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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

26 September 2026 at 18:00

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 Β°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 Β°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

Fine-grained Analysis of Stability and Generalization for Stochastic Bilevel Optimization

arXiv:2604.04090v1 Announce Type: cross Abstract: Stochastic bilevel optimization (SBO) has been integrated into many machine learning paradigms recently, including hyperparameter optimization, meta learning, and reinforcement learning. Along with the wide range of applications, there have been numerous studies on the computational behavior of SBO. However, the generalization guarantees of SBO methods are far less understood from the lens of statistical learning theory. In this paper, we provide a systematic generalization analysis of the first-order gradient-based bilevel optimization methods. Firstly, we establish the quantitative connections between the on-average argument stability and the generalization gap of SBO methods. Then, we derive the upper bounds of on-average argument stability for single-timescale stochastic gradient descent (SGD) and two-timescale SGD, where three settings (nonconvex-nonconvex (NC-NC), convex-convex (C-C), and strongly-convex-strongly-convex (SC-SC)) are considered respectively. Experimental analysis validates our theoretical findings. Compared with the previous algorithmic stability analysis, our results do not require reinitializing the inner-level parameters at each iteration and are applicable to more general objective functions.

Mastering Negation: Boosting Grounding Models via Grouped Opposition-Based Learning

arXiv:2603.12606v1 Announce Type: cross Abstract: Current vision-language detection and grounding models predominantly focus on prompts with positive semantics and often struggle to accurately interpret and ground complex expressions containing negative semantics. A key reason for this limitation is the lack of high-quality training data that explicitly captures discriminative negative samples and negation-aware language descriptions. To address this challenge, we introduce D-Negation, a new dataset that provides objects annotated with both positive and negative semantic descriptions. Building upon the observation that negation reasoning frequently appears in natural language, we further propose a grouped opposition-based learning framework that learns negation-aware representations from limited samples. Specifically, our method organizes opposing semantic descriptions from D-Negation into structured groups and formulates two complementary loss functions that encourage the model to reason about negation and semantic qualifiers. We integrate the proposed dataset and learning strategy into a state-of-the-art language-based grounding model. By fine-tuning fewer than 10 percent of the model parameters, our approach achieves improvements of up to 4.4 mAP and 5.7 mAP on positive and negative semantic evaluations, respectively. These results demonstrate that explicitly modeling negation semantics can substantially enhance the robustness and localization accuracy of vision-language grounding models.

The Curse of Depth in Large Language Models

arXiv:2502.05795v5 Announce Type: replace-cross Abstract: In this paper, we introduce the Curse of Depth, a concept that highlights, explains, and addresses the recent observation in modern Large Language Models (LLMs) where nearly half of the layers are less effective than expected. We first confirm the wide existence of this phenomenon across the most popular families of LLMs such as Llama, Mistral, DeepSeek, and Qwen. Our analysis, theoretically and empirically, identifies that the underlying reason for the ineffectiveness of deep layers in LLMs is the widespread usage of Pre-Layer Normalization (Pre-LN). While Pre-LN stabilizes the training of Transformer LLMs, its output variance exponentially grows with the model depth, which undesirably causes the derivative of the deep Transformer blocks to be an identity matrix, and therefore barely contributes to the training. To resolve this training pitfall, we propose LayerNorm Scaling (LNS), which scales the variance of output of the layer normalization inversely by the square root of its depth. This simple modification mitigates the output variance explosion of deeper Transformer layers, improving their contribution. Across a wide range of model sizes (130M to 7B), our experiments show that LNS consistently outperforms previous normalization and scaling techniques in enhancing LLM pre-training performance. Moreover, this improvement seamlessly carries over to supervised fine-tuning. All these gains can be attributed to the fact that LayerNorm Scaling enables deeper layers to contribute more effectively during training. Our code is available at \href{https://github.com/lmsdss/LayerNorm-Scaling}{LayerNorm-Scaling}.
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