arXiv subjects

Tamir Bendory

Publications and source records attributed to Tamir Bendory.

90 records · Page 5Linked to original sources

arXiv2018

Heterogeneous multireference alignment: a single pass approach

Multireference alignment (MRA) is the problem of estimating a signal from many noisy and cyclically shifted copies of itself. In this paper, we consider an extension called heterogeneous MRA, where $K$ signals must be estimated, and each observation comes from one of those signals, unknown to us. This is a simplified model for the heterogeneity problem notably arising in cryo-electron microscopy. We propose an algorithm which estimates the $K$ signals without estimating either the shifts or the classes of the observations. It requires only one pass over the data and is based on low-order moments that are invariant under cyclic shifts. Given sufficiently many measurements, one can estimate these invariant features averaged over the $K$ signals. We then design a smooth, non-convex optimization problem to compute a set of signals which are consistent with the estimated averaged features. We find that, in many cases, the proposed approach estimates the set of signals accurately despite non-convexity, and conjecture the number of signals $K$ that can be resolved as a function of the signal length $L$ is on the order of $\sqrt{L}$.

cs.IT↗

arXiv2018

3D ab initio modeling in cryo-EM by autocorrelation analysis

Single-Particle Reconstruction (SPR) in Cryo-Electron Microscopy (cryo-EM) is the task of estimating the 3D structure of a molecule from a set of noisy 2D projections, taken from unknown viewing directions. Many algorithms for SPR start from an initial reference molecule, and alternate between refining the estimated viewing angles given the molecule, and refining the molecule given the viewing angles. This scheme is called iterative refinement. Reliance on an initial, user-chosen reference introduces model bias, and poor initialization can lead to slow convergence. Furthermore, since no ground truth is available for an unsolved molecule, it is difficult to validate the obtained results. This creates the need for high quality ab initio models that can be quickly obtained from experimental data with minimal priors, and which can also be used for validation. We propose a procedure to obtain such an ab initio model directly from raw data using Kam's autocorrelation method. Kam's method has been known since 1980, but it leads to an underdetermined system, with missing orthogonal matrices. Until now, this system has been solved only for special cases, such as highly symmetric molecules or molecules for which a homologous structure was already available. In this paper, we show that knowledge of just two clean projections is sufficient to guarantee a unique solution to the system. This system is solved by an optimization-based heuristic. For the first time, we are then able to obtain a low-resolution ab initio model of an asymmetric molecule directly from raw data, without 2D class averaging and without tilting. Numerical results are presented on both synthetic and experimental data.

math.OC↗

arXiv2017

Fourier Phase Retrieval: Uniqueness and Algorithms

The problem of recovering a signal from its phaseless Fourier transform measurements, called Fourier phase retrieval, arises in many applications in engineering and science. Fourier phase retrieval poses fundamental theoretical and algorithmic challenges. In general, there is no unique mapping between a one-dimensional signal and its Fourier magnitude and therefore the problem is ill-posed. Additionally, while almost all multidimensional signals are uniquely mapped to their Fourier magnitude, the performance of existing algorithms is generally not well-understood. In this chapter we survey methods to guarantee uniqueness in Fourier phase retrieval. We then present different algorithmic approaches to retrieve the signal in practice. We conclude by outlining some of the main open questions in this field.

cs.IT↗

arXiv2017

Bispectrum Inversion with Application to Multireference Alignment

We consider the problem of estimating a signal from noisy circularly-translated versions of itself, called multireference alignment (MRA). One natural approach to MRA could be to estimate the shifts of the observations first, and infer the signal by aligning and averaging the data. In contrast, we consider a method based on estimating the signal directly, using features of the signal that are invariant under translations. Specifically, we estimate the power spectrum and the bispectrum of the signal from the observations. Under mild assumptions, these invariant features contain enough information to infer the signal. In particular, the bispectrum can be used to estimate the Fourier phases. To this end, we propose and analyze a few algorithms. Our main methods consist of non-convex optimization over the smooth manifold of phases. Empirically, in the absence of noise, these non-convex algorithms appear to converge to the target signal with random initialization. The algorithms are also robust to noise. We then suggest three additional methods. These methods are based on frequency marching, semidefinite relaxation and integer programming. The first two methods provably recover the phases exactly in the absence of noise. In the high noise level regime, the invariant features approach for MRA results in stable estimation if the number of measurements scales like the cube of the noise variance, which is the information-theoretic rate. Additionally, it requires only one pass over the data which is important at low signal-to-noise ratio when the number of observations must be large.

