Supporting data for “Deep learning methods and applications to digital health” by Shichao Ma (9399224)

“…</p><p dir="ltr">Several packges are mendatory to run the source code, including:</p><p dir="ltr">Python > 3.6 (3.11 preferred), TensorFlow > 2.16, Keras > 3.3, NumPy > 1.26, Pandas > 2.2, SciPy > 1.13</p><p><br></p>…”

Supporting data for "Optimisation of Trust in Collaborative Human-Machine Intelligence in Construction" by Hao Chen (9696848)

“…The second folder mirrors the structure of the first, encompassing Scopus data and Python source code used to generate the visualizations featured in Chapter 2. …”

MEG Dataset and Analysis Scripts for “The Effects of Task Similarity During Representation Learning in Brains and Neural Networks” by Nicholas Menghi (22426174)

“…</p><h3><b>Contents</b></h3><ul><li><b>MEG data</b> (results of the correlation between empirical and model matrices at different dimensionalities and domains)</li><li><b>Behavioral data</b> (behavioural accuracy performance: "Spatual Source Data")</li><li><b>Analysis script</b></li><li><b>Python package </b>developed to help with retrieving and computing simple operations</li></ul><h3><b>Data format</b></h3><p dir="ltr">Data are organized according to a structured folder layout (see <code>README.md</code> in the repository) and include:</p><ul><li><code>npy</code> MEG files (numpy)</li><li><code>.csv</code> behavioral files</li><li>Python scripts using MNE-Python for statistical analysis and visualization</li></ul><h3><b>Usage</b></h3><p dir="ltr">The provided scripts reproduce the statistical tests and figures presented in the manuscript. …”

DRLiPS: A Novel Method for Prediction of Druggable RNA-Small Molecule Binding Pockets Using Machine Learning by Sowmya Ramaswamy Krishnan (20867198)

Supplementary files for "A Guided Assistant for Building Machine Learning Models in Analytical Workflows" by An Le (20473628)

“…<table><tr><td><p><br></p></td></tr></table><p dir="ltr">app.py: Source code for the chatbot using the original system prompt (as demonstrated in the two case studies)</p><p dir="ltr">app_revised.py: Source code for the chatbot using the revised system prompt (incorporating enhancements from peer review)</p><p dir="ltr">test case 1.txt: Full conversation history for Test Case I (LFIA classification)</p><p dir="ltr">test case 2.txt: Full conversation history for Test Case II (LC-MS retention time regression)</p><p dir="ltr">revised_chat_history.txt: Test conversation illustrating new behaviors introduced by the revised system prompt</p><p dir="ltr">test case 1.py: Python script generated during Test Case I session for LFIA classification</p><p dir="ltr">test case 2.py: Python script generated during Test Case II session for retention-time regression</p><p dir="ltr"><br></p>…”

<b>Myelin Basic Protein (MBP) Degradome Foundation Atlas</b> by Axel Petzold (7076261)

“…</li></ul><p dir="ltr">Dataset Contents</p><p dir="ltr">The compressed archive includes:</p><ul><li>MBP_WT.csv — full degradome of wild-type MBP</li><li>MBP_R159K.csv — full degradome of the R159K MBP variant</li><li>MBP_Degradome_All.csv — merged and unified dataset combining all included MBP variants</li><li>Python source code used to generate all peptide fragments and compute peptide features</li><li>README.txt — structured technical documentation</li><li>requirements.txt — software dependency list for reproducibility</li></ul><h3>Data Format</h3><p dir="ltr">All files are provided in CSV (comma-separated values) format and include the following annotated fields:</p><ul><li><code>id</code> — structured peptide identifier (e.g., MBP_WT_10_42)</li><li><code>peptide</code> — amino acid sequence</li><li><code>start</code>, <code>stop</code> — cleavage positions</li><li><code>mz</code> — mass-to-charge ratio</li><li><code>Da</code> — molecular weight</li><li><code>Boman</code> — Boman index</li><li><code>charge</code> — net charge</li><li><code>pI</code> — isoelectric point</li><li><code>hydrophobicity</code></li><li><code>instability_index</code></li><li><code>aliphatic_index</code></li></ul><p dir="ltr">These properties enable integration into R, Python, SAS, Matlab, and machine learning workflows.…”

