Related papers: String Sampling with Bidirectional String Anchors
Domain shifts are ubiquitous in machine learning, and can substantially degrade a model's performance when deployed to real-world data. To address this, distribution alignment methods aim to learn feature representations which are invariant…
While a broad range of techniques have been proposed to tackle distribution shift, the simple baseline of training on an $\textit{undersampled}$ balanced dataset often achieves close to state-of-the-art-accuracy across several popular…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
Data selection is essential for training deep learning models. An effective data sampler assigns proper sampling probability for training data and helps the model converge to a good local minimum with high performance. Previous studies in…
We present a method for non-smooth convex minimization which is based on subgradient directions and string-averaging techniques. In this approach, the set of available data is split into sequences (strings) and a given iterate is processed…
We introduce Tiered Sampling, a novel technique for approximate counting sparse motifs in massive graphs whose edges are observed in a stream. Our technique requires only a single pass on the data and uses a memory of fixed size $M$, which…
It is a common contention that it is an ``impossible mission'' to exactly determine the minimum sample size for the estimation of a binomial parameter with prescribed margin of error and confidence level. In this paper, we investigate such…
The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
There has been a recent surge of interest in nonparametric bandit algorithms based on subsampling. One drawback however of these approaches is the additional complexity required by random subsampling and the storage of the full history of…
The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…
In bioinformatics, minimizers have become an inescapable method for handling $k$-mers (words of fixed size $k$) extracted from DNA or RNA sequencing, whether for sampling, storage, querying or partitioning. According to some fixed order on…
The problem of determining the correct order of fluctuation of the optimal alignment score of two random strings of length $n$ has been open for several decades. It is known that the biased expected effect of a random letter-change on the…
Constrained decoding enables Language Models (LMs) to produce samples that provably satisfy hard constraints. However, existing constrained-decoding approaches often distort the underlying model distribution, a limitation that is especially…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
Nested sampling is an iterative integration procedure that shrinks the prior volume towards higher likelihoods by removing a "live" point at a time. A replacement point is drawn uniformly from the prior above an ever-increasing likelihood…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Consistent sampling is a technique for specifying, in small space, a subset $S$ of a potentially large universe $U$ such that the elements in $S$ satisfy a suitably chosen sampling condition. Given a subset $\mathcal{I}\subseteq U$ it…
Generalized sampling consists in the recovery of a function $f$, from the samples of the responses of a collection of linear shift-invariant systems to the input $f$. The reconstructed function is typically a member of a finitely generated…