AI for Cytogenetics

As a Computer Science undergraduate student at PES University in Bangalore, India, I co-founded the startup CARAIO Technologies to develop AI-powered solutions for simplifying karyotyping, a commonly done cytogenetics test. Traditional karyotyping approaches are time-consuming and labor-intensive. The motivation for our work was to build an accessible, affordable, and efficient tool that automated chromosome segmentation and classification from metaphase images. 

Our product produced karyotypes within seconds, detecting presence of chromosomal disorders such as Down Syndrome (trisomy-21) and other numerical aneuploidies. I trained state-of-the-art deep learning models including SqueezeNet, EfficientNet, and transformers for classification and handled segmentation of complex metaphase images. My novel segmentation pipeline combined seed-based watershed and autoencoder image reconstruction to separate overlapping and clustered chromosomes. We eventually adopted zero-shot segmentation with Segment Anything Model (SAM) due to its superior performance with low annotation efforts. Additionaly, to integrate an LLM-based subject matter expert to our SaaS platform, I built a Cytogenetics Copilot chatbot with GPT-4, LangChain, and Pinecone during my participation at the 2023 UC Berkeley Cal Hacks hackathon.

Read more about how it all started here

Outcomes

• A. Pallavoor, P. Anagani, S. Tambarahalli, S. Pallavoor. Chromosome Segmentation Analysis Using Image Processing Techniques and Autoencoders. American Journal of Computer Science and Technology, 5(4), 210-216., 2022. (link to manuscript)

•  Selected Participant, UC Berkeley SkyDeck Pad-13 Batch 15 & 16 Incubation Program (2022-2023) 

•  A. Pallavoor and S. Pallavoor AI for Karyotyping: Automated Chromosome Analysis Using Deep Learning. Poster presented at BIOMEDevice Conference, Santa Clara (2022)

•  Developed a Cytogenetics Copilot chatbot with GPT-4, LangChain, and Pinecone as part of UC Berkeley Cal Hacks (2023)

• Participated at the G20-DIA Summit, Bangalore, India (2023)

• AI Keynote Speaker, iCARE-HS International Conference (2024)

• Invited Speaker, UC Berkeley ISPMA (2024): Challenges and Opportunities in Bringing AI to International Markets