Mexico Airports Traffic Statistics (2006–2025) by Montserrat Mora (20430644)

“…</li><li><b>Requirements File</b>: A <code>requirements.txt</code> file listing the Python dependencies needed to run the script.…”

The artifacts and data for the paper "DD4AV: Detecting Atomicity Violations in Interrupt-Driven Programs with Guided Concolic Execution and Filtering" (OOPSLA 2025) by zixuan yuan (17602152)

“…</li><li><code><strong>wllvm</strong></code>: The third-party library project WLLVM provides tools for building whole-program LLVM bitcode files from unmodified C or C++ source packages.…”

MLP_mod_application_v2.zip by Jian Li (20881226)

“…<p dir="ltr">The python source code for predicting the spatial location of macrophages using single cell dataset. …”

Discovery of a Latent Entropy-Based Physiologic State Variable Governing Multisystem Instability in Critical Illness by Jordan Rabbani (22800074)

“…Contents: notebook/ – A full Google Colab notebook exported as HTML and IPYNB, containing the exact code used for data cleaning, EI computation, EI_slope derivation, cross-correlation analysis, and multivariable regression. tables/ – CSV files of the processed ei_full dataframe, the xcorr_df table (lag-based cross-correlation results), and the ss_df table (two-variable OLS models for EI_slope). figures/ – Auto-generated plots of EI trajectories and regression diagnostics (if any were produced). metadata/ – Variable dictionaries, version information for Python, NumPy, Pandas, Statsmodels, and notes on reproducibility. …”

Curvature-Adaptive Embedding of Geographic Knowledge Graphs in Hyperbolic Space by chenchen Guo (21327470)

“…</p><h3>Requirements</h3><ul><li>Python 3.7</li><li>PyTorch 1.10.0 & CUDA 11.8</li></ul><h3>Main Result Running commands:</h3><p dir="ltr">Execute <code>.sh: bash .…”

Supplementary Material for review (<b>Revealing the co-occurrence patterns of public emotions from social media data</b>) by Yang Hua (21399140)

“…</p><p dir="ltr">This document provides a detailed explanation of how to reproduce all experimental results, figures and tables presented in the paper, and the key indicators in the abstract by using the shared datasets and source code. The aim is to ensure full reproducibility of the study.…”

Visitors to Mexico’s Archaeological Sites and Museums (1996-2025) by Montserrat Mora (20430644)

“…</li><li><b>Requirements File</b>: A <code>requirements.txt</code> file listing necessary Python dependencies for analysis.…”

<b>Tau Degradome Foundation Atlas</b> by Axel Petzold (7076261)

“…</li><li><b>Compression format:</b> Datasets are distributed in <code>.tar.gz</code> format and can be extracted with:</li></ul><pre></pre><pre><code>tar -xvzf FILENAME.tar.gz</code><br><br></pre><p dir="ltr"><b>Reproducibility and Methods</b><br>All datasets can be fully regenerated using open-source software tools, including <b>Python</b> and <b>SAS</b>. …”

Not All local LLMs Are Equal: A Benchmark of Energy and Performance by Simão Cunha (19712455)

