arXiv subjects

Anqi Liu

Publications and source records attributed to Anqi Liu.

At least 19 recordsLinked to original sources

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↗

arXiv2026

FOCUS: Active Critic Learning for Long-Horizon Language Model Agents

Sparse outcome rewards make it difficult for long-horizon language-model agents to assign credit to earlier actions. Learned critics provide value estimates for intermediate states, but these estimates can be inaccurate, while estimating intermediate values with repetitive continuation samples from points within a trajectory incurs substantial costs. To mitigate these issues, we introduce FOCUS, an RL method that uses selective branching to help the critic network learn its value estimator. The rollout controller facilitates active learning for the critic by sampling continuations from states that are expected to most reduce the critic's estimation error. These refined value estimates then score the segment between consecutive states with a TD($λ$) advantage, while the sampled evidence supplies training targets for the critic. FOCUS supports long-horizon agentic reinforcement learning through a modular context-management interface that decouples context management from rollout allocation. Our experiments show that using compaction-induced segment boundaries for value estimation and credit assignment, FOCUS outperforms GRPO and VinePPO with matched per-step generation budgets on legal reasoning, deep search, and code localization benchmarks, improving held-out accuracy at Qwen3.5-9B scale by 7.2 points over the strongest baseline on BrowseComp-Plus (55.4 vs. 48.2) and by 4.1 points on DeonticBench (56.5 vs. 52.4).

cs.LG↗

arXiv2026

RobustRLlib: A Unified Library and Benchmark for Robust Reinforcement Learning Algorithms

Robust reinforcement learning (RL) is critical for reliable real-world deployment, where policies may fail under diverse shifts and disruptions. Existing robust RL algorithms offer a rich set of mechanisms and principles, yet two major barriers limit their broader potential: limited algorithm reusability and an unclear empirical capability boundary. We introduce RobustRLlib, an algorithm-centric library and benchmark that addresses both challenges. It integrates 17 representative robust online, offline, and safe RL algorithms under a unified interface for substantially improved reusability, together with an enhanced evaluation platform spanning diverse real-world shifts and advanced humanoid and vision-language-action tasks. Systematic evaluation over 273 perturbation configurations provides an up-to-date capability map of current robust RL algorithms, revealing where they remain effective and where substantial robustness gaps persist. As an open-source, user-friendly platform, RobustRLlib offers a reproducible and extensible codebase for applying existing methods to new problems and developing new robust RL algorithms.

cs.LG↗

arXiv2026

Reading the Room: Foundations, Design, and Challenges of Normative Competence in LLMs

Human communities are governed by normative systems: shared standards that produce \textit{norms} dictating acceptable behavior, enforced through community sanctioning. Aligning increasingly autonomous AI systems with these norms is a central alignment challenge, complicated by the fact that norms are vast in number, change quickly, and are often arbitrary (e.g., dress or language conventions). Thus, alignment requires \textit{normative competence}: the ability to discern from interaction alone what norms a community enforces without relying on static pretrained knowledge. We introduce a multi-agent community debate setting, where access to debate is governed by synthetic norms, to study normative competence in isolation from pretraining exposure. We show that baseline LLM agents fail to learn norms even when doing so would improve their accuracy. We then experiment with various \textit{normative modules} -- architectural components for norm inference -- finding that norm-following is highly sensitive to both the style of norm and the model powering the normative module, suggesting a lack of generalizability. Furthermore, when idiosyncratic, non-normative behaviors accompany the true norm, LLM agents exhibit an unselective attribution failure: they indiscriminately copy idiosyncratic noise alongside enforced rules, a pattern that persists even when imitating unnecessary behaviors is explicitly penalized. To the best of our knowledge, our work is the first to operationalize and evaluate normative competence in LLMs, demonstrating that current AI systems excel at behavioral mimicry but lack the capacity to discern socially enforced order.

cs.AI↗

arXiv2026

Convergent Emergence of In-Context Learning Across Modalities

Few-shot in-context learning (ICL), the capacity of a model to infer abstract patterns from input-output examples provided in its prompt and apply them to new inputs, has been extensively studied in large language models trained for next-token prediction on human text. Recently, few-shot ICL has been demonstrated in autoregressive genomic models as well. This raises a question: does ICL emerge broadly across domains, and if so, what common structure is shared? To address both, we develop a controlled cross-modality framework that instantiates the same task suite in a variety of modalities to test what we call the Convergent Emergence Hypothesis: the idea that few-shot ICL, when it emerges, shares a common cross-modality difficulty profile - i.e., tasks that benefit from ICL in one modality tend to benefit in others. We show that paired-mapping ICL emerges across six modalities (language, genome, integer sequences, time series, images, and proteins), surpasses controlled baselines, and has correlated per-task effects across five of them. Together, these results provide support for the Convergent Emergence Hypothesis in some modalities, but not all.

