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Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by sampling from this DNA pool. Moreover, imperfections in writing (synthesis), reading (sequencing), storage, and handling of the DNA, in particular amplification via PCR, lead to a loss of DNA molecules and induce errors within the molecules. In order to design DNA storage systems, a qualitative and quantitative understanding of the errors and the loss of molecules is crucial. In this paper, we characterize those error probabilities by analyzing data from our own experiments as well as from experiments of two different groups. We find that errors within molecules are mainly due to synthesis and sequencing, while imperfections in handling and storage lead to a significant loss of sequences. The aim of our study is to help guide the design of future DNA data storage systems by providing a quantitative and qualitative understanding of the DNA data storage channel.

A common problem in machine learning is to rank a set of n items based on pairwise comparisons. Here ranking refers to partitioning the items into sets of pre-specified sizes according to their scores, which includes identification of the top-k items as the most prominent special case. The score of a given item is defined as the probability that it beats a randomly chosen other item. Finding an exact ranking typically requires a prohibitively large number of comparisons, but in practice, approximate rankings are often adequate. Accordingly, we study the problem of finding approximate rankings from pairwise comparisons. We analyze an active ranking algorithm that counts the number of comparisons won, and decides whether to stop or which pair of items to compare next, based on confidence intervals computed from the data collected in previous steps. We show that this algorithm succeeds in recovering approximate rankings using a number of comparisons that is close to optimal up to logarithmic factors. We also present numerical results, showing that in practice, approximation can drastically reduce the number of comparisons required to estimate a ranking., Comment: AISTATS 2017

We demonstrate a compact and easy-to-build computational camera for single-shot 3D imaging. Our lensless system consists solely of a diffuser placed in front of a standard image sensor. Every point within the volumetric field-of-view projects a unique pseudorandom pattern of caustics on the sensor. By using a physical approximation and simple calibration scheme, we solve the large-scale inverse problem in a computationally efficient way. The caustic patterns enable compressed sensing, which exploits sparsity in the sample to solve for more 3D voxels than pixels on the 2D sensor. Our 3D voxel grid is chosen to match the experimentally measured two-point optical resolution across the field-of-view, resulting in 100 million voxels being reconstructed from a single 1.3 megapixel image. However, the effective resolution varies significantly with scene content. Because this effect is common to a wide range of computational cameras, we provide new theory for analyzing resolution in such systems., Comment: The first two authors contributed equally

We consider the online one-class collaborative filtering (CF) problem that consists of recommending items to users over time in an online fashion based on positive ratings only. This problem arises when users respond only occasionally to a recommendation with a positive rating, and never with a negative one. We study the impact of the probability of a user responding to a recommendation, p_f, on the sample complexity, i.e., the number of ratings required to make `good' recommendations, and ask whether receiving positive and negative ratings, instead of positive ratings only, improves the sample complexity. Both questions arise in the design of recommender systems. We introduce a simple probabilistic user model, and analyze the performance of an online user-based CF algorithm. We prove that after an initial cold start phase, where recommendations are invested in exploring the user's preferences, this algorithm makes---up to a fraction of the recommendations required for updating the user's preferences---perfect recommendations. The number of ratings required for the cold start phase is nearly proportional to 1/p_f, and that for updating the user's preferences is essentially independent of p_f. As a consequence we find that, receiving positive and negative ratings instead of only positive ones improves the number of ratings required for initial exploration by a factor of 1/p_f, which can be significant., Comment: ICML 2017

Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current technological constraints on DNA synthesis and sequencing. Our model captures two key distinctive aspects of DNA storage systems: (1) the data is written onto many short DNA molecules that are stored in an unordered way and (2) the data is read by randomly sampling from this DNA pool. Under this model, we characterize the storage capacity, and show that a simple index-based coding scheme is optimal., Comment: To appear in Proc. of IEEE International Symposium on Information Theory (ISIT). Slightly extended version containing the proofs

Line spectral estimation is the problem of recovering the frequencies and amplitudes of a mixture of a few sinusoids from equispaced samples. However, in a variety of signal processing problems arising in imaging, radar, and localization we do not have access directly to such equispaced samples. Rather we only observe a severely undersampled version of these observations through linear measurements. This paper is about such generalized line spectral estimation problems. We reformulate these problems as sparse signal recovery problems over a continuously indexed dictionary which can be solved via a convex program. We prove that the frequencies and amplitudes of the components of the mixture can be recovered perfectly from a near-minimal number of observations via this convex program. This result holds provided the frequencies are sufficiently separated, and the linear measurements obey natural conditions that are satisfied in a variety of applications.

