Publications.

MIMYR: Generative modeling of missing tissue in spatial transcriptomics

Diffusion for tissue structure and transformers for gene expression.

First author

LLOKI: Cross-platform Spatial Transcriptomics Integration using Optimal Transport

Ellie Haber, Ajinkya Deshpande, Jian Ma, Spencer Krieger

Second author · Genome Research accepted September 2025

Natural Language to Class-level Code Generation by Iterative Tool-augmented Reasoning over Repository

Ajinkya Deshpande*, Anmol Agarwal*, Shashank Shet*, Arun Iyer, Aditya Kanade, Ram Bairi, Suresh Parthasarathy

Co-first author · Workshop paper

FiGURe: Simple and Efficient Unsupervised Node Representations with Filter Augmentations

Ajinkya P. Deshpande*, Chanakya Ekbote*, Arun Iyer, Ramakrishna Bairi, Sundararajan Sellamanickam

Co-first author · Also at MLG @ KDD 2024

Capturing Symmetries of Quantum Optimization Algorithms Using Graph Neural Networks

Ajinkya Deshpande, Alexey Melnikov