Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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APT-Agent: Automated Penetration Testing using Large Language Models
arXiv:2605.24949v1 Announce Type: cross Abstract: Penetration testing is essential to securing modern web infrastructures, yet traditional manual methods struggle to keep pace with their scale and complexity. Large Language Models (LLMs) offer new opportunities for automating these tasks, but existing approaches face two persistent challenges: hallucination of technical entities and insufficient long-term contextual memory. To address these issues, we present APT-Agent, a fully automated LLM-dr
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cs.AI, q-bio.NC updates on arXiv.org
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Contractual Skills: A GovernSpec Design Framework for Enterprise AI Agents
arXiv:2605.22634v2 Announce Type: replace-cross Abstract: Skills have become a practical packaging mechanism for agent instructions, workflows, scripts, and reference materials. In enterprise settings, however, a skill often needs to express more than task guidance: goals, input boundaries, permissions, human approval points, evidence requirements, output contracts, quality criteria, verification steps, and handoff rules. This paper proposes contractual skills, a GovernSpec-inspired design fram
Contractual Skills: A GovernSpec Design Framework for Enterprise AI Agents
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Cell
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Pan-neurodegeneration proteomics reveals disease subtypes and molecular signatures
A pan-neurodegeneration atlas built from multilayer, deep proteomics of 2,279 brain samples across 6 major diseases integrates whole proteome, detergent-insoluble proteome, and posttranslational modifications to enable intra- and inter-disease comparisons to reveal disease-specific subtypes and dysregulated pathways, while identifying shared changes such as GPNMB upregulation and NPTX2 downregulation.
Pan-neurodegeneration proteomics reveals disease subtypes and molecular signatures
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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WNT7A correlates with immunosuppression and predicts adverse prognosis in lung adenocarcinoma: Potential implication of the NF-kappaB/CCL2 Axis
Cytokine. 2026 Apr 6;202:157144. doi: 10.1016/j.cyto.2026.157144. Online ahead of print.ABSTRACTBACKGROUND: The remodeling of the tumor immune microenvironment (TME) is a pivotal determinant of therapeutic efficacy and clinical outcome in Lung Adenocarcinoma (LUAD). While WNT signaling is a known oncogenic driver, the specific immunomodulatory role of WNT7A and its potential crosstalk with inflammatory pathways in LUAD remain to be fully elucidated. We sought to define the prognostic value of WN
WNT7A correlates with immunosuppression and predicts adverse prognosis in lung adenocarcinoma: Potential implication of the NF-kappaB/CCL2 Axis
Cytokine. 2026 Apr 6;202:157144. doi: 10.1016/j.cyto.2026.157144. Online ahead of print.
ABSTRACT
BACKGROUND: The remodeling of the tumor immune microenvironment (TME) is a pivotal determinant of therapeutic efficacy and clinical outcome in Lung Adenocarcinoma (LUAD). While WNT signaling is a known oncogenic driver, the specific immunomodulatory role of WNT7A and its potential crosstalk with inflammatory pathways in LUAD remain to be fully elucidated. We sought to define the prognostic value of WNT7A and explore the molecular mechanisms by which it may foster an immunosuppressive TME.
METHODS: We performed a multi-omics analysis utilizing the TCGA-LUAD cohort (N = 508) and validated findings in an independent external cohort (GSE30219, N = 293). The prognostic significance of WNT7A was evaluated using Kaplan-Meier and multivariate Cox regression analyses. TME composition was dissected via ssGSEA, focusing on myeloid-derived suppressor cell (MDSC) infiltration. Mechanistic pathways were identified using Gene Set Enrichment Analysis (GSEA) and gene co-expression networks.
RESULTS: High WNT7A expression was identified as a significant predictor of poor Overall Survival (OS) in the TCGA cohort (P < 0.05) and validated in the external cohort (P < 0.05). Multivariate analysis confirmed WNT7A as an independent prognostic risk factor (HR = 1.085, P = 0.036). Immunologically, WNT7A expression was positively correlated with MDSC infiltration (R = 0.43, P < 0.001), suggesting a shift towards an immune-tolerant phenotype. Mechanistically, GSEA revealed a robust activation of inflammatory signaling in the high-WNT7A group. Specifically, the TNFA Signaling via NF-κB pathway was significantly enriched(NES = 2.52, P < 0.001). Consistent with this pathway activation, WNT7A showed a statistically significant positive correlation with CCL2 (P < 0.001), a critical chemokine for MDSC recruitment, implicating the NF-κB/CCL2 axis in this process.
