Related papers: SAMBLASTER: fast duplicate marking and structural …
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Automatic parallelization remains a challenging problem in software engineering, particularly in identifying code regions where loops can be safely executed in parallel on modern multi-core architectures. Traditional static analysis…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…
In many modern LLM applications, such as retrieval augmented generation, prompts have become programs themselves. In these settings, prompt programs are repeatedly called with different user queries or data instances. A big practical…
As genome sequencing is finding utility in a wide variety of domains beyond the confines of traditional medical settings, its computational pipeline faces two significant challenges. First, the creation of up to 0.5 GB of data per minute…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
In this paper, we explore a principal way to enhance the quality of widely pre-existing coarse masks, enabling them to serve as reliable training data for segmentation models to reduce the annotation cost. In contrast to prior refinement…
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to…
Early detection and resolution of duplicate and conflicting requirements can significantly enhance project efficiency and overall software quality. Researchers have developed various computational predictors by leveraging Artificial…
Unstructured text has long been difficult to automatically analyze at scale. Large language models (LLMs) now offer a way forward by enabling {\em semantic data processing}, where familiar data processing operators (e.g., map, reduce,…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
Dataset distillation plays a crucial role in creating compact datasets with similar training performance compared with original large-scale ones. This is essential for addressing the challenges of data storage and training costs. Prevalent…
We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the…
The development of parallel-processing image-analysis codes is generally a challenging task that requires complicated choreography of interprocessor communications. If, however, the image-analysis algorithm is embarrassingly parallel, then…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Sharpness-aware minimization (SAM) has been shown to improve the generalization of neural networks. However, each SAM update requires \emph{sequentially} computing two gradients, effectively doubling the per-iteration cost compared to base…
Existing approaches typically rely on large-scale fine-tuning to adapt LLMs for information reranking tasks, which is computationally expensive. In this work, we demonstrate that modern LLMs can be effectively adapted using only minimal,…
A method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing is presented. The manuscript focuses on…
Disassembly is fundamental to binary analysis and rewriting. We present a novel disassembly technique that takes a stripped binary and produces reassembleable assembly code. The resulting assembly code has accurate symbolic information,…
We propose Scrambler, and e-graph-based MBA obfuscation tool using Equality Expansion to efficiently generate complex and diverse expressions with equivalence guaranteed by construction. Experiments show Scrambler improves existing tools in…