Mechanomics Code - JVT حسب Carlo Vittorio Cannistraci (5854046)

"…At the beginning of the code, there is a help section that explains how to use it.<br></li><li>Python (written by Syed Shafat Ali and tested by Yan Ge): analogous functions of the MATLAB folder. …"

Spectral inclusion and pollution for a class of dissipative perturbations - data حسب Alexei Stepanenko (19655629)

"…The datasets are numpy array (Python programming language) saved as pickle files and can be opened using the pickle package  (see https://docs.python.org/3/library/pickle.html).…"

CpG Signature Profiling and Heatmap Visualization of SARS-CoV Genomes: Tracing the Genomic Divergence From SARS-CoV (2003) to SARS-CoV-2 (2019) حسب Tahir Bhatti (20961974)

"…</p><p dir="ltr">Tools and Libraries</p><p dir="ltr">The following tools and libraries were used in this analysis:</p><p dir="ltr">Programming Language :</p><p dir="ltr">Python 3.13</p><p dir="ltr">Libraries :</p><p dir="ltr">pandas: For data manipulation and cleaning.…"

ImproBR Replication Package حسب Anonymus (18533633)

"…**Preprocess**: Extract structured sections (LLM + heuristic fallback)<br>3. **Improve**: Enhance using knowledge retrieval and LLM generation<br><br>## RQ2 Evaluation Pipeline<br>To run the RQ2 evaluation pipeline that compares ImproBR-improved, ChatBR-improved, and raw bug reports against ground truth using similarity analysis on 37 duplicate pairs:<br>```bash<br>cd Modified_ChatBR_Similarity_Codes/RQ2/<br>```<br>Then follow the steps in: [`Modified_ChatBR_Similarity_Codes/RQ2/README.md`](<u>Modified_ChatBR_Similarity_Codes/RQ2/README.md</u>)<br><br><br>## Troubleshooting<br><br>### API Configuration Issues<br><br>**LLM Connection Errors:**<br>- Ensure `AZURE_API_KEY` is valid and not expired<br>- Verify `AZURE_RESOURCE_NAME` matches your Azure OpenAI resource<br>- Check that your deployment name is exactly "gpt-4o-mini"<br>- Confirm you have sufficient quota/credits in your Azure account<br><br>**Knowledge Base Missing:**<br>If you see "Vector store not found" error:<br>```bash<br>python data/build_full_knowledge_base.py<br>```<br><br>### Common Installation Issues<br><br>**ChromaDB Installation Problems:**<br>If ChromaDB fails to install, try:<br>```bash<br>pip install --upgrade pip<br>pip install chromadb==0.4.15 --no-cache-dir<br>```<br><br>Alternative: Install without ChromaDB and use local embeddings<br>```bash<br>pip install -r requirements.txt --exclude chromadb<br>```<br><br>**Requirements Installation Failures:**<br>If requirements.txt fails, install core dependencies first:<br>```bash<br>pip install torch==2.8.0 transformers==4.30.2 sentence-transformers==2.2.2<br>pip install azure-ai-inference==1.0.0b1 openai==1.107.0<br>pip install requests==2.32.5 tqdm==4.67.1 colorama==0.4.6<br>```<br><br>Then install remaining packages:<br>```bash<br>pip install -r requirements.txt<br>```<br><br>**Python Version Compatibility:**<br>- **Minimum**: Python 3.8<br>- **Maximum**: Python 3.11.x<br>- **Recommended**: Python 3.9-3.11<br>- **Known Issues**: Python 3.12+ not supported due to package conflicts<br><br>### Configuration Issues<br><br>**Missing config.py:**<br>Copy template and edit with your API keys:<br>```bash<br>cp config.py.template config.py<br>```<br>Edit config.py with your Azure OpenAI credentials.…"

Fusion API (Supplementary Information 3) from GrowCAD: Bioinspired Mathematical Design for Additive Manufacturing حسب Nasim Mahmoodi (11535135)

"…This Python program generates a 3D body using nonguided loft function from cloud points data…"

Fusion API (Supplementary Information 2) from GrowCAD: Bioinspired Mathematical Design for Additive Manufacturing حسب Nasim Mahmoodi (11535135)