CONCLUSION: WNT7A serves as a prognostic biomarker linked to immune evasion in LUAD, potentially by modulating the NF-κB/CCL2/MDSC axis. This study identifies WNT7A as a potential therapeutic target to remodel the immune microenvironment, providing a rationale for future investigations into WNT-targeted strategies to improve immunotherapy efficacy.
PMID:41946008 | DOI:10.1016/j.cyto.2026.157144
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Omics In Lung
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WNT7A correlates with immunosuppression and predicts adverse prognosis in lung adenocarcinoma: Potential implication of the NF-kappaB/CCL2 Axis
Cytokine. 2026 Apr 6;202:157144. doi: 10.1016/j.cyto.2026.157144. Online ahead of print.ABSTRACTBACKGROUND: The remodeling of the tumor immune microenvironment (TME) is a pivotal determinant of therapeutic efficacy and clinical outcome in Lung Adenocarcinoma (LUAD). While WNT signaling is a known oncogenic driver, the specific immunomodulatory role of WNT7A and its potential crosstalk with inflammatory pathways in LUAD remain to be fully elucidated. We sought to define the prognostic value of WN
WNT7A correlates with immunosuppression and predicts adverse prognosis in lung adenocarcinoma: Potential implication of the NF-kappaB/CCL2 Axis
Cytokine. 2026 Apr 6;202:157144. doi: 10.1016/j.cyto.2026.157144. Online ahead of print.
ABSTRACT
BACKGROUND: The remodeling of the tumor immune microenvironment (TME) is a pivotal determinant of therapeutic efficacy and clinical outcome in Lung Adenocarcinoma (LUAD). While WNT signaling is a known oncogenic driver, the specific immunomodulatory role of WNT7A and its potential crosstalk with inflammatory pathways in LUAD remain to be fully elucidated. We sought to define the prognostic value of WNT7A and explore the molecular mechanisms by which it may foster an immunosuppressive TME.
METHODS: We performed a multi-omics analysis utilizing the TCGA-LUAD cohort (N = 508) and validated findings in an independent external cohort (GSE30219, N = 293). The prognostic significance of WNT7A was evaluated using Kaplan-Meier and multivariate Cox regression analyses. TME composition was dissected via ssGSEA, focusing on myeloid-derived suppressor cell (MDSC) infiltration. Mechanistic pathways were identified using Gene Set Enrichment Analysis (GSEA) and gene co-expression networks.
RESULTS: High WNT7A expression was identified as a significant predictor of poor Overall Survival (OS) in the TCGA cohort (P < 0.05) and validated in the external cohort (P < 0.05). Multivariate analysis confirmed WNT7A as an independent prognostic risk factor (HR = 1.085, P = 0.036). Immunologically, WNT7A expression was positively correlated with MDSC infiltration (R = 0.43, P < 0.001), suggesting a shift towards an immune-tolerant phenotype. Mechanistically, GSEA revealed a robust activation of inflammatory signaling in the high-WNT7A group. Specifically, the TNFA Signaling via NF-κB pathway was significantly enriched(NES = 2.52, P < 0.001). Consistent with this pathway activation, WNT7A showed a statistically significant positive correlation with CCL2 (P < 0.001), a critical chemokine for MDSC recruitment, implicating the NF-κB/CCL2 axis in this process.
CONCLUSION: WNT7A serves as a prognostic biomarker linked to immune evasion in LUAD, potentially by modulating the NF-κB/CCL2/MDSC axis. This study identifies WNT7A as a potential therapeutic target to remodel the immune microenvironment, providing a rationale for future investigations into WNT-targeted strategies to improve immunotherapy efficacy.
