相关论文: Fast and sensitive read mapping with approximate s…

Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…

Learning suitable Whole slide images (WSIs) representations for efficient retrieval systems is a non-trivial task. The WSI embeddings obtained from current methods are in Euclidean space not ideal for efficient WSI retrieval. Furthermore,…

Summary: Raw nanopore signals can be analyzed while they are being generated, a process known as real-time analysis. Real-time analysis of raw signals is essential to utilize the unique features that nanopore sequencing provides, enabling…

Explainable artificial intelligence (XAI) enhances AI system transparency by framing interpretability as an optimization problem. However, this approach often necessitates numerous iterations of computationally intensive operations,…

In this paper we present an algorithm for rapid Bayesian analysis that combines the benefits of nested sampling and artificial neural networks. The blind accelerated multimodal Bayesian inference (BAMBI) algorithm implements the MultiNest…

Research on nearest-neighbor methods tends to focus somewhat dichotomously either on the statistical or the computational aspects -- either on, say, Bayes consistency and rates of convergence or on techniques for speeding up the proximity…

The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…

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…

We introduce PaSa, an advanced Paper Search agent powered by large language models. PaSa can autonomously make a series of decisions, including invoking search tools, reading papers, and selecting relevant references, to ultimately obtain…

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

Feeder reconfiguration is a critical operational strategy in power distribution systems. However, existing optimization approaches typically rely on explicit mathematical formulations and analytical models, which are often infeasible in…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

Third-generation nanopore sequencers offer a feature called selective sequencing or 'Read Until' that allows genomic reads to be analyzed in real-time and abandoned halfway, if not belonging to a genomic region of 'interest'. This selective…

In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…

Mass Spectrometry Imaging (MSI), using traditional rectilinear scanning, takes hours to days for high spatial resolution acquisitions. Given that most pixels within a sample's field of view are often neither relevant to underlying…

This paper introduces ASCAI, a novel adaptive sampling methodology that can learn how to effectively compress Deep Neural Networks (DNNs) for accelerated inference on resource-constrained platforms. Modern DNN compression techniques…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

DNA sequence alignment is an important workload in computational genomics. Reference-guided DNA assembly involves aligning many read sequences against candidate locations in a long reference genome. To reduce the computational load of this…

Traditional soil sampling and analysis methods are labor-intensive, time-consuming, and limited in spatial resolution, making them unsuitable for large-scale precision agriculture. To address these limitations, we present a robotic solution…