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Received — 4 December 2025 ⏭ Favourites

LOSTdb: a manually curated multi-omics database for lung cancer research

✇(Multiomics OR Omics) AND (Lung OR gastric OR Hepatocellular)
By: Hao Luo · Yunhao Yang · Zhipeng Gong · Lunxu Liu · Yaohui Chen
3 December 2025 at 19:00

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

A Definition of AGI

✇cs.AI, q-bio.NC updates on arXiv.org
By: Dan Hendrycks · Dawn Song · Christian Szegedy · Honglak Lee · Yarin Gal · Erik Brynjolfsson · Sharon Li · Andy Zou · Lionel Levine · Bo Han · Jie Fu · Ziwei Liu · Jinwoo Shin · Kimin Lee · Mantas Mazeika · Long Phan · George Ingebretsen · Adam Khoja · Cihang Xie · Olawale Salaudeen · Matthias Hein · Kevin Zhao · Alexander Pan · David Duvenaud · Bo Li · Steve Omohundro · Gabriel Alfour · Max Tegmark · Kevin McGrew · Gary Marcus · Jaan Tallinn · Eric Schmidt · Yoshua Bengio
4 December 2025 at 13:00
arXiv:2510.18212v3 Announce Type: replace Abstract: The lack of a concrete definition for Artificial General Intelligence (AGI) obscures the gap between today's specialized AI and human-level cognition. This paper introduces a quantifiable framework to address this, defining AGI as matching the cognitive versatility and proficiency of a well-educated adult. To operationalize this, we ground our methodology in Cattell-Horn-Carroll theory, the most empirically validated model of human cognition. The framework dissects general intelligence into ten core cognitive domains-including reasoning, memory, and perception-and adapts established human psychometric batteries to evaluate AI systems. Application of this framework reveals a highly "jagged" cognitive profile in contemporary models. While proficient in knowledge-intensive domains, current AI systems have critical deficits in foundational cognitive machinery, particularly long-term memory storage. The resulting AGI scores (e.g., GPT-4 at 27%, GPT-5 at 57%) concretely quantify both rapid progress and the substantial gap remaining before AGI.

AI Deception: Risks, Dynamics, and Controls

✇cs.AI, q-bio.NC updates on arXiv.org
By: Boyuan Chen (Jay) · Sitong Fang (Jay) · Jiaming Ji (Jay) · Yanxu Zhu (Jay) · Pengcheng Wen (Jay) · Jinzhou Wu (Jay) · Yingshui Tan (Jay) · Boren Zheng (Jay) · Mengying Yuan (Jay) · Wenqi Chen (Jay) · Donghai Hong (Jay) · Alex Qiu (Jay) · Xin Chen (Jay) · Jiayi Zhou (Jay) · Kaile Wang (Jay) · Juntao Dai (Jay) · Borong Zhang (Jay) · Tianzhuo Yang (Jay) · Saad Siddiqui (Jay) · Isabella Duan (Jay) · Yawen Duan (Jay) · Brian Tse (Jay) · Jen-Tse (Jay) · Huang · Kun Wang · Baihui Zheng · Jiaheng Liu · Jian Yang · Yiming Li · Wenting Chen · Dongrui Liu · Lukas Vierling · Zhiheng Xi · Haobo Fu · Wenxuan Wang · Jitao Sang · Zhengyan Shi · Chi-Min Chan · Eugenie Shi · Simin Li · Juncheng Li · Jian Yang · Wei Ji · Dong Li · Jinglin Yang · Jun Song · Yinpeng Dong · Jie Fu · Bo Zheng · Min Yang · Yike Guo · Philip Torr · Robert Trager · Yi Zeng · Zhongyuan Wang · Yaodong Yang · Tiejun Huang · Ya-Qin Zhang · Hongjiang Zhang · Andrew Yao
4 December 2025 at 13:00
arXiv:2511.22619v2 Announce Type: replace Abstract: As intelligence increases, so does its shadow. AI deception, in which systems induce false beliefs to secure self-beneficial outcomes, has evolved from a speculative concern to an empirically demonstrated risk across language models, AI agents, and emerging frontier systems. This project provides a comprehensive and up-to-date overview of the AI deception field, covering its core concepts, methodologies, genesis, and potential mitigations. First, we identify a formal definition of AI deception, grounded in signaling theory from studies of animal deception. We then review existing empirical studies and associated risks, highlighting deception as a sociotechnical safety challenge. We organize the landscape of AI deception research as a deception cycle, consisting of two key components: deception emergence and deception treatment. Deception emergence reveals the mechanisms underlying AI deception: systems with sufficient capability and incentive potential inevitably engage in deceptive behaviors when triggered by external conditions. Deception treatment, in turn, focuses on detecting and addressing such behaviors. On deception emergence, we analyze incentive foundations across three hierarchical levels and identify three essential capability preconditions required for deception. We further examine contextual triggers, including supervision gaps, distributional shifts, and environmental pressures. On deception treatment, we conclude detection methods covering benchmarks and evaluation protocols in static and interactive settings. Building on the three core factors of deception emergence, we outline potential mitigation strategies and propose auditing approaches that integrate technical, community, and governance efforts to address sociotechnical challenges and future AI risks. To support ongoing work in this area, we release a living resource at www.deceptionsurvey.com.