cs.AI↗

arXiv2026

WATCH: Adaptive Monitoring for AI Deployments via Weighted-Conformal Martingales

Responsibly deploying artificial intelligence (AI) / machine learning (ML) systems in high-stakes settings arguably requires not only proof of system reliability, but also continual, post-deployment monitoring to quickly detect and address any unsafe behavior. Methods for nonparametric sequential testing -- especially conformal test martingales (CTMs) and anytime-valid inference -- offer promising tools for this monitoring task. However, existing approaches are restricted to monitoring limited hypothesis classes or ``alarm criteria'' (e.g., detecting data shifts that violate certain exchangeability or IID assumptions), do not allow for online adaptation in response to shifts, and/or cannot diagnose the cause of degradation or alarm. In this paper, we address these limitations by proposing a weighted generalization of conformal test martingales (WCTMs), which lay a theoretical foundation for online monitoring for any unexpected changepoints in the data distribution while controlling false-alarms. For practical applications, we propose specific WCTM algorithms that adapt online to mild covariate shifts (in the marginal input distribution), quickly detect harmful shifts, and diagnose those harmful shifts as concept shifts (in the conditional label distribution) or extreme (out-of-support) covariate shifts that cannot be easily adapted to. On real-world datasets, we demonstrate improved performance relative to state-of-the-art baselines.

cs.LG↗

arXiv2026

Unlocking air traffic flow prediction through microscopic aircraft-state modeling

Short-term air traffic flow prediction in terminal airspace is essential for proactive air traffic management. Existing approaches predominantly model traffic flow as aggregated time series. However, traffic dynamics are governed by aircraft states and their interactions in continuous airspace. Such aggregation obscures fine-grained information, including aircraft kinematics, boundary interactions, and control-intent cues. Here we present AeroSense, a state-to-flow modeling paradigm that predicts future traffic flow directly from instantaneous airspace situations represented as dynamic sets of aircraft states derived from ADS-B trajectories. By establishing an end-to-end mapping from microscopic aircraft states to future regional traffic flow, AeroSense preserves aircraft-level dynamics while naturally accommodating varying traffic density, and avoids reliance on historical look-back windows. Experiments on a large-scale real-world dataset show that AeroSense exhibits strong predictive accuracy and robustness compared with time series-based forecasting approaches, without requiring exhaustive hyperparameter tuning. These findings suggest that aircraft-state situation modeling provides a promising alternative to conventional time-series forecasting in air traffic flow management.

cs.LG↗

arXiv2026

Conformal Policy Control

An agent must try new behaviors to explore and improve. In high-stakes environments, an agent that violates safety constraints may cause harm and must be taken offline, curtailing any future interaction. Imitating old behavior is safe, but excessive conservatism discourages exploration. How much behavior change is too much? We show how to use any safe reference policy as a probabilistic regulator for any optimized but untested policy. Conformal calibration on data from the safe policy determines how aggressively the new policy can act, while provably enforcing the user's declared risk tolerance. Unlike conservative optimization methods, we do not assume the user has identified the correct model class nor tuned any hyperparameters. Unlike previous conformal methods, our theory provides finite-sample guarantees even for non-monotonic bounded loss functions, and it introduces a new policy control setting. Our experiments on applications ranging from natural language question answering to biomolecular engineering show that safe exploration is not only possible from the first moment of deployment, but can also improve performance.

cs.AI↗

arXiv2026

Process Supervision of Confidence Margin for Calibrated LLM Reasoning

Scaling test-time computation with reinforcement learning (RL) has emerged as a reliable path to improve large language models (LLM) reasoning ability. Yet, outcome-based reward often incentivizes models to be overconfident, leading to hallucinations, unreliable confidence-based control, and unnecessary compute allocation. We introduce Reinforcement Learning with Confidence Margin (RLCM), a calibration-aware RL framework that jointly optimizes correctness and confidence reliability via a margin-enhanced process reward over intermediate-budget completions. Rather than aligning confidence to correctness likelihoods, RLCM encourages the model to widen the confidence margin between correct and incorrect steps within a single reasoning trajectory. Across mathematical, code, logic and science benchmarks, our method substantially improves calibration while maintaining or improving accuracy. We further show that, with calibrated confidence signals, the resulting models enable more efficient conformal risk control and effective confidence-weighted aggregation

