Trace Graph Research Articles

On the importance of assessing topological convergence in Bayesian phylogenetic inference.

Modern phylogenetics research is often performed within a Bayesian framework, using sampling algorithms such as Markov chain Monte Carlo (MCMC) to approximate the posterior distribution. These algorithms require careful evaluation of the quality of the generated samples. Within the field of phylogenetics, one frequently adopted diagnostic approach is to evaluate the effective sample size and to investigate trace graphs of the sampled parameters. A major limitation of these approaches is that they are developed for continuous parameters and therefore incompatible with a crucial parameter in these inferences: the tree topology. Several recent advancements have aimed at extending these diagnostics to topological space. In this reflection paper, we present two case studies-one on Ebola virus and one on HIV-illustrating how these topological diagnostics can contain information not found in standard diagnostics, and how decisions regarding which of these diagnostics to compute can impact inferences regarding MCMC convergence and mixing. Our results show the importance of running multiple replicate analyses and of carefully assessing topological convergence using the output of these replicate analyses. To this end, we illustrate different ways of assessing and visualizing the topological convergence of these replicates. Given the major importance of detecting convergence and mixing issues in Bayesian phylogenetic analyses, the lack of a unified approach to this problem warrants further action, especially now that additional tools are becoming available to researchers.

Graphs from matrices - a survey

Let R be a commutative ring with identity. For a positive integer n ≥ 2 , let M n ( R ) be the set of all n × n matrices over R and M n ( R ) * be the set of all non-zero matrices of M n ( R ) . The zero-divisor graph of M n ( R ) is a simple directed graph with vertex set the non-zero zero-divisors in M n ( R ) and two distinct matrices A and B are adjacent if their product is zero. Given a matrix A ∈ M n ( R ) , Tr(A) is the trace of the matrix A. The trace graph of the matrix ring M n ( R ) , denoted by Γ t ( M n ( R ) ) , is the simple undirected graph with vertex set { A ∈ M n ( R ) * : there exists B ∈ M n ( R ) * such that Tr ( AB ) = 0 } and two distinct vertices A and B are adjacent if and only if Tr ( AB ) = 0. For an ideal I of R, the notion of the ideal based trace graph, denoted by Γ I t ( M n ( R ) ) , is a simple undirected graph with vertex set M n ( R ) ∖ M n ( I ) and two distinct vertices A and B are adjacent if and only if Tr ( AB ) ∈ I . In this survey, we present several results concerning the zero-divisor graph, trace graph and the ideal based trace graph of matrices over R.

Design Space Exploration for Partitioning Dataflow Program on CPU-GPU Heterogeneous System

Dataflow programming is a methodology that enables the development of high-level, parametric programs that are independent of the underlying platform. This approach is particularly useful for heterogeneous platforms, as it eliminates the need to rewrite application software for each configuration. Instead, it only requires new low-level implementation code, which is typically automatically generated through code generation tools. The performance of programs running on heterogeneous parallel platforms is highly dependent on the partitioning and mapping of computation to different processing units. This is determined by parameters that govern the partitioning, mapping, scheduling, and allocation of data exchanges among the processing elements of the platform. Determining the appropriate parameters for a specific application and set of architectures is a complex task and is an active area of research. This paper presents a novel methodology for partitioning and mapping dataflow programs onto heterogeneous systems composed of both CPUs and GPUs. The objective is to identify the program configuration that provides the most efficient way to process a typical dataflow program by exploring its design space. This is an NP-complete problem that we have addressed by utilizing a design space exploration approach that leverages a Tabu search meta-heuristic optimization algorithm driven by analysis of the execution trace graph of the program. The heuristic algorithm effectively identifies a solution that maps actors to processing units while improving overall performance. The parameters of the heuristic algorithm, such as the time limit and the proportion of neighboring solutions explored during each iteration, can be fine-tuned for optimal results. Additionally, the proposed approach allows for the exploration of solutions that do not utilize all hardware resources if it results in better performance. The effectiveness of the proposed approach is demonstrated through experimental results on dataflow programs.

On Causal Equivalence by Tracing in String Rewriting

We introduce proof terms for string rewrite systems and, using these, show that various notions of equivalence on reductions known from the literature can be viewed as different perspectives on the notion of causal equivalence. In particular, we show that permutation equivalence classes (as known from the lambda-calculus and term rewriting) are uniquely represented both by trace graphs (known from physics as causal graphs) and by so-called greedy multistep reductions (as known from algebra). We present effective maps from the former to the latter, topological multi-sorting TM, and vice versa, the proof term algebra [[ ]].

