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PHOTONAI—A Python API for rapid machine learning model development

by Leenings, Ramona, Winter, Nils Ralf, Plagwitz, Lucas, Holstein, Vincent, Ernsting, Jan, Sarink, Kelvin, Fisch, Lukas, Steenweg, Jakob, Kleine-Vennekate, Leon, Gebker, Julian, Emden, Daniel, Grotegerd, Dominik, Opel, Nils, Risse, Benjamin, Jiang, Xiaoyi, Dannlowski, Udo, Hahn, Tim
Published in PloS one (21.07.2021)

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Navigating Drug-Induced Adversities: A Python-Based Console Application for Causality Assessment Using the Naranjo Algorithm

by Kumar, Masuram Bharath, Shaifali, Iram, Gairola, Bikash
Published in Curēus (Palo Alto, CA) (04.12.2023)

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RABiTPy: an open-source Python software for rapid, AI-powered bacterial tracking and analysis

by Sen, Samyabrata, Vairagare, Indraneel, Gosai, Jitendrapuri, Shrivastava, Abhishek
Published in BMC bioinformatics (18.05.2025)

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ETE: a python Environment for Tree Exploration

by Huerta-Cepas, Jaime, Dopazo, Joaquín, Gabaldón, Toni
Published in BMC bioinformatics (13.01.2010)

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LLM-IE: a python package for biomedical generative information extraction with large language models

by Hsu, Enshuo, Roberts, Kirk
Published in JAMIA open (01.04.2025)

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Fully-automated segmentation of muscle and inter-/intra-muscular fat from magnetic resonance images of calves and thighs: an open-source workflow in Python

by Tam, Kenneth, Liu, Si Wen, Costa, Sarah, Szabo, Eva, Reitsma, Shannon, Gillick, Hana, Adachi, Jonathan D., Wong, Andy Kin On
Published in Skeletal muscle (27.12.2024)

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Recent developments in the PHENIX software for automated crystallographic structure determination

by Adams, Paul D., Gopal, Kreshna, Grosse-Kunstleve, Ralf W., Hung, Li-Wei, Ioerger, Thomas R., McCoy, Airlie J., Moriarty, Nigel W., Pai, Reetal K., Read, Randy J., Romo, Tod D., Sacchettini, James C., Sauter, Nicholas K., Storoni, Laurent C., Terwilliger, Thomas C.
Published in Journal of synchrotron radiation (01.01.2004)

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Journal Article Conference Proceeding

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A statistical approach to automated analysis of the low‐contrast object detectability test for the large ACR MRI phantom

by Golestani, Ali M., Gee, Julia M.
Published in Journal of applied clinical medical physics (01.07.2025)

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Automation of image processing through ML algorithms of GRASS GIS using embedded Scikit-Learn library of Python

by Lemenkova, Polina
Published in Examples and counterexamples (01.06.2025)

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Automated Image Processing Workflow for Morphological Analysis of Fluorescence Microscopy Cell Images

by Voigt, Sven P., Ravikumar, K., Basu, Bikramjit, Kalidindi, Surya R.
Published in JOM (1989) (01.08.2021)

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An algorithm for automated extraction of resonance parameters from the stabilization method

by Langner, Johanna, Sadhukhan, Anjan, Saha, Jayanta K., Witek, Henryk A.
Published in Computer physics communications (01.11.2025)

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pyAKI—An open source solution to automated acute kidney injury classification

by Porschen, Christian, Ernsting, Jan, Brauckmann, Paul, Weiss, Raphael, Würdemann, Till, Booke, Hendrik, Amini, Wida, Maidowski, Ludwig, Risse, Benjamin, Hahn, Tim, von Groote, Thilo
Published in PloS one (03.01.2025)

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SPACIER: on-demand polymer design with fully automated all-atom classical molecular dynamics integrated into machine learning pipelines

by Nanjo, Shun, Arifin, Maeda, Hayato, Hayashi, Yoshihiro, Hatakeyama-Sato, Kan, Himeno, Ryoji, Hayakawa, Teruaki, Yoshida, Ryo
Published in npj computational materials (28.01.2025)

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PyRoboCOP: Python-Based Robotic Control and Optimization Package for Manipulation and Collision Avoidance

by Raghunathan, Arvind U., Jha, Devesh K., Romeres, Diego
Published in IEEE transactions on automation science and engineering (2024)

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Virtual-simulation boosted neural network dose calculation engine for intensity-modulated radiation therapy

by Li, Zirong, Liu, Yaoying, Shang, Xuying, Sheng, Huashan, Xie, Chuanbin, Zhao, Wei, Zhang, Gaolong, Zhou, Qichao, Xu, Shouping
Published in Australasian physical & engineering sciences in medicine (01.06.2025)

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Solving Spatial Optimization Problems via Lagrangian Relaxation and Automatic Gradient Computation

by Lei, Zhen, Lei, Ting L.
Published in ISPRS international journal of geo-information (01.01.2025)

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Causal chambers as a real-world physical testbed for AI methodology

by Gamella, Juan L., Peters, Jonas, Bühlmann, Peter
Published in Nature machine intelligence (01.01.2025)

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Calibrating activated sludge models through hyperparameter optimization: a new framework for wastewater treatment plant simulation

by Yu, Huarong, Wang, Yue, Li, Tan, Gan, Qibo, Qu, Dan, Qu, Fangshu
Published in npj clean water (23.08.2025)

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A New Tool for Extracting Static and Dynamic Parameters from [18F]F-DOPA PET/CT in Pediatric Gliomas

by Mureddu, Michele, Funck, Thomas, Morana, Giovanni, Rossi, Andrea, Ramaglia, Antonia, Milanaccio, Claudia, Verrico, Antonio, Bottoni, Gianluca, Fiz, Francesco, Piccardo, Arnoldo, Fato, Marco Massimo, Trò, Rosella
Published in Journal of clinical medicine (19.10.2024)

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Automated identification of bulk structures, two-dimensional materials, and interfaces using symmetry-based clustering

by Denell, Thea, Himanen, Lauri, Scheidgen, Markus, Draxl, Claudia
Published in npj computational materials (06.02.2025)

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