Discovering Coherent Biclusters from Gene Expression Data Using Zero-Suppressed Binary Decision Diagrams

The biclustering method can be a very useful analysis tool when some genes have multiple functions and experimental conditions are diverse in gene expression measurement. This is because the biclustering approach, in contrast to the conventional clustering techniques, focuses on finding a subset of the genes and a subset of the experimental conditions that together exhibit coherent behavior. However, the biclustering problem is inherently intractable, and it is often computationally costly to find biclusters with high levels of coherence. In this work, we propose a novel biclustering algorithm that exploits the zero-suppressed binary decision diagrams (ZBDDs) data structure to cope with the computational challenges. Our method can find all biclusters that satisfy specific input conditions, and it is scalable to practical gene expression data. We also present experimental results confirming the effectiveness of our approach

VLSI Design

This book provides some recent advances in design nanometer VLSI chips. The selected topics try to present some open problems and challenges with important topics ranging from design tools, new post-silicon devices, GPU-based parallel computing, emerging 3D integration, and antenna design. The book consists of two parts, with chapters such as: VLSI design for multi-sensor smart systems on a chip, Three-dimensional integrated circuits design for thousand-core processors, Parallel symbolic analysis of large analog circuits on GPU platforms, Algorithms for CAD tools VLSI design, A multilevel memetic algorithm for large SAT-encoded problems, etc

Universal Smart Grid Agent for Distributed Power Generation Management

"Somewhere, there is always wind blowing or the sun shining." This maxim could lead the global shift from fossil to renewable energy sources, suggesting that there is enough energy available to be turned into electricity. But the already impressive numbers that are available today, along with the European Union's 20-20-20 goal – to power 20% of the EU energy consumption from renewables until 2020 –, might mislead us over the problem that the go-to renewables readily available rely on a primary energy source mankind cannot control: the weather. At the same time, the notion of the smart grid introduces a vast array of new data coming from sensors in the power grid, at wind farms, power plants, transformers, and consumers. The new wealth of information might seem overwhelming, but can help to manage the different actors in the power grid. This book proposes to view the problem of power generation and distribution in the face of increased volatility as a problem of information distribution and processing. It enhances the power grid by turning its nodes into agents that forecast their local power balance from historical data, using artificial neural networks and the multi-part evolutionary training algorithm described in this book. They pro-actively communicate power demand and supply, adhering to a set of behavioral rules this book defines, and finally solve the 0-1 knapsack problem of choosing offers in such a way that not only solves the disequilibrium, but also minimizes line loss, by elegant modeling in the Boolean domain. The book shows that the Divide-et-Impera approach of a distributed grid control can lead to an efficient, reliable integration of volatile renewable energy sources into the power grid

Dynamic Trace Analysis with Zero-Suppressed BDDs

Instruction level parallelism (ILP) limitations have forced processor manufacturers to develop multi-core platforms with the expectation that programs will be able to exploit thread level parallelism (TLP). Multi-core programming shifts the burden of locating additional performance away from computer hardware to the software developers, who often attempt high-level redesigns focused on exposing thread level parallelism, as well as explore aggressive optimizations for sequential codes. Precise dynamic analysis can provide useful guidance for program optimization efforts, including efforts to find and extract thread level parallelism. Unfortunately, finding regions of code amenable to further optimization efforts requires analyzing traces that can quickly grow in size. Analysis of large dynamic traces (e.g. one billion instructions or more) is often impractical for commodity hardware. An ideal representation for dynamic trace data would provide compression. However, decompressing large software traces, even if decompressed data is never permanently stored, would make many analysis impractical. A better solution would allow analysis of the compressed data, without a costly decompression step. Prior works have developed trace compressors that generate an analyzable representation, but often limit the precision or scope of analyses. Zero-suppressed binary decision diagram (ZDDs) exhibit many of the desired properties of an ideal trace representation. This thesis shows: (1) dynamic trace data may be represented by zero-suppressed binary decision diagrams (ZDDs); (2) ZDDs allow many analyses to scale; (3) encoding traces as ZDDs can be performed in a reasonable amount of time; and, (4) ZDD-based analyses, such as irrelevant instruction detection and potential coarse-grained thread level parallelism extraction, can reveal a number of performanc

