Zhizhen Zhao

Lingda Wang, Savana Ammons, Vera Mikyoung Hur et al.

Predicting sea surface temperature (SST) within the El Niño-Southern Oscillation (ENSO) region has been extensively studied due to its significant influence on global temperature and precipitation patterns. Statistical models such as linear inverse model (LIM), analog forecasting (AF), and recurrent neural network (RNN) have been widely used for ENSO prediction, offering flexibility and relatively low computational expense compared to large dynamic models. However, these models have limitations in capturing spatial patterns in SST variability or relying on linear dynamics. Here we present a modified Convolutional Gated Recurrent Unit (ConvGRU) network for the ENSO region spatio-temporal sequence prediction problem, along with the Niño 3.4 index prediction as a down stream task. The proposed ConvGRU network, with an encoder-decoder sequence-to-sequence structure, takes historical SST maps of the Pacific region as input and generates future SST maps for subsequent months within the ENSO region. To evaluate the performance of the ConvGRU network, we trained and tested it using data from multiple large climate models. The results demonstrate that the ConvGRU network significantly improves the predictability of the Niño 3.4 index compared to LIM, AF, and RNN. This improvement is evidenced by extended useful prediction range, higher Pearson correlation, and lower root-mean-square error. The proposed model holds promise for improving our understanding and predicting capabilities of the ENSO phenomenon and can be broadly applicable to other weather and climate prediction scenarios with spatial patterns and teleconnections.

Yichi Zhang, Yici Yan, Alex Schwing et al.

We formulate a hierarchical rectified flow to model data distributions. It hierarchically couples multiple ordinary differential equations (ODEs) and defines a time-differentiable stochastic process that generates a data distribution from a known source distribution. Each ODE resembles the ODE that is solved in a classic rectified flow, but differs in its domain, i.e., location, velocity, acceleration, etc. Unlike the classic rectified flow formulation, which formulates a single ODE in the location domain and only captures the expected velocity field (sufficient to capture a multi-modal data distribution), the hierarchical rectified flow formulation models the multi-modal random velocity field, acceleration field, etc., in their entirety. This more faithful modeling of the random velocity field enables integration paths to intersect when the underlying ODE is solved during data generation. Intersecting paths in turn lead to integration trajectories that are more straight than those obtained in the classic rectified flow formulation, where integration paths cannot intersect. This leads to modeling of data distributions with fewer neural function evaluations. We empirically verify this on synthetic 1D and 2D data as well as MNIST, CIFAR-10, and ImageNet-32 data. Our code is available at: https://riccizz.github.io/HRF/.

Yichi Zhang, Yici Yan, Alex Schwing et al.

Flow matching has emerged as a compelling generative modeling approach that is widely used across domains. To generate data via a flow matching model, an ordinary differential equation (ODE) is numerically solved via forward integration of the modeled velocity field. To better capture the multi-modality that is inherent in typical velocity fields, hierarchical flow matching was recently introduced. It uses a hierarchy of ODEs that are numerically integrated when generating data. This hierarchy of ODEs captures the multi-modal velocity distribution just like vanilla flow matching is capable of modeling a multi-modal data distribution. While this hierarchy enables to model multi-modal velocity distributions, the complexity of the modeled distribution remains identical across levels of the hierarchy. In this paper, we study how to gradually adjust the complexity of the distributions across different levels of the hierarchy via mini-batch couplings. We show the benefits of mini-batch couplings in hierarchical rectified flow matching via compelling results on synthetic and imaging data. Code is available at https://riccizz.github.io/HRF_coupling.

