Five Operator Lattice Simulation by James McDaniel (22522571)

“…<p dir="ltr">This dataset contains the Python simulation code and supporting documentation for the paper <i>A Five-Operator Lattice of Consciousness: A Logical Framework for Mediation Between Implicit and Explicit Processing</i> (McDaniel, 2025).…”

Predicting coding regions on unassembled reads, how hard can it be? - Genome Informatics 2024 by Amanda Clare (98717)

“…The locations and directions of the predictions on the reads are then combined with the information about locations and directions of the reads on the genome using Python code to produce detailed results regarding the correct, incorrect and alternative starts and stops with respect to the genome-level annotation.…”

FlakyFix: Using Large Language Models for Predicting Flaky Test Fix Categories and Test Code Repair by Sakina Fatima (15362704)

“…<p dir="ltr">This is the replication package associated with the paper: 'FlakyFix: Using Large Language Models for Predicting Flaky Test Fix Categories and Test for Code Repair'</p><p><br></p><p dir="ltr">### Requirements</p><p dir="ltr">This is a list of all required python packages:</p><p dir="ltr">-imbalanced_learn==0.8.1</p><p dir="ltr">-numpy==1.19.5</p><p dir="ltr">-pandas==1.3.3</p><p dir="ltr">-transformers==4.10.2</p><p dir="ltr">-torch==1.5.0</p><p dir="ltr">-scikit_learn==0.24.2</p><p dir="ltr">-openai==v0.28.1</p><p><br></p><p dir="ltr">#Automated tool for labelling dataset with flaky test fix categories</p><p><br></p><p dir="ltr">This is a step-by-step guideline for automatically labelling dataset with flaky test fix categories</p><p><br></p><p><br></p><p dir="ltr">### Input Files:</p><p dir="ltr">This is a an input file that is required to accomplish this step:</p><p dir="ltr">* Data/IdoFT_dataset_filtered.csv</p><p dir="ltr">https://figshare.com/s/47f0fb6207ac3f9e2351</p><p><br></p><p dir="ltr">### Output Files:</p><p dir="ltr">* Results/IdoFT_dataset_filtered.csv</p><p><br></p><p><br></p><p dir="ltr">### Replicating the experiment</p><p><br></p><p dir="ltr">This experiment can be executed using the following commands after navigating to the `Code\` folder:</p><p><br></p><p dir="ltr">```console</p><p dir="ltr">bash Automated_labelling_tool.sh</p><p>```</p><p><br></p><p dir="ltr">It will generate the dataset required to run our prediction models to predict the category of the fix, given a flaky test code</p><p><br></p><p>---</p><p><br></p><p dir="ltr"># Prediction models for fix categories using the test case code</p><p><br></p><p dir="ltr">This is the guideline for replicating the experiments we used to evaluate our prediction models i.e. …”

Data and analysis codes for coarse-grained simulations of metal-organic cages by Emma Wolpert (21223817)

Supporting data for "Interpreting complex ecological patterns and processes across differentscales using Artificial Intelligence" by Yifei Gu (9507104)

“…The detailed implementation, source code and demo dataset are included in dedicated folders for each chapter.…”

Settings for ABC-SMC code. by Román Zapién-Campos (9592478)

The codes and data for "A Graph Convolutional Neural Network-based Method for Predicting Computational Intensity of Geocomputation" by FirstName LastName (20554465)

“…</p><p dir="ltr"><i>cd 1point2dem/CIPrediction</i></p><p dir="ltr"><i>python -u point_prediction.py --model [GCN|ChebNet|GATNet]</i></p><h3>step 4: Parallel computation</h3><p dir="ltr">This step uses the trained models to optimize parallel computation. …”

The codes and data for "A Graph Convolutional Neural Network-based Method for Predicting Computational Intensity of Geocomputation" by FirstName LastName (20554465)

“…</p><p dir="ltr"><i>cd 1point2dem/CIPrediction</i></p><p dir="ltr"><i>python -u point_prediction.py --model [GCN|ChebNet|GATNet]</i></p><h3>step 4: Parallel computation</h3><p dir="ltr">This step uses the trained models to optimize parallel computation. …”

