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Vancouver, British Columbia, Canada
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Toronto, Ontario, Canada
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Recent projects

Bioinformatics Algorithm Enhancement with Machine Learning
Re:Pair Genomics Inc. is seeking to enhance its bioinformatics algorithms by integrating machine learning techniques. The project aims to improve the accuracy and efficiency of genomic data analysis, which is crucial for identifying genetic variations and understanding complex biological processes. Learners will apply their machine learning knowledge to develop and refine components of an existing algorithm used in genomic data processing. The project will involve analyzing existing datasets, identifying patterns, and implementing machine learning models to optimize algorithm performance. This initiative provides an opportunity for learners to bridge the gap between theoretical knowledge and practical application in the field of bioinformatics. The project is designed to be completed by a team of learners specializing in computer science or bioinformatics, ensuring a focused and cohesive approach.

Enhancing Genomic Data Analysis with Machine Learning
Re:Pair Genomics Inc. is seeking to enhance its bioinformatics algorithms by integrating machine learning techniques to improve the accuracy and efficiency of genomic data analysis. The current algorithms, while effective, can benefit from the predictive power and adaptability of machine learning models. The project aims to identify specific areas within the existing bioinformatics pipeline where machine learning can be applied to optimize performance. Students will be tasked with researching and selecting appropriate machine learning models, training these models on existing genomic datasets, and evaluating their performance against current methods. The goal is to achieve a measurable improvement in data processing speed and accuracy, ultimately contributing to more precise genomic interpretations.

Enhancing Genomic Data Analysis with Machine Learning Part 2
Re:Pair Genomics Inc. is seeking to enhance its bioinformatics algorithms by integrating machine learning techniques to improve the accuracy and efficiency of genomic data analysis. The current algorithms, while effective, can benefit from the predictive power and adaptability of machine learning models. The project aims to identify specific areas within the existing bioinformatics pipeline where machine learning can be applied to optimize performance. Students will be tasked with researching and selecting appropriate machine learning models, training these models on existing genomic datasets, and evaluating their performance against current methods. The goal is to achieve a measurable improvement in data processing speed and accuracy, ultimately contributing to more precise genomic interpretations.
Personal projects
Math Visualization Assistant
February 2025 - Current
https://github.com/makaato53/RAG-projectOverview
This project implements a dual-function Retrieval-Augmented Generation (RAG) assistant that bridges the gap between complex theoretical research and practical implementation. It not only helps researchers and developers understand and implement ML/AI research papers with efficient CUDA optimization, but also breaks down complex mathematical topics into digestible, visually engaging animated explanations.
By combining paper comprehension, advanced mathematical summarization, and Manim-based animation with CUDA documentation retrieval, the system provides a comprehensive tool for both academic exploration and practical GPU programming.
Features
Scientific Paper & Math Processing:
Processes academic papers or math-heavy texts (PDF or plain text) to extract and preserve technical details and mathematical notation.
Uses advanced text chunking and embedding techniques to maintain context and isolate key concepts.
Generates concise summaries that break down complex math topics into step-by-step instructions suitable for visualization.
Manim-Based Animation Generation:
Automatically converts extracted mathematical concepts into detailed Manim animations.
Produces scene-by-scene breakdownsβfor example, plotting functions, highlighting transformations, and visualizing derivationsβto bring complex concepts to life in a style reminiscent of 3Blue1Brown.
Allows interactive adjustments of visualization parameters (such as domain, range, or color highlights).
CUDA Implementation Guidance:
Searches through CUDA documentation and NVIDIA best practices to provide targeted strategies for implementing and optimizing ML/AI algorithms on GPUs.
Utilizes vector search with FAISS to retrieve the most relevant documentation and presents contextually accurate solutions using LLM-generated responses.
LLM Integration:
Leverages Hugging Face's FLAN-T5 model for generating both context-aware paper summaries and detailed Manim scene instructions.
Ensures that responses are both theoretically sound and practically applicable for GPU programming and mathematical visualization.
Project Structure
graphql
Copy
Copyproject/
βββ notebooks/
β βββ 01_data_preparation.ipynb # PDF extraction, CUDA & math document processing
β βββ 02_embeddings.ipynb # Generating vector embeddings for papers and CUDA docs
β βββ 03_model_testing.ipynb # Testing response generation and animation pipelines
β βββ 04_quality_improvement.ipynb # Optimizing output quality for responses and animations
βββ app.py # Streamlit web application integrating both functionalities
βββ data/ # Datasets (e.g., paper PDFs, math text, annotated Manim prompts)
βββ src/
β βββ doc_processing/ # Code for processing papers and math content
β βββ visualization/ # Manim pipeline and math visualization tools
β βββ embeddings/ # Embedding generation and FAISS vector search
β βββ models/ # LLM and response generation models
β βββ utils/ # Utility functions and helpers
βββ requirements.txt # Project dependencies
βββ Dockerfile # Container configuration for deployment