scholarly journals Compacting points-to sets through object clustering

2021 ◽  
Vol 5 (OOPSLA) ◽  
pp. 1-27
Author(s):  
Mohamad Barbar ◽  
Yulei Sui
Keyword(s):  
Integer Programming ◽  
Open Source ◽  
Hierarchical Clustering ◽  
Data Structures ◽  
Constraint Solving ◽  
Memory Usage ◽  
Not Given ◽  
New Approach ◽  
Union Operation ◽  
Speed Up

Inclusion-based set constraint solving is the most popular technique for whole-program points-to analysis whereby an analysis is typically formulated as repeatedly resolving constraints between points-to sets of program variables. The set union operation is central to this process. The number of points-to sets can grow as analyses become more precise and input programs become larger, resulting in more time spent performing unions and more space used storing these points-to sets. Most existing approaches focus on improving scalability of precise points-to analyses from an algorithmic perspective and there has been less research into improving the data structures behind the analyses. Bit-vectors as one of the more popular data structures have been used in several mainstream analysis frameworks to represent points-to sets. To store memory objects in bit-vectors, objects need to mapped to integral identifiers. We observe that this object-to-identifier mapping is critical for a compact points-to set representation and the set union operation. If objects in the same points-to sets (co-pointees) are not given numerically close identifiers, points-to resolution can cost significantly more space and time. Without data on the unpredictable points-to relations which would be discovered by the analysis, an ideal mapping is extremely challenging. In this paper, we present a new approach to inclusion-based analysis by compacting points-to sets through object clustering. Inspired by recent staged analysis where an auxiliary analysis produces results approximating a more precise main analysis, we formulate points-to set compaction as an optimisation problem solved by integer programming using constraints generated from the auxiliary analysis’s results in order to produce an effective mapping. We then develop a more approximate mapping, yet much more efficiently, using hierarchical clustering to compact bit-vectors. We also develop an improved representation of bit-vectors (called core bit-vectors) to fully take advantage of the newly produced mapping. Our approach requires no algorithmic change to the points-to analysis. We evaluate our object clustering on flow sensitive points-to analysis using 8 open-source programs (>3.1 million lines of LLVM instructions) and our results show that our approach can successfully improve the analysis with an up to 1.83× speed up and an up to 4.05× reduction in memory usage.

Performance Comparison of Web Backend And Database: A Case Study Of Node.JS, Golang and MySQL, MongoDB

2019 ◽  
Vol 13 ◽  
Author(s):  
Faried Effendy ◽  
Taufik ◽  
Bramantyo Adhilaksono
Keyword(s):  
Response Time ◽  
Open Source ◽  
Poisson Distribution ◽  
Mobile Application ◽  
Web Applications ◽  
Performance Comparison ◽  
Memory Usage ◽  
Data Traffic ◽  
Cpu Utilization

: Substantial research has been conducted to compare web servers or to compare databases, but very limited research combines the two. Node.js and Golang (Go) are popular platforms for both web and mobile application back-ends, whereas MySQL and Go are among the best open source databases with different characters. Using MySQL and MongoDB as databases, this study aims to compare the performance of Go and Node.js as web applications back-end regarding response time, CPU utilization, and memory usage. To simulate the actual web server workload, the flow of data traffic on the server follows the Poisson distribution. The result shows that the combination of Go and MySQL is superior in CPU utilization and memory usage, while the Node.js and MySQL combination is superior in response time.

scholarly journals tidyMicro: a pipeline for microbiome data analysis and visualization using the tidyverse in R

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Charlie M. Carpenter ◽  
Daniel N. Frank ◽  
Kayla Williamson ◽  
Jaron Arbet ◽  
Brandie D. Wagner ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Open Source ◽  
Data Structures ◽  
Negative Binomial ◽  
Rocky Mountain ◽  
R Package ◽  
Microbiome Analysis ◽  
External Data ◽  
Data Tables ◽  
Microbiome Data

Abstract Background The drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial communities typically are of high dimensionality and can involve multiple data tables consisting of taxonomic or functional gene/pathway counts. Merging multiple high dimensional tables with study-related metadata can be challenging. Existing microbiome pipelines available in R have created their own data structures to manage this problem. However, these data structures may be unfamiliar to analysts new to microbiome data or R and do not allow for deviations from internal workflows. Existing analysis tools also focus primarily on community-level analyses and exploratory visualizations, as opposed to analyses of individual taxa. Results We developed the R package “tidyMicro” to serve as a more complete microbiome analysis pipeline. This open source software provides all of the essential tools available in other popular packages (e.g., management of sequence count tables, standard exploratory visualizations, and diversity inference tools) supplemented with multiple options for regression modelling (e.g., negative binomial, beta binomial, and/or rank based testing) and novel visualizations to improve interpretability (e.g., Rocky Mountain plots, longitudinal ordination plots). This comprehensive pipeline for microbiome analysis also maintains data structures familiar to R users to improve analysts’ control over workflow. A complete vignette is provided to aid new users in analysis workflow. Conclusions tidyMicro provides a reliable alternative to popular microbiome analysis packages in R. We provide standard tools as well as novel extensions on standard analyses to improve interpretability results while maintaining object malleability to encourage open source collaboration. The simple examples and full workflow from the package are reproducible and applicable to external data sets.

