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cs.AI, q-bio.NC updates on arXiv.org
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Is On-Policy Data always the Best Choice for Direct Preference Optimization-based LM Alignment?
arXiv:2508.10530v2 Announce Type: replace Abstract: The alignment of language models~(LMs) with human preferences is critical for building reliable AI systems. The problem is typically framed as optimizing an LM policy to maximize the expected reward that reflects human preferences. Recently, Direct Preference Optimization~(DPO) was proposed as a LM alignment method that directly optimize the policy from static preference data, and further improved by incorporating on-policy sampling~(i.e., pre
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cs.AI, q-bio.NC updates on arXiv.org
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Companion Agents: A Table-Information Mining Paradigm for Text-to-SQL
arXiv:2601.08838v1 Announce Type: cross Abstract: Large-scale Text-to-SQL benchmarks such as BIRD typically assume complete and accurate database annotations as well as readily available external knowledge, which fails to reflect common industrial settings where annotations are missing, incomplete, or erroneous. This mismatch substantially limits the real-world applicability of state-of-the-art (SOTA) Text-to-SQL systems. To bridge this gap, we explore a database-centric approach that leverages
Companion Agents: A Table-Information Mining Paradigm for Text-to-SQL
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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LOSTdb: a manually curated multi-omics database for lung cancer research
BMC Bioinformatics. 2025 Dec 3;26(1):290. doi: 10.1186/s12859-025-06319-6.ABSTRACTLung cancer is one of the most prevalent malignant tumors with high morbidity and mortality rates worldwide. Extensive multi-omics analyses have revealed significant intratumoral heterogeneity even within the same histopathological subtype. However, a database that systematically integrates multi-omics data for lung cancer research has long been lacking. Here, we developed LOSTdb, a molecular subtype annotation sys
LOSTdb: a manually curated multi-omics database for lung cancer research
BMC Bioinformatics. 2025 Dec 3;26(1):290. doi: 10.1186/s12859-025-06319-6.
ABSTRACT
Lung cancer is one of the most prevalent malignant tumors with high morbidity and mortality rates worldwide. Extensive multi-omics analyses have revealed significant intratumoral heterogeneity even within the same histopathological subtype. However, a database that systematically integrates multi-omics data for lung cancer research has long been lacking. Here, we developed LOSTdb, a molecular subtype annotation system for lung cancer that integrates multi-omics data and metadata. LOSTdb comprises 295 multi-omics datasets, including bulk RNA-seq, genomic, proteomic, methylation, and scRNA-seq data, with over 10,000 manually curated metadata entries. This resource encompasses high-quality clinical specimens, mouse models, and cell lines, totaling 34,393 samples and more than 1.2 million single cells. Each omics sample was annotated with both literature-based classical subtypes and NMF-derived meta-program (MP) subtypes. The platform supports cross-searching of omics and metadata at the gene and dataset levels, offers multiple visualization and analysis methods, and includes five tool modules, enabling functions such as integrated analysis, significance analysis between metadata as well as between genes and metadata, and target prediction for lung cancer molecular subtypes, serving as an essential tool for lung cancer precision medicine. LOSTdb is a user-friendly interactive database freely accessible at http://lostdbcancer.com:8080 .
PMID:41339793 | DOI:10.1186/s12859-025-06319-6
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Omics In Lung
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LOSTdb: a manually curated multi-omics database for lung cancer research
BMC Bioinformatics. 2025 Dec 3;26(1):290. doi: 10.1186/s12859-025-06319-6.ABSTRACTLung cancer is one of the most prevalent malignant tumors with high morbidity and mortality rates worldwide. Extensive multi-omics analyses have revealed significant intratumoral heterogeneity even within the same histopathological subtype. However, a database that systematically integrates multi-omics data for lung cancer research has long been lacking. Here, we developed LOSTdb, a molecular subtype annotation sys
LOSTdb: a manually curated multi-omics database for lung cancer research
BMC Bioinformatics. 2025 Dec 3;26(1):290. doi: 10.1186/s12859-025-06319-6.
ABSTRACT
Lung cancer is one of the most prevalent malignant tumors with high morbidity and mortality rates worldwide. Extensive multi-omics analyses have revealed significant intratumoral heterogeneity even within the same histopathological subtype. However, a database that systematically integrates multi-omics data for lung cancer research has long been lacking. Here, we developed LOSTdb, a molecular subtype annotation system for lung cancer that integrates multi-omics data and metadata. LOSTdb comprises 295 multi-omics datasets, including bulk RNA-seq, genomic, proteomic, methylation, and scRNA-seq data, with over 10,000 manually curated metadata entries. This resource encompasses high-quality clinical specimens, mouse models, and cell lines, totaling 34,393 samples and more than 1.2 million single cells. Each omics sample was annotated with both literature-based classical subtypes and NMF-derived meta-program (MP) subtypes. The platform supports cross-searching of omics and metadata at the gene and dataset levels, offers multiple visualization and analysis methods, and includes five tool modules, enabling functions such as integrated analysis, significance analysis between metadata as well as between genes and metadata, and target prediction for lung cancer molecular subtypes, serving as an essential tool for lung cancer precision medicine. LOSTdb is a user-friendly interactive database freely accessible at http://lostdbcancer.com:8080 .
PMID:41339793 | PMC:PMC12676782 | DOI:10.1186/s12859-025-06319-6
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Cell
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Identifying specific functional roles for senescence across cell types
A dual recombinase-mediated genetic system for cell-type-specific lineage tracing, ablation, and gene manipulation of senescent cells reveals distinct roles of senescence across cell types.