Related papers: Meraculous2: fast accurate short-read assembly of …

Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…

This paper presents the concepts behind the BrainScales (BSS) accelerated analog neuromorphic computing architecture. It describes the second-generation BrainScales-2 (BSS-2) version and its most recent in-silico realization, the HICANN-X…

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…

Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…

Speculative decoding emerges as a pivotal technique for enhancing the inference speed of Large Language Models (LLMs). Despite recent research aiming to improve prediction efficiency, multi-sample speculative decoding has been overlooked…

This work presents a novel four-stage open-domain QA pipeline R2-D2 (Rank twice, reaD twice). The pipeline is composed of a retriever, passage reranker, extractive reader, generative reader and a mechanism that aggregates the final…

DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying computational problem is hard, and many technical factors and limitations…

Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…

To compute robust 2D assembly plans, we present an approach that combines geometric planning with a deep neural network. We train the network using the Box2D physics simulator with added stochastic noise to yield robustness scores--the…

Fully-supervised polyp segmentation has accomplished significant triumphs over the years in advancing the early diagnosis of colorectal cancer. However, label-efficient solutions from weak supervision like scribbles are rarely explored yet…

The growing gap between the increasing complexity of large language models (LLMs) and the limited computational budgets of edge devices poses a key challenge for efficient on-device inference, despite gradual improvements in hardware…

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…

In this paper we introduce RADULS2, the fastest parallel sorter based on radix algorithm. It is optimized to process huge amounts of data making use of modern multicore CPUs. The main novelties include: extremely optimized algorithm for…

High backgrounds and detector ageing impact the track finding in the Belle II central drift chamber, reducing both track purity and track efficiency in events. This necessitates the development of new track finding algorithms to mitigate…

Two-dimensional (2D) heterojunctions display a remarkable potential for application in high performance, low power electro-optical systems. p-n junctions based on vertically stacked heterostructures have shown very promising performance as…

As deep learning models are increasingly deployed on mobile devices, modern mobile devices incorporate deep learning-specific accelerators to handle the growing computational demands, thus increasing their hardware heterogeneity. However,…

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…

Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…

Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and…

Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpora of malicious binaries, obtaining high-quality corpora of…