Normal view
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cs.AI, q-bio.NC updates on arXiv.org
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Test-Time Tuned Language Models Enable End-to-end De Novo Molecular Structure Generation from MS/MS Spectra
arXiv:2510.23746v1 Announce Type: new Abstract: Tandem Mass Spectrometry enables the identification of unknown compounds in crucial fields such as metabolomics, natural product discovery and environmental analysis. However, current methods rely on database matching from previously observed molecules, or on multi-step pipelines that require intermediate fragment or fingerprint prediction. This makes finding the correct molecule highly challenging, particularly for compounds absent from reference
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cs.AI, q-bio.NC updates on arXiv.org
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Generative AI for Healthcare: Fundamentals, Challenges, and Perspectives
arXiv:2510.24551v1 Announce Type: new Abstract: Generative Artificial Intelligence (GenAI) is taking the world by storm. It promises transformative opportunities for advancing and disrupting existing practices, including healthcare. From large language models (LLMs) for clinical note synthesis and conversational assistance to multimodal systems that integrate medical imaging, electronic health records, and genomic data for decision support, GenAI is transforming the practice of medicine and the
Generative AI for Healthcare: Fundamentals, Challenges, and Perspectives
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cs.AI, q-bio.NC updates on arXiv.org
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Integrating Genomics into Multimodal EHR Foundation Models
arXiv:2510.23639v1 Announce Type: cross Abstract: This paper introduces an innovative Electronic Health Record (EHR) foundation model that integrates Polygenic Risk Scores (PRS) as a foundational data modality, moving beyond traditional EHR-only approaches to build more holistic health profiles. Leveraging the extensive and diverse data from the All of Us (AoU) Research Program, this multimodal framework aims to learn complex relationships between clinical data and genetic predispositions. The
Integrating Genomics into Multimodal EHR Foundation Models
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cs.AI, q-bio.NC updates on arXiv.org
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Closing Gaps: An Imputation Analysis of ICU Vital Signs
arXiv:2510.24217v1 Announce Type: cross Abstract: As more Intensive Care Unit (ICU) data becomes available, the interest in developing clinical prediction models to improve healthcare protocols increases. However, the lack of data quality still hinders clinical prediction using Machine Learning (ML). Many vital sign measurements, such as heart rate, contain sizeable missing segments, leaving gaps in the data that could negatively impact prediction performance. Previous works have introduced num
Closing Gaps: An Imputation Analysis of ICU Vital Signs
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MRD
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Dynamic Monitoring of Recurrent Ovarian Cancer Using Serial ctDNA: A Real-World Case Series
Curr Oncol. 2025 Oct 21;32(10):585. doi: 10.3390/curroncol32100585.ABSTRACTRecurrent ovarian cancer (OC) is challenging to detect early using current methods like CA-125 and imaging. Circulating tumor DNA (ctDNA) may improve disease monitoring. Here, we assess the real-world clinical utility of serial ctDNA analyses in patients with recurrent OC. We analyzed serial plasma samples (N = 23) from six patients with recurrent OC using a tumor-informed next-generation sequencing assay targeting 68 can
Dynamic Monitoring of Recurrent Ovarian Cancer Using Serial ctDNA: A Real-World Case Series
Curr Oncol. 2025 Oct 21;32(10):585. doi: 10.3390/curroncol32100585.
ABSTRACT
Recurrent ovarian cancer (OC) is challenging to detect early using current methods like CA-125 and imaging. Circulating tumor DNA (ctDNA) may improve disease monitoring. Here, we assess the real-world clinical utility of serial ctDNA analyses in patients with recurrent OC. We analyzed serial plasma samples (N = 23) from six patients with recurrent OC using a tumor-informed next-generation sequencing assay targeting 68 cancer-related genes developed at the University of Washington. ctDNA variant allele frequencies (VAFs) were correlated with CA-125 levels, radiographic findings, and clinical outcomes. ctDNA levels generally reflected clinical status, accurately mirroring disease progression and therapeutic response. In one patient, rising ctDNA preceded clinical recurrence by four months, despite normal CA-125 and imaging, highlighting its potential advantage. Conversely, some patients exhibited clinical progression with undetectable ctDNA, indicating limitations in assay sensitivity, biological factors, or metastatic sites (e.g., brain metastases). ctDNA and CA-125 showed complementary value in most cases, suggesting potential combined use in clinical monitoring. Our findings demonstrate that ctDNA is a promising biomarker to complement existing monitoring approaches for recurrent OC. In some cases, capable of predicting relapse and treatment response ahead of current clinical indicators. However, identified discordances underscore technical and biological challenges that warrant further investigation. Larger prospective studies are necessary to refine ctDNA's clinical utility and integration into personalized OC care.