We consider sequential or active ranking of a set of n items based on noisy pairwise comparisons. Items are ranked according to the probability that a given item beats a randomly chosen item, and ranking refers to partitioning the items into sets of pre-specified sizes according to their scores. This notion of ranking includes as special cases the identification of the top-k items and the total ordering of the items. We first analyze a sequential ranking algorithm that counts the number of comparisons won, and uses these counts to decide whether to stop, or to compare another pair of items, chosen based on confidence intervals specified by the data collected up to that point. We prove that this algorithm succeeds in recovering the ranking using a number of comparisons that is optimal up to logarithmic factors. This guarantee does not require any structural properties of the underlying pairwise probability matrix, unlike a significant body of past work on pairwise ranking based on parametric models such as the Thurstone or Bradley-Terry-Luce models. It has been a long-standing open question as to whether or not imposing these parametric assumptions allows for improved ranking algorithms. For stochastic comparison models, in which the pairwise probabilities are bounded away from zero, our second contribution is to resolve this issue by proving a lower bound for parametric models. This shows, perhaps surprisingly, that these popular parametric modeling choices offer at most logarithmic gains for stochastic comparisons., Comment: improved log factor in main result; added discussion on comparison probabilities close to zero; added numerical results

A multiple input, multiple output (MIMO) radar emits probings signals with multiple transmit antennas and records the reflections from targets with multiple receive antennas. Estimating the relative angles, delays, and Doppler shifts from the received signals allows to determine the locations and velocities of the targets. Standard approaches to MIMO radar based on digital matched filtering or compressed sensing only resolve the angle-delay-Doppler triplets on a $(1/(N_T N_R), 1/B,1/T)$ grid, where $N_T$ and $N_R$ are the number of transmit and receive antennas, $B$ is the bandwidth of the probing signals, and $T$ is the length of the time interval over which the reflections are observed. In this work, we show that the \emph{continuous} angle-delay-Doppler triplets and the corresponding attenuation factors can be recovered perfectly by solving a convex optimization problem. This result holds provided that the angle-delay-Doppler triplets are separated either by $10/(N_T N_R-1)$ in angle, $10.01/B$ in delay, or $10.01/T$ in Doppler direction. Furthermore, this result is optimal (up to log factors) in the number of angle-delay-Doppler triplets that can be recovered., Comment: To appear in Proc. of IEEE International Symposium on Information Theory (ISIT), Barcelona, Spain, July 2016. Slightly extended version

We consider the problem of generating interpretable recommendations by identifying overlapping co-clusters of clients and products, based only on positive or implicit feedback. Our approach is applicable on very large datasets because it exhibits almost linear complexity in the input examples and the number of co-clusters. We show, both on real industrial data and on publicly available datasets, that the recommendation accuracy of our algorithm is competitive to that of state-of-art matrix factorization techniques. In addition, our technique has the advantage of offering recommendations that are textually and visually interpretable. Finally, we examine how to implement our technique efficiently on Graphical Processing Units (GPUs)., Comment: In IEEE International Conference on Data Engineering (ICDE) 2017

Subspace clustering refers to the problem of clustering unlabeled high-dimensional data points into a union of low-dimensional linear subspaces, whose number, orientations, and dimensions are all unknown. In practice one may have access to dimensionality-reduced observations of the data only, resulting, e.g., from undersampling due to complexity and speed constraints on the acquisition device or mechanism. More pertinently, even if the high-dimensional data set is available it is often desirable to first project the data points into a lower-dimensional space and to perform clustering there; this reduces storage requirements and computational cost. The purpose of this paper is to quantify the impact of dimensionality reduction through random projection on the performance of three subspace clustering algorithms, all of which are based on principles from sparse signal recovery. Specifically, we analyze the thresholding based subspace clustering (TSC) algorithm, the sparse subspace clustering (SSC) algorithm, and an orthogonal matching pursuit variant thereof (SSC-OMP). We find, for all three algorithms, that dimensionality reduction down to the order of the subspace dimensions is possible without incurring significant performance degradation. Moreover, these results are order-wise optimal in the sense that reducing the dimensionality further leads to a fundamentally ill-posed clustering problem. Our findings carry over to the noisy case as illustrated through analytical results for TSC and simulations for SSC and SSC-OMP. Extensive experiments on synthetic and real data complement our theoretical findings., Comment: new results for the noisy case, additional simulation work, additional discussions in the main body

