Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Grounded by Experience: Generative Healthcare Prediction Augmented with Hierarchical Agentic Retrieval
arXiv:2511.13293v1 Announce Type: new Abstract: Accurate healthcare prediction is critical for improving patient outcomes and reducing operational costs. Bolstered by growing reasoning capabilities, large language models (LLMs) offer a promising path to enhance healthcare predictions by drawing on their rich parametric knowledge. However, LLMs are prone to factual inaccuracies due to limitations in the reliability and coverage of their embedded knowledge. While retrieval-augmented generation (R
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cs.AI, q-bio.NC updates on arXiv.org
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SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
arXiv:2511.08151v2 Announce Type: replace Abstract: Recent advances in large language models have enabled AI systems to achieve expert-level performance on domain-specific scientific tasks, yet these systems remain narrow and handcrafted. We introduce SciAgent, a unified multi-agent system designed for generalistic scientific reasoning-the ability to adapt reasoning strategies across disciplines and difficulty levels. SciAgent organizes problem solving as a hierarchical process: a Coordinator A
SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
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(Multiomics OR Omics) AND (Pancreatic)
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The dual immunomodulatory role of B cells in tumorigenesis: mechanisms, microenvironment crosstalk, and therapeutic implications
Front Immunol. 2025 Oct 30;16:1649812. doi: 10.3389/fimmu.2025.1649812. eCollection 2025.ABSTRACTB lymphocytes exhibit a multifaceted and context-dependent role in tumor biology, acting as both promoters and suppressors of malignancy through dynamic interactions within the tumor microenvironment (TME). This review synthesizes current evidence on the dual functions of B cells in tumor immunity, highlighting their capacity to orchestrate antitumor responses via antigen presentation, antibody-depen
The dual immunomodulatory role of B cells in tumorigenesis: mechanisms, microenvironment crosstalk, and therapeutic implications
Front Immunol. 2025 Oct 30;16:1649812. doi: 10.3389/fimmu.2025.1649812. eCollection 2025.
ABSTRACT
B lymphocytes exhibit a multifaceted and context-dependent role in tumor biology, acting as both promoters and suppressors of malignancy through dynamic interactions within the tumor microenvironment (TME). This review synthesizes current evidence on the dual functions of B cells in tumor immunity, highlighting their capacity to orchestrate antitumor responses via antigen presentation, antibody-dependent cytotoxicity, and tertiary lymphoid structure (TLS)-mediated T cell activation, while paradoxically driving immunosuppression through regulatory B cells (Bregs), pro-angiogenic signaling, and immune checkpoint modulation. Key mechanisms include TLS formation, which enhances cytotoxic T cell priming and correlates with improved immunotherapy outcomes, and Breg-mediated secretion of IL-10/TGF-β, which fosters T cell exhaustion and myeloid-derived suppressor cell recruitment. Tumor-type specificity is evident: TLS-rich malignancies like melanoma and Non-Small Cell Lung Cancer (NSCLC) show B cell-driven immune activation, whereas pancreatic and hepatocellular carcinomas demonstrate B cell functional plasticity influenced by metabolic and epigenetic reprogramming. Therapeutically, B cell-targeted strategies-including CD20 antibodies, CAR-T cells, and B cell epitope vaccines-demonstrate efficacy in hematologic and solid tumors, yet face challenges due to subset heterogeneity and sex-specific response disparities. Emerging approaches combine immune checkpoint inhibitors (ICBs) with TLS-inducing agents or exploit B cell-derived biomarkers for personalized therapy. Future directions emphasize deciphering B cell metabolic-niche crosstalk, optimizing combinatorial regimens, and leveraging spatial multiomics to resolve functional heterogeneity. By bridging mechanistic insights with clinical translation, this work underscores B cells as pivotal regulators of tumor immunity and advocates for precision strategies to harness their antitumor potential while mitigating pro-tumor plasticity.
