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Confirmation bias, the tendency to interpret information in a way that aligns with one's preconceptions, can profoundly impact scientific research, leading to conclusions that reflect the researcher's hypotheses even when the observational data do not support them. This issue is especially critical in scientific fields involving highly noisy observations, such as cryo-electron microscopy. This study investigates confirmation bias in Gaussian mixture models. We consider the following experiment: A team of scientists assumes they are analyzing data drawn from a Gaussian mixture model with known signals (hypotheses) as centroids. However, in reality, the observations consist entirely of noise without any informative structure. The researchers use a single iteration of the K-means or expectation-maximization algorithms, two popular algorithms to estimate the centroids. Despite the observations being pure noise, we show that these algorithms yield biased estimates that resemble the initial hypotheses, contradicting the unbiased expectation that averaging these noise observations would converge to zero. Namely, the algorithms generate estimates that mirror the postulated model, although the hypotheses (the presumed centroids of the Gaussian mixture) are not evident in the observations. Specifically, among other results, we prove a positive correlation between the estimates produced by the algorithms and the corresponding hypotheses. We also derive explicit closed-form expressions of the estimates for a finite and infinite number of hypotheses. This study underscores the risks of confirmation bias in low signal-to-noise environments, provides insights into potential pitfalls in scientific methodologies, and highlights the importance of prudent data interpretation.

Semi-algebraic priors are ubiquitous in signal processing and machine learning. Prevalent examples include a) linear models where the signal lies in a low-dimensional subspace; b) sparse models where the signal can be represented by only a few coefficients under a suitable basis; and c) a large family of neural network generative models. In this paper, we prove a transversality theorem for semi-algebraic sets in orthogonal or unitary representations of groups: with a suitable dimension bound, a generic translate of any semi-algebraic set is transverse to the orbits of the group action. This, in turn, implies that if a signal lies in a low-dimensional semi-algebraic set, then it can be recovered uniquely from measurements that separate orbits. As an application, we consider the implications of the transversality theorem to the problem of recovering signals that are translated by random group actions from their second moment. As a special case, we discuss cryo-EM: a leading technology to constitute the spatial structure of biological molecules, which serves as our prime motivation. In particular, we derive explicit bounds for recovering a molecular structure from the second moment under a semi-algebraic prior and deduce information-theoretic implications. We also obtain information-theoretic bounds for three additional applications: factoring Gram matrices, multi-reference alignment, and phase retrieval. Finally, we deduce bounds for designing permutation invariant separators in machine learning.

The key ingredient to retrieving a signal from its Fourier magnitudes, namely, to solve the phase retrieval problem, is an effective prior on the sought signal. In this paper, we study the phase retrieval problem under the prior that the signal lies in a semi-algebraic set. This is a very general prior as semi-algebraic sets include linear models, sparse models, and ReLU neural network generative models. The latter is the main motivation of this paper, due to the remarkable success of deep generative models in a variety of imaging tasks, including phase retrieval. We prove that almost all signals in R^N can be determined from their Fourier magnitudes, up to a sign, if they lie in a (generic) semi-algebraic set of dimension N/2. The same is true for all signals if the semi-algebraic set is of dimension N/4. We also generalize these results to the problem of signal recovery from the second moment in multi-reference alignment models with multiplicity free representations of compact groups. This general result is then used to derive improved sample complexity bounds for recovering band-limited functions on the sphere from their noisy copies, each acted upon by a random element of SO(3).

In this paper, we study the problems of detection and recovery of hidden submatrices with elevated means inside a large Gaussian random matrix. We consider two different structures for the planted submatrices. In the first model, the planted matrices are disjoint, and their row and column indices can be arbitrary. Inspired by scientific applications, the second model restricts the row and column indices to be consecutive. In the detection problem, under the null hypothesis, the observed matrix is a realization of independent and identically distributed standard normal entries. Under the alternative, there exists a set of hidden submatrices with elevated means inside the same standard normal matrix. Recovery refers to the task of locating the hidden submatrices. For both problems, and for both models, we characterize the statistical and computational barriers by deriving information-theoretic lower bounds, designing and analyzing algorithms matching those bounds, and proving computational lower bounds based on the low-degree polynomials conjecture. In particular, we show that the space of the model parameters (i.e., number of planted submatrices, their dimensions, and elevated mean) can be partitioned into three regions: the impossible regime, where all algorithms fail; the hard regime, where while detection or recovery are statistically possible, we give some evidence that polynomial-time algorithm do not exist; and finally the easy regime, where polynomial-time algorithms exist., Comment: 36 pages

