Network descriptive statistics for the Deezer networks. by Alex Stivala (8356257)

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Example ALAAMEE goodness-of-fit output. by Alex Stivala (8356257)

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Global Aridity Index and Potential Evapotranspiration Climate Database v3.1 - Algorithm Code (Python) by Robert Zomer (12796235)

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)

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)

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

DeepB3Pred - code by Saleh Musleh (22263718)

Flowchart representation of lion optimization algorithm for hyperparameter tuning in the HCAP model. by Mohanad Faeq Ali (21354273)

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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)

DeepB3Pred_source_code by Muhammad Arif (17012472)

Code by Baoqiang Chen (21099509)

“…We divided the dataset into training and test sets, using 70% of the genes for training and 30% for testing. We implemented machine learning algorithms using the following R packages: rpart for Decision Trees, gbm for Gradient Boosting Machines (GBM), ranger for Random Forests, the glm function for Generalized Linear Models (GLM), and xgboost for Extreme Gradient Boosting (XGB). …”

RNA Velocity model simulation results. (A) Simulation results for RNA Velocity model without delay ( samples). The simulation is composed of an up-regulation phase (both production... by Ziyan Jin (21021976)

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Modeling lung cancer AST network and its perturbation with a SOX2 degrader. (A) Lung Cancer AST Network and the corresponding stochastic equations. Parameters are , , , , , , , , w... by Ziyan Jin (21021976)

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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).…”

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

BaNDyT: Bayesian Network Modeling of Molecular Dynamics Trajectories by Elizaveta Mukhaleva (20602550)

“…We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”