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Correction: Integrative multi-omics and machine learning reveals the spatial niche distribution and role of CYP27A1+TAMs in immunotherapy response in non-small cell lung cancer

Front Immunol. 2026 Mar 16;17:1822612. doi: 10.3389/fimmu.2026.1822612. eCollection 2026.

ABSTRACT

[This corrects the article DOI: 10.3389/fimmu.2026.1782545.].

PMID:41918731 | PMC:PMC13033988 | DOI:10.3389/fimmu.2026.1822612

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AI-guided multi-omics analysis identifies NPC1-modulated susceptibility to SARS-CoV-2 infection under PM(2.5) exposure

Nat Commun. 2026 Mar 30. doi: 10.1038/s41467-026-71196-3. Online ahead of print.

ABSTRACT

Exposure to airborne fine particulate matter (PM2.5) has been linked to increased risk of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, yet the underlying mechanisms remain unclear. Here, by leveraging a fine-tuned foundation model of single-cell transcriptomics, we uncover shared transcriptional signatures between PM2.5 exposure and SARS-CoV-2 infection. We further validate this association using population-level epidemiological analyses and perform genome-wide association studies (GWAS) to identify genetic variants that modulate infection risk under PM2.5 exposure. In addition, we identify NPC1 as a key modulator involved in SARS-CoV-2 infection efficiency under virus-laden PM2.5 exposure through integrative functional genomic analyses and in vitro experiments. Our findings suggest that PM2.5 facilitates viral entry through an NPC1-modulated endo-lysosomal pathway, providing a mechanistic explanation for observed pollution-related susceptibility. By integrating artificial intelligence (AI)-guided transcriptomics, epidemiology, GWAS, functional genomics, and in vitro verification, our study elucidates how environmental and genetic factors jointly influence SARS-CoV-2 susceptibility. This work highlights how AI-assisted multi-omics integration systematically decodes the health impacts of environmental exposures from molecular to population levels and informs air quality policy and infectious disease preparedness.

PMID:41912520 | DOI:10.1038/s41467-026-71196-3

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TRACE: A Multi-Agent System for Autonomous Physical Reasoning in Seismological

arXiv:2603.21152v2 Announce Type: replace-cross Abstract: Inferring the physical mechanisms that govern earthquake sequences from indirect geophysical observations remains difficult, particularly across tectonically distinct environments where similar seismic patterns can reflect different underlying processes. Current interpretations rely heavily on the expert synthesis of catalogs, spatiotemporal statistics, and candidate physical models, limiting reproducibility and the systematic transfer of insight across settings. Here we present TRACE (Trans-perspective Reasoning and Automated Comprehensive Evaluator), a multi-agent system that combines large language model planning with formal seismological constraints to derive auditable, physically grounded mechanistic inference from raw observations. Applied to the 2019 Ridgecrest sequence, TRACE autonomously identifies stress-perturbation-induced delayed triggering, resolving the cascading interaction between the Mw 6.4 and Mw 7.1 mainshocks; in the Santorini-Kolumbo case, the system identifies a structurally guided intrusion model, distinguishing fault-channeled episodic migration from the continuous propagation expected in homogeneous crustal failure. By providing a generalizable logical infrastructure for interpreting heterogeneous seismic phenomena, TRACE advances the field from expert-dependent analysis toward knowledge-guided autonomous discovery in Earth sciences.
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SFIBA: Spatial-based Full-target Invisible Backdoor Attacks

