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cs.AI, q-bio.NC updates on arXiv.org
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ToolMind Technical Report: A Large-Scale, Reasoning-Enhanced Tool-Use Dataset
arXiv:2511.15718v2 Announce Type: replace Abstract: Large Language Model (LLM) agents have developed rapidly in recent years to solve complex real-world problems using external tools. However, the scarcity of high-quality trajectories still hinders the development of stronger LLM agents. Most existing works on multi-turn dialogue synthesis validate correctness only at the trajectory level, which may overlook turn-level errors that can propagate during training and degrade model performance. To
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Journal of Medical Internet Research
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Considerations for Patient Privacy of Large Language Models in Health Care: Scoping Review
Background: The application of large language models (LLMs) in health care holds significant potential for enhancing patient care and advancing medical research. However, the protection of patient privacy remains a critical issue, especially when handling patient health information (PHI). Objective: This scoping review aims to evaluate the adequacy of current approaches and identify areas in need of improvement to ensure robust patient privacy protection in the existing studies about PHI-LLMs wi
Considerations for Patient Privacy of Large Language Models in Health Care: Scoping Review
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cs.AI, q-bio.NC updates on arXiv.org
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TeaRAG: A Token-Efficient Agentic Retrieval-Augmented Generation Framework
arXiv:2511.05385v1 Announce Type: cross Abstract: Retrieval-Augmented Generation (RAG) utilizes external knowledge to augment Large Language Models' (LLMs) reliability. For flexibility, agentic RAG employs autonomous, multi-round retrieval and reasoning to resolve queries. Although recent agentic RAG has improved via reinforcement learning, they often incur substantial token overhead from search and reasoning processes. This trade-off prioritizes accuracy over efficiency. To address this issue,
TeaRAG: A Token-Efficient Agentic Retrieval-Augmented Generation Framework
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Omics In Lung
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GASPS: A Multi-Omics Framework for Defining Genomic Aberration-Driven Signatures and Predicting Patient Outcomes in Lung Cancer
bioRxiv [Preprint]. 2025 Aug 25:2025.08.21.671519. doi: 10.1101/2025.08.21.671519.ABSTRACTLung cancer is the most common cause of cancer-related death worldwide. Recent advancements in targeted therapies and immunotherapies have achieved remarkable success. However, patient responses to treatments with lung cancer vary substantially. The mutation status of driver genes can direct personalized treatment, but their prognostic value and treatment efficacy are limited. In this study, we developed a
GASPS: A Multi-Omics Framework for Defining Genomic Aberration-Driven Signatures and Predicting Patient Outcomes in Lung Cancer
bioRxiv [Preprint]. 2025 Aug 25:2025.08.21.671519. doi: 10.1101/2025.08.21.671519.
ABSTRACT
Lung cancer is the most common cause of cancer-related death worldwide. Recent advancements in targeted therapies and immunotherapies have achieved remarkable success. However, patient responses to treatments with lung cancer vary substantially. The mutation status of driver genes can direct personalized treatment, but their prognostic value and treatment efficacy are limited. In this study, we developed a statistical framework named Genomic Aberration-Derived Signature for Patient Stratification (GASPS) to characterize the transcriptomic deregulation of driver genomic aberrations and stratify patients. By applying GASPS to The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data, we developed gene signatures for 38 driver genomic aberrations, including gene mutations, amplifications, and deletions. These signatures were applied to independent lung cancer transcriptomic datasets containing a total of 2,226 patient samples. Our results indicated that these driver gene signatures are much more prognostic than their corresponding genomic mutations. Interestingly, the two EGFR-related signatures characterizing EGFR mutation and amplification, respectively, exhibited contrasting associations with prognosis, treatment response, and immune infiltration in the tumor microenvironment. Moreover, the STK11 mutation signature, rather than the mutation status, was found to be predictive of the response and long-term benefit of patients treated with immune checkpoint blockade therapy in lung cancer. This framework is readily applicable to most cancer types using existing data to improve prognostic risk assessment and treatment efficacy by guiding personalized therapies.
PMID:40909579 | PMC:PMC12407784 | DOI:10.1101/2025.08.21.671519
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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GASPS: A Multi-Omics Framework for Defining Genomic Aberration-Driven Signatures and Predicting Patient Outcomes in Lung Cancer
bioRxiv [Preprint]. 2025 Aug 25:2025.08.21.671519. doi: 10.1101/2025.08.21.671519.ABSTRACTLung cancer is the most common cause of cancer-related death worldwide. Recent advancements in targeted therapies and immunotherapies have achieved remarkable success. However, patient responses to treatments with lung cancer vary substantially. The mutation status of driver genes can direct personalized treatment, but their prognostic value and treatment efficacy are limited. In this study, we developed a
GASPS: A Multi-Omics Framework for Defining Genomic Aberration-Driven Signatures and Predicting Patient Outcomes in Lung Cancer
bioRxiv [Preprint]. 2025 Aug 25:2025.08.21.671519. doi: 10.1101/2025.08.21.671519.
ABSTRACT
Lung cancer is the most common cause of cancer-related death worldwide. Recent advancements in targeted therapies and immunotherapies have achieved remarkable success. However, patient responses to treatments with lung cancer vary substantially. The mutation status of driver genes can direct personalized treatment, but their prognostic value and treatment efficacy are limited. In this study, we developed a statistical framework named Genomic Aberration-Derived Signature for Patient Stratification (GASPS) to characterize the transcriptomic deregulation of driver genomic aberrations and stratify patients. By applying GASPS to The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data, we developed gene signatures for 38 driver genomic aberrations, including gene mutations, amplifications, and deletions. These signatures were applied to independent lung cancer transcriptomic datasets containing a total of 2,226 patient samples. Our results indicated that these driver gene signatures are much more prognostic than their corresponding genomic mutations. Interestingly, the two EGFR-related signatures characterizing EGFR mutation and amplification, respectively, exhibited contrasting associations with prognosis, treatment response, and immune infiltration in the tumor microenvironment. Moreover, the STK11 mutation signature, rather than the mutation status, was found to be predictive of the response and long-term benefit of patients treated with immune checkpoint blockade therapy in lung cancer. This framework is readily applicable to most cancer types using existing data to improve prognostic risk assessment and treatment efficacy by guiding personalized therapies.
