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Pretrained large language models (LLMs) are currently state-of-the-art for solving the vast majority of natural language processing tasks. While many real-world applications still require fine-tuning to reach satisfactory levels of…
Joint modeling of longitudinal and survival data has become increasingly important in medical research, particularly for understanding disease progression in chronic conditions where both repeated biomarker measurements and time-to-event…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Brain networks has attracted the interests of many neuroscientists. From functional MRI (fMRI) data, statistical tools have been developed to recover brain networks. However, the dimensionality of whole-brain fMRI, usually in hundreds of…
Dynamic prediction of time-to-event outcomes using longitudinal data is highly useful in clinical research and practice. A common strategy is the joint modeling of longitudinal and time-to-event data. The shared random effect model has been…
Machine learning (ML) holds great promise for clinical applications but is often hindered by limited access to high-quality data due to privacy concerns, high costs, and long timelines associated with clinical trials. While large language…
Clinical trials are critical in advancing medical treatments but often suffer from immense time and financial burden. Advances in statistical methodologies and artificial intelligence (AI) present opportunities to address these…
Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…
Generalized linear mixed-effects models (GLMMs) are widely used to analyze grouped and hierarchical data. In a GLMM, each response is assumed to follow an exponential-family distribution where the natural parameter is given by a linear…
Latent Diffusion models (LDMs) have achieved remarkable results in synthesizing high-resolution images. However, the iterative sampling process is computationally intensive and leads to slow generation. Inspired by Consistency Models (song…
Statistical analysis of evolutionary-related protein sequences provides insights about their structure, function, and history. We show that Restricted Boltzmann Machines (RBM), designed to learn complex high-dimensional data and their…
In cancer biomarker development, a key objective is to evaluate whether a new biomarker, when combined with an established one, improves early cancer detection compared to using the established biomarker alone. Incremental value is often…
Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent…
The Linear Ballistic Accumulator (Brown & Heathcote, 2008) model is used as a measurement tool to answer questions about applied psychology. The analyses based on this model depend upon the model selected and its estimated parameters.…
Neuroimaging data, particularly from techniques like MRI or PET, offer rich but complex information about brain structure and activity. To manage this complexity, latent representation models - such as Autoencoders, Generative Adversarial…
The BioModels database is one of the premier databases for computational models in systems biology. The database contains over 1000 curated models and an even larger number of non-curated models. All the models are stored in the…
The amount of high-dimensional large-scale RNA sequencing data derived from multiple heterogeneous sources has increased exponentially in biological science. During data collection, significant technical noise or errors may occur. To…
We propose a random-effects approach to missing values for generalized linear mixed model (GLMM) analysis. The method converts a GLMM with missing covariates to another GLMM without missing covariates. The standard GLMM analysis tools for…
Generalized additive model is a powerful statistical learning and predictive modeling tool that has been applied in a wide range of applications. The need of high-dimensional additive modeling is eminent in the context of dealing with high…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…