Polarization and migration in the zebrafish posterior lateral line system. - Hildur Knutsdottir; Cole Zmurchok; Dhananjay Bhaskar; Eirikur Palsson; Damian Dalle Nogare; Ajay B. Chitnis; Leah Edelstein-Keshet (PLoS Comput. Biol., 2017)

Molecular Graph Generation via Geometric Scattering. - Dhananjay Bhaskar; Jackson D. Grady; Michael A. Perlmutter; Smita Krishnaswamy (CoRR, 2021)

Molecular Graph Generation via Geometric Scattering. - Dhananjay Bhaskar; Jackson D. Grady; Egbert Castro; Michael Perlmutter; Smita Krishnaswamy (MLSP, 2022)

Diffusion Curvature for Estimating Local Curvature in High Dimensional Data. - Dhananjay Bhaskar; Kincaid MacDonald; Oluwadamilola Fasina; Dawson Thomas; Bastian Rieck; Ian Adelstein; Smita Krishnaswamy (NeurIPS, 2022)

Guided Generative Protein Design using Regularized Transformers. - Egbert Castro; Abhinav Godavarthi; Julian A. Rubinfien; Kevin B. Givechian; Dhananjay Bhaskar; Smita Krishnaswamy (CoRR, 2022)

Transformer-based protein generation with regularized latent space optimization. - Egbert Castro; Abhinav Godavarthi; Julian A. Rubinfien; Kevin B. Givechian; Dhananjay Bhaskar; Smita Krishnaswamy (Nat. Mac. Intell., 2022)

Wire Before You Walk. - Tesfa Asmara; Dhananjay Bhaskar; Ian Adelstein; Smita Krishnaswamy; Michael Perlmutter (ACSSC, 2023)

Inferring Dynamic Regulatory Interaction Graphs From Time Series Data With Perturbations. - Dhananjay Bhaskar; Daniel Sumner Magruder; Matheo Morales; Edward De Brouwer; Aarthi Venkat; Frederik Wenkel; Guy Wolf; Smita Krishnaswamy (LoG, 2023)

A Flow Artist for High-Dimensional Cellular Data. - Kincaid MacDonald; Dhananjay Bhaskar; Guy Thampakkul; Nhi Nguyen; Joia Zhang; Michael Perlmutter; Ian Adelstein; Smita Krishnaswamy (MLSP, 2023)

Inferring dynamic regulatory interaction graphs from time series data with perturbations. - Dhananjay Bhaskar; Daniel Sumner Magruder; Edward De Brouwer; Aarthi Venkat; Frederik Wenkel; Guy Wolf; Smita Krishnaswamy (CoRR, 2023)

Graph topological property recovery with heat and wave dynamics-based features on graphs. - Dhananjay Bhaskar; Yanlei Zhang; Charles Xu 004; Xingzhi Sun 003; Oluwadamilola Fasina; Guy Wolf; Maximilian Nickel; Michael Perlmutter; Smita Krishnaswamy (CoRR, 2023)

Looking through the mind's eye via multimodal encoder-decoder networks. - Arman Afrasiyabi; Erica L. Busch; Rahul Singh; Dhananjay Bhaskar; Laurent Caplette; Nicholas B. Turk-Browne; Smita Krishnaswamy (CoRR, 2024)

ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics. - Siddharth Viswanath; Dhananjay Bhaskar; David R. Johnson; João F. Rocha; Egbert Castro; Jackson D. Grady; Alex T. Grigas; Michael A. Perlmutter; Corey S. O'Hern; Smita Krishnaswamy (CoRR, 2024)

Exploring the Manifold of Neural Networks Using Diffusion Geometry. - Elliott Abel; Peyton Crevasse; Yvan Grinspan; Selma Mazioud; Folu Ogundipe; Kristof Reimann; Ellie Schueler; Andrew J. Steindl; Ellen Zhang; Dhananjay Bhaskar; Siddharth Viswanath; Yanlei Zhang; et al. (CoRR, 2024)

Learnable Filters for Geometric Scattering Modules. - Alexander Tong 001; Frederik Wenkel; Dhananjay Bhaskar; Kincaid MacDonald; Jackson D. Grady; Michael Perlmutter; Smita Krishnaswamy; Guy Wolf (IEEE Trans. Signal Process., 2024)

Latent Representation Learning for Multimodal Brain Activity Translation. - Arman Afrasiyabi; Dhananjay Bhaskar; Erica L. Busch; Laurent Caplette; Rahul Singh; Guillaume Lajoie; Nicholas B. Turk-Browne; Smita Krishnaswamy (ICASSP, 2025)

Principal Curvatures Estimation with Applications to Single Cell Data. - Yanlei Zhang; Lydia Mezrag; Xingzhi Sun 003; Charles Xu 004; Kincaid MacDonald; Dhananjay Bhaskar; Smita Krishnaswamy; Guy Wolf; Bastian Rieck (ICASSP, 2025)

HiPoNet: A Topology-Preserving Multi-View Neural Network For High Dimensional Point Cloud and Single-Cell Data. - Siddharth Viswanath; Hiren Madhu; Dhananjay Bhaskar; Jake Kovalic; David R. Johnson; Rex Ying; Christopher J. Tape; Ian Adelstein; Michael Perlmutter; Smita Krishnaswamy (CoRR, 2025)

STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics. - João F. Rocha; Ke Xu 010; Xingzhi Sun 003; Ananya Krishna; Dhananjay Bhaskar; Blanche Mongeon; Morgan Craig; Mark Gerstein; Smita Krishnaswamy (CoRR, 2025)