Parallel implementation of the TRANSIMS micro-simulation

This paper describes the parallel implementation of the TRANSIMS traffic micro-simulation. The parallelization method is domain decomposition, which means that each CPU of the parallel computer is responsible for a different geographical area of the simulated region. We describe how information between domains is exchanged, and how the transportation network graph is partitioned. An adaptive scheme is used to optimize load balancing. We then demonstrate how computing speeds of our parallel micro-simulations can be systematically predicted once the scenario and the computer architecture are known. This makes it possible, for example, to decide if a certain study is feasible with a certain computing budget, and how to invest that budget. The main ingredients of the prediction are knowledge about the parallel implementation of the micro-simulation, knowledge about the characteristics of the partitioning of the transportation network graph, and knowledge about the interaction of these quantities with the computer system. In particular, we investigate the differences between switched and non-switched topologies, and the effects of 10 Mbit, 100 Mbit, and Gbit Ethernet. keywords: Traffic simulation, parallel computing, transportation planning, TRANSIM

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory network. Latest advances in transcriptomics have made it possible to infer basic topologies of pluripotency governing networks. The inferred network topologies, however, only encode boolean information while remaining silent about the roles of dynamics and molecular noise in gene expression. These features are widely considered essential for functional decision making. Herein we developed a framework for extending the boolean level networks into models accounting for individual genetic switches and promoter architecture which allows mechanistic interrogation of the roles of molecular noise, external signaling, and network topology. We demonstrate the pluripotent state of the network to be a broad attractor which is robust to variations of gene expression. Dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the molecular noise originating from genetic switching events which makes cells more responsive to extracellular signals. Lastly we show that steady state probability landscape can be significantly remodeled by global gene switching rates alone which can be taken as a proxy for how global epigenetic modifications exert control over stability of pluripotent states.Comment: 11 pages, 7 figure

Parameterized Model Checking of Token-Passing Systems

We revisit the parameterized model checking problem for token-passing systems and specifications in indexed $\textsf{CTL}^\ast \backslash \textsf{X}$. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed $\textsf{CTL}^\ast \backslash \textsf{X}$ in uni-directional token rings can be reduced to checking rings up to some \emph{cutoff} size. Clarke et al. (2004) have shown a similar result for general topologies and indexed $\textsf{LTL} \backslash \textsf{X}$, provided processes cannot choose the directions for sending or receiving the token. We unify and substantially extend these results by systematically exploring fragments of indexed $\textsf{CTL}^\ast \backslash \textsf{X}$ with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token.Comment: We had to remove an appendix until the proofs and notations there is cleare

A Review of Fault Diagnosing Methods in Power Transmission Systems

Transient stability is important in power systems. Disturbances like faults need to be segregated to restore transient stability. A comprehensive review of fault diagnosing methods in the power transmission system is presented in this paper. Typically, voltage and current samples are deployed for analysis. Three tasks/topics; fault detection, classification, and location are presented separately to convey a more logical and comprehensive understanding of the concepts. Feature extractions, transformations with dimensionality reduction methods are discussed. Fault classification and location techniques largely use artificial intelligence (AI) and signal processing methods. After the discussion of overall methods and concepts, advancements and future aspects are discussed. Generalized strengths and weaknesses of different AI and machine learning-based algorithms are assessed. A comparison of different fault detection, classification, and location methods is also presented considering features, inputs, complexity, system used and results. This paper may serve as a guideline for the researchers to understand different methods and techniques in this field

Efficient Synthesis of Network Updates

Software-defined networking (SDN) is revolutionizing the networking industry, but current SDN programming platforms do not provide automated mechanisms for updating global configurations on the fly. Implementing updates by hand is challenging for SDN programmers because networks are distributed systems with hundreds or thousands of interacting nodes. Even if initial and final configurations are correct, naively updating individual nodes can lead to incorrect transient behaviors, including loops, black holes, and access control violations. This paper presents an approach for automatically synthesizing updates that are guaranteed to preserve specified properties. We formalize network updates as a distributed programming problem and develop a synthesis algorithm based on counterexample-guided search and incremental model checking. We describe a prototype implementation, and present results from experiments on real-world topologies and properties demonstrating that our tool scales to updates involving over one-thousand nodes

Evolving Neural Networks through a Reverse Encoding Tree

NeuroEvolution is one of the most competitive evolutionary learning frameworks for designing novel neural networks for use in specific tasks, such as logic circuit design and digital gaming. However, the application of benchmark methods such as the NeuroEvolution of Augmenting Topologies (NEAT) remains a challenge, in terms of their computational cost and search time inefficiency. This paper advances a method which incorporates a type of topological edge coding, named Reverse Encoding Tree (RET), for evolving scalable neural networks efficiently. Using RET, two types of approaches -- NEAT with Binary search encoding (Bi-NEAT) and NEAT with Golden-Section search encoding (GS-NEAT) -- have been designed to solve problems in benchmark continuous learning environments such as logic gates, Cartpole, and Lunar Lander, and tested against classical NEAT and FS-NEAT as baselines. Additionally, we conduct a robustness test to evaluate the resilience of the proposed NEAT algorithms. The results show that the two proposed strategies deliver improved performance, characterized by (1) a higher accumulated reward within a finite number of time steps; (2) using fewer episodes to solve problems in targeted environments, and (3) maintaining adaptive robustness under noisy perturbations, which outperform the baselines in all tested cases. Our analysis also demonstrates that RET expends potential future research directions in dynamic environments. Code is available from https://github.com/HaolingZHANG/ReverseEncodingTree.Comment: Accepted to IEEE Congress on Evolutionary Computation (IEEE CEC) 2020. Lecture Presentatio

Verification and Synthesis of Symmetric Uni-Rings for Leads-To Properties

This paper investigates the verification and synthesis of parameterized protocols that satisfy leadsto properties $R \leadsto Q$ on symmetric unidirectional rings (a.k.a. uni-rings) of deterministic and constant-space processes under no fairness and interleaving semantics, where $R$ and $Q$ are global state predicates. First, we show that verifying $R \leadsto Q$ for parameterized protocols on symmetric uni-rings is undecidable, even for deterministic and constant-space processes, and conjunctive state predicates. Then, we show that surprisingly synthesizing symmetric uni-ring protocols that satisfy $R \leadsto Q$ is actually decidable. We identify necessary and sufficient conditions for the decidability of synthesis based on which we devise a sound and complete polynomial-time algorithm that takes the predicates $R$ and $Q$, and automatically generates a parameterized protocol that satisfies $R \leadsto Q$ for unbounded (but finite) ring sizes. Moreover, we present some decidability results for cases where leadsto is required from multiple distinct $R$ predicates to different $Q$ predicates. To demonstrate the practicality of our synthesis method, we synthesize some parameterized protocols, including agreement and parity protocols