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Dhananjay Bhaskar

Dhananjay Bhaskar

Assistant Professor

My lab develops novel computational methods for biomedical discovery at the intersection of machine learning, agent-based modeling, and geometric and topological data analysis. We are broadly engaged in AI for Science (AI4Science) and NeuroAI, with a focus on uncovering the structure and dynamics of complex biological systems. Applications of our work span drug discovery, cancer biology, cell communication and signaling, developmental biology, and neuroscience. By integrating mathematical principles and domain knowledge into learning algorithms, we aim to bridge data-driven modeling with mechanistic understanding.

Department

Biomedical Engineering

Contact

Engineering Centers Building
1550 Engineering Dr
Madison, WI

Featured news

Focus on new faculty: Dhananjay Bhaskar plays with the ‘shape’ of data

September 2, 2025

  • PhD 2021, Brown University
  • ScM 2021, Brown University
  • MS 2017, University of British Columbia
  • BS 2015, University of British Columbia

  • Computational Biology
  • Deep Learning
  • Graph Signal Processing
  • Mathematical Modeling
  • Representation Learning
  • Systems Neuroscience
  • Topological Data Analysis

  • 2025 APS, APS Forum on International Physics Distinguished Student Award
  • 2025 DAAD, DAAD Postdoc-NeT-AI Short Term Research Scholarship (Declined)
  • 2024 Kavli Institute for Neuroscience, Postdoctoral Fellowship
  • 2024 Eric and Wendy Schmidt Family Foundation, The Eric and Wendy Schmidt AI in Human Health Fellowship (Declined)
  • 2023 DAAD AINeT, Fellowship for Generative Models in Machine Learning
  • 2023 Yale Postdoctoral Association, Outstanding Contribution Award
  • 2021 Yale University, Boehringer Ingelheim Biomedical Data Science Fellowship
  • 2020 Brown University, Data Science Initiative Seed Grant
  • 2019 AMS MRC, Collaborative Research Travel Grant
  • 2017 Brown University, E Paul Sorensen Graduate Fellowship
  • 2016 UBC, Faculty of Science Graduate Award
  • 2016 The Tenth q-bio Summer School Scholarship
  • 2015 UBC, International Tuition Scholarship
  • 2014 UBC, International Undergraduate Summer Research Award

  • Koonce, N. L., Emerson, S. E., Bhaskar, D., Kuchroo, M., Moyle, M. W., Arroyo-Morales, P., Martínez, N. V., Emerson, J. I., Krishnaswamy, S., Mohler, W., & Colón-Ramos, D. (2025). NeuroSC: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks. eLife, 13 https://doi.org/10.7554/eLife.103977.2
  • Sun, X., Gupta, S., Tong, A., Kuchroo, M., Bhaskar, D., Liu, C., Venkat, A., Juan, B. P., Rangel, L., Rodriguez, V., Lock, J. G., Chaffer, C. L., & Krishnaswamy, S. (2025). Revealing dynamic temporal trajectories and underlying regulatory networks with Cflows https://doi.org/10.1101/2023.03.28.534644
  • Rocha, J. F., Xu, K., Sun, X., Krishna, A., Bhaskar, D., Mongeon, B., Craig, M., Gerstein, M., & Krishnaswamy, S. (2025). STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics https://doi.org/10.48550/arXiv.2507.11660
  • Bhaskar, D., Zhang, Y., Moore, J., Gao, F., Rieck, B., Wolf, G., Khasawneh, F., Munch, E., Noah, J. A., Pushkarskaya, H., Pittenger, C., Greco, V., & Krishnaswamy, S. (2025). Neurospectrum: A Geometric and Topological Deep Learning Framework for Uncovering Spatiotemporal Signatures in Neural Activity https://doi.org/10.1101/2023.03.22.533807
  • Afrasiyabi, A., Bhaskar, D., Busch, E. L., Caplette, L., Singh, R., Lajoie, G., Turk-Browne, N. B., & Krishnaswamy, S. (2025). Latent Representation Learning for Multimodal Brain Activity Translation. In ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (p. 1-5) https://doi.org/10.1109/ICASSP49660.2025.10887834
  • Zhang, Y., Mezrag, L., Sun, X., Xu, C., Macdonald, K., Bhaskar, D., Krishnaswamy, S., Wolf, G., & Rieck, B. (2025). Principal Curvatures Estimation with Applications to Single Cell Data. In ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (p. 1-5) https://doi.org/10.1109/ICASSP49660.2025.10888433
  • Singh, R., Zhang, Y., Bhaskar, D., Srihari, V., Tek, C., Zhang, X., Noah, J. A., Krishnaswamy, S., & Hirsch, J. (2025). Deep multimodal representations and classification of first-episode psychosis via live face processing. Frontiers in Psychiatry, 16 https://doi.org/10.3389/fpsyt.2025.1518762
  • Viswanath, S., Madhu, H., Bhaskar, D., Kovalic, J., Johnson, D., Ying, R., Tape, C., Adelstein, I., Perlmutter, M., & Krishnaswamy, S. (2025). HiPoNet: A Topology-Preserving Multi-View Neural Network For High Dimensional Point Cloud and Single-Cell Data https://doi.org/10.48550/arXiv.2502.07746
  • Abel, E., Steindl, A. J., Mazioud, S., Schueler, E., Ogundipe, F., Zhang, E., Grinspan, Y., Reimann, K., Crevasse, P., Bhaskar, D., Viswanath, S., Zhang, Y., Rudner, T. G., Adelstein, I., & Krishnaswamy, S. (2024). Exploring the Manifold of Neural Networks Using Diffusion Geometry https://doi.org/10.48550/arXiv.2411.12626
  • Bhaskar, D., Moore, J., Zhang, Y., Gao, F., Rieck, B., Wolf, G., Pushkarskaya, H., Khasawneh, F., Munch, E., Greco, V., Pittenger, C., & Krishnaswamy, S. (2024). Neuro-GSTH: A Geometric Scattering and Persistent Homology Framework for Uncovering Spatiotemporal Signatures in Neural Activity https://doi.org/10.1101/2023.03.22.533807