Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies

Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual information (MI) which is, in principle, an objective and model independent similarity measure. MI can be estimated by concatenating and zipping sequences, yielding thereby the "normalized compression distance". So far this has produced promising results, but with uncontrolled errors. We describe a simple approach to get robust estimates of MI from global pairwise alignments. Using standard alignment algorithms, this gives for animal mitochondrial DNA estimates that are strikingly close to estimates obtained from the alignment free methods mentioned above. Our main result uses algorithmic (Kolmogorov) information theory, but we show that similar results can also be obtained from Shannon theory. Due to the fact that it is not additive, normalized compression distance is not an optimal metric for phylogenetics, but we propose a simple modification that overcomes the issue of additivity. We test several versions of our MI based distance measures on a large number of randomly chosen quartets and demonstrate that they all perform better than traditional measures like the Kimura or log-det (resp. paralinear) distances. Even a simplified version based on single letter Shannon entropies, which can be easily incorporated in existing software packages, gave superior results throughout the entire animal kingdom. But we see the main virtue of our approach in a more general way. For example, it can also help to judge the relative merits of different alignment algorithms, by estimating the significance of specific alignments.Comment: 19 pages + 16 pages of supplementary materia

The Vadalog System: Datalog-based Reasoning for Knowledge Graphs

Over the past years, there has been a resurgence of Datalog-based systems in the database community as well as in industry. In this context, it has been recognized that to handle the complex knowl\-edge-based scenarios encountered today, such as reasoning over large knowledge graphs, Datalog has to be extended with features such as existential quantification. Yet, Datalog-based reasoning in the presence of existential quantification is in general undecidable. Many efforts have been made to define decidable fragments. Warded Datalog+/- is a very promising one, as it captures PTIME complexity while allowing ontological reasoning. Yet so far, no implementation of Warded Datalog+/- was available. In this paper we present the Vadalog system, a Datalog-based system for performing complex logic reasoning tasks, such as those required in advanced knowledge graphs. The Vadalog system is Oxford's contribution to the VADA research programme, a joint effort of the universities of Oxford, Manchester and Edinburgh and around 20 industrial partners. As the main contribution of this paper, we illustrate the first implementation of Warded Datalog+/-, a high-performance Datalog+/- system utilizing an aggressive termination control strategy. We also provide a comprehensive experimental evaluation.Comment: Extended version of VLDB paper <https://doi.org/10.14778/3213880.3213888

Practical Minimum Cut Algorithms

The minimum cut problem for an undirected edge-weighted graph asks us to divide its set of nodes into two blocks while minimizing the weight sum of the cut edges. Here, we introduce a linear-time algorithm to compute near-minimum cuts. Our algorithm is based on cluster contraction using label propagation and Padberg and Rinaldi's contraction heuristics [SIAM Review, 1991]. We give both sequential and shared-memory parallel implementations of our algorithm. Extensive experiments on both real-world and generated instances show that our algorithm finds the optimal cut on nearly all instances significantly faster than other state-of-the-art algorithms while our error rate is lower than that of other heuristic algorithms. In addition, our parallel algorithm shows good scalability

Solving Parity Games in Scala

Parity games are two-player games, played on directed graphs, whose nodes are labeled with priorities. Along a play, the maximal priority occurring infinitely often determines the winner. In the last two decades, a variety of algorithms and successive optimizations have been proposed. The majority of them have been implemented in PGSolver, written in OCaml, which has been elected by the community as the de facto platform to solve efficiently parity games as well as evaluate their performance in several specific cases. PGSolver includes the Zielonka Recursive Algorithm that has been shown to perform better than the others in randomly generated games. However, even for arenas with a few thousand of nodes (especially over dense graphs), it requires minutes to solve the corresponding game. In this paper, we deeply revisit the implementation of the recursive algorithm introducing several improvements and making use of Scala Programming Language. These choices have been proved to be very successful, gaining up to two orders of magnitude in running time