arXiv:2504.21052v2 Announce Type: replace-cross Abstract: Multi-target backdoor attacks pose significant security threats to deep neural networks, as they can preset multiple target classes through a single backdoor injection. This allows attackers to control the model to misclassify poisoned samples with triggers into any desired target class during inference, exhibiting superior attack performance compared with conventional backdoor attacks. However, existing multi-target backdoor attacks fail to guarantee trigger specificity and stealthiness in black-box settings, resulting in two main issues. First, they are unable to simultaneously target all classes when only training data can be manipulated, limiting their effectiveness in realistic attack scenarios. Second, the triggers often lack visual imperceptibility, making poisoned samples easy to detect. To address these problems, we propose a Spatial-based Full-target Invisible Backdoor Attack, called SFIBA. It restricts triggers for different classes to specific local spatial regions and morphologies in the pixel space to ensure specificity, while employing a frequency-domain-based trigger injection method to guarantee stealthiness. Specifically, for injection of each trigger, we first apply fast fourier transform to obtain the amplitude spectrum of clean samples in local spatial regions. Then, we employ discrete wavelet transform to extract the features from the amplitude spectrum and use singular value decomposition to integrate the trigger. Subsequently, we selectively filter parts of the trigger in pixel space to implement trigger morphology constraints and adjust injection coefficients based on visual effects. We conduct experiments on multiple datasets and models. The results demonstrate that SFIBA can achieve excellent attack performance and stealthiness, while preserving the model's performance on benign samples, and can also bypass existing backdoor defenses.
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Can Multimodal LLMs See Science Instruction? Benchmarking Pedagogical Reasoning in K-12 Classroom Videos

arXiv:2602.18466v1 Announce Type: cross Abstract: K-12 science classrooms are rich sites of inquiry where students coordinate phenomena, evidence, and explanatory models through discourse; yet, the multimodal complexity of these interactions has made automated analysis elusive. Existing benchmarks for classroom discourse focus primarily on mathematics and rely solely on transcripts, overlooking the visual artifacts and model-based reasoning emphasized by the Next Generation Science Standards (NGSS). We address this gap with SciIBI, the first video benchmark for analyzing science classroom discourse, featuring 113 NGSS-aligned clips annotated with Core Instructional Practices (CIP) and sophistication levels. By evaluating eight state-of-the-art LLMs and Multimodal LLMs, we reveal fundamental limitations: current models struggle to distinguish pedagogically similar practices, suggesting that CIP coding requires instructional reasoning beyond surface pattern matching. Furthermore, adding video input yields inconsistent gains across architectures. Crucially, our evidence-based evaluation reveals that models often succeed through surface shortcuts rather than genuine pedagogical understanding. These findings establish science classroom discourse as a challenging frontier for multimodal AI and point toward human-AI collaboration, where models retrieve evidence to accelerate expert review rather than replace it.
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Foundation and Large-Scale AI Models in Neuroscience: A Comprehensive Review

arXiv:2510.16658v2 Announce Type: replace Abstract: The development of large-scale artificial intelligence (AI) models is influencing neuroscience research by enabling end-to-end learning from raw brain signals and neural data. In this paper, we review applications of large-scale AI models across five major neuroscience domains: neuroimaging and data processing, brain-computer interfaces and neural decoding, clinical decision support and translational frameworks, and disease-specific applications across neurological and psychiatric disorders. These models show potential to address major computational neuroscience challenges, including multimodal neural data integration, spatiotemporal pattern interpretation, and the development of translational frameworks for clinical research. Moreover, the interaction between neuroscience and AI has become increasingly reciprocal, as biologically informed architectural constraints are now incorporated to develop more interpretable and computationally efficient models. This review highlights both the promise of such technologies and critical implementation considerations, with particular emphasis on rigorous evaluation frameworks, effective integration of domain knowledge, prospective clinical validation, and comprehensive ethical guidelines. Finally, a systematic listing of critical neuroscience datasets used to develop and evaluate large-scale AI models across diverse research applications is provided.
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SelfAI: A self-directed framework for long-horizon scientific discovery

arXiv:2512.00403v2 Announce Type: replace-cross Abstract: Scientific discovery increasingly entails long-horizon exploration of complex hypothesis spaces, yet most existing approaches emphasize final performance while offering limited insight into how scientific exploration unfolds over time, particularly balancing efficiency-diversity trade-offs and supporting reproducible, human-in-the-loop discovery workflows. We introduce SelfAI, a self-directed, multi-agent-enabled discovery system that automates scientific exploration as a strategic, trajectory-driven decision-making process. SelfAI translates high-level research intent into executable experiments, reasons over accumulated experimental trajectories to guide subsequent exploration, and applies adaptive stopping decisions to terminate unproductive search paths within a closed-loop workflow governed by explicit efficiency-diversity trade-offs. Evaluated using real-world experiments spanning domains from machine learning to drug discovery, SelfAI consistently discovers high-quality solutions with substantially fewer redundant trials than classical optimization and recent LLM-based baselines. The proposed methods establish a general framework for organizing long-horizon scientific discovery and adaptive decision-making in complex scientific and engineering systems.
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Group Representational Position Encoding