E. A. Huerta, Zhizhen Zhao

We live in momentous times. The science community is empowered with an arsenal of cosmic messengers to study the Universe in unprecedented detail. Gravitational waves, electromagnetic waves, neutrinos and cosmic rays cover a wide range of wavelengths and time scales. Combining and processing these datasets that vary in volume, speed and dimensionality requires new modes of instrument coordination, funding and international collaboration with a specialized human and technological infrastructure. In tandem with the advent of large-scale scientific facilities, the last decade has experienced an unprecedented transformation in computing and signal processing algorithms. The combination of graphics processing units, deep learning, and the availability of open source, high-quality datasets, have powered the rise of artificial intelligence. This digital revolution now powers a multi-billion dollar industry, with far-reaching implications in technology and society. In this chapter we describe pioneering efforts to adapt artificial intelligence algorithms to address computational grand challenges in Multi-Messenger Astrophysics. We review the rapid evolution of these disruptive algorithms, from the first class of algorithms introduced in early 2017, to the sophisticated algorithms that now incorporate domain expertise in their architectural design and optimization schemes. We discuss the importance of scientific visualization and extreme-scale computing in reducing time-to-insight and obtaining new knowledge from the interplay between models and data.

Renjie Liao, Zhizhen Zhao, Raquel Urtasun et al.

We propose the Lanczos network (LanczosNet), which uses the Lanczos algorithm to construct low rank approximations of the graph Laplacian for graph convolution. Relying on the tridiagonal decomposition of the Lanczos algorithm, we not only efficiently exploit multi-scale information via fast approximated computation of matrix power but also design learnable spectral filters. Being fully differentiable, LanczosNet facilitates both graph kernel learning as well as learning node embeddings. We show the connection between our LanczosNet and graph based manifold learning methods, especially the diffusion maps. We benchmark our model against several recent deep graph networks on citation networks and QM8 quantum chemistry dataset. Experimental results show that our model achieves the state-of-the-art performance in most tasks. Code is released at: \url{https://github.com/lrjconan/LanczosNetwork}.

Hongyu Shen, Zhizhen Zhao

Despite empirical risk minimization (ERM) is widely applied in the machine learning community, its performance is limited on data with spurious correlation or subpopulation that is introduced by hidden attributes. Existing literature proposed techniques to maximize group-balanced or worst-group accuracy when such correlation presents, yet, at the cost of lower average accuracy. In addition, many existing works conduct surveys on different subpopulation methods without revealing the inherent connection between these methods, which could hinder the technology advancement in this area. In this paper, we identify important sampling as a simple yet powerful tool for solving the subpopulation problem. On the theory side, we provide a new systematic formulation of the subpopulation problem and explicitly identify the assumptions that are not clearly stated in the existing works. This helps to uncover the cause of the dropped average accuracy. We provide the first theoretical discussion on the connections of existing methods, revealing the core components that make them different. On the application side, we demonstrate a single estimator is enough to solve the subpopulation problem. In particular, we introduce the estimator in both attribute-known and -unknown scenarios in the subpopulation setup, offering flexibility in practical use cases. And empirically, we achieve state-of-the-art performance on commonly used benchmark datasets.

Hongyu Shen, Yici Yan, Zhizhen Zhao

Model-X knockoff has garnered significant attention among various feature selection methods due to its guarantees for controlling the false discovery rate (FDR). Since its introduction in parametric design, knockoff techniques have evolved to handle arbitrary data distributions using deep learning-based generative models. However, we have observed limitations in the current implementations of the deep Model-X knockoff framework. Notably, the "swap property" that knockoffs require often faces challenges at the sample level, resulting in diminished selection power. To address these issues, we develop "Deep Dependency Regularized Knockoff (DeepDRK)," a distribution-free deep learning method that effectively balances FDR and power. In DeepDRK, we introduce a novel formulation of the knockoff model as a learning problem under multi-source adversarial attacks. By employing an innovative perturbation technique, we achieve lower FDR and higher power. Our model outperforms existing benchmarks across synthetic, semi-synthetic, and real-world datasets, particularly when sample sizes are small and data distributions are non-Gaussian.

Mona Zehni, Zhizhen Zhao

The goal of 2D tomographic reconstruction is to recover an image given its projections from various views. It is often presumed that projection angles associated with the projections are known in advance. Under certain situations, however, these angles are known only approximately or are completely unknown. It becomes more challenging to reconstruct the image from a collection of random projections. We propose an adversarial learning based approach to recover the image and the projection angle distribution by matching the empirical distribution of the measurements with the generated data. Fitting the distributions is achieved through solving a min-max game between a generator and a critic based on Wasserstein generative adversarial network structure. To accommodate the update of the projection angle distribution through gradient back propagation, we approximate the loss using the Gumbel-Softmax reparameterization of samples from discrete distributions. Our theoretical analysis verifies the unique recovery of the image and the projection distribution up to a rotation and reflection upon convergence. Our extensive numerical experiments showcase the potential of our method to accurately recover the image and the projection angle distribution under noise contamination.