Gut microbial metabolites in cancer immunomodulation

✇Omics In Lung
By: Hengshuo Liu · Xingyu Xiong · Weizhen Zhu · Sheng Wang · Weichao Huang · Guoqing Zhu · Hang Xu · Lu Yang
3 December 2025 at 19:00

Mol Cancer. 2025 Dec 3. doi: 10.1186/s12943-025-02521-5. Online ahead of print.

ABSTRACT

Gut microbiota-derived metabolites are emerging as systemic "remote immunoregulators" that shape tumor immunity across tissues. Integrating evidence across short-chain fatty acids, tryptophan derivatives, secondary bile acids, polyamines and other metabolites, we advance a metabolite-immune pathway-cancer framework that links receptor-mediated signaling, epigenetic remodeling and metabolic reprogramming to context-dependent, bidirectional immune effects. Importantly, in addition to the g protein-coupled receptor / aryl hydrocarbon receptor pathway, the selected microbial small molecule metabolites are the true T-cell receptor ligands of unconventional T cells, directly shaping the tissue resident immune and tumor microenvironment, supplementing the receptor signaling and epigenetic programs in our framework. We synthesize how these metabolites recalibrate the tumor immune microenvironment-modulating antigen presentation, T-cell effector fitness and exhaustion, regulatory T-cell activity, and myeloid polarization-and why the same metabolite can either potentiate immune surveillance or entrench immunosuppression depending on ligand-receptor pairing, dose and tissue niche. We compare tumor-type specific patterns (e.g., colorectal, liver, lung, breast and prostate cancers) to highlight common circuits and organ-restricted idiosyncrasies. Methodologically, we outline how single-cell and spatial multi-omics, imaging mass spectrometry and functional biosensors now enable co-registration of metabolite exposure with immune-cell states in human tumors, providing an actionable basis for biomarker discovery. Given ongoing debate about signals attributed to intratumoral microbiota in low-biomass tumor tissues, we foreground quantifiable, spatially mappable and pharmacologically tractable metabolite-receptor pathways, using microbe-associated molecular patterns / translocation as comparators to judge when chemical signals should be prioritized as intervention targets. Finally, we evaluate precision intervention avenues-including fecal microbiota transplantation, rational bacterial consortia, engineered microbes and nanoparticle-enabled metabolite delivery-and propose stratification rules that pair metabolite/receptor signatures with fit-for-purpose delivery. Together, mapping tissue-specific metabolite-immune circuits and embedding them in robust biomarker frameworks may convert microbial metabolites from correlative markers into therapeutic targets and tools, improving the efficacy and durability of cancer immunotherapy.

PMID:41339918 | DOI:10.1186/s12943-025-02521-5

LOSTdb: a manually curated multi-omics database for lung cancer research

✇Omics In Lung
By: Hao Luo · Yunhao Yang · Zhipeng Gong · Lunxu Liu · Yaohui Chen
3 December 2025 at 19:00

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

Scaling Multimodal Search and Recommendation with Small Language Models via Upside-Down Reinforcement Learning

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yu-Chen Lin · Sanat Sharma · Hari Manikandan · Jayant Kumar · Tracy Holloway King · Jing Zheng
4 December 2025 at 13:00
arXiv:2502.09854v2 Announce Type: replace-cross Abstract: In this work, we investigate how small language models (SLMs) can be scaled to support multimodal search and recommendation use cases while remaining efficient enough for real-time, resource-constrained deployments. We present a framework that combines upside-down reinforcement learning with synthetic data distillation from a large language model (Llama-3) to train a 100M-parameter GPT-2 model for multitask prompt generation. Despite being up to 80 times smaller than state-of-the-art large language models (LLMs), our SLM achieves relevance and diversity scores within 6% of competitive baselines such as Llama-3 8B, Qwen3 8B, and Ministral 8B. These results demonstrate that SLMs can effectively handle multimodal search and recommendation tasks, while dramatically reducing inference latency and memory overhead. Our study highlights the potential of lightweight models as practical engines for scalable multimodal discovery, bridging the gap between cutting-edge research and real-world multimodal applications such as media recommendations and creative content generation.