PMID:41149505 | PMC:PMC12563156 | DOI:10.3390/curroncol32100585
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cs.AI, q-bio.NC updates on arXiv.org
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Tongyi DeepResearch Technical Report
arXiv:2510.24701v1 Announce Type: cross Abstract: We present Tongyi DeepResearch, an agentic large language model, which is specifically designed for long-horizon, deep information-seeking research tasks. To incentivize autonomous deep research agency, Tongyi DeepResearch is developed through an end-to-end training framework that combines agentic mid-training and agentic post-training, enabling scalable reasoning and information seeking across complex tasks. We design a highly scalable data syn
Tongyi DeepResearch Technical Report
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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
Agent Data Protocol: Unifying Datasets for Diverse, Effective Fine-tuning of LLM Agents
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Omics in Gastric
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The Role of Omentin in Gastrointestinal Cancer: Diagnostic, Prognostic, and Therapeutic Perspectives
Metabolites. 2025 Sep 30;15(10):649. doi: 10.3390/metabo15100649.ABSTRACTBackground/Objectives: Omentin, also known as intelectin-1, is a secreted adipokine with anti-inflammatory, insulin-sensitizing, and immune-modulatory functions, primarily expressed in visceral adipose tissue. While omentin has been associated with favorable metabolic outcomes, its role in cancer pathogenesis appears context-dependent and remains poorly understood. This review investigates the biological functions, expressi
The Role of Omentin in Gastrointestinal Cancer: Diagnostic, Prognostic, and Therapeutic Perspectives
Metabolites. 2025 Sep 30;15(10):649. doi: 10.3390/metabo15100649.
ABSTRACT
Background/Objectives: Omentin, also known as intelectin-1, is a secreted adipokine with anti-inflammatory, insulin-sensitizing, and immune-modulatory functions, primarily expressed in visceral adipose tissue. While omentin has been associated with favorable metabolic outcomes, its role in cancer pathogenesis appears context-dependent and remains poorly understood. This review investigates the biological functions, expression patterns, and clinical relevance of omentin across gastrointestinal malignancies. Methods: A comprehensive review of the literature was conducted using PubMed, Scopus, and Web of Science up to August 2025 to evaluate the role of omentin in gastrointestinal cancers. Both preclinical and clinical studies evaluating omentin, its analogues and omentin-enhancing agents in gastric, colorectal, hepatic, pancreatic, and esophageal cancers were included. Results: Omentin exhibits anti-proliferative, anti-inflammatory, and anti-angiogenic effects within the tumor microenvironment in several GI malignancies. However, evidence also indicates a dual role. High intratumoral omentin expression correlates with improved prognosis in colorectal, gastric, and hepatic cancers; in contrast, elevated circulating levels-particularly in colorectal and pancreatic cancers-have been paradoxically associated with increased cancer risk and poor outcomes. Mechanistically, omentin modulates PI3K/Akt, NF-κB, AMPK, and oxidative stress pathways, and interacts with TMEM207. However, most available studies are small-scale and heterogeneous, with methodological inconsistencies and limited multi-omics integration, leaving major knowledge gaps. Conclusions: This review highlights omentin's distinct systemic and local roles across GI cancers, underscoring its translational implications. Omentin emerges as a promising but context-dependent biomarker and therapeutic target, with future research needed to address heterogeneity, standardize assays, and validate its clinical utility in large-scale prospective studies.
PMID:41149627 | PMC:PMC12566161 | DOI:10.3390/metabo15100649
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(Multiomics OR Omics) AND (Pancreatic)
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Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.ABSTRACTRecent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pan
Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.
ABSTRACT
Recent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pancreatic, and glioblastoma. Despite these advances, challenges remain, such as the integration of disparate data types and the interpretation of complex biological interactions. However, developments in proteogenomics and mass spectrometry have enhanced the correlation between molecular profiles and clinical features, refining the prediction of therapeutic responses. Future research in cancer drug discovery is poised to benefit from multi-omics approaches, improving the precision and efficacy of personalized therapies. By developing integrative network-based models, researchers aim to address challenges related to heterogeneity, reproducibility, and data interpretation. A standardized framework for multi-omics data integration could revolutionize cancer research, optimizing the identification of novel drug targets and enhancing our understanding of cancer biology. This complete approach holds the promise of advancing personalized therapies by fully characterizing the molecular landscape of cancer, ultimately improving patient outcomes through more effective and targeted treatment strategies. This narrative review underscores the potential of multi-omics approaches to transform cancer research and improve patient outcomes through more precise and effective treatments.
