Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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NED-Tree: Bridging the Semantic Gap with Nonlinear Element Decomposition Tree for LLM Nonlinear Optimization Modeling
arXiv:2604.01588v1 Announce Type: new Abstract: Automating the translation of Operations Research (OR) problems from natural language to executable models is a critical challenge. While Large Language Models (LLMs) have shown promise in linear tasks, they suffer from severe performance degradation in real-world nonlinear scenarios due to semantic misalignment between mathematical formulations and solver codes, as well as unstable information extraction. In this study, we introduce NED-Tree, a s
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cs.AI, q-bio.NC updates on arXiv.org
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LiteInception: A Lightweight and Interpretable Deep Learning Framework for General Aviation Fault Diagnosis
arXiv:2604.01725v1 Announce Type: new Abstract: General aviation fault diagnosis and efficient maintenance are critical to flight safety; however, deploying deep learning models on resource-constrained edge devices poses dual challenges in computational capacity and interpretability. This paper proposes LiteInception--a lightweight interpretable fault diagnosis framework designed for edge deployment. The framework adopts a two-stage cascaded architecture aligned with standard maintenance workfl
LiteInception: A Lightweight and Interpretable Deep Learning Framework for General Aviation Fault Diagnosis
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cs.AI, q-bio.NC updates on arXiv.org
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World Action Verifier: Self-Improving World Models via Forward-Inverse Asymmetry
arXiv:2604.01985v1 Announce Type: cross Abstract: General-purpose world models promise scalable policy evaluation, optimization, and planning, yet achieving the required level of robustness remains challenging. Unlike policy learning, which primarily focuses on optimal actions, a world model must be reliable over a much broader range of suboptimal actions, which are often insufficiently covered by action-labeled interaction data. To address this challenge, we propose World Action Verifier (WAV)
World Action Verifier: Self-Improving World Models via Forward-Inverse Asymmetry
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cs.AI, q-bio.NC updates on arXiv.org
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Unified Optimization of Source Weights and Transfer Quantities in Multi-Source Transfer Learning: An Asymptotic Framework
arXiv:2601.10779v2 Announce Type: replace-cross Abstract: In multi-source transfer learning, a key challenge lies in how to appropriately differentiate and utilize heterogeneous source tasks. However, existing multi-source methods typically focus on optimizing either the source weights or the amount of transferred samples, largely neglecting their joint consideration. In this work, we propose a theoretical framework, Unified Optimization of Weights and Quantities (UOWQ), that jointly determines
Unified Optimization of Source Weights and Transfer Quantities in Multi-Source Transfer Learning: An Asymptotic Framework
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cs.AI, q-bio.NC updates on arXiv.org
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Improving Ensemble Forecasts of Abnormally Deflecting Tropical Cyclones with Fused Atmosphere-Ocean-Terrain Data
arXiv:2603.29200v2 Announce Type: replace-cross Abstract: Deep learning-based tropical cyclone (TC) forecasting methods have demonstrated significant potential and application advantages, as they feature much lower computational cost and faster operation speed than numerical weather prediction models. However, existing deep learning methods still have key limitations: they can only process a single type of sequential trajectory data or homogeneous meteorological variables, and fail to achieve a
Improving Ensemble Forecasts of Abnormally Deflecting Tropical Cyclones with Fused Atmosphere-Ocean-Terrain Data
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response
Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.ABSTRACTImmunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcripto
Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response
Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.
ABSTRACT
Immunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcriptomics to dissect the spatial localization of these regulators. We identified the SNHG6-BIRC5 axis as a critical driver of the "immune-cold" phenotype in lung adenocarcinoma. We provide visual evidence that this axis localizes to tumor nests and negatively correlates with T- cell infiltration, elucidating a mechanism of spatial immune exclusion. Validating the clinical relevance of these findings, genome-scale CRISPR-Cas9 screening data confirmed the functional essentiality of these targets for cancer cell survival. Furthermore, pharmacogenomic analysis revealed that high expression of this axis correlates with sensitivity to chemotherapy agents like Vinblastine, suggesting a potential stratification strategy for patients with immune-excluded tumors. To expand the clinical utility to immunotherapy prediction, we developed a pan-cancer XGBoost machine learning model incorporating 14 high-performance regulatory features. This model achieved robust performance in distinguishing immunotherapy responders from non-responders with an AUC of 0.771, outperforming traditional markers such as PD-L1. Collectively, this study highlights spatial determinants of immune exclusion and chemotherapy sensitivity- and presents a generalized machine- learning tool for precision immunotherapy stratification. The developed online resource is freely available to facilitate community-wide biomarker discovery.
PMID:41925746 | DOI:10.1007/s00262-026-04374-3
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Omics In Lung
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Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response
Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.ABSTRACTImmunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcripto
Integrated spatial transcriptomics and pan-cancer XGBoost modeling uncover spatial drivers of immune exclusion and predict immunotherapy response
Cancer Immunol Immunother. 2026 Apr 2;75(4):131. doi: 10.1007/s00262-026-04374-3.