cs.LG↗

arXiv2026

Decoding the Micromagnetic Hamiltonian from Magnetic Fingerprints

Extracting intrinsic magnetic Hamiltonians directly from magnetometry is challenging due to the high dimensionality of the parameter space and the degeneracy induced by ensemble averaging. Here, we introduce a collection of deep convolutional neural networks (CNNs) to extract the full phenomenological micromagnetic Hamiltonian directly from the magnetic fingerprints encoded within First-Order Reversal Curves (FORCs). We validate this approach via closed-loop verification, re-creating the input magnetometry for both simulated and experimental FORCs. To mitigate false positives, we deploy an `Alice--Bob' parallel network that quantifies prediction uncertainty based on solely the information in FORCs without any additional ground-truth knowledge. This framework provides a robust, machine-learning-assisted approach to unravel the underlying spin behaviors in complex magnetic systems

cond-mat.mtrl-sci↗

arXiv2026

Estimating Rare Events in Language Models with Proper Evaluation

Quantifying the risk of rare failures in language models, such as those triggered by adversarial distribution shifts or very large-scale deployments, requires estimating probabilities far too small for random sampling. While recent work has formalized Low Probability Estimation, existing pipelines remain fragile in the rarest regimes: estimators can suffer zero-estimate collapse or systematic bias, and standard evaluation losses can become unstable or poorly matched to asymmetric safety costs. In this work, we introduce Gradient Activation Adaptive Multi-Level Splitting (GA-AMLS), which adapts rare-event Monte Carlo methods to the continuous activation space of language models. Specifically, GA-AMLS uses a gradient-based MCMC kernel to navigate activation space, eliminating the zero-estimate collapse of input-space search and replacing the independence assumptions of prior activation-space estimators with conditional sampling under an explicit, heavier-tailed activation prior. We also propose the Shifted-Power Bregman (SPB) Loss, a proper scoring rule that remains finite for zero-estimates and offers tunable asymmetry between underestimation and overestimation penalties. Experiments on small transformer models reveal a bias-variance tradeoff: GA-AMLS achieves the lowest loss under symmetric evaluation, reducing average log-space squared error relative to the strongest baseline across model sizes, while methods with overestimation bias prevail under asymmetric penalties. Our findings highlight that estimator choice should be matched to deployment context. More broadly, our work establishes activation space as a tractable domain for rare-event estimation in language models, circumventing the brittleness of discrete input-space search.

cs.LG↗

arXiv2026

Full-Pipeline Inference Optimization for MiMo-V2.5 Series: Pushing Hybrid SWA Efficiency to the Limit

We present a full-pipeline inference optimization for the MiMo-V2.5 model family, which combines Hybrid Sliding Window Attention (Hybrid SWA), sparse Mixture-of-Experts (MoE), and multimodal encoders. While Hybrid SWA can ideally reduce both attention compute and KVCache storage significantly compared to Full Attention, realizing these gains in production requires substantial engineering effort. We systematically optimize the KVCache system with layerwise prefetch, SWA-aware prefix cache trees, and specialized placement strategies, achieving strict $O(W)$ SWA storage and high cache hit rates. We further build GCache, a high-performance distributed cache infrastructure with RDMA-optimized networking, and develop a KVCache-affinity router to reduce computation while preserving load balancing. We also optimize for multimodal inputs, including GPU image preprocessing, parallel video decoding, and multimodal cache sharing. Together, these optimizations constitute the first large-scale LLM serving system in production that efficiently covers the Hybrid SWA + MoE + multimodal composite architecture.

cs.AR↗

arXiv2026

Toward Calibrated Mixture-of-Experts Under Distribution Shift

Calibration aligns a model's predictive uncertainty with the frequencies of its empirical outcomes and is important for understanding and trusting reported probabilities. Recent work shows that enforcing calibration at the level of individual predictors can improve ensemble accuracy and calibration, with mixture-of-experts (MoE) models showing strong empirical improvements in particular; however, the conditions under which calibration helps MoE are not well understood. In this work, we study how MoE models behave under distribution shift, focusing on how routing mechanisms interact with expert-level calibration. We show that expert calibration is sufficient to ensure calibration of the overall model under a broad class of distribution shifts in hard-routed models, but is insufficient for calibrating soft-routed models. To address this, we propose an adversarial reweighting that penalizes calibration errors of the routed aggregate under distribution shift, and we demonstrate that it improves the accuracy-calibration tradeoff both on average and on difficult subsets of the data, across model classes, prediction tasks, and distribution shifts.