"…This Python program generates a 3D body using a guided rails loft function from cloud points data…"

The Improved Hydro-Sediment Numerical Model and Machine Learning Models حسب Yuning Tan (20580932)

"…The hydro-sediment model was implemented in the C# programming language using Visual Studio, while the machine learning models were developed in Python.…"

ML-UrineQuant حسب Warren Hill (20108487)

"…<p dir="ltr">ML-UrineQuant is a machine learning program written in Python for identifying and quantifying mouse urine on absorbent paper. …"

Coverage Optimized Stochastic Reinforcement Learning for Lines حسب Gusiyuan Wang (21196376)

"…</p><p dir="ltr">We use Python API provided by the IBM ILOG CPLEX 22.1.0 to solve MILP models. …"

MPCID: A new high-resolution multi-precipitation concentration indicators dataset for mainland China حسب 栋洋 张 (20515496)

"…</li><li>Data Format<br>CSV files: The station - based annual data in CSV format can be easily opened and analyzed using spreadsheet software like Microsoft Excel or programming languages such as Python with libraries like Pandas.…"

software code of NeoDesign حسب Wenqian Yu (19730101)

"…Before running the program, it is necessary to check or download python packages and local functions as follow:</p><ul><li>gor4</li><li>mhcflurry</li><li>NetMHCpan4.1</li><li>NetChop3.1</li><li>pepsickle</li><li>hmmer(>3.4)</li></ul><h3>See the read.md file for instructions on how to use the code.…"

Fuzzing: On Benchmarking Outcome as a Function of Benchmark Properties حسب Dylan Wolff (13565191)

"…Also contains some pre- and post-processing scripts for gathering data</p><p dir="ltr"><code>final-data-analysis</code> -- An R Jupyter notebook and Python scripts used to generate the figures in the paper, along with the cleaned and aggregated data in CSV files</p><p dir="ltr"><code>delay</code> -- Python scripts used to generate the figures for e0 (injecting delays) in the paper</p><p dir="ltr"><code>raw-data</code> -- The raw files output by Fuzzbench for our experiments</p><p dir="ltr">The notebook and scripts should be runnable on the CSV files in that directory without modification. …"

Projected HST/STIS images of Jupiter's FUV aurora حسب Jonathan Nichols (17840543)

"…The images are in kR projected onto a stereographic projection and, like the NIRCam images, can be read using the accompanying Python code in hstimage.py:</p><p dir="ltr">im = HSTProjImage(filename)</p><p dir="ltr">im.readHSTFile()</p><p dir="ltr">im.tvPolar()</p>…"

Coverage Optimized Stochastic Reinforcement Learning for Lines حسب Gusiyuan Wang (21196376)

"…<p dir="ltr"><b>About this project</b></p><p dir="ltr">This project is a deep reinforcement learning (DRL)-driven optimization framework called Coverage Optimized Stochastic Reinforcement Learning for Lines (COSRL) model, designed to solve MCLP-Line problems under demand uncertainty due to the use of binary coverage relationship evaluation. …"

Cheyenne River Flood Frequency حسب Earth Lab (3386570)

"…<p dir="ltr">Streamflow data retrieved from the USGS National Water Information Service (NWIS) with the <code>dataretrievals</code> library with the following query: </p><ul><li>Cheyenne River near Wasta site (site number 06423500)</li><li>Starting 1934-10-01</li><li>Ending 2024-09-30</li></ul><p dir="ltr">Data used in the ESIIL Stars program flood frequency coding challenge and published online on the ESIIL Environmental Data Science Learning Portal.…"

<b>Analysis of Cost Leadership Strategy in Low-Cost Airline Enterprises with Deep Learning Method</b> حسب ZEHRA YARDI (20284389)

"…The tweets of Ryanair were processed using a program called Knime, which is one of the useful programs. …"

DevCMG: Developer-Centric Automated Commit Message Generation حسب ZN (21452111)

