Russell Kunes

Russell Kunes

PhD Student in Statistics at Columbia University

Research

My research interests are centered around developing computational methods for analyzing genomics data. In particular, here are a few topics which I’m currently thinking about:

  • Learning about gene regulation from single cell data - Broadly, I’m interested in extracting rules of transcription from single cell gene expression and chromatin accessibility data using machine learning and interfacing with wet lab biologists to test these rules.
  • Variational Inference for Discrete Latents - I’m developing gradient estimation methods for stochastic gradient descent for discrete models where the gradient of the evidence lower bound can’t be tractably computed.

Papers

  • R. Kunes*, T. Walle*, T. Nawy, D. Pe’er. Supervised discovery of interpretable gene programs from single-cell data. 2023. (link)
  • J. Remsik, X. Tong, R. Kunes … D. Pe’er, A. Boire. Leptomeningeal anti-tumor immunity follows unique signaling principles. (link)
  • R. Kunes, Mingzhang Yin, Max Land, D. Pe’er, S.Tavaré. Gradient Estimation for Binary Latent Variables via Gradient Variance Clipping. 2023. AAAI Conference on Artificial Intelligence Oral Presentation.(link)
  • S. Mani, D. Haviv, R. Kunes, D. Pe’er. SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments. ICML Workshop in Computational Biology 2023 (link)
  • T. Walle … R. Kunes … Cytokine release syndrome-like serum responses after Covid-19 vaccination are frequent but clinically inapparent in patients under immune checkpoint therapy. Nature Cancer 2022 (link)
  • Y. Xiao … R. Kunes … Cross-platform analysis reveals cellular and molecular landscape of glioblastoma invasion. Neuro-oncology. 2022 (link)
  • R. Kunes, S. He, Y. Xiao, S. Tavare, D. Knowles. (2020) Supervised Tumor Cell Subtype Identification via SCAN. ICML Workshop in Computational Biology 2020.(link)
  • R. Kunes*, J. Ren*, F. Doshi Velez. (2020) Prediction Focused Topic Models via Vocab Filtering. In AISTATS ‘20 (link)
  • R. Kunes*, J. Ren*, F. Doshi Velez. (2019) Prediction Focused Topic Models for Electronic Health Records. Neural Information Processing Sytems Workshop in Machine Learning for Healthcare ‘19 (link)

Collaborations

  • Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing. Cell. 2019. (link)