thoeris system via producing 3′cADPR. This study demonstrates that the TIR signaling requirements for plant and prokaryotic immune systems are distinct and that TIRs across kingdoms generate a diversity of small-molecule products

SAT modulo monotonic theories

Satisfiability Modulo Theories (SMT) solvers are a class of efficient constraint solvers which form integral parts of many algorithms. Over the years, dozens of different Satisfiability Modulo Theories solvers have been developed, supporting dozens of different logics. However, there are still many important applications for which specialized SMT solvers have not yet been developed. We develop a framework for easily building efficient SMT solvers for previously unsupported logics. Our techniques apply to a wide class of logics which we call monotonic theories, which include many important elements of graph theory and automata theory. Using this SAT Modulo Monotonic Theories framework, we created a new SMT solver, MonoSAT. We demonstrate that MonoSAT improves the state of the art across a wide body of applications, ranging from circuit layout and data center management to protocol synthesis - and even to video game design.Science, Faculty ofComputer Science, Department ofGraduat

VNF chain allocation and management at data center scale

Algorithms and the Foundations of Software technolog

Proteomic analysis of microtubule inner proteins (MIPs) in Rib72 null Tetrahymena cells reveals functional MIPs.

The core structure of motile cilia and flagella, the axoneme, is built from a stable population of doublet microtubules. This unique stability is brought about, at least in part, by a network of microtubule inner proteins (MIPs) that are bound to the luminal side of the microtubule walls. Rib72A and Rib72B were identified as MIPs in the motile cilia of the protist Tetrahymena thermophila. Loss of these proteins leads to ciliary defects and loss of additional MIPs. We performed mass spectrometry coupled with proteomic analysis and bioinformatics to identify the MIPs lost in RIB72A/B knockout Tetrahymena axonemes. We identified a number of candidate MIPs and pursued one, Fap115, for functional characterization. We find that loss of Fap115 results in disrupted cell swimming and aberrant ciliary beating. Cryo-electron tomography reveals that Fap115 localizes to MIP6a in the A-tubule of the doublet microtubules. Overall, our results highlight the complex relationship between MIPs, ciliary structure, and ciliary function