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  • The Missing Layer of AGI: From Pattern Alchemy to Coordination Physics Edward Y. Chang
    arXiv:2512.05765v1 Announce Type: new Abstract: Influential critiques argue that Large Language Models (LLMs) are a dead end for AGI: "mere pattern matchers" structurally incapable of reasoning or planning. We argue this conclusion misidentifies the bottleneck: it confuses the ocean with the net. Pattern repositories are the necessary System-1 substrate; the missing component is a System-2 coordination layer that selects, constrains, and binds these patterns. We formalize this layer via UCCT, a
     

The Missing Layer of AGI: From Pattern Alchemy to Coordination Physics

arXiv:2512.05765v1 Announce Type: new Abstract: Influential critiques argue that Large Language Models (LLMs) are a dead end for AGI: "mere pattern matchers" structurally incapable of reasoning or planning. We argue this conclusion misidentifies the bottleneck: it confuses the ocean with the net. Pattern repositories are the necessary System-1 substrate; the missing component is a System-2 coordination layer that selects, constrains, and binds these patterns. We formalize this layer via UCCT, a theory of semantic anchoring that models reasoning as a phase transition governed by effective support (rho_d), representational mismatch (d_r), and an adaptive anchoring budget (gamma log k). Under this lens, ungrounded generation is simply an unbaited retrieval of the substrate's maximum likelihood prior, while "reasoning" emerges when anchors shift the posterior toward goal-directed constraints. We translate UCCT into architecture with MACI, a coordination stack that implements baiting (behavior-modulated debate), filtering (Socratic judging), and persistence (transactional memory). By reframing common objections as testable coordination failures, we argue that the path to AGI runs through LLMs, not around them.

XR-DT: Extended Reality-Enhanced Digital Twin for Agentic Mobile Robots

arXiv:2512.05270v1 Announce Type: cross Abstract: As mobile robots increasingly operate alongside humans in shared workspaces, ensuring safe, efficient, and interpretable Human-Robot Interaction (HRI) has become a pressing challenge. While substantial progress has been devoted to human behavior prediction, limited attention has been paid to how humans perceive, interpret, and trust robots' inferences, impeding deployment in safety-critical and socially embedded environments. This paper presents XR-DT, an eXtended Reality-enhanced Digital Twin framework for agentic mobile robots, that bridges physical and virtual spaces to enable bi-directional understanding between humans and robots. Our hierarchical XR-DT architecture integrates virtual-, augmented-, and mixed-reality layers, fusing real-time sensor data, simulated environments in the Unity game engine, and human feedback captured through wearable AR devices. Within this framework, we design an agentic mobile robot system with a unified diffusion policy for context-aware task adaptation. We further propose a chain-of-thought prompting mechanism that allows multimodal large language models to reason over human instructions and environmental context, while leveraging an AutoGen-based multi-agent coordination layer to enhance robustness and collaboration in dynamic tasks. Initial experimental results demonstrate accurate human and robot trajectory prediction, validating the XR-DT framework's effectiveness in HRI tasks. By embedding human intention, environmental dynamics, and robot cognition into the XR-DT framework, our system enables interpretable, trustworthy, and adaptive HRI.

Simulating Life Paths with Digital Twins: AI-Generated Future Selves Influence Decision-Making and Expand Human Choice

arXiv:2512.05397v1 Announce Type: cross Abstract: Major life transitions demand high-stakes decisions, yet people often struggle to imagine how their future selves will live with the consequences. To support this limited capacity for mental time travel, we introduce AI-enabled digital twins that have ``lived through'' simulated life scenarios. Rather than predicting optimal outcomes, these simulations extend prospective cognition by making alternative futures vivid enough to support deliberation without assuming which path is best. We evaluate this idea in a randomized controlled study (N=192) using multimodal synthesis - facial age progression, voice cloning, and large language model dialogue - to create personalized avatars representing participants 30 years forward. Young adults 18 to 28 years old described pending binary decisions and were assigned to guided imagination or one of four avatar conditions: single-option, balanced dual-option, or expanded three-option with a system-generated novel alternative. Results showed asymmetric effects: single-sided avatars increased shifts toward the presented option, while balanced presentation produced movement toward both. Introducing a system-generated third option increased adoption of this new alternative compared to control, suggesting that AI-generated future selves can expand choice by surfacing paths that might otherwise go unnoticed. Participants rated evaluative reasoning and eudaimonic meaning-making as more important than emotional or visual vividness. Perceived persuasiveness and baseline agency predicted decision change. These findings advance understanding of AI-mediated episodic prospection and raise questions about autonomy in AI-augmented decisions.