cs.AI↗

arXiv2026

Masked Symmetric Nonnegative Matrix Factorization for Community Detection in Incomplete Networks

Community detection in complex networks is frequently challenged by incomplete or noisy adjacency matrices. Traditional symmetric nonnegative matrix factorization methods typically rely on zero-imputation for unobserved entries, which compromises clustering reliability. This paper proposes a Masked Symmetric Nonnegative Matrix Factorization (Masked SymNMF) framework designed to factorize partially observed networks directly. By defining a masking operator over the observed entries, the proposed model restricts the objective evaluation exclusively to valid data. To overcome the severe non-convexity inherent in the symmetric factorization, we formulate an asymmetric relaxation penalized by a regularization term. We prove the exact penalty property of this reformulated model, establishing its theoretical equivalence to the original symmetric problem under sufficient regularization. Furthermore, an alternating nonnegative least squares framework is developed, yielding tailored update rules for Multiplicative Updates, Hierarchical Alternating Least Squares, and Projected Gradient Descent algorithms. Extensive numerical experiments on synthetic datasets and real-world networks demonstrate that the proposed Masked SymNMF outperforms baseline imputation methods across varying observation densities, providing a theoretically sound and practically efficient approach for community detection in incomplete networks.

math.OC↗

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

Efficient and Uncertainty-Aware Diffusion Framework for Offline-to-Online Reinforcement Learning

Offline-to-Online Reinforcement Learning (O2O-RL) leverages an offline, pre-trained policy to minimize costly online interactions. Although data-efficient, O2O-RL is susceptible to shifts between offline and online distributions. Existing work aims to mitigate the harm of this shift by finetuning the policy on trajectory data sampled from a diffusion model. Inspired by this line of work, we propose DUAL: an efficient \textbf{D}iffusion \textbf{U}ncertainty-\textbf{A}ware framework for offline-to-online reinforcement \textbf{L}earning. DUAL utilizes the prior knowledge of the diffusion model to distill a fast-sampling diffusion actor policy and transition model in the offline phase. DUAL also employs a Laplace approximation and distance transition-state-shift detection, thereby using uncertainty quantification to improve exploration versus exploitation in the online phase. We formally show that our actor loss with the Laplace approximation provides a proxy for a principled estimate of epistemic uncertainty. Empirically, DUAL improves the online expected return over O2O-RL baselines across multiple settings and environments.

cs.LG↗

arXiv2026

Configurable Reward Model for Balanced Safety Alignment

Aligning large language models (LLMs) to heterogeneous and rapidly evolving safety requirements remains a critical challenge. Existing instruction-tuned LLMs and standalone safety classifiers often fail to generalize to new safety configurations, motivating the need for Reward Models (RMs) that are explicitly configurable to changing specifications. We introduce the Configurable Safety Reward Model (CSRM), which is jointly optimized for calibrated safety compliance and reward modeling. Our approach is supported by configuration-targeted data augmentation that enforces instruction adherence while preserving relative severity structure. The resulting RM is sensitive to fine-grained safety configurations and conversational nuances, substantially improving generalization to previously unseen safety configurations. CSRM achieves state-of-the-art performance on recent configurable safety benchmarks, including CoSApien (94.6% F1) and DynaBench (75.8% F1), without requiring additional human annotation. When used for downstream safety alignment, CSRM yields LLMs with a significantly improved helpfulness-safety tradeoff compared to existing baselines.

cs.CL↗

arXiv2026

Controlling the Risk of Corrupted Contexts for Language Models via Early-Exiting

Large language models (LLMs) can be influenced by harmful or irrelevant context, which can significantly harm model performance on downstream tasks. This motivates principled designs in which LLM systems include built-in mechanisms to guard against such "garbage in, garbage out" scenarios. We propose a novel approach to limit the degree to which harmful context can degrade model performance. First, we define a baseline "safe" behavior for the model -- the model's performance given no context at all (zero-shot). Next, we apply distribution-free risk control (DFRC) to control the extent to which the user-provided context can decay performance below this safe zero-shot baseline. We achieve this by leveraging dynamic early exit prediction, ignoring later attention heads that attend the most to the unsafe inputs. Finally, we propose modifications to DFRC that allow it to both control risk for harmful inputs \textit{and} leverage performance and efficiency gains on helpful inputs. We present both theoretical and empirical results across 9 tasks spanning in-context learning and open-ended question answering, showing that our approach can effectively control risk for harmful context and simultaneously achieve substantial computational efficiency gains with helpful context.

cs.AI↗