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Neural Scalable Symbolic Search Framework for Complex Logical Queries with Multiple Free Variables

✇cs.AI, q-bio.NC updates on arXiv.org
By: Weizhi Fei · Hang Yin · Zihao Wang · Shukai Zhao · Wei Zhang · Yangqiu Song
arXiv:2605.25985v1 Announce Type: new Abstract: Complex Query Answering (CQA) is a fundamental knowledge representation and reasoning task over incomplete knowledge graphs (KGs). Answering existential first-order queries with $k$ free variables (i.e., $\text{EFO}_k$ queries) is a crucial yet challenging problem, as it requires ranking answer tuples in $\mathcal{E}^k$, where $\mathcal{E}$ denotes the entity set of a KG. This quickly becomes intractable as $k$ grows. Consequently, existing benchmarks and methods rely on marginal rankings over individual variables; however, marginal rankings are a poor proxy for the true joint ranking of tuples. Building on neural symbolic search for $\text{EFO}_1$ queries, we propose Neural Scalable Symbolic Search (NS3), a budgeted framework that approximates joint ranking without enumerating $\mathcal{E}^k$. NS3 (i) answers marginalized sub-queries to obtain necessary candidate sets, (ii) merges multiple free variables into hypernodes whose domains are pruned and controlled by a dynamic budget $B$, and (iii) progressively reduces an $\text{EFO}_k$ query to an $\text{EFO}_{k-1}$ query over a budgeted reduced domain. Across three standard KG datasets, NS3 substantially improves joint ranking performance while retaining strong marginal accuracy. We further release a joint-ranking benchmark that extends existing $\text{EFO}_1$ datasets to $k=3$, enabling systematic evaluation of multi-variable queries. Our code is provided in https://github.com/HKUST-KnowComp/NS3_KDD2026.
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Towards Evaluation Engineering: An Empirical Study of ML Evaluation Harnesses in the Wild

✇cs.AI, q-bio.NC updates on arXiv.org
By: Zhimin Zhao · Zehao Wang · Abdul Ali Bangash · Bram Adams · Ahmed E. Hassan
arXiv:2605.24213v1 Announce Type: cross Abstract: Evaluation harnesses are software systems that orchestrate model evaluation by managing model invocation, data loading, metric computation, and result reporting. Despite their critical role in machine learning infrastructure, their operational challenges and engineering concerns have received limited attention so far. We present an empirical study of 57 evaluation harnesses, deriving a five-stage harness model and classifying 16,560 issues by workflow stage and root cause. Most harness operational challenges concentrate in the Specification stage (41.4% of issues), where harnesses integrate external models, datasets, and scoring judges. The three most frequent root causes of operational challenges are unimplemented features (24.3%), documentation gaps (20.3%), and missing input validation (17.2%), which together account for 61.7% of classified issues, spanning both defects in existing functionality and capability gaps that block intended workflows. Root causes also vary by workflow stage: environment incompatibility and external dependency breakage account for 36.2% of provisioning issues, whereas algorithmic error (25.9%) and validation gap (22.5%) dominate assessment issues. Together, these contributions establish an empirical foundation for treating evaluation engineering as a distinct software engineering concern.
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CollectionLoRA: Collecting 50 Effects in 1 LoRA via Multi-Teacher On-Policy Distillation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Fangtai Wu · Hailong Guo · Shijie Huang · Jiayi Song · Yubo Huang · Mushui Liu · Zhao Wang · Yunlong Yu · Jiaming Liu · Ruihua Huang
arXiv:2605.25378v1 Announce Type: cross Abstract: Customized image editing aims to equip pre-trained diffusion models with specific visual effects using limited paired data, typically via Low-Rank Adaptation (LoRA). As the number of desired effects grows, storing and dynamically loading numerous these effect LoRAs significantly increases deployment overhead. Furthermore, current pipelines typically cascade these effect LoRAs with acceleration modules for fast generation, which triggers severe parameter interference and results in concept bleeding and style degradation. We propose CollectionLoRA, a multi-teacher on-policy distillation framework capable of distilling the concepts of up to 50 different effect LoRAs along with few-step generation capabilities into a single LoRA. This fundamentally resolves the feature interference issue and significantly reduces deployment costs. Specifically, the method introduces (i) a Probabilistic Dual-Stream Routing mechanism that enables the model to randomly switch between data sources during training, effectively enhancing its generalization in unseen scenarios; (ii) an Asymmetric Orthogonal Prompting strategy to achieve concept isolation within the prompt space; (iii) a Coarse-to-Fine Distillation Objective to mitigate the distribution gap between the teacher and student models. Extensive evaluations show that CollectionLoRA distills all customized effects and few-step generation into a single LoRA, reducing deployment overhead while achieving concept fidelity comparable to or better than independently trained teacher models.
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Efficient and Scalable Neural Symbolic Search for Knowledge Graph Complex Query Answering

