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Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major…
Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…
Understanding the strengths and weaknesses of machine learning (ML) algorithms is crucial for determine their scope of application. Here, we introduce the DIverse and GENerative ML Benchmark (DIGEN) - a collection of synthetic datasets for…
Ultrafast multidimensional spectroscopies are powerful tools that can access charge and energy flow in complex materials, shifting chemical kinetics, and even many-body interactions in correlated matter. However, current implementations…
An accurate method for enumerating pathogen indicators, such as Escherichia coli (E. coli), and Salmonella spp. is important for assessing the safety of compost samples. This study aimed to determine the occurrence of pathogen indicators in…
Multivariate time series (MTS) data, when sampled irregularly and asynchronously, often present extensive missing values. Conventional methodologies for MTS analysis tend to rely on temporal embeddings based on timestamps that necessitate…
Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has become a cornerstone technology in clinical microbiology, enabling rapid and accurate microbial identification. However, the development of…
The DNA sequencing is the process of identifying the exact order of nucleotides within a given DNA molecule. The new portable and relatively inexpensive DNA sequencers, such as Oxford Nanopore MinION, have the potential to move DNA…
Medical coding is essential for standardizing clinical data and communication but is often time-consuming and prone to errors. Traditional Natural Language Processing (NLP) methods struggle with automating coding due to the large label…
We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure…
The role of Artificial Intelligence (AI) is growing in every stage of drug development. Nevertheless, a major challenge in drug discovery AI remains: Drug pharmacokinetic (PK) and Drug-Target Interaction (DTI) datasets collected in…
Inference from interaction maps, such as centromere identification from genome-wide chromosome conformation capture techniques -- notably Hi-C -- can be formulated as a generic inverse problem: infer a set of parameters given a map…
Common Data Elements (CDEs) standardize data collection and sharing across studies, enhancing data interoperability and improving research reproducibility. However, implementing CDEs presents challenges due to the broad range and variety of…
Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…
Background: While the importance of gene-gene interactions in human diseases has been well recognized, identifying them has been a great challenge, especially through association studies with millions of genetic markers and thousands of…
The discovery of new multicomponent inorganic compounds can provide direct solutions to many scientific and engineering challenges, yet the vast size of the uncharted material space dwarfs current synthesis throughput. While the…
This paper presents a novel framework, MGNER, for Multi-Grained Named Entity Recognition where multiple entities or entity mentions in a sentence could be non-overlapping or totally nested. Different from traditional approaches regarding…
To detect large-variance code clones (i.e. clones with relatively more differences) in large-scale code repositories is difficult because most current tools can only detect almost identical or very similar clones. It will make promotion and…
Next-generation sequencing techniques have facilitated a large scale analysis of human genetic variation. Despite the advances in sequencing speeds, the computational discovery of structural variants is not yet standard. It is likely that…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…