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Yash-Dhanawate/README.md

πŸ‘‹ Hi, I'm Yash Dhanawate

AI for Drug Discovery β€’ Explainable AI β€’ Cheminformatics β€’ Machine Learning

Building trustworthy machine learning models for molecular property prediction, virtual screening, and computational drug discovery.

LinkedIn Email


πŸ”¬ About Me

I'm a Computational Chemist and Machine Learning enthusiast passionate about developing AI-driven solutions for drug discovery.

My work focuses on combining Graph Neural Networks, Explainable AI (XAI), QSAR, Active Learning, and Molecular Modeling to build reliable and interpretable models for molecular property prediction and virtual screening.

I enjoy working on projects that bridge Machine Learning with Medicinal Chemistry, transforming raw chemical data into scientifically meaningful insights.


πŸš€ Current Focus

  • 🧠 Explainable AI (Integrated Gradients, Model Interpretation)
  • 🧬 Graph Neural Networks for Molecular Property Prediction
  • πŸ’Š AI-assisted Drug Discovery & Virtual Screening
  • πŸ“ˆ QSAR Modeling & Molecular Machine Learning
  • 🎯 Active Learning & Uncertainty Estimation
  • βš—οΈ Cheminformatics using RDKit
  • πŸ”¬ Molecular Dynamics & Computational Chemistry

πŸ“Œ Featured Projects

🧠 Explainable AI for Molecular Property Prediction

Developed a hybrid Graph Neural Network framework that combines molecular graph representations with Explainable AI techniques to interpret atom-level contributions and investigate whether the model learns meaningful chemistry rather than dataset-specific bias.

Tech: PyTorch Geometric β€’ RDKit β€’ Captum β€’ Integrated Gradients


🎯 Active Learning for Virtual Screening

Designed a temporal active learning workflow using uncertainty estimation and conformal prediction to prioritize compounds for experimental screening under realistic chronological evaluation.

Tech: Scikit-learn β€’ MAPIE β€’ RDKit β€’ Python


πŸ’Š QSAR Pipeline for Drug Discovery

Built end-to-end QSAR workflows including molecular standardization, feature engineering, model development, hyperparameter optimization, and model interpretation.


πŸ›  Tech Stack

Machine Learning

Python β€’ PyTorch β€’ Scikit-learn β€’ LightGBM β€’ XGBoost β€’ Optuna

AI for Drug Discovery

RDKit β€’ PyTorch Geometric β€’ Captum β€’ QSAR β€’ Molecular Fingerprints β€’ Molecular Descriptors

Molecular Modeling

GROMACS β€’ AutoDock Vina β€’ Molecular Dynamics β€’ Docking

Data Science

Pandas β€’ NumPy β€’ Matplotlib β€’ MLflow β€’ MySQL

Tools

Git β€’ Linux β€’ Streamlit


🌱 Currently Learning

  • Large Language Models for Scientific Applications
  • Generative AI for Molecule Generation
  • Advanced Graph Neural Networks
  • MLOps for Machine Learning Systems
  • Explainable AI for Drug Discovery

πŸ“« Let's Connect

I'm always interested in collaborating on projects involving

  • Explainable AI
  • Drug Discovery
  • Molecular Machine Learning
  • Graph Neural Networks
  • QSAR
  • Computational Chemistry

Feel free to connect with me on LinkedIn or explore my repositories below.


πŸŽ“ Certifications

Python for Data Science and Machine Learning Bootcamp β€” Udemy

Pinned Loading

  1. Cheminformatics-Active-Learning-Conformal-Prediction Cheminformatics-Active-Learning-Conformal-Prediction Public

    End-to-end prospective drug discovery pipeline for the Dopamine Receptor D2 (DRD2) utilizing Morgan fingerprints, UMAP, Optuna-tuned LightGBM, Split Conformal Prediction (MAPIE) with mathematical g…

    Jupyter Notebook

  2. PharmaGNN-XAI PharmaGNN-XAI Public

    Graph Neural Networks for molecular property prediction with Explainable AI (XAI) to identify important pharmacophore regions and understand model predictions.

    Jupyter Notebook

  3. toxicity toxicity Public

    Jupyter Notebook

  4. ptp1b-activity ptp1b-activity Public

    Jupyter Notebook

  5. VEGFR2_QSAR VEGFR2_QSAR Public

    Jupyter Notebook