ToolMind Technical Report: A Large-Scale, Reasoning-Enhanced Tool-Use Dataset

arXiv:2511.15718v2 Announce Type: replace Abstract: Large Language Model (LLM) agents have developed rapidly in recent years to solve complex real-world problems using external tools. However, the scarcity of high-quality trajectories still hinders the development of stronger LLM agents. Most existing works on multi-turn dialogue synthesis validate correctness only at the trajectory level, which may overlook turn-level errors that can propagate during training and degrade model performance. To address these limitations, we introduce ToolMind, a large-scale, high-quality tool-agentic dataset with 160k synthetic data instances generated using over 20k tools and 200k augmented open-source data instances. Our data synthesis pipeline first constructs a function graph based on parameter correlations and then uses a multi-agent framework to simulate realistic user-assistant-tool interactions. Beyond trajectory-level validation, we employ fine-grained turn-level filtering to remove erroneous or suboptimal steps, ensuring that only high-quality reasoning traces are retained. This approach mitigates error amplification during training while preserving self-corrective reasoning signals essential for robust tool-use learning. Models fine-tuned on ToolMind show significant improvements over baselines on several benchmarks.

The AI Productivity Index (APEX)

arXiv:2509.25721v4 Announce Type: replace-cross Abstract: We present an extended version of the AI Productivity Index (APEX-v1-extended), a benchmark for assessing whether frontier models are capable of performing economically valuable tasks in four jobs: investment banking associate, management consultant, big law associate, and primary care physician (MD). This technical report details the extensions to APEX-v1, including an increase in the held-out evaluation set from n = 50 to n = 100 cases per job (n = 400 total) and updates to the grading methodology. We present a new leaderboard, where GPT5 (Thinking = High) remains the top performing model with a score of 67.0%. APEX-v1-extended shows that frontier models still have substantial limitations when performing typical professional tasks. To support further research, we are open sourcing n = 25 non-benchmark example cases per role (n = 100 total) along with our evaluation harness.

Exploring a Digital Health Solution to Collect and Manage Health-Related Needs for Patients Who Undergo Complex Surgery: Mixed Methods Study

Background: Patients who undergo complex surgery (e.g., esophagectomy, liver resection) often experience substantial burden of health-related needs (medical, social, and behavioral health). A closed loop digital solution could facilitate the collection and resolution of health-related needs by care team members for patients who undergo complex surgery. A digital solution may facilitate adherence to a clear treatment plan and concomitantly reduce surgical complications and readmissions associated with unmet health-related needs, which remain persistent challenges across health care settings. Objective: To establish problems and gaps in the collection, integration, and management of health-related needs and identify a set of user specifications for a digital solution to collect and manage health-related needs, specifically medical, social, and behavioral needs for patients who undergo complex surgery. Methods: We applied the Double Diamond Framework and organized the study into two sequential phases: (1) qualitative methods to discover patients’ and care team members’ perspectives on health-related needs; (2) participatory design sessions to gain feedback and sentiment about ideal features of a digital solution. Both phases were conducted between December 2023 and March 2025. We supplemented both phases with analysis of electronic health record (EHR) data for patients who underwent complex surgery at our academic medical center (AMC). Results: Extensive themes emerged from interviews with patients (n=20) and care team members (n=24), capturing their health-related and surgical experiences as well as desired features for a proposed digital solution. Our swim lane diagram demonstrated four critical gaps in workflow: (1) heterogeneity in the approach to screening, monitoring, and managing health-related needs; (2) patients felt uncomfortable reporting health-related needs, particularly behavioral and social needs, to their care team; (3) lack of access to referral resources to resolve needs; and (4) the need for a closed loop intervention for patients and care team members. A subset of participants from Phase 1 (n=5 patients and n=9 care team members) provided feedback on preferred features, drawing from digital tools currently available in the EHR at our AMC. Among four existing EHR tools tested, there were notable variations in how patients and care team members felt about their potential use. Participants also provided extensive feedback for preferred components (e.g., goals and active plans) that should be available in an existing or custom digital solution to manage health-related needs. Findings from the qualitative interviews and design sessions were corroborated with EHR documentation. Conclusions: Digital solutions could provide a streamlined approach for collection and management of health-related needs in surgery, with the goal of addressing unmet needs and improving patient activation. This approach is critical to ensure patients, especially patients who undergo complex surgery, have positive health outcomes. We identified preferences for specific features in a proposed digital solution based on our systematic assessment that will inform future work.