Enhanced system for ns2 trace file analysis with network performance evaluation

One of the critical challenges facing operators around the world is how to ensure that everything is running smoothly as well as how to analyze the performance of the network. Nonetheless, the analytic system must be precise, user-friendly, and quick enough to depict network performance in real time. Network performance is essential for ensuring service quality. In this light, the Network Simulator NS-2 is generally employed for network research on the widely-used UNIX and Windows systems. Next, the network scenarios are generated using network simulation scripts, and upon completion of the simulation, trace files that record network events are generated. Information that might be utilized in a performance study could be recorded in trace files. This could include the total number of packets sent, their arrival times, any delays or losses, and so on. This trace file analysis problem arises mostly because NS-2 does not provide any visualization options for analyzing simulation results (trace files). A system is proposed to analyze the NS2 trace file and facilitate data extraction and evaluation. The main feature of this system is the Java language for network performance evaluation. And to prove the validity of the system, the system was compared with the Trace graph, where the speed of the new system was very high.

Constructions of DNA and polypeptide cages based on plane graphs and odd crossing [formula omitted]-junctions

The constructions of three-dimensional synthetic DNA and polypeptide structures with a single closed DNA strand and polypeptide chain are mathematically based on strong traces of polyhedral graphs. However, a method developed for constructing such a DNA and polypeptide structure may impose additional restrictions on the types of strong traces and polyhedral graphs. In this paper, we show that strong traces for certain 2-connected plane graphs (allowed to have multiple edges) can be obtained using thickened graphs (sometimes called ribbon graphs) constructed with only two types of junctions : 0-crossing junction and special d(v)-crossing junction (called π-junction), where d(v) is the degree of the vertex v at which the d(v)-crossing junction is to be placed. The π-junctions are only applicable to vertices with odd degrees (≥3). We characterize the 2-connected plane graphs to which our approach can be applied and provide a brief guideline for the implementation of our method. This approach provides the theory, as well as a set of candidates, for designing and constructing stable DNA and polypeptide molecules needing only a method capable of creating the 0-crossing and π-junctions in a 2-connected plane graph.

Real-time FMR lorentzian visualization through a novel synchronous VNA-FMR measurement apparatus.

It is shown in this work that a synchronous measurement setup is able to conveniently and accurately retrieve ferromagnetic resonance's (FMR) main physical properties from a permalloy sample. The apparatus used comprises a vector network analyzer (VNA), coupled with external DC coils, driven by a controllable power supply. A permalloy thin film sample was subjected to a microwave signal through a grounded coplanar waveguide. A square wave signal generated by an Arduino microcontroller drives the coils to a triangular, 65.4ms period magnetic field. This field's half-cycle is synchronized to match a zero-span sampling time at the VNA. The system has the advantage of fast results, as the typical FMR lorentzian curve is completed in a few seconds and shown immediately on the VNA's scattering parameter S21 trace graph. The system showed an improved signal-to-noise ratio of 51.7 at 10GHz over 24.3 for the 100nm thick permalloy- sample used in this work. A magnetic field resonance point, collected at 10GHz, showed a five-fold improvement in the standard-error.

Analisis Graph Mining dalam Penentuan Senyawa Dan Tanaman Obat Indonesia Sebagai Antihipertensi

Hypertension, also known as high blood pressure, is a degenerative disease whose prevalence tends to increase every year. People in Indonesia generally treat this disease by using a mixture of several types of herbal plants or so-called herbs. This study aims to find out the potential of compounds and plants that have effectiveness as antihypertensives by combining the concept of multicomponent-multi-target with a bioinformatics approach. This study aims to find out the potential of compounds and medicinal plants in Indonesia that have effectiveness as antihypertensives using graph mining analysis. Graph tracing techniques can be applied to search for compounds and plants related to target proteins in a disease. Patikan kebo (Euphorbia factor Ti2, betaAmyrin, alpha-Amyrin), mango (3-Carene, L-Histidine), cayenne pepper (Capsanthin, Capsorubin, Solasonine), papaya (L-Histidine, Sterol, Caffeine), and fenugreek ( L-Histidine) is the best plant that acts as an antihypertensive agent by targeting 4 proteins or about 80% of the total 5 significant proteins in hypertension.