✇cs.AI, q-bio.NC updates on arXiv.org
By: Weizhi Fei · Zihao Wang · hang Yin · Shukai Zhao · Wei Zhang · Yangqiu Song
arXiv:2505.08155v4 Announce Type: replace Abstract: Complex Query Answering (CQA) is a crucial reasoning task over Knowledge Graphs (KGs), which aims to answer first-order logical queries from incomplete KGs. While existing neural-symbolic methods achieve strong performance, they face significant complexity bottlenecks: quadratic data complexity scaling with the number of entities, and NP-hard query complexity for cyclic queries. Consequently, these approaches struggle to scale effectively to large knowledge graphs and complex queries. To address these limitations, we propose an efficient and scalable symbolic search method comprising two key components: (1) constraint strategies that drastically reduce the variable search domain, lowering data complexity; and (2) a local search algorithm that approximately solves NP-hard cyclic queries. Experiments on various CQA benchmarks demonstrate that, for tree-form queries, our method achieves 97% relative MRR with a 10$\times$ speedup using only 10% of the search space. Furthermore, it demonstrates robust performance on complex cyclic queries and large-scale KGs, effectively alleviating efficiency and scalability challenges. Our code is provided in https://github.com/HKUST-KnowComp/NLISA_KDD2026.
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Kolmogorov-Arnold Fourier Networks

✇cs.AI, q-bio.NC updates on arXiv.org
By: Jusheng Zhang · Yijia Fan · Kaitong Cai · Keze Wang · Wenhao Wang
arXiv:2502.06018v3 Announce Type: replace-cross Abstract: Although Kolmogorov-Arnold-based interpretable networks (KANs) possess strong theoretical expressiveness, they suffer from severe parameter explosion and limited ability to capture high-frequency features in high-dimensional tasks. To address these issues, we propose the Kolmogorov-Arnold Fourier Network (KAF), which fundamentally redefines the KAN paradigm through spectral reparameterization. Our key contributions include: (1) proposing a fundamental basis transformation from the local, grid-based B-spline representation to a global, adaptive spectral representation. This shift changes the network's inductive bias, reducing parameter complexity from $O(G)$ to $O(1)$ while preserving expressiveness; (2) introducing trainable Random Fourier Features (RFF) initialized via a spectral alignment strategy, which allows the model to break the smoothness limitation of fixed kernels and accurately capture high-frequency components; and (3) implementing an adaptive hybrid GELU-Fourier activation mechanism that progressively enhances frequency representation during training. Comprehensive experiments demonstrate the superiority of KAF across computer vision (CV), natural language processing (NLP), audio, and partial differential equation (PDE) solving tasks, achieving state-of-the-art performance with improved efficiency. The code is available at https://github.com/kolmogorovArnoldFourierNetwork/KAF.
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PiXTime: A Model for Federated Time Series Forecasting with Heterogeneous Data across Nodes

