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cs.AI, q-bio.NC updates on arXiv.org
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DeKeyNLU: Enhancing Natural Language to SQL Generation through Task Decomposition and Keyword Extraction
arXiv:2509.14507v2 Announce Type: replace Abstract: Natural Language to SQL (NL2SQL) provides a new model-centric paradigm that simplifies database access for non-technical users by converting natural language queries into SQL commands. Recent advancements, particularly those integrating Retrieval-Augmented Generation (RAG) and Chain-of-Thought (CoT) reasoning, have made significant strides in enhancing NL2SQL performance. However, challenges such as inaccurate task decomposition and keyword ex
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cs.AI, q-bio.NC updates on arXiv.org
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Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CT
arXiv:2511.16698v1 Announce Type: cross Abstract: SNOMED CT is a biomedical ontology with a hierarchical representation of large-scale concepts. Knowledge retrieval in SNOMED CT is critical for its application, but often proves challenging due to language ambiguity, synonyms, polysemies and so on. This problem is exacerbated when the queries are out-of-vocabulary (OOV), i.e., having no equivalent matchings in the ontology. In this work, we focus on the problem of hierarchical concept retrieval
Hierarchical Retrieval with Out-Of-Vocabulary Queries: A Case Study on SNOMED CT
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cs.AI, q-bio.NC updates on arXiv.org
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From Passive to Proactive: A Multi-Agent System with Dynamic Task Orchestration for Intelligent Medical Pre-Consultation
arXiv:2511.01445v1 Announce Type: new Abstract: Global healthcare systems face critical challenges from increasing patient volumes and limited consultation times, with primary care visits averaging under 5 minutes in many countries. While pre-consultation processes encompassing triage and structured history-taking offer potential solutions, they remain limited by passive interaction paradigms and context management challenges in existing AI systems. This study introduces a hierarchical multi-ag
From Passive to Proactive: A Multi-Agent System with Dynamic Task Orchestration for Intelligent Medical Pre-Consultation
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Nature Medicine
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An eyecare foundation model for clinical assistance: a randomized controlled trial
Nature Medicine, Published online: 28 August 2025; doi:10.1038/s41591-025-03900-7Trained and validated on multimodal data from 14.5 million images from multicountry datasets, a foundation model is shown to increase diagnostic and referral accuracy of clinicians when used as an assistant in a trial involving 16 ophthalmologists and 668 patients.
An eyecare foundation model for clinical assistance: a randomized controlled trial
Nature Medicine, Published online: 28 August 2025; doi:10.1038/s41591-025-03900-7
Trained and validated on multimodal data from 14.5 million images from multicountry datasets, a foundation model is shown to increase diagnostic and referral accuracy of clinicians when used as an assistant in a trial involving 16 ophthalmologists and 668 patients.-
(Multiomics OR Omics) AND (Pancreatic)
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Targeting spermine metabolism to overcome immunotherapy resistance in pancreatic cancer
Nat Commun. 2025 Aug 22;16(1):7827. doi: 10.1038/s41467-025-63146-2.ABSTRACTWhile dysregulation of polyamine metabolism is frequently observed in cancer, it is unknown how polyamines alter the tumor microenvironment (TME) and contribute to therapeutic resistance. Analysis of polyamines in the plasma of pancreatic cancer patients reveals that spermine levels are significantly elevated and correlate with poor prognosis. Using a multi-omics approach, we identify Serpinb9 as a vulnerability in sperm
Targeting spermine metabolism to overcome immunotherapy resistance in pancreatic cancer
Nat Commun. 2025 Aug 22;16(1):7827. doi: 10.1038/s41467-025-63146-2.
ABSTRACT
While dysregulation of polyamine metabolism is frequently observed in cancer, it is unknown how polyamines alter the tumor microenvironment (TME) and contribute to therapeutic resistance. Analysis of polyamines in the plasma of pancreatic cancer patients reveals that spermine levels are significantly elevated and correlate with poor prognosis. Using a multi-omics approach, we identify Serpinb9 as a vulnerability in spermine metabolism in pancreatic cancer. Serpinb9, a serine protease inhibitor, directly interacts with spermine synthase (SMS), impeding its lysosome-mediated degradation and thereby augmenting spermine production and secretion. Mechanistically, the accumulation of spermine in the TME alters the metabolic landscape of immune cells, promoting CD8+ T cell dysfunction and pro-tumor polarization of macrophages, thus creating an immunosuppressive microenvironment. Small peptides that disrupt the Serpinb9-SMS interaction significantly enhance the efficacy of immune checkpoint blockade therapy. Together, our findings suggest that targeting spermine metabolism is a promising strategy to improve pancreatic cancer immunotherapy.
PMID:40846845 | PMC:PMC12373741 | DOI:10.1038/s41467-025-63146-2
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses
Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.ABSTRACTImmune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (
Interplay between gut microbial communities and metabolites modulates pan-cancer immunotherapy responses
Cell Metab. 2025 Jan 28:S1550-4131(24)00495-9. doi: 10.1016/j.cmet.2024.12.013. Online ahead of print.
ABSTRACT
Immune checkpoint blockade (ICB) therapy has revolutionized cancer treatment but remains effective in only a subset of patients. Emerging evidence suggests that the gut microbiome and its metabolites critically influence ICB efficacy. In this study, we performed a multi-omics analysis of fecal microbiomes and metabolomes from 165 patients undergoing anti-programmed cell death protein 1 (PD-1)/programmed death ligand 1 (PD-L1) therapy, identifying microbial and metabolic entities associated with treatment response. Integration of data from four public metagenomic datasets (n = 568) uncovered cross-cohort microbial and metabolic signatures, validated in an independent cohort (n = 138). An integrated predictive model incorporating these features demonstrated robust performance. Notably, we characterized five response-associated enterotypes, each linked to specific bacterial taxa and metabolites. Among these, the metabolite phenylacetylglutamine (PAGln) was negatively correlated with response and shown to attenuate anti-PD-1 efficacy in vivo. This study sheds light on the interplay among the gut microbiome, the gut metabolome, and immunotherapy response, identifying potential biomarkers to improve treatment outcomes.
PMID:39909032 | DOI:10.1016/j.cmet.2024.12.013