We consider the finite alphabet phase retrieval problem: recovering a signal whose entries lie in a small alphabet of possible values from its Fourier magnitudes. This problem arises in the celebrated technology of X-ray crystallography to determine the atomic structure of biological molecules. Our main result states that for generic values of the alphabet, two signals have the same Fourier magnitudes if and only if several partitions have the same difference sets. Thus, the finite alphabet phase retrieval problem reduces to the combinatorial problem of determining a signal from those difference sets. Notably, this result holds true when one of the letters of the alphabet is zero, namely, for sparse signals with finite alphabet, which is the situation in X-ray crystallography.

Multi-reference alignment (MRA) is the problem of recovering a signal from its multiple noisy copies, each acted upon by a random group element. MRA is mainly motivated by single-particle cryo-electron microscopy (cryo-EM) that has recently joined X-ray crystallography as one of the two leading technologies to reconstruct biological molecular structures. Previous papers have shown that in the high noise regime, the sample complexity of MRA and cryo-EM is $n=\omega(\sigma^{2d})$, where $n$ is the number of observations, $\sigma^2$ is the variance of the noise, and $d$ is the lowest-order moment of the observations that uniquely determines the signal. In particular, it was shown that in many cases, $d=3$ for generic signals, and thus the sample complexity is $n=\omega(\sigma^6)$. In this paper, we analyze the second moment of the MRA and cryo-EM models. First, we show that in both models the second moment determines the signal up to a set of unitary matrices, whose dimension is governed by the decomposition of the space of signals into irreducible representations of the group. Second, we derive sparsity conditions under which a signal can be recovered from the second moment, implying sample complexity of $n=\omega(\sigma^4)$. Notably, we show that the sample complexity of cryo-EM is $n=\omega(\sigma^4)$ if at most one third of the coefficients representing the molecular structure are non-zero; this bound is near-optimal. The analysis is based on tools from representation theory and algebraic geometry. We also derive bounds on recovering a sparse signal from its power spectrum, which is the main computational problem of X-ray crystallography.

The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we consider the effect of imposing sparsity priors on the molecule. We use techniques from signal processing, optimization, and applied algebraic geometry to obtain new theoretical and computational contributions for this challenging non-linear inverse problem with sparsity constraints. We prove that molecular structures modeled as sums of Gaussians are uniquely determined by the second-order autocorrelation of their projection images, implying that the sample complexity is proportional to the square of the variance of the noise. This theory improves upon the non-sparse case, where the third-order autocorrelation is required for uniformly-oriented particle images and the sample complexity scales with the cube of the noise variance. Furthermore, we build a computational framework to reconstruct molecular structures which are sparse in the wavelet basis. This method combines the sparse representation for the molecule with projection-based techniques used for phase retrieval in X-ray crystallography., Comment: 31 pages, 5 figures, 1 movie

The purpose of this article is to discuss recent advances in the growing field of phase retrieval, and to publicize open problems that we believe will be of interest to mathematicians in general, and algebraists in particular.

This paper studies the sample complexity of learning the $k$ unknown centers of a balanced Gaussian mixture model (GMM) in $\mathbb{R}^d$ with spherical covariance matrix $\sigma^2\mathbf{I}$. In particular, we are interested in the following question: what is the maximal noise level $\sigma^2$, for which the sample complexity is essentially the same as when estimating the centers from labeled measurements? To that end, we restrict attention to a Bayesian formulation of the problem, where the centers are uniformly distributed on the sphere $\sqrt{d}\mathcal{S}^{d-1}$. Our main results characterize the exact noise threshold $\sigma^2$ below which the GMM learning problem, in the large system limit $d,k\to\infty$, is as easy as learning from labeled observations, and above which it is substantially harder. The threshold occurs at $\frac{\log k}{d} = \frac12\log\left( 1+\frac{1}{\sigma^2} \right)$, which is the capacity of the additive white Gaussian noise (AWGN) channel. Thinking of the set of $k$ centers as a code, this noise threshold can be interpreted as the largest noise level for which the error probability of the code over the AWGN channel is small. Previous works on the GMM learning problem have identified the minimum distance between the centers as a key parameter in determining the statistical difficulty of learning the corresponding GMM. While our results are only proved for GMMs whose centers are uniformly distributed over the sphere, they hint that perhaps it is the decoding error probability associated with the center constellation as a channel code that determines the statistical difficulty of learning the corresponding GMM, rather than just the minimum distance., Comment: COLT 2022