In this paper we study the identification of a time-varying linear system from its response to a known input signal. More specifically, we consider systems whose response to the input signal is given by a weighted superposition of delayed and Doppler shifted versions of the input. This problem arises in a multitude of applications such as wireless communications and radar imaging. Due to practical constraints, the input signal has finite bandwidth B, and the received signal is observed over a finite time interval of length T only. This gives rise to a delay and Doppler resolution of 1/B and 1/T. We show that this resolution limit can be overcome, i.e., we can exactly recover the continuous delay-Doppler pairs and the corresponding attenuation factors, by solving a convex optimization problem. This result holds provided that the distance between the delay-Doppler pairs is at least 2.37/B in time or 2.37/T in frequency. Furthermore, this result allows the total number of delay-Doppler pairs to be linear up to a log-factor in BT, the dimensionality of the response of the system, and thereby the limit for identifiability. Stated differently, we show that we can estimate the time-frequency components of a signal that is S-sparse in the continuous dictionary of time-frequency shifts of a random window function, from a number of measurements, that is linear up to a log-factor in S., Comment: Revised version; fixed an error in the proof of Lemma 6

Subspace clustering refers to the problem of clustering unlabeled high-dimensional data points into a union of low-dimensional linear subspaces, assumed unknown. In practice one may have access to dimensionality-reduced observations of the data only, resulting, e.g., from "undersampling" due to complexity and speed constraints on the acquisition device. More pertinently, even if one has access to the high-dimensional data set it is often desirable to first project the data points into a lower-dimensional space and to perform the clustering task there; this reduces storage requirements and computational cost. The purpose of this paper is to quantify the impact of dimensionality-reduction through random projection on the performance of the sparse subspace clustering (SSC) and the thresholding based subspace clustering (TSC) algorithms. We find that for both algorithms dimensionality reduction down to the order of the subspace dimensions is possible without incurring significant performance degradation. The mathematical engine behind our theorems is a result quantifying how the affinities between subspaces change under random dimensionality reducing projections., Comment: ISIT 2014

Subspace clustering refers to the problem of clustering high-dimensional data points into a union of low-dimensional linear subspaces, where the number of subspaces, their dimensions and orientations are all unknown. In this paper, we propose a variation of the recently introduced thresholding-based subspace clustering (TSC) algorithm, which applies spectral clustering to an adjacency matrix constructed from the nearest neighbors of each data point with respect to the spherical distance measure. The new element resides in an individual and data-driven choice of the number of nearest neighbors. Previous performance results for TSC, as well as for other subspace clustering algorithms based on spectral clustering, come in terms of an intermediate performance measure, which does not address the clustering error directly. Our main analytical contribution is a performance analysis of the modified TSC algorithm (as well as the original TSC algorithm) in terms of the clustering error directly., Comment: ICASSP 2014

We propose a method for inferring the conditional indepen- dence graph (CIG) of a high-dimensional discrete-time Gaus- sian vector random process from finite-length observations. Our approach does not rely on a parametric model (such as, e.g., an autoregressive model) for the vector random process; rather, it only assumes certain spectral smoothness proper- ties. The proposed inference scheme is compressive in that it works for sample sizes that are (much) smaller than the number of scalar process components. We provide analytical conditions for our method to correctly identify the CIG with high probability., Comment: to appear in Proc. IEEE ICASSP 2014

The problem of clustering noisy and incompletely observed high-dimensional data points into a union of low-dimensional subspaces and a set of outliers is considered. The number of subspaces, their dimensions, and their orientations are assumed unknown. We propose a simple low-complexity subspace clustering algorithm, which applies spectral clustering to an adjacency matrix obtained by thresholding the correlations between data points. In other words, the adjacency matrix is constructed from the nearest neighbors of each data point in spherical distance. A statistical performance analysis shows that the algorithm exhibits robustness to additive noise and succeeds even when the subspaces intersect. Specifically, our results reveal an explicit tradeoff between the affinity of the subspaces and the tolerable noise level. We furthermore prove that the algorithm succeeds even when the data points are incompletely observed with the number of missing entries allowed to be (up to a log-factor) linear in the ambient dimension. We also propose a simple scheme that provably detects outliers, and we present numerical results on real and synthetic data., Comment: final version, to appear in the IEEE Transactions on Information Theory

We consider the problem of clustering noisy high-dimensional data points into a union of low-dimensional subspaces and a set of outliers. The number of subspaces, their dimensions, and their orientations are unknown. A probabilistic performance analysis of the thresholding-based subspace clustering (TSC) algorithm introduced recently in [1] shows that TSC succeeds in the noisy case, even when the subspaces intersect. Our results reveal an explicit tradeoff between the allowed noise level and the affinity of the subspaces. We furthermore find that the simple outlier detection scheme introduced in [1] provably succeeds in the noisy case., Comment: Presented at the IEEE Int. Symp. Inf. Theory (ISIT) 2013, Istanbul, Turkey. The version posted here corrects a minor error in the published version. Specifically, the exponent -c n_l in the success probability of Theorem 1 and in the corresponding proof outline has been corrected to -c(n_l-1)

