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Sparse regularized regression methods are now widely used in genome-wide association studies (GWAS) to address the multiple testing burden that limits discovery of potentially important predictors. Linear mixed models (LMMs) have become an…
The denoising diffusion probabilistic model (DDPM) has emerged as a mainstream generative model in generative AI. While sharp convergence guarantees have been established for the DDPM, the iteration complexity is, in general, proportional…
Transformers have emerged as the backbone of large language models (LLMs). However, generation remains inefficient due to the need to store in memory a cache of key-value representations for past tokens, whose size scales linearly with the…
Dose-response prediction in cancer is an active application field in machine learning. Using large libraries of \textit{in-vitro} drug sensitivity screens, the goal is to develop accurate predictive models that can be used to guide…
According to the 2021 World Health Organization (WHO) Classification scheme for gliomas, glioma segmentation is a very important basis for diagnosis and genotype prediction. In general, 3D multimodal brain MRI is an effective diagnostic…
Accurate characterization of glioma is crucial for clinical decision making. A delineation of the tumor is also desirable in the initial decision stages but is a time-consuming task. Leveraging the latest GPU capabilities, we developed a…
We consider the problem of clustering grouped data for which the observations may include group-specific variables in addition to the variables that are shared across groups. This type of data is common in cancer genomics where the…
We consider the estimation of Dirichlet Process Mixture Models (DPMMs) in distributed environments, where data are distributed across multiple computing nodes. A key advantage of Bayesian nonparametric models such as DPMMs is that they…
Knowledge of molecular subtypes of gliomas can provide valuable information for tailored therapies. This study aimed to investigate the use of deep convolutional neural networks (DCNNs) for noninvasive glioma subtyping with radiological…
The Dirichlet process (DP) is a fundamental mathematical tool for Bayesian nonparametric modeling, and is widely used in tasks such as density estimation, natural language processing, and time series modeling. Although MCMC inference…
Acute Myeloid Leukemia (AML) remains a clinical challenge due to its extreme molecular heterogeneity and high relapse rates. While precision medicine has introduced mutation-specific therapies, many patients still lack effective,…
Model-based clustering is widely used for identifying and distinguishing types of diseases. However, modern biomedical data coming with high dimensions make it challenging to perform the model estimation in traditional cluster analysis. The…
To identify novel dynamic patterns of gene expression, we develop a statistical method to cluster noisy measurements of gene expression collected from multiple replicates at multiple time points, with an unknown number of clusters. We…
Drug repurposing is often framed as a candidate identification task, but existing approaches provide limited guidance for distinguishing biologically plausible candidates from historically well-connected ones. Here we introduce DrugKLM, a…
High-dimensional data of discrete and skewed nature is commonly encountered in high-throughput sequencing studies. Analyzing the network itself or the interplay between genes in this type of data continues to present many challenges. As…
Autoregressive Models (ARMs) have long dominated the landscape of Large Language Models. Recently, a new paradigm has emerged in the form of diffusion-based Large Language Models (dLLMs), which generate text by iteratively denoising masked…
Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…
A key aim of systems biology is the reconstruction of molecular networks, however we do not yet have networks that integrate information from all datasets available for a particular clinical condition. This is in part due to the limited…
It is increasingly common clinically for cancer specimens to be examined using techniques that identify somatic mutations. In principle these mutational profiles can be used to diagnose the tissue of origin, a critical task for the 3-5% of…
Biophysical modeling, particularly involving partial differential equations (PDEs), offers significant potential for tailoring disease treatment protocols to individual patients. However, the inverse problem-solving aspect of these models…