ARTICLE | doi:10.20944/preprints202108.0156.v1
Online: 6 August 2021 (10:25:25 CEST)
Modern scientific research particularly radio astronomi- cal spectroscopic observations cannot be imagined without appropriate software suite. That is necessary because of two reasons 1) data are in digital form and 2) data processing is a complex multi-step process. In this paper created in VIRAC data processing suite for a single radio telescope, space maser observations are presented. Software Defined Radio (SDR) backend data processing is described. Implementation of the frequency switching algorithm, acquisition of observation data and their format for storing are discussed. Multiple ways to display the observation results are highlighted.
ARTICLE | doi:10.20944/preprints202301.0030.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: OpenCV; Python; objects; object detection; card
Online: 3 January 2023 (09:40:17 CET)
Computer vision is a rapidly developing field that focuses on highly sophisticated picture analysis, manipulation, and comprehension. Its objective is to analyze what is happening in front of a camera and utilize that understanding to control a computer or robotic system or to present users with fresh visuals that are more enlightening or appealing than the original camera images. Computer vision technologies make it feasible for new user interfaces, augmented reality gaming, biometrics, automobile, photography, movie creation, Web search, and many more applications. This essay seeks to explain how computer vision can be utilized to play blackjack successfully.
ARTICLE | doi:10.20944/preprints202212.0543.v1
Subject: Computer Science And Mathematics, Signal Processing Keywords: OpenCV; Python; objects; object detection; card
Online: 28 December 2022 (12:42:17 CET)
Computer vision is a fast-expanding discipline focusing on analyzing, altering, and comprehending images at a high level. Its goal is to figure out what's going on in front of a camera and use that knowledge to manage a computer or robotic system or to show people new visuals that are more instructive or attractive than the original camera photos. Video surveillance, biometrics, automotive, photography, movie production, Web search, medicine, augmented reality gaming, new user interfaces, and many other applications are all possible with computer vision technologies. This paper aims to describe how computer vision will be used to play a winning game of blackjack.
Subject: Biology And Life Sciences, Immunology And Microbiology Keywords: Chryseobacterium indologenes; Oral abscess; Ball Python
Online: 11 May 2021 (14:53:22 CEST)
Abstract: Chryseobacterium indologenes is an opportunistic pathogen isolated from human infec-tions and rarely from some aquatic animals. A 3-year-old male ball python (Python regius) was admitted to the veterinary clinic by a pet owner because of acute respiratory and swallowing failure. During physical examinations, oral secretions and abscesses were observed on the mouth cavity and throat of the animal. After microbiological analysis including isolation, identi-fication, and 16s rRNA sequencing; Ch. indologenes was detected as the main cause of the oral abscess in this case. Phylogenetic relatedness analysis showed a close relationship between this isolate and other strains isolated from human infections. Antimicrobial susceptibility testing re-vealed that the isolate was multi-drug resistant. However, it was very sensitive to minocycline, ceftazidime, and tetracycline. The patient was treated by antibiotic therapy and completely re-covered after two weeks. To our best knowledge, this is the first incidence of Ch. indologenes in an oral abscess in a ball python. As result we would consider this organism as an opportunistic animal pathogen with zoonotic potentiality.
ARTICLE | doi:10.20944/preprints202012.0577.v1
Subject: Business, Economics And Management, Accounting And Taxation Keywords: GIS; QGIS; Zotero; Python; Georeference; Citations
Online: 23 December 2020 (09:41:08 CET)
Here we introduce Literature Mapper, a Python QGIS plugin that provides a method for creating a spatial bibliography manager as well as a specification for storing spatial data in a bibliography manager. Literature Mapper uses QGIS’ spatial capabilities to allow users to add location information to a Zotero library, a free and open source bibliography manager. Literature Mapper enhances the citations in a user’s online Zotero database with geo-locations by storing spatial coordinates as part of traditional citation entries. Literature Mapper receives data from and sends data to the user’s online database via Zotero’s web API. By using Zotero as the backend data storage, Literature Mapper benefits from all of its features including shared citation Collections, public sharing, and an open web API usable by additional applications, such as web mapping libraries. We evaluate Literature Mapper’s ability to provide insights into the spatial distribution of published literature by mapping the study sites described in academic publications related to California’s coastal strand vegetation. The results of this exercise are presented in static and web map form.
ARTICLE | doi:10.20944/preprints202309.2177.v1
Subject: Engineering, Mechanical Engineering Keywords: particle image velocimetry; OpenPIV; python; image processing
Online: 30 September 2023 (09:59:14 CEST)
Particle Image Velocimetry (PIV) is a widely used experimental technique for measuring flow. In recent years, open-source PIV software has become more popular as it offers researchers and practitioners enhanced computational capabilities. Software development for graphical processing unit (GPU) architectures requires careful algorithm design and data structure selection for optimal performance. PIV software, optimized for central processing units (CPUs), offer an alternative to specialized GPU software. In the present work, an improved algorithm for the OpenPIV-Python software is presented and implemented under a traditional CPU framework. The Python language was selected due to its versatility and widespread adoption. The algorithm was also tested on a supercomputing cluster, a workstation, and Google Colaboratory during the development phase. Using a known velocity field, the algorithm precisely captured the time-average flow, monetary velocity fields, and vortices.