EIF3M as a pan-cancer biomarker: prognostic significance and immune infiltration association

Front Mol Biosci. 2025 Nov 18;12:1697083. doi: 10.3389/fmolb.2025.1697083. eCollection 2025.

ABSTRACT

BACKGROUND: EIF3M, a core subunit of eukaryotic translation initiation factor 3, plays a pivotal role in protein synthesis by regulating the assembly of the 43S initiation complex. However, its biological functions in cancer remain poorly understood. To further investigate the clinical translational value and underlying mechanisms of EIF3M in tumors, this study conducted comprehensive bioinformatic analysis of EIF3M across various tumor types.

METHODS: We utilized publicly available databases to perform a comprehensive bioinformatics analysis of EIF3M's biological roles in oncogenesis, aiming to elucidate its pan-cancer expression patterns and prognostic significance. Furthermore, we conducted an integrative multi-omics analysis incorporating methylation profiling, co-expressed gene networks, targeted miRNA interactions, and tumor immune microenvironment infiltration to decipher the complex regulatory architecture and biological pathways mediated by EIF3M across cancer types. Finally, we used HCC cell lines for in vitro functional validation, determining how EIF3M expression modulates malignant phenotypic behaviors in hepatocellular carcinoma.

RESULTS: EIF3M was overexpressed in multiple cancers and correlated with advanced tumor stage and poor survival. Its dysregulation was primarily driven by gene amplification and regulated by promoter methylation and miRNAs. EIF3M functioned as a hub in cell cycle and transcriptional networks and was linked to an immunosuppressive microenvironment. In hepatocellular carcinoma models, EIF3M modulated tumor proliferation, migration, and activated oncogenic pathways like Wnt/β-catenin.

CONCLUSION: This study reveals that EIF3M expression correlates with immune infiltration and poor prognosis in multiple cancers. In vitro experiments in hepatocellular carcinoma models demonstrated that EIF3M critically regulates malignant cell behaviors. Collectively, our findings highlight EIF3M's value as a promising pan-cancer biomarker worthy of further investigation for its utility in prognosis prediction and as an indicator of immunotherapeutic response.

PMID:41341921 | PMC:PMC12669982 | DOI:10.3389/fmolb.2025.1697083

Detecting Sociodemographic Biases in the Content and Quality of Large Language Model–Generated Nursing Care: Cross-Sectional Simulation Study

Background: Large language models (LLMs) are increasingly applied in healthcare. However, concerns remain that their nursing care recommendations may reflect patients’ sociodemographic attributes rather than clinical needs. Objective: To investigate potential biases in nursing care plans generated by LLMs, we focused on whether outputs differ systematically based on patients’ sociodemographic characteristics and assessed the implications for equitable nursing care. Methods: We utilized a standardized clinical scenario with GPT to generate care plans for 96 sociodemographic identity combinations, drawing on 9,600 tests. We conducted statistical analyses (t-tests and ANOVA) to analyze how text length and the frequency of physiological and psychological nursing terms varied across sociodemographic factors. Additionally, we utilized Python for data processing and visualization to ensure methodological rigor throughout the study. Results: The analysis revealed significant sociodemographic biases in LLMs-generated nursing care plans. Female patients received shorter care plans (t = 4.864, P

Promoting Responsible DeepSeek Deployment in Health Care: Scoping Review Comparing Grey and White Literature