"…<br><br>---<br><br>## **Datasets**<br>The `dataset` folder contains all 2,683 commits used in this study, covering the following five programming languages:<br>- C++<br>- C#<br>- Java<br>- JavaScript<br>- Python<br><br>---<br><br>## **Baselines**<br>### **State-of-the-Art (SOTA):**<br>- KADEL<br>- OMEGA<br>- DeepSeek-V3<br><br>### **Other Tools:**<br>- GPT-3.5<br>- CmtGen<br>- CoRec<br>- NMT<br>- NNGen<br>- Ptr-net<br><br>---<br><br>## **Experiments**<br><br>### **RQ1: Effectiveness of DevCMG**<br>Commands to run the experiments:<br>python message_generation.py<br>python llm_judge_metrics.py<br><br>## **RQ2: Ablation Study Results**<br><br>| **Approach**                  | **Reasonableness** | **Comprehensiveness** | **Succinctness** | **Normativity** | **Weighted Average** |<br>|-------------------------------|--------------------|-----------------------|------------------|-----------------|-----------------------|<br>| Baseline                      | 3.36              | 2.99                 | 3.32             | 2.18            | 2.9445                |<br>| Without behavior clustering   | 3.39              | 3.37                 | 2.61             | 2.22            | 2.919                 |<br>| Without CCS classification    | 3.59              | 3.18                 | 3.33             | 3.20            | 3.3725                |<br>| **Our approach**              | **3.99**          | **3.91**             | **3.65**         | **3.87**        | **3.891**             |<br><br>---<br><br># **RQ3: Rankings from Different Evaluators**<br><br>| **Evaluator**     | **Ranking**                                                                                                  |<br>|-------------------|------------------------------------------------------------------------------------------------------------|<br>| **Gemini-2.5**    | DevCMG, Zero-Shot, GPT-3.5, OMEGA, KADEL, NNgen, Ptr-net, CmtGen, CoRec, NMT                               |<br>| **GPT-4o**        | DevCMG, Zero-Shot, OMEGA, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **DeepSeek-R1**   | DevCMG, Zero-Shot, OMEGA, GPT-3.5, KADEL, NNgen, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **Qwen-3**        | DevCMG, Zero-Shot, GPT-3.5, OMEGA, KADEL, NNgen, Ptr-net, CoRec, NMT, CmtGen                               |<br>| **ChatGLM-4**     | DevCMG, OMEGA, Zero-Shot, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br>| **Human**         | DevCMG, Zero-Shot, OMEGA, GPT-3.5, NNgen, KADEL, Ptr-net, CoRec, CmtGen, NMT                               |<br><br>## **RQ4: User Study Results**<br><br>The user study results are available in the `/experiments/RQ4` folder. …"

The perceived wealth and physical disorder scores prediction dataset for urban China حسب Yanji Zhang (22363905)

"…They can be processed using GIS software such as ArcGIS and QGIS, as well as Python programming language packages such as Rasterio. …"

Fire Ecology Database: Database exports for fire-related plant traits and vegetation responses to fire حسب José R. Ferrer-Paris (592994)

"…Data was exported from the database (<b>version 1.1</b>) and formatted in CSV and XLSX formats using customised Python scripts.</p><p dir="ltr">Contents:</p><ul><li>Fire-related trait records (fireveg-trait-records-model.xlsx)</li><li>Summary of fire-related information per species (fireveg-trait-report-model.xlsx)</li><li>Fire-related trait records (fireveg-trait-records.csv)</li><li>Fire-related trait records with problems for data curation (fireveg-trait-records-curation.xlsx)</li><li>Vegetation response to fire events, field data (fireveg-field-report-model.xlsx)</li><li>Vegetation response to fire events, field data (fireveg-field-records.csv)</li><li>List of references (fireveg-db-references.xlsx)</li><li>Two files with definitions of fire-related traits and attributes of field data</li></ul><p><br></p>…"

HISTORECO: Historical Spanish transition database on climate, geography, and economics of the 20th-21st Century حسب Guillermo Rodríguez López (19872589)

"…</p><p dir="ltr">The dataset combines information from twenty sources (databases/articles), harmonizing and downscaling them to the municipal level using GIS and programming tools (mainly QGIS, R, and Python). …"