cs.IT↗

arXiv2017

Non-Convex Phase Retrieval from STFT Measurements

The problem of recovering a one-dimensional signal from its Fourier transform magnitude, called Fourier phase retrieval, is ill-posed in most cases. We consider the closely-related problem of recovering a signal from its phaseless short-time Fourier transform (STFT) measurements. This problem arises naturally in several applications, such as ultra-short laser pulse characterization and ptychography. The redundancy offered by the STFT enables unique recovery under mild conditions. We show that in some cases the unique solution can be obtained by the principal eigenvector of a matrix, constructed as the solution of a simple least-squares problem. When these conditions are not met, we suggest using the principal eigenvector of this matrix to initialize non-convex local optimization algorithms and propose two such methods. The first is based on minimizing the empirical risk loss function, while the second maximizes a quadratic function on the manifold of phases. We prove that under appropriate conditions, the proposed initialization is close to the underlying signal. We then analyze the geometry of the empirical risk loss function and show numerically that both gradient algorithms converge to the underlying signal even with small redundancy in the measurements. In addition, the algorithms are robust to noise.

cs.IT↗

arXiv2017

On the Uniqueness of FROG Methods

The problem of recovering a signal from its power spectrum, called phase retrieval, arises in many scientific fields. One of many examples is ultra-short laser pulse characterization in which the electromagnetic field is oscillating with ~10^15 Hz and phase information cannot be measured directly due to limitations of the electronic sensors. Phase retrieval is ill-posed in most cases as there are many different signals with the same Fourier transform magnitude. To overcome this fundamental ill-posedness, several measurement techniques are used in practice. One of the most popular methods for complete characterization of ultra-short laser pulses is the Frequency-Resolved Optical Gating (FROG). In FROG, the acquired data is the power spectrum of the product of the unknown pulse with its delayed replica. Therefore the measured signal is a quartic function of the unknown pulse. A generalized version of FROG, where the delayed replica is replaced by a second unknown pulse, is called blind FROG. In this case, the measured signal is quadratic with respect to both pulses. In this letter we introduce and formulate FROG-type techniques. We then show that almost all band-limited signals are determined uniquely, up to trivial ambiguities, by blind FROG measurements (and thus also by FROG), if in addition we have access to the signals power spectrum.

cs.IT↗

arXiv2017

Robust Recovery of Positive Stream of Pulses

The problem of estimating the delays and amplitudes of a positive stream of pulses appears in many applications, such as single-molecule microscopy. This paper suggests estimating the delays and amplitudes using a convex program, which is robust in the presence of noise (or model mismatch). Particularly, the recovery error is proportional to the noise level. We further show that the error grows exponentially with the density of the delays and also depends on the localization properties of the pulse.

cs.IT↗

arXiv2016

Robust Recovery of Stream of Pulses using Convex Optimization

This paper considers the problem of recovering the delays and amplitudes of a weighted superposition of pulses. This problem is motivated by a variety of applications such as ultrasound and radar. We show that for univariate and bivariate stream of pulses, one can recover the delays and weights to any desired accuracy by solving a tractable convex optimization problem, provided that a pulse-dependent separation condition is satisfied. The main result of this paper states that the recovery is robust to additive noise or model mismatch.

cs.IT↗

arXiv2016

Sparse Sampling in Helical Cone-Beam CT Perfect Reconstruction Algorithms

In the current paper we consider the Helical Cone Beam CT. This scanning method exposes the patient to large quantities of radiation and results in very large amounts of data being collected and stored. Both these facts are prime motivators for the development of an efficient, reduced rate, sampling pattern. We calculate bounds on the support in the frequency domain of the collected data and use these to suggest an efficient sampling pattern. A reduction of up to a factor of 2 in sampling rate is suggested. Indeed, we show that reconstruction quality is not affected by this reduction of sampling rates.

cs.IT↗

arXiv2015

Stable Support Recovery of Stream of Pulses with Application to Ultrasound Imaging

This paper considers the problem of estimating the delays of a weighted superposition of pulses, called stream of pulses, in a noisy environment. We show that the delays can be estimated using a tractable convex optimization problem with a localization error proportional to the square root of the noise level. Furthermore, all false detections produced by the algorithm have small amplitudes. Numerical and in-vitro ultrasound experiments corroborate the theoretical results and demonstrate their applicability for the ultrasound imaging signal processing.

cs.IT↗

arXiv2015

A Least Squares Approach for Stable Phase Retrieval from Short-Time Fourier Transform Magnitude

