Related papers: biobambam: tools for read pair collation based alg…

Recovering texture information from the aliasing regions has always been a major challenge for Single Image Super Resolution (SISR) task. These regions are often submerged in noise so that we have to restore texture details while…

Duplicate marking is a critical preprocessing step in gene sequence analysis to flag redundant reads arising from polymerase chain reaction(PCR) amplification and sequencing artifacts. Although Picard MarkDuplicates is widely recognized as…

Vision-and-language multi-modal pretraining and fine-tuning have shown great success in visual question answering (VQA). Compared to general domain VQA, the performance of biomedical VQA suffers from limited data. In this paper, we propose…

For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…

Motivation: Seed location 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. State-of-the-art read…

This paper describes some of the recent work of project AMALGAM (automatic mapping among lexico-grammatical annotation models). We are investigating ways to map between the leading corpus annotation schemes in order to improve their…

Although data is abundant, data labeling is expensive. Semi-supervised learning methods combine a few labeled samples with a large corpus of unlabeled data to effectively train models. This paper introduces our proposed method LiDAM, a…

Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…

Recent advances in deep neural networks have been developed via architecture search for stronger representational power. In this work, we focus on the effect of attention in general deep neural networks. We propose a simple and effective…

Large data sets are increasingly common in cloud and virtualized environments. For example, transfers of multiple gigabytes are commonplace, as are replicated blocks of such sizes. There is a need for fast error-correction or data…

We propose a new approach to determine correspondences between image pairs in the wild under large changes in illumination, viewpoint, context, and material. While other approaches find correspondences between pairs of images by treating…

A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the…

Variant detection from high-throughput sequencing data is an essential step in identification of alleles involved in complex diseases and cancer. To deal with these massive data, elaborated sequence analysis pipelines are employed. A core…

With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…

A new variant of bit interleaved coded modulation (BICM) is proposed. In the new scheme, called Parallel BICM, L identical binary codes are used in parallel using a mapper, a newly proposed finite-length interleaver and a binary dither…

This study introduces bifurcated attention, a method designed to enhance language model inference in shared-context batch decoding scenarios. Our approach addresses the challenge of redundant memory IO costs, a critical factor contributing…

Motivation: With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…

This paper presents a novel beacon light coding protocol, which enables fast and accurate identification of the beacons in an image. The protocol is provably robust to a predefined set of detection and decoding errors, and does not require…

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data…

In-memory database query processing frequently involves substantial data transfers between the CPU and memory, leading to inefficiencies due to Von Neumann bottleneck. Processing-in-Memory (PIM) architectures offer a viable solution to…