Background: The rapid deployment of DeepSeek, an open-source large language model has sparked concerns of its impact on patient outcomes and safety. However, little is known about how DeepSeek is used and regulated in these facilities. Objective: This study aimed to 1) systematically review the characteristics of deployed DeepSeek in the top 100 hospitals in China; and 2) compare performances and risks from hospital disclosure with research evidence. Methods: We performed a scoping review of gray and white literature, collecting data from the top 100 Chinese hospitals. We extracted basic characteristics of DeepSeek, its aim, evaluation approach, performance, risk and hospital regulation. A coding framework was developedcovering LLMs application scenario, evaluation dimension and source of risk. Results: We identified a total of 58 DeepSeek models in 48 out of the top 100 Chinese hospitals as well as 27 studies. We observed deployed DeepSeek mainly intended to assist clinical decision making, such as patient diagnosis and treatment recommendation. However, only 36.2% hospital-deployed models clearly indicated a pre-deployment assessment, 22.4% presented assessment results, and 8.6% identified potential risks and countermeasures. We found poor transparency in hospital reporting, with none presenting evaluation details. Hospitals were likely to report DeepSeek’s higher performance and fewer risks. Conclusions: The irresponsible deployment of DeepSeek in Chinese leading hospitals poses potential risks to patient outcomes and safety. We highlight the urgent need that existing regulations should be expanded to the downstream developers and users and hospitals need to perform a more rigorous validation and transparent reporting.

Listening to Patients’ Voices on the Use of AI in Health Care: Cross-Sectional Study

Background: Artificial intelligence (AI) holds great promise in transforming healthcare delivery. However, successful implementation of AI projects in healthcare depends on patients' acceptance and trust. There is only limited empirical research examining public perceptions, particularly on the use of personal health data in AI applications in healthcare. Objective: To examine public knowledge and comfort levels with AI use in healthcare, including use of personal health data with and without consent, and to assess how sociodemographic factors, digital literacy, and health conditions influence these perceptions. Methods: We analyzed data from 6,904 Canadian adults who participated in the 2023 Canadian Digital Health Survey. AI-related knowledge and comfort levels were measured using ordinal scales. Sociodemographic characteristics, digital health literacy, and self-reported chronic health conditions were included as predictors. Ordinal logistic regression models were used to assess associations between these factors and AI-related attitudes. Results: 42.3% reported moderate knowledge of AI, while only 7.8% described themselves as very knowledgeable. Overall, 44.6% were comfortable with AI use in healthcare, increasing to 64.7% when personal health data were used with consent, but decreasing when used without consent (52.6% uncomfortable). Respondents were most comfortable with AI use for epidemic tracking and workflow management, and less so for clinical tasks. Fully weighted ordinal logistic regression models indicated that men (OR=1.57, p<.001 non-citizens higher-income respondents p those with graduate education higher digital health literacy and more chronic conditions exhibited greater odds of reporting ai knowledge. for comfort use in healthcare aged men .001 or comfort. lower-income white reported lower levels. using personal data consent adults were less comfortable than showed while other racial groups without contrast black conclusions: the findings point to enhancing transparent policies ethical governance as key increasing public trust ai-driven healthcare.>

EIF3M as a pan-cancer biomarker: prognostic significance and immune infiltration association

Front Mol Biosci. 2025 Nov 18;12:1697083. doi: 10.3389/fmolb.2025.1697083. eCollection 2025.

ABSTRACT

BACKGROUND: EIF3M, a core subunit of eukaryotic translation initiation factor 3, plays a pivotal role in protein synthesis by regulating the assembly of the 43S initiation complex. However, its biological functions in cancer remain poorly understood. To further investigate the clinical translational value and underlying mechanisms of EIF3M in tumors, this study conducted comprehensive bioinformatic analysis of EIF3M across various tumor types.

METHODS: We utilized publicly available databases to perform a comprehensive bioinformatics analysis of EIF3M's biological roles in oncogenesis, aiming to elucidate its pan-cancer expression patterns and prognostic significance. Furthermore, we conducted an integrative multi-omics analysis incorporating methylation profiling, co-expressed gene networks, targeted miRNA interactions, and tumor immune microenvironment infiltration to decipher the complex regulatory architecture and biological pathways mediated by EIF3M across cancer types. Finally, we used HCC cell lines for in vitro functional validation, determining how EIF3M expression modulates malignant phenotypic behaviors in hepatocellular carcinoma.