PMID:41246318 | PMC:PMC12611826 | DOI:10.3389/fimmu.2025.1649812
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cs.AI, q-bio.NC updates on arXiv.org
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MedFuse: Multiplicative Embedding Fusion For Irregular Clinical Time Series
arXiv:2511.09247v1 Announce Type: new Abstract: Clinical time series derived from electronic health records (EHRs) are inherently irregular, with asynchronous sampling, missing values, and heterogeneous feature dynamics. While numerical laboratory measurements are highly informative, existing embedding strategies usually combine feature identity and value embeddings through additive operations, which constrains their ability to capture value-dependent feature interactions. We propose MedFuse, a
MedFuse: Multiplicative Embedding Fusion For Irregular Clinical Time Series
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Cell
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Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
Stereo-seq V2 facilitates single-cell-resolution spatial RNA mapping in FFPE samples through random primer capture, uncovering ncRNAs, host-pathogen transcriptome profiling, and spatial immune repertoires in situ.
Stereo-seq V2: Spatial mapping of total RNA on FFPE sections with high resolution
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cs.AI, q-bio.NC updates on arXiv.org
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SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
arXiv:2511.08151v1 Announce Type: new Abstract: Recent advances in large language models have enabled AI systems to achieve expert-level performance on domain-specific scientific tasks, yet these systems remain narrow and handcrafted. We introduce SciAgent, a unified multi-agent system designed for generalistic scientific reasoning-the ability to adapt reasoning strategies across disciplines and difficulty levels. SciAgent organizes problem solving as a hierarchical process: a Coordinator Agent
SciAgent: A Unified Multi-Agent System for Generalistic Scientific Reasoning
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Nature Biotechnology - Issue - nature.com science feeds
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Publisher Correction: Deep-learning-based virtual screening of antibacterial compounds
Nature Biotechnology, Published online: 07 November 2025; doi:10.1038/s41587-025-02941-0Publisher Correction: Deep-learning-based virtual screening of antibacterial compounds
Publisher Correction: Deep-learning-based virtual screening of antibacterial compounds
Nature Biotechnology, Published online: 07 November 2025; doi:10.1038/s41587-025-02941-0
Publisher Correction: Deep-learning-based virtual screening of antibacterial compounds-
cs.AI, q-bio.NC updates on arXiv.org
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AIMeter: Measuring, Analyzing, and Visualizing Energy and Carbon Footprint of AI Workloads
arXiv:2506.20535v2 Announce Type: replace-cross Abstract: The rapid advancement of AI, particularly large language models (LLMs), has raised significant concerns about the energy use and carbon emissions associated with model training and inference. However, existing tools for measuring and reporting such impacts are often fragmented, lacking systematic metric integration and offering limited support for correlation analysis among them. This paper presents AIMeter, a comprehensive software tool
AIMeter: Measuring, Analyzing, and Visualizing Energy and Carbon Footprint of AI Workloads
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Nanomaterial-assisted immunodiagnostic profiling and therapeutic targeting of hepatocellular carcinoma: from molecular biomarkers to clinical applications
Front Immunol. 2025 Oct 14;16:1668630. doi: 10.3389/fimmu.2025.1668630. eCollection 2025.ABSTRACTAIMS AND OBJECTIVES: This study aimed to identify immunologically relevant transcriptomic and proteomic biomarkers in hepatocellular carcinoma (HCC) and to characterize their B-cell epitopes for potential integration into nanomaterial-based biosensors and immunomodulatory platforms for early diagnosis and targeted therapy.METHODS: We conducted a comprehensive multi-omics analysis by integrating trans
Nanomaterial-assisted immunodiagnostic profiling and therapeutic targeting of hepatocellular carcinoma: from molecular biomarkers to clinical applications
Front Immunol. 2025 Oct 14;16:1668630. doi: 10.3389/fimmu.2025.1668630. eCollection 2025.
ABSTRACT
AIMS AND OBJECTIVES: This study aimed to identify immunologically relevant transcriptomic and proteomic biomarkers in hepatocellular carcinoma (HCC) and to characterize their B-cell epitopes for potential integration into nanomaterial-based biosensors and immunomodulatory platforms for early diagnosis and targeted therapy.
METHODS: We conducted a comprehensive multi-omics analysis by integrating transcriptomic (TCGA-LIHC) and proteomic data to identify differentially expressed genes (DEGs) in HCC. Protein-protein interaction networks and pathway enrichment were used to prioritize hub genes. Five candidate biomarkers, RFC2, HSP90AB1, YWHAZ, CYP2E1, and ADH4, were selected for qRT-PCR and serum ELISA validation in clinical cohorts comprising 85 HCC patients and 50 healthy controls. B-cell epitope prediction was performed using BepiPred 2.0 and validated through synthetic peptide-based ELISA in the same cohort to assess immunoreactivity. Diagnostic performance was evaluated using ROC curve analysis.