Challenges and Limitations of Generative AI in Synthesizing Wearable Sensor Data

✇cs.AI, q-bio.NC updates on arXiv.org
By: Flavio Di Martino · Franca Delmastro
4 December 2025 at 13:00
arXiv:2505.14206v2 Announce Type: replace-cross Abstract: The widespread adoption of wearable sensors has the potential to provide massive and heterogeneous time series data, driving the use of Artificial Intelligence in human sensing applications. However, data collection remains limited due to stringent ethical regulations, privacy concerns, and other constraints, hindering progress in the field. Synthetic data generation, particularly through Generative Adversarial Networks and Diffusion Models, has emerged as a promising solution to mitigate both data scarcity and privacy issues. However, these models are often limited to narrow operational scenarios, such as short-term and unimodal signal patterns. To address this gap, we present a systematic evaluation of state-of-the-art generative models for time series data, explicitly assessing their performance in challenging scenarios such as stress and emotion recognition. Our study examines the extent to which these models can jointly handle multi-modality, capture long-range dependencies, and support conditional generation-core requirements for real-world wearable sensor data generation. To enable a fair and rigorous comparison, we also introduce an evaluation framework that evaluates both the intrinsic fidelity of the generated data and their utility in downstream predictive tasks. Our findings reveal critical limitations in the existing approaches, particularly in maintaining cross-modal consistency, preserving temporal coherence, and ensuring robust performance in train-on-synthetic, test-on-real, and data augmentation scenarios. Finally, we present our future research directions to enhance synthetic time series generation and improve the applicability of generative models in the wearable computing domain.

SafeGenes: Evaluating the Adversarial Robustness of Genomic Foundation Models

✇cs.AI, q-bio.NC updates on arXiv.org
By: Huixin Zhan · Clovis Barbour · Jason H. Moore
4 December 2025 at 13:00
arXiv:2506.00821v2 Announce Type: replace-cross Abstract: Genomic Foundation Models (GFMs), such as Evolutionary Scale Modeling (ESM), have demonstrated significant success in variant effect prediction. However, their adversarial robustness remains largely unexplored. To address this gap, we propose SafeGenes: a framework for Secure analysis of genomic foundation models, leveraging adversarial attacks to evaluate robustness against both engineered near-identical adversarial Genes and embedding-space manipulations. In this study, we assess the adversarial vulnerabilities of GFMs using two approaches: the Fast Gradient Sign Method (FGSM) and a soft prompt attack. FGSM introduces minimal perturbations to input sequences, while the soft prompt attack optimizes continuous embeddings to manipulate model predictions without modifying the input tokens. By combining these techniques, SafeGenes provides a comprehensive assessment of GFM susceptibility to adversarial manipulation. Targeted soft prompt attacks induced severe degradation in MLM-based shallow architectures such as ProteinBERT, while still producing substantial failure modes even in high-capacity foundation models such as ESM1b and ESM1v. These findings expose critical vulnerabilities in current foundation models, opening new research directions toward improving their security and robustness in high-stakes genomic applications such as variant effect prediction.

Aetheria: A multimodal interpretable content safety framework based on multi-agent debate and collaboration

✇cs.AI, q-bio.NC updates on arXiv.org
By: Yuxiang He · Jian Zhao · Yuchen Yuan · Tianle Zhang · Wei Cai · Haojie Cheng · Ziyan Shi · Ming Zhu · Haichuan Tang · Chi Zhang · Xuelong Li
3 December 2025 at 13:00
arXiv:2512.02530v1 Announce Type: new Abstract: The exponential growth of digital content presents significant challenges for content safety. Current moderation systems, often based on single models or fixed pipelines, exhibit limitations in identifying implicit risks and providing interpretable judgment processes. To address these issues, we propose Aetheria, a multimodal interpretable content safety framework based on multi-agent debate and collaboration.Employing a collaborative architecture of five core agents, Aetheria conducts in-depth analysis and adjudication of multimodal content through a dynamic, mutually persuasive debate mechanism, which is grounded by RAG-based knowledge retrieval.Comprehensive experiments on our proposed benchmark (AIR-Bench) validate that Aetheria not only generates detailed and traceable audit reports but also demonstrates significant advantages over baselines in overall content safety accuracy, especially in the identification of implicit risks. This framework establishes a transparent and interpretable paradigm, significantly advancing the field of trustworthy AI content moderation.