PMID:41946008 | DOI:10.1016/j.cyto.2026.157144
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cs.AI, q-bio.NC updates on arXiv.org
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Readable Minds: Emergent Theory-of-Mind-Like Behavior in LLM Poker Agents
arXiv:2604.04157v1 Announce Type: new Abstract: Theory of Mind (ToM) -- the ability to model others' mental states -- is fundamental to human social cognition. Whether large language models (LLMs) can develop ToM has been tested exclusively through static vignettes, leaving open whether ToM-like reasoning can emerge through dynamic interaction. Here we report that autonomous LLM agents playing extended sessions of Texas Hold'em poker progressively develop sophisticated opponent models, but only
Readable Minds: Emergent Theory-of-Mind-Like Behavior in LLM Poker Agents
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Oncogene - Issue - nature.com science feeds
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S100A6 promotes liver metastasis by activating FGFR3 signaling in <i>BAP1</i>-deficient uveal melanoma
Oncogene, Published online: 04 April 2026; doi:10.1038/s41388-026-03766-0S100A6 promotes liver metastasis by activating FGFR3 signaling in BAP1-deficient uveal melanoma
S100A6 promotes liver metastasis by activating FGFR3 signaling in <i>BAP1</i>-deficient uveal melanoma
Oncogene, Published online: 04 April 2026; doi:10.1038/s41388-026-03766-0
S100A6 promotes liver metastasis by activating FGFR3 signaling in BAP1-deficient uveal melanoma-
cs.AI, q-bio.NC updates on arXiv.org
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Countering Catastrophic Forgetting of Large Language Models for Better Instruction Following via Weight-Space Model Merging
arXiv:2604.01538v1 Announce Type: cross Abstract: Large language models have been adopted in the medical domain for clinical documentation to reduce clinician burden. However, studies have reported that LLMs often "forget" a significant amount of instruction-following ability when fine-tuned using a task-specific medical dataset, a critical challenge in adopting general-purpose LLMs for clinical applications. This study presents a model merging framework to efficiently adapt general-purpose LLM
Countering Catastrophic Forgetting of Large Language Models for Better Instruction Following via Weight-Space Model Merging
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npj Digital Medicine
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Integrating large language models for enhanced predictive analytics in healthcare
npj Digital Medicine, Published online: 02 April 2026; doi:10.1038/s41746-026-02572-yIntegrating large language models for enhanced predictive analytics in healthcare
Integrating large language models for enhanced predictive analytics in healthcare
npj Digital Medicine, Published online: 02 April 2026; doi:10.1038/s41746-026-02572-y
Integrating large language models for enhanced predictive analytics in healthcare-
Nature - Issue - nature.com science feeds
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Structure of the mouse cytoplasmic lattice
Nature, Published online: 31 March 2026; doi:10.1038/s41586-026-10442-6Structure of the mouse cytoplasmic lattice
Structure of the mouse cytoplasmic lattice
Nature, Published online: 31 March 2026; doi:10.1038/s41586-026-10442-6
Structure of the mouse cytoplasmic lattice-
AAAS: Table of Contents
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High-temperature memristors enabled by interfacial engineering
Science, Ahead of Print.
High-temperature memristors enabled by interfacial engineering
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Omics In Lung
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Dual Antitumor Effects of Solanum incanum L. in Lung and Colonic Adenocarcinomas via TRAIL-Mediated Extrinsic Apoptotic Pathway: A Network Pharmacology and Multi-Omics Investigation
Curr Med Chem. 2026 Mar 17. doi: 10.2174/0109298673415187251212085809. Online ahead of print.ABSTRACTBACKGROUND: Solanum incanum L. (S. incanum) is a Traditional Chinese Medicine (TCM) known for its heat-clearing and detoxifying properties. This study evaluates the anti-cancer potential of S. incanum in lung and colorectal adenocarcinoma. Also, we aim to confirm the connection between the lung and the large intestine, as proposed in TCM theory.METHODS: This study employed network pharmacology an
Dual Antitumor Effects of Solanum incanum L. in Lung and Colonic Adenocarcinomas via TRAIL-Mediated Extrinsic Apoptotic Pathway: A Network Pharmacology and Multi-Omics Investigation
Curr Med Chem. 2026 Mar 17. doi: 10.2174/0109298673415187251212085809. Online ahead of print.
ABSTRACT
BACKGROUND: Solanum incanum L. (S. incanum) is a Traditional Chinese Medicine (TCM) known for its heat-clearing and detoxifying properties. This study evaluates the anti-cancer potential of S. incanum in lung and colorectal adenocarcinoma. Also, we aim to confirm the connection between the lung and the large intestine, as proposed in TCM theory.
METHODS: This study employed network pharmacology analysis, MTT and morphological analysis, Western blotting, and molecular docking to investigate the anti-cancer effects of S. incanum, particularly through its activation of the TRAIL-mediated extrinsic apoptotic pathway.
RESULTS: This study identified 15 active compounds in S. incanum, with glycosylated alkaloids such as α-solanine and solasonine highlighted as key bioactive compounds. KEGG and GO analyses revealed that S. incanum influences apoptosis-related pathways, particularly the extrinsic apoptotic pathway, regulating mediators such as CASP3, CASP8, and various TNF- related receptors. The anticancer potential was assessed through cellular studies using A549 and HT29 cell lines, with MTT cell viability assays showing that α-solanine induces apoptosis, with IC50 values between 20 and 30 μM. Western blot analysis demonstrated that S. incanum activates apoptosis via the TRAIL-mediated extrinsic apoptotic pathway, promoting CASP8, CASP3, and PARP1 cleavage in a dose-dependent manner, affecting DNA synthesis. Molecular docking further identified α-solanine and solasonine as compounds that bind to critical proteins in the TRAIL-related apoptotic pathway, confirming their roles in promoting apoptosis.
