Related papers: KeBaB: $k$-mer based breaking for finding long MEM…

In a K-best detector for multiple-input-multiple-output(MIMO) systems, the value of K needs to be sufficiently large to achieve near-maximum-likelihood (ML) performance. By treating K as a variable that can be adjusted according to a…

Genome-Scale Metabolic Models (GEMs) describe the interactions between genes, proteins, and the biochemical reactions that underpin an organism's metabolism aiming to computationally simulate functions at the cellular level. While many…

Fine-tuning large language models (LLMs) with backpropagation\textemdash even for a subset of parameters such as LoRA\textemdash can be much more memory-consuming than inference and is often deemed impractical for resource-constrained…

Multi-arm bandit (MAB) algorithms have been used to learn optimal beams for millimeter wave communication systems. Here, the complexity of learning the optimal beam linearly scales with the number of beams, leading to high latency when…

Online machine learning (OML) algorithms do not need any training phase and can be deployed directly in an unknown environment. OML includes multi-armed bandit (MAB) algorithms that can identify the best arm among several arms by achieving…

The Mixture-of-Experts (MoE) architecture has become a predominant paradigm for scaling large language models (LLMs). Despite offering strong performance and computational efficiency, large MoE-based LLMs like DeepSeek-V3-0324 and…

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…

Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…

In generating large quantities of DNA data, high-throughput sequencing technologies require advanced bioinformatics infrastructures for efficient data analysis. k-mer counting, the process of quantifying the frequency of fixed-length k DNA…

One of the primary uses for transmission electron microscopy (TEM) is to measure diffraction pattern images in order to determine a crystal structure and orientation. In nanobeam electron diffraction (NBED) we scan a moderately converged…

Pipeline parallelism enables efficient training of Large Language Models (LLMs) on large-scale distributed accelerator clusters. Yet, pipeline bubbles during startup and tear-down reduce the utilization of accelerators. Although efficient…

DNA sequence classification is a fundamental task in computational biology with vast implications for applications such as disease prevention and drug design. Therefore, fast high-quality sequence classifiers are significantly important.…

Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped…

With the booming of Large Language Models (LLMs), prompt-learning has become a promising method mainly researched in various research areas. Recently, many attempts based on prompt-learning have been made to improve the performance of text…

Advances in gene sequencing have enabled in silico analyses of microbial genomes and have led to the revision of concepts of microbial taxonomy and evolution. We explore deficiencies in existing multiple sequence global alignment algorithms…

Bloom Filter is extensively deployed data structure in various applications and research domain since its inception. Bloom Filter is able to reduce the space consumption in an order of magnitude. Thus, Bloom Filter is used to keep…

Metacells are disjoint and homogeneous groups of single-cell profiles, representing discrete and highly granular cell states. Existing metacell algorithms tend to use only one modality to infer metacells, even though single-cell multi-omics…

Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…

Micro-Electro-Mechanical Systems (MEMS) comb drives are used for both as sensors and actuators. As a result, they have been considered to be very important in MEMS technology and has been under intense study for last few years. The…

We propose RoCoFT, a parameter-efficient fine-tuning method for large-scale language models (LMs) based on updating only a few rows and columns of the weight matrices in transformers. Through extensive experiments with medium-size LMs like…