Yun Gong

Lei Huang, Hui Shen, Kuan-Jui Su et al.

Genotype-based cis-expression prediction depends on accurately modeling local regulatory architecture. We present block-sparse Bayesian sparse linear mixed model (bsBSLMM), an extension of Bayesian sparse linear mixed model (BSLMM) that incorporates linkage disequilibrium (LD)-block spike-and-slab sparsity and a transcription start site (TSS)-informed SNP inclusion prior. Across 23,098 genes from GEUVADIS European-ancestry lymphoblastoid cell lines, bsBSLMM retained more predictable genes than BSLMM, LASSO, BLUP, TIGAR elastic net, and TIGAR Dirichlet-process regression under matched evaluation criteria. Compared with BSLMM, bsBSLMM improved held-out prediction performance for most shared genes, with gains driven primarily by LD-block sparsity and further enhanced by the TSS-informed prior. Variants selected by bsBSLMM showed stronger enrichment in GM12878 DNase and H3K27ac regulatory regions than variants selected by BSLMM. In transcriptome-wide association study (TWAS) analysis, bsBSLMM recovered established inflammatory bowel disease signals, including IL23R, and identified additional genome-wide significant genes not detected by BSLMM. Independent validation in the Louisiana Osteoporosis Study reproduced the increased prediction yield across ancestries and recovered biologically relevant bone mineral density pathways in downstream TWAS and gene set enrichment analyses. These results demonstrate that incorporating LD-block structure and biologically informed SNP priors improves cis-expression prediction and enhances downstream TWAS discovery.

Lei Huang, Chuan Qiu, Kuan-Jui Su et al.

Genotype imputation enables dense variant coverage for genome-wide association and risk-prediction studies, yet conventional reference-panel methods remain limited by ancestry bias and reduced rare-variant accuracy. We present Genotype Bidirectional Encoder Representations from Transformers (GenoBERT), a transformer-based, reference-free framework that tokenizes phased genotypes and uses a self-attention mechanism to capture both short- and long-range linkage disequilibrium (LD) dependencies. Benchmarking on two independent datasets including the Louisiana Osteoporosis Study (LOS) and the 1000 Genomes Project (1KGP) across ancestry groups and multiple genotype missingness levels (5-50%) shows that GenoBERT achieves the highest overall accuracy compared to four baseline methods (Beagle5.4, SCDA, BiU-Net, and STICI). At practical sparsity levels (up to 25% missing), GenoBERT attains high overall imputation accuracy ($r^2 approx 0.98$) across datasets, and maintains robust performance ($r^2 > 0.90$) even at 50% missingness. Experimental results across different ancestries confirm consistent gains across datasets, with resilience to small sample sizes and weak LD. A 128-SNP (single-nucleotide polymorphism) context window (approximately 100 Kb) is validated through LD-decay analyses as sufficient to capture local correlation structures. By eliminating reference-panel dependence while preserving high accuracy, GenoBERT provides a scalable and robust solution for genotype imputation and a foundation for downstream genomic modeling.

Yun Gong, Zebang Shen, Niao He

Potential functions in highly pertinent applications, such as deep learning in over-parameterized regime, are empirically observed to admit non-isolated minima. To understand the convergence behavior of stochastic dynamics in such landscapes, we propose to study the class of \logPLmeasure\ measures $μ_ε\propto \exp(-V/ε)$, where the potential $V$ satisfies a local Polyak-Łojasiewicz (PŁ) inequality, and its set of local minima is provably \emph{connected}. Notably, potentials in this class can exhibit local maxima and we characterize its optimal set S to be a compact $\mathcal{C}^2$ \emph{embedding submanifold} of $\mathbb{R}^d$ without boundary. The \emph{non-contractibility} of S distinguishes our function class from the classical convex setting topologically. Moreover, the embedding structure induces a naturally defined Laplacian-Beltrami operator on S, and we show that its first non-trivial eigenvalue provides an \emph{$ε$-independent} lower bound for the \Poincare\ constant in the \Poincare\ inequality of $μ_ε$. As a direct consequence, Langevin dynamics with such non-convex potential $V$ and diffusion coefficient $ε$ converges to its equilibrium $μ_ε$ at a rate of $\tilde{\mathcal{O}}(1/ε)$, provided $ε$ is sufficiently small. Here $\tilde{\mathcal{O}}$ hides logarithmic terms.