We consider the problem of clustering a set of high-dimensional data points into sets of low-dimensional linear subspaces. The number of subspaces, their dimensions, and their orientations are unknown. We propose a simple and low-complexity clustering algorithm based on thresholding the correlations between the data points followed by spectral clustering. A probabilistic performance analysis shows that this algorithm succeeds even when the subspaces intersect, and when the dimensions of the subspaces scale (up to a log-factor) linearly in the ambient dimension. Moreover, we prove that the algorithm also succeeds for data points that are subject to erasures with the number of erasures scaling (up to a log-factor) linearly in the ambient dimension. Finally, we propose a simple scheme that provably detects outliers., Comment: ICASSP 2013

We consider a generalization of the multiple measurement vector (MMV) problem, where the measurement matrices are allowed to differ across measurements. This problem arises naturally when multiple measurements are taken over time, e.g., and the measurement modality (matrix) is time-varying. We derive probabilistic recovery guarantees showing that---under certain (mild) conditions on the measurement matrices---l2/l1-norm minimization and a variant of orthogonal matching pursuit fail with a probability that decays exponentially in the number of measurements. This allows us to conclude that, perhaps surprisingly, recovery performance does not suffer from the individual measurements being taken through different measurement matrices. What is more, recovery performance typically benefits (significantly) from diversity in the measurement matrices; we specify conditions under which such improvements are obtained. These results continue to hold when the measurements are subject to (bounded) noise., Comment: Allerton 2012

Nested canalizing Boolean (NCF) functions play an important role in biological motivated regulative networks and in signal processing, in particular describing stack filters. It has been conjectured that NCFs have a stabilizing effect on the network dynamics. It is well known that the average sensitivity plays a central role for the stability of (random) Boolean networks. Here we provide a tight upper bound on the average sensitivity for NCFs as a function of the number of relevant input variables. As conjectured in literature this bound is smaller than 4/3 This shows that a large number of functions appearing in biological networks belong to a class that has very low average sensitivity, which is even close to a tight lower bound., Comment: revised submission to PLOS ONE

We consider the problem of identifying a linear deterministic operator from its response to a given probing signal. For a large class of linear operators, we show that stable identifiability is possible if the total support area of the operator's spreading function satisfies D<=1/2. This result holds for an arbitrary (possibly fragmented) support region of the spreading function, does not impose limitations on the total extent of the support region, and, most importantly, does not require the support region to be known prior to identification. Furthermore, we prove that stable identifiability of almost all operators is possible if D<1. This result is surprising as it says that there is no penalty for not knowing the support region of the spreading function prior to identification. Algorithms that provably recover all operators with D<=1/2, and almost all operators with D<1 are presented., Comment: To appear in IEEE Trans. Inf. Theory

Consider a large Boolean network with a feed forward structure. Given a probability distribution on the inputs, can one find, possibly small, collections of input nodes that determine the states of most other nodes in the network? To answer this question, a notion that quantifies the determinative power of an input over the states of the nodes in the network is needed. We argue that the mutual information (MI) between a given subset of the inputs X = {X_1, ..., X_n} of some node i and its associated function f_i(X) quantifies the determinative power of this set of inputs over node i. We compare the determinative power of a set of inputs to the sensitivity to perturbations to these inputs, and find that, maybe surprisingly, an input that has large sensitivity to perturbations does not necessarily have large determinative power. However, for unate functions, which play an important role in genetic regulatory networks, we find a direct relation between MI and sensitivity to perturbations. As an application of our results, we analyze the large-scale regulatory network of Escherichia coli. We identify the most determinative nodes and show that a small subset of those reduces the overall uncertainty of the network state significantly. Furthermore, the network is found to be tolerant to perturbations of its inputs.

We consider the problem of identifying a linear deterministic operator from an input-output measurement. For the large class of continuous (and hence bounded) operators, under additional mild restrictions, we show that stable identifiability is possible if the total support area of the operator's spreading function satisfies D <= 1/2. This result holds for arbitrary (possibly fragmented) support regions of the spreading function, does not impose limitations on the total extent of the support region, and, most importantly, does not require the support region of the spreading function to be known prior to identification. Furthermore, we prove that asking for identifiability of only almost all operators, stable identifiability is possible if D <= 1. This result is surprising as it says that there is no penalty for not knowing the support region of the spreading function prior to identification., Comment: To be presented at IEEE Int. Symp. Inf. Theory 2011, St Petersburg, Russia