scholarly journals An Open-Source Cloud-FPGA Gene Regulatory Accelerator

2021 ◽  
Author(s):  
Lucas Bragança ◽  
Jeronimo Penha ◽  
Michael Canesche ◽  
Dener Ribeiro ◽  
José Augusto M. Nacif ◽  
...  
Keyword(s):  
Open Source ◽  
Gene Regulatory Networks ◽  
High Performance ◽  
Regulatory Networks ◽  
Cloud Services ◽  
On Demand ◽  
Speed Up ◽  
Gene Regulatory ◽  
High Level ◽  
Better Than

FPGAs are suitable to speed up gene regulatory network (GRN) algorithms with high throughput and energy efficiency. In addition, virtualizing FPGA using hardware generators and cloud resources increases the computing ability to achieve on-demand accelerations across multiple users. Recently, Amazon AWS provides high-performance Cloud's FPGAs. This work proposes an open source accelerator generator for Boolean gene regulatory networks. The generator automatically creates all hardware and software pieces from a high-level GRN description. We evaluate the accelerator performance and cost for CPU, GPU, and Cloud FPGA implementations by considering six GRN models proposed in the literature. As a result, the FPGA accelerator is at least 12x faster than the best GPU accelerator. Furthermore, the FPGA reaches the best performance per dollar in cloud services, at least 5x better than the best GPU accelerator.

scholarly journals FIPS: An R Package for Biomathematical Modelling of Human Fatigue Related Impairment

2020 ◽  
Author(s):  
Michael David Wilson ◽  
Luke Joseph Gough Strickland ◽  
Timothy Ballard
Keyword(s):  
Mathematical Models ◽  
Open Source ◽  
Data Structures ◽  
R Package ◽  
System Safety ◽  
Model Interpretation ◽  
Performance Impairment ◽  
Significant Barrier ◽  
Human Fatigue ◽  
Interpretation Model

In many workplace contexts, accurate predictions of a human’s fatigue state can drastically improve system safety. Biomathematical models of fatigue (BMMs) are a family of dynamic phenomenological models that predict the neurobehavioural outcomes of fatigue (e.g., sleepiness, performance impairment) based on sleep/wake history (Dawson, Darwent, & Roach, 2017). However, to-date there are no open source implementations of BMMs, and this presents a significant barrier to their broadscale adoption by researchers and industry practitioners. FIPS is an open source R package (R Core Team, 2020) to facilitate BMM research and simulation. FIPS has implementations of several published bio-mathematical models and includes functions for easily manipulating sleep history data into the required data structures. FIPS also includes default plot and summary methods to aid model interpretation. Model objects follow tidy data conventions (Wickham, 2014), enabling FIPS to be integrated into existing research workflows of R users.

Mobile E-Health Information System

2011 ◽  
Vol 2 (4) ◽  
pp. 1-28
Author(s):  
Flora S. Tsai
Keyword(s):  
Health Care ◽  
Information System ◽  
Open Source ◽  
Health Information ◽  
Smart Card ◽  
Mobile Applications ◽  
Health Information System ◽  
Order Entry ◽  
Medical Centers ◽  
Speed Up

A mobile e-Health information system (MEHIS) aims to speed up the operations of health care in medical centers and hospitals. However, the proper implementation of MEHIS involves integrating many subsystems for MEHIS to be properly executed. A typical MEHIS can consist of many components and subsystems, such as appointments and scheduling; admission, discharge, and transfer (ADT); prescription order entry; dietary planning; and smart card sign-on. This paper describes the development of a MEHIS with open-source Eclipse, using currently available health care standards. The author discusses the issues of building a mobile e-Health information system which can help achieve the goal of ubiquitous and mobile applications for the personalization of e-Health.

