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Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…
The BDD package Adiar manipulates Binary Decision Diagrams (BDDs) in external memory. This enables handling big BDDs, but the performance suffers when dealing with moderate-sized BDDs. This is mostly due to initializing expensive external…
A matrix $M: A \times X \rightarrow \{-1,1\}$ corresponds to the following learning problem: An unknown element $x \in X$ is chosen uniformly at random. A learner tries to learn $x$ from a stream of samples, $(a_1, b_1), (a_2, b_2) \ldots$,…
We present a sublinear randomized algorithm to compute a sparse Fourier transform for nonequispaced data. Suppose a signal S is known to consist of N equispaced samples, of which only L<N are available. If the ratio p=L/N is not close to 1,…
The increasing complexity of transformer models in artificial intelligence expands their computational costs, memory usage, and energy consumption. Hardware acceleration tackles the ensuing challenges by designing processors and…
When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…
The Burrows-Wheeler Transform (BWT) is a fundamental component in many data structures for text indexing and compression, widely used in areas such as bioinformatics and information retrieval. The extended BWT (eBWT) generalizes the…
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…
Recent years has witnessed dramatic progress of neural machine translation (NMT), however, the method of manually guiding the translation procedure remains to be better explored. Previous works proposed to handle such problem through…
The transformer architecture has been widely applied to many machine learning tasks. A main bottleneck in the time to perform transformer computations is a task called attention computation. [Alman and Song, NeurIPS 2023] have shown that in…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
We engineer algorithms for sorting huge data sets on massively parallel machines. The algorithms are based on the multiway merging paradigm. We first outline an algorithm whose I/O requirement is close to a lower bound. Thus, in contrast to…
An external memory data structure is presented for maintaining a dynamic set of $N$ two-dimensional points under the insertion and deletion of points, and supporting 3-sided range reporting queries and top-$k$ queries, where top-$k$ queries…
The $B^{\epsilon}$-tree [Brodal and Fagerberg 2003] is a simple I/O-efficient external-memory-model data structure that supports updates orders of magnitude faster than B-tree with a query performance comparable to the B-tree: for any…
Memory-augmented neural networks consisting of a neural controller and an external memory have shown potentials in long-term sequential learning. Current RAM-like memory models maintain memory accessing every timesteps, thus they do not…
In this paper, we develop semi-external and external memory algorithms for graph partitioning and clustering problems. Graph partitioning and clustering are key tools for processing and analyzing large complex networks. We address both…
Recent research in the field of machine learning has increasingly focused on the memorization capacity of Transformers, but how efficient they are is not yet well understood. We demonstrate that Transformers can memorize labels with…
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…
Transformer models gain popularity because of their superior inference accuracy and inference throughput. However, the transformer is computation-intensive, causing a long inference time. The existing works on transformer inference…
Wheeler automata were introduced in 2017 as a tool to generalize existing indexing and compression techniques based on the Burrows-Wheeler transform. Intuitively, an automaton is said to be Wheeler if there exists a total order on its…