ARTICLE | doi:10.20944/preprints202301.0557.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: PDF; Malware; Machine Learning; Python; Random Forest
Online: 30 January 2023 (12:55:47 CET)
Portable Document Format (PDF) is one of the most widely used files types worldwide in data exchange, this has encourage hackers to utilize such files to spread any malicious content through PDF, utilizing different methods and techniques to accomplish that, on the other hand, security researches kept trying to improve detection methods to cope up to the rapidly increasing number of malwares daily, one of the commonly used detection technique nowadays is by utilizing artificial intelligence and Machine learning classificat; thision to help detecting PDF Malwares, in this paper, we utilize machine learning classifier Random Forest on a newly released PDF Malware dataset CIC-Evasive-PDFMal2022 to achieve the main goal of detecting malicious PDF documents, results showing a detection accuracy of around 99.5%
ARTICLE | doi:10.20944/preprints202211.0556.v2
Subject: Medicine And Pharmacology, Epidemiology And Infectious Diseases Keywords: Agent-based-model; epidemiology; python; zoonotic diseases
Online: 1 December 2022 (02:09:32 CET)
Agent-based models (ABMs) are computational models for simulating the actions and interactions of autonomous agents in time and space. These models allow users to simulate the complex interactions between individual agents and the landscapes they inhabit and are increasingly used in epidemiology to understand complex phenomena and make predictions. However, as the complexity of the simulated systems increases, notably when disease control interventions are considered, model flexibility and processing speed can become limiting. Here we introduce SamPy, an open-source Python library for stochastic agent-based modeling of epidemics. SamPy is a modular toolkit for model development, providing adaptable modules that capture host movement, disease dynamics, and disease control interventions. Memory optimization and design provide high computational efficiency allowing modelling of large, spatially-explicit populations of agents over extensive geographical areas. In this article, we demonstrate the high flexibility and processing speed of this new library. The version of SamPy considered in this paper is available at https://github.com/sampy-project/sampy-paper .
Subject: Environmental And Earth Sciences, Geophysics And Geology Keywords: Python; QGIS plugin; geodatabase; Seismic microzonation; SpatiaLite.
Online: 7 September 2021 (11:53:51 CEST)
MzSTools is a plugin for QGIS developed by the Institute of Environmental Geology and Geoengineering of the National Research Council (CNR-IGAG). The plugin has been designed as a set of practical and easy-to-use tools to carry out seismic microzonation (SM) studies, by producing standard compliant geographic database and maps, thus making them accurate, homogeneous and uniform for all municipalities in Italy. A geodatabase based on SQLite/SpatiaLite Relational Database Management System (RDBMS) has been designed to collect and store data related to elements such as: geognostic surveys; bedrocks and cover terrains; superficial and buried geomorphological elements; tectonic-structural elements; elements of geological instability such as landslide zones, liquefaction zones and zones affected by active and capable faults; homogeneous microzones in seismic perspective, microzones characterized by a seismic amplification factor. MzSTools assembles in a single software environment a set of useful tools in a configurable QGIS project template, comprising layers, symbol libraries, cartographic styles and print layouts for the SM maps. The plugin is open source and hosted on the GitHub platform, and available via the official QGIS plugins repository (https://plugins.qgis.org/plugins/MzSTools/).
ARTICLE | doi:10.20944/preprints202108.0185.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: AES; Audio analysis; Authenticated encryption; Cryptography; Python
Online: 9 August 2021 (09:31:46 CEST)
The focus of this research is to analyze the results of encrypting audio using various authenticated encryption algorithms implemented in the Python cryptography library for ensuring authenticity and confidentiality of the original contents. The Advanced Encryption Standard (AES) is used as the underlying cryptographic primitive in conjunction with various modes including Galois Counter Mode (GCM), Counter with Cipher Block Chaining Message Authentication Code (CCM), and Cipher Block Chaining (CBC) with Keyed-Hashing for encrypting a relatively small audio file. The resulting encrypted audio shows similarity in the variance when encrypting using AES-GCM and AES-CCM. There is a noticeable reduction in variance of the performed encodings and an increase in the amount of time it takes to encrypt and decrypt the same audio file using AES-CBC with Keyed-Hashing. In addition, the corresponding encrypted using this mode audio spans a longer duration. As a result, AES should either have GCM or CCM for an efficient and reliable authenticated encryption integration within a workflow.
ARTICLE | doi:10.20944/preprints202307.1849.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: block-based Python Programming; programming environment; programming learning
Online: 27 July 2023 (10:19:16 CEST)
Advancements in computing technology have resulted in significant changes in education, healthcare, and manufacturing fields. Thus, personnel training in computer-related fields is directly related to national competitiveness. Therefore, the importance of programming education has been emphasized worldwide. Programming education has been conducted since the 1980s, however beginners often find programming tedious and difficult because of the cognitive burden of using text commands. Therefore, block-based programming environments, such as Scratch and Code.org, and beginner-oriented programming environments, such as Blockly and Pencil Code, have been de-veloped. However, they have limitations when transitioning from block to text-based programming. In this study, we conducted one semester of classes for 128 middle school, high school, and uni-versity students to determine whether an environment that allows using a text-based programming language in a block-based programming environment aids beginners’ understanding of program-ming instructions, command usage confidence, and programming usefulness. The results confirm that the usability of a block-based environment positively influences programming perception. This study is significant because it verifies the necessity and effectiveness of a block-based environment that employs a text-based programming language in programming education for beginners.
