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We overview Bayesian estimation, hypothesis testing, and model-averaging and illustrate how they benefit parametric survival analysis. We contrast the Bayesian framework to the currently dominant frequentist approach and highlight…
BERT4Rec is an effective model for sequential recommendation based on the Transformer architecture. In the original publication, BERT4Rec claimed superiority over other available sequential recommendation approaches (e.g. SASRec), and it is…
Mathematical models support inference and forecasting in ecology and epidemiology, but results depend on the estimation framework. We compare Bayesian and Frequentist approaches across three biological models using four datasets:…
Biofilms are spatially organized microorganism colonies embedded in a self-produced matrix, conferring to the microbial community resistance to environmental stresses. Motile bacteria have been observed swimming in the matrix of pathogenic…
An antibiogram is a periodic summary of antibiotic resistance results of organisms from infected patients to selected antimicrobial drugs. Antibiograms help clinicians to understand regional resistance rates and select appropriate…
This paper presents a non-parametric classification technique for identifying a candidate bi-allelic genetic marker set that best describes disease susceptibility in gene-gene interaction studies. The developed technique functions by…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
We introduce a model called Host-Pathogen game for studying biological competitions. Notably, we focus on the invasive dynamics of external agents, like bacteria, within a host organism. The former are mapped to a population of defectors…
The outcomes of evolution are determined by which mutations occur and fix. In rapidly adapting microbial populations, this process is particularly hard to predict because lineages with different beneficial mutations often spread…
Recently, pretrained language models based on BERT have been introduced for the French biomedical domain. Although these models have achieved state-of-the-art results on biomedical and clinical NLP tasks, they are constrained by a limited…
Recently, ChatGPT has attracted great attention, as it can generate fluent and high-quality responses to human inquiries. Several prior studies have shown that ChatGPT attains remarkable generation ability compared with existing models.…
Penalized variable selection for high dimensional longitudinal data has received much attention as accounting for the correlation among repeated measurements and providing additional and essential information for improved identification and…
Microbiomes not only underpin Earth's biogeochemical cycles but also play crucial roles in both engineered and natural ecosystems, such as the soil, wastewater treatment, and the human gut. However, microbiome engineering faces significant…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…
Nowadays, recommendation systems have become crucial to online platforms, shaping user exposure by accurate preference modeling. However, such an exposure strategy can also reinforce users' existing preferences, leading to a notorious…
Detecting and predicting septic shock early is crucial for the best possible outcome for patients. Accurately forecasting the vital signs of patients with sepsis provides valuable insights to clinicians for timely interventions, such as…
Personal health analytics systems face a persistent cold-start dilemma: users expect meaningful insights early in data collection, while conventional statistical inference requires data volumes that often exceed engagement horizons.…
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…
We survey and show our earlier results about three different ways of fluctuation-enhanced sensing of bio agent, the phage-based method for bacterium detection published earlier; sensing and evaluating the odors of microbes; and spectral and…
Ongoing advances in microbiome profiling have allowed unprecedented insights into the molecular activities of microbial communities. This has fueled a strong scientific interest in understanding the critical role the microbiome plays in…