Jiangran Wang, Zhuo Chen, Di Luo et al.

We develop a spacetime neural network method with second order optimization for solving quantum dynamics from the high dimensional Schrödinger equation. In contrast to the standard iterative first order optimization and the time-dependent variational principle, our approach utilizes the implicit mid-point method and generates the solution for all spatial and temporal values simultaneously after optimization. We demonstrate the method in the Schrödinger equation with a self-normalized autoregressive spacetime neural network construction. Future explorations for solving different high dimensional differential equations are discussed.

Parisa Karimi, Mark Butala, Zhizhen Zhao et al.

The evolution of images with physics-based dynamics is often spatially localized and nonlinear. A switching linear dynamic system (SLDS) is a natural model under which to pose such problems when the system's evolution randomly switches over the observation interval. Because of the high parameter space dimensionality, efficient and accurate recovery of the underlying state is challenging. The work presented in this paper focuses on the common cases where the dynamic evolution may be adequately modeled as a collection of decoupled, locally concentrated dynamic operators. Patch-based hybrid estimators are proposed for real-time reconstruction of images from noisy measurements given perfect or partial information about the underlying system dynamics. Numerical results demonstrate the effectiveness of the proposed approach for denoising in a realistic data-driven simulation of remotely sensed cloud dynamics.

Mona Zehni, Zhizhen Zhao

Tomographic reconstruction recovers an unknown image given its projections from different angles. State-of-the-art methods addressing this problem assume the angles associated with the projections are known a-priori. Given this knowledge, the reconstruction process is straightforward as it can be formulated as a convex problem. Here, we tackle a more challenging setting: 1) the projection angles are unknown, 2) they are drawn from an unknown probability distribution. In this set-up our goal is to recover the image and the projection angle distribution using an unsupervised adversarial learning approach. For this purpose, we formulate the problem as a distribution matching between the real projection lines and the generated ones from the estimated image and projection distribution. This is then solved by reaching the equilibrium in a min-max game between a generator and a discriminator. Our novel contribution is to recover the unknown projection distribution and the image simultaneously using adversarial learning. To accommodate this, we use Gumbel-softmax approximation of samples from categorical distribution to approximate the generator's loss as a function of the unknown image and the projection distribution. Our approach can be generalized to different inverse problems. Our simulation results reveal the ability of our method in successfully recovering the image and the projection distribution in various settings.

Di Luo, Zhuo Chen, Kaiwen Hu et al.

Symmetries such as gauge invariance and anyonic symmetry play a crucial role in quantum many-body physics. We develop a general approach to constructing gauge invariant or anyonic symmetric autoregressive neural network quantum states, including a wide range of architectures such as Transformer and recurrent neural network (RNN), for quantum lattice models. These networks can be efficiently sampled and explicitly obey gauge symmetries or anyonic constraint. We prove that our methods can provide exact representation for the ground and excited states of the 2D and 3D toric codes, and the X-cube fracton model. We variationally optimize our symmetry incorporated autoregressive neural networks for ground states as well as real-time dynamics for a variety of models. We simulate the dynamics and the ground states of the quantum link model of $\text{U(1)}$ lattice gauge theory, obtain the phase diagram for the 2D $\mathbb{Z}_2$ gauge theory, determine the phase transition and the central charge of the $\text{SU(2)}_3$ anyonic chain, and also compute the ground state energy of the SU(2) invariant Heisenberg spin chain. Our approach provides powerful tools for exploring condensed matter physics, high energy physics and quantum information science.

Lingda Wang, Bingcong Li, Huozhi Zhou et al.

