Related papers: XORRO: Rapid Paired-End Read Overlapper
Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
Many recent algorithms for approximate model counting are based on a reduction to combinatorial searches over random subsets of the space defined by parity or XOR constraints. Long parity constraints (involving many variables) provide…
Large-scale, weakly-supervised speech recognition models, such as Whisper, have demonstrated impressive results on speech recognition across domains and languages. However, their application to long audio transcription via buffered or…
Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…
Enhancing the efficiency of iterative computation on graphs has garnered considerable attention in both industry and academia. Nonetheless, the majority of efforts focus on expediting iterative computation by minimizing the running time per…
Retrieval-Augmented Generation (RAG) has revolutionized natural language processing by dynamically integrating external knowledge into Large Language Models (LLMs), addressing their limitation of static training datasets. Recent…
In this paper, we propose a novel method based on character sequence-to-sequence models to correct documents already processed with Optical Character Recognition (OCR) systems. The main contribution of this paper is a set of strategies to…
Group Relative Policy Optimization (GRPO) enhances policy learning by computing gradients from relative comparisons among candidate outputs that share a common input prefix. Despite its effectiveness, GRPO introduces substantial…
We describe a new parallel implementation, mplrs, of the vertex enumeration code lrs that uses the MPI parallel environment and can be run on a network of computers. The implementation makes use of a C wrapper that essentially uses the…
Maintaining a dynamic $k$-core decomposition is an important problem that identifies dense subgraphs in dynamically changing graphs. Recent work by Liu et al. [SPAA 2022] presents a parallel batch-dynamic algorithm for maintaining an…
Accurate and robust disassembly of stripped binaries is challenging. The root of the difficulty is that high-level structures, such as instruction and function boundaries, are absent in stripped binaries and must be recovered based on…
Sequential computation is well understood but does not scale well with current technology. Within the next decade, systems will contain large numbers of processors with potentially thousands of processors per chip. Despite this, many…
Efficient parallelization of Large Language Models (LLMs) with long sequences is essential but challenging due to their significant computational and memory demands, particularly stemming from communication bottlenecks in attention…
Lossy compression is one of the most efficient solutions to reduce storage overhead and improve I/O performance for HPC applications. However, existing parallel I/O libraries cannot fully utilize lossy compression to accelerate parallel…
As high-throughput sequencers become standard equipment outside of sequencing centers, there is an increasing need for efficient methods for pre-processing and primary analysis. While a vast literature proposes methods for HTS data…
Instantaneous Noise-Based Logic (INBL) presents a classical noise-based computing framework as an alternative to quantum computation, though some logic gates remain unimplemented for achieving universality over superpositions. INBL encodes…
Coding over subsets (known as generations) rather than over all content blocks in P2P distribution networks and other applications is necessary for a number of practical reasons such as computational complexity. A penalty for coding only…
To reduce computational complexity and delay in randomized network coded content distribution, and for some other practical reasons, coding is not performed simultaneously over all content blocks, but over much smaller, possibly overlapping…
In runtime verification, pattern matching, which searches for occurrences of a specific pattern within a word, provides more information than a simple violation detection of the monitored property, by locating concrete evidence of the…
We present a fast general-purpose algorithm for high-throughput clustering of data "with a two dimensional organization". The algorithm is designed to be implemented with FPGAs or custom electronics. The key feature is a processing time…