arXiv:2512.07805v4 Announce Type: replace-cross Abstract: We present GRAPE (Group Representational Position Encoding), a unified framework for positional encoding based on group actions. GRAPE unifies two families of mechanisms: (i) multiplicative rotations (Multiplicative GRAPE) in $\operatorname{SO}(d)$ and (ii) additive logit biases (Additive GRAPE) arising from unipotent actions in the general linear group $\mathrm{GL}$. In Multiplicative GRAPE, a position $n \in \mathbb{Z}$ (or $t \in \mathbb{R}$) acts as $\mathbf{G}(n) = \exp(n \, \omega \, \mathbf{L})$ with a rank-2 skew-symmetric generator $\mathbf{L} \in \mathbb{R}^{d \times d}$, yielding a relative, compositional, norm-preserving map with a closed-form matrix exponential. RoPE is recovered exactly when the $d/2$ planes correspond to canonical coordinate pairs with a log-uniform spectrum. Learned commuting subspaces and compact non-commuting mixtures strictly extend this geometry to capture cross-subspace feature coupling at $O(d)$ and $O(r d)$ cost per head, respectively. In Additive GRAPE, additive logits arise from rank-1 (or low-rank) unipotent actions, recovering ALiBi and the Forgetting Transformer (FoX) as exact special cases while preserving an exact relative law and streaming cacheability. Overall, GRAPE provides a principled design space for positional geometry in long-context models, subsuming RoPE and ALiBi as special cases. Project page: https://github.com/model-architectures/GRAPE.
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One Token Is Enough: Improving Diffusion Language Models with a Sink Token

arXiv:2601.19657v4 Announce Type: replace-cross Abstract: Diffusion Language Models (DLMs) have emerged as a compelling alternative to autoregressive approaches, enabling parallel text generation with competitive performance. Despite these advantages, there is a critical instability in DLMs: the moving sink phenomenon. Our analysis indicates that sink tokens exhibit low-norm representations in the Transformer's value space, and that the moving sink phenomenon serves as a protective mechanism in DLMs to prevent excessive information mixing. However, their unpredictable positions across diffusion steps undermine inference robustness. To resolve this, we propose a simple but effective extra sink token implemented via a modified attention mask. Specifically, we introduce a special token constrained to attend solely to itself, while remaining globally visible to all other tokens. Experimental results demonstrate that introducing a single extra token stabilizes attention sinks, substantially improving model performance. Crucially, further analysis confirms that the effectiveness of this token is independent of its position and characterized by negligible semantic content, validating its role as a robust and dedicated structural sink.
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Step 3.5 Flash: Open Frontier-Level Intelligence with 11B Active Parameters

arXiv:2602.10604v2 Announce Type: replace-cross Abstract: We introduce Step 3.5 Flash, a sparse Mixture-of-Experts (MoE) model that bridges frontier-level agentic intelligence and computational efficiency. We focus on what matters most when building agents: sharp reasoning and fast, reliable execution. Step 3.5 Flash pairs a 196B-parameter foundation with 11B active parameters for efficient inference. It is optimized with interleaved 3:1 sliding-window/full attention and Multi-Token Prediction (MTP-3) to reduce the latency and cost of multi-round agentic interactions. To reach frontier-level intelligence, we design a scalable reinforcement learning framework that combines verifiable signals with preference feedback, while remaining stable under large-scale off-policy training, enabling consistent self-improvement across mathematics, code, and tool use. Step 3.5 Flash demonstrates strong performance across agent, coding, and math tasks, achieving 85.4% on IMO-AnswerBench, 86.4% on LiveCodeBench-v6 (2024.08-2025.05), 88.2% on tau2-Bench, 69.0% on BrowseComp (with context management), and 51.0% on Terminal-Bench 2.0, comparable to frontier models such as GPT-5.2 xHigh and Gemini 3.0 Pro. By redefining the efficiency frontier, Step 3.5 Flash provides a high-density foundation for deploying sophisticated agents in real-world industrial environments.
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