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.
Xiao Liang, Zhong-Zhi Li, Zhenghao Lin Microsoft, Eric Hanchen Jiang, Hengyuan Zhang, Yelong Shen, Kai-Wei Chang University of California, Los Angeles and Amazon, Ying Nian Wu 等 10 位作者
Large language models (LLMs) have demonstrated strong reasoning capabilities through step-by-step chain-of-thought (CoT) reasoning. Nevertheless, at the limits of model capability, CoT often proves insufficient, and its strictly sequential nature constrains test-time scalability. A potential alternative is divide-and-conquer (DAC) reasoning, which decomposes a complex problem into subproblems to facilitate more effective exploration of the solution space. Although promising, our analysis reveals a fundamental misalignment between general-purpose post-training and DAC-style inference, which limits the model’s capacity to fully leverage this potential. To bridge this gap and fully unlock LLMs’ reasoning capabilities on the most challenging tasks, we propose an end-to-end reinforcement learning (RL) framework to enhance their DAC-style reasoning capacity. At each step, the policy decomposes a problem into a group of subproblems, solves them sequentially, and addresses the original problem conditioned on the subproblem solutions, with both decomposition and solution integrated into RL training. Under comparable training settings, our DAC-style framework endows the model with a higher performance ceiling and stronger test-time scalability, surpassing CoT by 8.6% in Pass@1 and 6.3% in Pass@32 on competition-level benchmarks. The code is available at the provided link.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Zhong-Zhi Li, Xiao Liang, Zihao Tang, Lei Ji, Peijie Wang, Haotian Xu, Xing W, Haizhen Huang 等 14 位作者
Large Language Models (LLMs) have recently achieved remarkable progress on complex reasoning tasks by leveraging extended Chain-of-Thought (CoT) techniques. These reasoning processes can be roughly categorized into System-1 (fast and intuitive) and System-2 (slow and deliberate) paradigms. However, excessive reliance on lengthy System-2-style reasoning during inference can produce extremely long outputs, thereby reducing efficiency. In this work, we propose Thinking Length Data Re-weighting (TLDR), that does not rely on sophisticated data annotations or interpolation between multiple models. We continuously balance the weights between the model’s System-1 and System-2 data to eliminate redundant reasoning processes while preserving the model’s reasoning capability. We validate our method across multiple base models, including Deepseek-R1-Distilled Qwen models, as well as on a diverse benchmarks with varying difficulty levels. Our method significantly reduces the number of output tokens by nearly 40% while maintaining the accuracy of the reasoning.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Kailai Yang University of Manchester, Xiao Liu Microsoft Research Asia, Lei Ji, Hao Li, Xiao Liang, Zhiwei Liu, Yeyun Gong, Peng Cheng Microsoft Research 等 9 位作者
Continual pre-training on small-scale task-specific data is an effective method for improving large language models in new target fields, yet it risks catastrophic forgetting of their original capabilities. A common solution is to re-weight training data mixtures from source and target fields on a domain space to achieve balanced performance. Previous domain reweighting strategies rely on manual designation with certain heuristics based on human intuition or empirical results. In this work, we prove that more general heuristics can be parameterized by proposing Data Mixing Agent, the first model-based, end-to-end framework that learns to re-weight domains. The agent learns generalizable heuristics through reinforcement learning on large quantities of data mixing trajectories with corresponding feedback from an evaluation environment. Experiments in continual pre-training on math reasoning show that Data Mixing Agent outperforms strong baselines in achieving balanced performance across source and target field benchmarks. Furthermore, it generalizes well across unseen source fields, target models, and domain spaces without retraining. Direct application to the code generation field also indicates its adaptability across target domains. Further analysis showcases the agents’ well-aligned heuristics with human intuitions and their efficiency in achieving superior model performance with less source-field data.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Boyan Duan, Xiao Liang, Shuai Lu JD.com, Yaoxiang Wang, Yelong Shen, Kai-Wei Chang University of California, Los Angeles and Amazon, Ying Nian Wu, Mao Yang 等 10 位作者
Automated theorem proving in Euclidean geometry, particularly for International Mathematical Olympiad (IMO) level problems, remains a major challenge and an important research focus in Artificial Intelligence. In this paper, we present a highly efficient method for geometry theorem proving that runs entirely on CPUs without relying on neural network–based inference. Our initial study shows that a simple random strategy for adding auxiliary points can achieve ”silver-medal” level human performance on IMO. Building on this, we propose HAGeo, a Heuristic-based method for adding Auxiliary points in Geometric deduction that solves 28 of 30 problems on the IMO-30 benchmark, achieving “gold-medal” level performance and surpassing AlphaGeometry, a competitive neural network–based approach, by a notable margin. To evaluate our method and existing approaches more comprehensively, we further construct HAGeo, a benchmark consisting of 409 geometry problems with human-assessed difficulty levels. Compared with the widely used IMO-30, our benchmark poses greater challenges and provides a more precise evaluation, setting a higher bar for geometry theorem proving.
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cs.CL · cs.AI
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表