ARTICLE | doi:10.20944/preprints202307.1666.v1
Subject: Computer Science And Mathematics, Security Systems Keywords: cybersecurity; digital forensics; cyber threats; forensic investigator; python
Online: 25 July 2023 (07:56:11 CEST)
This article delves deeply into digital forensics, covering computer forensics, network 1 forensics, and mobile device forensics. It analyzes the techniques and methodologies used by forensic 2 investigators in various disciplines. It underlines the diffculties investigators encounter and the 3 importance of thorough investigations to combat ever-increasing cyber risks. The paper emphasizes 4 the necessity of leveraging digital forensic tools to improve cybersecurity and provides a thorough 5 list of widely used Python libraries suitable for each investigation strategy, allowing for effective 6 comparison. Furthermore, it emphasizes the availability and suitability of these Python libraries in 7 computer device investigations (PyTSK3, Volatility, Pyregf, and Pyevtx), mobile device investigations 8 (Pytsk3, Volatility, Pyewf, dfVFS, Androguard, and pyMobileDevice), and network forensics (Scapy, 9 Bro/Zeek, Dpkt, pypcap, and NetworkX). The creation of these libraries recognizes the complexities 10 of digital crimes and the importance of applying modern techniques in forensic investigations. 11 Particularly, digital forensics plays an important role for healthcare providers because modern 12 medical devices produce, store, and transmit large amounts of patient and therapy information, 13 which could provide a forensic investigator with a treasure trove of potential digital evidence.
TECHNICAL NOTE | doi:10.20944/preprints202012.0179.v1
Subject: Engineering, Automotive Engineering Keywords: Python; Molecular Dynamics; Scientific Computing; Periodic Boundary Condition
Online: 8 December 2020 (06:47:59 CET)
In this paper, we introduce a simple yet powerful and working version of the molecular dynamics code using the Python 3.9 language. The code contents are published in the link given in the appendix 1. The structure and components of the program is given in detail using flowcharts and code snippets. The program consists of major features like velocity verlet integrator, thermostats, COM removal, input and output modules, virial, pressure, and other thermodynamic quantities estimation etc. The author believes that this program will be helpful to graduate students who perform research in molecular dynamics simulations who intend to write their own code instead of the sophisticated open source packages.
ARTICLE | doi:10.20944/preprints201805.0470.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: remote sensing; python; data management; landsat; open-source
Online: 31 May 2018 (11:12:27 CEST)
Many remote sensing analytical data products are most useful when they are in an appropriate regional or national projection, rather than globally based projections like Universal Transverse Mercator (UTM) or geographic coordinates, i.e., latitude and longitude. Furthermore, leaving data in the global systems can create problems, either due to misprojection of imagery because of UTM zone boundaries, or because said projections are not optimised for local use. We developed the open-source Irish Earth Observation (IEO) Python module to maintain a local remote sensing data library for Ireland. This pure Python module, in conjunction with the IEOtools Python scripts, utilises the Geospatial Data Abstraction Library (GDAL) for its geoprocessing functionality. At present, the module supports only Landsat TM/ETM+/OLI/TIRS data that have been corrected to surface reflectance using the USGS/ESPA LEDAPS/ LaSRC Collection 1 architecture. This module and the IEOtools catalogue available Landsat data from the USGS/EROS archive, and includes functions for the importation of imagery into a defined local projection and calculation of cloud-free vegetation indices. While this module is distributed with default values and data for Ireland, it can be adapted for other regions with simple modifications to the configuration files and geospatial data sets.
ARTICLE | doi:10.20944/preprints202309.1375.v1
Subject: Environmental And Earth Sciences, Remote Sensing Keywords: flood; radar imagery; Sentinel-1; Google Earth Engine; Python
Online: 20 September 2023 (09:47:41 CEST)
This paper presents an operational approach for detecting floods and establishing flood extent using Sentinel-1 radar imagery with Google Earth Engine. Flooded areas are identified using a change-detection method based on the normalized difference. The HAND algorithm is used to delineate zones for processing. The approach was tested and calibrated at small scale to identify optimal parameters for flood detection. It was then applied to the whole of the island of Madagascar after the cyclone Batsirai in 2022. The proposed method is enabled by the computing power and data availability of Google Earth Engine and Google Colab. The results show satisfactory accuracy in delineating flooded areas. The advantages of this approach are its rapidity, online availability and ability to detect floods over a wide area. The approach relying on Google tools thus offers an effective solution for generating a large-scale synoptic picture to inform hazard management decision-making. However, one of the method’s drawbacks is that it depends to a large extent on frequent radar imagery being available at the time of flood events and on free access to the platform. These drawbacks will need to be taken into account in an operational scenario.
