SemanticDrugSim

Author	GitHub
Stephen Borja	@OutForMilks
Erin Chua	@chua-e
Gideon Chua	@hootawsneaks
Zhean Ganituen	@zrygan	Correspondence
Nathaniel Oco		Faculty Adviser

Public GitHub repository for computing semantic drug similarity by unsupervised learning using PubMed corpus and a fastText model.

This work has been accepted as a conference proceeding of the 28th International Conference of Oriental COCOSDA and will be presented on November 12–14, 2025, at Universitas Kristen Duta Wacana (UKDW), Yogyakarta, Indonesia.

Supplementary Heatmaps

The conference proceeding references additional heatmaps not included in the paper.
These supplementary materials are available in the heatmaps/ directory.

Getting Started

Simply clone the repository:

$ git clone https://github.com/Mango-Cats/SemanticDrugSim

This project uses uv for package and project management. The provided init.ps1 script handles setup: it installs uv if necessary, creates a Python virtual environment, and adds all dependencies. Simply run:

.\init.ps1

What this does: it checks if uv installed and downloads it if not. Then, activate the Python virtual environments (venv) and adds all dependencies to it.

Repository Structure

• main.py — entry point for running the project.
• heatmaps/
• similarity/ — scripts for computing semantic and orthographic similarity.
• train/ — scripts for training the fastText model.
• visualize/ — scripts for creating heatmaps.
• corpus/ — Go and PowerShell scripts for extracting and parsing the corpus.
• vendor/ — fastText .whl file.

Citation

BibTeX:

  @software{Ganituen2025Software,
    author    = {Ganituen, Zhean Robby and Borja, Stephen and Chua, Erin Gabrielle and Chua, Gideon},
    title     = {{SemanticDrugSim}}
  }

  @inproceedings{Ganituen2025,
    author    = {Ganituen, Zhean Robby and Borja, Stephen and Chua, Erin Gabrielle and Chua, Gideon and Oco, Nathaniel},
    title     = {Integrating Semantic and Orthographic Features for Drug Name Similarity Analysis},
    booktitle = {Proceedings of the 28th International Conference of Oriental COCOSDA},
    year      = {2025},
    address   = {Yogyakarta, Indonesia},
    month     = {November}
  }

Also see CITATION.cff