RESULTS: EIF3M was overexpressed in multiple cancers and correlated with advanced tumor stage and poor survival. Its dysregulation was primarily driven by gene amplification and regulated by promoter methylation and miRNAs. EIF3M functioned as a hub in cell cycle and transcriptional networks and was linked to an immunosuppressive microenvironment. In hepatocellular carcinoma models, EIF3M modulated tumor proliferation, migration, and activated oncogenic pathways like Wnt/β-catenin.

CONCLUSION: This study reveals that EIF3M expression correlates with immune infiltration and poor prognosis in multiple cancers. In vitro experiments in hepatocellular carcinoma models demonstrated that EIF3M critically regulates malignant cell behaviors. Collectively, our findings highlight EIF3M's value as a promising pan-cancer biomarker worthy of further investigation for its utility in prognosis prediction and as an indicator of immunotherapeutic response.

PMID:41341921 | PMC:PMC12669982 | DOI:10.3389/fmolb.2025.1697083

Harnessing human-AI collaboration for an AI roadmap that moves beyond pilots

The past year has marked a turning point in the corporate AI conversation. After a period of eager experimentation, organizations are now confronting a more complex reality: While investment in AI has never been higher, the path from pilot to production remains elusive. Three-quarters of enterprises remain stuck in experimentation mode, despite mounting pressure to convert early tests into operational gains.

“Most organizations can suffer from what we like to call PTSD, or process technology skills and data challenges,” says Shirley Hung, partner at Everest Group. “They have rigid, fragmented workflows that don’t adapt well to change, technology systems that don’t speak to each other, talent that is really immersed in low-value tasks rather than creating high impact. And they are buried in endless streams of information, but no unified fabric to tie it all together.”

The central challenge, then, lies in rethinking how people, processes, and technology work together.

Across industries as different as customer experience and agricultural equipment, the same pattern is emerging: Traditional organizational structures—centralized decision-making, fragmented workflows, data spread across incompatible systems—are proving too rigid to support agentic AI. To unlock value, leaders must rethink how decisions are made, how work is executed, and what humans should uniquely contribute.

“It is very important that humans continue to verify the content. And that is where you’re going to see more energy being put into,” Ryan Peterson, EVP and chief product officer at Concentrix.

Much of the conversation centered on what can be described as the next major unlock: operationalizing human-AI collaboration. Rather than positioning AI as a standalone tool or a “virtual worker,” this approach reframes AI as a system-level capability that augments human judgment, accelerates execution, and reimagines work from end to end. That shift requires organizations to map the value they want to create; design workflows that blend human oversight with AI-driven automation; and build the data, governance, and security foundations that make these systems trustworthy.

“My advice would be to expect some delays because you need to make sure you secure the data,” says Heidi Hough, VP for North America aftermarket at Valmont. “As you think about commercializing or operationalizing any piece of using AI, if you start from ground zero and have governance at the forefront, I think that will help with outcomes.”

Early adopters are already showing what this looks like in practice: starting with low-risk operational use cases, shaping data into tightly scoped enclaves, embedding governance into everyday decision-making, and empowering business leaders, not just technologists, to identify where AI can create measurable impact. The result is a new blueprint for AI maturity grounded in reengineering how modern enterprises operate.

“Optimization is really about doing existing things better, but reimagination is about discovering entirely new things that are worth doing,” says Hung.

Watch the webcast.

This webcast is produced in partnership with Concentrix.

This content was produced by Insights, the custom content arm of MIT Technology Review. It was not written by MIT Technology Review’s editorial staff. It was researched, designed, and written by human writers, editors, analysts, and illustrators. This includes the writing of surveys and collection of data for surveys. AI tools that may have been used were limited to secondary production processes that passed thorough human review.

A typology of physician input approaches to using AI chatbots for clinical decision-making

npj Digital Medicine, Published online: 05 December 2025; doi:10.1038/s41746-025-02184-y

A typology of physician input approaches to using AI chatbots for clinical decision-making

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

A Definition of AGI

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

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

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

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

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.

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

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.
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