This paper studies the adversarial graphical contextual bandits, a variant of adversarial multi-armed bandits that leverage two categories of the most common side information: \emph{contexts} and \emph{side observations}. In this setting, a learning agent repeatedly chooses from a set of $K$ actions after being presented with a $d$-dimensional context vector. The agent not only incurs and observes the loss of the chosen action, but also observes the losses of its neighboring actions in the observation structures, which are encoded as a series of feedback graphs. This setting models a variety of applications in social networks, where both contexts and graph-structured side observations are available. Two efficient algorithms are developed based on \texttt{EXP3}. Under mild conditions, our analysis shows that for undirected feedback graphs the first algorithm, \texttt{EXP3-LGC-U}, achieves the regret of order $\mathcal{O}(\sqrt{(K+α(G)d)T\log{K}})$ over the time horizon $T$, where $α(G)$ is the average \emph{independence number} of the feedback graphs. A slightly weaker result is presented for the directed graph setting as well. The second algorithm, \texttt{EXP3-LGC-IX}, is developed for a special class of problems, for which the regret is reduced to $\mathcal{O}(\sqrt{α(G)dT\log{K}\log(KT)})$ for both directed as well as undirected feedback graphs. Numerical tests corroborate the efficiency of proposed algorithms.

Bingcong Li, Lingda Wang, Georgios B. Giannakis et al.

Aiming at convex optimization under structural constraints, this work introduces and analyzes a variant of the Frank Wolfe (FW) algorithm termed ExtraFW. The distinct feature of ExtraFW is the pair of gradients leveraged per iteration, thanks to which the decision variable is updated in a prediction-correction (PC) format. Relying on no problem dependent parameters in the step sizes, the convergence rate of ExtraFW for general convex problems is shown to be ${\cal O}(\frac{1}{k})$, which is optimal in the sense of matching the lower bound on the number of solved FW subproblems. However, the merit of ExtraFW is its faster rate ${\cal O}\big(\frac{1}{k^2} \big)$ on a class of machine learning problems. Compared with other parameter-free FW variants that have faster rates on the same problems, ExtraFW has improved rates and fine-grained analysis thanks to its PC update. Numerical tests on binary classification with different sparsity-promoting constraints demonstrate that the empirical performance of ExtraFW is significantly better than FW, and even faster than Nesterov's accelerated gradient on certain datasets. For matrix completion, ExtraFW enjoys smaller optimality gap, and lower rank than FW.

E. A. Huerta, Gabrielle Allen, Igor Andreoni et al.

Multi-messenger astrophysics is a fast-growing, interdisciplinary field that combines data, which vary in volume and speed of data processing, from many different instruments that probe the Universe using different cosmic messengers: electromagnetic waves, cosmic rays, gravitational waves and neutrinos. In this Expert Recommendation, we review the key challenges of real-time observations of gravitational wave sources and their electromagnetic and astroparticle counterparts, and make a number of recommendations to maximize their potential for scientific discovery. These recommendations refer to the design of scalable and computationally efficient machine learning algorithms; the cyber-infrastructure to numerically simulate astrophysical sources, and to process and interpret multi-messenger astrophysics data; the management of gravitational wave detections to trigger real-time alerts for electromagnetic and astroparticle follow-ups; a vision to harness future developments of machine learning and cyber-infrastructure resources to cope with the big-data requirements; and the need to build a community of experts to realize the goals of multi-messenger astrophysics.

Lingda Wang, Huozhi Zhou, Bingcong Li et al.

Cascading bandit (CB) is a popular model for web search and online advertising, where an agent aims to learn the $K$ most attractive items out of a ground set of size $L$ during the interaction with a user. However, the stationary CB model may be too simple to apply to real-world problems, where user preferences may change over time. Considering piecewise-stationary environments, two efficient algorithms, \texttt{GLRT-CascadeUCB} and \texttt{GLRT-CascadeKL-UCB}, are developed and shown to ensure regret upper bounds on the order of $\mathcal{O}(\sqrt{NLT\log{T}})$, where $N$ is the number of piecewise-stationary segments, and $T$ is the number of time slots. At the crux of the proposed algorithms is an almost parameter-free change-point detector, the generalized likelihood ratio test (GLRT). Comparing with existing works, the GLRT-based algorithms: i) are free of change-point-dependent information for choosing parameters; ii) have fewer tuning parameters; iii) improve at least the $L$ dependence in regret upper bounds. In addition, we show that the proposed algorithms are optimal (up to a logarithm factor) in terms of regret by deriving a minimax lower bound on the order of $Ω(\sqrt{NLT})$ for piecewise-stationary CB. The efficiency of the proposed algorithms relative to state-of-the-art approaches is validated through numerical experiments on both synthetic and real-world datasets.

