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memgonzales/README.md

Hello 👋 I'm Mark Edward

I am a Bachelor of Science – Master of Science in Computer Science (Honors) student at De La Salle University, Manila. I enjoy working on challenges that bring together AI and software engineering.

Currently, I am in a three-month research attachment with the Agency for Science, Technology and Research (A*STAR), Singapore, under the Singapore International Pre-Graduate Award. At A*STAR, I develop algorithms and AI models for large (gigapixel-scale) tissue images. I have also worked on machine learning, data science, and software engineering projects with the Asian Development Bank (ADB) and the International Rice Research Institute (IRRI).

In 2023, I was conferred the second prize in the Magsaysay Future Engineers/Technologists Award by the National Academy of Science and Technology, Philippines. Here are some of my recent publications:

  • 🧬 Bioinformatics
    • Predicting which bacteria are attacked by "good" viruses using protein language models
      PLOS ONE (Code | Paper)
  • 👁️ Computer Vision
    • Lightweight deep learning model for detecting mirrors and reflective surfaces
      2023 International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision (Code | Paper)
  • 🗣️ Natural Language Processing
    • Tracking the evolution of Filipino word meanings using sentence embeddings and network science
      2023 International Conference on Asian Language Processing (Code | Paper)
  • 💻 Programming Language Design and Implementation
    • Novice-friendly programming language for 2D drawing and animation
      2024 Philippine Computing Science Congress (Code | Paper)Awarded Best Student Paper
  • 🛢️ Database Design and Data Visualization
    • Transforming chatbot dialogues into a data mart schema for data visualization
      2023 Philippine Computing Science Congress (Paper)

Here are some of my software engineering projects:

  • 🌾 RicePilaf. Web dashboard and novel bioinformatics pipeline for analyzing rice genomes. Published in GigaScience and developed with the International Rice Research Institute (IRRI). Written in Python and R, uses Dash and Flask as framework, and containerized via Docker
  • 🎨 Artemis. Art-sharing Android app where the community of users can post, bookmark, and provide feedback on members' works, as well as share these artworks on their Facebook accounts. Written in Kotlin and uses Firebase
  • Powerzone Inventory. Web-based inventory, transaction, and delivery management system for a fuel company in Bicol, Philippines. Built with MongoDB, Express.js, and Node.js and includes a CI/CD pipeline

I also enjoy competitive programming. In the 2022 International Collegiate Programming Contest (ICPC) Asia-Manila Regionals, our team ranked fifth overall and was recognized as the top Philippine team and the first to solve a problem.

Beyond coding, my passion lies in strengthening tech education. Since 2017, I have been serving as a mentor for the Asian MathSci League, Inc. (AMSLI), an organization that trains and selects representatives for international math and informatics competitions. I designed the curriculum and wrote handouts for its advanced programming classes.

I also contribute questions to the International Bebras Challenge on Informatics and Computational Thinking, an annual contest joined by over 4 million students from 70 countries. My 2023 problem proposal was awarded Best Task, and my 2022 and 2024 proposals were nominated for this recognition.

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  1. bioinfodlsu/phage-host-prediction bioinfodlsu/phage-host-prediction Public

    Published in PLOS ONE. Phage-host interaction prediction tool that uses protein language models to represent the receptor-binding proteins of phages. It presents improvements over using handcrafted…

    Jupyter Notebook 13 2

  2. sliding-puzzle sliding-puzzle Public

    8-puzzle game that features a walkthrough of the optimal solution and allows users to customize the tiles using photos from their Gallery

    Kotlin 11 8

  3. meta-learning-clustering meta-learning-clustering Public

    Presented at the 2022 IEEE Region 10 Conference (TENCON 2022). Our main contribution is twofold: (1) the construction of a meta-learning model for recommending a distance metric for k-means cluster…

    Jupyter Notebook 3

  4. mirror-segmentation mirror-segmentation Public

    Presented at the 2023 International Conference in Central Europe on Computer Graphics, Visualization and Computer Vision (WSCG 2023). Lightweight mirror segmentation CNN that uses an EfficientNet b…

    Python 2

  5. medical-expert-ehrlich medical-expert-ehrlich Public

    Backward-chaining medical expert system that specializes in selected autoimmune diseases and employs MYCIN-style computations to handle uncertainty

    Prolog 7

  6. bioinfodlsu/rice-pilaf bioinfodlsu/rice-pilaf Public

    Published in GigaScience. Web app for post-GWAS/QTL analysis that performs a slew of novel bioinformatics analyses to cross-reference GWAS/QTL mapping results with a host of publicly available rice…

    Python 1 1