We study the problem of recovering a signal $x\in\mathbb{C}^N$ from samples of its phaseless periodic short-time Fourier transform (STFT): the magnitude of the Fourier transform of the signal multiplied by a sliding window $w\in \mathbb{C}^W$. We show that if the window $w$ is known, then a generic signal can be recovered, up to a global phase, from less than 4N phaseless STFT measurements. In the blind case, when the window is unknown, we show that the signal and the window can be determined simultaneously, up to a group of unavoidable ambiguities, from less than 4N+2W measurements. In both cases, our bounds are optimal, up to a constant smaller than two.

Motivated by the problem of determining the atomic structure of macromolecules using single-particle cryo-electron microscopy (cryo-EM), we study the sample and computational complexities of the sparse multi-reference alignment (MRA) model: the problem of estimating a sparse signal from its noisy, circularly shifted copies. Based on its tight connection to the crystallographic phase retrieval problem, we establish that if the number of observations is proportional to the square of the variance of the noise, then the sparse MRA problem is statistically feasible for sufficiently sparse signals. To investigate its computational hardness, we consider three types of computational frameworks: projection-based algorithms, bispectrum inversion, and convex relaxations. We show that a state-of-the-art projection-based algorithm achieves the optimal estimation rate, but its computational complexity is exponential in the sparsity level. The bispectrum framework provides a statistical-computational trade-off: it requires more observations (so its estimation rate is suboptimal), but its computational load is provably polynomial in the signal's length. The convex relaxation approach provides polynomial time algorithms (with a large exponent) that recover sufficiently sparse signals at the optimal estimation rate. We conclude the paper by discussing potential statistical and algorithmic implications for cryo-EM.

We study the dihedral multi-reference alignment problem of estimating the orbit of a signal from multiple noisy observations of the signal, acted on by random elements of the dihedral group. We show that if the group elements are drawn from a generic distribution, the orbit of a generic signal is uniquely determined from the second moment of the observations. This implies that the optimal estimation rate in the high noise regime is proportional to the square of the variance of the noise. This is the first result of this type for multi-reference alignment over a non-abelian group with a non-uniform distribution of group elements. Based on tools from invariant theory and algebraic geometry, we also delineate conditions for unique orbit recovery for multi-reference alignment models over finite groups (namely, when the dihedral group is replaced by a general finite group) when the group elements are drawn from a generic distribution. Finally, we design and study numerically three computational frameworks for estimating the signal based on group synchronization, expectation-maximization, and the method of moments.

The $q$-th order spectrum is a polynomial of degree $q$ in the entries of a signal $x\in\mathbb{C}^N$, which is invariant under circular shifts of the signal. For $q\geq 3$, this polynomial determines the signal uniquely, up to a circular shift, and is called a high-order spectrum. The high-order spectra, and in particular the bispectrum ($q=3$) and the trispectrum ($q=4$), play a prominent role in various statistical signal processing and imaging applications, such as phase retrieval and single-particle reconstruction. However, the dimension of the $q$-th order spectrum is $N^{q-1}$, far exceeding the dimension of $x$, leading to increased computational load and storage requirements. In this work, we show that it is unnecessary to store and process the full high-order spectra: a signal can be characterized uniquely, up to symmetries, from only $N+1$ linear measurements of its high-order spectra. The proof relies on tools from algebraic geometry and is corroborated by numerical experiments.

