Erdem Varol

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Erdem Varol, Ph.D.
Grossman Center for the Statistics of Mind
Zuckerman Institute, Center for Theoretical Neuroscience
Department of Statistics
Columbia University
email: ev2430@columbia.edu
address: 3227 Broadway, New York, NY 10027
Google scholar page


I'm currently a post-doctoral fellow at the Center for Theoretical Neuroscience at Columbia University working with Liam Paninski and collaborating heavily with Oliver Hobert.

Current areas of research: biomedical image and video analysis, single cell sequencing analysis, and connectomics.

I was a Ph.D. student at the Electrical and Systems Engineering department, University of Pennsylvania. My advisor was Christos Davatzikos. I have defended my thesis on April 2018. My Ph.D. research has focused on statistics, machine learning and optimization and their applications to neuroimaging analysis.

News

April 29, 2021 - Video presentation on “Decentralized motion inference and registration of Neuropixels data” posted to YouTube.

April 28, 2021 - Manuscript on “Multi-scale semi-supervised clustering of brain images: deriving disease subtypes” available at bioRxiv.

April 6, 2021 - Manuscript on “Visualizing the organization and differentiation of the male-specific nervous system of C. elegans” available at bioRxiv.

January 29, 2021 - Paper on “Decentralized motion inference and registration of Neuropixels data” accepted at ICASSP ’21.

January 18, 2021 - Abstract on “Decentralized motion inference and registration of Neuropixels data” accepted at COSYNE ’21. Code available at Github.

December 29, 2020 - Paper on “NeuroPAL: A Multicolor Atlas for Whole-Brain Neuronal Identification in C. elegans” published at Cell.

December 16, 2020 - Manuscript on “Molecular topography of an entire nervous system” available at bioRxiv. Code available at Github.

December 15, 2020 - Paper on “Neuron Matching in C. elegans With Robust Approximate Linear Regression Without Correspondence” available at WACV ’21.

November 13, 2020 - Gave a nominated talk on “Neuropixels registration” at ZIPS.

October 20, 2020 - Manuscript on “Decentralized motion inference and registration of Neuropixels data” submitted to ICASSP 2021. Code available at Github.

October 1, 2020 - 4 MICCAI papers available online: 1) Statistical Atlas of C. elegans Neurons, 2) Demixing Calcium Imaging Data in C. elegans via Deformable Non-negative Matrix Factorization, 3) Probabilistic Joint Segmentation and Labeling of C. elegans Neurons, 4) MAGIC: Multi-scale Heterogeneity Analysis and Clustering for Brain Diseases.

August 20, 2020 - Paper on how “Unique homeobox codes delineate all the neuron classes of C. elegans” published at Nature.

July 8, 2020 - Manuscript on “Extracting neural signals from semi-immobilized animals with deformable non-negative matrix factorization” available at bioRxiv.

June 30, 2020 - Manuscript on “Sinkhorn EM: An Expectation-Maximization algorithm based on entropic optimal transport” available at arXiv.

June 23, 2020 - 2 more MICCAI 2020 papers accepted after rebuttal: “Probabilistic Segmentation and Labeling of C. elegans Neurons”, “MAGIC: Multi-scale Heterogeneity Analysis and Clustering for Brain Diseases”.

May 18, 2020 - 2 MICCAI 2020 papers provisionally accepted: “Deformable non-negative matrix factorization” and “Statistical atlas of C. elegans neurons”.

December 9, 2019 - CVPR pre-print on “Temporal Wasserstein non-negative matrix factorization for non-rigid motion segmentation and spatiotemporal deconvolution” available at arXiv.

December 6, 2019 - NeurIPS Workshop on Learning Meaningful Representations of Life poster on “Probabilistic Atlases of C.elegans Neurons in NeuroPAL” posted here.

December 6, 2019 - Advances in Approximate Bayesian Inference (AABI) 2020 paper on “Sinkhorn Permutation Variational Marginal Inference” available at OpenReview + Poster.

October 31, 2019 - Two COSYNE 2020 extended abstracts,“Non-linear matrix factorization methods for extracting calcium traces in moving C. elegans videos” and “Joint segmentation and labeling of C. elegans neurons” posted.

October 25, 2019 - ICASSP 2020 pre-print of “Wasserstein total variation filtering” available at arXiv.

June 20, 2019 - Pre-print of “NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans” available at bioRxiv.

May 23, 2019 - NeurIPS 2019 pre-print on “Robust approximate linear regression without correspondence” available at arXiv.

September 17, 2018 - I will be giving a talk on generative-discriminative regression at MICCAI 2018 in Granada, Spain.

September 1, 2018 - I have started working at the Center for Theoretical Neuroscience at Columbia University as a post-doctoral fellow with Liam Paninski.