ARTICLE | doi:10.20944/preprints202012.0516.v1
Subject: Computer Science And Mathematics, Algebra And Number Theory Keywords: benefits; c++; comparative study; execution speed; memory management; python
Online: 21 December 2020 (11:57:01 CET)
In this era of technology, programming has become more significant than ever before. Python and C++ are both widely used programming languages. Python, the most popular programming language in today’s world, is a high-level object-oriented language whereas C++, the language behind most operating systems, is a low-level object-oriented language. In this paper, we present a comparative study of Python and C++. This paper discusses the introduction to these languages, their memory management techniques, and the reasons behind their program execution speed. Furthermore, we analyzed the execution time and memory used by multiple algorithms in both the languages with best, average, and worst cases. They are also compared with respect to the benefits and issues related to them. Results indicate that C++ is faster than Python in execution speed but Python serves as a better language for beginners due to its simplicity. Moreover, for the best results, the language should be selected according to the type of project.
ARTICLE | doi:10.20944/preprints202306.1016.v1
Subject: Environmental And Earth Sciences, Water Science And Technology Keywords: Decision Tree; linear regression; Naïve Bayes; Python; Support Vector Machine
Online: 14 June 2023 (08:40:50 CEST)
Water pollution is a common problem for dams situated within an urban or agricultural catchment. This can negatively affect the hydro ecosystem, drinking, recreational and other uses of water. In this study, the drinking water quality class of the Roodeplaat Dam, South Africa which faces pollution problems was modeled using machine learning algorisms in Python Jupyter Notebook 6.0.0. Eleven monthly water quality parameters recorded at five sampling stations from January 1981 to September 2017 were used for training and testing the model. Five machine learning classifiers: Gaussian Naïve Bayes (GNB), K-nearest neighbors (KNN), Decision Tree (DT), Support Vector Machines (SVM), and Linear Regression (LR) at a test size of 20%, 25%, 30%, and 40% were used to classify water into five classes (Excellent to Very bad). It was investigated that the dam water has only three classes good, medium, and bad. The prediction accuracies of machine learning algorithms from the highest to the lowest were 96.39%, 96.17%, 92.25%, 90.20, and 54.19% for KNN, DT, SVM, GNB, and LR, respectively. Therefore, KNN at a test size of 30% was recommended to classify the water quality of Roodeplat Dam accurately. Hence, machine learning algorithms can be used to identify the class of water quality before the water is treated and distributed for drinking use.
TECHNICAL NOTE | doi:10.20944/preprints202103.0194.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Active Learning, Classification, Machine Learning, Python, Github, Repository, Open Source
Online: 5 March 2021 (21:14:20 CET)
Machine learning applications often need large amounts of training data to perform well. Whereas unlabeled data can be easily gathered, the labeling process is difficult, time-consuming, or expensive in most applications. Active learning can help solve this problem by querying labels for those data points that will improve the performance the most. Thereby, the goal is that the learning algorithm performs sufficiently well with fewer labels. We provide a library called scikit-activeml that covers the most relevant query strategies and implements tools to work with partially labeled data. It is programmed in Python and builds on top of scikit-learn.
Subject: Computer Science And Mathematics, Software Keywords: ARBTools, Python, three-dimensional interpolation, spline, vector field, scalar field, smoothing
Online: 28 March 2019 (11:13:31 CET)
ARBTools is a Python library containing a Lekien-Marsden type tricubic spline method for interpolating three-dimensional scalar or vector fields presented as a set of discrete data points on a regular cuboid grid. ARBTools was developed for simulations of magnetic molecular traps, in which the magnitude, gradient and vector components of a magnetic field are required. Numerical integrators for solving particle trajectories are included, but the core interpolator can be used for any scalar or vector field. The only additional system requirements are NumPy.
ARTICLE | doi:10.20944/preprints202306.0309.v1
Subject: Computer Science And Mathematics, Software Keywords: search engine optimization; seo techniques; python seo tool; machine learning seo
Online: 5 June 2023 (10:38:37 CEST)
In the present-day digital landscape, websites have increasingly relied on digital marketing practices, notably search engine optimization (SEO), as a vital component in promoting sustainable growth. The traffic a website receives directly determines its development and success. As such, website owners frequently engage the services of SEO experts to enhance their website's visibility and increase traffic. These specialists employ premium SEO audit tools that crawl the website's source code to identify structural changes necessary to comply with specific ranking criteria, commonly called SEO factors. Working collaboratively with developers, SEO specialists implement technical changes to the source code and await the results. The cost of purchasing premium SEO audit tools or hiring an SEO specialist typically ranges in the thousands of dollars per year. Against this backdrop, this research endeavors to provide an open-source Python-based Machine Learning SEO software tool to the general public, catering to the needs of both website owners and SEO specialists. The tool analyzes the top-ranking websites for a given search term, assessing their on-page and off-page SEO strategies, and provides recommendations to enhance a website's performance to surpass its competition. The tool yields remarkable results, boosting average daily organic traffic from 10 to 143 visitors.
