Related papers: biobambam: tools for read pair collation based alg…
Training with larger mini-batches improves the convergence rate and can yield superior performance. However, training with large mini-batches becomes prohibitive for Large Language Models (LLMs), due to the large GPU memory requirement. To…
Cross-modal alignment is crucial for multimodal representation fusion due to the inherent heterogeneity between modalities. While Transformer-based methods have shown promising results in modeling inter-modal relationships, their quadratic…
The emergence of Phase-Change Memory (PCM) provides opportunities for directly connecting persistent memory to main memory bus. While PCM achieves high read throughput and low standby power, the critical concerns are its poor write…
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…
Mamba and Vision Mamba (Vim) models have shown their potential as an alternative to methods based on Transformer architecture. This work introduces Fast Mamba for Vision (Famba-V), a cross-layer token fusion technique to enhance the…
In deep active learning, it is especially important to choose multiple examples to markup at each step to work efficiently, especially on large datasets. At the same time, existing solutions to this problem in the Bayesian setup, such as…
Traditional KV cache eviction strategies, which discard less critical KV-pairs based on attention scores, often degrade generation quality, causing context loss or hallucinations. Recent efforts shift toward KV merging, merging eviction…
Feature-level fusion shows promise in collaborative perception (CP) through balanced performance and communication bandwidth trade-off. However, its effectiveness critically relies on input feature quality. The acquisition of high-quality…
Tandem repeats in proteins identification, classification and curation is a complex process that requires manual processing from experts, processing power and time. There are recent and relevant advances applying machine learning for…
Merging two sorted arrays is a prominent building block for sorting and other functions. Its efficient parallelization requires balancing the load among compute cores, minimizing the extra work brought about by parallelization, and…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Scientific documents often contain a large number of acronyms. Disambiguation of these acronyms will help researchers better understand the meaning of vocabulary in the documents. In the past, thanks to large amounts of data from English…
In recent years microbiome studies have become increasingly prevalent and large-scale. Through high-throughput sequencing technologies and well-established analytical pipelines, relative abundance data of operational taxonomic units and…
We show that the wavefront algorithm can achieve higher pairwise read alignment throughput on a UPMEM PIM system than on a server-grade multi-threaded CPU system.
Automatic segmentation methods are important tools for quantitative analysis of Magnetic Resonance Images (MRI). Recently, patch-based label fusion approaches have demonstrated state-of-the-art segmentation accuracy. In this paper, we…
Adapted from biological sequence alignment, trace alignment is a process mining technique used to visualize and analyze workflow data. Any analysis done with this method, however, is affected by the alignment quality. The best existing…
Many practical applications of AI in medicine consist of semi-supervised discovery: The investigator aims to identify features of interest at a resolution more fine-grained than that of the available human labels. This is often the scenario…
In the last decade a number of algorithms and associated software have been developed to align next generation sequencing (NGS) reads with relevant reference genomes. The accuracy of these programs may vary significantly, especially when…
The explosion of short videos has dramatically reshaped the manners people socialize, yielding a new trend for daily sharing and access to the latest information. These rich video resources, on the one hand, benefited from the…
This paper presents a new multi-layered algorithm for motion planning under motion and sensing uncertainties for Linear Temporal Logic specifications. We propose a technique to guide a sampling-based search tree in the combined task and…