Simultaneous sparse approximation via greedy pursuit

A simple sparse approximation problem requests an approximation of a given input signal as a linear combination of T elementary signals drawn from a large, linearly dependent collection. An important generalization is simultaneous sparse approximation. Now one must approximate several input signals at once using different linear combinations of the same T elementary signals. This formulation appears, for example, when analyzing multiple observations of a sparse signal that have been contaminated with noise. A new approach to this problem is presented here: a greedy pursuit algorithm called simultaneous orthogonal matching pursuit. The paper proves that the algorithm calculates simultaneous approximations whose error is within a constant factor of the optimal simultaneous approximation error. This result requires that the collection of elementary signals be weakly correlated, a property that is also known as incoherence. Numerical experiments demonstrate that the algorithm often succeeds, even when the inputs do not meet the hypotheses of the proof

Algorithmic linear dimension reduction in the l_1 norm for sparse vectors

This paper develops a new method for recovering m-sparse signals that is simultaneously uniform and quick. We present a reconstruction algorithm whose run time, O(m log^2(m) log^2(d)), is sublinear in the length d of the signal. The reconstruction error is within a logarithmic factor (in m) of the optimal m-term approximation error in l_1. In particular, the algorithm recovers m-sparse signals perfectly and noisy signals are recovered with polylogarithmic distortion. Our algorithm makes O(m log^2 (d)) measurements, which is within a logarithmic factor of optimal. We also present a small-space implementation of the algorithm. These sketching techniques and the corresponding reconstruction algorithms provide an algorithmic dimension reduction in the l_1 norm. In particular, vectors of support m in dimension d can be linearly embedded into O(m log^2 d) dimensions with polylogarithmic distortion. We can reconstruct a vector from its low-dimensional sketch in time O(m log^2(m) log^2(d)). Furthermore, this reconstruction is stable and robust under small perturbations

Improved sparse approximation over quasi-incoherent dictionaries

This paper discusses a new greedy algorithm for solving the sparse approximation problem over quasi-incoherent dictionaries. These dictionaries consist of waveforms that are uncorrelated "on average," and they provide a natural generalization of incoherent dictionaries. The algorithm provides strong guarantees on the quality of the approximations it produces, unlike most other methods for sparse approximation. Moreover, very efficient implementations are possible via approximate nearest-neighbor data structure

Approximate Sparse Recovery: Optimizing Time and Measurements

An approximate sparse recovery system consists of parameters $k,N$, an $m$-by-$N$ measurement matrix, $\Phi$, and a decoding algorithm, $\mathcal{D}$. Given a vector, $x$, the system approximates $x$ by $\widehat x =\mathcal{D}(\Phi x)$, which must satisfy $\| \widehat x - x\|_2\le C \|x - x_k\|_2$, where $x_k$ denotes the optimal $k$-term approximation to $x$. For each vector $x$, the system must succeed with probability at least 3/4. Among the goals in designing such systems are minimizing the number $m$ of measurements and the runtime of the decoding algorithm, $\mathcal{D}$. In this paper, we give a system with $m=O(k \log(N/k))$ measurements--matching a lower bound, up to a constant factor--and decoding time $O(k\log^c N)$, matching a lower bound up to $\log(N)$ factors. We also consider the encode time (i.e., the time to multiply $\Phi$ by $x$), the time to update measurements (i.e., the time to multiply $\Phi$ by a 1-sparse $x$), and the robustness and stability of the algorithm (adding noise before and after the measurements). Our encode and update times are optimal up to $\log(N)$ factors

124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics

Optical super-resolution techniques reach unprecedented spatial resolution down to a few nanometers. However, efficient multiplexing strategies for the simultaneous detection of hundreds of molecular species are still elusive. Here, we introduce an entirely new approach to multiplexed super-resolution microscopy by designing the blinking behavior of targets with engineered binding frequency and duration in DNA-PAINT. We assay this kinetic barcoding approach in silico and in vitro using DNA origami structures, show the applicability for multiplexed RNA and protein detection in cells, and finally experimentally demonstrate 124-plex super-resolution imaging within minutes.We thank Martin Spitaler and the imaging facility of the MPI of Biochemistry for confocal imaging support