ABSTRACT
Immunotherapy has revolutionized cancer treatment, yet characterizing the spatial complexity of the tumor immune microenvironment remains a challenge. In this study, we established a comprehensive computational framework integrating multi-omics profiling across 27 cancer types to decode immune-related non-coding RNA regulatory networks. Moving beyond traditional bulk analysis, we utilized spatial transcriptomics to dissect the spatial localization of these regulators. We identified the SNHG6-BIRC5 axis as a critical driver of the "immune-cold" phenotype in lung adenocarcinoma. We provide visual evidence that this axis localizes to tumor nests and negatively correlates with T- cell infiltration, elucidating a mechanism of spatial immune exclusion. Validating the clinical relevance of these findings, genome-scale CRISPR-Cas9 screening data confirmed the functional essentiality of these targets for cancer cell survival. Furthermore, pharmacogenomic analysis revealed that high expression of this axis correlates with sensitivity to chemotherapy agents like Vinblastine, suggesting a potential stratification strategy for patients with immune-excluded tumors. To expand the clinical utility to immunotherapy prediction, we developed a pan-cancer XGBoost machine learning model incorporating 14 high-performance regulatory features. This model achieved robust performance in distinguishing immunotherapy responders from non-responders with an AUC of 0.771, outperforming traditional markers such as PD-L1. Collectively, this study highlights spatial determinants of immune exclusion and chemotherapy sensitivity- and presents a generalized machine- learning tool for precision immunotherapy stratification. The developed online resource is freely available to facilitate community-wide biomarker discovery.
PMID:41925746 | PMC:PMC13046951 | DOI:10.1007/s00262-026-04374-3
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Cell
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New approach methodologies for drug discovery
New approach methodologies that are human-centered, such as stem cells, organoids, and in silico models, can span the full drug discovery pipeline—from disease modeling to efficacy testing—and hold promise as both tools for drug discovery and potential therapies.
New approach methodologies for drug discovery
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Cell Death Discovery nature.com science feeds
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Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection
Cell Death Discovery, Published online: 02 April 2026; doi:10.1038/s41420-026-03031-zExcessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection
Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection
Cell Death Discovery, Published online: 02 April 2026; doi:10.1038/s41420-026-03031-z
Excessive pyroptosis mediates the exacerbation of pneumonia caused by low-lethality influenza virus and secondary MRSA co-infection-
cs.AI, q-bio.NC updates on arXiv.org
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PAR$^2$-RAG: Planned Active Retrieval and Reasoning for Multi-Hop Question Answering
arXiv:2603.29085v1 Announce Type: new Abstract: Large language models (LLMs) remain brittle on multi-hop question answering (MHQA), where answering requires combining evidence across documents through retrieval and reasoning. Iterative retrieval systems can fail by locking onto an early low-recall trajectory and amplifying downstream errors, while planning-only approaches may produce static query sets that cannot adapt when intermediate evidence changes. We propose \textbf{Planned Active Retrie
PAR$^2$-RAG: Planned Active Retrieval and Reasoning for Multi-Hop Question Answering
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cs.AI, q-bio.NC updates on arXiv.org
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Predicting Neuromodulation Outcome for Parkinson's Disease with Generative Virtual Brain Model
arXiv:2603.29176v1 Announce Type: new Abstract: Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promising therapies, inter-individual variability limits empirical treatment selection, increasing non-negligible surgical risk and cost. Previous explorations either resort to limited statistical biomarkers that are insufficient to characterize variability, or employ AI-driven methods which is prone to overf
Predicting Neuromodulation Outcome for Parkinson's Disease with Generative Virtual Brain Model
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cs.AI, q-bio.NC updates on arXiv.org
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Route-Induced Density and Stability (RIDE): Controlled Intervention and Mechanism Analysis of Routing-Style Meta Prompts on LLM Internal States
arXiv:2603.29206v1 Announce Type: new Abstract: Routing is widely used to scale large language models, from Mixture-of-Experts gating to multi-model/tool selection. A common belief is that routing to a task ``expert'' activates sparser internal computation and thus yields more certain and stable outputs (the Sparsity--Certainty Hypothesis). We test this belief by injecting routing-style meta prompts as a textual proxy for routing signals in front of frozen instruction-tuned LLMs. We quantify (C
Route-Induced Density and Stability (RIDE): Controlled Intervention and Mechanism Analysis of Routing-Style Meta Prompts on LLM Internal States
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cs.AI, q-bio.NC updates on arXiv.org
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PSPA-Bench: A Personalized Benchmark for Smartphone GUI Agent
arXiv:2603.29318v1 Announce Type: new Abstract: Smartphone GUI agents execute tasks by operating directly on app interfaces, offering a path to broad capability without deep system integration. However, real-world smartphone use is highly personalized: users adopt diverse workflows and preferences, challenging agents to deliver customized assistance rather than generic solutions. Existing GUI agent benchmarks cannot adequately capture this personalization dimension due to sparse user-specific d