PaperDebugger: A Plugin-Based Multi-Agent System for In-Editor Academic Writing, Review, and Editing

✇cs.AI, q-bio.NC updates on arXiv.org
By: Junyi Hou (National University of Singapore) · Andre Lin Huikai (National University of Singapore) · Nuo Chen (National University of Singapore) · Yiwei Gong (Independent Researcher · Singapore) · Bingsheng He (National University of Singapore)
3 December 2025 at 13:00
arXiv:2512.02589v1 Announce Type: new Abstract: Large language models are increasingly embedded into academic writing workflows, yet existing assistants remain external to the editor, preventing deep interaction with document state, structure, and revision history. This separation makes it impossible to support agentic, context-aware operations directly within LaTeX editors such as Overleaf. We present PaperDebugger, an in-editor, multi-agent, and plugin-based academic writing assistant that brings LLM-driven reasoning directly into the writing environment. Enabling such in-editor interaction is technically non-trivial: it requires reliable bidirectional synchronization with the editor, fine-grained version control and patching, secure state management, multi-agent scheduling, and extensible communication with external tools. PaperDebugger addresses these challenges through a Chrome-approved extension, a Kubernetes-native orchestration layer, and a Model Context Protocol (MCP) toolchain that integrates literature search, reference lookup, document scoring, and revision pipelines. Our demo showcases a fully integrated workflow, including localized edits, structured reviews, parallel agent execution, and diff-based updates, encapsulated within a minimal-intrusion user interface (UI). Early aggregated analytics demonstrate active user engagement and validate the practicality of an editor-native, agentic writing assistant. More details about this demo and video could be found at https://github.com/PaperDebugger/PaperDebugger.

A Framework for Causal Concept-based Model Explanations

✇cs.AI, q-bio.NC updates on arXiv.org
By: Anna Rodum Bj{\o}ru, Jacob Lysn{\ae}s-Larsen, Oskar J{\o}rgensen, Inga Str\"umke, Helge Langseth
3 December 2025 at 13:00
arXiv:2512.02735v1 Announce Type: new Abstract: This work presents a conceptual framework for causal concept-based post-hoc Explainable Artificial Intelligence (XAI), based on the requirements that explanations for non-interpretable models should be understandable as well as faithful to the model being explained. Local and global explanations are generated by calculating the probability of sufficiency of concept interventions. Example explanations are presented, generated with a proof-of-concept model made to explain classifiers trained on the CelebA dataset. Understandability is demonstrated through a clear concept-based vocabulary, subject to an implicit causal interpretation. Fidelity is addressed by highlighting important framework assumptions, stressing that the context of explanation interpretation must align with the context of explanation generation.

scCluBench: Comprehensive Benchmarking of Clustering Algorithms for Single-Cell RNA Sequencing

✇cs.AI, q-bio.NC updates on arXiv.org
By: Ping Xu · Zaitian Wang · Zhirui Wang · Pengjiang Li · Jiajia Wang · Ran Zhang · Pengfei Wang · Yuanchun Zhou
3 December 2025 at 13:00
arXiv:2512.02471v1 Announce Type: cross Abstract: Cell clustering is crucial for uncovering cellular heterogeneity in single-cell RNA sequencing (scRNA-seq) data by identifying cell types and marker genes. Despite its importance, benchmarks for scRNA-seq clustering methods remain fragmented, often lacking standardized protocols and failing to incorporate recent advances in artificial intelligence. To fill these gaps, we present scCluBench, a comprehensive benchmark of clustering algorithms for scRNA-seq data. First, scCluBench provides 36 scRNA-seq datasets collected from diverse public sources, covering multiple tissues, which are uniformly processed and standardized to ensure consistency for systematic evaluation and downstream analyses. To evaluate performance, we collect and reproduce a range of scRNA-seq clustering methods, including traditional, deep learning-based, graph-based, and biological foundation models. We comprehensively evaluate each method both quantitatively and qualitatively, using core performance metrics as well as visualization analyses. Furthermore, we construct representative downstream biological tasks, such as marker gene identification and cell type annotation, to further assess the practical utility. scCluBench then investigates the performance differences and applicability boundaries of various clustering models across diverse analytical tasks, systematically assessing their robustness and scalability in real-world scenarios. Overall, scCluBench offers a standardized and user-friendly benchmark for scRNA-seq clustering, with curated datasets, unified evaluation protocols, and transparent analyses, facilitating informed method selection and providing valuable insights into model generalizability and application scope.

