Lei Huang, Chuan Qiu, Kuan-Jui Su, Anqi Liu, Yun Gong, Weiqiang Lin, Lindong Jiang, Chen Zhao 等 16 位作者
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.
Fact-checking explanations help Web users understand why a claim receives its verdict, yet the same explanation may not satisfy readers with different backgrounds and preferences. We formulate Faithful Personalized Fact-Checking Explanation Rewriting, which adapts an existing explanation to individual readers while preserving factual fidelity. Rather than relying on reader-written reference explanations, we learn personalized rewriting from the relative preferences of LLM-simulated readers. However, this presents two challenges: distinguishing persona-specific preferences from general explanation quality and learning beyond a limited set of predefined explanation styles. To address these challenges, we propose Personalized Explanation Rewriting via Preference Learning (PERPL), a framework consisting of two components. Simulated Preference Construction derives persona-specific supervision from simulated reader preferences through cross-persona reciprocal pairing. Progressive Preference Learning first trains a lightweight rewriter on the constructed supervision and then refines it through exploration-guided preference optimization, enabling it to discover preferred explanations beyond the predefined styles. Extensive experiments demonstrate that PERPL outperforms much larger general-purpose LLMs in personalized preference alignment while maintaining high factual fidelity.