We address the problem of recovering a signal (up to global phase) from its short-time Fourier transform (STFT) magnitude measurements. This problem arises in several applications, including optical imaging and speech processing. In this paper we suggest three interrelated algorithms. The first algorithm estimates the signal efficiently from noisy measurements by solving a simple least-squares (LS) problem. In contrast to previously proposed algorithms, the LS approach has stability guarantees and does not require any prior knowledge on the sought signal. However, the recovery is guaranteed under relatively strong restrictions on the STFT window. The second approach is guaranteed to recover a non-vanishing signal efficiently from noise-free measurements, under very moderate conditions on the STFT window. Finally, the third method estimates the signal robustly from noisy measurements by solving a semi-definite program (SDP). The proposed SDP algorithm contains an inherent trade-off between its robustness and the restrictions on the STFT windows that can be used.

cs.IT↗

arXiv2015

Recovery of Sparse Positive Signals on the Sphere from Low Resolution Measurements

This letter considers the problem of recovering a positive stream of Diracs on a sphere from its projection onto the space of low-degree spherical harmonics, namely, from its low-resolution version. We suggest recovering the Diracs via a tractable convex optimization problem. The resulting recovery error is proportional to the noise level and depends on the density of the Diracs. We validate the theory by numerical experiments.

cs.IT↗

arXiv2015

Convex Optimization Approach for Stable Decomposition of Stream of Pulses

This paper deals with the problem of estimating the delays and amplitudes of a weighted superposition of pulses, called stream of pulses. This problem is motivated by a variety of applications, such as ultrasound and radar. This paper shows that the recovery error of a tractable convex optimization problem is proportional to the noise level. Additionally, the estimated delays are clustered around the true delays. This holds provided that the pulse meets a few mild localization properties and that a separation condition holds. If the amplitudes are known to be positive, the separation is unnecessary. In this case, the recovery error is proportional to the noise level and depends on the maximal number of delays within a resolution cell.

cs.IT↗

arXiv2015

Unified Convex Optimization Approach to Super-Resolution Based on Localized Kernels

The problem of resolving the fine details of a signal from its coarse scale measurements or, as it is commonly referred to in the literature, the super-resolution problem arises naturally in engineering and physics in a variety of settings. We suggest a unified convex optimization approach for super-resolution. The key is the construction of an interpolating polynomial based on localized kernels. We also show that the localized kernels act as the connecting thread to another wide-spread problem of stream of pulses.

cs.IT↗

arXiv2015

Super-resolution on the Sphere using Convex Optimization

This paper considers the problem of recovering an ensemble of Diracs on a sphere from its low resolution measurements. The Diracs can be located at any location on the sphere, not necessarily on a grid. We show that under a separation condition, one can recover the ensemble with high precision by a three-stage algorithm, which consists of solving a semi-definite program, root finding and least-square fitting. The algorithm's computation time depends solely on the number of measurements, and not on the required solution accuracy. We also show that in the special case of non-negative ensembles, a sparsity condition is sufficient for recovery. Furthermore, in the discrete setting, we estimate the recovery error in the presence of noise as a function of the noise level and the super-resolution factor.

cs.IT↗

arXiv2014

Exact recovery of non-uniform splines from the projection onto spaces of algebraic polynomials

In this work we consider the problem of recovering non-uniform splines from their projection onto spaces of algebraic polynomials. We show that under a certain Chebyshev-type separation condition on its knots, a spline whose inner-products with a polynomial basis and boundary conditions are known, can be recovered using Total Variation norm minimization. The proof of the uniqueness of the solution uses the method of `dual' interpolating polynomials and is based on \cite{SR}, where the theory was developed for trigonometric polynomials. We also show results for the multivariate case.

cs.IT↗

arXiv2014

Edge Preserving Multi-Modal Registration Based On Gradient Intensity Self-Similarity

Image registration is a challenging task in the world of medical imaging. Particularly, accurate edge registration plays a central role in a variety of clinical conditions. The Modality Independent Neighbourhood Descriptor (MIND) demonstrates state of the art alignment, based on the image self-similarity. However, this method appears to be less accurate regarding edge registration. In this work, we propose a new registration method, incorporating gradient intensity and MIND self-similarity metric. Experimental results show the superiority of this method in edge registration tasks, while preserving the original MIND performance for other image features and textures.

cs.CV↗

arXiv2014

Exact recovery of Dirac ensembles from the projection onto spaces of spherical harmonics

In this work we consider the problem of recovering an ensemble of Diracs on the sphere from its projection onto spaces of spherical harmonics. We show that under an appropriate separation condition on the unknown locations of the Diracs, the ensemble can be recovered through Total Variation norm minimization. The proof of the uniqueness of the solution uses the method of `dual' interpolating polynomials and is based on [8], where the theory was developed for trigonometric polynomials. We also show that in the special case of non-negative ensembles, a sparsity condition is sufficient for exact recovery.

cs.IT↗