Related papers: External memory BWT and LCP computation for sequen…

We propose the design and an implementation of a bulk-parallel external memory priority queue to take advantage of both shared-memory parallelism and high external memory transfer speeds to parallel disks. To achieve higher performance by…

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…

In the reordering buffer problem (RBP), a server is asked to process a sequence of requests lying in a metric space. To process a request the server must move to the corresponding point in the metric. The requests can be processed slightly…

We study the problem of optimizing Large Language Model (LLM) inference scheduling to minimize total latency. LLM inference is an online and multi-task service process and also heavily energy consuming by which a pre-trained LLM processes…

Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…

Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…

The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Large language models (LLMs) increasingly play an important role in a wide range of information processing and management tasks in industry. Many of these tasks are performed in large batches or even offline, and the performance indicator…

Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…

In this work, we define the generalized wake-up problem, $GWU(s)$, for a shared memory asynchronous system with $n$ processes. Informally, the problem, which is parametrized by an increasing sequence $s = s_1,\ldots,s_p$, asks that at least…

We present an algorithm for building the extended BWT (eBWT) of a string collection from its grammar-compressed representation. Our technique exploits the string repetitions captured by the grammar to boost the computation of the eBWT.…

Memory-augmented LLM agents offer an appealing shortcut to continual learning: rather than updating model parameters, they accumulate experience in external memory, seemingly sidestepping the stability-plasticity dilemma of parametric…

Major challenges in LLMs inference remain frequent memory bandwidth bottlenecks, computational redundancy, and inefficiencies in long-sequence processing. To address these issues, we propose LLM-CoOpt, a comprehensive algorithmhardware…

We consider the problem of neural association for a network of non-binary neurons. Here, the task is to first memorize a set of patterns using a network of neurons whose states assume values from a finite number of integer levels. Later,…

A practical large language model (LLM) service may involve a long system prompt, which specifies the instructions, examples, and knowledge documents of the task and is reused across requests. However, the long system prompt causes…

The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…

Memorization presents a challenge for several constrained Natural Language Generation (NLG) tasks such as Neural Machine Translation (NMT), wherein the proclivity of neural models to memorize noisy and atypical samples reacts adversely with…

Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…