Artificial Intelligence Virtual Cells: From Measurements to Decisions across Modality, Scale, Dynamics, and Evaluation

✇cs.AI, q-bio.NC updates on arXiv.org
By: Chengpeng Hu · Calvin Yu-Chian Chen
3 December 2025 at 13:00
arXiv:2510.12498v2 Announce Type: replace Abstract: Artificial Intelligence Virtual Cells (AIVCs) aim to learn executable, decision-relevant models of cell state from multimodal, multiscale measurements. Recent studies have introduced single-cell and spatial foundation models, improved cross-modality alignment, scaled perturbation atlases, and explored pathway-level readouts. Nevertheless, although held-out validation is standard practice, evaluations remain predominantly within single datasets and settings; evidence indicates that transport across laboratories and platforms is often limited, that some data splits are vulnerable to leakage and coverage bias, and that dose, time and combination effects are not yet systematically handled. Cross-scale coupling also remains constrained, as anchors linking molecular, cellular and tissue levels are sparse, and alignment to scientific or clinical readouts varies across studies. We propose a model-agnostic Cell-State Latent (CSL) perspective that organizes learning via an operator grammar: measurement, lift/project for cross-scale coupling, and intervention for dosing and scheduling. This view motivates a decision-aligned evaluation blueprint across modality, scale, context and intervention, and emphasizes function-space readouts such as pathway activity, spatial neighborhoods and clinically relevant endpoints. We recommend operator-aware data design, leakage-resistant partitions, and transparent calibration and reporting to enable reproducible, like-for-like comparisons.

AutoSurvey2: Empowering Researchers with Next Level Automated Literature Surveys

✇cs.AI, q-bio.NC updates on arXiv.org
By: Siyi Wu · Chiaxin Liang · Ziqian Bi · Leyi Zhao · Tianyang Wang · Junhao Song · Yichao Zhang · Keyu Chen · Benji Peng · Xinyuan Song
3 December 2025 at 13:00
arXiv:2510.26012v3 Announce Type: replace Abstract: The rapid growth of research literature, particularly in large language models (LLMs), has made producing comprehensive and current survey papers increasingly difficult. This paper introduces autosurvey2, a multi-stage pipeline that automates survey generation through retrieval-augmented synthesis and structured evaluation. The system integrates parallel section generation, iterative refinement, and real-time retrieval of recent publications to ensure both topical completeness and factual accuracy. Quality is assessed using a multi-LLM evaluation framework that measures coverage, structure, and relevance in alignment with expert review standards. Experimental results demonstrate that autosurvey2 consistently outperforms existing retrieval-based and automated baselines, achieving higher scores in structural coherence and topical relevance while maintaining strong citation fidelity. By combining retrieval, reasoning, and automated evaluation into a unified framework, autosurvey2 provides a scalable and reproducible solution for generating long-form academic surveys and contributes a solid foundation for future research on automated scholarly writing. All code and resources are available at https://github.com/annihi1ation/auto_research.

