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Simran-Sodhi/README.md

Simran Sodhi

I work at the intersection of machine learning and computational biology, building models and pipelines for protein modeling and single-cell analysis. Currently pursuing an MS in Automated Science at Carnegie Mellon University. Previously, worked as a Software Development Engineer at Amazon.

Featured Projects

  • Puncta CSAT Pipeline – End-to-end microscopy analysis pipeline for studying phase separation
  • ASR Project 2025 – Active learning framework for improving cell segmentation in microscopy
  • Drug Design Dynamics – Protein–ligand interaction prediction using Metropolis simulations + ML models (Go, Python, R Shiny)
  • ExpresSeekers – RNA-seq analysis pipeline for clustering and differential expression across large-scale cancer datasets

Current Work

  • Protein variant effect prediction (ESM-2)
  • Hybrid Transformer + State Space models

Tech

Python · PyTorch · Scanpy · AWS · Java · Go

Links

Pinned Loading

  1. puncta_csat_pipeline puncta_csat_pipeline Public

    End-to-end pipeline for segmentation and quantitative analysis of fluorescence microscopy data to study phase separation

    Jupyter Notebook

  2. asrProject2025 asrProject2025 Public

    Active learning framework for improving cell segmentation in microscopy images using uncertainty and diversity-based sampling

    Jupyter Notebook

  3. drug-design-dynamics drug-design-dynamics Public

    Protein–ligand interaction prediction using Metropolis simulations and machine learning models across molecular datasets

    Go 1

  4. ExpresSeekers ExpresSeekers Public

    RNA-seq analysis pipeline for clustering, differential expression, and classification across cancer datasets

    Jupyter Notebook