Multi-reference alignment entails estimating a signal in $\mathbb{R}^L$ from its circularly-shifted and noisy copies. This problem has been studied thoroughly in recent years, focusing on the finite-dimensional setting (fixed $L$). Motivated by single-particle cryo-electron microscopy, we analyze the sample complexity of the problem in the high-dimensional regime $L\to\infty$. Our analysis uncovers a phase transition phenomenon governed by the parameter $\alpha = L/(\sigma^2\log L)$, where $\sigma^2$ is the variance of the noise. When $\alpha>2$, the impact of the unknown circular shifts on the sample complexity is minor. Namely, the number of measurements required to achieve a desired accuracy $\varepsilon$ approaches $\sigma^2/\varepsilon$ for small $\varepsilon$; this is the sample complexity of estimating a signal in additive white Gaussian noise, which does not involve shifts. In sharp contrast, when $\alpha\leq 2$, the problem is significantly harder and the sample complexity grows substantially quicker with $\sigma^2$.

We study super-resolution multi-reference alignment, the problem of estimating a signal from many circularly shifted, down-sampled, and noisy observations. We focus on the low SNR regime, and show that a signal in $\mathbb{R}^M$ is uniquely determined when the number $L$ of samples per observation is of the order of the square root of the signal's length $(L=O(\sqrt{M}))$. Phrased more informally, one can square the resolution. This result holds if the number of observations is proportional to at least 1/SNR$^3$. In contrast, with fewer observations recovery is impossible even when the observations are not down-sampled ($L=M$). The analysis combines tools from statistical signal processing and invariant theory. We design an expectation-maximization algorithm and demonstrate that it can super-resolve the signal in challenging SNR regimes.

Motivated by the X-ray crystallography technology to determine the atomic structure of biological molecules, we study the crystallographic phase retrieval problem, arguably the leading and hardest phase retrieval setup. This problem entails recovering a K-sparse signal of length N from its Fourier magnitude or, equivalently, from its periodic auto-correlation. Specifically, this work focuses on the fundamental question of uniqueness: what is the maximal sparsity level K/N that allows unique mapping between a signal and its Fourier magnitude, up to intrinsic symmetries. We design a systemic computational technique to affirm uniqueness for any specific pair (K,N), and establish the following conjecture: the Fourier magnitude determines a generic signal uniquely, up to intrinsic symmetries, as long as K<=N/2. Based on group-theoretic considerations and an additional computational technique, we formulate a second conjecture: if K

The properties of gradient techniques for the phase retrieval problem have received a considerable attention in recent years. In almost all applications, however, the phase retrieval problem is solved using a family of algorithms that can be interpreted as variants of Douglas-Rachford splitting. In this work, we establish a connection between Douglas-Rachford and gradient algorithms. Specifically, we show that in some cases a generalization of Douglas-Rachford, called relaxed-reflect-reflect (RRR), can be viewed as gradient descent on a certain objective function. The solutions coincide with the critical points of that objective, which---in contrast to standard gradient techniques---are not its minimizers. Using the objective function, we give simple proofs of some basic properties of the RRR algorithm. Specifically, we describe its set of solutions, show a local convexity around any solution, and derive stability guarantees. Nevertheless, in its present state, the analysis does not elucidate the remarkable empirical performance of RRR and its global properties.

In recent years, an abundance of new molecular structures have been elucidated using cryo-electron microscopy (cryo-EM), largely due to advances in hardware technology and data processing techniques. Owing to these new exciting developments, cryo-EM was selected by Nature Methods as Method of the Year 2015, and the Nobel Prize in Chemistry 2017 was awarded to three pioneers in the field. The main goal of this article is to introduce the challenging and exciting computational tasks involved in reconstructing 3-D molecular structures by cryo-EM. Determining molecular structures requires a wide range of computational tools in a variety of fields, including signal processing, estimation and detection theory, high-dimensional statistics, convex and non-convex optimization, spectral algorithms, dimensionality reduction, and machine learning. The tools from these fields must be adapted to work under exceptionally challenging conditions, including extreme noise levels, the presence of missing data, and massively large datasets as large as several Terabytes. In addition, we present two statistical models: multi-reference alignment and multi-target detection, that abstract away much of the intricacies of cryo-EM, while retaining some of its essential features. Based on these abstractions, we discuss some recent intriguing results in the mathematical theory of cryo-EM, and delineate relations with group theory, invariant theory, and information theory.

