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A list of main papers
Selected (see Longer list below for details)
Longer list
(number of pages included for ML conference papers per suggestion from my mathematician friends, unless i forgot to add)
Complexity Analysis of Normalizing Constant Estimation: from Jarzynski Equality to Annealed Importance Sampling and beyond
Wei Guo, Molei Tao, and Yongxin Chen
submitted, 2025
arXiv probabilistic methods
Fast Solvers for Discrete Diffusion Models: Theory and Applications of High-Order Algorithms
Yinuo Ren, Haoxuan Chen, Yuchen Zhu, Wei Guo, Yongxin Chen, Grant M. Rotskoff, Molei Tao, and Lexing Ying.
submitted, 2025
arXiv GenAI, probablistic methods
Trivialized Momentum Facilitates Diffusion Generative Modeling on Lie Groups
Yuchen Zhu, Tianrong Chen, Lingkai Kong, Evangelos A. Theodorou, and Molei Tao.
ICLR, 2025
arXiv GenAI, AI4Science, probablistic methods
Provable Benefit of Annealed Langevin Monte Carlo for Non-log-concave Sampling
Wei Guo, Molei Tao, and Yongxin Chen
ICLR, 2025
arXiv probabilistic methods
Diffusion Generative Modeling for Spatially Resolved Gene Expression Inference from Histology Images
Sichen Zhu, Yuchen Zhu, Molei Tao*, and Peng Qiu*
ICLR, 2025
arXiv GenAI, AI4Science, probablistic methods
Variational Schrodinger Momentum Diffusion
Kevin Rojas, Yixin Tan, Molei Tao, Yuriy Nevmyvaka, and Wei Deng
AISTATS, 2025
TBA GenAI, probablistic methods
Robust First and Second-Order Differentiation for Regularized Optimal Transport
Xingjie Li, Fei Lu, Molei Tao, and Felix X.-F. Ye.
SIAM Journal on Scientific Computing, 2025
arXiv probablistic methods
SODA: Spectral Orthogonal Decomposition Adaptation for Diffusion Models
Xinxi Zhang, Song Wen, Ligong Han, Felix Juefei-Xu, Akash Srivastava, Junzhou Huang, Hao Wang, Molei Tao, and Dimitris N. Metaxas.
WACV, 2025
arXiv GenAI, optimization
Plug-and-Play Controllable Generation for Discrete Masked Models
Wei Guo, Yuchen Zhu, Molei Tao, and Yongxin Chen.
TBA, 2024
arXiv GenAI, AI4Science, probablistic methods
DeepTTV: Deep Learning Prediction of Hidden Exoplanet From Transit Timing Variations
Chen Chen, Lingkai Kong, Gongjie Li, Molei Tao
TBA, 2024
arXiv AI4Science
Evaluating the Design Space of Diffusion-Based Generative Models
Yuqing Wang, Ye He, and Molei Tao.
NeurIPS, 2024
arXiv deep learning theory, optimization, GenAI, probablistic methods
Zeroth-Order Sampling Methods for Non-Log-Concave Distributions: Alleviating Metastability by Denoising Diffusion
Ye He, Kevin Rojas, and Molei Tao.
NeurIPS, 2024
arXiv probablistic methods, GenAI
Provable Acceleration of Nesterov's Accelerated Gradient for Asymmetric Matrix Factorization and Linear Neural Networks
Zhenghao Xu, Yuqing Wang, Tuo Zhao, Rachel Ward, and Molei Tao.
NeurIPS, 2024
arXiv optimization, deep learning theory
Quantum State Generation with Structure-Preserving Diffusion Model
Yuchen Zhu, Tianrong Chen, Evangelos A. Theodorou, Xie Chen, Molei Tao.
TBA, 2024
arXiv AI4Science, GenAI, probablistic methods
Can Specific THz Fields Induce Collective Base-Flipping in DNA? A Stochastic Averaging and Resonant Enhancement Investigation Based on a New Mesoscopic Model
Wang Sang Koon, Houman Owhadi, Molei Tao, and Tomohiro Yanao (alphabetical, led by Koon).
