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Domain Knowledge Matters: Improving Prompts with Fix Templates for Repairing Python Type Errors by Peng, Yun, Gao, Shuzheng, Gao, Cuiyun, Huo, Yintong, Lyu, Michael R.

“…As a dynamic programming language, Python has become increasingly popular in recent years…”
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Discovering Repetitive Code Changes in Python ML Systems by Dilhara, Malinda, Ketkar, Ameya, Sannidhi, Nikhith, Dig, Danny

“… Despite the extraordinary rise in popularity of Python-based ML systems, they do not benefit from these advances…”
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PyTy: Repairing Static Type Errors in Python by Chow, Yiu Wai, Di Grazia, Luca, Pradel, Michael

“… As more and more code bases get type-annotated, static type checkers detect an increasingly large number of type errors…”
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A Python Instrument Control and Data Acquisition Suite for Reproducible Research by Koerner, Lucas J., Caswell, Thomas A., Allan, Daniel B., Campbell, Stuart I.

“… The National Synchrotron Light Source-II (NSLS-II) has generated an open-source Python data acquisition, management, and analysis software suite that automates X-ray…”
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Bloat beneath Python’s Scales: A Fine-Grained Inter-Project Dependency Analysis by Drosos, Georgios-Petros, Sotiropoulos, Thodoris, Spinellis, Diomidis, Mitropoulos, Dimitris

“… In this work, we conduct a large-scale, fine-grained analysis to understand bloated dependency code in the PyPI ecosystem…”
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SpotFlow: Tracking Method Calls and States at Runtime by Hora, Andre

“… In this paper, we propose SpotFlow, a tool to ease the runtime analysis of Python programs. With Spot-Flow, practitioners and researchers can easily extract information…”
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CoverUp: Effective High Coverage Test Generation for Python by Altmayer Pizzorno, Juan, Berger, Emery D.

“… We evaluate our prototype CoverUp implementation across a benchmark of challenging code derived from open-source Python projects and show that CoverUp substantially improves on the state of the art…”
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SNPAAMapper-Python: A highly efficient genome-wide SNP variant analysis pipeline for Next-Generation Sequencing data by Li, Chang, Ma, Kevin, Xu, Nicole, Fu, Chenjian, He, Andrew, Liu, Xiaoming, Bai, Yongsheng

“… In this study, we updated SNPAAMapper, a variant annotation pipeline by converting perl codes to python for generating annotation output with an improved computational efficiency and updated…”
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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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Restoring Reproducibility of Jupyter Notebooks by Wang, Jiawei, Kuo, Tzu-yang, Li, Li, Zeller, Andreas

“…Jupyter notebooks-documents that contain live code, equations, visualizations, and narrative text-now are among the most popular means to compute, present, discuss and disseminate scientific findings…”
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Lost in Translation: A Study of Bugs Introduced by Large Language Models While Translating Code by Pan, Rangeet, Ibrahimzada, Ali Reza, Krishna, Rahul, Sankar, Divya, Wassi, Lambert Pougeum, Merler, Michele, Sobolev, Boris, Pavuluri, Raju, Sinha, Saurabh, Jabbarvand, Reyhaneh

“… The prerequisite for advancing the state of LLM-based code translation is to understand their promises and limitations over existing techniques…”
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MolProbity: More and better reference data for improved all‐atom structure validation by Williams, Christopher J., Headd, Jeffrey J., Moriarty, Nigel W., Prisant, Michael G., Videau, Lizbeth L., Deis, Lindsay N., Verma, Vishal, Keedy, Daniel A., Hintze, Bradley J., Chen, Vincent B., Jain, Swati, Lewis, Steven M., Arendall, W. Bryan, Snoeyink, Jack, Adams, Paul D., Lovell, Simon C., Richardson, Jane S., Richardson, David C.