Symmetric and efficient synthesis

Since the formulation of the synthesis problem for reactive systems by Church in the 60s, research on synthesis has lead to both theoretical insights and practical approaches for automatically constructing systems from their specifications. While the first solution of the problem was given by Büchi as early as 1969, only very recently, focus has shifted towards identifying ways to exploit the structure in reactive system specifications in order to lift the scalability of synthesis to industrial-sized designs. The recent progress in synthesis not only lead to a renewed interest in the subject, but also shed light onto the downsides of current synthesis approaches. In the original formulation of the problem, the structure of the produced solutions was not a concern. Experiments with current synthesis approaches has however shown that the computed implementations are usually very hard to understand and have little of the structure that manually constructed implementations have. Furthermore, the scalability of current synthesis approaches is still deemed to be insufficient for many industrial application scenarios, which prevents the introduction of reactive synthesis technology into industrial design flows. In this thesis, we tackle both of these problems for reactive synthesis. To counter the insufficient structure in the solutions, we analyse the problem of symmetric synthesis. In this alternative synthesis problem, the aim is to compute a solution that consists of multiple copies of the same process such that the overall system satisfies the specification. Such systems have no centralised control units, and are considered to be more robust and easier to maintain. We characterise undecidable and decidable cases of the problem, and provide a synthesis algorithm for rotation-symmetric architectures, which capture many cases of practical relevance. To improve the scalability in synthesis, we start with a simple but scalable approach to reactive synthesis that has shown its principal applicability in the field, and extend its main idea both in terms of scope and usability. We enhance its expressivity in a way that allows to synthesise robust systems, and remove its limitation to specifications of a very special form. Both improvements yield theoretical insights into the synthesis problem: we characterise which specification classes can be supported in synthesis approaches that use parity games with a fixed number of colours as the underlying computation model, and examine the properties of universal very-weak automata, on which we base a synthesis workflow that combines ease of specification with a low complexity of the underlying game solving step. As a side-result, we also obtain the first procedure to translate a formula in linear-time temporal logic (LTL) to a computation tree logic (CTL) formula with only universal path quantifiers, whenever possible. The new results on symmetric and efficient reactive synthesis are complemented by an easily accessible introductory chapter to the field of reactive synthesis that can also be read in isolation.paddle apparatus with membrane holder were identified.Trotz der Vorzüge der Synthese reaktiver Systeme gegenüber der manuellen Konstruktion solcher Systeme ist Synthese noch nicht als Teil industrieller Vorgehensmodelle etabliert. Als Hauptgrund für diese Diskrepanz gilt allgemein, dass sowohl die Qualität der synthetisierten Systeme bei Anwendung bisheriger Methoden unzureichend ist, als auch die Skalierbarkeit aktueller Syntheseverfahren der Verbesserung bedarf. Diese Dissertation behandelt beide diese Probleme der Synthese reaktiver Systeme auf breiter Front. Zur Verbesserung der Qualität synthetisierter Systeme wird die Synthese von strukturierten Systemen betrachtet. Experimente mit aktuellen Syntheseverfahren haben gezeigt, dass die erzeugten Implementierungen oft schwer zu verstehen sind und anders als handgeschriebene Implementierungen kaum Struktur haben. Abhilfe verschafft die Beschränkung auf die Erzeugung symmetrischer Systeme, die aus mehreren Kopien des selben Prozesses bestehen, so dass das Gesamtsystem die Spezifikation erfüllt. Solche Systeme haben keine zentrale Koordinationskomponente und werden allgemein als robuster und einfacher zu warten eingestuft. In dieser Dissertation werden entscheidbare und unentscheidbare Fälle des symmetrischen Syntheseproblems identifiziert und ein Synthesealgorithmus für rotationssymmetrische Systeme beschrieben. Diese Systemklasse deckt viele praktisch relevante Architekturen ab. Um das Problem der mangelnden Skalierbarkeit anzugehen, wird die Hauptidee des Generalised Reactivity(1) Syntheseansatzes, welcher seine praktische Anwendbarkeit bereits unter Beweis gestellt hat, aufgegriffen und sowohl bezüglich der Expressivität als auch der Benutzbarkeit vervollständigt. Die Erweiterung der Expressivität ermöglicht es, den resultierenden Ansatz für die Synthese robuster Systeme zu nutzen, während die Benutzbarkeit für industrielle Anwendungen durch die Aufhebung der Beschränkung, dass die Spezifikation eine sehr spezielle Form haben muss, erreicht wird. Beide Erweiterungen geben Einsicht in die Theorie der Synthese: Zum einen wird die Klasse der Spezifikationen, die in Syntheseansätzen verwendet werden können, die auf dem Lösen von Paritätsspielen mit einer vordefinierten Anzahl von Farben basieren, charakterisiert. Zum anderen wird Einsicht in die Eigenschaften universeller sehr schwacher Automaten gegeben. Ein Nebenprodukt der neuen Syntheseverfahren ist die erste Prozedur, um einen Ausdruck in linear-time temporal logic (LTL) in computation tree logic mit universellen Pfadquantoren (ACTL) zu übersetzen, wann immer dies möglich ist. Die Resultate zur symmetrischen und effizienten reaktiven Synthese werden von einer didaktisch aufbereiteten Einführung in das Gebiet der reaktiven Synthese begleitet, welche auch unabhängig von den übrigen Teilen der Dissertation gelesen werden kann