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

“…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 describe here the software’s uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. …”

Data Sheet 1_COCαDA - a fast and scalable algorithm for interatomic contact detection in proteins using Cα distance matrices.pdf by Rafael Pereira Lemos (9104911)

“…Here, we introduce COCαDA (COntact search pruning by Cα Distance Analysis), a Python-based command-line tool for improving search pruning in large-scale interatomic protein contact analysis using alpha-carbon (Cα) distance matrices. …”

A multi-hop example from the BibSQL dataset. by Zhenyu Wang (580934)

“…While acknowledging limitations such as potential logic errors in complex queries and reliance on domain-specific knowledge, the proposed framework shows strong generalizability and practical applicability. By uniquely integrating semantic similarity learning, RAG, and PoT prompting, this work establishes a scalable foundation for future intelligent bibliographic retrieval systems and domain-specific Text-to-SQL applications.…”

Detailed statistics of the BibSQL dataset. by Zhenyu Wang (580934)

“…While acknowledging limitations such as potential logic errors in complex queries and reliance on domain-specific knowledge, the proposed framework shows strong generalizability and practical applicability. By uniquely integrating semantic similarity learning, RAG, and PoT prompting, this work establishes a scalable foundation for future intelligent bibliographic retrieval systems and domain-specific Text-to-SQL applications.…”

Genosophus: A Dynamical-Systems Diagnostic Engine for Neural Representation Analysis by Alan Glanz (22109698)

“…</p><h2><b>Included Files</b></h2><h3><b>1. </b><code><strong>GenosophusV2.py</strong></code></h3><p dir="ltr">Executable Python implementation of the Genosophus Engine.…”

Fast, FAIR, and Scalable: Managing Big Data in HPC with Zarr by Alfonso Ladino (21447002)

“…(NEXRAD), using open-source tools from the Python ecosystem such as Xarray, Xradar, and Dask to enable efficient parallel processing and scalable analysis. …”

Appendix_SRD_Manual.docx by Doron Nakar (21664370)

Comprehensive Fluid and Gravitational Dynamics Script for General Symbolic Navier-Stokes Calculations and Validation by Stylianos Touloumidis (19938747)

“…It provides a flexible foundation on which theoretical assumptions can be validated, and practical calculations performed. Implemented in Python with symbolic calculations, the script facilitates in-depth analysis of complex flow patterns and makes advanced mathematical computations more accessible. …”

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)

“…</p><pre><pre>sudo apt-get install -y wget git build-essential python3 python python-pip python3-pip tmux cmake libtool libtool-bin automake autoconf autotools-dev m4 autopoint libboost-dev help2man gnulib bison flex texinfo zlib1g-dev libexpat1-dev libfreetype6 libfreetype6-dev libbz2-dev liblzo2-dev libtinfo-dev libssl-dev pkg-config libswscale-dev libarchive-dev liblzma-dev liblz4-dev doxygen libncurses5 vim intltool gcc-multilib sudo --fix-missing<br></pre></pre><pre><pre>pip install numpy && pip3 install numpy && pip3 install sysv_ipc<br></pre></pre><h4><b>Download the Code</b></h4><p dir="ltr">Download <b>DD4AV</b> from the Figshare website to your local machine and navigate to the project directory:</p><pre><pre>cd DD4AV<br></pre></pre><h4><b>Configure Environment and Install the Tool</b></h4><p dir="ltr">For convenience, we provide shell scripts to automate the installation process. …”

Artifact for the IJCAI 2024 paper "Solving Long-run Average Reward Robust MDPs via Stochastic Games" by Krishnendu Chatterjee (15367413)

“…<br></pre></pre><h2>Structure and How to run</h2><p dir="ltr">There are four Python files in the repository.</p><pre><pre>(i) `StrategyIteration.py` is the backend code, containing the implementation of the RPPI algorithm described in the paper.…”

<b>Anthropogenic nutrient inputs cause excessive algal growth for nearly half the world’s population</b> by Richard McDowell (7311011)

“…<p dir="ltr">Contains</p><p dir="ltr">Final Analysis Output.xlsx: Current and reference concentrations of DRP, TP, NO3-N and TN along with pivot table analysis</p><p dir="ltr">Code: Python code used to implement the model in ArcGIS Pro.…”

Probabilistic-QSR-GeoQA by Mohammad Kazemi (19442467)

“…</p><p><br></p><p><br></p><p dir="ltr"><b>Perquisites</b></p><p dir="ltr">Two spatial reasoning tools, SparQ for conventional reasoning and Probcog for probabilistic reasoning need to be installed:</p><p><br></p><p dir="ltr">- Probcog ( Follow the their github repo in https://github.com/opcode81/ProbCog)</p><p dir="ltr">- SparQ (Follow their manual in https://www.uni-bamberg.de/fileadmin/sme/SparQ/SparQ-Manual.pdf)</p><p><br></p><p><br></p><p dir="ltr"><b>Materials</b></p><p dir="ltr">This includes codes, data, evidence sets, and mln folders for two experiments:</p><p dir="ltr">- Code: This folder includes questionGenerator.py and answerExtraction.py for generating synthetic questions and post-processing of inferences from Probcog and SparQ reasoners. …”

