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We present a new approximation algorithm for the treewidth problem which finds an upper bound on the treewidth and constructs a corresponding tree decomposition as well. Our algorithm is a faster variation of Reed's classical algorithm. For…
We show how to distinguish circuits with $\log k$ negations (a.k.a $k$-monotone functions) from uniformly random functions in $\exp\left(\tilde{O}\left(n^{1/3}k^{2/3}\right)\right)$ time using random samples. The previous best…
The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
Pseudo-random number generators (PRNGs) are widely used in modern computing and are expected to exhibit excellent statistical performance and repeatability. This study evaluates and compares modern PRNGs used in high performance computing…
Given a sequence $s_1$ of $n$ letters drawn i.i.d. from an alphabet of size $\sigma$ and a mutated substring $s_2$ of length $m < n$, we often want to recover the mutation history that generated $s_2$ from $s_1$. Modern sequence aligners…
An $(n, k)$-Poisson Multinomial Distribution (PMD) is a random variable of the form $X = \sum_{i=1}^n X_i$, where the $X_i$'s are independent random vectors supported on the set of standard basis vectors in $\mathbb{R}^k.$ In this paper, we…
We present a new perfect simulation algorithm for stationary chains having unbounded variable length memory. This is the class of infnite memory chains for which the family of transition probabilities is represented by a probabilistic…
Background: We study the statistical properties of fragment coverage in genome sequencing experiments. In an extension of the classic Lander-Waterman model, we consider the effect of the length distribution of fragments. We also introduce…
We analyze a sublinear RAlSFA (Randomized Algorithm for Sparse Fourier Analysis) that finds a near-optimal B-term Sparse Representation R for a given discrete signal S of length N, in time and space poly(B,log(N)), following the approach…
Pseudo-random number generators (PRNGs) are essential in a wide range of applications, from cryptography to statistical simulations and optimization algorithms. While uniform randomness is crucial for security-critical areas like…
Parallel supercomputer-based Monte Carlo and stochastic simulations require pseudorandom number generators that can produce distinct pseudorandom streams across many independent processes. We propose a scalable class of parallel and…
We consider the model of random trees introduced by Devroye [SIAM J. Comput. 28 (1999) 409-432]. The model encompasses many important randomized algorithms and data structures. The pieces of data (items) are stored in a randomized fashion…
Langevin Dynamics, Monte Carlo, and all-atom Molecular Dynamics simulations in implicit solvent, widely used to access the microscopic transitions in biomolecules, require a reliable source of random numbers. Here we present the two main…
The authors prove that the probability of choosing a nonlinear filter of m-sequences with optimal properties, that is, maximum period and maximum linear complexity, tends assymptotically to 1 as the linear feedback shift register length…
Folded Reed-Solomon (FRS) codes are a well-studied family of codes, known for achieving list decoding capacity. In this work, we give improved deterministic and randomized algorithms for list decoding FRS codes of rate $R$ up to radius…
Guessing Random Additive Noise Decoding (GRAND) is a universal decoding algorithm that has been recently proposed as a practical way to perform maximum likelihood decoding. It generates a sequence of possible error patterns and applies them…
In this paper, we show that while almost all functions require exponential size branching programs to compute, for all functions $f$ there is a branching program computing a doubly exponential number of copies of $f$ which has linear size…
Following [OW16], we continue our analysis of: (1) "Quantum tomography", i.e., learning a quantum state, i.e., the quantum generalization of learning a discrete probability distribution; (2) The distribution of Young diagrams output by the…
In the classical linear degeneracy testing problem, we are given $n$ real numbers and a $k$-variate linear polynomial $F$, for some constant $k$, and have to determine whether there exist $k$ numbers $a_1,\ldots,a_k$ from the set such that…