PMID:40909579 | PMC:PMC12407784 | DOI:10.1101/2025.08.21.671519
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Biomarkers associated with cancer-related anorexia in lung cancer: a scoping review
Support Care Cancer. 2025 Jun 19;33(7):596. doi: 10.1007/s00520-025-09670-9.ABSTRACTPURPOSE: Anorexia is a frequent and serious symptom in patients with lung cancer, often leading to malnutrition and cachexia, and negatively affecting quality of life and survival. This scoping review systematically synthesizes current evidence on biomarkers associated with cancer-related anorexia (CRA) in lung cancer, aiming to clarify biological mechanisms and inform targeted interventions.METHODS: We performed
Biomarkers associated with cancer-related anorexia in lung cancer: a scoping review
Support Care Cancer. 2025 Jun 19;33(7):596. doi: 10.1007/s00520-025-09670-9.
ABSTRACT
PURPOSE: Anorexia is a frequent and serious symptom in patients with lung cancer, often leading to malnutrition and cachexia, and negatively affecting quality of life and survival. This scoping review systematically synthesizes current evidence on biomarkers associated with cancer-related anorexia (CRA) in lung cancer, aiming to clarify biological mechanisms and inform targeted interventions.
METHODS: We performed a comprehensive literature search of studies evaluating the associations between CRA and various biomarkers in patients with lung cancer. Data were extracted and analyzed for pathway, genomic, transcriptomic, epigenetic, proteomic, metabolic, and composite biomarkers.
RESULTS: A total of 33 studies were included, identifying more than 100 biomarkers closely associated with CRA in lung cancer. These include inflammatory cytokines, energy metabolism markers, epigenetic and transcriptomic alterations, and disruptions in multiple cellular signaling pathways. Our analysis demonstrates that CRA is not the result of a single factor but reflects widespread dysregulation across metabolic, immune, and signaling networks. Some studies suggest that nutritional and anti-inflammatory interventions, such as n-3 fatty acid and antioxidant supplementation, can modulate biomarker profiles and potentially improve clinical outcomes.
CONCLUSION: CRA in lung cancer is a multifactorial syndrome involving complex interactions among inflammatory, metabolic, and signaling pathways. Multi-omics biomarker integration holds promise for early detection and individualized treatment, but larger, multi-center studies are needed to confirm clinical utility and optimize management strategies. Precision interventions based on biomarker profiles should be further explored in future research and practice.
PMID:40536584 | DOI:10.1007/s00520-025-09670-9
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Pulmonary nodule
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Early Screening and Subtype Identification of High-Risk Lung Nodules via Breathprint by Graphene eNose Platform: A Large Cohort Study
ACS Sens. 2025 Apr 25;10(4):3101-3111. doi: 10.1021/acssensors.5c00314. Epub 2025 Apr 7.ABSTRACTEarly screening of individuals with high-risk lung nodules can significantly improve the prognosis of lung cancer patients, and accurate identification of lung nodule subtypes can provide guidance for medical treatment. Exhaled breath (EB) analysis via eNoses offers a quick and noninvasive approach, but current eNose technology lacks quality control and solid validation in large population studies. He
Early Screening and Subtype Identification of High-Risk Lung Nodules via Breathprint by Graphene eNose Platform: A Large Cohort Study
ACS Sens. 2025 Apr 25;10(4):3101-3111. doi: 10.1021/acssensors.5c00314. Epub 2025 Apr 7.
ABSTRACT
Early screening of individuals with high-risk lung nodules can significantly improve the prognosis of lung cancer patients, and accurate identification of lung nodule subtypes can provide guidance for medical treatment. Exhaled breath (EB) analysis via eNoses offers a quick and noninvasive approach, but current eNose technology lacks quality control and solid validation in large population studies. Herein, an eNose platform integrated with a metal ion-decorated graphene sensor array and a breath sampling accessory was established. EB samples from 427 healthy subjects and 2586 subjects with lung nodules, including various benign and malignant subtypes, were collected through the breath sampling accessory for quality control. The large-cohort clinical EB samples were analyzed by the eNose platform to acquire the cross-reactive resistance response. Breathprint analysis for high-risk lung nodules using SVM and age-matched training sets yielded strong and robust performance. Combined with baseline data, the model achieved an AUC of 0.93 (95% CI, 0.89-0.96) on the external test set, with 97% sensitivity and 73% specificity. Moreover, dimensionality reduction analysis of breathprints demonstrated separability across different lung nodule subtypes. This study demonstrates the reliability of the graphene eNose platform to identify high-risk lung nodules and classify lung nodule subtypes in a noninvasive and rapid method.
PMID:40193324 | DOI:10.1021/acssensors.5c00314
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Most Recent Articles: Clinical Epigenetics
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Tissue of origin prediction for cancer of unknown primary using a targeted methylation sequencing panel
Cancer of unknown primary (CUP) is a group of rare malignancies with poor prognosis and unidentifiable tissue-of-origin. Distinct DNA methylation patterns in different tissues and cancer types enable the ident...