arXiv:2609.10055v1 Announce Type: new Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

arXiv:2605.24598v1 Announce Type: new Abstract: Large language model (LLM) agents excel at solving complex long-horizon tasks through autonomous interaction with environments. However, their real-world deployment faces a fundamental device--cloud dilemma: on-device models are efficient but often brittle, while cloud models are stronger but costly in computation. State-of-the-art LLM device--cloud routers usually make coarse task-level decisions, which cannot adapt to the changing difficulty of multi-step agent interactions. To address this issue, we present Hera, a step-level device--cloud LLM agent coordinator for long-horizon tasks achieving a strong performance--cost Pareto frontier. Hera adopts a novel two-stage training paradigm: (1) imitation learning for cold-start, followed by (2) reinforcement learning that jointly optimizes task success and cloud usage efficiency. The first stage casts step-level routing as a supervised classification problem: the device agent is replayed on cloud trajectories, with each state labeled by the agreement between device and cloud actions. In the second stage, we perform cost-aware reinforcement learning by grouping identical states across trajectories and updating Hera with labels favoring higher expected return and fewer future cloud calls. We evaluate Hera on ALFWorld, WebShop, and AppWorld, where it consistently outperforms prior methods, achieving 92.5% of the cloud-only success rate with cloud use in only 46.3% of steps.

arXiv:2605.24993v1 Announce Type: new Abstract: Current fMRI decoders face a performance-fidelity trade-off where efficient ID encoders outperform geometrically faithful surface-based models. We argue this is partly driven by inefficient surface tokenization and the failure to use anatomy as a predictive signal. We present NeurIPS, a framework that improves surface-based decoding by reframing anatomical variation from a nuisance to a powerful inductive prior. NeurIPS unites two innovations: a Selective ROI Spherical Tokenizer (SRST) for efficient geometric encoding, and a Structure-Guided Mixture of Experts (SG-MoE) that explicitly models individual anatomy using cortical features. On the Natural Scenes Dataset, NeurIPS establishes a new state-of-the-art for surface decoders and achieves performance comparable to strong 1D baselines. This is achieved with unprecedented efficiency, as the model converges dramatically faster (10 vs. 600 epochs). This efficiency enables rapid adaptation to new subjects using only 20% of data and ensures robust scalability as the training cohort is expanded. Ablations provide causal evidence that these gains are driven by the model's use of cortical features, not by memorizing subject IDs. By leveraging anatomical priors, NeurIPS provides a principled and scalable path toward robust, generalizable brain decoding.

arXiv:2402.03627v4 Announce Type: replace-cross Abstract: As Large Language Models make a breakthrough in natural language processing tasks (NLP), multimodal technique becomes extremely popular. However, it has been shown that multimodal NLP are vulnerable to adversarial attacks, where the outputs of a model can be dramatically changed by a perturbation to the input. While several defense techniques have been proposed both in computer vision and NLP models, the multimodal robustness of models have not been fully explored. In this paper, we study the adversarial robustness provided by modifying loss function of pre-trained multimodal models, by restricting top K softmax outputs. Based on the evaluation and scoring, our experiments show that after a fine-tuning, adversarial robustness of pre-trained models can be significantly improved, against popular attacks. Further research should be studying, such as output diversity, generalization and the robustness-performance trade-off of this kind of loss functions. Our code will be available after this paper is accepted

arXiv:2411.10406v3 Announce Type: replace-cross Abstract: In the span of four decades, quantum computation has evolved from an intellectual curiosity to a potentially realizable technology. Today, small-scale demonstrations have become possible for quantum algorithmic primitives on hundreds of physical qubits. Nevertheless, there are significant outstanding challenges in quantum hardware, fabrication, software architecture, and algorithms on the path towards a full-stack scalable quantum computing technology. Here, we provide a comprehensive review of these scaling challenges. We show how to facilitate scaling by adopting existing semiconductor technology to build much higher-quality qubits, employing systems engineering approaches, and performing distributed heterogeneous quantum-classical computing. We provide a detailed resource and sensitivity analysis for quantum applications on surface-code error-corrected quantum computers given current, target, and desired hardware specifications based on superconducting qubits, accounting for a realistic distribution of errors. We provide comprehensive resource estimates for several utility-scale applications including quantum chemistry calculations, catalyst design, NMR spectroscopy, and Fermi-Hubbard simulation. We show that orders of magnitude enhancement in performance could be obtained by a combination of hardware improvements and tight quantum-HPC integration. Furthermore, we introduce high-performance architectures for quantum-probabilistic computing with custom-designed accelerators to tackle today's industry-scale classical optimization, machine learning, and quantum simulation tasks in a cost-effective manner.

