Software

The following papers have associated software packages.

  • Unbiasing Procedures for Scale-invariant Multi-reference Alignment.
    With Anna Little.
    2021.
    pdf, arXiv.
    Software page.
  • MagNet: A Magnetic Neural Network for Directed Graphs.
    With Xitong Zhang, Yixuan He, Nathan Brugnone, and Michael Perlmutter.
    In Advances in Neural Information Processing Systems 34, 2021.
    pdf, arXiv, NeurIPS.
    Software page.
  • ClassicalGSG: Prediction of logP Using Classical Molecular Force Fields and Geometric Scattering for Graphs.
    With Nazanin Donyapour and Alex Dickson.
    Journal of Computational Chemistry, volume 42, issues 14, pages 1006-1017, 2021.
    pdf, ChemRxiv, Journal of Comp. Chem.
    Software page.
  • Wavelet invariants for statistically robust multi-reference alignment.
    With Anna Little.
    Information and Inference: A Journal of the IMA, in press, 2020.
    pdf, arXiv, IMA.
    Software page.
  • Kymatio: Scattering Transforms in Python.
    With Mathieu Andreux, Tomás Angles, Georgios Exarchakis, Roberto Leonarduzzi, Gasper Rochette, Louis Thiry, John Zarka, Stéphane Mallat, Joakim Andén, Eugene Belilovsky, Joan Bruna, Vincent Lostanlen, Muawiz Chaudhary, Edouard Oyallon, Sixhin Zhang, Carmine Cella, Michael Eickenberg.
    Journal of Machine Learning Research, volume 21, number 60, pages 1-6, 2020.
    pdf, arXiv, JMLR.
    Software page
  • Coarse Graining of Data via Inhomogeneous Diffusion Condensation.
    With Nathan Brugnone, Alex Gonopolskiy, Mark W. Moyle, Manik Kuchroo, David van Dijk, Kevin R. Moon, Daniel Colon-Ramos, Guy Wolf and Smita Krishnaswamy.
    In Proceedings of the 2019 IEEE International Conference on Big Data, pages 2624–2633, 2019.
    pdf, arXiv, IEEE Xplore.
    Software page
  • Visualizing Structure and Transitions for Biological Data Exploration (PHATE).
    With Kevin R. Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel Burkhardt, William Chen, Kristina Yim, Antonia van den Elzen, Ronald R. Coifman, Natalia B. Ivanova, Guy Wolf and Smita Krishnaswamy.
    Nature Biotechnology, volume 37, pages 1482–1492, 2019.
    pdf (journal version), pdf (complete version, very large > 100 mb), bioRxiv, Nature Biotechnology.
    Software page
  • Solid Harmonic Wavelet Scattering for Predictions of Molecule Properties (Editor’s Pick).
    With Michael Eickenberg, Georgios Exarchakis, Stéphane Mallat and Louis Thiry.
    Journal of Chemical Physics, volume 148, issue 24, 241732, 2018.
    pdf, arXiv, AIP.
    Software page
  • Wavelet Scattering Regression of Quantum Chemical Energies.
    With Stéphane Mallat and Nicolas Poilvert.
    Multiscale Modeling and Simulation, volume 15, issue 2, pages 827-863, 2017.
    pdf, arXiv, MMS.
    Software page
  • Computing minimal interpolants in  C^{1,1}(\mathbb{R}^d).
    With Ariel Herbert-Voss and Frederick McCollum.
    Revista Matemática Iberoamericana, volume 33, issue 1, pages 29-66, 2017.
    pdf, arXiv, RMI.
    Software page
  • Diffusion maps for changing data.
    With Ronald R. Coifman.
    Applied and Computational Harmonic Analysis, volume 36, issue 1, pages 79-107, January 2014.
    pdf, arXiv, ScienceDirect.
    Software page