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Metadata plays a critical role in indexing, documenting, and analyzing scientific literature, yet extracting it accurately and efficiently remains a challenging task. Traditional approaches often rely on rule-based or task-specific models,…

Modern deep neural networks achieved remarkable progress in medical image segmentation tasks. However, it has recently been observed that they tend to produce overconfident estimates, even in situations of high uncertainty, leading to…

Parameter Efficient Fine-Tuning (PEFT) methods have been extensively utilized in Large Language Models (LLMs) to improve the down-streaming tasks without the cost of fine-tuing the whole LLMs. Recent studies have shown how to effectively…

Adequate read filtering is critical when processing high-throughput data in marker-gene-based studies. Sequencing errors can cause the mis-clustering of otherwise similar reads, artificially increasing the number of retrieved Operational…

Next-generation sequencing (NGS) is a pivotal technique in genome sequencing due to its high throughput, rapid results, cost-effectiveness, and enhanced accuracy. Its significance extends across various domains, playing a crucial role in…

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…

Expectation Propagation (EP)-based Multiple-Input Multiple-Output (MIMO) detector is regarded as a state-of-the-art MIMO detector because of its exceptional performance. However, we find that the EP MIMO detector cannot guarantee to achieve…

The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…

Reading a qubit is a fundamental operation in quantum computing. It translates quantum information into classical information enabling subsequent classification to assign the qubit states `0' or `1'. Unfortunately, qubit readout is one of…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

Data selection for fine-tuning large language models (LLMs) aims to choose a high-quality subset from existing datasets, allowing the trained model to outperform baselines trained on the full dataset. However, the expanding body of research…

One of the key requirements for incorporating machine learning into the drug discovery process is complete reproducibility and traceability of the model building and evaluation process. With this in mind, we have developed an end-to-end…

Quantum error mitigation (QEM) has been proposed as a class of hardware-friendly error suppression techniques. While QEM has been primarily studied for mitigating errors in the estimation of expectation values of observables, recent works…

The advent of DNA and RNA sequencing has revolutionized the study of genomics and molecular biology. Next generation sequencing (NGS) technologies like Illumina, Ion Torrent, SOLiD sequencing etc. have brought about a quick and cheap way to…

DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…

Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…

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…

PySEMTools is a Python-based library for post-processing simulation data produced with high-order hexahedral elements in the context of the spectral element method in computational fluid dynamics. It aims to minimize intermediate steps…

Software engineering activities frequently involve edits to existing code. However, contemporary code language models (LMs) lack the ability to handle diverse types of code-edit requirements. In this work, we attempt to overcome this…

A large item catalogue is a major challenge for deploying modern sequential recommender models, since it makes the memory footprint of the model large and increases inference latency. One promising approach to address this is RecJPQ, which…