RESULTS: RFC2, HSP90AB1, and YWHAZ were significantly upregulated (|log2FC|>0.2) and showed high serological expression, whereas CYP2E1 and ADH4 were consistently downregulated. Predicted B-cell epitopes from RFC2, HSP90AB1, and YWHAZ exhibited strong immunoreactivity (AUC>0.84), indicating their diagnostic potential. Enrichment analysis revealed that upregulated DEGs were involved in cell cycle and mitotic progression, while downregulated genes were linked to immune suppression and metabolic dysfunction. These validated immunogenic epitopes offer promising anchors for nanomaterial-functionalized biosensors, such as gold nanoparticle-conjugated ELISA, graphene-based electrochemical platforms, and peptide-coated quantum dots, for ultrasensitive and multiplexed HCC detection.
CONCLUSION: By integrating transcriptomic and proteomic screening with epitope-level validation, we identified a novel panel of immunogenic biomarkers suitable for nanomaterial-enabled diagnostics in HCC. These findings support the translational potential of peptide-nano scaffold conjugates in developing minimally invasive, immune-responsive biosensing and therapeutic tools tailored for early-stage liver cancer management.
PMID:41164201 | PMC:PMC12558944 | DOI:10.3389/fimmu.2025.1668630
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Omics In Lung
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Prospective proteomics for discovering biomarkers in lung adenocarcinoma: a literature review
Transl Cancer Res. 2025 Sep 30;14(9):6102-6117. doi: 10.21037/tcr-2025-1092. Epub 2025 Sep 26.ABSTRACTBACKGROUND AND OBJECTIVE: Lung adenocarcinoma (LUAD), as the main subtype of non-small cell lung cancer (NSCLC), faces clinical challenges including molecular heterogeneity, late diagnosis, and aggressive growth, leading to a low 5-year survival rate. Biomarkers are critical for early detection, accurate differentiation of benign/malignant lesions, and guiding personalized treatment strategies.
Prospective proteomics for discovering biomarkers in lung adenocarcinoma: a literature review
Transl Cancer Res. 2025 Sep 30;14(9):6102-6117. doi: 10.21037/tcr-2025-1092. Epub 2025 Sep 26.
ABSTRACT
BACKGROUND AND OBJECTIVE: Lung adenocarcinoma (LUAD), as the main subtype of non-small cell lung cancer (NSCLC), faces clinical challenges including molecular heterogeneity, late diagnosis, and aggressive growth, leading to a low 5-year survival rate. Biomarkers are critical for early detection, accurate differentiation of benign/malignant lesions, and guiding personalized treatment strategies. Proteomic technologies using liquid biopsy show potential by analyzing protein changes and post-translational modifications (PTMs) to identify novel biomarkers and unravel cancer mechanisms. This review examines proteomic advances in LUAD, compares platform strengths, lists validated protein markers, and discusses challenges like specificity and regulations. It aims to develop a precision medicine framework by integrating multi-omics data for improved diagnosis and treatment.
METHODS: This study conducted a literature review by searching the PubMed and Web of Science databases for original articles written in English from 2002 to 2025, using the keywords "lung adenocarcinoma" OR "LUAD" AND "biomarkers" AND "proteomics" OR "SomaScan" OR "spatial proteomics" to identify the latest research findings in the field of proteomics technology and LUAD biomarkers. The included studies mainly focused on the current landscape of biomarkers in the diagnosis, treatment, and prognosis of LUAD.
KEY CONTENT AND FINDINGS: This review discusses high-throughput methods for comprehensive protein profiling in accessible biospecimens (tissues, blood, urine) to identify biomarkers for LUAD. We systematically evaluate emerging proteomic strategies, including mass spectrometry (MS), proximity extension assays (PEAs), spatial proteomics techniques, and SomaScan platforms-coupled with innovative computational frameworks have revolutionized biomarkers discovery and their translational potential in developing precision diagnostics and targeted therapies. Additionally, the review addresses challenges in integrating proteomics with genomics, transcriptomics, and metabolomics, offering new methodologies and expanding research in life sciences. As technological advancements continue, it is anticipated that more potential biomarkers will be conducted to validate the broader application in LUAD treatment, addressing early-stage disease complexities and aiding in selecting more effective treatment strategies.
