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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…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
Accurate molecular identification of metabolites can unlock new areas of the molecular universe and allow greater insight into complex biological and environmental systems than currently possible. Analytical approaches for measuring the…
As data science continues to grow in popularity, there will be an increasing need to make data science tools more scalable, flexible, and accessible. In particular, automated machine learning (AutoML) systems seek to automate the process of…
Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and…
The rapid expansion of the Industrial Internet of Things (IIoT) has significantly advanced digital technologies and interconnected industrial systems, creating substantial opportunities for growth. However, this growth has also heightened…
The design of protein sequences with desired functionalities is a fundamental task in protein engineering. Deep generative methods, such as autoregressive models and diffusion models, have greatly accelerated the discovery of novel protein…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this assembly process are regulated by the complementary…
Recently, the Diffusion Probabilistic Model (DPM)-based methods have achieved substantial success in the field of medical image segmentation. However, most of these methods fail to enable the diffusion model to learn edge features and…
Open-set recognition (OSR) aims to simultaneously detect unknown-class samples and classify known-class samples. Most of the existing OSR methods are inductive methods, which generally suffer from the domain shift problem that the learned…
Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS$^2$) is the major analytical technique in…
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…
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium ${\it Escherichia coli}$, for $\approx$ 65$\%$ of the promoters we remain completely ignorant of…
Numerous algorithms have been proposed for detecting anomalies (outliers, novelties) in an unsupervised manner. Unfortunately, it is not trivial, in general, to understand why a given sample (record) is labelled as an anomaly and thus…
Integrated sensing and communication (ISAC) is a key feature of future cellular systems, enabling applications such as intruder detection, monitoring, and tracking using the same infrastructure. However, its potential for structural health…
Intrusion Detection System (IDS) is one of the security measures being used as an additional defence mechanism to prevent the security breaches on web. It has been well known methodology for detecting network-based attacks but still…
Network intrusions have become a significant threat in recent years as a result of the increased demand of computer networks for critical systems. Intrusion detection system (IDS) has been widely deployed as a defense measure for computer…
Locating the promoter region in DNA sequences is of paramount importance in the field of bioinformatics. This is a problem widely studied in the literature, however, not yet fully resolved. Some researchers have presented remarkable results…
Tumour-infiltrating lymphocytes (TILs) are considered as a valuable prognostic markers in both triple-negative and human epidermal growth factor receptor 2 (HER2) positive breast cancer. In this study, we introduce an innovative deep…