Chaos, 2024
arXiv applied dynamical systems in physical problems
Extragradient Type Methods for Riemannian Variational Inequality Problems
Zihao Hu, Guanghui Wang, Xi Wang, Andre Wibisono, Jacob Abernethy, Molei Tao.
AISTATS, 2024
arXiv optimization
Automated construction of effective potential via algorithmic implicit bias
Xingjie Helen Li and Molei Tao.
Journal of Computational Physics, 2024
arXiv applied dynamical systems in physical problem, deep learning theory
Good regularity creates large learning rate implicit biases: edge of stability, balancing, and catapult
Yuqing Wang, Zhenghao Xu, Tuo Zhao, and Molei Tao.
NeurIPS workshop (short version, long version in review), 2023
arXiv deep learning theory, optimization, applied dynamical systems
Dual Fourier Unet: scale-robust diffusion model for zero-shot super-resolution image generation
Alexander Havrilla, Kevin Rojas, Wenjing Liao, and Molei Tao.
NeurIPS workshop, 2023
arXiv GenAI
Mirror Diffusion Models for Constrained and Watermarked Generation
Guan-Horng Liu, Tianrong Chen, Evangelos A. Theodorou, and Molei Tao.
NeurIPS, 2023
arXiv GenAI, probablistic methods
Deep Multi-Marginal Momentum Schrodinger Bridge
Tianrong Chen, Guan-Horng Liu, Molei Tao, and Evangelos A. Theodorou.
NeurIPS, 2023
arXiv GenAI, probablistic methods
Markov chain Monte Carlo for Gaussian: A linear control perspective
Bo Yuan, Jiaojiao Fan, Yuqing Wang, Molei Tao, and Yongxin Chen.
IEEE Control Systems Letters, 2023
paper probablistic methods
Landscape classification through coupling method
Yao Li, Molei Tao, and Shirou Wang.
submitted, 2023
arXiv probablistic methods
gDDIM: generalized denoising diffusion implicit models
Qinsheng Zhang, Molei Tao, and Yongxin Chen.
ICLR, 2023
arXiv GenAI, probablistic methods
Momentum Stiefel Optimizer, with Applications to Suitably-Orthogonal Attention, and Optimal Transport
Lingkai Kong, Yuqing Wang, and Molei Tao.
ICLR, 2023
arXiv optimization, GenAI, probablistic methods
code
Electromechanical frequency comb generation in fluid media with a parametrically driven capacitive microresonator
Sushruta Surappa, Charles Wei, Molei Tao, and F Levent Degertekin.
Physical Review Applied, 2023
TBA applied dynamical systems in physical problems
NySALT: Nyström-type inference-based schemes adaptive to large time-stepping
Xingjie Li, Fei Lu, Molei Tao, Felix Ye (alphabetical).
Journal of Computational Physics, 2022
arXiv
Data-driven discovery of non-Newtonian astronomy via learning non-Euclidean Hamiltonian
Oswin So, Gongjie Li, Evangelos A. Theodorou, Molei Tao.
NeurIPS workshop, 2022
pdf AI4Science
Alternating Mirror Descent for Constrained Min-Max Games
Andre Wibisono, Molei Tao, and Georgios Piliouras.
NeurIPS, 2022
arXiv, 45 pages optimization
Low spin-axis variations of circumbinary planets
Renyi Chen, Gongjie Li, and Molei Tao.
Monthly Notices of the Royal Astronomical Society, 2022
arXiv applied dynamical systems in physical problems
Hessian-Free High-Resolution Nesterov Acceleration for Sampling
Ruilin Li, Hongyuan Zha, and Molei Tao.
ICML, 2022
arXiv, 38 pages probablistic methods
The Mirror Langevin Algorithm Converges with Vanishing Bias
Ruilin Li, Molei Tao, Santosh S. Vempala, and Andre Wibisono (alphabetical).