CONCLUSIONS: By synthesizing cutting-edge evidence on proteome-driven LUAD biomarkers, this review elucidates actionable strategies to refine early detection protocols and mechanism-informed personalized treatment frameworks, directly advancing precision oncology initiatives for this prevalent malignancy through biomarker-guided clinical decision-making and multi-omics integration.
PMID:41158224 | PMC:PMC12554480 | DOI:10.21037/tcr-2025-1092
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cs.AI, q-bio.NC updates on arXiv.org
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From Detection to Discovery: A Closed-Loop Approach for Simultaneous and Continuous Medical Knowledge Expansion and Depression Detection on Social Media
arXiv:2510.23626v1 Announce Type: cross Abstract: Social media user-generated content (UGC) provides real-time, self-reported indicators of mental health conditions such as depression, offering a valuable source for predictive analytics. While prior studies integrate medical knowledge to improve prediction accuracy, they overlook the opportunity to simultaneously expand such knowledge through predictive processes. We develop a Closed-Loop Large Language Model (LLM)-Knowledge Graph framework tha
From Detection to Discovery: A Closed-Loop Approach for Simultaneous and Continuous Medical Knowledge Expansion and Depression Detection on Social Media
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cs.AI, q-bio.NC updates on arXiv.org
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Tongyi DeepResearch Technical Report
arXiv:2510.24701v1 Announce Type: cross Abstract: We present Tongyi DeepResearch, an agentic large language model, which is specifically designed for long-horizon, deep information-seeking research tasks. To incentivize autonomous deep research agency, Tongyi DeepResearch is developed through an end-to-end training framework that combines agentic mid-training and agentic post-training, enabling scalable reasoning and information seeking across complex tasks. We design a highly scalable data syn
Tongyi DeepResearch Technical Report
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cs.AI, q-bio.NC updates on arXiv.org
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Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
arXiv:2510.21293v2 Announce Type: replace Abstract: Background: Trustworthy AI serves as a foundational pillar for two major AI ethics conferences: AIES and FAccT. However, current research often adopts techno-centric approaches, focusing primarily on technical attributes such as reliability, robustness, and fairness, while overlooking the sociotechnical dimensions critical to understanding AI trustworthiness in real-world contexts. Objectives: This scoping review aims to examine how the AIES
Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Integrating deep learning and multi-omics features in radiation pneumonitis prediction for lung cancer patients using PET/CT
BMC Med Imaging. 2025 Oct 27;25(1):426. doi: 10.1186/s12880-025-01971-z.ABSTRACTBACKGROUND: To investigate the feasibility and accuracy of PET radiomics features, along with their combination with CT radiomics, dosiomics, and deep learning (DL) features, in predicting radiation pneumonitis (RP) in lung cancer patients treated with volumetric modulated arc therapy (VMAT).METHODS: A total of 206 and 27 lung cancer patients who underwent VMAT with pre-treatment PET/CT imaging were enrolled from Hos
Integrating deep learning and multi-omics features in radiation pneumonitis prediction for lung cancer patients using PET/CT
BMC Med Imaging. 2025 Oct 27;25(1):426. doi: 10.1186/s12880-025-01971-z.
ABSTRACT
BACKGROUND: To investigate the feasibility and accuracy of PET radiomics features, along with their combination with CT radiomics, dosiomics, and deep learning (DL) features, in predicting radiation pneumonitis (RP) in lung cancer patients treated with volumetric modulated arc therapy (VMAT).
METHODS: A total of 206 and 27 lung cancer patients who underwent VMAT with pre-treatment PET/CT imaging were enrolled from Hospital One and Hospital Two for model training and external validation, respectively. Four machine learning (ML) methods were applied to build radiomics models with features extracted from CT (R_CT), PET (R_PET), radiomics features fused PET/CT (R_fFU) and fused PET/CT images (R_ iFU), as well dosiomics features (D). Three DL models were built to extract features from PET (DL_PET), CT (DL_CT), and fused PET/CT images (DL_FU). The best-performing radiomics and DL models were combined with dosiomics to create the final joint model. ROC curves with AUC, accuracy, sensitivity, and specificity evaluated the performance. A nomogram was constructed using top-performing model features, parameters, and relevant clinical factors.
