Related papers: MONI can find k-MEMs
We propose a novel method to sparsify attention in the Transformer model by learning to select the most-informative token representations during the training process, thus focusing on the task-specific parts of an input. A reduction of…
Suppose we have n algorithms, quantum or classical, each computing some bit-value with bounded error probability. We describe a quantum algorithm that uses O(sqrt{n}) repetitions of the base algorithms and with high probability finds the…
We present an optimal data structure for submatrix maximum queries in n x n Monge matrices. Our result is a two-way reduction showing that the problem is equivalent to the classical predecessor problem in a universe of polynomial size. This…
Motivation: Building the histogram of occurrences of every $k$-symbol long substring of nucleotide data is a standard step in many bioinformatics applications, known under the name of $k$-mer counting. Its applications include developing de…
Given a pattern $p = s_1x_1s_2x_2\cdots s_{r-1}x_{r-1}s_r$ such that $x_1,x_2,\ldots,x_{r-1}\in\{x,\overset{{}_{\leftarrow}}{x}\}$, where $x$ is a variable and $\overset{{}_{\leftarrow}}{x}$ its reversal, and $s_1,s_2,\ldots,s_r$ are…
The number of n-gram features grows exponentially in n, making it computationally demanding to compute the most frequent n-grams even for n as small as 3. Motivated by our production machine learning system built on n-gram features, we ask:…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
In online learning, a decision maker repeatedly selects one of a set of actions, with the goal of minimizing the overall loss incurred. Following the recent line of research on algorithms endowed with additional predictive features, we…
We prove that for any real-valued matrix $X \in \R^{m \times n}$, and positive integers $r \ge k$, there is a subset of $r$ columns of $X$ such that projecting $X$ onto their span gives a $\sqrt{\frac{r+1}{r-k+1}}$-approximation to best…
We assume the permutation $\pi$ is given by an $n$-element array in which the $i$-th element denotes the value $\pi(i)$. Constructing its inverse in-place (i.e. using $O(\log{n})$ bits of additional memory) can be achieved in linear time…
Consider the following generalization of the classic binary search problem: a searcher is required to find a hidden vertex $x$ in a tree $T$. To do so, they iteratively perform queries to an oracle, each about a chosen vertex $v$. After…
Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…
We show how to represent sets in a linear space data structure such that expressions involving unions and intersections of sets can be computed in a worst-case efficient way. This problem has applications in e.g. information retrieval and…
The k-means method is one of the most widely used clustering algorithms, drawing its popularity from its speed in practice. Recently, however, it was shown to have exponential worst-case running time. In order to close the gap between…
Repeat finding in strings has important applications in subfields such as computational biology. Surprisingly, all prior work on repeat finding did not consider the constraint on the locality of repeats. In this paper, we propose and study…
Referring multi-object tracking (RMOT) is an emerging cross-modal task that aims to locate an arbitrary number of target objects and maintain their identities referred by a language expression in a video. This intricate task involves the…
Motion correction (MoCo) in radial MRI is a particularly challenging problem due to the unpredictability of subject movement. Current state-of-the-art (SOTA) MoCo algorithms often rely on extensive high-quality MR images to pre-train neural…
State-of-the-art speech-to-text models typically employ Transformer-based encoders that model token dependencies via self-attention mechanisms. However, the quadratic complexity of self-attention in both memory and computation imposes…
The k-means algorithm is a well-known method for partitioning n points that lie in the d-dimensional space into k clusters. Its main features are simplicity and speed in practice. Theoretically, however, the best known upper bound on its…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…