Article
Ecology
Hui Yu, Marcel Klaassen
Summary: The study introduces a package called rabc to assist researchers in developing animal behavior classifiers using supervised classification approach. This package includes workflow for accelerometer data visualization, feature calculation, selection, extreme gradient boost model training, validation, and demonstration of behavior classification results using an example dataset on white stork.
ECOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Ting Wei, Jinfu Nie, Nicholas B. Larson, Zhenqing Ye, Jeanette E. Eckel-Passow, Keith D. Robertson, Jean-Pierre A. Kocher, Liguo Wang
Summary: The CpGtools package is designed to analyze DNA methylation data, including CpG positions, DNA methylation values, and differential CpG analysis between groups using various statistical methods.
Article
Green & Sustainable Science & Technology
Thi-Thu-Huong Le, Yustus Eko Oktian, Howon Kim
Summary: The Industrial Internet of Things (IIoT) provides growth opportunities for industrial businesses but also faces cybersecurity challenges. Machine learning-based Intrusion Detection Systems (IDS) are attractive for improving attack detection accuracy in imbalanced IIoT datasets.
Article
Biochemical Research Methods
Matteo Manica, Charlotte Bunne, Roland Mathis, Joris Cadow, Mehmet Eren Ahsen, Gustavo A. Stolovitzky, Maria Rodriguez Martinez
Summary: The emergence of high-throughput technologies allows for measurements of numerous molecular entities, but inferring networks from this data remains a challenge. COSIFER is a package that offers a selection of network inference methodologies and consensus strategies to create robust network predictions.
Article
Biochemical Research Methods
Nicholas Mateyko, Omar Tariq, Xinyi E. Chen, Will Cheney, Asfar Lathif Salaudeen, Ishika Luthra, Najmeh Nikpour, Abdul Muntakim Rafi, Hadis Kamali Deghan, Cassandra Jensen, Carl de Boer
Summary: Generate Indexes for Libraries (GIL) is a software tool that generates primers for multiplexed sequencing libraries. It can be customized to meet user specifications and produces ordering and demultiplexing-ready outputs.
Article
Biochemical Research Methods
Marie Mille, Julie Ripoll, Bastien Cazaux, Eric Rivals
Summary: This study proposes a Python package called dipwmsearch, which offers an original and efficient algorithm for searching for occurrences of dinucleotide PWMs in sequences. The package allows the enumeration of matching words and simultaneous searching in the sequence, even if it contains IUPAC codes. Users can easily install dipwmsearch via Pypi or conda, and they also have access to comprehensive documentation and executable scripts for using dinucleotide PWMs.
Article
Biochemical Research Methods
Quan Do, Ho Bich Hai, Pierre Larmande
Summary: This article introduces PyRice, a Python package that provides a unified programming API to quickly collect gene information for Oryza sativa species and combine it logically to facilitate scientific research. PyRice's modular design and smart query system optimize query speed and produce intuitive results.
Article
Biochemical Research Methods
Jan Ludwiczak, Aleksander Winski, Stanislaw Dunin-Horkawicz
Summary: This study developed localpdb, a versatile Python library for managing protein structures and annotations. It features a flexible plugin system for unifying structural data with diverse auxiliary resources, suitable for bioinformatic tasks, especially large-scale protein structural analysis and machine learning.
Article
Computer Science, Interdisciplinary Applications
Stephen Eckel, Daniel S. Barker, Eric B. Norrgard, Julia Scherschligt
Summary: The Python computer program presented in this study simulates various aspects of laser cooling physics. Users can specify parameters and choose from different levels of approximation for computational efficiency. The software successfully reproduces well-known phenomena such as Rabi flopping, electromagnetically induced transparency, and optical molasses.