ARTICLE | doi:10.20944/preprints202211.0507.v1
Subject: Engineering, Civil Engineering Keywords: cementitious materials; concrete; mortar; freeze-thaw resistance; durability; 3D-scan; Python
Online: 28 November 2022 (09:09:08 CET)
Deterioration of concrete subjected to freezing and thawing climatic conditions is one of most important factors affecting the durability of concrete infrastructure in cold climates. The freeze-thaw resistance of cementitious materials like concrete and mortar can be determined by the CDF test (Capillary Suction of De-icing chemicals and Freeze-Thaw Test). Here, concrete specimens are subjected to repeated freeze-thaw cycles with simultaneous addition of de-icing salt and the amount of material weathered near the surface is determined. For concretes with adequate freeze-thaw resistance, this test method works very well. However, specimens with inadequate or unknown performance often experience increased edge weathering, which is caused by the detachment of the lateral isolation tape. The increasing edge influence thus leads to a falsification of the results and consequently to an underestimation of the actual freeze-thaw resistance of the material. In materials research in particular, however, concretes with high levels of weathering are studied in order to be able to investigate various factors of influence on the freeze-thaw resistance of concretes in a targeted manner. This paper presents a novel methodology that delivers new information regarding the weathering of CDF test samples and the associated distribution function of the height decrease using high resolution 3D scan data. The results indicate a correlation between the progression of the distribution function and the sample's maximum aggregate size. The change of the sample volume can be used to support the weathering results of the standard CDF methodology. The increase of the surface area is used to estimate the tortuosity of the sample surface. It indicates an asymptotic curve approaching a specific maximum value, which is dependent on the the weathering depth of the sample.
ARTICLE | doi:10.20944/preprints202108.0138.v2
Subject: Chemistry And Materials Science, Nanotechnology Keywords: inorganic nanoparticles; in silico; optimization; theranostic; therapeutic; diagnostic; computation; coding; Python
Online: 7 September 2021 (11:57:23 CEST)
Inorganic nanoparticles are utilized for therapeutic, diagnostic, or in combination, theranostic purposes. The latter involves simultaneous sensing, imaging, or tracking of drug delivery. Furthermore, these nanoparticles can differ in their morphologies, which affect outcomes such as the effectiveness of hyperthermia, induction, drug loading, circulation time by escaping the body's immune system, imaging modality clarity, and biosensing. However, design of these theranostics is limited by the lack of a method to predict their therapeutic efficacy. Herein, we report a simple and novel computational approach via algebraic and geometric calculations of surface area (SA) to volume (V) ratios (SA:V) which can help predict the efficacy of the inorganic nanoparticles of the investigated morphologies. The approach comprises a coding platform for the program and uses Python 3 on a Windows 10 operating system. Analyses of 29 polyhedral morphologies that inorganic nanoparticles could assume ex silico showed that only particular concave and convex morphologies in this size regime are more productive over the standard sizes as well as a few noted in literature for baseline comparison. Our results provide a method that can aid in predicting the efficacy of inorganic nanoparticles with certain morphology giving rise to their fundamental basis and eventual implementation ex silico.
ARTICLE | doi:10.20944/preprints202005.0354.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: ensemble learning; machine learning; Python; spatial distance; statistical distance; weighted ensemble
Online: 23 May 2020 (04:54:39 CEST)
In this paper, we introduce deboost, a Python library devoted to weighted distance ensembling of predictions for regression and classification tasks. Its backbone resides on the scikit-learn library for default models and data preprocessing functions. It offers flexible choices of models for the ensemble as long as they contain the predict method, like the models available from scikit-learn. deboost is released under the MIT open-source license and can be downloaded from the Python Package Index (PyPI) at https://pypi.org/project/deboost. The source scripts are also available on a GitHub repository at https://github.com/weihao94/DEBoost.
ARTICLE | doi:10.20944/preprints202003.0043.v1
Subject: Environmental And Earth Sciences, Environmental Science Keywords: Groundwater Modeling; Hydrologic Monitoring Network; American Samoa; Jupyter Notebooks; GitHub; Python
Online: 3 March 2020 (11:45:15 CET)
Recent advancements in cloud-computing and social-networking are influencing how we communicate professionally, work collaboratively, and approach data-science tasks. Here we show how the groundwater modeling field is well positioned to benefit from these advancements. We present a case study detailing a vertically-integrated, collaborative modeling framework jointly developed by participants at the American Samoa Power Authority and at the University of Hawaii Water Resources Research Center. The framework components include direct collection and analysis of climatic and streamflow data, development of a water budget model, and initiation of a dynamic groundwater modeling process. The framework is entirely open-source and applies newly available data-science infrastructure using Python-based tools compiled with Jupyter Notebooks and cloud computing services such as GitHub. These resources allow for seamless integration of multiple computational components into a dynamic cloud-based workflow that is immediately accessible to stakeholders, resource managers, or anyone with an internet connection
ARTICLE | doi:10.20944/preprints202302.0317.v1
Subject: Computer Science And Mathematics, Computer Science Keywords: SBOannotator; ontologies; SBO terms; Python; software; automated assignment; computational modeling; systems biology
Online: 20 February 2023 (03:57:56 CET)
The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and reproducible manner is challenging. Using precisely defined ontologies enables the encoding of field-specific knowledge and the association of disparate data types. In computational modeling, the medium for representing domain knowledge is the set of orthogonal structured controlled vocabularies named Systems Biology Ontology ( SBO). The SBO terms enable modelers to explicitly define and unambiguously describe model entities, including their roles and characteristics. Here, we present the first standalone tool that automatically assigns SBO terms to multiple entities of a given SBML model, named the SBOannotator. The main focus lies on the reactions, as the correct assignment of precise SBO annotations requires their extensive classification. Our implementation does not consider only top-level terms but examines the functionality of the underlying enzymes to allocate precise and highly specific ontology terms to biochemical reactions. Transport reactions are examined separately and are classified based on the mechanism of molecule transport. Pseudo-reactions that serve modeling purposes are given reasonable terms to distinguish between biomass production and the import or export of metabolites. Finally, other model entities, such as metabolites and genes, are annotated with appropriate terms. Including SBO annotations in the models will enhance the reproducibility, usability, and analysis of biochemical networks. Availability: The open-source project SBOannotator is freely available under the terms of LGPL version 3.0 from https://github.com/draeger-lab/SBOannotator/.