Yifeng Fan, Tingran Gao, Zhizhen Zhao

We introduce a novel co-learning paradigm for manifolds naturally equipped with a group action, motivated by recent developments on learning a manifold from attached fibre bundle structures. We utilize a representation theoretic mechanism that canonically associates multiple independent vector bundles over a common base manifold, which provides multiple views for the geometry of the underlying manifold. The consistency across these fibre bundles provide a common base for performing unsupervised manifold co-learning through the redundancy created artificially across irreducible representations of the transformation group. We demonstrate the efficacy of the proposed algorithmic paradigm through drastically improved robust nearest neighbor search and community detection on rotation-invariant cryo-electron microscopy image analysis.

Yifeng Fan, Zhizhen Zhao

We introduce multi-frequency vector diffusion maps (MFVDM), a new framework for organizing and analyzing high dimensional datasets. The new method is a mathematical and algorithmic generalization of vector diffusion maps (VDM) and other non-linear dimensionality reduction methods. MFVDM combines different nonlinear embeddings of the data points defined with multiple unitary irreducible representations of the alignment group that connect two nodes in the graph. We illustrate the efficacy of MFVDM on synthetic data generated according to a random graph model and cryo-electron microscopy image dataset. The new method achieves better nearest neighbor search and alignment estimation than the state-of-the-arts VDM and diffusion maps (DM) on extremely noisy data.

Yifeng Fan, Tingran Gao, Zhizhen Zhao

We develop in this paper a novel intrinsic classification algorithm -- multi-frequency class averaging (MFCA) -- for classifying noisy projection images obtained from three-dimensional cryo-electron microscopy (cryo-EM) by the similarity among their viewing directions. This new algorithm leverages multiple irreducible representations of the unitary group to introduce additional redundancy into the representation of the optimal in-plane rotational alignment, extending and outperforming the existing class averaging algorithm that uses only a single representation. The formal algebraic model and representation theoretic patterns of the proposed MFCA algorithm extend the framework of Hadani and Singer to arbitrary irreducible representations of the unitary group. We conceptually establish the consistency and stability of MFCA by inspecting the spectral properties of a generalized local parallel transport operator through the lens of Wigner $D$-matrices. We demonstrate the efficacy of the proposed algorithm with numerical experiments.

Yifeng Fan, Zhizhen Zhao

Cryo-electron microscopy (EM) single particle reconstruction is an entirely general technique for 3D structure determination of macromolecular complexes. However, because the images are taken at low electron dose, it is extremely hard to visualize the individual particle with low contrast and high noise level. In this paper, we propose a novel approach called multi-frequency vector diffusion maps (MFVDM) to improve the efficiency and accuracy of cryo-EM 2D image classification and denoising. This framework incorporates different irreducible representations of the estimated alignment between similar images. In addition, we propose a graph filtering scheme to denoise the images using the eigenvalues and eigenvectors of the MFVDM matrices. Through both simulated and publicly available real data, we demonstrate that our proposed method is efficient and robust to noise compared with the state-of-the-art cryo-EM 2D class averaging and image restoration algorithms.

Ishan Deshpande, Yuan-Ting Hu, Ruoyu Sun et al.