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yiming Zhou · Jiahao Wang · Mingyue Cheng · Hao Wang · Defu Lian · Enhong Chen
arXiv:2601.05613v2 Announce Type: replace-cross Abstract: While collaborative forecasting on distributed time series is highly desirable, directly pooling localized datasets is often impractical due to data sharing constraints. Federated learning offers a promising alternative, yet conventional federated learning algorithms require homogeneous model architectures, which are incompatible with the structural discrepancies, such as unaligned temporal resolutions and mismatched variable channels, commonly observed across decentralized nodes. To bridge this gap, we introduce PiXTime, a novel Transformer-based framework designed to natively accommodate and leverage structurally heterogeneous temporal data. At its core, PiXTime adopts a parameter-decoupling architecture, strategically partitioning the model into localized personalized modules and a globally aggregated shared backbone. Specifically, node-specific local modules act as dimensional adapters, projecting raw sequences of diverse lengths into a unified representation space. Concurrently, a globally synchronized VE Table injects consistent categorical identities into the feature space, allowing the shared backbone to collaboratively learn and generalize representations across inconsistent variable distributions. Comprehensive evaluations on multiple benchmarks demonstrate that PiXTime achieves state-of-the-art performance in heterogeneous federated environments, while maintaining robust superiority in standard homogeneous and centralized forecasting settings.
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BEAR: Towards Beam-Search-Aware Optimization for Recommendation with Large Language Models

✇cs.AI, q-bio.NC updates on arXiv.org
By: Weiqin Yang · Bohao Wang · Zhenxiang Xu · Jiawei Chen · Shengjia Zhang · Jingbang Chen · Canghong Jin · Can Wang
arXiv:2601.22925v3 Announce Type: replace-cross Abstract: Recent years have seen a rapid surge in research leveraging Large Language Models (LLMs) for recommendation. These methods typically employ supervised fine-tuning (SFT) to adapt LLMs to recommendation scenarios, and utilize beam search during inference to efficiently retrieve $B$ top-ranked recommended items. However, we identify a critical training-inference inconsistency: while SFT optimizes the overall probability of positive items, it does not guarantee that such items will be retrieved by beam search even if they possess high overall probabilities. Due to the greedy pruning mechanism, beam search can prematurely discard a positive item once its prefix probability is insufficient. To address this inconsistency, we propose BEAR (Beam-SEarch-Aware Regularization), a novel fine-tuning objective that explicitly accounts for beam search behavior during training. Rather than directly simulating beam search for each instance during training, which is computationally prohibitive, BEAR enforces a relaxed necessary condition: each token in a positive item must rank within the top-$B$ candidate tokens at each decoding step. This objective effectively mitigates the risk of incorrect pruning while incurring negligible computational overhead compared to standard SFT. Extensive experiments across four real-world datasets demonstrate that BEAR significantly outperforms strong baselines. Code is available at https://github.com/Tiny-Snow/BEAR-SIGIR-2026 .
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Prism: Spectral-Aware Block-Sparse Attention

✇cs.AI, q-bio.NC updates on arXiv.org
By: Xinghao Wang · Pengyu Wang · Xiaoran Liu · Fangxu Liu · Jason Chu · Kai Song · Xipeng Qiu
arXiv:2602.08426v2 Announce Type: replace-cross Abstract: Block-sparse attention is promising for accelerating long-context LLM pre-filling, yet identifying relevant blocks efficiently remains a bottleneck. Existing methods typically employ coarse-grained attention as a proxy for block importance estimation, but often resort to expensive token-level searching or scoring, resulting in significant selection overhead. In this work, we trace the inaccuracy of standard coarse-grained attention via mean pooling to a theoretical root cause: the interaction between mean pooling and Rotary Positional Embeddings (RoPE). We prove that mean pooling acts as a low-pass filter that induces destructive interference in high-frequency dimensions, effectively creating a "blind spot" for local positional information (e.g., slash patterns). To address this, we introduce Prism, a training-free spectral-aware approach that decomposes block selection into high-frequency and low-frequency branches. By applying energy-based temperature calibration, Prism restores the attenuated positional signals directly from pooled representations, enabling block importance estimation using purely block-level operations, thereby improving efficiency. Extensive evaluations confirm that Prism maintains accuracy parity with full attention while delivering up to $\mathbf{5.1\times}$ speedup.
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PRXL2B facilitates the progression of hepatocellular carcinoma and the therapeutic efficacy of oncolytic adenovirus H101 through the PI3K/AKT/PD-L1 axis

✇Omics in Hepatocellular
By: Ziqi Zhang · Hongli Chen · Yangming Liu · Hao Wang · You Yan · Yanxi Yu · Zuotian Huang · Yanyao Liu · Wei Li · Zhongjun Wu · Meiqing Kang · Xiaoyong Luo · Ping Che · Rui Liao

Biosci Trends. 2026 May 21. doi: 10.5582/bst.2026.01000. Online ahead of print.

