Synthesizing Finite-state Protocols from Scenarios and Requirements

Scenarios, or Message Sequence Charts, offer an intuitive way of describing the desired behaviors of a distributed protocol. In this paper we propose a new way of specifying finite-state protocols using scenarios: we show that it is possible to automatically derive a distributed implementation from a set of scenarios augmented with a set of safety and liveness requirements, provided the given scenarios adequately \emph{cover} all the states of the desired implementation. We first derive incomplete state machines from the given scenarios, and then synthesis corresponds to completing the transition relation of individual processes so that the global product meets the specified requirements. This completion problem, in general, has the same complexity, PSPACE, as the verification problem, but unlike the verification problem, is NP-complete for a constant number of processes. We present two algorithms for solving the completion problem, one based on a heuristic search in the space of possible completions and one based on OBDD-based symbolic fixpoint computation. We evaluate the proposed methodology for protocol specification and the effectiveness of the synthesis algorithms using the classical alternating-bit protocol.Comment: This is the working draft of a paper currently in submission. (February 10, 2014

Error and Attack Tolerance of Layered Complex Networks

Many complex systems may be described not by one, but by a number of complex networks mapped one on the other in a multilayer structure. The interactions and dependencies between these layers cause that what is true for a distinct single layer does not necessarily reflect well the state of the entire system. In this paper we study the robustness of three real-life examples of two-layer complex systems that come from the fields of communication (the Internet), transportation (the European railway system) and biology (the human brain). In order to cover the whole range of features specific to these systems, we focus on two extreme policies of system's response to failures, no rerouting and full rerouting. Our main finding is that multilayer systems are much more vulnerable to errors and intentional attacks than they seem to be from a single layer perspective.Comment: 5 pages, 3 figure

Priority diffusion model in lattices and complex networks

We introduce a model for diffusion of two classes of particles ($A$ and $B$) with priority: where both species are present in the same site the motion of $A$'s takes precedence over that of $B$'s. This describes realistic situations in wireless and communication networks. In regular lattices the diffusion of the two species is normal but the $B$ particles are significantly slower, due to the presence of the $A$ particles. From the fraction of sites where the $B$ particles can move freely, which we compute analytically, we derive the diffusion coefficients of the two species. In heterogeneous networks the fraction of sites where $B$ is free decreases exponentially with the degree of the sites. This, coupled with accumulation of particles in high-degree nodes leads to trapping of the low priority particles in scale-free networks.Comment: 5 pages, 3 figure

Supporting User-Defined Functions on Uncertain Data

Uncertain data management has become crucial in many sensing and scientific applications. As user-defined functions (UDFs) become widely used in these applications, an important task is to capture result uncertainty for queries that evaluate UDFs on uncertain data. In this work, we provide a general framework for supporting UDFs on uncertain data. Specifically, we propose a learning approach based on Gaussian processes (GPs) to compute approximate output distributions of a UDF when evaluated on uncertain input, with guaranteed error bounds. We also devise an online algorithm to compute such output distributions, which employs a suite of optimizations to improve accuracy and performance. Our evaluation using both real-world and synthetic functions shows that our proposed GP approach can outperform the state-of-the-art sampling approach with up to two orders of magnitude improvement for a variety of UDFs. 1

On the Suitability of Estelle for Multimedia Systems

Formal Description Techniques have been widely used for the specification of traditional networked applications. They have not been applied to the specification of new applications such as multimedia systems yet. In this paper, we examine the FDT Estelle with respect to its suitability for multimedia system specification and automatic derivation of efficient implementations. We show that it is possible to specify certain aspects of multimedia systems, but that Estelle is not sufficient for others. The derived implementations often perform badly. We show the reasons and propose to use a slightly modified Estelle syntax and semantics to solve the problems. The implemented solution was tested successfully

Fluorescence activated cell sorting followed by small RNA sequencing reveals stable microRNA expression during cell cycle progression.

BACKGROUND: Previously, drug-based synchronization procedures were used for characterizing the cell cycle dependent transcriptional program. However, these synchronization methods result in growth imbalance and alteration of the cell cycle machinery. DNA content-based fluorescence activated cell sorting (FACS) is able to sort the different cell cycle phases without perturbing the cell cycle. MiRNAs are key transcriptional regulators of the cell cycle, however, their expression dynamics during cell cycle has not been explored. METHODS: Following an optimized FACS, a complex initiative of high throughput platforms (microarray, Taqman Low Density Array, small RNA sequencing) were performed to study gene and miRNA expression profiles of cell cycle sorted human cells originating from different tissues. Validation of high throughput data was performed using quantitative real time PCR. Protein expression was detected by Western blot. Complex statistics and pathway analysis were also applied. RESULTS: Beyond confirming the previously described cell cycle transcriptional program, cell cycle dependently expressed genes showed a higher expression independently from the cell cycle phase and a lower amplitude of dynamic changes in cancer cells as compared to untransformed fibroblasts. Contrary to mRNA changes, miRNA expression was stable throughout the cell cycle. CONCLUSIONS: Cell cycle sorting is a synchronization-free method for the proper analysis of cell cycle dynamics. Altered dynamic expression of universal cell cycle genes in cancer cells reflects the transformed cell cycle machinery. Stable miRNA expression during cell cycle progression may suggest that dynamical miRNA-dependent regulation may be of less importance in short term regulations during the cell cycle

Controlling Window Protocols for Time-Constrained Communication in a Multiple Access Environment

For many time-constrained communication applications, such as packetized voice, a critical performance measure is the percentage of messages which are transmitted within a given amount of time after their arrival at a sending station. We examine the use of a group random access protocol based on time windows for achieving time-constrained communication in a multiple access environment. First, we formulate a policy for controlling protocol operation in order to minimize the percentage of messages with waiting times greater than some given bound. A semi-Markov decision model is then developed for protocol operation and three of the four optimal control elements of this policy are then determined. Although the semi-Markov decision model can also be used to obtain performance results, the procedure is too computationally expensive to be of practical use. Thus, an alternate performance model based on a centralized queueing system with impatient customers is developed. Protocol performance under the optimal elements of the control policy shows significant improvements over cases in which the protocol is not controlled in this manner. Simulation results are also presented to corroborate the analytic results