Smriti Vaidyanathan

I'm an incoming Computational Biology PhD student at UC Berkeley (Fall 2026).

I completed my Master's in Computer Science at Columbia University, where I conducted research at the New York Genome Center in the Knowles Lab, developing deep learning models for integrative analysis of gene expression and alternative splicing in single-cell transcriptomic data.

Before that, I earned my Sc.B. in Computational Biology from Brown University, where I studied alternative splicing regulation by RNA-binding protein condensates using computational analysis of bioimages in the Larschan Lab.

smritivaidyanathan [at] berkeley [dot] edu

Projects

SpliceVI

Research project within the Knowles Lab. A multimodal VAE integrating gene expression and splicing signals from scRNA-seq data (see preprint), built using scvi-tools, inspired by and adapted from MultiVI. Also includes a single-modality splicing VAE with a partial encoder and linear decoder.

iSTAR-C

Final project for Columbia's BMCS E4480. Extended iSTAR (Zhang et al., 2024) with biologically informed supervision for pixel-level cell-type prediction, using Starfysh-derived spot-level compositions and optional heat-diffusion pseudo-labels for out-of-spot supervision.

Remembering to Learn: A Brain-Inspired Approach to Catastrophic Forgetting in AI

Final project for Columbia's COMS E6998. Extended FlyModel with BI-R, EWC, and cascade synapses to improve continual learning on CIFAR-100. Cascade synapses notably reduced memory loss without replay.

Brain Tumor Segmentation and Survival Prediction (BRATS 2020)

Final project for Columbia's COMS W4995: Deep Learning for Computer Vision. Segmented tumor regions and predicted survival outcomes from BRATS 2020 MRI scans using U-Net and ResNet-based models.

3D Speckle Volume Quantifier

Custom analysis tool developed for my undergraduate honors thesis at Brown University in the Larschan Lab. Quantifies nuclear speckle volumes from confocal z-stacks to study how the GA-binding transcription factor CLAMP influences splicing condensate formation in Drosophila embryos.