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In this paper, we present a method to encrypt dynamic controllers that can be implemented through most homomorphic encryption schemes, including somewhat, leveled fully, and fully homomorphic encryption. To this end, we represent the output of the given controller as a linear combination of a fixed number of previous inputs and outputs. As a result, the encrypted controller involves only a limited number of homomorphic multiplications on every encrypted data, assuming that the output is re-encrypted and transmitted back from the actuator. A guidance for parameter choice is also provided, ensuring that the encrypted controller achieves predefined performance for an infinite time horizon. Furthermore, we propose a customization of the method for Ring-Learning With Errors (Ring-LWE) based cryptosystems, where a vector of messages can be encrypted into a single ciphertext and operated simultaneously, thus reducing computation and communication loads. Unlike previous results, the proposed customization does not require extra algorithms such as rotation, other than basic addition and multiplication. Simulation results demonstrate the effectiveness of the proposed method.

Positive linear programs (LPs) model many graph and operations research problems. One can solve for a $(1+\epsilon)$-approximation for positive LPs, for any selected $\epsilon$, in polylogarithmic depth and near-linear work via variations of the multiplicative weight update (MWU) method. Despite extensive theoretical work on these algorithms through the decades, their empirical performance is not well understood. In this work, we implement and test an efficient parallel algorithm for solving positive LP relaxations, and apply it to graph problems such as densest subgraph, bipartite matching, vertex cover and dominating set. We accelerate the algorithm via a new step size search heuristic. Our implementation uses sparse linear algebra optimization techniques such as fusion of vector operations and use of sparse format. Furthermore, we devise an implicit representation for graph incidence constraints. We demonstrate the parallel scalability with the use of threading OpenMP and MPI on the Stampede2 supercomputer. We compare this implementation with exact libraries and specialized libraries for the above problems in order to evaluate MWU's practical standing for both accuracy and performance among other methods. Our results show this implementation is faster than general purpose LP solvers (IBM CPLEX, Gurobi) in all of our experiments, and in some instances, outperforms state-of-the-art specialized parallel graph algorithms.

Time-series datasets are central in numerous fields of science and engineering, such as biomedicine, Earth observation, and network analysis. Extensive research exists on state-space models (SSMs), which are powerful mathematical tools that allow for probabilistic and interpretable learning on time series. Estimating the model parameters in SSMs is arguably one of the most complicated tasks, and the inclusion of prior knowledge is known to both ease the interpretation but also to complicate the inferential tasks. Very recent works have attempted to incorporate a graphical perspective on some of those model parameters, but they present notable limitations that this work addresses. More generally, existing graphical modeling tools are designed to incorporate either static information, focusing on statistical dependencies among independent random variables (e.g., graphical Lasso approach), or dynamic information, emphasizing causal relationships among time series samples (e.g., graphical Granger approaches). However, there are no joint approaches combining static and dynamic graphical modeling within the context of SSMs. This work proposes a novel approach to fill this gap by introducing a joint graphical modeling framework that bridges the static graphical Lasso model and a causal-based graphical approach for the linear-Gaussian SSM. We present DGLASSO (Dynamic Graphical Lasso), a new inference method within this framework that implements an efficient block alternating majorization-minimization algorithm. The algorithm's convergence is established by departing from modern tools from nonlinear analysis. Experimental validation on synthetic and real weather variability data showcases the effectiveness of the proposed model and inference algorithm.

In this paper we study a Separation Logic of Relations (SLR) and compare its expressiveness to (Monadic)Second Order Logic (M)SO. SLR is based on the well-known Symbolic Heap fragment of Separation Logic, whose formulae are composed of points-to assertions, inductively defined predicates, with the separating conjunction as the only logical connective. SLR generalizes the Symbolic Heap fragment by supporting general relational atoms, instead of only points-to assertions. In this paper, we restrict ourselves to finite relational structures, and hence only consider Weak (M)SO, where quantification ranges over finite sets. Our main results are that SLR and MSO are incomparable on structures of unbounded treewidth, while SLR can be embedded in SO in general. Furthermore, MSO becomes a strict subset of SLR, when the treewidth of the models is bounded by a parameter and all vertices attached to some hyperedge belong to the interpretation of a fixed unary relation symbol. We also discuss the problem of identifying a fragment of SLR that is equivalent to MSO over models of bounded treewidth.