arXiv:2603.07472v1 Announce Type: cross Abstract: In this study, we present a conditional diffusion-transformer framework for generating ensembles of three-dimensional Escherichia coli genome conformations guided by Hi-C contact maps. Instead of producing a single deterministic structure, we formulate genome reconstruction as a conditional generative modeling problem that samples heterogeneous conformations whose ensemble-averaged contacts are consistent with the input Hi-C data. A synthetic dataset is constructed using coarse-grained molecular dynamics simulations to generate chromatin ensembles and corresponding Hi-C maps under circular topology. Our models operate in a latent diffusion setting with a variational autoencoder that preserves per-bin alignment and supports replication-aware representations. Hi-C information is injected through a transformer-based encoder and cross-attention, enforcing a physically interpretable one-way constraint from Hi-C to structure. The model is trained using a flow-matching objective for stable optimization. On held-out ensembles, generated structures reproduce the input Hi-C distance-decay and structural correlation metrics while maintaining substantial conformational diversity, demonstrating the effectiveness of diffusion-based generative modeling for ensemble-level 3D genome reconstruction.

arXiv:2602.20980v2 Announce Type: replace-cross Abstract: Multimodal Large Language Models (MLLMs) have achieved remarkable performance by integrating powerful language backbones with large-scale visual encoders. Among these, latent Chain-of-Thought (CoT) methods enable implicit reasoning in continuous hidden states, facilitating seamless vision-language integration and faster inference. However, existing heuristically predefined supervision signals in latent CoT provide limited guidance for preserving critical visual information in intermediate latent states. To address this limitation, we propose CrystaL (Crystallized Latent Reasoning), a single-stage framework with two paths to process intact and corrupted images, respectively. By explicitly aligning the attention patterns and prediction distributions across the two paths, CrystaL crystallizes latent representations into task-relevant visual semantics, without relying on auxiliary annotations or external modules. Extensive experiments on perception-intensive benchmarks demonstrate that CrystaL consistently outperforms state-of-the-art baselines, achieving substantial gains in fine-grained visual understanding while maintaining robust reasoning capabilities.

arXiv:2603.03325v1 Announce Type: cross Abstract: Large language models (LLMs) have become integral to modern Human-AI collaboration workflows, where accurately understanding user intent serves as a crucial step for generating satisfactory responses. Context-aware intent understanding, which involves inferring user intentions from situational environments, is inherently challenging because it requires reasoning over both the immediate context and the user's underlying motivations that drive their behavior. Moreover, existing approaches often treat intent understanding as a static recognition task, overlooking users' accumulated intent patterns that could provide valuable references for more accurate and generalizable understanding. To address this gap, we propose IntPro, a proxy agent that learns to adapt to individual users via retrieval-conditioned intent inference. We design intent explanations that abstract how contextual signals connect to expressed intents, and store them in an individual intent history library for retrieval. We train IntPro through supervised fine-tuning on retrieval-conditioned trajectories and multi-turn Group Relative Policy Optimization (GRPO) with tool-aware reward functions, enabling the agent to learn when to leverage historical intent patterns and when to infer directly. Experiments across three diverse scenarios (Highlight-Intent, MIntRec2.0, and Weibo Post-Sync) demonstrate that IntPro achieves strong intent understanding performance with effective context-aware reasoning capabilities across different scenarios and model types.

arXiv:2602.19416v1 Announce Type: new Abstract: Reinforcement Learning from Human Feedback (RLHF) enables powerful LLM alignment but can introduce reward hacking - models exploit spurious correlations in proxy rewards without genuine alignment. Compounding this, the objectives internalized during RLHF remain opaque, making hacking behaviors difficult to detect or correct. We introduce IR3 (Interpretable Reward Reconstruction and Rectification), a framework that reverse-engineers, interprets, and surgically repairs the implicit objectives driving RLHF-tuned models. We propose Contrastive Inverse Reinforcement Learning (C-IRL), which reconstructs the implicit reward function by contrasting paired responses from post-alignment and baseline policies to explain behavioral shifts during RLHF. We then decompose the reconstructed reward via sparse autoencoders into interpretable features, enabling identification of hacking signatures through contribution analysis. Finally, we propose mitigation strategies - clean reward optimization, adversarial shaping, constrained optimization, and feature-guided distillation - that target problematic features while preserving beneficial alignment. Experiments across multiple reward model configurations show that IR3 achieves 0.89 correlation with ground-truth rewards, identifies hacking features with over 90% precision, and significantly reduces hacking behaviors while maintaining capabilities within 3% of the original model.

arXiv:2505.06595v3 Announce Type: replace-cross Abstract: In this paper, we propose a method for transferring feature representation to lightweight student models from larger teacher models. We mathematically define a new notion called \textit{perception coherence}. Based on this notion, we propose a loss function, which takes into account the dissimilarities between data points in feature space through their ranking. At a high level, by minimizing this loss function, the student model learns to mimic how the teacher model \textit{perceives} inputs. More precisely, our method is motivated by the fact that the representational capacity of the student model is weaker than the teacher model. Hence, we aim to develop a new method allowing for a better relaxation. This means that, the student model does not need to preserve the absolute geometry of the teacher one, while preserving global coherence through dissimilarity ranking. Importantly, while rankings are defined only on finite sets, our notion of \textit{perception coherence} extends them into a probabilistic form. This formulation depends on the input distribution and applies to general dissimilarity metrics. Our theoretical insights provide a probabilistic perspective on the process of feature representation transfer. Our experiments results show that our method outperforms or achieves on-par performance compared to strong baseline methods for representation transferring.