相关论文: Family based HLA imputation and optimization of ha…
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the…
Analysis of genomic segments shared identical-by-descent (IBD) between individuals is fundamental to many genetic applications, from demographic inference to estimating the heritability of diseases, but IBD detection accuracy in…
Generative machine learning models offer a powerful framework for therapeutic design by efficiently exploring large spaces of biological sequences enriched for desirable properties. Unlike supervised learning methods, which require both…
Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…
Genomic imprinting and maternal effects are two epigenetic factors that have been increasingly explored for their roles in the etiology of complex diseases. This is part of a concerted effort to find the "missing heritability." Accordingly,…
In this paper we develop the Greedy Recombination Interpolation Method (GRIM) for finding sparse approximations of functions initially given as linear combinations of some (large) number of simpler functions. In a similar spirit to the…
The collection of immunoglobulin genes in an individual's germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of…
In genetic studies, haplotype data provide more refined information than data about separate genetic markers. However, large-scale studies that genotype hundreds to thousands of individuals may only provide results of pooled data, where…
The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian…
Large-scale biobanks are being collected around the world in efforts to better understand human health and risk factors for disease. They often survey hundreds of thousands of individuals, combining questionnaires with clinical, genetic,…
Genotyping errors are known to influence the power of both family-based and case-control studies in the genetics of complex disease. Estimating genotyping error rate in a given dataset can be complex, but when family information is…
This paper presents a novel method for statistical inference in high-dimensional binary models with unspecified structure, where we leverage a (potentially misspecified) sparsity-constrained working generalized linear model (GLM) to…
Human leukocyte antigen (HLA) genes are associated with a variety of diseases, however direct typing of HLA is time and cost consuming. Thus various imputation methods using sequential SNPs data have been proposed based on statistical or…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Inference-time computation is a powerful paradigm to enhance the performance of large language models (LLMs), with Best-of-N sampling being a widely used technique. However, this method is computationally expensive, requiring both (1) an…
Bayesian nonparametric mixtures and random partition models are powerful tools for probabilistic clustering. However, standard independent mixture models can be restrictive in some applications such as inference on cell lineage due to the…
Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level…
Motivation: Seed location filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. State-of-the-art read…
The vast majority of biological sequences encode unknown functions and bear little resemblance to experimentally characterized proteins, limiting both our understanding of biology and our ability to harness functional potential for the…
With generative models becoming increasingly sophisticated and diverse, detecting AI-generated images has become increasingly challenging. While existing AI-genereted Image detectors achieve promising performance on in-distribution…