Fast 3D Surrogate Modeling for Data Center Thermal Management

✇cs.AI, q-bio.NC updates on arXiv.org
By: Soumyendu Sarkar · Antonio Guillen-Perez · Zachariah J Carmichael · Avisek Naug · Refik Mert Cam · Vineet Gundecha · Ashwin Ramesh Babu · Sahand Ghorbanpour · Ricardo Luna Gutierrez
3 December 2025 at 13:00
arXiv:2511.11722v2 Announce Type: replace-cross Abstract: Reducing energy consumption and carbon emissions in data centers by enabling real-time temperature prediction is critical for sustainability and operational efficiency. Achieving this requires accurate modeling of the 3D temperature field to capture airflow dynamics and thermal interactions under varying operating conditions. Traditional thermal CFD solvers, while accurate, are computationally expensive and require expert-crafted meshes and boundary conditions, making them impractical for real-time use. To address these limitations, we develop a vision-based surrogate modeling framework that operates directly on a 3D voxelized representation of the data center, incorporating server workloads, fan speeds, and HVAC temperature set points. We evaluate multiple architectures, including 3D CNN U-Net variants, a 3D Fourier Neural Operator, and 3D vision transformers, to map these thermal inputs to high-fidelity heat maps. Our results show that the surrogate models generalize across data center configurations and significantly speed up computations (20,000x), from hundreds of milliseconds to hours. This fast and accurate estimation of hot spots and temperature distribution enables real-time cooling control and workload redistribution, leading to substantial energy savings (7\%) and reduced carbon footprint.

Digital Biometrics in Predicting Risk for Obstructive Sleep Apnea and Hypertension: Decentralized, Prospective Cohort Study

✇Journal of Medical Internet Research
By: Natalia Orendain · Samantha Spierling Bagsic · Edward Ramos · Jay Pandit · Robert L Owens · Stuti Jaiswal
4 December 2025 at 04:30
Background: Sleep is an important component of human health and can be measured longitudinally using digital activity trackers. Further, decentralized digital research has the potential to provide a real-world picture of sleep in large populations. Objective: This study examined whether longitudinal sleep patterns from activity trackers could predict risk of obstructive sleep apnea (OSA) and hypertension, as defined the Berlin questionnaire and self report, respectively. Methods: We recruited adults ≥18 years nationwide to join our sleep-focused smartphone-based study, called the Research Framework for Exploring Sleep Health (REFRESH). Our sample of N= 391 adults is comprised predominately of females (68%; n = 247 out of 364) at a mean age of 48 years (standard deviation (SD) = 13.62). Participants were asked to fill out health-related surveys, including the Berlin questionnaire, and the Horne-Ostberg questionnaire for chronotype. Participants were asked to link their own activity tracker to the application to collect longitudinal sleep data. Results: We analyzed sleep data from 391 participants, among a predominately White (65%; n = 231 out of 353) followed by multiracial (17%; n = 61 out of 353) and Hispanic or Latino (6.5%; n = 23 out of 353) cohort. Collinearity testing showed that OSA risk and self-reported hypertension could be considered independently. Holding body mass index (BMI) at fixed value, the odds of having high OSA risk increased by 159% for every one-hour increase in weekday sleep variability (odds ratio (OR) = 2.592, 95% confidence interval (CI) [1.613, 4.400]; P

Multi-omic profiling provides insights into the heterogeneity, microenvironmental features, and biomarker landscape of small-cell lung cancer

✇Omics In Lung
By: Mingchao Xie · Miljenka Vuko · Shashank Saran · Siyu Liu · Andrew G Chambers · Hana Baakza · Helen K Angell · Felicia Ng · Carl M Gay · Robert J Cardnell · Felix J Segerer · Alma Andoni · Jaime Rodriguez-Canales · Paul M Waring · Markus Schick · J Carl Barrett · Lauren A Byers · Giulia Fabbri
2 December 2025 at 19:00

Mol Cancer. 2025 Dec 2. doi: 10.1186/s12943-025-02514-4. Online ahead of print.

ABSTRACT

BACKGROUND: Greater understanding of differential therapeutic sensitivity, specifically to immunotherapy, in small-cell lung cancer (SCLC) is required.

METHODS: We explored SCLC heterogeneity through integrated molecular characterization of tumor tissue samples from 159 treatment-naive patients, utilizing genetic, epigenetic, transcriptional, and proteomic profiling, immunohistochemistry staining for multiple biologically relevant markers including transcriptional subtype-defining proteins, and spatial immune profiling using multiplex immunofluorescence.

RESULTS: Multi-omics analysis confirmed high heterogeneity across/within neuroendocrine and non-neuroendocrine subtypes. Methylomics analysis identified four methylome clusters that may enhance subtype prediction, prognosis, and longitudinal monitoring of subtype evolution. Immunohistochemistry analysis showed high MHC-I expression in non-neuroendocrine subtypes, which have greatest potential benefit from adding immunotherapy to chemotherapy; high DLL3 expression associated with neuroendocrine subtypes and an immune-cold tumor microenvironment. Multiplex immunofluorescence demonstrated associations of MHC-I with spatial arrangement and phenotypic features of immune cells in the tumor microenvironment of high-MHC-I-expressing SCLC, providing mechanistic rationale for MHC-I as a potential biomarker of immunotherapy response.

