Conic Optimization Theory: Convexification Techniques and Numerical Algorithms

Optimization is at the core of control theory and appears in several areas of this field, such as optimal control, distributed control, system identification, robust control, state estimation, model predictive control and dynamic programming. The recent advances in various topics of modern optimization have also been revamping the area of machine learning. Motivated by the crucial role of optimization theory in the design, analysis, control and operation of real-world systems, this tutorial paper offers a detailed overview of some major advances in this area, namely conic optimization and its emerging applications. First, we discuss the importance of conic optimization in different areas. Then, we explain seminal results on the design of hierarchies of convex relaxations for a wide range of nonconvex problems. Finally, we study different numerical algorithms for large-scale conic optimization problems.Comment: 18 page

Grothendieck inequalities for semidefinite programs with rank constraint

Grothendieck inequalities are fundamental inequalities which are frequently used in many areas of mathematics and computer science. They can be interpreted as upper bounds for the integrality gap between two optimization problems: a difficult semidefinite program with rank-1 constraint and its easy semidefinite relaxation where the rank constrained is dropped. For instance, the integrality gap of the Goemans-Williamson approximation algorithm for MAX CUT can be seen as a Grothendieck inequality. In this paper we consider Grothendieck inequalities for ranks greater than 1 and we give two applications: approximating ground states in the n-vector model in statistical mechanics and XOR games in quantum information theory.Comment: 22 page

BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Distributed execution of bigraphical reactive systems

The bigraph embedding problem is crucial for many results and tools about bigraphs and bigraphical reactive systems (BRS). Current algorithms for computing bigraphical embeddings are centralized, i.e. designed to run locally with a complete view of the guest and host bigraphs. In order to deal with large bigraphs, and to parallelize reactions, we present a decentralized algorithm, which distributes both state and computation over several concurrent processes. This allows for distributed, parallel simulations where non-interfering reactions can be carried out concurrently; nevertheless, even in the worst case the complexity of this distributed algorithm is no worse than that of a centralized algorithm

Bigraphical models for protein and membrane interactions

We present a bigraphical framework suited for modeling biological systems both at protein level and at membrane level. We characterize formally bigraphs corresponding to biologically meaningful systems, and bigraphic rewriting rules representing biologically admissible interactions. At the protein level, these bigraphic reactive systems correspond exactly to systems of kappa-calculus. Membrane-level interactions are represented by just two general rules, whose application can be triggered by protein-level interactions in a well-de\"ined and precise way. This framework can be used to compare and merge models at different abstraction levels; in particular, higher-level (e.g. mobility) activities can be given a formal biological justification in terms of low-level (i.e., protein) interactions. As examples, we formalize in our framework the vesiculation and the phagocytosis processes

Innocent strategies as presheaves and interactive equivalences for CCS

Seeking a general framework for reasoning about and comparing programming languages, we derive a new view of Milner's CCS. We construct a category E of plays, and a subcategory V of views. We argue that presheaves on V adequately represent innocent strategies, in the sense of game semantics. We then equip innocent strategies with a simple notion of interaction. This results in an interpretation of CCS. Based on this, we propose a notion of interactive equivalence for innocent strategies, which is close in spirit to Beffara's interpretation of testing equivalences in concurrency theory. In this framework we prove that the analogues of fair and must testing equivalences coincide, while they differ in the standard setting.Comment: In Proceedings ICE 2011, arXiv:1108.014