arXiv:2603.03655v1 Announce Type: new Abstract: Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

arXiv:2603.04135v1 Announce Type: cross Abstract: Group Relative Policy Optimization (GRPO) effectively scales LLM reasoning but incurs prohibitive computational costs due to its extensive group-based sampling requirement. While recent selective data utilization methods can mitigate this overhead, they could induce estimation bias by altering the underlying sampling distribution, compromising theoretical rigor and convergence behavior. To address this limitation, we propose Dynamic Pruning Policy Optimization (DPPO), a framework that enables dynamic pruning while preserving unbiased gradient estimation through importance sampling-based correction. By incorporating mathematically derived rescaling factors, DPPO significantly accelerates GRPO training without altering the optimization objective of the full-batch baseline. Furthermore, to mitigate the data sparsity induced by pruning, we introduce Dense Prompt Packing, a window-based greedy strategy that maximizes valid token density and hardware utilization. Extensive experiments demonstrate that DPPO consistently accelerates training across diverse models and benchmarks. For instance, on Qwen3-4B trained on MATH, DPPO achieves 2.37$\times$ training speedup and outperforms GRPO by 3.36% in average accuracy across six mathematical reasoning benchmarks.

arXiv:2603.02265v1 Announce Type: cross Abstract: In order to evaluate the invulnerability of networks against various types of attacks and provide guidance for potential performance enhancement as well as controllability maintenance, network controllability robustness (NCR) has attracted increasing attention in recent years. Traditionally, controllability robustness is determined by attack simulations, which are computationally time-consuming and only applicable to small-scale networks. Although some machine learning-based methods for predicting network controllability robustness have been proposed, they mainly focus on pairwise interactions in complex networks, and the underlying relationships between high-order structural information and controllability robustness have not been explored. In this paper, a dual hypergraph attention neural network model based on high-order knowledge (NCR-HoK) is proposed to accomplish robustness learning and controllability robustness curve prediction. Through a node feature encoder, hypergraph construction with high-order relations, and a dedicated dual hypergraph attention module, the proposed method can effectively learn three types of network information simultaneously: explicit structural information in the original graph, high-order connection information in local neighborhoods, and hidden features in the embedding space. Notably, we explore for the first time the impact of high-order knowledge on network controllability robustness. Compared with state-of-the-art methods for network robustness learning, the proposed method achieves superior performance on both synthetic and real-world networks with low computational overhead.

arXiv:2603.02406v1 Announce Type: cross Abstract: Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43\% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8\% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling. The code is available at: https://github.com/ZhanghanNi/RigidSSL.git.

arXiv:2510.14686v2 Announce Type: replace-cross Abstract: We introduce xLLM, an intelligent and efficient Large Language Model (LLM) inference framework designed for high-performance, large-scale enterprise-grade serving, with deep optimizations for diverse AI accelerators. To address these challenges, xLLM builds a novel decoupled service-engine architecture. At the service layer, xLLM-Service features an intelligent scheduling module that efficiently processes multimodal requests and co-locates online and offline tasks through unified elastic scheduling to maximize cluster utilization. This module also relies on a workload-adaptive dynamic Prefill-Decode (PD) disaggregation policy and a novel Encode-Prefill-Decode (EPD) disaggregation policy designed for multimodal inputs. Furthermore, it incorporates a distributed architecture to provide global KV Cache management and robust fault-tolerant capabilities for high availability. At the engine layer, xLLM-Engine co-optimizes system and algorithm designs to fully saturate computing resources. This is achieved through comprehensive multi-layer execution pipeline optimizations, an adaptive graph mode and an xTensor memory management. xLLM-Engine also further integrates algorithmic enhancements such as optimized speculative decoding and dynamic EPLB, collectively serving to substantially boost throughput and inference efficiency. Extensive evaluations demonstrate that xLLM delivers significantly superior performance and resource efficiency. Under identical TPOT constraints, xLLM achieves throughput up to 1.7x that of MindIE and 2.2x that of vLLM-Ascend with Qwen-series models, while maintaining an average throughput of 1.7x that of MindIE with Deepseek-series models. xLLM framework is publicly available at https://github.com/jd-opensource/xllm and https://github.com/jd-opensource/xllm-service.