In the infection courses of different SARS-CoV-2 variants, disease outcomes and signatures were delineated by physiological changes, viral load, pathology, and pulmonary transcriptome analysis. This multi-dimensional landscape of disease outcomes and underlying mechanisms might provide important clues for immunotherapy of SARS-CoV-2 infection and pneumonia caused by other respiratory viruses.

arXiv:2605.24489v1 Announce Type: new Abstract: Enzyme-reaction retrieval is a fundamental problem in computational biology, underpinning enzyme characterization, reaction mechanism elucidation, and the rational design of metabolic pathways and biocatalysts. As a bidirectional task, it entails both enzyme-to-reaction and reaction-to-enzyme mapping. However, existing approaches suffer from poor generalization across tasks and distributions, with performance highly sensitive to dataset splits and substantial asymmetry between retrieval directions. To address these challenges, we present TIGER, a Text-Informed Generalized Enzyme-Reaction Retrieval framework that leverages protein-to-text generation models to distill textual semantic knowledge from enzyme sequences, providing a generalized representation that bridges enzymes and biochemical reactions. To ensure the quality and reliability of textual semantics, we design a Dynamic Gating Network that adaptively fuses text-derived knowledge with sequence features, enabling more consistent and informative enzyme representations, while a Structure-Shared Feature Projector aligns enzyme and reaction representations within a unified latent space. Extensive experiments demonstrate that, under bidirectional retrieval supervision, TIGER significantly outperforms state-of-the-art baselines across diverse distributions and exhibits strong robustness and transferability across tasks.

arXiv:2605.24686v1 Announce Type: new Abstract: As large language models (LLMs) are increasingly integrated into emotionally sensitive domains, the structural integrity of their emotional intelligence (EI) becomes a critical frontier for safety and alignment. Current benchmarks often conflate superficial politeness with deep affective reasoning, failing to distinguish between perceptual accuracy and interactive efficacy. Here, we introduce FACET (Functional Affective Competence and Empathy Test), a psychometrically grounded framework comprising 480 expert-crafted items. Unlike previous metrics, FACET is theoretically anchored in the Mayer-Salovey-Caruso four-branch ability model, operationalizing EI through perception, facilitation, understanding, and management of emotions. Through an evaluation of nine frontier models (including GPT-5, Claude-Sonnet-4), we demonstrate that emotional intelligence is not a monolithic capability but is fragmented across cognitive and interactive dimensions. While frontier models demonstrate robust proficiency in objective emotion recognition and social reasoning, this does not consistently translate to interactive success. We categorize these discrepancies into three distinct performance profiles: cognitive-dominant, interactive-dominant, and context-dependent. These typologies indicate that emotional skills do not scale uniformly with general intelligence or model size; rather, they are shaped by specific alignment paradigms. Notably, we identify hidden emotion recognition as a universal performance bottleneck across all architectures. Our results suggest that current RLHF processes may optimize for "stochastic empathy", a statistical mimicry of emotional syntax, at the expense of integrated affective reasoning. These findings challenge the assumption of linear emotional scaling and provide a rigorous roadmap for developing socially aware agents capable of genuine clinical resonance.

arXiv:2511.04556v2 Announce Type: replace Abstract: Urban flooding triggered by intense rainfall is becoming increasingly frequent and widespread. While flood prediction and monitoring in high spatio-temporal resolution are desired, practical constraints in time, budget, and technology hinder its full implementation. How to monitor urban drainage networks and predict flow conditions under constrained resources is a major challenge. To address this, we introduced a data-driven sparse sensing (DSS) approach, demonstrated via a digital-twin of the Woodland catchment in Duluth, Minnesota. Specifically, we coupled EPA-SWMM with singular value decomposition and QR factorization-based sensor selection to optimize monitoring locations for system-level flow reconstruction. An ensemble of SWMM simulations, driven by diverse scenarios, provided the necessary hydraulic data to extract the reduced basis and identify informative sensor locations. Cross-event validation showed that three strategically placed sensors among 77 candidate nodes achieved a mean system-level Nash-Sutcliffe efficiency (NSE) of 0.949 across observed storm events. The QR-selected sensor sets were benchmarked against reference sensor configurations obtained from exhaustive searches and Monte Carlo random-placements. This comparison further showed that flow reconstruction based on QR-selected sensors closely tracked the exhaustive optimum while substantially outperforming random placements. We further evaluated the framework's robustness by introducing multiplicative Gaussian noise and simulating individual sensor failures. While the model is relatively resilient to noise, the impact of sensor dropouts depends heavily on the number of sensors allocated and their specific locations.