International Conference on Algorithmic Learning Theory, 2022
pdf, 25 pages probablistic methods
Improving sampling accuracy of SG-MCMC methods via non-uniform subsampling of gradients
Ruilin Li, Xin Wang, Hongyuan Zha, and Molei Tao.
Discrete & Continuous Dynamical SystemsS, 2021
arXiv probablistic methods
Variational Symplectic Accelerated Optimization on Lie Groups
Taeyoung Lee, Molei Tao, and Melvin Leok.
Conference on Decision and Control (CDC), 2021
arXiv optimization
GRIT: a package for structure-preserving simulations of gravitationally interacting rigid-bodies
Renyi Chen, Gongjie Li, and Molei Tao.
The Astrophysical Journal, 2021
arXiv applied dynamical systems in physical problems, computational math in physical problems
code
Data-driven Prediction of General Hamiltonian Dynamics via Learning Exactly-Symplectic Maps
Renyi Chen and Molei Tao.
ICML 2021
arXiv, 17 pages applied dynamical systems in physical problems, AI4Science
a 5-min talk for this work
Why Do Deep Residual Networks Generalize Better than Deep Feedforward Networks? -A Neural Tangent Kernel Perspective
Kaixuan Huang^, Yuqing Wang^, Molei Tao, and Tuo Zhao (^ joint first author).
NeurIPS 2020
pdf, 28 pages deep learning theory, optimization, applied dynamical systems
a 3-min talk for this work by my student Yuqing Wang
A Derivative-Free Optimization Method with Application to Functions with Exploding and Vanishing Gradients
Said Al-Abri, Tony X. Lin, Molei Tao, and Fumin Zhang
IEEE Control Systems Letters, 2020
pdf optimization
Variational Optimization on Lie Groups, with Examples of Leading (Generalized) Eigenvalue Problems
Molei Tao and Tomoki Ohsawa.
AISTATS, 2020 (best paper award)
pdf, 17 pages optimization
a 13-min talk for this work
AhKin: a modular and efficient code for the Doppler Shift Attenuation Method
Alejandro Garzon, Wilmar Rodriguez, Fernando Cristancho, and Molei Tao.
Computer Physics Communications, 2020
pdf (old descriptions from here on. not updated. who cares?), stochastic, physics
Space-time phononic crystals with anomalous topological edge states
Mourad Oudich, Yuanchen Deng, Molei Tao, and Yun Jing.
Physical Review Research, 2019
pdf nonlinear, multiscale, engineering
Dynamic mode decomposition for multiscale nonlinear physics
Daniel Dylewsky, Molei Tao, and J. Nathan Kutz.
Physical Review E, 2019
pdf data, multiscale, nonlinear
Analysis and design of capacitive parametric ultrasonic transducers for efficient ultrasonic power transfer based on a 1D lumped model
Sushruta Surappa, Molei Tao, and F. Levent Degertekin.
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, 2018
pdf multiscale, engineering
Explicit symplectic approximation of nonseparable Hamiltonians: algorithm and long time performance
Molei Tao.
Physical Review E, 2016
pdf symplectic, multiscale, nonlinear, numerical analysis
Uncovering circumbinary planetary architectural properties from selection biases
Gongjie Li, Matthew J. Holman, and Molei Tao.
The Astrophysical Journal, 2016
pdf exoplanetary, nonlinear
Explicit high-order symplectic integrators for charged particles in general electromagnetic fields
Molei Tao.
Journal of Computational Physics, 2016
pdf symplectic, nonlinear, numerical analysis
Temporal homogenization of linear ODEs, with applications to parametric super-resonance and energy harvest
Molei Tao and Houman Owhadi.
Archive for Rational Mechanics and Analysis, 2016
pdf multiscale, engineering, nonlinear
Variational and linearly-implicit integrators, with applications
Molei Tao and Houman Owhadi.
IMA Journal of Numerical Analysis, 2016
pdf symplectic, multiscale, numerical analysis
Convex optimal uncertainty quantification
Shuo Han, Molei Tao, Ufuk Topcu, Houman Owhadi, and Richard M. Murray.