ABSTRACT

Oncolytic adenovirus H101 has shown antitumor activity in hepatocellular carcinoma (HCC), but the molecular determinants of treatment response remain unclear. In this study, a Hepa1-6 subcutaneous tumor model was established in C57BL/6 mice and treated with intratumoral H101, followed by integrated transcriptomic and proteomic analyses to identify candidate genes associated with H101 response. PRXL2B was selected for further investigation using public multi-omics datasets, tissue microarray-based immunohistochemistry, in vitro functional assays, mechanistic analyses, and in vivo validation experiments. Integrated multi-omics analyses identified PRXL2B as a candidate gene downregulated after H101 treatment. Public datasets and tissue-based validation further showed that PRXL2B was upregulated in HCC tissues. In MHCC97H and HCCLM3 cells, PRXL2B knockdown inhibited proliferation, migration, and invasion, promoted apoptosis and cell-cycle arrest, and enhanced the antitumor effect of H101. Mechanistically, PRXL2B silencing reduced AKT phosphorylation and PD-L1 expression. In vivo, PRXL2B knockdown suppressed tumor growth, and the combination of PRXL2B knockdown and H101 produced the strongest antitumor effect. These findings indicate that PRXL2B promotes malignant phenotypes in HCC and may modulate H101 efficacy through the PI3K/AKT/PD-L1 axis. Targeting PRXL2B may therefore represent a potential strategy to enhance the therapeutic efficacy of oncolytic virus therapy in HCC.

PMID:42161529 | DOI:10.5582/bst.2026.01000

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Proteomic and lipidomic analyses reveal molecular subtypes and potential targets in early-stage lung adenocarcinoma among non-smokers

✇Pulmonary nodule
By: Yaohui Sun · Jian Liu · Xin Xu · Qiqi Liu · Hua Cheng · Wenwen Huo · Ronghao Wang · Qingdong Cao

Cell Rep. 2026 May 26;45(5):117215. doi: 10.1016/j.celrep.2026.117215. Epub 2026 Apr 28.

ABSTRACT

Early-stage lung adenocarcinoma (LUAD) in never smokers exhibits distinct biological features, yet the metabolic programs driving early invasion remain unclear. We integrate proteomic and lipidomic profiling of primary LUAD tumors from never smokers, matched normal adjacent tissues (NATs), and benign pulmonary nodules (BPNs). Integrated multi-omics analysis reveals coordinated dysregulation of lipid metabolism and immune signaling in early LUAD. Proteome-based network fusion stratifies invasive LUAD into immune-metabolic synergistic (IMS) and metabolic-stress-driven (MSD) subtypes. IMS tumors retain apolipoprotein-associated lipid modules and favorable immune features, whereas MSD tumors exhibit stress-response programs. Mechanistically, APOA1 and APOC1 emerge as key nodes linking lipid homeostasis to invasion, and their depletion promotes LUAD cell migration and invasion. We establish a two-protein, four-lipid diagnostic panel demonstrating robust performance across tissue and plasma cohorts. These findings provide a molecular basis for early detection and risk stratification in never smokers.

PMID:42054209 | DOI:10.1016/j.celrep.2026.117215

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An activated wheat CCG10-NLR immune receptor forms an octameric resistosome

✇Cell
By: Guanghao Guo · He Zhao · Kaihong Bai · Jian Lu · Qiuhong Wu · Lei Lu · Yue Zhang · Lingli Dong · Guangwei Li · Yongxing Chen · Yikun Hou · Ping Lu · Miaomiao Li · Huaizhi Zhang · Gaojie Wang · Keyu Zhu · Baoge Huang · Xuejia Cui · Hongkui Fu · Chenchen Hu · Zhiying Chu · Xue Lyu · Sophien Kamoun · Chao Wang · Zhiyong Liu · Muniyandi Selvaraj · Jonathan D.G. Jones
An activated CCG10-NLR WAI3 plant immune receptor forms an octameric resistosome, which induces calcium influx and immune responses through a unique channel architecture.
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