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cs.AI, q-bio.NC updates on arXiv.org
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Agent Data Protocol: Unifying Datasets for Diverse, Effective Fine-tuning of LLM Agents
arXiv:2510.24702v1 Announce Type: cross Abstract: Public research results on large-scale supervised finetuning of AI agents remain relatively rare, since the collection of agent training data presents unique challenges. In this work, we argue that the bottleneck is not a lack of underlying data sources, but that a large variety of data is fragmented across heterogeneous formats, tools, and interfaces. To this end, we introduce the agent data protocol (ADP), a light-weight representation languag
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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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(Multiomics OR Omics) AND (Pancreatic)
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High-Sensitive Spatial Proteomics for Pancreatic Cancer Progression Analysis
bioRxiv [Preprint]. 2025 May 5:2025.05.01.651678. doi: 10.1101/2025.05.01.651678.ABSTRACTPancreatic cancer remains as one of the most challenging malignancies to diagnose and treat due to the late development of symptoms and limited early diagnostic options. Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursors to invasive pancreatic ductal adenocarcinoma (PDAC)and an understanding of the changes in patterns of protein expression that accompany the progression from normal
High-Sensitive Spatial Proteomics for Pancreatic Cancer Progression Analysis
bioRxiv [Preprint]. 2025 May 5:2025.05.01.651678. doi: 10.1101/2025.05.01.651678.
ABSTRACT
Pancreatic cancer remains as one of the most challenging malignancies to diagnose and treat due to the late development of symptoms and limited early diagnostic options. Intraductal papillary mucinous neoplasms (IPMNs) are non-invasive precursors to invasive pancreatic ductal adenocarcinoma (PDAC)and an understanding of the changes in patterns of protein expression that accompany the progression from normal ductal (ND) cell, to IPMN to PDAC may provide avenues for improved earlier detection. In this study, we present an optimized spatial tissue proteomics workflow, termed SP-Max (Spatial Proteomics Optimized for Maximum Sensitivity and Reproducibility in Minimal Sample), designed to maximize protein recovery and quantification from limited laser micro dissected (LMD) samples. Our workflow enabled the identification of more than 6,000 proteins and the quantification of over 5,200 protein groups from FFPE tissue contours of pancreatic tissues. Comparative analyses across ND, IPMN, and PDAC revealed critical molecular differences in protein pathways and potential markers of progression. SP-Max provides a systematic, reproducible approach that significantly enhances our ability to study precancerous lesions and cancer progression in pancreatic tissues at unprecedented resolution.
PMID:40654937 | PMC:PMC12247709 | DOI:10.1101/2025.05.01.651678
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Most Recent Articles: Clinical Epigenetics
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Epigenetic regulatory protein chromobox family regulates multiple signalling pathways and mechanisms in cancer
Signal transduction plays a pivotal role in modulating a myriad of critical processes, including the tumour microenvironment (TME), cell cycle arrest, proliferation and apoptosis of tumour cells, as well as th...
Epigenetic regulatory protein chromobox family regulates multiple signalling pathways and mechanisms in cancer
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Cell Death Discovery nature.com science feeds
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Ferroptosis: a new hunter of hepatocellular carcinoma
Cell Death Discovery, Published online: 13 March 2024; doi:10.1038/s41420-024-01863-1Ferroptosis: a new hunter of hepatocellular carcinoma
Ferroptosis: a new hunter of hepatocellular carcinoma
Cell Death Discovery, Published online: 13 March 2024; doi:10.1038/s41420-024-01863-1
Ferroptosis: a new hunter of hepatocellular carcinoma