The Independent Cutset problem asks whether there is a set of vertices in a given graph that is both independent and a cutset. Such a problem is $\textsf{NP}$-complete even when the input graph is planar and has maximum degree five. In this paper, we first present a $\mathcal{O}^*(1.4423^{n})$-time algorithm for the problem. We also show how to compute a minimum independent cutset (if any) in the same running time. Since the property of having an independent cutset is MSO$_1$-expressible, our main results are concerned with structural parameterizations for the problem considering parameters that are not bounded by a function of the clique-width of the input. We present $\textsf{FPT}$-time algorithms for the problem considering the following parameters: the dual of the maximum degree, the dual of the solution size, the size of a dominating set (where a dominating set is given as an additional input), the size of an odd cycle transversal, the distance to chordal graphs, and the distance to $P_5$-free graphs. We close by introducing the notion of $\alpha$-domination, which allows us to identify more fixed-parameter tractable and polynomial-time solvable cases.

Discrete chemical reaction networks formalize the interactions of molecular species in a well-mixed solution as stochastic events. Given their basic mathematical and physical role, the computational power of chemical reaction networks has been widely studied in the molecular programming and distributed computing communities. While for Turing-universal systems there is a universal measure of optimal information encoding based on Kolmogorov complexity, chemical reaction networks are not Turing universal unless error and unbounded molecular counts are permitted. Nonetheless, here we show that the optimal number of reactions to generate a specific count $x \in \mathbb{N}$ with probability $1$ is asymptotically equal to a ``space-aware'' version of the Kolmogorov complexity of $x$, defined as $\mathrm{\widetilde{K}s}(x) = \min_p\left\{\lvert p \rvert / \log \lvert p \rvert + \log(\texttt{space}(\mathcal{U}(p))) : \mathcal{U}(p) = x \right\}$, where $p$ is a program for universal Turing machine $\mathcal{U}$. This version of Kolmogorov complexity incorporates not just the length of the shortest program for generating $x$, but also the space usage of that program. Probability $1$ computation is captured by the standard notion of stable computation from distributed computing, but we limit our consideration to chemical reaction networks obeying a stronger constraint: they ``know when they are done'' in the sense that they produce a special species to indicate completion. As part of our results, we develop a module for encoding and unpacking any $b$ bits of information via $O(b/\log{b})$ reactions, which is information-theoretically optimal for incompressible information. Our work provides one answer to the question of how succinctly chemical self-organization can be encoded -- in the sense of generating precise molecular counts of species as the desired state.

Optimization tasks are crucial in statistical machine learning. Recently, there has been great interest in leveraging tools from dynamical systems to derive accelerated and robust optimization methods via suitable discretizations of continuous-time systems. However, these ideas have mostly been limited to Euclidean spaces and unconstrained settings, or to Riemannian gradient flows. In this work, we propose a dissipative extension of Dirac's theory of constrained Hamiltonian systems as a general framework for solving optimization problems over smooth manifolds, including problems with nonlinear constraints. We develop geometric/symplectic numerical integrators on manifolds that are "rate-matching," i.e., preserve the continuous-time rates of convergence. In particular, we introduce a dissipative RATTLE integrator able to achieve optimal convergence rate locally. Our class of (accelerated) algorithms are not only simple and efficient but also applicable to a broad range of contexts.

In this work, we further investigate the application of the well-known Richardson extrapolation (RE) technique to accelerate the convergence of sequences resulting from linear multistep methods (LMMs) for numerically solving initial-value problems of systems of ordinary differential equations. By extending the ideas of our previous paper, we now utilize some advanced versions of RE in the form of repeated RE (RRE). Assume that the underlying LMM -- the base method -- has order $p$ and RE is applied $l$ times. Then we prove that the accelerated sequence has convergence order $p+l$. The version we present here is global RE (GRE, also known as passive RE), since the terms of the linear combinations are calculated independently. Thus, the resulting higher-order LMM-RGRE methods can be implemented in a parallel fashion and existing LMM codes can directly be used without any modification. We also investigate how the linear stability properties of the base method (e.g. $A$- or $A(\alpha)$-stability) are preserved by the LMM-RGRE methods.

Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.

Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.