A Hybrid Ensemble-Based Parallel Learning Framework for Multi-Omics Data Integration and Cancer Subtype Classification by Mohammed Nasser Al-Andoli (21431681)

“…<p dir="ltr">The code supports replication of results on TCGA Pan-cancer and BRCA datasets and includes data preprocessing, model training, and evaluation scripts:<br>Python scripts for data preprocessing and integration</p><ul><li>Autoencoder implementation for multimodal feature learning</li><li>Hybrid ensemble training code (DL/ML models and meta-learner)</li><li>PSO and backpropagation hybrid optimization code</li><li>Parallel execution scripts</li><li>Instructions for replicating results on TCGA Pan-cancer and BRCA datasets</li></ul><p></p>…”

<b>Algorithm Pseudocode</b> by Yibin Zhao (22425801)

“…The model generates point forecasts and forecast interval boundaries for short-term loads, providing important support for risk quantification and decision-making in power systems. The pseudo-code follows standard Python syntax specifications for functions and loops and is easy to understand and implement. …”

<b>Anonymous, runnable artifact for </b><b>Testing AI Applications Under Nondeterminism, Drift, and Resource Constraints: A Problem‑Driven Multi‑Layer Approach</b> by Nariman Mani (21380459)

“…</b> The anonymized archive includes a dependency‑free Python implementation of all five layers (oracle, coverage, drift mapping, prioritization, resource scheduling), an orchestrator, and synthetic datasets with 50 test cases per sub‑application (LLM assistant, retrieval with citation, vision calories, notification/social). …”

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 .…”

Void-Center Galaxies and the Gravity of Probability Framework: Pre-DESI Consistency with VGS 12 and NGC 6789 by Jordan Waters (21620558)

“…<br><br><br><b>ORCID ID: https://orcid.org/0009-0009-0793-8089</b><br></p><p dir="ltr"><b>Code Availability:</b></p><p dir="ltr"><b>All Python tools used for GoP simulations and predictions are available at:</b></p><p dir="ltr"><b>https://github.com/Jwaters290/GoP-Probabilistic-Curvature</b><br><br>The Gravity of Probability framework is implemented in this public Python codebase that reproduces all published GoP predictions from preexisting DESI data, using a single fixed set of global parameters. …”

Leveraging explainable causal artificial intelligence to study forest gross primary productivity dynamics in China's protected areas by Pedro Cabral (18947566)

“…<p dir="ltr">A Python script used for modeling forest GPP in China´s Protected Areas, including mean encoding of the categorical variable climate zone (CZ), multicollinearity testing using Variance Inflation Factor (VIF), implementation of four machine learning models to predict forest GPP, XAI and causality analysis.…”

MCCN Case Study 3 - Select optimal survey locality by Donald Hobern (21435904)

“…</p><p dir="ltr">This is a simple implementation that uses four environmental attributes imported for all Australia (or a subset like NSW) at a moderate grid scale:</p><ol><li>Digital soil maps for key soil properties over New South Wales, version 2.0 - SEED - see <a href="https://esoil.io/TERNLandscapes/Public/Pages/SLGA/ProductDetails-SoilAttributes.html" target="_blank">https://esoil.io/TERNLandscapes/Public/Pages/SLGA/ProductDetails-SoilAttributes.html</a></li><li>ANUCLIM Annual Mean Rainfall raster layer - SEED - see <a href="https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-rainfall-raster-layer" target="_blank">https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-rainfall-raster-layer</a></li><li>ANUCLIM Annual Mean Temperature raster layer - SEED - see <a href="https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-temperature-raster-layer" target="_blank">https://datasets.seed.nsw.gov.au/dataset/anuclim-annual-mean-temperature-raster-layer</a></li></ol><h4><b>Dependencies</b></h4><ul><li>This notebook requires Python 3.10 or higher</li><li>Install relevant Python libraries with: <b>pip install mccn-engine rocrate</b></li><li>Installing mccn-engine will install other dependencies</li></ul><h4><b>Overview</b></h4><ol><li>Generate STAC metadata for layers from predefined configuratiion</li><li>Load data cube and exclude nodata values</li><li>Scale all variables to a 0.0-1.0 range</li><li>Select four layers for comparison (soil organic carbon 0-30 cm, soil pH 0-30 cm, mean annual rainfall, mean annual temperature)</li><li>Select 10 random points within NSW</li><li>Generate 10 new layers representing standardised environmental distance between one of the selected points and all other points in NSW</li><li>For every point in NSW, find the lowest environmental distance to any of the selected points</li><li>Select the point in NSW that has the highest value for the lowest environmental distance to any selected point - this is the most different point</li><li>Clean up and save results to RO-Crate</li></ol><p><br></p>…”