Related papers: BGT: efficient and flexible genotype query across …
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
Personalized medicine is expected to maximize the intended drug effects and minimize side effects by treating patients based on their genetic profiles. Thus, it is important to generate drugs based on the genetic profiles of diseases,…
The Burrows-Wheeler transform (BWT) is integral to the FM-index, which is used extensively in text compression, indexing, pattern search, and bioinformatic problems as de novo assembly and read alignment. Thus, efficient construction of the…
Graph Transformers (GTs) have recently demonstrated remarkable performance across diverse domains. By leveraging attention mechanisms, GTs are capable of modeling long-range dependencies and complex structural relationships beyond local…
Graph neural networks (GNNs) have extended the success of deep neural networks (DNNs) to non-Euclidean graph data, achieving ground-breaking performance on various tasks such as node classification and graph property prediction.…
Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…
We introduce the Byte Latent Transformer (BLT), a new byte-level LLM architecture that, for the first time, matches tokenization-based LLM performance at scale with significant improvements in inference efficiency and robustness. BLT…
The Bidirectional Encoder Representations from Transformers (BERT) model has been radically improving the performance of many Natural Language Processing (NLP) tasks such as Text Classification and Named Entity Recognition (NER)…
In recent years, the focus of bioinformatics research has moved from individual sequences to collections of sequences. Given the fundamental role of the Burrows-Wheeler Transform (BWT) in string processing, a number of dedicated tools have…
We propose an efficient batching strategy for variable-length decoding on GPU architectures. During decoding, when candidates terminate or are pruned according to heuristics, our streaming approach periodically "refills" the batch before…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
Graph-based computations are crucial in a wide range of applications, where graphs can scale to trillions of edges. To enable efficient training on such large graphs, mini-batch subgraph sampling is commonly used, which allows training…
Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transfer, and analysis. FASTQ, the standard format for over two decades, stores one byte per…
Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…
Graph neural networks (GNNs) have delivered remarkable results in various fields. However, the rapid increase in the scale of graph data has introduced significant performance bottlenecks for GNN inference. Both computational complexity and…
Over the past years, substantial numbers of microbial species' genomes have been deposited outside of conventional INSDC databases. The GlobDB aggregates 14 independent genomic catalogues to provide a comprehensive database of…
High-throughput sequencing technologies have led to explosive growth of genomic databases; one of which will soon reach hundreds of terabytes. For many applications we want to build and store indexes of these databases but constructing such…
Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic…
Table understanding (TU) has achieved promising advancements, but it faces the challenges of the scarcity of manually labeled tables and the presence of complex table structures.To address these challenges, we propose HGT, a framework with…
Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…