ARTICLE | doi:10.20944/preprints202205.0185.v1
Subject: Computer Science And Mathematics, Information Systems Keywords: AMS; Face Recognition; AAMS; Face Detector; Python; Monitoring; RFID; Arduino Uno; IoT
Online: 13 May 2022 (09:40:48 CEST)
The 21st century, where all things are depending upon technology, almost all the human tasks are being done with the help of technology to save a lot of time and make our life much more comfortable. The monitoring of students’ attendance is a crucial task for faculty in today’s world. There are more chances of errors while entering the students’ attendance records in the primary system, primarily when the class was over. The main concern of this study is to build an IoT-based automated attendance management system for educational institutes by biometric recognition to incorporate fake/proxy attendance and errors of entry and to replace old manual methods of taking students’ attendance by calling their names or roll numbers. The AAS will click the image of the classroom, and it will automatically detect the faces of students sitting in the lecture room and recognize them during lectures then mark their attendance daily to keep a record of their presence and also maintain and manage it for the management staff of the institution for future by using web services.
ARTICLE | doi:10.20944/preprints201908.0098.v1
Subject: Biology And Life Sciences, Food Science And Technology Keywords: community food environment; nutrition environment; geographical information systems (GIS); Facility List Coder; Python
Online: 7 August 2019 (16:53:36 CEST)
A community food environment plays an essential role in explaining the healthy life-style patterns of its community members. However, there is a lack of compelling quantitative approaches to evaluate these environments. This study introduces and validates a new tool named the Facility List Coder (FLC), whose purpose is to assess food environments based on data sources and classification algorithms. Using the case of Mataró (Spain), we randomly selected 301 grids areas (100 m2) where we conducted street audits in order to physically identify all the facilities by name, address and type. Then, audit-identified facilities were matched with those automatically-identified and were classified using the FLC in order to determine its quality. Our results suggest that automatically-identified and audit-identified food environments have a high level of agreement. The ICC estimates and their respective 95% confidence intervals for the overall sample, yield the result “excellent” (ICC ≥ 0.9) for the level of reliability of the FLC.
ARTICLE | doi:10.20944/preprints201810.0372.v1
Subject: Engineering, Control And Systems Engineering Keywords: teaching robotics; science teaching; STEM; robotic tool; python; Raspberry Pi; PiCamera; vision system
Online: 17 October 2018 (05:53:30 CEST)
This paper presents the robotic platform, PiBot, that has been developed and that is aimed at improving the teaching of Robotics with vision to secondary students. Its computational core is the Raspberry Pi 3 controller board, and the greatest novelty of this prototype is the support developed for the powerful camera mounted on board, the PiCamera. An open software infrastructure written in Python language was implemented so that the student may use this camera, or even a WebCam, as the main sensor of this robotic platform. Also, higher level commands have been provided to enhance the learning outcome for beginners. In addition, a PiBot 3D printable model and the counterpart for the Gazebo simulator were also developed and fully supported. They are publicly available so that students and educational centers that do not have the physical robot or can not afford the costs of these, can nevertheless practice and learn or teach Robotics using these open platforms: DIY-PiBot and/or simulated-PiBot.
ARTICLE | doi:10.20944/preprints201710.0085.v1
Subject: Environmental And Earth Sciences, Atmospheric Science And Meteorology Keywords: volcanic gases; SO2; remote sensing; UV cameras; image processing; analysis software; Python 2.7
Online: 13 October 2017 (04:00:49 CEST)
UV SO2 cameras have become a common tool to measure and monitor SO2-emission-rates, mostly from volcanoes but also from anthropogenic sources (e.g. power plants or ships). In the past years, the analysis of UV SO2 camera data has seen many improvements. As a result, for many of the required analysis steps, several alternatives exist today. This inspired the development of Pyplis, an open-source software toolbox written in Python 2.7, which aims to unify the most prevalent methods from literature within a single, cross-platform analysis framework. Pyplis comprises a vast collection of algorithms relevant for the analysis of UV SO2 camera data. These include several routines to retrieve plume background radiances as well as routines for cell and DOAS based camera calibration. The latter includes two independent methods to identify the DOAS field-of-view within the camera images. Plume velocities can be retrieved using an optical flow algorithm as well as signal cross-correlation. Furthermore, Pyplis includes a routine to perform a first order correction of the signal dilution effect. All required geometrical calculations are performed within a 3D model environment allowing for distance retrievals to plume and local terrain features on a pixel basis. SO2-emission-rates can be retrieved simultaneously for an arbitrary number of plume intersections. Pyplis has been extensively and successfully tested using data from several field campaigns. Here, the main features are introduced using a dataset obtained at Mt. Etna, Italy on 16 September 2015.