Motivated by the structure reconstruction problem in single-particle cryo-electron microscopy, we consider the multi-target detection model, where multiple copies of a target signal occur at unknown locations in a long measurement, further corrupted by additive Gaussian noise. At low noise levels, one can easily detect the signal occurrences and estimate the signal by averaging. However, in the presence of high noise, which is the focus of this paper, detection is impossible. Here, we propose two approaches---autocorrelation analysis and an approximate expectation maximization algorithm---to reconstruct the signal without the need to detect signal occurrences in the measurement. In particular, our methods apply to an arbitrary spacing distribution of signal occurrences. We demonstrate reconstructions with synthetic data and empirically show that the sample complexity of both methods scales as 1/SNR^3 in the low SNR regime., Comment: 13 pages, 8 figures

We consider the multi-target detection problem of recovering a set of signals that appear multiple times at unknown locations in a noisy measurement. In the low noise regime, one can estimate the signals by first detecting occurrences, then clustering and averaging them. In the high noise regime however, neither detection nor clustering can be performed reliably, so that strategies along these lines are destined to fail. Notwithstanding, using autocorrelation analysis, we show that the impossibility to detect and cluster signal occurrences in the presence of high noise does not necessarily preclude signal estimation. Specifically, to estimate the signals, we derive simple relations between the autocorrelations of the observation and those of the signals. These autocorrelations can be estimated accurately at any noise level given a sufficiently long measurement. To recover the signals from the observed autocorrelations, we solve a set of polynomial equations through nonlinear least-squares. We provide analysis regarding well-posedness of the task, and demonstrate numerically the effectiveness of the method in a variety of settings. The main goal of this work is to provide theoretical and numerical support for a recently proposed framework to image 3-D structures of biological macromolecules using cryo-electron microscopy in extreme noise levels., Comment: arXiv admin note: text overlap with arXiv:1810.00226

Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces images called micrographs. Projections of the molecule of interest are embedded in the micrographs at unknown locations, and under unknown viewing directions. Standard imaging techniques first locate these projections (detection) and then reconstruct the 3-D structure from them. Unfortunately, high noise levels hinder detection. When reliable detection is rendered impossible, the standard techniques fail. This is a problem, especially for small molecules. In this paper, we pursue a radically different approach: we contend that the structure could, in principle, be reconstructed directly from the micrographs, without intermediate detection. The aim is to bring small molecules within reach for cryo-EM. To this end, we design an autocorrelation analysis technique that allows to go directly from the micrographs to the sought structures. This involves only one pass over the micrographs, allowing online, streaming processing for large experiments. We show numerical results and discuss challenges that lay ahead to turn this proof-of-concept into a complementary approach to state-of-the-art algorithms., Comment: Older citations to this paper refer to version arXiv:1810.00226v1, parts of which now appear in: Tamir Bendory, Nicolas Boumal, William Leeb, Eitan Levin, and Amit Singer. "Multi-target detection with application to cryo-electron microscopy." Inverse Problems 35, no. 10 (2019): 104003

The problem of recovering a pair of signals from their blind phaseless short-time Fourier transform measurements arises in several important phase retrieval applications, including ptychography and ultra-short pulse characterization. In this paper, we prove that in order to determine a pair of generic signals uniquely, up to trivial ambiguities, the number of phaseless measurements one needs to collect is, at most, five times the number of parameters required to describe the signals. This result improves significantly upon previous papers, which required the number of measurements to be quadratic in the number of parameters rather than linear. In addition, we consider the simpler problem of recovering a pair of generic signals from their blind short-time Fourier transform, when the phases are known. In this setting, which can be understood as a special case of the blind deconvolution problem, we show that the number of measurements required to determine the two signals, up to trivial ambiguities, equals exactly the number of parameters to be recovered. As a side result, we study the classical phase retrieval problem---that is, recovering a signal from its Fourier magnitudes---when some entries of the signal are known apriori. We derive a bound on the number of required measurements as a function of the size of the set of known entries. Specifically, we show that if most of the signal's entries are known, then only a few Fourier magnitudes are necessary to determine a signal uniquely.

