Jixuan Ruan, Zhuo Cui, Zhengding Hu, Zhongkai Yu, Xiang Fang, Yue Guan, Jason Ludmir, Phillip E. Weinberg 等 13 位作者
Large Language Models (LLMs) offer an adaptable alternative to traditional quantum compilation heuristics, which bottleneck progress by demanding costly manual redesigns whenever hardware evolves. However, naive single-pass LLM approaches fail under the unique challenges introduced by quantum compilation. We introduce Qubrio, a practical agentic framework that significantly reduces heuristic redesigns through a three-level decomposition. By (1) partitioning programs into sequential operation stages, (2) deploying specialized agents for placement, routing and optimization, and (3) using disaggregated feedback for precise error correction, our system reliably navigates complex physical constraints. Beyond serving as a direct compiler, our LLM framework also uncovers novel strategies that facilitate convoy-style shuttling, substantially enhancing hardware concurrency without sacrificing fidelity. We further integrate these strategies into the previous state-of-the-art (SOTA) compiler, recovering a significant fraction of the LLM's performance advantages. On realistic workloads, our compiler achieves significant improvements in hardware runtime and program fidelity over the SOTA baseline PowerMove, seamlessly adapting to new hardware capabilities. Qubrio features an open user interface for practical use, and its code is publicly available at https://github.com/crosaa/Qubrio.
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.