SIAM Journal on Optimization, 2015
pdf optimization, stochastic
An improved wave-vector-frequency-domain method for nonlinear wave modeling
Yun Jing, Molei Tao, and Jonathan Cannata.
IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control, 2014
pdf multiscale, engineering, numerical analysis
Convex optimal uncertainty quantification: algorithms and a case study in energy storage placement
Shuo Han, Ufuk Topcu, Molei Tao, Houman Owhadi, and Richard M. Murray.
American Control Conference, 2013
pdf optimization, stochastic, engineering
Variational integrators for electric circuits
Sina Ober-Bloebaum, Molei Tao, Mulin Cheng, Houman Owhadi, and Jerrold E. Marsden.
Journal of Computational Physics, 2013
pdf symplectic, multiscale, numerical analysis, engineering
Control of a Model of DNA Division via Parametric Resonance
Wang Sang Koon*, Houman Owhadi, Molei Tao, and Tomohiro Yanao (alphabetical).
Chaos, 2013
pdf nonlinear, multiscale
Statistics of Dislocation Slip Avalanches in Nanosized Single Crystals Show Tuned Critical Behavior Predicted by a Simple Mean Field Model
Nir Friedman, Andrew T. Jennings, Georgios Tsekenis, Ju-Young Kim, Molei Tao, Jonathan T. Uhl, Julia R. Greer, and Karin A. Dahmen.
Physical Review Letters, 2012
pdf nonlinear, physics, experiment
From efficient symplectic exponentiation of matrices to symplectic integration of high-dimensional Hamiltonian systems with slowly varying quadratic stiff potentials
Molei Tao, Houman Owhadi, and Jerrold E. Marsden.
Applied Mathematics Research eXpress, 2011
pdf symplectic, numerical analysis, multiscale
Space-time FLAVORS: finite difference, multisymplectic, and pseudospectral integrators for multiscale PDEs
Molei Tao, Houman Owhadi, and Jerrold E. Marsden.
Dynamics of Partial Differential Equations, 2011
pdf symplectic, multiscale, numerical analysis
Evaluation of a wave vector frequency domain method for nonlinear wave propagation
Yun Jing, Molei Tao, and Gregory T. Clement.
The Journal of the Acoustical Society of America, 2011
pdf multiscale, engineering
Nonintrusive and structure preserving multiscale integration of stiff ODEs, SDEs and Hamiltonian systems with hidden slow dynamics via flow averaging
Molei Tao, Houman Owhadi, and Jerrold E. Marsden.
SIAM: Multiscale Modeling and Simulation, 2010
pdf multiscale, numerical analysis, symplectic, stochastic
A fast and reliable two-sequence local alignment algorithm
Qiming Hou, Molei Tao, and Yanda Li.
China National Computer Conference, 2005
(in Chinese) bioinformatics
Not peer-reviewed
Multiscale geometric integration of deterministic and stochastic systems
Molei Tao.
Caltech Ph.D. Dissertation, 2011
link multiscale, numerical analysis, symplectic, stochastic
Structure preserving stochastic impulse methods for stiff Langevin systems with a uniform global error of order 1 or 1/2 on position
Molei Tao, Houman Owhadi, and Jerrold E. Marsden.
arXiv supplement to [Tao et al. AMRX 2011], 2010
arXiv multiscale, numerical analysis, symplectic, stochastic
Temperature and Friction Accelerated Sampling of Boltzmann-Gibbs Distribution
Molei Tao, Houman Owhadi, and Jerrold E. Marsden.
unpublished but not wrong, 2010
arXiv numerical analysis, symplectic, stochastic
Thermodynamic and structural consensus principle predicts mature miRNA location and structure, categorizes conserved interspecies miRNA subgroups, and hints new possible mechanisms of miRNA maturization
Molei Tao.
Tsinghua Bachelor Thesis, 2007
arXiv bioinformatics, data
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