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Rushin Gindra

Doctoral Researcher | Painter | Mountain Bike rider

Education

Doctoral Researcher, Experimental Medicine

Technische Universität München (TUM), Germany
2022 - Present

MSc in Computer Science

Rutgers, The state university of New Jersey, USA
2018 - 2020

B.Tech in Computer Engineering

Mumbai University
2014 - 2018

Languages

  • English (Native)
  • German (A2)
  • Hindi (Native)
  • Marathi (Native)

Interests

  • Bike-packing
  • Climbing
  • Photography

Career Profile

Just a chill guy. Need to update though.

Experiences

Doctoral Researcher

2022 - Present
Helmholtz Munich & TUM, Germany
  • Image integrated tools for Spatial Transcriptomics analysis
  • Spatial-omics, Self-supervised learning, Multi-modal learning

Bioinformatics Analyst

2020 - 2023
Boston University school of medicine, USA
  • Graph Networks and Transformers for cancer detection
  • Self-supervised learning, Multi-cohort training to minimize batch effect, Semantic segmentation for tissue-subtyping.

Research Assistant, MS Thesis

2019 - 2020
Center for computational biomedicine, Rutgers University, USA
  • Unsupervised shared GANs, Domain Adaptation
  • Atrous convolutions, Multi-scale convolutions for cardiac segmentation

Research Intern

2017
Srujana Innovation Lab, L. V. Prasad Eye Institute
  • Fractal analysis based retinal vessel density quantification
  • Clinical validation focused statistical correlations.

Projects

Ask me about the projects. I am most reponsive on twitter or linkedin

SpatialCLIP - Spatialomics based contrastive pre-training improves pathology foundation models on molecular subtyping tasks
CARTerrain - Development of CAR-T cells in Pancreas using spatial resolved gene-expression profiling
Sphoenix - Generative models for multi-modal spatial-omics dataset generation.

Publications

If you can’t find an open-access link to the publication, ping me, I am happy to share the article. Happy reading :)

  • SpatialCLIP - Spatialomics based contrastive pre-training improves pathology foundation models on molecular subtyping tasks
    • Rushin Gindra*, Mathias Nguyen*, Giovanni Palla, Manuel Tran, Dieter Saur, Tingying Peng
    in preparation
  • Current best practices for Batch Effect Correction in Histopathological analysis
    • Rushin Gindra*, Sayedali Boushehri*, Sophia Wagner*, Manuel Tran*, Dominik Winter, Carsten Marr, Tingying Peng
    under review
  • Graph Perceiver Network for Lung Tumor and Bronchial Premalignant Lesion Stratification from Histopathology
    • Rushin Gindra, Yi Zheng, Emily J. Green, Mary E. Reid, Sarah A. Mazzilli, Daniel T. Merrick, Eric J. Burks, Vijaya B. Kolachalama, Jennifer E. Beane
    The American Journal of Pathology 2024
  • A graph-transformer for whole slide image classification
    • Yi Zheng, Rushin Gindra, Emily Green, Eric J. Burks, Margrit Betke, Jennifer E. Beane, Vijaya B Kolachalama
    IEEE Transactions on Medical Imaging 2022
  • Improvements on Cardiac Segmentation for cross-modality domain adaptation frameworks
    • Rushin Gindra, Dimitris Metaxas
    Rutgers University Community Repository (RUcore) 2020
  • OCT angiography fractal analysis-based quantification of macular vascular density in BRVO eyes.
    • Dave V., Pappuru R.R., Gindra R., Ananthakrishnan A., Modi S., Trivedi M., Harikumar P.
    Canadian Journal of Ophthalmology 2019

    Skills & Proficiency

    Python & PyTorch

    SpatialData, Scanpy

    Git, Wandb, Slurm, Linux

    Mountain Biking

    Climbing

    Humour