PSPA-Bench: A Personalized Benchmark for Smartphone GUI Agent
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cs.AI, q-bio.NC updates on arXiv.org
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Owl-AuraID 1.0: An Intelligent System for Autonomous Scientific Instrumentation and Scientific Data Analysis
arXiv:2603.29828v1 Announce Type: new Abstract: Scientific discovery increasingly depends on high-throughput characterization, yet automation is hindered by proprietary GUIs and the limited generalizability of existing API-based systems. We present Owl-AuraID, a software-hardware collaborative embodied agent system that adopts a GUI-native paradigm to operate instruments through the same interfaces as human experts. Its skill-centric framework integrates Type-1 (GUI operation) and Type-2 (data
Owl-AuraID 1.0: An Intelligent System for Autonomous Scientific Instrumentation and Scientific Data Analysis
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cs.AI, q-bio.NC updates on arXiv.org
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ATP-Bench: Towards Agentic Tool Planning for MLLM Interleaved Generation
arXiv:2603.29902v1 Announce Type: new Abstract: Interleaved text-and-image generation represents a significant frontier for Multimodal Large Language Models (MLLMs), offering a more intuitive way to convey complex information. Current paradigms rely on either image generation or retrieval augmentation, yet they typically treat the two as mutually exclusive paths, failing to unify factuality with creativity. We argue that the next milestone in this field is Agentic Tool Planning, where the model
ATP-Bench: Towards Agentic Tool Planning for MLLM Interleaved Generation
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cs.AI, q-bio.NC updates on arXiv.org
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Improving Ensemble Forecasts of Abnormally Deflecting Tropical Cyclones with Fused Atmosphere-Ocean-Terrain Data
arXiv:2603.29200v1 Announce Type: cross Abstract: Deep learning-based tropical cyclone (TC) forecasting methods have demonstrated significant potential and application advantages, as they feature much lower computational cost and faster operation speed than numerical weather prediction models. However, existing deep learning methods still have key limitations: they can only process a single type of sequential trajectory data or homogeneous meteorological variables, and fail to achieve accurate
Improving Ensemble Forecasts of Abnormally Deflecting Tropical Cyclones with Fused Atmosphere-Ocean-Terrain Data
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cs.AI, q-bio.NC updates on arXiv.org
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RAAP: Retrieval-Augmented Affordance Prediction with Cross-Image Action Alignment
arXiv:2603.29419v1 Announce Type: cross Abstract: Understanding object affordances is essential for enabling robots to perform purposeful and fine-grained interactions in diverse and unstructured environments. However, existing approaches either rely on retrieval, which is fragile due to sparsity and coverage gaps, or on large-scale models, which frequently mislocalize contact points and mispredict post-contact actions when applied to unseen categories, thereby hindering robust generalization.
RAAP: Retrieval-Augmented Affordance Prediction with Cross-Image Action Alignment
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cs.AI, q-bio.NC updates on arXiv.org
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An Empirical Study of Multi-Agent Collaboration for Automated Research
arXiv:2603.29632v1 Announce Type: cross Abstract: As AI agents evolve, the community is rapidly shifting from single Large Language Models (LLMs) to Multi-Agent Systems (MAS) to overcome cognitive bottlenecks in automated research. However, the optimal multi-agent coordination framework for these autonomous agents remains largely unexplored. In this paper, we present a systematic empirical study investigating the comparative efficacy of distinct multi-agent structures for automated machine lear
An Empirical Study of Multi-Agent Collaboration for Automated Research
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cs.AI, q-bio.NC updates on arXiv.org
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A Semi-amortized Lifted Learning-to-Optimize Masked (SALLO-M) Transformer Model for Scalable and Generalizable Beamforming
arXiv:2510.13077v3 Announce Type: replace-cross Abstract: We develop an unsupervised deep learning framework for real-time scalable and generalizable downlink beamforming in multi-user multiple-input single-output (MU-MISO) systems. The proposed semi-amortized lifted learning-to-optimize (SALLO) framework employs a multi-layer Transformer to iteratively refine an auxiliary variable and the beamformer solution, with a few projected gradient ascent steps at each layer. A key feature of our SALLO
A Semi-amortized Lifted Learning-to-Optimize Masked (SALLO-M) Transformer Model for Scalable and Generalizable Beamforming
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cs.AI, q-bio.NC updates on arXiv.org
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VLA Models Are More Generalizable Than You Think: Revisiting Physical and Spatial Modeling
arXiv:2512.02902v2 Announce Type: replace-cross Abstract: Vision-language-action (VLA) models achieve strong in-distribution performance but degrade sharply under novel camera viewpoints and visual perturbations. We show that this brittleness primarily arises from misalignment in Spatial Modeling, rather than Physical Modeling. To address this, we propose a one-shot adaptation framework that recalibrates visual representations through lightweight, learnable updates. Our first method, Feature To