ARTICLE | doi:10.20944/preprints202112.0352.v1
Subject: Engineering, Control And Systems Engineering Keywords: Ball-Plate System; STEM; USB HD camera; Python scripts; ready-made functions; PID controller
Online: 22 December 2021 (11:20:19 CET)
This paper presents the process of designing, fabrication, assembling, programming and optimizing a prototype of a nonlinear mechatronic Ball-Plate System (BPS) as a laboratory platform for STEM engineer education. Due to the nonlinearity and complexity of BPS, task presents challenging issues, such as: 1) difficulties in controlling the stabilization of a given position point known as steady state error, 2) position resolution known as specific distance error and 3) adverse environmental effects - light shadow error, also discussed in this paper. The laboratory BPS prototype for education was designed, manufactured and installed at the Karlovac University of Applied Sciences at the Department of Mechanical Engineering, Study of mechatronics. The low-cost two degrees BPS system uses a USB HD camera for computer vision as feedback and two DC servomotors as actuators. Due to controlling problems, an advanced block diagram of control system is proposed and discussed. An open-source control system based on Python scripts that allows the use of ready-made functions from the library allows changing the color of the ball and the parameters of the PID controller, thus indirectly simplifying control system and directly the mathematical calculation. The authors will continue their research on this BPS mechatronic platform and control algorithms.
ARTICLE | doi:10.20944/preprints202212.0567.v1
Subject: Computer Science And Mathematics, Artificial Intelligence And Machine Learning Keywords: Voice Assistance, Machine Learning, Virtual Assistance, Artificial Intelligence, Selection Bias, Sample Population, Python 3.10, Pyttsx3, PyTorch, JSON
Online: 30 December 2022 (02:12:34 CET)
In recent times, voice assistants have become a part of our day-to-day lives, allowing information retrieval by voice synthesis, voice recognition, and natural language processing. These voice assistants can be found in many modern-day devices such as Apple, Amazon, Google, and Samsung. This project is primarily focused on Virtual Assistance in Natural Language Processing. Natural Language Processing is a form of AI that helps machines understand people and create feedback loops. This project will use deep learning to create a Voice Recognizer and use Commonvoice and data collected from the local community for model training using Google Colaboratory. After recognizing a command, the AI assistant will be able to perform the most suitable actions and then give a response. The motivation for this project comes from the race and gender bias that exists in many virtual assistants. The computer industry is primarily dominated by the male gender, and because of this, many of the products produced do not regard women. This bias has an impact on natural language processing. This project will be utilizing various open-source projects to implement machine learning algorithms and train the assistant algorithm to recognize different types of voices, accents, and dialects. Through this project, the goal to use voice data from underrepresented groups to build a voice assistant that can recognize voices regardless of gender, race, or accent. Increasing the representation of women in the computer industry is important for the future of the industry. By representing women in the initial study of voice assistants, it can be shown that females play a vital role in the development of this technology. In line with related work, this project will use first-hand data from the college population and middle-aged adults to train voice assistants to combat gender bias.
REVIEW | doi:10.20944/preprints202204.0047.v1
Subject: Computer Science And Mathematics, Computational Mathematics Keywords: Artificial Intelligence; Bottom-up Parser; Context-Free-Grammar; English Grammar; Python; Parse Table; Semantic Parser; Top-downParser
Online: 6 April 2022 (12:42:37 CEST)
The objective of parsing is to transform a natural language sentence it in to a standard order. and in a same way a sentence is tokenized with an appropriate format. There are certain English grammar evaluation rules and the parsing approach which is to be followed for the proper formation of a particular sentence syntactically and semantically using the parsing approach. A sentence in English language is the main element in the semantic parser, which creates a parse tree with the help of applying semantic dating technique to a number of phrases. A parser divides a token into smaller components by applying sets of guidelines that characterize and a series of the tokens to determine its structure of the language, which specified by grammar. The illustration provides easy records on grammatical connections, which can simply know and put into practice with those who have no prior knowledge of the language, such as those who need to obtain textual family members. The semantic family members represent the relationships of a number of the words in the sentence. We advocate utilizing our parser to acquire the tagged sets as well as a context-free layout grammatical representation for the source form. All pronouns, adverbs, singular, plural, nouns, verbs, people, adjectives, tenses and other words are kept in a database.
ARTICLE | doi:10.20944/preprints202307.1831.v1
Subject: Medicine And Pharmacology, Veterinary Medicine Keywords: machine learning; veterinary medical education; random forest; medical education; artificial intelligence; Python; R; veterinary educators; educational data mining; learning analytics
Online: 26 July 2023 (14:02:31 CEST)
Machine learning (ML) offers potential opportunities to enhance the learning, teaching and assessments within veterinary medical education including but not limited to assisting with admissions processes as well as student progress evaluations. The purpose of this primer is to assist veterinary educators in appraising and potentially adopting these rapid upcoming advances in data science and technology. In the first section, we introduce ML concepts and highlight similarities/differences between ML and classical statistics. In the second section, we provide a step-by-step worked example using simulated veterinary student data to answer a hypothesis driven question. Python syntax with explanations is provided within the text to create a random forest ML prediction model and within each step, specific considerations such as how to manage incomplete student records are highlighted when applying ML algorithms within the veterinary education field. The results from the simulated data demonstrate how decisions by the veterinary educator during ML model creation may impact the most important features contributing to the model. These results highlight the need for the veterinary educator to be fully transparent during the creation of ML models and future research is needed to establish guidelines for handling data not missing at random in medical education, and preferred methods for model evaluation.