Automorphism group of the symmetry trace graph of real matrices

Let be the real field and be the set of all m × n matrices over where For a square matrix denotes the trace of A (the sum of all diagonal entries of A). The symmetry trace graph of is defined to be a graph with vertex set of all nonzero matrices in and two vertices A and B are adjacent if and only if where is the transpose of B. Clearly, is undirected and without loops. In the present paper, by studying maximum cliques of we determine the form of an arbitrary automorphism of

Optimization of Breadth-First Search Algorithm for Path Solutions in Mazyin Games

A game containing elements of artificial intelligence, of course, requires an algorithm in its application. One example of a game that includes elements of artificial intelligence is the Labyrinth game. Maze is a simple educational game. This game is known as finding a way out of the maze to arrive at a predetermined goal. The labyrinth encounters numerous obstacles along the way, such as dead ends and parapets, to reach the target location. In this game, players are required to think logically about how to find the right maze path. The obstacle faced in this game is that sometimes players have difficulty finding a way out, especially if the game level has reached a high level in the process of finding a way out. To solve this problem, a graph tracing technique is needed. The Breadth-First Search (BFS) strategy can be used in conjunction with various graph search algorithms. An example of a broad search method is the Breadth-First Search Algorithm, which works by visiting nodes at level n first before moving on to nodes at level n+1. The advantage of the Breadth-First Search algorithm is that it can find a solution as the shortest path and find the minimum solution if there is more than one solution. This study will discuss how to find a path for the Labyrinth using the BFS algorithm. The result of applying this BFS algorithm is the shortest route solution raised so that the Labyrinth can arrive at the destination point through the route provided.

Evaluating DoS jamming attack on reactive routing protocol in wireless sensor networks

Wireless sensor networks (WSNs) over the years have emerged as the enabling underlining infrastructure for new wireless technology trends such as Internet-of Things (IoT) and Fog Computing. Its application has spread across diverse fields such as agriculture, military, healthcare and home automation. Despite its promising attributes, it is characterized by its extremely limited resources such as battery energy and memory. Additionally, its deployment in hostile and unattended areas make it vulnerable to security attacks. One of such attacks is the denial of service (DoS) jamming attack that is perpetrated by malicious nodes emitting radio frequency signals to disrupt and interfere with the normal functions of the sensor nodes in the network. This eventually causes a denial of service in the network. Different routing protocols have been proposed over the years to guarantee reliable communication and maintain the network lifetime and functionality for a reasonable duration, notwithstanding DoS jamming attack. Therefore, in this work, we evaluate the effect of a constant jamming DoS attack on two key reactive routing protocols in WSN, ad hoc on-demand distance vector (AODV) and dynamic source routing (DSR). Metrics such as packet sending ratio (PSR), packet loss (PL) and transmitted packets are used to measure the impact of constant jamming DoS attack in the network. Simulation results using network simulation 2 (NS2) and trace graph show that, irrespective of the adopted reactive routing protocol, the impact of the jamming attack is the same.

Hamiltonian trace graph of matrices

Let [Formula: see text] be a commutative ring with identity, [Formula: see text] be a positive integer and [Formula: see text] be the set of all [Formula: see text] matrices over [Formula: see text] For a matrix [Formula: see text] Tr[Formula: see text] is the trace of [Formula: see text] The trace graph of the matrix ring [Formula: see text] denoted by [Formula: see text] is the simple undirected graph with vertex set [Formula: see text][Formula: see text] and two distinct vertices [Formula: see text] and [Formula: see text] are adjacent if and only if Tr[Formula: see text] The ideal-based trace graph of the matrix ring [Formula: see text] with respect to an ideal [Formula: see text] of [Formula: see text] denoted by [Formula: see text] is the simple undirected graph with vertex set [Formula: see text] and two distinct vertices [Formula: see text] and [Formula: see text] are adjacent if and only if Tr[Formula: see text] In this paper, we investigate some properties and structure of [Formula: see text] Further, it is proved that both [Formula: see text] and [Formula: see text] are Hamiltonian.

