Related papers: XORRO: Rapid Paired-End Read Overlapper
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
With the rapid advancements of deep learning in recent years, hardware accelerators are continuously deployed in more and more safety-critical applications such as autonomous driving and robotics. While the accelerators are usually…
The growing demand for real-time data processing in applications such as neural networks and embedded control systems has spurred the search for faster, more efficient alternatives to traditional electronic systems. In response, we…
Computation of a signal's estimated covariance matrix is an important building block in signal processing, e.g., for spectral estimation. Each matrix element is a sum of products of elements in the input matrix taken over a sliding window.…
Recent advances in reasoning models have demonstrated significant improvements in accuracy by employing detailed and comprehensive reasoning processes. However, generating these lengthy reasoning sequences is computationally expensive and…
Existing research on instruction following largely focuses on tasks with simple instructions and short responses. In this work, we explore multi-constraint instruction following for generating long-form text. We create Suri, a dataset with…
In the last decade, an impressive increase in software adaptions has led to a surge in log data production, making manual log analysis impractical and establishing the necessity for automated methods. Conversely, most automated analysis…
Motivation: Illumina Sequencing data can provide high coverage of a genome by relatively short (100 bp150 bp) reads at a low cost. Our goal is to produce trimmed and error-corrected reads to improve genome assemblies. Our error correction…
The proliferation of high-throughput sequencing machines ensures rapid generation of up to billions of short nucleotide fragments in a short period of time. This massive amount of sequence data can quickly overwhelm today's storage and…
Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…
This paper presents a novel approach to network coding for distribution of large files. Instead of the usual approach of splitting packets into disjoint classes (also known as generations) we propose the use of overlapping classes. The…
Speech processing systems currently do not support the vast majority of languages, in part due to the lack of data in low-resource languages. Cross-lingual transfer offers a compelling way to help bridge this digital divide by incorporating…
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…
Arikan has shown that systematic polar codes (SPC) outperform nonsystematic polar codes (NSPC). However, the performance gain comes at the price of elevated encoding complexity, i.e., compared to NSPC, the available encoding methods for SPC…
Quad-level cell (QLC) flash offers significant benefits in cost and capacity, but its limited reliability leads to frequent read retries, which severely degrade read performance. A common strategy in high-density flash storage is to program…
Parameter-efficient fine-tuning enables fast personalization of text-to-image diffusion models, but composing multiple custom concepts remains challenging due to representation interference. Existing modular methods either rely on expensive…
Read-optimized columnar databases use differential updates to handle writes by maintaining a separate write-optimized delta partition which is periodically merged with the read-optimized and compressed main partition. This merge process…
To obtain a better understanding of the trade-offs between various objectives, Bi-Objective Integer Programming (BOIP) algorithms calculate the set of all non-dominated vectors and present these as the solution to a BOIP problem.…
VLM-based OCR models have become the de facto choice for document parsing, as they can accurately extract page-level elements (e.g., paragraphs within individual pages) together with their bounding boxes and textual content. However,…
Computer Emergency Response Teams (CERTs) face increasing challenges processing the growing volume of security-related information. Daily manual analysis of threat reports, security advisories, and vulnerability announcements leads to…