ARTICLE | doi:10.20944/preprints202103.0189.v1
Subject: Computer Science And Mathematics, Robotics Keywords: Flying Social Robot; Autonomous Unmanned Aerial Vehicle (UAV); Emotion Recognition; Convolution Neural Network (CNN); Virtual Reality (VR); Unity; MATLAB/Simulink; Python
Online: 5 March 2021 (11:52:50 CET)
This work is part of an ongoing research project to develop an unmanned flying social robot to monitor dependants at home in order to detect the person’s state and bring the necessary assistance. In this sense, this paper focuses on the description of a virtual reality (VR) simulation platform for the monitoring process of an avatar in a virtual home by a rotatory-wing autonomous unmanned aerial vehicle (UAV). This platform is based on a distributed architecture composed of three modules communicated through the Message Queue Telemetry Transport (MQTT) protocol: the UAV Simulator implemented in MATLAB/Simulink, the VR Visualiser developed in Unity, and the new emotion recognition (ER) System developed in Python. Using a face detection algorithm and a convolutional neural network (CNN), the ER System is able to detect the person’s face in the image captured by the UAV’s on-board camera and classify the emotion among seven possible ones (surprise, fear, happiness, sadness, disgust, anger or neutral expression). The experimental results demonstrate the correct integration of this new computer vision module within the VR platform, as well as the good performance of the designed CNN, with around 85% in the F1-score, a mean of the precision and recall of the model. The developed emotion detection system can be used in the future implementation of the assistance UAV that monitors dependent people in a real environment, since the methodology used is valid for images of real people.
ARTICLE | doi:10.20944/preprints202308.0102.v1
Subject: Computer Science And Mathematics, Data Structures, Algorithms And Complexity Keywords: Bayesian Multi-Change Point Analysis; Linear Trend Segment Fit; Computationally Efficient Open-Source Python Implementation; S&P500; Mean Market Correlation; Economic Crises; Econophysics
Online: 2 August 2023 (02:40:56 CEST)
Identifying macroeconomic events that are responsible for dramatic changes of economy is of particular relevance to understand the overall economic dynamics. We introduce an open-source available efficient Python implementation of a Bayesian multi-trend change point analysis which solves significant memory and computing time limitations to extract crisis information from a correlation metric. Therefore, we focus on the recently investigated S&P500 mean market correlation in a period of roughly 20 years that includes the dot-com bubble, the global financial crisis and the Euro crisis. The analysis is performed two-fold: first, in retrospect on the whole dataset and second, in an on-line adaptive manner in pre-crisis segments. The on-line sensitivity horizon is roughly determined to be 80 up to 100 trading days after a crisis onset. A detailed comparison to global economic events supports the interpretation of the mean market correlation as an informative macroeconomic measure by a rather good agreement of change point distributions and major crisis events. Furthermore, the results hint to the importance of the U.S. housing bubble as trigger of the global financial crisis, provide new evidence for the general reasoning of locally (meta)stable economic states and could work as a comparative impact rating of specific economic events.
ARTICLE | doi:10.20944/preprints202203.0290.v3
Subject: Biology And Life Sciences, Biology And Biotechnology Keywords: host-virus interactions; tissue-specific model; COVID-19; SARS-CoV-2; antiviral targets; flux balance analysis; flux variability analysis; reaction knockout; host-derived enforcement; metabolic modeling; virus mutations; software engineering; Python
Online: 17 January 2023 (01:50:23 CET)
COVID-19 is one of the deadliest respiratory diseases, and its emergence caught the pharmaceutical industry off guard. While vaccines have been rapidly developed, treatment options for infected people remain scarce, and COVID-19 poses a substantial global threat. This study presents a novel workflow to predict robust druggable targets against emerging RNA viruses using metabolic networks and information of the viral structure and its genome sequence. For this purpose, we implemented pymCADRE and PREDICATE to create tissue-specific metabolic models, construct viral biomass functions and predict host-based antiviral targets from more than one genome. We observed that pymCADRE reduces the computational time of flux variability analysis for internal optimizations. We applied these tools to create a new metabolic network of primary bronchial epithelial cells infected with SARS-CoV-2 and identified enzymatic reactions with inhibitory effects. The most promising reported targets were from the purine metabolism, while targeting the pyrimidine and carbohydrate metabolisms seemed to be promising approaches to enhance viral inhibition. Finally, we computationally tested the robustness of our targets in all known variants of concern, verifying our targets’ inhibitory effects. Since laboratory tests are time-consuming and involve complex readouts to track processes, our workflow focuses on metabolic fluxes within infected cells and is applicable for rapid hypothesis-driven identification of potentially exploitable antivirals concerning various viruses and host cell types.