DISCUSSION: The shared activation of the TRAIL-mediated apoptotic pathway in both lung and colorectal adenocarcinoma models suggests a common molecular mechanism. These findings provide experimental evidence linking traditional ethnopharmacological concepts with apoptosis-related anti-cancer activity.
CONCLUSIONS: This study emphasizes that the main compound of S. incanum, α-solanine, supports the ethnopharmacological concept of "Exterior-interior Pairing of the Lung and Large Intestine", thereby demonstrating that both lung and colorectal adenocarcinomas share a common anticancer pathway through a TRAIL-related apoptotic mechanism.
PMID:41863159 | DOI:10.2174/0109298673415187251212085809
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Cell
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Human-specific features of the cerebellum and ZP2-regulated synapse development
Human-specific transcriptomic and regulatory features are present in the cerebellum, with ZP2 playing a key role in synapse regulation. ZP2 expression is induced by pontine mossy fibers, leading to decreased synaptic proteins and neuronal activity, which provides insights into the evolutionary development of the human cerebellum.
Human-specific features of the cerebellum and ZP2-regulated synapse development
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Pulmonary nodule
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NFATC2::NUTM2 Fusion Defines a Novel Primary Pulmonary Epithelial Tumor With a Distinctive Immunophenotype
Am J Surg Pathol. 2026 Jun 1;50(6):695-704. doi: 10.1097/PAS.0000000000002533. Epub 2026 Mar 13.ABSTRACTWith the application of molecular techniques in pathologic diagnosis, several novel primary pulmonary epithelial tumors have been continuously discovered and classified under the WHO classification of thoracic tumors. Recently, a pulmonary tumor with NFATC2 :: NUTM2B fusion was first documented, but the spectrum of NFATC2::NUTM2 fusion variants and their associated pathologic features remains
NFATC2::NUTM2 Fusion Defines a Novel Primary Pulmonary Epithelial Tumor With a Distinctive Immunophenotype
Am J Surg Pathol. 2026 Jun 1;50(6):695-704. doi: 10.1097/PAS.0000000000002533. Epub 2026 Mar 13.
ABSTRACT
With the application of molecular techniques in pathologic diagnosis, several novel primary pulmonary epithelial tumors have been continuously discovered and classified under the WHO classification of thoracic tumors. Recently, a pulmonary tumor with NFATC2 :: NUTM2B fusion was first documented, but the spectrum of NFATC2::NUTM2 fusion variants and their associated pathologic features remains incompletely characterized. Coincidentally, we also found and described 6 primary pulmonary tumors harboring recurrent NFATC2::NUTM2A/E fusions through integrated genomic analysis. These patients, including 4 females and 2 males, with a median age of 53 years, presented with incidentally detected peripheral lung nodules composed of monotonous epithelioid cells arranged in cords, nests, and trabeculae within a prominent desmoplastic stroma. All tumors exhibited a consistent immunophenotype: CK5/6+/GATA3+/calponin+/EMA+/DOG1 (perinuclear dot-like staining)/p63-. High-throughput chromosome conformation capture (Hi-C) analysis showed the structural variation of NFATC2::NUTM2E in all 6 cases, whereas RNA sequencing detected the fusion transcripts in 5 cases ( NFATC2::NUTM2A , n=2; NFATC2::NUTM2E , n=3). Ultrastructural examination of 1 case suggested epithelial differentiation. All patients remained disease-free after complete resection (median follow-up: 24 mo; range: 9 to 41 mo). These findings define a novel primary pulmonary tumor entity driven by NFATC2::NUTM2 fusions, and characterized by a distinctive immunophenotype, expanding the spectrum of NUTM2 -associated neoplasms. Our study underscores the utility of multiomics approaches for characterizing rare neoplasms and provides a diagnostic framework for this entity.
