Related papers: On k-Mer-Based and Maximum Likelihood Estimation A…
Motivated by the established notion of storage codes, we consider sets of infinite sequences over a finite alphabet such that every $k$-tuple of consecutive entries is uniquely recoverable from its $l$-neighborhood in the sequence. We…
We propose a Bayesian expectation-maximization (EM) algorithm for reconstructing Markov-tree sparse signals via belief propagation. The measurements follow an underdetermined linear model where the regression-coefficient vector is the sum…
Many different metrics exist for evaluating parsing results, including Viterbi, Crossing Brackets Rate, Zero Crossing Brackets Rate, and several others. However, most parsing algorithms, including the Viterbi algorithm, attempt to optimize…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
We consider the phase retrieval problem, in which the observer wishes to recover a $n$-dimensional real or complex signal $\mathbf{X}^\star$ from the (possibly noisy) observation of $|\mathbf{\Phi} \mathbf{X}^\star|$, in which…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
We propose a method to reconstruct sparse signals degraded by a nonlinear distortion and acquired at a limited sampling rate. Our method formulates the reconstruction problem as a nonconvex minimization of the sum of a data fitting term and…
We consider the Top-$K$ selection problem, which aims to identify the largest $K$ elements in an array. Top-$K$ selection arises in many machine learning algorithms and often becomes a bottleneck on accelerators, which are optimized for…
Top-$k$ decoding is a widely used method for sampling from LLMs: at each token, only the largest $k$ next-token-probabilities are kept, and the next token is sampled after re-normalizing them to sum to unity. Top-$k$ and other sampling…
Reconstructing weighted networks from partial information is necessary in many important circumstances, e.g. for a correct estimation of systemic risk. It has been shown that, in order to achieve an accurate reconstruction, it is crucial to…
We demonstrate how we can practically incorporate multi-step future information into a decoder of maximum likelihood sequence models. We propose a "k-step look-ahead" module to consider the likelihood information of a rollout up to k steps.…
We propose a new and computationally efficient algorithm for maximizing the observed log-likelihood for a multivariate normal data matrix with missing values. We show that our procedure based on iteratively regressing the missing on the…
Existing tracking methods mainly focus on learning better target representation or developing more robust prediction models to improve tracking performance. While tracking performance has significantly improved, the target loss issue occurs…
Suppose we wish to recover a signal x in C^n from m intensity measurements of the form |<x,z_i>|^2, i = 1, 2,..., m; that is, from data in which phase information is missing. We prove that if the vectors z_i are sampled independently and…
When working with quantum states, analysis of the final quantum state generated through probabilistic measurements is essential. This analysis is typically conducted by constructing the density matrix from either partial or full tomography…
Most Relevant Explanation (MRE) is a method for finding multivariate explanations for given evidence in Bayesian networks [12]. This paper studies the theoretical properties of MRE and develops an algorithm for finding multiple top MRE…
With the rise of the Internet of Things, strategies for effectively processing big data are essential for discovering meaningul insights. The time series datasets produced by groups of interconnected devices contain valuable underlying…
Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains to be challenging. We articulate a statistical inference…
In this paper, we put forth a new joint sparse recovery algorithm called signal space matching pursuit (SSMP). The key idea of the proposed SSMP algorithm is to sequentially investigate the support of jointly sparse vectors to minimize the…