arXiv:2605.10989v3 Announce Type: replace-cross Abstract: The training of Binary Neural Networks (BNNs) is fundamentally based on gradient approximation for non-differentiable binarization operations (e.g., sign function). However, prevailing methods including the Straight-Through Estimator (STE) and its improved variants, rely on hand-crafted designs that suffer from gradient mismatch problem and information loss induced by fixed-range gradient clipping. To address this, we propose SURrogate GradiEnt Adaptation (SURGE), a novel learnable gradient compensation framework with theoretical grounding. SURGE mitigates gradient mismatch through auxiliary backpropagation. Specifically, we design a Dual-Path Gradient Compensator (DPGC) that constructs a parallel full-precision auxiliary branch for each binarized layer, decoupling gradient flow via output decomposition during backpropagation. DPGC enables bias-reduced gradient estimation by leveraging the full-precision branch to estimate components beyond STE's first-order approximation. To further enhance training stability, we introduce an Adaptive Gradient Scaler (AGS) based on an optimal scale factor to dynamically balance inter-branch gradient contributions via norm-based scaling. Experiments on image classification, object detection, and language understanding tasks demonstrate that SURGE performs best over state-of-the-art methods.

arXiv:2604.01452v1 Announce Type: new Abstract: Scientific discovery is slowed by fragmented literature that requires excessive human effort to gather, analyze, and understand. AI tools, including autonomous summarization and question answering, have been developed to aid in understanding scientific literature. However, these tools lack the structured, multi-step approach necessary for extracting deep insights from scientific literature. Large Language Models (LLMs) offer new possibilities for literature analysis, but remain unreliable due to hallucinations and incomplete extraction. We introduce Elhuyar, a multi-agent, human-in-the-loop system that integrates LLMs, structured AI, and human scientists to extract, analyze, and iteratively refine insights from scientific literature. The framework distributes tasks among specialized agents for filtering papers, extracting data, fitting models, and summarizing findings, with human oversight ensuring reliability. The system generates structured reports with extracted data, visualizations, model equations, and text summaries, enabling deeper inquiry through iterative refinement. Deployed in materials science, it analyzed literature on tungsten under helium-ion irradiation, showing experimentally correlated exponential helium bubble growth with irradiation dose and temperature, offering insight for plasma-facing materials (PFMs) in fusion reactors. This demonstrates how AI-assisted literature review can uncover scientific patterns and accelerate discovery.

arXiv:2604.01461v1 Announce Type: new Abstract: Reducing hallucinations in Large Language Models (LLMs) is essential for improving the accuracy of data extraction from large text corpora. Current methods, like prompt engineering and chain-of-thought prompting, focus on individual documents but fail to consider relationships across a corpus. This paper introduces Peer Context Outlier Detection (P-COD), a novel approach that uses the relationships between documents to improve extraction accuracy. Our application domain is in scientific literature summarization, where papers with similar experiment settings should draw similar conclusions. By comparing extracted data to validated peer information within the corpus, we adjust confidence scores and flag low-confidence results for expert review. High-confidence results, supported by peer validation, are considered reliable. Our experiments demonstrate up to 98% precision in outlier detection across 6 domains of science, demonstrating that our design reduces hallucinations, enhances trust in automated systems, and allows researchers to focus on ambiguous cases, streamlining the data extraction workflows.

arXiv:2603.22466v1 Announce Type: cross Abstract: Always-on sensing is essential for next-generation edge/wearable AI systems, yet continuous high-fidelity RGB video capture remains prohibitively expensive for resource-constrained mobile and edge platforms. We present a new paradigm for efficient streaming video understanding: grayscale-always, color-on-demand. Through preliminary studies, we discover that color is not always necessary. Sparse RGB frames suffice for comparable performance when temporal structure is preserved via continuous grayscale streams. Building on this insight, we propose ColorTrigger, an online training-free trigger that selectively activates color capture based on windowed grayscale affinity analysis. Designed for real-time edge deployment, ColorTrigger uses lightweight quadratic programming to detect chromatic redundancy causally, coupled with credit-budgeted control and dynamic token routing to jointly reduce sensing and inference costs. On streaming video understanding benchmarks, ColorTrigger achieves 91.6% of full-color baseline performance while using only 8.1% RGB frames, demonstrating substantial color redundancy in natural videos and enabling practical always-on video sensing on resource-constrained devices.