PMID:41821426 | DOI:10.1097/PAS.0000000000002533
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Omics In Lung
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NFATC2::NUTM2 Fusion Defines a Novel Primary Pulmonary Epithelial Tumor With a Distinctive Immunophenotype
Am J Surg Pathol. 2026 Mar 13. doi: 10.1097/PAS.0000000000002533. Online ahead of print.ABSTRACTWith the application of molecular techniques in pathologic diagnosis, several novel primary pulmonary epithelial tumors have been continuously discovered and classified under the WHO classification of thoracic tumors. Recently, a pulmonary tumor with NFATC2::NUTM2B fusion was first documented, but the spectrum of NFATC2::NUTM2 fusion variants and their associated pathologic features remains incomplete
NFATC2::NUTM2 Fusion Defines a Novel Primary Pulmonary Epithelial Tumor With a Distinctive Immunophenotype
Am J Surg Pathol. 2026 Mar 13. doi: 10.1097/PAS.0000000000002533. Online ahead of print.
ABSTRACT
With the application of molecular techniques in pathologic diagnosis, several novel primary pulmonary epithelial tumors have been continuously discovered and classified under the WHO classification of thoracic tumors. Recently, a pulmonary tumor with NFATC2::NUTM2B fusion was first documented, but the spectrum of NFATC2::NUTM2 fusion variants and their associated pathologic features remains incompletely characterized. Coincidentally, we also found and described 6 primary pulmonary tumors harboring recurrent NFATC2::NUTM2A/E fusions through integrated genomic analysis. These patients, including 4 females and 2 males, with a median age of 53 years, presented with incidentally detected peripheral lung nodules composed of monotonous epithelioid cells arranged in cords, nests, and trabeculae within a prominent desmoplastic stroma. All tumors exhibited a consistent immunophenotype: CK5/6+/GATA3+/calponin+/EMA+/DOG1 (perinuclear dot-like staining)/p63-. High-throughput chromosome conformation capture (Hi-C) analysis showed the structural variation of NFATC2::NUTM2E in all 6 cases, whereas RNA sequencing detected the fusion transcripts in 5 cases (NFATC2::NUTM2A, n=2; NFATC2::NUTM2E, n=3). Ultrastructural examination of 1 case suggested epithelial differentiation. All patients remained disease-free after complete resection (median follow-up: 24 mo; range: 9 to 41 mo). These findings define a novel primary pulmonary tumor entity driven by NFATC2::NUTM2 fusions, and characterized by a distinctive immunophenotype, expanding the spectrum of NUTM2-associated neoplasms. Our study underscores the utility of multiomics approaches for characterizing rare neoplasms and provides a diagnostic framework for this entity.
PMID:41821426 | DOI:10.1097/PAS.0000000000002533
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cs.AI, q-bio.NC updates on arXiv.org
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T2S-Bench & Structure-of-Thought: Benchmarking and Prompting Comprehensive Text-to-Structure Reasoning
arXiv:2603.03790v1 Announce Type: cross Abstract: Think about how human handles complex reading tasks: marking key points, inferring their relationships, and structuring information to guide understanding and responses. Likewise, can a large language model benefit from text structure to enhance text-processing performance? To explore it, in this work, we first introduce Structure of Thought (SoT), a prompting technique that explicitly guides models to construct intermediate text structures, con
T2S-Bench & Structure-of-Thought: Benchmarking and Prompting Comprehensive Text-to-Structure Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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IDER: IDempotent Experience Replay for Reliable Continual Learning
arXiv:2603.00624v2 Announce Type: replace-cross Abstract: Catastrophic forgetting, the tendency of neural networks to forget previously learned knowledge when learning new tasks, has been a major challenge in continual learning (CL). To tackle this challenge, CL methods have been proposed and shown to reduce forgetting. Furthermore, CL models deployed in mission-critical settings can benefit from uncertainty awareness by calibrating their predictions to reliably assess their confidences. Howeve
IDER: IDempotent Experience Replay for Reliable Continual Learning
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cs.AI, q-bio.NC updates on arXiv.org
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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 (N
Can Multimodal LLMs See Science Instruction? Benchmarking Pedagogical Reasoning in K-12 Classroom Videos
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cs.AI, q-bio.NC updates on arXiv.org
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Temporal-Aware Heterogeneous Graph Reasoning with Multi-View Fusion for Temporal Question Answering
arXiv:2602.19569v1 Announce Type: cross Abstract: Question Answering over Temporal Knowledge Graphs (TKGQA) has attracted growing interest for handling time-sensitive queries. However, existing methods still struggle with: 1) weak incorporation of temporal constraints in question representation, causing biased reasoning; 2) limited ability to perform explicit multi-hop reasoning; and 3) suboptimal fusion of language and graph representations. We propose a novel framework with temporal-aware que