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cs.AI, q-bio.NC updates on arXiv.org
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A Framework for Responsible AI Systems: Building Societal Trust through Domain Definition, Trustworthy AI Design, Auditability, Accountability, and Governance
arXiv:2503.04739v2 Announce Type: replace-cross Abstract: Responsible Artificial Intelligence (RAI) addresses the ethical and regulatory challenges of deploying AI systems in high-risk scenarios. This paper proposes a comprehensive framework for the design of an RAI system (RAIS) that integrates five key dimensions: domain definition, trustworthy AI design, auditability, accountability, and governance. Unlike prior work that treats these components in isolation, our proposal emphasizes their in
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cs.AI, q-bio.NC updates on arXiv.org
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AIRepr: An Analyst-Inspector Framework for Evaluating Reproducibility of LLMs in Data Science
arXiv:2502.16395v3 Announce Type: replace-cross Abstract: Large language models (LLMs) are increasingly used to automate data analysis through executable code generation. Yet, data science tasks often admit multiple statistically valid solutions, e.g. different modeling strategies, making it critical to understand the reasoning behind analyses, not just their outcomes. While manual review of LLM-generated code can help ensure statistical soundness, it is labor-intensive and requires expertise.
AIRepr: An Analyst-Inspector Framework for Evaluating Reproducibility of LLMs in Data Science
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cs.AI, q-bio.NC updates on arXiv.org
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LGM: Enhancing Large Language Models with Conceptual Meta-Relations and Iterative Retrieval
arXiv:2511.03214v1 Announce Type: cross Abstract: Large language models (LLMs) exhibit strong semantic understanding, yet struggle when user instructions involve ambiguous or conceptually misaligned terms. We propose the Language Graph Model (LGM) to enhance conceptual clarity by extracting meta-relations-inheritance, alias, and composition-from natural language. The model further employs a reflection mechanism to validate these meta-relations. Leveraging a Concept Iterative Retrieval Algorithm
LGM: Enhancing Large Language Models with Conceptual Meta-Relations and Iterative Retrieval
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Oncogene - Issue - nature.com science feeds
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Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation
Oncogene, Published online: 22 February 2025; doi:10.1038/s41388-025-03309-zSingle-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation
Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation
Oncogene, Published online: 22 February 2025; doi:10.1038/s41388-025-03309-z
Single-cell multiomics reveals a gene regulatory circuit driving leukemia cell differentiation-
Omics In Lung
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Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer
Cancer Cell. 2025 Feb 14:S1535-6108(25)00030-3. doi: 10.1016/j.ccell.2025.01.012. Online ahead of print.ABSTRACTRecent advances have shed light on the molecular heterogeneity of small cell lung cancer (SCLC), yet the spatial organizations and cellular interactions in tumor immune microenvironment remain to be elucidated. Here, we employ co-detection by indexing (CODEX) and multi-omics profiling to delineate the spatial landscape for 165 SCLC patients, generating 267 high-dimensional images encom
Integrative spatial analysis reveals tumor heterogeneity and immune colony niche related to clinical outcomes in small cell lung cancer
Cancer Cell. 2025 Feb 14:S1535-6108(25)00030-3. doi: 10.1016/j.ccell.2025.01.012. Online ahead of print.
ABSTRACT
Recent advances have shed light on the molecular heterogeneity of small cell lung cancer (SCLC), yet the spatial organizations and cellular interactions in tumor immune microenvironment remain to be elucidated. Here, we employ co-detection by indexing (CODEX) and multi-omics profiling to delineate the spatial landscape for 165 SCLC patients, generating 267 high-dimensional images encompassing over 9.3 million cells. Integrating CODEX and genomic data reveals a multi-positive tumor cell neighborhood within ASCL1+ (SCLC-A) subtype, characterized by high SLFN11 expression and associated with poor prognosis. We further develop a cell colony detection algorithm (ColonyMap) and reveal a spatially assembled immune niche consisting of antitumoral macrophages, CD8+ T cells and natural killer T cells (MT2) which highly correlates with superior survival and predicts improving immunotherapy response in an independent cohort. This study serves as a valuable resource to study SCLC spatial heterogeneity and offers insights into potential patient stratification and personalized treatments.
PMID:39983726 | DOI:10.1016/j.ccell.2025.01.012
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Cell
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A multi-tissue metabolome atlas of primate pregnancy
A multi-tissue metabolome atlas of 23 maternal tissues from pregnant monkeys revealed dynamic metabolic coupling, core pathways, and a multitude of pregnancy-adaptive metabolites during normal primate pregnancy, with implications for female health.