Vatsal Patel

Research Engineer | AI & Machine Learning Specialist

Leveraging a strong mathematical foundation and extensive experience in bioinformatics to build cutting-edge AI solutions, driving innovation in biomedical research since 2020.

About Me

Vatsal Patel

I am a dedicated Research Engineer with a deep passion for applying Machine Learning and Artificial Intelligence to solve complex real-world problems, particularly within the biomedical domain. My journey into AI began in 2020, driven by a fascination with data-driven discovery, which I pursued alongside my Bachelor’s degree in Mathematics from St. Xavier's College, Mumbai. This strong quantitative background provides a robust foundation for my work in ML.

For 3.5 years (Sep 2021 - Mar 2025), I contributed significantly at the National Institute of Biomedical Genomics (NIBMG), initially as a Senior Project Consultant and later as a Bioinformatics Research Engineer. My role focused on integrating advanced ML techniques, including Deep Learning (TensorFlow, PyTorch) and Graph Neural Networks, into cancer genomics research.

I thrive on tackling challenging projects, from developing patent‑pending models for patient risk stratification using pathology images (PIONEER) to creating novel multi‑omics integration methods with Graph Attention Networks (presented in Hamburg). I am also the creator of the Machine Learning Copilot Agent, an AI tool designed to automate ML workflows.

My goal is to continue pushing the boundaries of AI and contribute to impactful research and technological advancements.

Research Engineer Highlight 2020 Specialization Highlight Bachelor’s Degree Certificate NIBMG Experience Deep Learning Specialization Highlight GNN Highlight PIONEER Highlight Presented in Hamburg Highlight ML Copilot Code Example Highlight

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Technical Expertise

Python

TensorFlow

PyTorch

(inc. Geometric)

Graph Neural Networks

Deep Learning

Scikit-learn

Pandas

Unix/Linux

Hugging Face

Docker/Singularity

GPU Training

Langchain

LlamaIndex

Bioinformatics

Vision Transformers

CLIP

LLMs (GPT, Llama)

Google Cloud

Multiple Instance Learning

Mathematics

(Foundation)

Professional Experience

Bioinformatics Research Engineer

Sep 2021 – Mar 2025 (3.5 Years)

National Institute of Biomedical Genomics (NIBMG), Kalyani, India

Contributed to the National Supercomputing Mission (NSM) Platform for Genomics and Drug Discovery.

Key Responsibilities:

  • Implemented novel Machine Learning solutions for complex cancer genomics research problems.
  • Tracked and presented key findings from ML publications in genomics & pathology to the research team.
  • Developed and deployed scalable GPU pipelines for feature extraction using open-source foundation models (e.g., Pathology Vision Models).
  • Led independent research initiatives, notably applying Graph Neural Networks for Multi-Omics integration.

Key Achievements:

  • Developed PIONEER: A pathology-immune-omics model predicting high-risk HNSCC patients from WSI with AUC > 0.80. (Patent Pending)
  • Created a Graph Attention Autoencoder for multi-omics risk stratification (AUC ~0.98), presented at Helmholtz AI Conference, Germany.
  • Bridged communication between technical and non-technical team members, explaining complex ML concepts effectively.

Featured Projects

ML Copilot Agent

Machine Learning Copilot Agent

© 2024 Vatsal Patel. All rights reserved.

An AI‑driven agent (GPT‑4o + LlamaIndex) automating ML classification workflows via natural language commands and real-time code execution.

PIONEER Project

PIONEER: Pathology‑Immune‑Omics Alignment

Patent Pending

Novel vision foundation model aligning immune-multi-omics features with histopathology images (WSI) to predict high-risk HNSCC patients (AUC > 0.80).

Role: ML Engineer (Equal Contribution)

Graph Attention Autoencoder

Graph Attention Autoencoder for Multi-Omics

Presented: Helmholtz AI Conf. 2023

Integrated multi‑omics data using GATs for risk stratification (AUC ~0.98) and biomarker identification in HNSCC.

MedDiscover RAG-LLM

MedDiscover: RAG‑LLM for Biomedicine

Portable RAG system using LLMs for biomedical knowledge extraction from user-defined literature. Includes GUI.

M.Sc. Thesis Project (Grade: 1.0)

Weather Chatbot Phi3

Weather Chatbot (Phi‑3 Mini)

LLM agent executing real‑time OpenWeather API calls via Langchain, with a Gradio chat interface.

Publications & Preprints

An ensemble machine learning-based performance evaluation...

Jan 2025 (Contributing Author)

Multi-faceted dysregulated immune response for COVID-19...

Dec 2023 (Contributing Author)

Deep Learning Model to automate the process of mapping cancer cells...

Aug 2021 (First Author)

Convergence of Gradient Descent after Homeomorphic Transformation.

June 2021 (First Author)

Graph Attention Networks for Biomedical Insights...

In Academic Review / Preprint (First Author)

View on Zenodo

Leveraging Retrieval-Augmented Generation with Large Language Models...

In Preparation (First Author)

Machine Learning Copilot Agent.

In Preparation (First Author)

Certifications & Specializations

Building expertise since 2020

TensorFlow Developer Certificate

DeepLearning.AI TensorFlow Developer

Professional Certificate (4 Courses)

Issued: July 2020

Verify Certificate
Machine Learning on Google Cloud Certificate

Machine Learning with TensorFlow on Google Cloud

Specialization (5 Courses)

Issued: July 2020

Verify Certificate
Mathematics for Machine Learning Certificate

Mathematics for Machine Learning

Specialization (3 Courses - Imperial College London)

Issued: Sep 2020

Verify Certificate

Academic Background

M.Sc. Artificial Intelligence

IU International University...

Grade: 1.9 / 4.0...

Thesis Grade: 1.0...

B.Sc. Mathematics

St. Xavier's College, Mumbai...

CGPA: 9.31 / 10.0

Class XII (GSHSEB)

St. Joseph E.T High School...

Percentage: 80%

Class XI (GSEB)

St. Joseph E.T High School...

Percentage: 80%

Get In Touch

I'm always open to discussing new projects...