The Applicability of Process-Orientation to Software Development Projects

2019 ◽  
Vol 10 (2) ◽  
pp. 1-7
Author(s):  
Viktorija Ponomarenko
Keyword(s):  
Technology Transfer ◽  
Software Development ◽  
Development Projects ◽  
New Approach ◽  
Eu Member States ◽  
New Information ◽  
Europe 2020 ◽  
Europe 2020 Strategy ◽  
Speed Up ◽  
Additional Value

The progress in the digital single market (DSM) has been acknowledged as one of the 10 political priorities by the European Commission since 2015. It could contribute € 415 billion per year (GDP) to the economy of the 28 EU Member States and create hundreds of thousands of new jobs. Nowadays, the ICT sector and the European Digital Agenda have declared it as one of the seven pillars of the Europe 2020 strategy. In order to speed up the development of new information technology and its commercialisation, it is necessary to increase software quality aimed at accelerating and improving technology transfer, taking into account process quality management. The aim of this article is to give an overview of a new approach to producing an additional value of the software development projects to improve the technology transfer process.

TACTICAL ROUTE PLANNING: NEW ALGORITHMS FOR DECOMPOSING THE MAP

1996 ◽  
Vol 05 (01n02) ◽  
pp. 199-218 ◽  
Author(s):  
J.R. BENTON ◽  
S.S. IYENGAR ◽  
W. DENG ◽  
N. BRENER ◽  
V.S. SUBRAHMANIAN
Keyword(s):  
Data Structures ◽  
Fundamental Problem ◽  
Route Planning ◽  
Decomposition Methods ◽  
Search Algorithms ◽  
Experimental Results ◽  
New Approach ◽  
Robotic Vehicles ◽  
New Algorithms ◽  
Large Grid

This paper defines a new approach and investigates a fundamental problem in route planners. This capability is important for robotic vehicles(Martian Rovers, etc.) and for planning off-road military maneuvers. The emphasis throughout this paper will be on the design and analysis and hieiaichical implementation of our route planner. This work was motivated by anticipation of the need to search a grid of a trillion points for optimum routes. This cannot be done simply by scaling upward from the algorithms used to search a grid of 10,000 points. Algorithms sufficient for the small grid are totally inadequate for the large grid. Soon, the challenge will be to compute off-road routes more than 100 km long and with a one or two-meter grid. Previous efforts are reviewed and the data structures, decomposition methods and search algorithms are analyzed and limitations are discussed. A detailed discussion of a hieraichical implementation is provided and the experimental results are analyzed.

3D Printing Complex Structures Using Modeling and Simulation

2015 ◽  
Author(s):  
Hammad Mazhar
Keyword(s):  
3D Printing ◽  
Open Source ◽  
Data Structures ◽  
Large Scale ◽  
Selective Layer ◽  
Parallel Data ◽  
Wide Range ◽  
Data Structures And Algorithms ◽  
Multi Body ◽  
Dynamics Problems

This paper describes an open source parallel simulation framework capable of simulating large-scale granular and multi-body dynamics problems. This framework, called Chrono::Parallel, builds upon the modeling capabilities of Chrono::Engine, another open source simulation package, and leverages parallel data structures to enable scalable simulation of large problems. Chrono::Parallel is somewhat unique in that it was designed from the ground up to leverage parallel data structures and algorithms so that it scales across a wide range of computer architectures and yet has a rich modeling capability for simulating many different types of problems. The modeling capabilities of Chrono::Parallel will be demonstrated in the context of additive manufacturing and 3D printing by modeling the Selective Layer Sintering layering process and simulating large complex interlocking structures which require compression and folding to fit into a 3D printer’s build volume.

scholarly journals Existence and uniqueness of monotone wavefronts in a nonlocal resource-limited model

2019 ◽  
Vol 150 (5) ◽  
pp. 2462-2483 ◽  
Author(s):  
Elena Trofimchuk ◽  
Manuel Pinto ◽  
Sergei Trofimchuk
Keyword(s):  
Existence And Uniqueness ◽  
Propagation Speed ◽  
New Approach ◽  
Resource Limited ◽  
Model Dynamics ◽  
Small Parameters ◽  
Speed Up ◽  
Spatio Temporal ◽  
Travelling Fronts ◽  
Nonlocal Reaction

AbstractWe are revisiting the topic of travelling fronts for the food-limited (FL) model with spatio-temporal nonlocal reaction. These solutions are crucial for understanding the whole model dynamics. Firstly, we prove the existence of monotone wavefronts. In difference with all previous results formulated in terms of ‘sufficiently small parameters’, our existence theorem indicates a reasonably broad and explicit range of the model key parameters allowing the existence of monotone waves. Secondly, numerical simulations realized on the base of our analysis show appearance of non-oscillating and non-monotone travelling fronts in the FL model. These waves were never observed before. Finally, invoking a new approach developed recently by Solar et al., we prove the uniqueness (for a fixed propagation speed, up to translation) of each monotone front.

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