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Despite the successes of large language models (LLMs), they exhibit significant drawbacks, particularly when processing long contexts. Their inference cost scales quadratically with respect to sequence length, making it expensive for…

We study allowing large language models (LLMs) to process arbitrarily long prompts through the lens of inference-time scaling. We propose Recursive Language Models (RLMs), a general inference paradigm that treats long prompts as part of an…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

Although masked language models are highly performant and widely adopted by NLP practitioners, they can not be easily used for autoregressive language modelling (next word prediction and sequence probability estimation). We present an…

In this paper, we present a compressed data structure for moving object trajectories in a road network, which are represented as sequences of road edges. Unlike existing compression methods for trajectories in a network, our method supports…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…

In this paper, we propose a novel approach to combine \emph{compact directed acyclic word graphs} (CDAWGs) and grammar-based compression. This leads us to an efficient self-index, called Linear-size CDAWGs (L-CDAWGs), which can be…

Neural information retrieval architectures based on transformers such as BERT are able to significantly improve system effectiveness over traditional sparse models such as BM25. Though highly effective, these neural approaches are very…

Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…

Large language models (LLMs) have brought a great breakthrough to the natural language processing (NLP) community, while leading the challenge of handling concurrent customer queries due to their high throughput demands. Data multiplexing…

We introduce Transformer Grammars (TGs), a novel class of Transformer language models that combine (i) the expressive power, scalability, and strong performance of Transformers and (ii) recursive syntactic compositions, which here are…

The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…

It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…

Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…

The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…

Large Language Models (LLMs) have exhibited exceptional performance across a broad range of tasks and domains. However, they still encounter difficulties in solving mathematical problems due to the rigorous and logical nature of…

We show how to modify the linear-time construction algorithm for suffix arrays based on induced sorting (Nong et al., DCC'09) such that it computes the array of longest common prefixes (LCP-array) as well. Practical tests show that this…

In this work, we propose Reinforced Functional Token Tuning (RFTT), a novel reinforced fine-tuning framework that empowers Large Language Models (LLMs) with self-play learn-to-reason capabilities. Unlike prior prompt-driven reasoning…

Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…