Zilu Zhang, Jing Bao, Lifeng Qiao, Sheng Xu, Qiantai Feng, Siqi Sun, Yang Yang
Protein-complex structure prediction with AlphaFold 3 depends on MSA content, depth, and cross-chain pairing. Current pipelines apply uniform recipes, typically maximizing depth and pairing by species, yet even whether cross-chain pairing helps AF3 remains contested. We show that the value of both depth and pairing is strongly target-dependent, so no single recipe is optimal across interfaces. We introduce an autonomous agent that treats a frozen AF3 as a black-box experimental instrument. For each target, the agent formulates biological hypotheses, analyzes and reorganizes the MSA, and iteratively refines sequence selection and pairing using predictor label-free signals alone. On 1{,}015 protein--protein interfaces from three benchmarks released after AF3's training cutoff, the agent improves overall interface DockQ over AF3's default pipeline and fixed MSA recipes on every benchmark, while using on average 60\% fewer MSA sequences than the default. Gains are largest for inter-species heteromers, where species-based pairing is unreliable: mean DockQ increases from 0.465 to 0.612 on FoldBench and from 0.482 to 0.562 on HD439. The improvements arise from both sequence construction and pairing policy, including deliberate non-pairing. These results recast MSA design as a target-specific problem and show that an autonomous agent can adapt it at test time through biological reasoning and self-directed, confidence-guided experimentation.
Anqi Yu, Xudong Xu, Jianzhi Lu, Yuqi Sun, Bingguo Chen, Chenxi Ma, Weimin Tan, Bo Yan
Spatial multi-omics technologies jointly profile diverse molecular modalities with spatial context, providing a comprehensive view of cellular heterogeneity and tissue organization. To integrate spatial multi-omics data and identify spatial domains, a wide range of unsupervised methods has been proposed. However, recent approaches rely on single-step fusion, directly aggregating heterogeneous modalities into a shared representation, making embeddings sensitive to modality imbalance and measurement noise that are inherent to spatial multi-omics data, as well as unstable optimization under weak supervision. Here, we propose ILR-SMO (Iterative Latent Refinement for Spatial Multi-Omics), a unified self-supervised framework that reformulates multimodal integration as a stability-aware refinement process over a shared latent representation. Instead of single-step plain fusion, ILR-SMO progressively integrates modality-specific information through sequential updates, allowing information to be injected in a controlled manner. This incremental refinement enables later updates to correct or compensate for earlier deviations, resulting in more stable and robust representation learning under heterogeneous and noisy modalities. ILR-SMO further incorporates reliability-aware modality gating for adaptive modulation of modality contributions, and employs a joint objective to enforce spatial coherence while preventing representation collapse. Extensive experiments on five spatial multi-omics benchmarks demonstrate that ILR-SMO consistently outperforms seven state-of-the-art methods and exhibits strong robustness across diverse settings.
Large language model (LLM) agents have demonstrated strong capabilities in automating complex information-seeking and transactional tasks across the open web. However, their real-world reliability remains limited by access barriers, such as dead links, authentication walls, rate limits, and anti-scraping defenses. These barriers block the primary execution path, causing agents to abort prematurely, loop indefinitely, or quietly compromise the user's original constraints. Existing evaluations either implicitly assume that target resources are freely accessible or focus on transient perturbations that simple retries can resolve, failing to capture scenarios where agents must actively reroute around impassable bottlenecks. To bridge this gap, this paper introduces AgentHeal, a comprehensive benchmark evaluating goal-preserving resource recovery, defined as the ability of web agents to detect non-transient access barriers, pivot to legitimate alternative sources, and fulfill the user's exact original objective. Spanning nine barrier families across a counterfactual sandbox and real-website replay, our experiments on leading LLM backbones show that average task success drops sharply from 89.4% to 43.7% under access barriers. Further analysis reveals that agents frequently fall for deceptive look-alikes, fail to escalate to users when necessary, violate access policies, or waste computation on futile retries, providing actionable diagnostics for developing resilient web agents.
Neural representation has emerged as a powerful tool to mitigate the demand for increasingly higher-resolution images. However, a fundamental trade-off remains between structured (e.g., feature grids, which offer spatial consistency) and unstructured (e.g., 2D Gaussians, which adaptively capture local variances) representations. This choice significantly affects how well an algorithm represents an image. Here, we present Gaussian-Grid, a hybrid neural representation that adaptively integrates structured and unstructured primitives. By dynamically partitioning computation between 2D Gaussian distributions and their attached multi-resolution feature grids based on the local frequency content, Gaussian-Grid automatically optimizes its architecture to match the underlying complexity of the target signal. We evaluate our approach using high-resolution natural images and demonstrate its applications as GPU-native dataset storage, showing $1.24$-$2.14\times$ decoding speed improvement and PCIe data traffic reduction of $23\times$-$176\times$ over JPEG + ZIP data archiving. The results show that Gaussian-Grid maintains small memory footprints while achieving high reconstruction fidelity across a variety of datasets.
Junpeng Ding, Zichen Tang Beijing University of Posts and Telecommunications, Haihong E Beijing University of Post and Telecommunication, Mengyuan Ji, Yang Liu, Haolin Tian, Haiyang Sun, Pengqi Sun 等 20 位作者
We introduce SPUR, a comprehensive benchmark for scientific experimental image perception, understanding, and reasoning, comprising 4,264 question-answering (QA) pairs derived from 1,084 expert-curated images. SPUR features three key innovations: (1) Panel-Level Fine-Grained Perception: evaluating the visual perception of multimodal large language models (MLLMs) across three dimensions (numerical, morphological, and information localization) on six fine-grained panel types; (2) Cross-Panel Relation Understanding: utilizing complex images with an average of 14.3 panels per sample to evaluate MLLMs’ ability to decipher intricate cross-panel relations; (3) Expert-Level Reasoning: assessment of qualitative and quantitative reasoning across five experimental paradigms to determine if models can infer conclusions from evidence as human experts do. Comprehensive evaluation of 20 MLLMs and four multimodal Chain-of-Thought (MCoT) methods reveals that current models fall significantly short of the expert-level requirements for scientific image interpretation, underscoring a critical bottleneck in AI for Science (AI4S) research.
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cs.CL · cs.CV
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表