Python scripts and notebooks by Ismail Belgacem (20845811)

Python code for hierarchical cluster analysis of detected R-strategies from rule-based NLP on 500 circular economy definitions by Zahir Barahmand (18008947)

“…</p><p dir="ltr">This Python code was optimized and debugged using ChatGPT-4o to ensure implementation efficiency, accuracy, and clarity.…”

Fitting a feast/famine cycle to a glycolysis model. by Paul van Lent (16876977)

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Jaxkineticmodel allows for hybridizing kinetic models with neural networks. by Paul van Lent (16876977)

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Analysis of convergence properties for a collection of SBML models. by Paul van Lent (16876977)

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Overview of the SBML models used in this study. The collection of models was retrieved from Biomodels [43] and a previously reported collection of SBML benchmark models [11]. The n... by Paul van Lent (16876977)

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Finites differences python code to solve CH equation with a source term and Comsol routine to solve Brusselator equation in radial domains. by Giulio Facchini (9031490)

“…<p dir="ltr"><b><i>* Cahn-Hilliard simulations *</i></b><br>Finite difference code implementing the modified Cahn Hilliard equation with a forward Euler scheme and the possibility to parallelize the solver using the numba python library.…”

EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit by Gonzalo Colmenarejo (650249)

“…In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. …”

2D Orthogonal Planes Split: <b>Python</b> and <b>MATLAB</b> code | <b>Source Images</b> for Figures by Nektarios Valous (20715650)

“…The output files generated by the code include results from both Python and MATLAB implementations; these output images are provided as validation, demonstrating that both implementations produce matching results.…”

Prediction accuracy analysis over time steps. by Mohanad Faeq Ali (21354273)

“…The recurrent networks, specifically Long Short Term Memory (LSTM), process data from healthcare devices, identifying abnormal patterns that indicate potential cyberattacks over time. The created system was implemented using Python, and various metrics, including false positive and false negative rates, accuracy, precision, recall, and computational efficiency, were used for evaluation. …”

FPR and FNR analysis based on different time steps. by Mohanad Faeq Ali (21354273)

Design and implementation of DelaySSA. The input data for DelaySSA are reaction information, initial states, parameters and delays. Combining these into the simulation function, th... by Ziyan Jin (21021976)

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Illustration of the text transformation process before and after synonym replacement: The process begins with a sample initial text segment (Sample text before synonym replacement’... by Enock Niyonkuru (21246879)

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Schematic of the approach: This schematic illustrates the entire workflow of the project. by Enock Niyonkuru (21246879)

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Text Transformation Pipeline: An example of the multi-stage text transformation pipeline applied to a sample abstract (PMID: 30609739). by Enock Niyonkuru (21246879)

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Comparative analysis of WordNet replacement impact on data distribution. by Enock Niyonkuru (21246879)

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Comparison of window size for embedding with Wordnet synonym replacement (WN) and without (PM). While Table 1 compared the effects of different values of using a window size of 10,... by Enock Niyonkuru (21246879)

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Non-biomedical word replacement algorithm: This algorithm outlines the process for replacing non-biomedical words in a corpus using WordNet. by Enock Niyonkuru (21246879)

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Comparison of mean interconcept distance for embedding with WordNet synonym replacement (WN) and without (PM). The initial number of unique concepts in the total corpus was 3,018,9... by Enock Niyonkuru (21246879)

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Comparative analysis of WN and PM methodologies: Figure (a) displays the bar chart comparing WN and PM across five distinct concept sets (Methods), highlighting the number of conce... by Enock Niyonkuru (21246879)

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