相关论文: PhaVIP: Phage VIrion Protein classification based …
\textbf{Introduction:} Accurate prediction of Phage Virion Proteins (PVP) is essential for genomic studies due to their crucial role as structural elements in bacteriophages. Computational tools, particularly machine learning, have emerged…
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection, replication, and evolution. Although a large number of new…
Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently,…
Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers…
Pangenome variation graphs (PVGs) allow for the representation of genetic diversity in a more nuanced way than traditional reference-based approaches. Here we focus on how PVGs are a powerful tool for studying genetic variation in viruses,…
A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…
Bayesian inference has become an important tool to solve inverse problems and to quantify uncertainties in their solutions. Variational inference is a method that provides probabilistic, Bayesian solutions efficiently by using optimization.…
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to…
Transfer learning has become an essential tool in modern computer vision, allowing practitioners to leverage backbones, pretrained on large datasets, to train successful models from limited annotated data. Choosing the right backbone is…
The escalating frequency and scale of recent malware attacks underscore the urgent need for swift and precise malware classification in the ever-evolving cybersecurity landscape. Key challenges include accurately categorizing closely…
Many animals and humans process the visual field with a varying spatial resolution (foveated vision) and use peripheral processing to make eye movements and point the fovea to acquire high-resolution information about objects of interest.…
Vision Transformers (ViTs) have emerged as the state-of-the-art architecture in representation learning, leveraging self-attention mechanisms to excel in various tasks. ViTs split images into fixed-size patches, constraining them to a…
Virus-like particles (VLPs) are valuable for vaccine development due to their immune-triggering properties. Understanding their stoichiometry, the number of protein subunits to form a VLP, is critical for vaccine optimisation. However,…
Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The success of these applications depends on accurately determining…
The most recent year has witnessed the success of applying the Vision Transformer (ViT) for image classification. However, there are still evidences indicating that ViT often suffers following two aspects, i) the high computation and the…
Flow-Imaging Microscopy (FIM) is commonly used in both academia and industry to characterize subvisible particles (those $\le 25 \mu m$ in size) in protein therapeutics. Pharmaceutical companies are required to record vast volumes of FIM…
Image Classification is a fundamental task in the field of computer vision that frequently serves as a benchmark for gauging advancements in Computer Vision. Over the past few years, significant progress has been made in image…
Neural networks are widely adopted to solve complex and challenging tasks. Especially in high-stakes decision-making, understanding their reasoning process is crucial, yet proves challenging for modern deep networks. Feature visualization…
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields…
Accurate identification of antiviral peptides (AVPs) is critical for accelerating novel drug development. However, current computational methods struggle to capture intricate sequence dependencies and effectively handle ambiguous,…