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Combined Transcriptomic and Histological Profiling Uncover Hepatic Regulatory Hierarchy of Triploid <em>Oncorhynchus mykiss</em> Under Interactive Salinity, Temperature and Body Weight Regimes

Biology (Basel). 2026 Sep 17;15(18):1646. doi: 10.3390/biology15181646.

ABSTRACT

Salinity, temperature and body weight dominate seawater acclimation in rainbow trout (Oncorhynchus mykiss), yet few studies simultaneously explore their main effects and potential correlative interactive patterns in hepatic responses. A 60-day L9 (33) orthogonal trial was performed on triploid rainbow trout with three gradients of body weight, temperature and salinity. Hepatic transcriptomics revealed that salinity drove global transcriptional remodeling and high salinity induced far fewer DEGs than medium salinity. WGCNA screened a salinity-positive blue module (r = 0.408, p = 0.0346), while alternative splicing confirmed extensive salinity-dependent post-transcriptional regulation. Semi-quantitative histology showed that 20 °C was associated with more pronounced salinity-caused hepatocellular vacuolation and karyopyknosis in the orthogonal test. Survival statistics indicated that salinity was the only factor with significant main effects (p < 0.05), and the 500 g-10 °C-10 ppt group obtained the highest survival. This multi-omics and histological dataset reveals a suggestive regulatory hierarchy-like pattern: salinity acts as the primary driver, temperature serves as a synergistic amplifier, and body weight plays a minor modulatory role. These findings provide a theoretical basis for developing size-specific salinity acclimation protocols in commercial triploid rainbow trout farming.

PMID:42792591 | PMC:PMC13604319 | DOI:10.3390/biology15181646

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LightNav-0: Eliciting VLM Spatial Intelligence for Generalist Embodied Navigation

arXiv:2608.30935v2 Announce Type: replace-cross Abstract: Embodied navigation requires agents to translate heterogeneous goals and visual observations into actions across tasks, environments, and robot embodiments. Modern vision-language models (VLMs) already encode spatial priors for visual grounding, spatial reasoning, and pointing, but these capabilities are rarely elicited directly for robot control. Existing navigation systems instead rely on task- or embodiment-specific components, fragmenting perception, reasoning, and action while offering limited generalization. Here we present LightNav-0, a compact generalist embodied navigation model that elicits the spatial intelligence of a pretrained VLM and aligns it with navigation, without task-specific prediction heads. LightNav-0 represents diverse navigation tasks through a unified token interface: dual-channel pointing expresses task-, scene-, and embodiment-agnostic spatial intent, while a residual vector-quantized action tokenizer maps this intent to precise, embodiment-specific trajectories. Together with temporally aware visual history compression, ER mid-training, supervised fine-tuning, and reinforcement learning, this formulation supports instruction following, open-vocabulary object navigation, and visual tracking within a single model. The navigation training corpus spans 2K+ scenes and 4K+ hours of embodied navigation data. LightNav-ER, the embodied-reasoning checkpoint used to initialize LightNav-0, attains the highest complete-set average across 8 embodied-reasoning benchmarks, while LightNav-0 achieves state-of-the-art monocular success rates across all 10 public navigation simulation settings. Real-world evaluations further demonstrate zero-shot generalization across robot embodiments, diverse scenes, and static and dynamic targets. These results establish compact VLMs as a unified and transferable backbone for generalist embodied navigation.
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Robust Fuzzy Multi-view Learning under View Conflict

arXiv:2605.24475v1 Announce Type: cross Abstract: Trusted multi-view classification aims to deliver reliable fusion for accurate predictions and has recently attracted substantial attention in both academia and industry. However, existing TMVC methods typically assume strict alignment across different views during both training and testing phases, which is often impractical in real-world scenarios. This limitation motivates us to revisit TMVC and extend it to a more challenging setting: how to mitigate the impact of view conflict (VC) during both training and inference. To tackle this setting, existing TMVC methods suffer from three critical limitations: underestimated uncertainty, misleading decisions, and overfitting to VC. To address these issues, this paper proposes a novel Robust Fuzzy Multi-View Learning (R-FUML) framework grounded in Fuzzy Set Theory. Specifically, R-FUML models network outputs as fuzzy memberships to quantify category credibility and uses an entropy-based method for reliable multi-view fusion. To this end, we present a Robust Multi-view Fusion (RMF) strategy that accounts for both view-specific uncertainty and inter-view conflicts, thereby alleviating the adverse impacts of VC on decision-making. To identify and conquer VC during training, we further design a Robust Learning Against VC (RLVC) framework. RLVC isolates conflicting samples by leveraging neural networks' memory effects and then retrains the model by applying a penalty to these conflicting views. Extensive experiments across eight public datasets demonstrate that R-FUML consistently outperforms 15 state-of-the-art baselines in robustness and uncertainty estimation. The code will be released upon acceptance.
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Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics

arXiv:2510.09901v2 Announce Type: replace Abstract: Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery across varying levels of autonomy. These language agents provide a flexible and versatile framework that orchestrates interactions with human scientists, natural language, computer language and code, and physics. This paper presents our view and vision of LLM-based scientific agents and their growing role in transforming the scientific discovery lifecycle, from hypothesis discovery, experimental design and execution, to result analysis and refinement. We critically examine current methodologies, emphasizing key innovations, practical achievements, and outstanding limitations. Additionally, we identify open research challenges and outline promising directions for building more robust, generalizable, and adaptive scientific agents. Our analysis highlights the transformative potential of autonomous agents to accelerate scientific discovery across diverse domains.
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MELT: Improve Composed Image Retrieval via the Modification Frequentation-Rarity Balance Network