PMID:41147019 | PMC:PMC12553891 | DOI:10.1177/11795549251384582
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cs.AI, q-bio.NC updates on arXiv.org
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Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
arXiv:2510.21293v2 Announce Type: replace Abstract: Background: Trustworthy AI serves as a foundational pillar for two major AI ethics conferences: AIES and FAccT. However, current research often adopts techno-centric approaches, focusing primarily on technical attributes such as reliability, robustness, and fairness, while overlooking the sociotechnical dimensions critical to understanding AI trustworthiness in real-world contexts. Objectives: This scoping review aims to examine how the AIES
Understanding AI Trustworthiness: A Scoping Review of AIES & FAccT Articles
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(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
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Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.ABSTRACTRecent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pan
Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.
ABSTRACT
Recent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pancreatic, and glioblastoma. Despite these advances, challenges remain, such as the integration of disparate data types and the interpretation of complex biological interactions. However, developments in proteogenomics and mass spectrometry have enhanced the correlation between molecular profiles and clinical features, refining the prediction of therapeutic responses. Future research in cancer drug discovery is poised to benefit from multi-omics approaches, improving the precision and efficacy of personalized therapies. By developing integrative network-based models, researchers aim to address challenges related to heterogeneity, reproducibility, and data interpretation. A standardized framework for multi-omics data integration could revolutionize cancer research, optimizing the identification of novel drug targets and enhancing our understanding of cancer biology. This complete approach holds the promise of advancing personalized therapies by fully characterizing the molecular landscape of cancer, ultimately improving patient outcomes through more effective and targeted treatment strategies. This narrative review underscores the potential of multi-omics approaches to transform cancer research and improve patient outcomes through more precise and effective treatments.
PMID:41147019 | PMC:PMC12553891 | DOI:10.1177/11795549251384582
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cs.AI, q-bio.NC updates on arXiv.org
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Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality
arXiv:2503.05860v2 Announce Type: replace-cross Abstract: Benchmarks are essential for unified evaluation and reproducibility. The rapid rise of Artificial Intelligence for Software Engineering (AI4SE) has produced numerous benchmarks for tasks such as code generation and bug repair. However, this proliferation has led to major challenges: (1) fragmented knowledge across tasks, (2) difficulty in selecting contextually relevant benchmarks, (3) lack of standardization in benchmark creation, and (
Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality
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Omics In Lung
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Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.ABSTRACTRecent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pan
Navigating Cancer Complexity: Integrative Multi-Omics Methodologies for Clinical Insights
Clin Med Insights Oncol. 2025 Oct 21;19:11795549251384582. doi: 10.1177/11795549251384582. eCollection 2025.
ABSTRACT
Recent advancements in cancer multi-omics have transformed our understanding of cancer biology by integrating genomics, transcriptomics, proteomics, and metabolomics. These integrative approaches have led to the identification of novel biomarkers and therapeutic targets, offering deeper insights into the molecular intricacies of various cancers, including breast, lung, gastric, pancreatic, and glioblastoma. Despite these advances, challenges remain, such as the integration of disparate data types and the interpretation of complex biological interactions. However, developments in proteogenomics and mass spectrometry have enhanced the correlation between molecular profiles and clinical features, refining the prediction of therapeutic responses. Future research in cancer drug discovery is poised to benefit from multi-omics approaches, improving the precision and efficacy of personalized therapies. By developing integrative network-based models, researchers aim to address challenges related to heterogeneity, reproducibility, and data interpretation. A standardized framework for multi-omics data integration could revolutionize cancer research, optimizing the identification of novel drug targets and enhancing our understanding of cancer biology. This complete approach holds the promise of advancing personalized therapies by fully characterizing the molecular landscape of cancer, ultimately improving patient outcomes through more effective and targeted treatment strategies. This narrative review underscores the potential of multi-omics approaches to transform cancer research and improve patient outcomes through more precise and effective treatments.
PMID:41147019 | PMC:PMC12553891 | DOI:10.1177/11795549251384582
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cs.AI, q-bio.NC updates on arXiv.org
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Robustness is Important: Limitations of LLMs for Data Fitting
arXiv:2508.19563v3 Announce Type: replace-cross Abstract: Large Language Models (LLMs) are being applied in a wide array of settings, well beyond the typical language-oriented use cases. In particular, LLMs are increasingly used as a plug-and-play method for fitting data and generating predictions. Prior work has shown that LLMs, via in-context learning or supervised fine-tuning, can perform competitively with many tabular supervised learning techniques in terms of predictive performance. Howev