Code for the HIVE Appendicitis prediction modelRepository with LLM_data_extractor_optuna for automated feature extraction by Anoeska Schipper (18513465)

“…</p><p dir="ltr"><b>LLM Data Extractor optuna repo</b> is a Python framework for generating and evaluating clinical text predictions using large language models (LLMs) like <code>qwen2.5</code>. …”

Supplementary data for PCI-based pavement modelling: code, presentation, and additional analysis by Azam Amir (21505033)

Code by Baoqiang Chen (21099509)

“…</p><p><br></p><p dir="ltr">For the 5′ UTR library, we developed a Python script to extract sequences and Unique Molecular Identifiers (UMIs) from the FASTQ files. …”

Analysis Codes for "Gene Signatures Predict Metastatic Organotropism in Breast Cancer: A Machine Learning Analysis of Single-Cell Data" by Ardo Sanjaya (18321300)

OVEP code by Yuanfang Guan (22258765)

“…/usr/bin/env python3</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/plot/plot_auc_nucleotide_length.py` </p><p dir="ltr"> Script related to: plot auc nucleotide length.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/plot/plot_scatter_auc_length.py` </p><p dir="ltr"> Script related to: plot scatter auc length.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_attention/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_attention/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_attention/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_attention/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_1024/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_1024/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_1024/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_1024/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_nonbinary_train_and_predict_5fold_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindelonlyintrain_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindelonlyintrain_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindelonlyintrain_masklabel/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindelonlyintrain_indelonlyintest_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindelonlyintrain_indelonlyintest_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonlyonlyintrain_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonlyonlyintrain_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonlyonlyintrain_masklabel/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_nonbinary_5fold_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_4096/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_4096/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_4096/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_4096/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_512/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_512/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_512/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel_512/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindel_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindel_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindel_masklabel/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_nonindel_masklabel/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonlyonlyintrain_nonindelonlyintest_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonlyonlyintrain_nonindelonlyintest_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_masklabel/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonly_masklabel/predict_nucleotide_plot.py` </p><p dir="ltr"> Script related to: predict nucleotide plot.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonly_masklabel/predict_train.py` </p><p dir="ltr"> Script related to: predict train.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonly_masklabel/plot_auc_compare_base.py` </p><p dir="ltr"> Script related to: plot auc compare base.py</p><p dir="ltr">- `rate_code/code_halftrainmaskmissing_masklabel/base_excludeN_5fold_indelonly_masklabel/plot_auc.py` </p><p dir="ltr"> Script related to: plot auc.py</p><p><br></p><p>---</p><p><br></p><p dir="ltr">## Reproducibility hints</p><p><br></p><p dir="ltr">While this snapshot does not include data/configs, common entry points typically look like:</p><p><br></p><p dir="ltr">- `*predict_train*.py` — training loop (likely 5-fold CV; see corresponding `predict_nucleotide_plot.py` for visualization).…”

Local Python Code Protector Script: A Tool for Source Code Protection and Secure Code Sharing by Pavel Izosimov (20096259)

“…</p><h2>Key Features</h2><ul><li><a href="https://xn--mxac.net/secure-python-code-manager.html" target="_blank"><b>Code Obfuscation in Python</b></a>: Implements multi-level protection with dynamic encryption and obfuscation techniques, making it an effective <a href="https://xn--mxac.net/secure-python-code-manager.html" target="_blank"><b>Python obfuscator</b></a>.…”

Bursty model and Refractory model simulation results. (A) Bursty model simulation results ( samples). The production of nascent mRNA occurs in bursts and degrade after delay time <... by Ziyan Jin (21021976)

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

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

MMRCC_original code by Rui Chen (21529631)

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

6. Motif Code Theory by William Terry (22279591)

“…<p dir="ltr">The Motif Code Theory (MCT) simulation code, mct_unified_code.py, is a Python 3.9 script that models the universe as a time-dependent directed multigraph G(t) = (V(t), E(t)) with N=10^7 vertices (representing quantum fields/particles) and edges (interactions). …”