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Screening is a time-consuming and labour-intensive yet required task for medical systematic reviews, as tens of thousands of studies often need to be screened. Prioritising relevant studies to be screened allows downstream systematic review…
Motivation: Machine learning methods can be used to support scientific discovery in healthcare-related research fields. However, these methods can only be reliably used if they can be trained on high-quality and curated datasets. Currently,…
Motivation: Post-database searching is a key procedure in peptide dentification with tandem mass spectrometry (MS/MS) strategies for refining peptide-spectrum matches (PSMs) generated by database search engines. Although many statistical…
Possessing the five-year durability rate of nearly 5%, currently, the fourth leading cause for cancer-related deaths is pancreatic cancer. Previously, several works have resolved that early diagnosis performs a meaningful function in…
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…
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,…
Metaproteomics are becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS)…
Debiased collaborative filtering aims to learn an unbiased prediction model by removing different biases in observational datasets. To solve this problem, one of the simple and effective methods is based on the propensity score, which…
Breast cancer is one of the leading fatal disease worldwide with high risk control if early discovered. Conventional method for breast screening is x-ray mammography, which is known to be challenging for early detection of cancer lesions.…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
Clinical cystoscopy, the current standard for bladder cancer diagnosis, suffers from significant reliance on physician expertise, leading to variability and subjectivity in diagnostic outcomes. There is an urgent need for objective,…
One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…
This paper introduces a novel approach for dengue fever classification based on online learning paradigms. The proposed approach is suitable for practical implementation as it enables learning using only a few training samples. With time,…
Breast cancer is one of the most threatening diseases in women's life; thus, the early and accurate diagnosis plays a key role in reducing the risk of death in a patient's life. Mammography stands as the reference technique for breast…
Similar question retrieval is a core task in community-based question answering (CQA) services. To balance the effectiveness and efficiency, the question retrieval system is typically implemented as multi-stage rankers: The first-stage…
Classification tasks in NLP are typically addressed by selecting a pre-trained language model (PLM) from a model hub, and fine-tuning it for the task at hand. However, given the very large number of PLMs that are currently available, a…
Gallbladder cancer (GBC) is the most frequent cause of disease among biliary tract neoplasms. Identifying the molecular mechanisms and biomarkers linked to GBC progression has been a significant challenge in scientific research. Few recent…
Although click data is widely used in search systems in practice, so far the inherent bias, most notably position bias, has prevented it from being used in training of a ranker for search, i.e., learning-to-rank. Recently, a number of…
Molecular and genomic properties are critical in selecting cancer treatments to target individual tumors, particularly for immunotherapy. However, the methods to assess such properties are expensive, time-consuming, and often not routinely…
The development of molecular diagnostic tools to achieve individualized medicine requires identifying predictive biomarkers associated with subgroups of individuals who might receive beneficial or harmful effects from different available…