Zuverlässige und Energieeffiziente gemischt-kritische Echtzeit On-Chip Systeme

Multi- and many-core embedded systems are increasingly becoming the target for many applications that require high performance under varying conditions. A resulting challenge is the control, and reliable operation of such complex multiprocessing architectures under changes, e.g., high temperature and degradation. In mixed-criticality systems where many applications with varying criticalities are consolidated on the same execution platform, fundamental isolation requirements to guarantee non-interference of critical functions are crucially important. While Networks-on-Chip (NoCs) are the prevalent solution to provide scalable and efficient interconnects for the multiprocessing architectures, their associated energy consumption has immensely increased. Specifically, hard real-time NoCs must manifest limited energy consumption as thermal runaway in such a core shared resource jeopardizes the whole system guarantees. Thus, dynamic energy management of NoCs, as opposed to the related work static solutions, is highly necessary to save energy and decrease temperature, while preserving essential temporal requirements. In this thesis, we introduce a centralized management to provide energy-aware NoCs for hard real-time systems. The design relies on an energy control network, developed on top of an existing switch arbitration network to allow isolation between energy optimization and data transmission. The energy control layer includes local units called Power-Aware NoC controllers that dynamically optimize NoC energy depending on the global state and applications’ temporal requirements. Furthermore, to adapt to abnormal situations that might occur in the system due to degradation, we extend the concept of NoC energy control to include the entire system scope. That is, online resource management employing hierarchical control layers to treat system degradation (imminent core failures) is supported. The mechanism applies system reconfiguration that involves workload migration. For mixed-criticality systems, it allows flexible boundaries between safety-critical and non-critical subsystems to safely apply the reconfiguration, preserving fundamental safety requirements and temporal predictability. Simulation and formal analysis-based experiments on various realistic usecases and benchmarks are conducted showing significant improvements in NoC energy-savings and in treatment of system degradation for mixed-criticality systems improving dependability over the status quo.Eingebettete Many- und Multi-core-Systeme werden zunehmend das Ziel für Anwendungen, die hohe Anfordungen unter unterschiedlichen Bedinungen haben. Für solche hochkomplexed Multi-Prozessor-Systeme ist es eine grosse Herausforderung zuverlässigen Betrieb sicherzustellen, insbesondere wenn sich die Umgebungseinflüsse verändern. In Systeme mit gemischter Kritikalität, in denen viele Anwendungen mit unterschiedlicher Kritikalität auf derselben Ausführungsplattform bedient werden müssen, sind grundlegende Isolationsanforderungen zur Gewährleistung der Nichteinmischung kritischer Funktionen von entscheidender Bedeutung. Während On-Chip Netzwerke (NoCs) häufig als skalierbare Verbindung für die Multiprozessor-Architekturen eingesetzt werden, ist der damit verbundene Energieverbrauch immens gestiegen. Daher sind dynamische Plattformverwaltungen, im Gegensatz zu den statischen, zwingend notwendig, um ein System an die oben genannten Veränderungen anzupassen und gleichzeitig Timing zu gewährleisten. In dieser Arbeit entwickeln wir energieeffiziente NoCs für harte Echtzeitsysteme. Das Design basiert auf einem Energiekontrollnetzwerk, das auf einem bestehenden Switch-Arbitration-Netzwerk entwickelt wurde, um eine Isolierung zwischen Energieoptimierung und Datenübertragung zu ermöglichen. Die Energiesteuerungsschicht umfasst lokale Einheiten, die als Power-Aware NoC-Controllers bezeichnet werden und die die NoC-Energie in Abhängigkeit vom globalen Zustand und den zeitlichen Anforderungen der Anwendungen optimieren. Darüber hinaus wird das Konzept der NoC-Energiekontrolle zur Anpassung an Anomalien, die aufgrund von Abnutzung auftreten können, auf den gesamten Systemumfang ausgedehnt. Online- Ressourcenverwaltungen, die hierarchische Kontrollschichten zur Behandlung Abnutzung (drohender Kernausfälle) einsetzen, werden bereitgestellt. Bei Systemen mit gemischter Kritikalität erlaubt es flexible Grenzen zwischen sicherheitskritischen und unkritischen Subsystemen, um die Rekonfiguration sicher anzuwenden, wobei grundlegende Sicherheitsanforderungen erhalten bleiben und Timing Vorhersehbarkeit. Experimente werden auf der Basis von Simulationen und formalen Analysen zu verschiedenen realistischen Anwendungsfallen und Benchmarks durchgeführt, die signifikanten Verbesserungen bei On-Chip Netzwerke-Energieeinsparungen und bei der Behandlung von Abnutzung für Systeme mit gemischter Kritikalität zur Verbesserung die Systemstabilität gegenüber dem bisherigen Status quo zeigen

Individual Tariffs for Mobile Services: Analysis of Operator Business and Risk Consequences

A design approach is offered for individual tariffs for mass customized mobile service products, whereby operators can determine their contract acceptance rules to guarantee with a set probability their minimum profit and risk levels. It uses realistic improvements to earlier reported negotiation algorithms [1], and a full operator operational model including infrastructure and content acquisition. Value at risk and profit are analyzed when a random user has consistent characteristics to a survey group, so that risk and profits are pooled. This analysis is necessary to give the supplier business guarantees to enter individual tariff agreements. A full numerical case is given for a class of mobile service.risks;mobile communication services;Individual tariffs

PowerModels.jl: An Open-Source Framework for Exploring Power Flow Formulations

In recent years, the power system research community has seen an explosion of novel methods for formulating and solving power network optimization problems. These emerging methods range from new power flow approximations, which go beyond the traditional DC power flow by capturing reactive power, to convex relaxations, which provide solution quality and runtime performance guarantees. Unfortunately, the sophistication of these emerging methods often presents a significant barrier to evaluating them on a wide variety of power system optimization applications. To address this issue, this work proposes PowerModels, an open-source platform for comparing power flow formulations. From its inception, PowerModels was designed to streamline the process of evaluating different power flow formulations on shared optimization problem specifications. This work provides a brief introduction to the design of PowerModels, validates its implementation, and demonstrates its effectiveness with a proof-of-concept study analyzing five different formulations of the Optimal Power Flow problem