We study the ubiquitous super-resolution problem, in which one aims at localizing positive point sources in an image, blurred by the point spread function of the imaging device. To recover the point sources, we propose to solve a convex feasibility program, which simply finds a nonnegative Borel measure that agrees with the observations collected by the imaging device. In the absence of imaging noise, we show that solving this convex program uniquely retrieves the point sources, provided that the imaging device collects enough observations. This result holds true if the point spread function of the imaging device can be decomposed into horizontal and vertical components, and if the translations of these components form a Chebyshev system, i.e., a system of continuous functions that loosely behave like algebraic polynomials. Building upon recent results for one-dimensional signals [1], we prove that this super-resolution algorithm is stable, in the generalized Wasserstein metric, to model mismatch (i.e., when the image is not sparse) and to additive imaging noise. In particular, the recovery error depends on the noise level and how well the image can be approximated with well-separated point sources. As an example, we verify these claims for the important case of a Gaussian point spread function. The proofs rely on the construction of novel interpolating polynomials---which are the main technical contribution of this paper---and partially resolve the question raised in [2] about the extension of the standard machinery to higher dimensions.

In the multireference alignment model, a signal is observed by the action of a random circular translation and the addition of Gaussian noise. The goal is to recover the signal's orbit by accessing multiple independent observations. Of particular interest is the sample complexity, i.e., the number of observations/samples needed in terms of the signal-to-noise ratio (the signal energy divided by the noise variance) in order to drive the mean-square error (MSE) to zero. Previous work showed that if the translations are drawn from the uniform distribution, then, in the low SNR regime, the sample complexity of the problem scales as $\omega(1/\text{SNR}^3)$. In this work, using a generalization of the Chapman--Robbins bound for orbits and expansions of the $\chi^2$ divergence at low SNR, we show that in the same regime the sample complexity for any aperiodic translation distribution scales as $\omega(1/\text{SNR}^2)$. This rate is achieved by a simple spectral algorithm. We propose two additional algorithms based on non-convex optimization and expectation-maximization. We also draw a connection between the multireference alignment problem and the spiked covariance model.

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 $\sqrt{L}$., Comment: 6 pages, 3 figures

Phase retrieval refers to recovering a signal from its Fourier magnitude. This problem arises naturally in many scientific applications, such as ultra-short laser pulse characterization and diffraction imaging. Unfortunately, phase retrieval is ill-posed for almost all one-dimensional signals. In order to characterize a laser pulse and overcome the ill-posedness, it is common to use a technique called Frequency-Resolved Optical Gating (FROG). In FROG, the measured data, referred to as FROG trace, is the Fourier magnitude of the product of the underlying signal with several translated versions of itself. The FROG trace results in a system of phaseless quartic Fourier measurements. In this paper, we prove that it suffices to consider only three translations of the signal to determine almost all bandlimited signals, up to trivial ambiguities. In practice, one usually also has access to the signal's Fourier magnitude. We show that in this case only two translations suffice. Our results significantly improve upon earlier work.

In recent years, the mathematical and algorithmic aspects of the phase retrieval problem have received considerable attention. Many papers in this area mention crystallography as a principal application. In crystallography, the signal to be recovered is periodic and comprised of atomic distributions arranged homogeneously in the unit cell of the crystal. The crystallographic problem is both the leading application and one of the hardest forms of phase retrieval. We have constructed a graded set of benchmark problems for evaluating algorithms that perform this type of phase retrieval. The data, publicly available online, is provided in an easily interpretable format. We also propose a simple and unambiguous success/failure criterion based on the actual needs in crystallography. Baseline runtimes were obtained with an iterative algorithm that is similar but more transparent than those used in crystallography. Empirically, the runtimes grow exponentially with respect to a new hardness parameter: the sparsity of the signal autocorrelation. We also review the algorithms used by the leading software packages. This set of benchmark problems, we hope, will encourage the development of new algorithms for the phase retrieval problem in general, and crystallography in particular., Comment: 27 pages, 10 figures, new references, modified appendix, improved presentation

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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., Comment: Small modifications