Generative adversarial nets (GANs) and variational auto-encoders have significantly improved our distribution modeling capabilities, showing promise for dataset augmentation, image-to-image translation and feature learning. However, to model high-dimensional distributions, sequential training and stacked architectures are common, increasing the number of tunable hyper-parameters as well as the training time. Nonetheless, the sample complexity of the distance metrics remains one of the factors affecting GAN training. We first show that the recently proposed sliced Wasserstein distance has compelling sample complexity properties when compared to the Wasserstein distance. To further improve the sliced Wasserstein distance we then analyze its `projection complexity' and develop the max-sliced Wasserstein distance which enjoys compelling sample complexity while reducing projection complexity, albeit necessitating a max estimation. We finally illustrate that the proposed distance trains GANs on high-dimensional images up to a resolution of 256x256 easily.

Hongyu Shen, E. A. Huerta, Eamonn O'Shea et al.

We introduce deep learning models to estimate the masses of the binary components of black hole mergers, $(m_1,m_2)$, and three astrophysical properties of the post-merger compact remnant, namely, the final spin, $a_f$, and the frequency and damping time of the ringdown oscillations of the fundamental $\ell=m=2$ bar mode, $(ω_R, ω_I)$. Our neural networks combine a modified $\texttt{WaveNet}$ architecture with contrastive learning and normalizing flow. We validate these models against a Gaussian conjugate prior family whose posterior distribution is described by a closed analytical expression. Upon confirming that our models produce statistically consistent results, we used them to estimate the astrophysical parameters $(m_1,m_2, a_f, ω_R, ω_I)$ of five binary black holes: $\texttt{GW150914}, \texttt{GW170104}, \texttt{GW170814}, \texttt{GW190521}$ and $\texttt{GW190630}$. We use $\texttt{PyCBC Inference}$ to directly compare traditional Bayesian methodologies for parameter estimation with our deep-learning-based posterior distributions. Our results show that our neural network models predict posterior distributions that encode physical correlations, and that our data-driven median results and 90$\%$ confidence intervals are similar to those produced with gravitational wave Bayesian analyses. This methodology requires a single V100 $\texttt{NVIDIA}$ GPU to produce median values and posterior distributions within two milliseconds for each event. This neural network, and a tutorial for its use, are available at the $\texttt{Data and Learning Hub for Science}$.

Gabrielle Allen, Igor Andreoni, Etienne Bachelet et al.

This report provides an overview of recent work that harnesses the Big Data Revolution and Large Scale Computing to address grand computational challenges in Multi-Messenger Astrophysics, with a particular emphasis on real-time discovery campaigns. Acknowledging the transdisciplinary nature of Multi-Messenger Astrophysics, this document has been prepared by members of the physics, astronomy, computer science, data science, software and cyberinfrastructure communities who attended the NSF-, DOE- and NVIDIA-funded "Deep Learning for Multi-Messenger Astrophysics: Real-time Discovery at Scale" workshop, hosted at the National Center for Supercomputing Applications, October 17-19, 2018. Highlights of this report include unanimous agreement that it is critical to accelerate the development and deployment of novel, signal-processing algorithms that use the synergy between artificial intelligence (AI) and high performance computing to maximize the potential for scientific discovery with Multi-Messenger Astrophysics. We discuss key aspects to realize this endeavor, namely (i) the design and exploitation of scalable and computationally efficient AI algorithms for Multi-Messenger Astrophysics; (ii) cyberinfrastructure requirements to numerically simulate astrophysical sources, and to process and interpret Multi-Messenger Astrophysics data; (iii) management of gravitational wave detections and triggers to enable electromagnetic and astro-particle follow-ups; (iv) a vision to harness future developments of machine and deep learning and cyberinfrastructure resources to cope with the scale of discovery in the Big Data Era; (v) and the need to build a community that brings domain experts together with data scientists on equal footing to maximize and accelerate discovery in the nascent field of Multi-Messenger Astrophysics.