“…<br><br>To execute the program, run the following command, changing the parameters as needed:<br><br>```bash<br>#!/bin/bash<br><br>source ../env/bin/activate<br><br>export PYTHONPATH=$PYTHONPATH:$(pwd)<br>export WEGGLI_PATH=weggli<br>export PATH="$HOME/.cargo/bin:$PATH"<br><br>python3 main.py \<br> --llm_path llms/models/codellama-7b-instruct.Q5_K_M.gguf \<br> --benchmarks humaneval_x/\<br> --max_tokens 512 \<br> --n_ctx 4098 \<br> --seed 42 \<br> --top_p 0.95 \<br> --temperature 0.6 \<br> --n_times 1 \<br> --sleep_time 1.0 \<br> --save_output yes \<br> --n_shot_prompting 0 \<br> --pass_k 1 \<br> --samples_interval all<br><br>deactivate<br>```<br><br><b>Note:</b> You may need to create the <code>__init__.py</code> files manually, as Figshare does not allow uploading files with zero bytes.…”

SpaMask: Dissecting spatial domains in spatial transcriptomics by a masked graph attention autoencoder by Yi Liu (17324461)

“…<br>(2) Tutorial for domain identification on 10x Visium human dorsolateral prefrontal cortex (DLPFC) dataset can be found here: Train_151674.ipynb.<br>Python source code, tutorials and datasets can be also accessed at https://github.com/LYxiaotai/SpaMask.…”

<b>Myelin oligodendrocyte glycoprotein (MOG) Degradome Foundation Atlas</b> by Axel Petzold (7076261)

“…</li></ul><h3>Reproducibility and Code Availability</h3><p dir="ltr">Dataset generation is fully reproducible using open-source tools:</p><ul><li>Python</li><li>SAS</li></ul><p dir="ltr">All required scripts are included in the repository and are well documented to support local replication and custom adaptations. …”

A Human Brain Map of Mitochondrial Respiratory Capacity and Diversity by Eugene V. Mosharov (20543317)

“…Python code used for the conversion of the image of the brain slab to Neuroimaging Informatics Technology Initiative (NIfTI) format.…”

Albumin Degradome Foundation Atlas by Axel Petzold (7076261)

“…</p><h2><b>Data Format and Access</b></h2><ul><li><b>Primary file:</b> <code>Albumin_Degradome_Foundation_Atlas_v1.tar.xz</code><br>(contains all peptide tables in standard CSV format)</li><li><b>File Type:</b> ASCII comma-separated values (CSV)</li><li><b>Compression:</b> <code>xz -9 -T0</code> for maximal CPU-parallelised compression</li><li><b>Compatibility:</b></li><li><ul><li>R, Python, MATLAB, SAS</li><li>Excel, LibreOffice</li><li>Any proteomics workflow (e.g., Skyline, MaxQuant preprocessing, MS/MS spectral libraries)</li></ul></li></ul><h2><b>FAIR Principles</b></h2><p dir="ltr">This dataset is fully aligned with FAIR data standards:</p><ul><li><b>Findable:</b> Rich metadata, stable DOI, search-optimised description</li><li><b>Accessible:</b> Open-access Figshare repository</li><li><b>Interoperable:</b> Standard numeric and CSV formats</li><li><b>Reusable:</b> Transparent, reproducible Python source code included</li></ul><h2><b>Applications</b></h2><p dir="ltr">The Albumin Degradome Foundation Atlas supports research across multiple biomedical domains:</p><ul><li>Biomarker development in liver disease, kidney dysfunction, inflammation, and systemic disorders</li><li>Mass-spectrometry method development</li><li>Computational proteomics and peptide modelling</li><li>Autoimmunity and neo-epitope analysis</li><li>Protein–peptide interaction studies</li><li>Proteolytic pathway mapping and degradomics</li></ul><h2><b>Versioning and Future Work</b></h2><p dir="ltr">This is <b>Version 1</b> of the Albumin Degradome Foundation Atlas. …”

Seismic-Acoustic Dataset of Coastal Bryde’s Whales in the Beibu Gulf by Yue Wang (22435645)

“…</p></td></tr><tr><td><p dir="ltr"><code>requirements.txt</code></p></td><td><p dir="ltr">Python dependencies for environment setup.…”