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新论文 · v1arXiv:2611.09377

KineCouple: Substrate-conditioned residual readout for enzyme kinetic prediction

Chun Kang, Yunbo Zhang, Fanhu Zeng, Jian Liu, Siwei Deng, Lei Sha

原文摘要

Accurate prediction of enzyme kinetic parameters can support enzyme engineering and metabolic modeling by complementing experimental characterization. Existing prediction methods often pool residue-level protein features before combining them with substrate features. Such substrate-independent pooling cannot adapt residue weighting to the substrate during aggregation, potentially diluting information relevant to a specific enzyme-substrate pair. Since the contributions of individual residues to catalysis can depend on the substrate, substrate-conditioned aggregation offers a way to emphasize residue features relevant to the prediction. We introduce KineCouple, which uses substrate queries and residue-level keys and values in cross-attention, allowing the substrate to guide residue selection before aggregation. The model preserves the global protein representation and adds a gated correction defined as the difference between the conditioned readout and a uniform readout. ProtT5 and MolT5 remain frozen, and separate models predict kcat and Km on a logarithmic scale. In pooled out-of-fold predictions on the CataPro benchmarks, KineCouple reduces kcat RMSE from 1.333 to 1.330 and increases PCC from 0.492 to 0.496 relative to reproduced CataPro. For Km, RMSE decreases from 0.998 to 0.997 and PCC increases from 0.633 to 0.634. Spearman correlation also improves for both tasks.

cs.AI · q-bio.QM

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arXiv ↗PDF ↗
版本更新 · v2arXiv:2610.33745

POD-RoPE: Rotary Position Encoding over Physical Observation Distributions for Embodied AI

Xiaodi Huang, Zilin Wang, Jinpeng Liu, Pengchuan Xiao, Zhenlei Shao, Zhang Zhang

原文摘要

Embodied perception requires positional representations that capture both physical geometry and the spatial and temporal extent of observations. We introduce POD-RoPE (Physical Observation Distribution RoPE), which represents token observation footprints as distributions over camera centers, viewing directions, and sampling times. Under independent sampling, expected rotations encode relative relationships between distributions; when each distribution collapses to a single address, the construction recovers pointwise RoPE. The same rotation statistics support Q/K matching and coherence-dependent V/O transformations, allowing observation geometry to guide both information selection and content aggregation. Per-token pre-aggregation avoids increasing sequence length or processing pairs of observation nodes. We evaluate POD-RoPE across four robot policy architectures, simulation and real-world manipulation, and complementary reconstruction, depth-estimation, and novel-view-synthesis tasks. Integrating POD-RoPE into Fast-WAM improves mean success from 91.83% to 92.88% across all 50 RoboTwin 2.0 tasks, and from 32.5% to 52.5% on two real-robot tasks on Sharpa North. Controlled reconstruction ablations support the contributions of distribution encoding and V/O transformations. In H20 model-block benchmarks, POD-RoPE achieves median forward-plus-backward speedups of $1.91\times$ over P-RoPE and $5.34\times$ over RayRoPE, with a median latency overhead of 17.4% over Standard RoPE. These results support physical observation distributions as an effective and computationally efficient basis for geometry-aware attention.

cs.RO · cs.AI

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arXiv ↗PDF ↗
首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.1168ACL Anthology · ACL 2026

SafetyMem: Adaptive Jailbreak Defense via Dual-Component Safety Memory

Hao Wang, Ziyi Ni, Huacan Wang QuantaAlpha, Pin Lyu Institute of automation, Chinese academy of science, Chinese Academy of Sciences, Lei Sha Beihang University

原文摘要

Current defenses for Large Language Models (LLMs) often suffer from a ”memory gap”: parameter-modifying methods are computationally rigid, while inference-time filters cannot retain or reuse defense knowledge across interactions. To address this, we propose SafetyMem, a novel framework that secures LLMs through a dual-component safety memory system. SafetyMem consists of Semantic Safety Memory (SSM), which consolidates diverse jailbreak attempts into a structured knowledge base of attack patterns, and Episodic Safety Memory (ESM), which maintains an evolving set of procedural rules refined from historical detection failures. Unlike static defenses, SafetyMem allows the model to ”remember” and adapt to emerging adversarial strategies without parameter retraining. To further enhance robustness, we introduce an adversarial memory expansion mechanism that proactively generates challenging variants to solidify these memories. Experiments on standard and stealthy jailbreak benchmarks show that SafetyMem substantially reduces attack success rates while preserving efficiency and interpretability, consistently outperforming state-of-the-art baselines across multiple LLMs.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.1496ACL Anthology · ACL 2026

Self-SoftCoT: A Self-Consistent Framework via Position-Aware Latent Space Reinforcement Learning

Liangliang Dong Jilin University, Lianlei Shan, Shuaimin Li

原文摘要

While Chain-of-Thought (CoT) reasoning empowers Large Language Models (LLMs) to tackle complex tasks, its reliance on discrete token decoding imposes an inherent Discreteness Bottleneck, limiting expressiveness within a restricted vocabulary space. Existing continuous reasoning approaches, such as SoftCoT, mitigate this but typically rely on external auxiliary models, resulting in complex deployment and fractured inference pipelines. To address these challenges, we propose Self-SoftCoT, a self-contained framework that enables a frozen LLM to internally generate and consume latent thoughts without external assistants. By establishing a single-stream “Thinking → Speaking” closed-loop, we decouple latent planning from explicit generation. Furthermore, we adopt Group Sequence Policy Optimization (GSPO) to stabilize learning and employ Position-Aware Independent Projection to mitigate representation homogenization. Experimental results on five reasoning benchmarks demonstrate that our method significantly improves the reasoning performance of frozen LLMs. Specifically, our Qwen2.5-based model uses only N=2 soft tokens to outperform the SoftCoT baseline (N=4), improving the average accuracy from 75.06% to 78.42%. Similarly, LLaMA-3.1 performance increases from 70.52% to 74.55%.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表