On trace graph of matrices over fields

For a finite commutative ring R and a positive integer $$n\ge 2,$$ let $$M_n(R)$$ be the set of all $$n\times n$$ matrices over R and $$M_n(R)^*$$ be the set of all non-zero matrices of $$M_n(R).$$ For $$A\in M_n(R),$$ Tr(A) denotes the trace of the matrix A. The trace graph $$\varGamma _t(M_n(R))$$ of the matrix ring $$M_n(R)$$ is the simple undirected graph with vertex set $$\{A\in M_n(R)^*: \text {there exists } B\in M_n(R)^*$$ $$\text {such that Tr}(AB)=0\}$$ and two distinct vertices A and B are adjacent if and only if Tr $$(AB) = 0.$$ For an ideal I of R, the ideal based trace graph $$\varGamma _{I^t}(M_n(R))$$ of the matrix ring $$M_n(R)$$ is the simple undirected graph with vertex set $$M_n(R){\setminus } M_n(I)$$ and two distinct vertices A and B are adjacent if and only if Tr $$(AB)\in I.$$ For any field $${\mathbb {F}},$$ we prove that the zero divisor graph of $$M_n({\mathbb {F}})$$ is an induced subgraph of the trace graph $$\varGamma _t(M_n({\mathbb {F}}))$$ if and only if $$n=2.$$ Further, we obtain the value of certain domination parameters of $$\varGamma _t(M_n(R))$$ and $$\varGamma _{I^t}(M_n(R)).$$ We prove that, for any two finite fields $$F_1,F_2$$ and integers $$n_1,n_2\ge 2,$$ if $$\varGamma _t(M_{n_1}(F_1))\cong \varGamma _t(M_{n_2}(F_2)),$$ then $$n_1=n_2$$ and $$F_1\cong F_2.$$ In particular, it was proved that the domination number of the trace graph of matrices over a field $${\mathbb {F}}$$ is $$|{\mathbb {F}}|+1.$$ Thereafter, we provide properties of ideal based trace graphs.

Analyzing Impact of Distributed PV Generation on Integrated Transmission & Distribution System Voltage Stability—A Graph Trace Analysis Based Approach

The use of a Graph Trace Analysis (GTA)-based power flow for analyzing the voltage stability of integrated Transmission and Distribution (T&D) networks is discussed in the context of distributed Photovoltaic (PV) generation. The voltage stability of lines and the load carrying capability of buses is analyzed at various PV penetration levels. It is shown that as the PV generation levels increase, an increase in the steady state voltage stability of the system is observed. Moreover, within certain regions of stability margin changes, changes in voltage stability margins of transmission lines are shown to be linearly related to changes in the loading of the lines. Two case studies are presented, where one case study involves a model with eight voltage levels and 784,000 nodes. In one case study, a voltage-stability heat map is used to demonstrate the identification of weak lines and buses.

Ideal based trace graph of matrices

Let $R$ be a commutative ring and $M_n(R)$ be the set of all $n\times n$ matrices over $R$ where $n\geq 2.$ The trace graph of the matrix ring $M_n(R)$ with respect to an ideal $I$ of $R,$ denoted by $\Gamma_{I^t}(M_n(R)),$ is the simple undirected graph with vertex set $M_n(R)\setminus M_n(I)$ and two distinct vertices $A$ and $B$ are adjacent if and only if Tr$(AB) \in I.$ Here Tr$(A)$ represents the trace of the matrix $A.$ In this paper, we exhibit some properties and structure of $\Gamma_{I^t}(M_n(R)).$

Unicast based reactive & proactive routing simulation in MANET: A comparative study for protocols in mobility scenarios

A challenging issue for (MANETs) is finding an effective routing mechanism, the wireless connection must have the capability to interact while traveling randomly, since MANETs are self-configuring mobile node networks. Traditional fixed network routing protocols are useless with MANET. Based on this, MANETs introduced new routing protocols. In this study, the routing process was investigated, particularly (DSR), (AODV) and (DSDV). Simulations are implemented in the NS2 simulation environment and evaluated their performance under various scenarios. The results of the simulation study were summarized with a number of graphs using NAM (Network Animation Environment) and Trace Graph programs and a general evaluation was made. The results of the simulation studies presented that DSR and AODV showed better efficiency than the table based DSDV protocol. In addition, DSR and AODV protocols may present a variable performance for the different data packets and network sizes due to their algorithmic differences.