Zhizhen Zhao, Lydia T. Liu, Amit Singer

In photon-limited imaging, the pixel intensities are affected by photon count noise. Many applications, such as 3-D reconstruction using correlation analysis in X-ray free electron laser (XFEL) single molecule imaging, require an accurate estimation of the covariance of the underlying 2-D clean images. Accurate estimation of the covariance from low-photon count images must take into account that pixel intensities are Poisson distributed, hence the classical sample covariance estimator is sub-optimal. Moreover, in single molecule imaging, including in-plane rotated copies of all images could further improve the accuracy of covariance estimation. In this paper we introduce an efficient and accurate algorithm for covariance matrix estimation of count noise 2-D images, including their uniform planar rotations and possibly reflections. Our procedure, steerable $e$PCA, combines in a novel way two recently introduced innovations. The first is a methodology for principal component analysis (PCA) for Poisson distributions, and more generally, exponential family distributions, called $e$PCA. The second is steerable PCA, a fast and accurate procedure for including all planar rotations for PCA. The resulting principal components are invariant to the rotation and reflection of the input images. We demonstrate the efficiency and accuracy of steerable $e$PCA in numerical experiments involving simulated XFEL datasets and rotated Yale B face data.

E. A. Huerta, Daniel George, Zhizhen Zhao et al.

We discuss the development of novel deep learning algorithms to enable real-time regression analysis for time series data. We showcase the application of this new method with a timely case study, and then discuss the applicability of this approach to tackle similar challenges across science domains.

Hongyu Shen, Daniel George, E. A. Huerta et al.

Gravitational wave astronomy is a rapidly growing field of modern astrophysics, with observations being made frequently by the LIGO detectors. Gravitational wave signals are often extremely weak and the data from the detectors, such as LIGO, is contaminated with non-Gaussian and non-stationary noise, often containing transient disturbances which can obscure real signals. Traditional denoising methods, such as principal component analysis and dictionary learning, are not optimal for dealing with this non-Gaussian noise, especially for low signal-to-noise ratio gravitational wave signals. Furthermore, these methods are computationally expensive on large datasets. To overcome these issues, we apply state-of-the-art signal processing techniques, based on recent groundbreaking advancements in deep learning, to denoise gravitational wave signals embedded either in Gaussian noise or in real LIGO noise. We introduce SMTDAE, a Staired Multi-Timestep Denoising Autoencoder, based on sequence-to-sequence bi-directional Long-Short-Term-Memory recurrent neural networks. We demonstrate the advantages of using our unsupervised deep learning approach and show that, after training only using simulated Gaussian noise, SMTDAE achieves superior recovery performance for gravitational wave signals embedded in real non-Gaussian LIGO noise.

Zhizhen Zhao, Yoel Shkolnisky, Amit Singer

Cryo-electron microscopy nowadays often requires the analysis of hundreds of thousands of 2D images as large as a few hundred pixels in each direction. Here we introduce an algorithm that efficiently and accurately performs principal component analysis (PCA) for a large set of two-dimensional images, and, for each image, the set of its uniform rotations in the plane and their reflections. For a dataset consisting of $n$ images of size $L \times L$ pixels, the computational complexity of our algorithm is $O(nL^3 + L^4)$, while existing algorithms take $O(nL^4)$. The new algorithm computes the expansion coefficients of the images in a Fourier-Bessel basis efficiently using the non-uniform fast Fourier transform. We compare the accuracy and efficiency of the new algorithm with traditional PCA and existing algorithms for steerable PCA.

Zhizhen Zhao, Amit Singer

We introduce a new rotationally invariant viewing angle classification method for identifying, among a large number of Cryo-EM projection images, similar views without prior knowledge of the molecule. Our rotationally invariant features are based on the bispectrum. Each image is denoised and compressed using steerable principal component analysis (PCA) such that rotating an image is equivalent to phase shifting the expansion coefficients. Thus we are able to extend the theory of bispectrum of 1D periodic signals to 2D images. The randomized PCA algorithm is then used to efficiently reduce the dimensionality of the bispectrum coefficients, enabling fast computation of the similarity between any pair of images. The nearest neighbors provide an initial classification of similar viewing angles. In this way, rotational alignment is only performed for images with their nearest neighbors. The initial nearest neighbor classification and alignment are further improved by a new classification method called vector diffusion maps. Our pipeline for viewing angle classification and alignment is experimentally shown to be faster and more accurate than reference-free alignment with rotationally invariant K-means clustering, MSA/MRA 2D classification, and their modern approximations.