arXiv:2603.07131v1 Announce Type: cross Abstract: Large Vision Language Models (LVLMs) show immense potential for automated ophthalmic diagnosis. However, their clinical deployment is severely hindered by lacking domain-specific knowledge. In this work, we identify two structural deficiencies hindering reliable medical reasoning: 1) the Perception Gap, where general-purpose visual encoders fail to resolve fine-grained pathological cues (e.g., microaneurysms); and 2) the Reasoning Gap, where sparse visual evidence is progressively overridden by massive language priors in deeper transformer layers, leading to ungrounded hallucinations. To bridge these gaps, we propose EyExIn, a data-efficient framework designed to anchor retinal VLMs with expert knowledge via a Deep Expert Injection mechanism. Our architecture employs an Expert-Aware Dual-Stream encoding strategy that decouples visual representation into a general stream for anatomical context and a specialized expert stream for pathological semantics. To ensure high-fidelity integration, we design a Semantic-Adaptive Gated Fusion module, which dynamically amplifies subtle lesion signals while filtering irrelevant background noise. Furthermore, we introduce Adaptive Deep Expert Injection to embed persistent "Vision Anchors" by integrating fused visual features as residual biases directly into intermediate LLM layers. This mechanism creates a visual shortcut that forces the reasoning stack to remain strictly grounded in visual evidence. Extensive experiments across four benchmarks demonstrate that our model consistently outperforms massive proprietary systems. EyExIn significantly enhances domain-specific knowledge embedding and achieves state-of-the-art precision in ophthalmic visual question answering, advancing the development of trustworthy ophthalmic AI.

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:2510.07181v3 Announce Type: replace-cross Abstract: Vision-Language Models (VLMs) have shown remarkable capabilities in spatial reasoning, yet they remain fundamentally limited to qualitative precision and lack the computational precision required for real-world robotics. Current approaches fail to leverage metric cues from depth sensors and camera calibration, instead reducing geometric problems to pattern recognition tasks that cannot deliver the centimeter-level accuracy essential for robotic manipulation. We present TIGeR (Tool-Integrated Geometric Reasoning), a novel framework that transforms VLMs from perceptual estimators to geometric computers by enabling them to generate and execute precise geometric computations through external tools. Rather than attempting to internalize complex geometric operations within neural networks, TIGeR empowers models to recognize geometric reasoning requirements, synthesize appropriate computational code, and invoke specialized libraries for exact calculations. To support this paradigm, we introduce TIGeR-300K, a comprehensive tool-invocation-oriented dataset covering point transformations, pose estimation, and spatial compatibility verification, complete with tool invocation sequences and intermediate computations. Through a two-stage training pipeline combining supervised fine-tuning (SFT) and reinforcement fine-tuning (RFT) with our proposed hierarchical reward design, TIGeR achieves SOTA performance on geometric reasoning benchmarks while demonstrating centimeter-level precision in real-world robotic manipulation tasks.

arXiv:2504.06193v3 Announce Type: replace-cross Abstract: Link prediction is a crucial graph-learning task with applications including citation prediction and product recommendation. Distilling Graph Neural Networks (GNNs) teachers into Multi-Layer Perceptrons (MLPs) students has emerged as an effective approach to achieve strong performance and reducing computational cost by removing graph dependency. However, existing distillation methods only use standard GNNs and overlook alternative teachers such as specialized model for link prediction (GNN4LP) and heuristic methods (e.g., common neighbors). This paper first explores the impact of different teachers in GNN-to-MLP distillation. Surprisingly, we find that stronger teachers do not always produce stronger students: MLPs distilled from GNN4LP can underperform those distilled from simpler GNNs, while weaker heuristic methods can teach MLPs to near-GNN performance with drastically reduced training costs. Building on these insights, we propose Ensemble Heuristic-Distilled MLPs (EHDM), which eliminates graph dependencies while effectively integrating complementary signals via a gating mechanism. Experiments on ten datasets show an average 7.93% improvement over previous GNN-to-MLP approaches with 1.95-3.32 times less training time, indicating EHDM is an efficient and effective link prediction method. Our code is available at https://github.com/ZongyueQin/EHDM

arXiv:2601.23232v3 Announce Type: replace-cross Abstract: In recent years, large language models (LLMs) have made rapid progress in information retrieval, yet existing research has mainly focused on text or static multimodal settings. Open-domain video shot retrieval, which involves richer temporal structure and more complex semantics, still lacks systematic benchmarks and analysis. To fill this gap, we introduce ShotFinder, a benchmark that formalizes editing requirements as keyframe-oriented shot descriptions and introduces five types of controllable single-factor constraints: Temporal order, Color, Visual style, Audio, and Resolution. We curate 1,210 high-quality samples from YouTube across 20 thematic categories, using large models for generation with human verification. Based on the benchmark, we propose ShotFinder, a text-driven three-stage retrieval and localization pipeline: (1) query expansion via video imagination, (2) candidate video retrieval with a search engine, and (3) description-guided temporal localization. Experiments on multiple closed-source and open-source models reveal a significant gap to human performance, with clear imbalance across constraints: temporal localization is relatively tractable, while color and visual style remain major challenges. These results reveal that open-domain video shot retrieval is still a critical capability that multimodal large models have yet to overcome.