Search Results - (( (stateni OR studies) python code analysis ) OR ( state python code analysis ))~

Analysis methods and code for very high-precision mass measurements of unstable isotopes by Karthein, J., Atanasov, D., Blaum, K., Lunney, D., Manea, V., Mougeot, M.

“…We present a robust analysis code developed in the Python language and incorporating libraries of the ROOT data analysis framework for the state-of-the-art mass spectrometry method called phase…”
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A Study of Large Language Models in Detecting Python Code Violations by Mohammed Salih, Hekar A., Sarhan, Qusay I.

“… This study investigates the effectiveness of large language models (LLMs) compared to traditional static code analysis tools in detecting Python coding violations…”
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PBjam: A Python Package for Automating Asteroseismology of Solar-like Oscillators by Nielsen, M. B., Davies, G. R., Ball, W. H., Lyttle, A. J., Li 李坦, T. 达, Hall, O. J., Chaplin, W. J., Gaulme, P., Carboneau, L., Ong 王加, J. M. J. 冕, García, R. A., Mosser, B., Roxburgh, I. W., Corsaro, E., Benomar, O., Moya, A., Lund, M. N.

“… So far the process of performing an asteroseismic analysis of a star has remained somewhat esoteric and inaccessible to nonexperts…”
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SBML2HYB: a Python interface for SBML compatible hybrid modeling by Pinto, José, Costa, Rafael S, Alexandre, Leonardo, Ramos, João, Oliveira, Rui

“…Abstract Summary Here, we present sbml2hyb, an easy-to-use standalone Python tool that facilitates the conversion of existing mechanistic models of biological systems in Systems Biology Markup Language (SBML…”
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Snakes on a Spaceship - An Overview of Python in Heliophysics by Burrell, A.G., Halford, A., Klenzing, J., Stoneback, R. A., Morley, S. K., Annex, A. M., Laundal, K. M., Kellerman, A. C., Stansby, D., Ma, J.

“…Computational analysis has become ubiquitous within the heliophysics community. However, community standards for peer review of codes and analysis have lagged behind these developments…”
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MechElastic: A Python library for analysis of mechanical and elastic properties of bulk and 2D materials by Singh, Sobhit, Lang, Logan, Dovale-Farelo, Viviana, Herath, Uthpala, Tavadze, Pedram, Coudert, François-Xavier, Romero, Aldo H.

“…The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix (Cij…”
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Python code smells detection using conventional machine learning models by Sandouka, Rana, Aljamaan, Hamoud

“… Therefore, code smell detection is important in software building. Recent studies utilized machine learning algorithms for code smell detection…”
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GPT-4.1 Sets the Standard in Automated Experiment Design Using Novel Python Libraries by Fachada, Nuno, Fernandes, Daniel, Fernandes, Carlos M., Ferreira-Saraiva, Bruno D., Matos-Carvalho, João P.

“… unfamiliar Python APIs for complex computational experiments remains poorly characterized. This study systematically benchmarks a selection of state-of-the-art LLMs in generating functional Python code for two increasingly challenging scenarios…”
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pyMBE: The Python-based molecule builder for ESPResSo by Beyer, David, Torres, Paola B, Pineda, Sebastian P, Narambuena, Claudio F, Grad, Jean-Noël, Košovan, Peter, Blanco, Pablo M

“…We present the Python-based Molecule Builder for ESPResSo (pyMBE), an open source software application to design custom coarse-grained (CG…”
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VAMPyR-A high-level Python library for mathematical operations in a multiwavelet representation by Bjørgve, Magnar, Tantardini, Christian, Jensen, Stig Rune, Gerez S, Gabriel A, Wind, Peter, Di Remigio Eikås, Roberto, Dinvay, Evgueni, Frediani, Luca

“…), they provide a framework that narrows the gap between the theoretical formalism of the fundamental equations and the practical implementation in a working code…”
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COBRApy: COnstraints-Based Reconstruction and Analysis for Python by Ebrahim, Ali, Lerman, Joshua A, Palsson, Bernhard O, Hyduke, Daniel R

“…Background COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes…”
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Gnocis: An integrated system for interactive and reproducible analysis and modelling of cis-regulatory elements in Python 3 by Bredesen-Aa, Bjørn André, Rehmsmeier, Marc

“… methods for the genome-wide prediction of candidate CREs. We here present Gnocis, a Python package that streamlines the analysis and the modelling of CRE sequences…”
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PETAL: a Python tool for deep analysis of biological pathways by Sgroi, Giuseppe, Russo, Giulia, Pappalardo, Francesco

“… Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth search…”
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Pytim: A python package for the interfacial analysis of molecular simulations by Sega, Marcello, Hantal, György, Fábián, Balázs, Jedlovszky, Pál

“… The code implements several algorithms for the identification of instantaneous interfaces of arbitrary shape, and analysis tools written specifically for the study of interfacial properties, such as intrinsic profiles…”
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Kssdtree: an interactive Python package for phylogenetic analysis based on sketching technique by Yang, Hang, Lu, Xiaoxin, Chang, Jiaxing, Chang, Qing, Zheng, Wen, Chen, Zehua, Yi, Huiguang

“… These limitations collectively impede the overall convenience and efficiency of the analysis. In this study, we introduce Kssdtree, an interactive Python package designed to address these challenges…”
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Pyleoclim: Paleoclimate Timeseries Analysis and Visualization With Python by Khider, Deborah, Emile‐Geay, Julien, Zhu, Feng, James, Alexander, Landers, Jordan, Ratnakar, Varun, Gil, Yolanda

“…We present a Python package geared toward the intuitive analysis and visualization of paleoclimate timeseries, Pyleoclim. The code is open‐source, object…”
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MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics by Haiman, Zachary B., Zielinski, Daniel C., Koike, Yuko, Yurkovich, James T., Palsson, Bernhard O.

“… MASSpy adds dynamic modeling tools to the COnstraint-Based Reconstruction and Analysis Python (COBRApy…”
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LLM-Based Test-Driven Interactive Code Generation: User Study and Empirical Evaluation by Fakhoury, Sarah, Naik, Aaditya, Sakkas, Georgios, Chakraborty, Saikat, Lahiri, Shuvendu K.

“… Through a mixed methods user study with 15 programmers, we present an empirical evaluation of the effectiveness of the workflow to improve code generation accuracy…”
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Discovering Repetitive Code Changes in Python ML Systems by Dilhara, Malinda, Ketkar, Ameya, Sannidhi, Nikhith, Dig, Danny

“… To fill the knowledge gap and advance the science and tooling in ML software evolution, we conducted the first and most fine-grained study on code change patterns in a diverse corpus of 1000 top…”
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ColiCoords: A Python package for the analysis of bacterial fluorescence microscopy data by Smit, Jochem H., Li, Yichen, Warszawik, Eliza M., Herrmann, Andreas, Cordes, Thorben

“…Single-molecule fluorescence microscopy studies of bacteria provide unique insights into the mechanisms of cellular processes and protein machineries in ways that are unrivalled by any other…”
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