RESULTS: The extreme gradient boosting (XGBoost) and 18-layer residual neural network (Resnet-18) achieved the best performance. The R+D+DL model combined radiomics, dosiomics, and DL features achieved AUCs of 0.93, 0.92 and 0.89 in the training, internal validaiton and external validation cohorts, respectively. A nomogram constructed with gender, Adaptive RT, SUVp90, and XGBoost-score achieved an AUC of 0.94 for RP prediction in VMAT-treated lung cancer patients using PET/CT.
CONCLUSION: Integrating radiomics, DL, dosiomics features and SUVp90 is promising in the RP prediction for lung cancer patients underwent VMAT using PET/CT images.
PMID:41146084 | DOI:10.1186/s12880-025-01971-z
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cs.AI, q-bio.NC updates on arXiv.org
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Learned, Lagged, LLM-splained: LLM Responses to End User Security Questions
arXiv:2411.14571v2 Announce Type: replace-cross Abstract: Answering end user security questions is challenging. While large language models (LLMs) like GPT, LLAMA, and Gemini are far from error-free, they have shown promise in answering a variety of questions outside of security. We studied LLM performance in the area of end user security by qualitatively evaluating 3 popular LLMs on 900 systematically collected end user security questions. While LLMs demonstrate broad generalist ``knowledge'
Learned, Lagged, LLM-splained: LLM Responses to End User Security Questions
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cs.AI, q-bio.NC updates on arXiv.org
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Multimodal 3D Genome Pre-training
arXiv:2504.09060v2 Announce Type: replace-cross Abstract: Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored. Here, we propose MIX-HIC, the first multimodal foundation model of 3D genome that integrates both 3D genome structure and epigenomic tracks, which obtains unified and comprehensive semantics. For accurate heterogeneous semantic
Multimodal 3D Genome Pre-training
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Nature Medicine
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A full life cycle biological clock based on routine clinical data and its impact in health and diseases
Nature Medicine, Published online: 27 October 2025; doi:10.1038/s41591-025-04006-wThe biological clock model LifeClock predicts biological age across all life stages from routine clinical data, revealing distinct pediatric and adult disease risk patterns.
A full life cycle biological clock based on routine clinical data and its impact in health and diseases
Nature Medicine, Published online: 27 October 2025; doi:10.1038/s41591-025-04006-w
The biological clock model LifeClock predicts biological age across all life stages from routine clinical data, revealing distinct pediatric and adult disease risk patterns.-
cs.AI, q-bio.NC updates on arXiv.org
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MedAlign: A Synergistic Framework of Multimodal Preference Optimization and Federated Meta-Cognitive Reasoning
arXiv:2510.21093v1 Announce Type: new Abstract: Recently, large models have shown significant potential for smart healthcare. However, the deployment of Large Vision-Language Models (LVLMs) for clinical services is currently hindered by three critical challenges: a tendency to hallucinate answers not grounded in visual evidence, the inefficiency of fixed-depth reasoning, and the difficulty of multi-institutional collaboration. To address these challenges, in this paper, we develop MedAlign, a n
MedAlign: A Synergistic Framework of Multimodal Preference Optimization and Federated Meta-Cognitive Reasoning
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cs.AI, q-bio.NC updates on arXiv.org
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Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
arXiv:2510.21293v1 Announce Type: new Abstract: Background: Trustworthy AI serves as a foundational pillar for two major AI ethics conferences: AIES and FAccT. However, current research often adopts techno-centric approaches, focusing primarily on technical attributes such as reliability, robustness, and fairness, while overlooking the sociotechnical dimensions critical to understanding AI trustworthiness in real-world contexts. Objectives: This scoping review aims to examine how the AIES and
Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
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cs.AI, q-bio.NC updates on arXiv.org
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Benchmarking GPT-5 for biomedical natural language processing
arXiv:2509.04462v2 Announce Type: replace-cross Abstract: Biomedical literature and clinical narratives pose multifaceted challenges for natural language understanding, from precise entity extraction and document synthesis to multi-step diagnostic reasoning. This study extends a unified benchmark to evaluate GPT-5 and GPT-4o under zero-, one-, and five-shot prompting across five core biomedical NLP tasks: named entity recognition, relation extraction, multi-label document classification, summar