arXiv subjects

Yun Gong

Publications and source records attributed to Yun Gong.

7 recordsLinked to original sources

arXiv2026

Annotation-Informed Block-Sparse Bayesian Modeling for cis-Expression Prediction

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.

q-bio.GN↗

arXiv2026

GenoBERT: A Language Model for Accurate Genotype Imputation

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.

q-bio.GN↗

arXiv2025

Poincare Inequality for Local Log-Polyak-Łojasiewicz Measures: Non-asymptotic Analysis in Low-temperature Regime

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 log-PŁ$^\circ$ 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 connected. Notably, potentials in this class can exhibit local maxima and we characterize its optimal set $S$ to be a compact ${C}^2$ embedding submanifold of ${R}^d$ without boundary. The 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 $ε$-independent lower bound for the Poincaré constant in the Poincaré 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 $\tilde{O}(1/ε)$, provided $ε$ is sufficiently small. Here $\tilde{O}$ hides logarithmic terms.

math.PR↗

arXiv2025

Poincaré Inequality for Local Log-Polyak-Lojasiewicz Measures : Non-asymptotic Analysis in Low-temperature Regime

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.

cs.LG↗

arXiv2024

Propagation of Chaos for 2D Log Gas on the Whole Space

We derive the quantitative propagation of chaos in the sense of relative entropy for the first time for the 2D Log gas or the weakly interacting particle systems with 2D Coulomb interactions on the whole space. We resolve this problem by adapting the modulated free energy method in [BJW23] to the whole space setting and establishing the crucial logarithmic growth estimates for the mean-field Poisson-Nernst-Planck (PNP) equation of single component via the parabolic maximum principle.

math.AP↗

arXiv2024

Personalized Playback Technology: How Short Video Services Create Excellent User Experience

Short-form video content has become increasingly popular and influential in recent years. Its concise yet engaging format aligns well with todays' fast-paced and on-the-go lifestyles, making it a dominating trend in the digital world. As one of the front runners in the short video platform space, ByteDance has been highly successful in delivering a one-of-a-kind short video experience and attracting billions of users worldwide. One key contributing factor is its advanced end-to-end personalized short video playback technology, where we pioneered and developed the new technical field over the past five years to optimize user experience. This paper introduces the major concepts and methodologies of this personalized video playback technology that distinguish it from traditional multimedia technologies. More details, including goal setting, iterative process, modeling, experimental methods and required supporting systems, are also provided to encourage deeper research in this area.

cs.MM↗

arXiv2024

Uniform-in-time propagation of chaos for second order interacting particle systems

We study the long time behavior of second order particle systems interacting through global Lipschitz kernels. Combining hypocoercivity method in [37] and relative entropy method in [25], we are able to overcome the degeneracy of diffusion in position direction by controlling the relative entropy and relative Fisher information together. This implies the uniform-in-time propagation of chaos through the strong convergence of all marginals. Our method works at the level of Liouville equation and relies on the log Sobolev inequality of equilibrium of Vlasov-Fokker-Planck equation.

math.AP↗