arXiv:2603.29291v1 Announce Type: cross Abstract: Composed Image Retrieval (CIR) uses a reference image and a modification text as a query to retrieve a target image satisfying the requirement of ``modifying the reference image according to the text instructions''. However, existing CIR methods face two limitations: (1) frequency bias leading to ``Rare Sample Neglect'', and (2) susceptibility of similarity scores to interference from hard negative samples and noise. To address these limitations, we confront two key challenges: asymmetric rare semantic localization and robust similarity estimation under hard negative samples. To solve these challenges, we propose the Modification frEquentation-rarity baLance neTwork MELT. MELT assigns increased attention to rare modification semantics in multimodal contexts while applying diffusion-based denoising to hard negative samples with high similarity scores, enhancing multimodal fusion and matching. Extensive experiments on two CIR benchmarks validate the superior performance of MELT. Codes are available at https://github.com/luckylittlezhi/MELT.
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Hierarchical Dual-Change Collaborative Learning for UAV Scene Change Captioning

arXiv:2603.12832v1 Announce Type: cross Abstract: This paper proposes a novel task for UAV scene understanding - UAV Scene Change Captioning (UAV-SCC) - which aims to generate natural language descriptions of semantic changes in dynamic aerial imagery captured from a movable viewpoint. Unlike traditional change captioning that mainly describes differences between image pairs captured from a fixed camera viewpoint over time, UAV scene change captioning focuses on image-pair differences resulting from both temporal and spatial scene variations dynamically captured by a moving camera. The key challenge lies in understanding viewpoint-induced scene changes from UAV image pairs that share only partially overlapping scene content due to viewpoint shifts caused by camera rotation, while effectively exploiting the relative orientation between the two images. To this end, we propose a Hierarchical Dual-Change Collaborative Learning (HDC-CL) method for UAV scene change captioning. In particular, a novel transformer, \emph{i.e.} Dynamic Adaptive Layout Transformer (DALT) is designed to adaptively model diverse spatial layouts of the image pair, where the interrelated features derived from the overlapping and non-overlapping regions are learned within the flexible and unified encoding layer. Furthermore, we propose a Hierarchical Cross-modal Orientation Consistency Calibration (HCM-OCC) method to enhance the model's sensitivity to viewpoint shift directions, enabling more accurate change captioning. To facilitate in-depth research on this task, we construct a new benchmark dataset, named UAV-SCC dataset, for UAV scene change captioning. Extensive experiments demonstrate that the proposed method achieves state-of-the-art performance on this task. The dataset and code will be publicly released upon acceptance of this paper.
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Rel-MOSS: Towards Imbalanced Relational Deep Learning on Relational Databases

arXiv:2603.07916v1 Announce Type: new Abstract: In recent advances, to enable a fully data-driven learning paradigm on relational databases (RDB), relational deep learning (RDL) is proposed to structure the RDB as a heterogeneous entity graph and adopt the graph neural network (GNN) as the predictive model. However, existing RDL methods neglect the imbalance problem of relational data in RDBs and risk under-representing the minority entities, leading to an unusable model in practice. In this work, we investigate, for the first time, class imbalance problem in RDB entity classification and design the relation-centric minority synthetic over-sampling GNN (Rel-MOSS), in order to fill a critical void in the current literature. Specifically, to mitigate the issue of minority-related information being submerged by majority counterparts, we design the relation-wise gating controller to modulate neighborhood messages from each individual relation type. Based on the relational-gated representations, we further propose the relation-guided minority synthesizer for over-sampling, which integrates the entity relational signatures to maintain relational consistency. Extensive experiments on 12 entity classification datasets provide compelling evidence for the superiority of Rel-MOSS, yielding an average improvement of up to 2.46% and 4.00% in terms of Balanced Accuracy and G-Mean, compared with SOTA RDL methods and classic methods for handling class imbalance.
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Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset

arXiv:2406.06512v2 Announce Type: replace-cross Abstract: The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin.
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Model-agnostic Selective Labeling with Provable Statistical Guarantees

arXiv:2510.14581v3 Announce Type: replace-cross Abstract: Obtaining high-quality labels for large datasets is expensive, requiring massive annotations from human experts. While AI models offer a cost-effective alternative by predicting labels, their label quality is compromised by the unavoidable labeling errors. Existing methods mitigate this issue through selective labeling, where AI labels a subset and human labels the remainder. However, these methods lack theoretical guarantees on the quality of AI-assigned labels, often resulting in unacceptably high labeling error within the AI-labeled subset. To address this, we introduce \textbf{Conformal Labeling}, a novel method to identify instances where AI predictions can be provably trusted. This is achieved by controlling the false discovery rate (FDR), the proportion of incorrect labels within the selected subset. In particular, we construct a conformal $p$-value for each test instance by comparing AI models' predicted confidence to those of calibration instances mislabeled by AI models. Then, we select test instances whose $p$-values are below a data-dependent threshold, certifying AI models' predictions as trustworthy. We provide theoretical guarantees that Conformal Labeling controls the FDR below the nominal level, ensuring that a predefined fraction of AI-assigned labels is correct on average. Extensive experiments demonstrate that our method achieves tight FDR control with high power across various tasks, including image and text labeling, and LLM QA.
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