“… There have been many infrastructure improvements, including rewrite of previous Java utilities to now use existing or newly written Python utilities in the open…”
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Detecting and Explaining Anomalies Caused by Web Tamper Attacks via Building Consistency-based Normality by Liao, Yifan, Xu, Ming, Lin, Yun, Teoh, Xiwen, Xie, Xiaofei, Feng, Ruitao, Liauw, Frank, Zhang, Hongyu, Dong, Jin Song

“… However, their frontend can be manipulable by the clients (e.g., the frontend code can be modified to bypass some validation steps…”
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ThinCurr: An open-source 3D thin-wall eddy current modeling code for the analysis of large-scale systems of conducting structures by Hansen, Christopher, Battey, Alexander, Braun, Anson, Miller, Sander, Lagieski, Michael, Stewart, Ian, Sweeney, Ryan, Paz-Soldan, Carlos

“… The new code, part of the broader Open FUSION Toolkit, is open-source and designed for ease of use without sacrificing capability and speed through a combination of Python, Fortran, and C/C++ components…”
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A NICER View of the Massive Pulsar PSR J0740+6620 Informed by Radio Timing and XMM-Newton Spectroscopy by Riley, Thomas E., Watts, Anna L., Ray, Paul S., Bogdanov, Slavko, Guillot, Sebastien, Morsink, Sharon M., Bilous, Anna V., Arzoumanian, Zaven, Choudhury, Devarshi, Deneva, Julia S., Gendreau, Keith C., Harding, Alice K., Ho, Wynn C. G., Lattimer, James M., Loewenstein, Michael, Ludlam, Renee M., Markwardt, Craig B., Okajima, Takashi, Prescod-Weinstein, Chanda, Remillard, Ronald A., Wolff, Michael T., Fonseca, Emmanuel, Cromartie, H. Thankful, Kerr, Matthew, Pennucci, Timothy T., Parthasarathy, Aditya, Ransom, Scott, Stairs, Ingrid, Guillemot, Lucas, Cognard, Ismael

“…We report on Bayesian estimation of the radius, mass, and hot surface regions of the massive millisecond pulsar PSR J0740+6620, conditional on pulse-profile…”
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Decoding the JAK-STAT Axis in Colorectal Cancer with AI-HOPE-JAK-STAT: A Conversational Artificial Intelligence Approach to Clinical–Genomic Integration by Yang, Ei-Wen, Waldrup, Brigette, Velazquez-Villarreal, Enrique

“…: AI-HOPE-JAK-STAT combines large language models (LLMs), a natural language-to-code engine, and harmonized public CRC datasets from cBioPortal…”
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Introduction to computational causal inference using reproducible Stata, R, and Python code: A tutorial by Smith, Matthew J., Mansournia, Mohammad A., Maringe, Camille, Zivich, Paul N., Cole, Stephen R., Leyrat, Clémence, Belot, Aurélien, Rachet, Bernard, Luque‐Fernandez, Miguel A.

“…The main purpose of many medical studies is to estimate the effects of a treatment or exposure on an outcome. However, it is not always possible to randomize…”
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Python Data Analyst's Toolkit - Learn Python and Python-Based Libraries with Applications in Data Analysis and Statistics by Rajagopalan, Gayathri

“… The code is presented in Jupyter notebooks that can further be adapted and extended. This book is divided into three parts - programming with Python, data analysis and visualization, and statistics…”
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LiPydomics: A Python Package for Comprehensive Prediction of Lipid Collision Cross Sections and Retention Times and Analysis of Ion Mobility-Mass Spectrometry-Based Lipidomics Data by Ross, Dylan H, Cho, Jang Ho, Zhang, Rutan, Hines, Kelly M, Xu, Libin

“… Existing solutions for these data analysis challenges (i.e., multivariate statistics and lipid identification…”
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Python for MATLAB Development - Extend MATLAB with 300,000+ Modules from the Python Package Index by Danial, Albert

“…This book shows you how to enhance MATLAB with Python solutions to a vast array of computational problems in science, engineering, optimization, statistics, finance, and simulation…”
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