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CPSea: Large-scale cyclic peptide-protein complex dataset for machinelearning in cyclic peptide design

Neural Information Processing Systems

Cyclic peptides exhibit better binding affinity and proteolytic stability compared to their linear counterparts. However, the development of cyclic peptide design models is hindered by the scarcity of data. To address this, we introduce CPSea(Cyclic Peptide Sea), a dataset of 2.71 million cyclic peptide-receptor complexes, curated through systematic mining of the AlphaFold Database (AFDB). Our pipeline extracts compact domains from AFDB, identifies cyclization sites using the ฮฒ-carbon (Cฮฒ) distance thresholds, and applies multi-stage filtering to ensure structure fidelity and binding compatibility. Compared with experimental data of cyclic peptides, CPSea shows similar distributions in metrics on structure fidelity and wet-lab compatibility. To our knowledge, CPSea is the largest cyclic peptide-receptor dataset to date, enabling end-to-end model training for the first time.


C2Prompt: Class-aware Client Knowledge Interaction for Federated Continual Learning

Neural Information Processing Systems

Federated continual learning (FCL) tackles scenarios of learning from continuously emerging task data across distributed clients, where the key challenge lies in addressing both temporal forgetting over time and spatial forgetting simultaneously. Recently, prompt-based FCL methods have shown advanced performance through task-wise prompt communication. In this study, we underscore that the existing prompt-based FCL methods are prone to class-wise knowledge coherence between prompts across clients. The class-wise knowledge coherence includes two aspects: (1) intra-class distribution gap across clients, which degrades the learned semantics across prompts, (2) inter-prompt class-wise relevance, which highlights crossclass knowledge confusion. During prompt communication, insufficient classwise coherence exacerbates knowledge conflicts among new prompts and induces interference with old prompts, intensifying both spatial and temporal forgetting. To address these issues, we propose a novel Class-aware Client Knowledge Interaction (C2Prompt) method that explicitly enhances class-wise knowledge coherence during prompt communication. Specifically, a local class distribution compensation mechanism (LCDC) is introduced to reduce intra-class distribution disparities across clients, thereby reinforcing intra-class knowledge consistency. Additionally, a class-aware prompt aggregation scheme (CPA) is designed to alleviate interclass knowledge confusion by selectively strengthening class-relevant knowledge aggregation. Extensive experiments on multiple FCL benchmarks demonstrate that C2Prompt achieves state-of-the-art performance.


Empirical Study on Robustness and Resilience in Cooperative Multi-Agent Reinforcement Learning

Neural Information Processing Systems

In cooperative Multi-Agent Reinforcement Learning (MARL), it is a common practice to tune hyperparameters in ideal simulated environments to maximize cooperative performance. However, policies tuned for cooperation often fail to maintain robustness and resilience under real-world uncertainties. Building trustworthy MARL systems requires a deep understanding of robustness, which ensures stability under uncertainties, and resilience, the ability to recover from disruptions--a concept extensively studied in control systems but largely overlooked in MARL. In this paper, we present a large-scale empirical study comprising over 82,620 experiments to evaluate cooperation, robustness, and resilience in MARL across 4 real-world environments, 13 uncertainty types, and 15 hyperparameters. Our key findings are: (1) Under mild uncertainty, optimizing cooperation improves robustness and resilience, but this link weakens as perturbations intensify. Robustness and resilience also varies by algorithm and uncertainty type.


Uni-LoRA: One Vector is All You Need

Neural Information Processing Systems

Low-Rank Adaptation (LoRA) has become the de facto parameter-efficient finetuning (PEFT) method for large language models (LLMs) by constraining weight updates to low-rank matrices. Recent works such as Tied-LoRA, VeRA, and VBLoRA push efficiency further by introducing additional constraints to reduce the trainable parameter space. In this paper, we show that the parameter space reduction strategies employed by these LoRA variants can be formulated within a unified framework, Uni-LoRA, where the LoRA parameter space, flattened as a highdimensional vector space RD, can be reconstructed through a projection from a subspace Rd, with d D. We demonstrate that the fundamental difference among various LoRA methods lies in the choice of the projection matrix, P RD d. Most existing LoRA variants rely on layer-wise or structure-specific projections that limit cross-layer parameter sharing, thereby compromising parameter efficiency. In light of this, we introduce an efficient and theoretically grounded projection matrix that is isometric, enabling global parameter sharing and reducing computation overhead. Furthermore, under the unified view of Uni-LoRA, this design requires only a single trainable vector to reconstruct LoRA parameters for the entire LLM - making UniLoRA both a unified framework and a "one-vector-only" solution. Extensive experiments on GLUE, mathematical reasoning, and instruction tuning benchmarks demonstrate that Uni-LoRA achieves state-of-the-art parameter efficiency while outperforming or matching prior approaches in predictive performance.


Russian warship fires warning shots near UK-registered yacht in Channel

BBC News

'It was surreal': British couple describe having warning shots fired near them by Russian warship A retired British couple who were on a yacht which had warning shots fired near it by a Russian warship in the English Channel have told the BBC the experience was surreal. Jane and Alan Kelvey were sailing 23 miles (37km) off the Isle of Wight in international waters when they came into close contact with the Russian frigate, the Admiral Grigorovich on Tuesday. Sir Keir Starmer said firing shots into the path of a UK-registered yacht was reckless - an incident the Ministry of Defence has described as an isolated one. Russia's Defence Ministry said the yacht had been on a dangerous approach towards the warship but the couple said they were not on a collision course. The incident comes days after Royal Marine Commandos intercepted a Russian shadow fleet tanker carrying sanctioned oil in the Channel on Sunday, in the first operation of its kind carried out by the British military.


