Boneshwar V K

B.S. & M.S., Biological Sciences · IIT Madras

Researcher in machine learning for genomics and precision medicine.
Computational Biology · AI for Healthcare.

View CV Publications
Portrait of Boneshwar V K

About

Hi, I'm Boneshwar, a Machine Learning Scientist at PopVax, India. I build interpretable, robust models that generalize across biological modalities, from graph neural networks for single-cell genomics to generative, knowledge-grounded systems for clinical reasoning and frontier deep learning models for de novo protein design. I was fortunate to be advised by Prof. Babji Srinivasan and Prof. Bala Natarajan, under whom I worked on scRNA-seq and multi-omic analysis with deep neural architectures such as graph neural networks and graph transformers. My goal is to make AI a dependable instrument for detecting cancer at its earliest stages and curing it.

Research interests: graph neural networks, single-cell genomics, generative modeling, knowledge graphs, topological data analysis, and LLMs for healthcare.

Research

What I work on

My research sits at the intersection of representation learning and biology: designing models that are accurate, efficient, and interpretable enough to trust in a clinical setting.

i.

Single-cell genomics

Inductive graph neural networks for imputation, clustering, and trajectory inference on sparse, noisy scRNA-seq atlases.

ii.

Generative & structured models

Graph transformers, VAEs, and masked transformers that capture position and structure relationships in biological sequences and networks.

iii.

Knowledge-grounded AI

Ontology and knowledge-graph grounded LLMs for interpretable, traceable clinical decision support and differential diagnosis.

Highlights

Recent news

Selected work

Featured publication

  1. Journal · 2025

    Inductive graph neural network framework for imputation of single-cell RNA sequencing data

    Boneshwar V K, Deepesh Agarwal, Bala Natarajan, Babji Srinivasan

    Computers & Chemical Engineering, vol. 195 (2025), 109031

    Read article All publications

Background

Education & skills

B.S. & M.S. in Biological Sciences

Indian Institute of Technology Madras · Dual Degree

  • Specialization: Computational Biology
  • Thesis: Bioinformatics, graph neural networks, and generative modeling for scRNA-seq

Languages

  • Python
  • C++
  • C#
  • R

ML & data

  • PyTorch
  • PyG
  • DGL
  • TensorFlow
  • scikit-learn
  • NetworkX
  • Pandas

Scientific computing

  • GROMACS
  • AutoDock
  • PyMOL
  • VMD
  • Weka
  • Blender

Wet lab

  • Molecular cloning
  • Colony PCR
  • CFU quantification