Unicast based reactive & proactive routing simulation in MANET: A comparative study for protocols in mobility scenarios

A challenging issue for (MANETs) is finding an effective routing mechanism, the wireless connection must have the capability to interact while traveling randomly, since MANETs are self-configuring mobile node networks. Traditional fixed network routing protocols are useless with MANET. Based on this, MANETs introduced new routing protocols. In this study, the routing process was investigated, particularly (DSR), (AODV) and (DSDV). Simulations are implemented in the NS2 simulation environment and evaluated their performance under various scenarios. The results of the simulation study were summarized with a number of graphs using NAM (Network Animation Environment) and Trace Graph programs and a general evaluation was made. The results of the simulation studies presented that DSR and AODV showed better efficiency than the table based DSDV protocol. In addition, DSR and AODV protocols may present a variable performance for the different data packets and network sizes due to their algorithmic differences.

On the trace graph of matrices

Let R be a commutative ring with identity, $${M_n(R)}$$ be the set of all $${n \times n}$$ matrices over R and $${M_n(R) ^{*} }$$ be the set of all non-zero matrices of $${M_n(R)}$$ where $${n \geq 2}$$ . For a matrix $${A \in M_n(R)}$$ , $${{\rm Tr} (A)}$$ is the trace of A. The trace graph of the matrix ring $${M_n(R)}$$ , denoted by $${\Gamma_t(M_n(R))}$$ , is the simple undirected graph denoted by $${\Gamma_t(M_n(R))}$$ with vertex set $$\{{A \in M_n(R) ^{*} : }$$ there exists $${B \in M_n(R) ^{*} }$$ such that $${{\rm Tr}(AB)=0}\}$$ and two distinct vertices A and B are adjacent if and only if $${{\rm Tr} (AB) = 0}$$ . First, we prove that $${\Gamma_t(M_n(R))}$$ is 2-connected and hence obtain Eulerian properties of $${\Gamma_t(M_n(R))}$$ . Also we obtain the domination number of $${\Gamma_t(M_n(R))}$$ of a commutative semisimple ring R and obtain the domination number for $${\Gamma_t(M_n(\mathbb Z_2^m))}$$ . Finally, it is proved that for a commutative ring R with identity, $${\Gamma_t(M_n(R))}$$ is non-planar and classified all finite commutative rings R with identity for which the trace graph has thickness 2.

Execution Trace Graph of Dataflow Process Networks

The paper introduces and specifies a formalism that provides complete representations of dataflow process network (DPN) program executions, by means of directed acyclic graphs. Such graphs, also known as execution trace graphs (ETG), are composed of nodes representing each action firing and by directed arcs representing the dataflow program execution constraints between two action firings. Action firings are atomic operations that encompass the algorithmic part of the action executions applied to both, the input data and the actor state variables. The paper describes how an ETG can be effectively derived from a dataflow program, specifies the type of dependencies that need to be included, and the processing that need to be applied so that an ETG become capable of representing all the admissible trajectories that dynamic dataflow programs can execute. The paper also describes how some characteristics of the ETG, related to specific implementations of the dataflow program, can be evaluated by means of high-level and architecture-independent executions of the program. Furthermore, some examples are provided showing how the analysis of the ETGs can support efficient explorations, reductions, and optimizations of the design space, providing results in terms of design alternatives, without requiring any partial implementation or reduction of the expressiveness of the original DPN dataflow program.

Tracing of large‐scale actor systems

SummaryIn large‐scale and distributed actor systems, there are situations where processing messages within one of the actors fails, often due to failures that had occurred earlier in the system. In such cases, tracing down the origin of the failure is difficult since existing monitoring tools only provide ways to collect metrics and statistical information about system execution. In this paper, we describe a new tool for tracing distributed actor systems, Akka Tracing Tool, a library that allows users to generate a trace graph of messages. To address the distributed nature of the environment, we proposed an efficient data collection mechanism based on the one‐way replication technique implemented in CouchDB, a popular document database. The tool was evaluated in a distributed environment of up to 50 nodes set up in the Amazon Web Services (AWS) computing cloud on a real application: car traffic simulation. The measured overhead when tracing all messages was between 39% to 45% on average. The library also proved to be scalable with respect to the number of nodes in the actor system and to be user‐friendly. Owing to these properties, we expect that the tool can simplify finding errors and speed up the development process of actor systems.