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PyCG: Practical Call Graph Generation in Python by Salis, Vitalis, Sotiropoulos, Thodoris, Louridas, Panos, Spinellis, Diomidis, Mitropoulos, Dimitris

“… We propose a pragmatic, static approach for call graph generation in Python. We compute all assignment relations between program identifiers of functions, variables, classes, and modules through an inter-procedural analysis…”
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A Study of Large Language Models in Detecting Python Code Violations by Mohammed Salih, Hekar A., Sarhan, Qusay I.

“… Common static code analysis tools for Python, such as Pylint and Flake8, are widely used to enforce code quality by detecting coding violations without executing the code…”
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Evaluating Large Language Models in Class-Level Code Generation by Du, Xueying, Liu, Mingwei, Wang, Kaixin, Wang, Hanlin, Liu, Junwei, Chen, Yixuan, Feng, Jiayi, Sha, Chaofeng, Peng, Xin, Lou, Yiling

“…Recently, many large language models (LLMs) have been proposed, showing advanced proficiency in code generation…”
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NeuroPycon: An open-source python toolbox for fast multi-modal and reproducible brain connectivity pipelines by Meunier, David, Pascarella, Annalisa, Altukhov, Dmitrii, Jas, Mainak, Combrisson, Etienne, Lajnef, Tarek, Bertrand-Dubois, Daphné, Hadid, Vanessa, Alamian, Golnoush, Alves, Jordan, Barlaam, Fanny, Saive, Anne-Lise, Dehgan, Arthur, Jerbi, Karim

“… NeuroPycon is an open-source multi-modal brain data analysis toolkit which provides Python-based template pipelines for advanced multi-processing of MEG, EEG, functional and anatomical MRI data…”
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mesas.py v1.0: a flexible Python package for modeling solute transport and transit times using StorAge Selection functions by Harman, Ciaran J., Xu Fei, Esther

“…, and in the transport dynamics. SAS is currently the state-of-the-art approach to interpreting tracer transport…”
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Hitac: a hierarchical taxonomic classifier for fungal ITS sequences compatible with QIIME2 by Miranda, Fábio M., Azevedo, Vasco C., Ramos, Rommel J., Renard, Bernhard Y., Piro, Vitor C.

“…Background Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants…”
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Percolation theory using Python by Malthe-Sørenssen, Anders

“… Readers will learn how to generate, analyze, and comprehend data and models, with detailed theoretical discussions complemented by accessible computer codes…”
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Understanding the Robustness of Transformer-Based Code Intelligence via Code Transformation: Challenges and Opportunities by Li, Yaoxian, Qi, Shiyi, Gao, Cuiyun, Peng, Yun, Lo, David, Lyu, Michael R., Xu, Zenglin

“…Transformer-based models have demonstrated state-of-the-art performance in various intelligent coding tasks such as code comment generation and code completion…”
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Integrated reliability analysis procedure for spatially variable soil slopes using recursive FORM algorithm enhanced by importance sampling: Abaqus via Python implementations by Ji, Jian, Liao, Wenwang, Hu, Yining, Lü, Qing

“… The improved Hasofer-Lind-Rackwitz-Fiessler (iHLRF) recursive algorithm is adopted to implement the FORM procedure when coupled with finite element codes for slope stability analysis, and the KL is used to reduce the dimension of random variables…”
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Statistics Using Python by Campesato, Oswald

“…This book is designed to offer a fast-paced yet thorough introduction to essential statistical concepts using Python code samples, and aims to assist data scientists in their daily endeavors…”
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Single-cell sequencing to multi-omics: technologies and applications by Wu, Xiangyu, Yang, Xin, Dai, Yunhan, Zhao, Zihan, Zhu, Junmeng, Guo, Hongqian, Yang, Rong

“… Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity…”
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PyPIMalDet: A malicious PyPI package detection method combining code features and metadata features by Yan, Jiale, Zhao, Bo

“… Given the vast number of software packages and frequent updates on PyPI, existing detection methods based on dynamic analysis or large language models are computationally and time-consuming…”
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Leveraging Python to Process Cross-Cultural Temperament Interviews: A Novel Platform for Text Analysis by Underwood, Joshua J., Kirchhoff, Cornelia, Warwick, Haven, Gartstein, Maria A.

“… Specifically, we used Python natural language processing capabilities to analyze semistructured temperament interviews conducted with U.S…”
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BGC-val: a model- and grid-independent Python toolkit to evaluate marine biogeochemical models by de Mora, Lee, Yool, Andrew, Palmieri, Julien, Sellar, Alistair, Kuhlbrodt, Till, Popova, Ekaterina, Jones, Colin, Allen, J. Icarus

“…The biogeochemical evaluation toolkit, BGC-val, is a model- and grid-independent Python toolkit that has been built to evaluate marine biogeochemical models using a simple interface…”
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PeptideBuilder: A simple Python library to generate model peptides by Tien, Matthew Z., Sydykova, Dariya K., Meyer, Austin G., Wilke, Claus O.

“… For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code…”
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Mathematical Modeling in Systems Biology

“…The reprint presents a collection of systems biology-related topics and new studies that utilize computational, mathematical, and systems-oriented approaches…”
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From code to reliability: Python-powered Paraconsistent Logic for alarm detection in the power gris/ Do codigo a confiabilidade: Logica Paraconsistente impulsionada por Python para a deteccao de alarmes na rede de energia by de Oliveira, Joseffe Barroso, Gino, Joao Vitor Santa Rosa, de Lima, Carlos Jose, Filho, Joao Inacio da Silva

“… This application enables the comparison of triggered alarms with the resultant logical states obtained during the analysis…”
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Raw Data to Results: A Hands-On Introduction and Overview of Computational Analysis for Single-Molecule Localization Microscopy by Martens, Koen J. A., Turkowyd, Bartosz, Endesfelder, Ulrike

“… Importantly, user-friendly, ready-to-use and well-documented code in Python and MATLAB with exemplary data is provided as an interactive experience for the reader, as well as a starting…”
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BASIN-3D: A brokering framework to integrate diverse environmental data by Varadharajan, Charuleka, Hendrix, Valerie C., Christianson, Danielle S., Burrus, Madison, Wong, Catherine, Hubbard, Susan S., Agarwal, Deborah A.

“…Diverse observational and simulation datasets are needed to understand and predict complex ecosystem behavior over seasonal to decadal and century time-scales…”
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MultiNMRFit: a software to fit 1D and pseudo-2D NMR spectra by Millard, Pierre, Le Grégam, Loïc, Dubiley, Svetlana, Gabrielli, Valeria, Gosselin-Monplaisir, Thomas, Lippens, Guy, Charlier, Cyril

“…Abstract Motivation Nuclear Magnetic Resonance (NMR) is widely used for quantitative analysis of metabolic systems…”
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