COMPUTER PHYSICS COMMUNICATIONS
(2022)
Article
Chemistry, Medicinal
Jan-Oliver Kapp-Joswig, Bettina G. Keller
Summary: Density-based clustering procedures are widely used due to their ability to find arbitrary shaped clusters and their robustness against outliers. They have been proven effective in molecular dynamics simulations for identifying relevant molecular conformations. The open-source Python project CommonNNClustering provides a convenient reimplementation of the common-nearestneighbor method, offering hierarchical clustering and result evaluation functionalities with a focus on flexibility and customization through a generic API design.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Computer Science, Artificial Intelligence
Ana Marta Sequeira, Diana Lousa, Miguel Rocha
Summary: The field of protein data mining has been rapidly growing, but tools and platforms for protein sequence analysis and classification still have limitations. To address these limitations, ProPythia, a versatile and easy-to-use Python package, has been proposed to deploy machine learning and deep learning approaches for protein sequence analysis and classification.
Article
Biochemical Research Methods
Jin Xu, Jessie Jiang, Herbert M. Sauro
Summary: SBMLDiagrams is a new Python package that allows users to add and retrieve layout and render information in SBML. It uses skia-python to support diagram rendering, allowing export to common image formats.
Article
Computer Science, Interdisciplinary Applications
Tobias Kohne, Bryan Riel, Mark Simons
Summary: Dense, regional-scale, continuously-operating GNSS networks allow for the monitoring of plate motion and regional surface deformation. This article introduces DISSTANS, a Python package that aims to analyze the observation records from these networks, taking advantage of their spatial structure and enabling uncertainty propagation.
COMPUTERS & GEOSCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Tao Ma, Lizhou Wu, Shuairun Zhu, Hongzhou Zhu
Summary: This study investigates the performance of extreme gradient boosting (XGBoost) in predicting multiclass clay sensitivity and the ability of synthetic minority over-sampling technique (SMOTE) in addressing imbalanced categories. The results show that XGBoost performs the best in the prediction of clay sensitivity, while SMOTE is useful in addressing imbalanced issues.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemistry & Molecular Biology
Xin Huang, Patricia Kruisz, Martin Kuhlwilm
Summary: S* is a widely used statistic for detecting archaic admixture from population genetic data. We implemented sstar, which is robust to differences in demographic models and can be used for detecting introgressed fragments in various scenarios and in non-human species.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Chen Wang, Xiaomei Yang, Shaomin Fei, Kai Zhou, Xiaofeng Gong, Miao Du, Ruisen Luo
Summary: This paper investigates the application of scalar quantization based on sparse least square optimization, proposing multiple quantization algorithms based on different regularization criteria, and comparing and testing them through iterative methods and clustering-based methods.
IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
(2021)
Article
Computer Science, Artificial Intelligence
Chen Wang, Chengyuan Deng, Zhoulu Yu, Dafeng Hui, Xiaofeng Gong, Ruisen Luo
Summary: The study introduces a novel dynamic ensemble method AER to address the overfitting issue in binary imbalanced data classification through regularization and utilizing global geometry of data, demonstrating superior performance in experiments.
INFORMATION FUSION
(2021)
Proceedings Paper
Computer Science, Theory & Methods
Sepehr Assadi, Chen Wang
PROCEEDINGS OF THE 52ND ANNUAL ACM SIGACT SYMPOSIUM ON THEORY OF COMPUTING (STOC '20)
(2020)
Article
Computer Science, Information Systems
Songyi Dian, Peng Cheng, Qiang Ye, Jirong Wu, Ruisen Luo, Chen Wang, Dafeng Hui, Ning Zhou, Dong Zou, Qin Yu, Xiaofeng Gong
Proceedings Paper
Automation & Control Systems
Luo Ruisen, Dian Songyi, Wang Chen, Cheng Peng, Tang Zuodong, Yu YanMei, Wang Shixiong
3RD INTERNATIONAL CONFERENCE ON AUTOMATION, CONTROL AND ROBOTICS ENGINEERING (CACRE 2018)
(2018)
Article
Computer Science, Hardware & Architecture
Shixiong Wang, Jianhua He, Chen Wang, Xitong Li
COMPUTER SYSTEMS SCIENCE AND ENGINEERING
(2018)
Article
Computer Science, Information Systems
Ruisen Luo, Qian Feng, Chen Wang, Xiaomei Yang, Haiyan Tu, Qin Yu, Shaomin Fei, Xiaofeng Gong