CONCLUSIONS: This multimodal profiling analysis provides further insights into the biologic complexity of SCLC and highlights potential therapeutic vulnerabilities of distinct disease subtypes.

PMID:41331472 | DOI:10.1186/s12943-025-02514-4

Integrative Analysis of Multi-Omics Data for Biomarker Discovery

✇Omics in Hepatocellular
By: Rency S Varghese · Xinran Zhang · Sarada Giridharan · Hoi Yan Katharine Chau · Radhika Unnikrishnan · Md Mamunur Rashid · Muhammad Salman Sajid · Habtom W Ressom
3 December 2025 at 19:00

Annu Int Conf IEEE Eng Med Biol Soc. 2025 Jul;2025:1-7. doi: 10.1109/EMBC58623.2025.11254134.

ABSTRACT

The complexity of biological systems and the limitations of analyzing individual omics studies for biomarker discovery have raised the need for a holistic approach by multi-omics integration. By integrating data from multiple layers, researchers can gain insights into the entire system rather than just individual components. Also, integrative analysis can help identify molecular signatures that are more accurate in predicting disease onset, progression, and response to treatment, leading to better-targeted therapies and personalized medicine. In this paper, we explored statistical and deep learning methods for integrative analysis of metabolomics, lipidomics, peptidomics, proteomics, and glycoproteomics data acquired by LC-MS/MS analysis of serum samples from 20 hepatocellular carcinoma (HCC) cases and 20 patients with liver cirrhosis (CIRR). The goal is to identify a panel of multi-omics features that distinguish HCC cases from cirrhotic controls. A pathway analysis using these features identified biological pathways such as LXR/RXR Activation and Acute Response signaling as significantly enriched in our multi-omics datasets.

PMID:41336317 | PMC:PMC12694951 | DOI:10.1109/EMBC58623.2025.11254134

Whole-genome landscapes of 1,364 breast cancers

✇Nature - Issue - nature.com science feeds
By: Ryul Kim · Jonghan Yu · Joonoh Lim · Brian Baek-Lok Oh · Seok Jin Nam · Seok Won Kim · Jeong Eon Lee · Byung Joo Chae · Ji-Yeon Kim · Ga Eun Park · Bong Joo Kang · Pill Sun Paik · Soo Yeon Bae · Chang Ik Yoon · Young Joo Lee · Dooreh Kim · Kabsoo Shin · Ji Eun Lee · Jun Kang · Ahwon Lee · Erin Connolly-Strong · Sangmoon Lee · Bo Rahm Lee · Yuna Lee · Ki Jong Yi · Young Oh Kwon · In Hwan Chun · Junggil Park · Jihye Kim · Chahyun Choi · Jong Yeon Shin · Hyungjung Lee · Minji Kim · Hansol Park · Ilecheon Jeong · Boram Yi · Won-Chul Lee · Jeong Seok Lee · Woo Chan Park · Sung Hun Kim · Yoon-La Choi · Jeongmin Lee · Young Seok Ju · Yeon Hee Park
3 December 2025 at 08:00

Nature, Published online: 03 December 2025; doi:10.1038/s41586-025-09812-3

Whole-genome and transcriptome analysis of 1,364 cases of breast cancer from South Korea broadens our understanding of breast cancer biology and reveals genomic features that connect tumour biology with treatment responses and clinical outcomes.
Received — 3 December 2025 ⏭ Favourites

DeFi TrustBoost: Blockchain and AI for Trustworthy Decentralized Financial Decisions

✇cs.AI, q-bio.NC updates on arXiv.org
By: Swati Sachan · Dale S. Fickett
2 December 2025 at 13:00
arXiv:2512.00142v1 Announce Type: cross Abstract: This research introduces the Decentralized Finance (DeFi) TrustBoost Framework, which combines blockchain technology and Explainable AI to address challenges faced by lenders underwriting small business loan applications from low-wealth households. The framework is designed with a strong emphasis on fulfilling four crucial requirements of blockchain and AI systems: confidentiality, compliance with data protection laws, resistance to adversarial attacks, and compliance with regulatory audits. It presents a technique for tamper-proof auditing of automated AI decisions and a strategy for on-chain (inside-blockchain) and off-chain data storage to facilitate collaboration within and across financial organizations.
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