On the SAC-BL Algorithm for Anomaly Detection

Neural Information Processing Systems

Visual anomaly detection is significant in safety-critical and reliability-sensitive scenarios. Prior studies mainly emphasize the design and training of scoring functions, while little effort has been devoted to constructing decision rules based on these score functions. A recent work Ma et al. (2025b) highlights this issue and proposes the SAC-BL algorithm to address it. This method consists of a strong anomaly constraint (SAC) network and a betting-like (BL) algorithm serving as the decision rule. The SAC-BL algorithm can control the false discovery rate (FDR).


Towards Thinking-Optimal Scaling of Test-Time Compute for LLMReasoning

Neural Information Processing Systems

Recent studies have shown that making a model spend more time thinking through longer Chain of Thoughts (CoTs) enables it to gain significant improvements in complex reasoning tasks. While current researches continue to explore the benefits of increasing test-time compute by extending the CoT lengths of Large Language Models (LLMs), we are concerned about a potential issue hidden behind the current pursuit of test-time scaling: Would excessively scaling the CoT length actually bring adverse effects to a model's reasoning performance? Our explorations on mathematical reasoning tasks reveal an unexpected finding that scaling with longer CoTs can indeed impair the reasoning performance of LLMs in certain domains. Moreover, we discover that there exists an optimal scaled length distribution that differs across different domains. Based on these insights, we propose a ThinkingOptimal Scaling strategy. Our method first uses a small set of seed data with varying response length distributions to teach the model to adopt different reasoning efforts for deep thinking. Then, the model selects its shortest correct response under different reasoning efforts on additional problems for self-improvement. Our self-improved models built upon Qwen2.5-32B-Instruct


Self-Verifying Reflection Helps Transformers with CoTReasoning

Neural Information Processing Systems

Advanced large language models (LLMs) frequently reflect in reasoning chainof-thoughts (CoTs), where they self-verify the correctness of current solutions and explore alternatives. However, given recent findings that LLMs detect limited errors in CoTs, how reflection contributes to empirical improvements remains unclear. To analyze this issue, in this paper, we present a minimalistic reasoning framework to support basic self-verifying reflection for small transformers without natural language, which ensures analytic clarity and reduces the cost of comprehensive experiments. Theoretically, we prove that self-verifying reflection guarantees improvements if verification errors are properly bounded. Experimentally, we show that tiny transformers, with only a few million parameters, benefit from self-verification in both training and reflective execution, reaching remarkable LLM-level performance in integer multiplication and Sudoku. Similar to LLM results, we find that reinforcement learning (RL) improves in-distribution performance and incentivizes frequent reflection for tiny transformers, yet RL mainly optimizes shallow statistical patterns without faithfully reducing verification errors.


Switchable Token-Specific Codebook Quantization For Face Image Compression

Neural Information Processing Systems

With the ever-increasing volume of visual data, the efficient and lossless transmission, along with its subsequent interpretation and understanding, has become a critical bottleneck in modern information systems. The emerged codebook-based solution utilize a globally shared codebook to quantize and dequantize each token, controlling the bpp by adjusting the number of tokens or the codebook size. However, for facial images--which are rich in attributes--such global codebook strategies overlook both the category-specific correlations within images and the semantic differences among tokens, resulting in suboptimal performance, especially at low bpp. Motivated by these observations, we propose a Switchable Token-Specific Codebook Quantization for face image compression, which learns distinct codebook groups for different image categories and assigns an independent codebook to each token. By recording the codebook group to which each token belongs with a small number of bits, our method can reduce the loss incurred when decreasing the size of each codebook group. This enables a larger total number of codebooks under a lower overall bpp, thereby enhancing the expressive capability and improving reconstruction performance. Owing to its generalizable design, our method can be integrated into any existing codebook-based representation learning approach and has demonstrated its effectiveness on face recognition datasets, achieving an average accuracy of 93.51% for reconstructed images at 0.05 bpp.


Hessian-guided Perturbed Wasserstein Gradient Flows for Escaping Saddle Points

Neural Information Processing Systems

Wasserstein gradient flow (WGF) is a common method to perform optimization over the space of probability measures. While WGF is guaranteed to converge to a first-order stationary point, for nonconvex functionals the converged solution does not necessarily satisfy the second-order optimality condition; i.e., it could converge to a saddle point. In this work, we propose a new algorithm for probability measure optimization, perturbed Wasserstein gradient flow (PWGF), that achieves second-order optimality for general nonconvex objectives. PWGF enhances WGF by injecting noisy perturbations near saddle points via a Gaussian process-based scheme. By pushing the measure forward along a random vector field generated from a Gaussian process, PWGF helps the solution escape saddle points efficiently by perturbing the solution towards the smallest eigenvalue direction of the Wasserstein Hessian. We theoretically derive the computational complexity for PWGF to achieve a second-order stationary point. Furthermore, we prove that PWGF converges to a global optimum in polynomial time for strictly benign objectives.