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9 recordsLinked to original sources
PubMed2026

CAUSAL artificial intelligence and data-driven decision intelligence in personalized medicine: a review of healthcare informatics systems.

This review examines the integration of causal artificial intelligence (AI) and data-driven decision intelligence within healthcare informatics systems to advance personalized medicine and clinical decision-making. A narrative review methodology was employed, synthesizing interdisciplinary literature from major databases, including PubMed, Scopus, Web of Science, IEEE Xplore, and ScienceDirect. Studies focusing on causal inference, decision intelligence, and healthcare informatics applications in personalized medicine were included. Data were extracted on methodological approaches, healthcare settings, analytical techniques, and clinical applications, followed by thematic synthesis. Findings indicate that causal AI enhances clinical decision support by enabling estimation of treatment effects and simulation of intervention outcomes at the individual patient level. Integration of multimodal health data such as electronic health records, genomic data, and real-time monitoring improves prediction accuracy and supports tailored treatment strategies. Additionally, causal models improve interpretability, fostering clinician trust and facilitating transparent decision-making. Robust healthcare informatics infrastructures, including interoperable systems and data warehouses, were identified as critical enablers of causal analytics. Overall, causal AI represents a transformative advancement in healthcare analytics, supporting more informed, individualized, and evidence-based clinical decisions. Its integration within healthcare informatics systems has significant potential to improve patient outcomes and guide the future of intelligent, personalized healthcare delivery.

Precision Medicine↗
PubMed2026

Emulated trial of artificial intelligence use and subsequent depressive outcomes in a survey of US adults.

BACKGROUND: Generative artificial intelligence (AI) use has been suggested to have adverse mental health consequences but a causal relationship has not been examined. OBJECTIVE: To simulate a randomised controlled trial of AI use in a work, school or personal context by applying target trial emulation to multiple waves of data from a nationally representative survey. METHODS: We conducted a target trial emulation using non-probability survey data from three waves of a nationally representative survey conducted between 18 June 2024 and 8 January 2025. Participants aged ≥18 years reported generative AI use frequency at baseline. High-frequency use was defined as multiple times per week or more. The primary outcome was depressive symptom severity measured using the Patient Health Questionnaire 9-item (PHQ-9) at follow-up. Generalised causal forests assessed heterogeneity of treatment effects. FINDINGS: Among 19 099 participants assessed at baseline, 2862 (15.0%) reported AI use at least multiple times per week. A subset of 3109 (16.3%) returned for follow-up. In the primary weighted analysis, high-frequency use was not significantly associated with change in PHQ-9 score at follow-up (mean difference -0.18, 95% CI -0.94 to 0.59; p=0.65). Multiple sensitivity analyses using alternate outcome definitions also did not identify significant causal effects. Generalised causal forests yielded no significant evidence of heterogeneity of effect (p=0.81). CONCLUSIONS: In an emulated randomised trial among US adults, generative AI use was not associated with subsequent depressive symptoms. This result does not support the premise that AI use causes greater depressive symptoms, although adverse outcomes among vulnerable individuals cannot be excluded. CLINICAL IMPLICATIONS: AI use is unlikely to cause increased depressive symptoms among most US adults. Continued monitoring should clarify potential risks among vulnerable populations.

Humans↗
PubMed2026

Exposome influences: a multi-omics perspective on the combined toxic effects of pharmaceuticals and personal care products in Alzheimer's disease.

According to WHO data, approximately 57 million people worldwide were affected by dementia in 2021, with prevalence projected to rise. Alzheimer's disease (AD), responsible for 60%-80% of dementia cases, continues to be a leading cause of mortality, with current treatments offering limited efficacy and disease-modifying therapies lacking widespread adoption or conclusive safety evidence, shifting the focus toward prevention and risk modification. Risk factors for AD include both non-modifiable elements, such as age, genetics, and gender, and modifiable factors, like environmental pollution, health status, and diet. While age remains the primary non-modifiable risk factor, early-onset dementia represents only up to 9% of cases. Addressing modifiable factors is essential, as it could prevent or delay almost half of dementia cases, with interventions-such as increased physical activity, smoking cessation, alcohol limitation, and overall health management-being significantly associated with a reduced risk. In this context, the exposome approach offers a comprehensive, integrative framework in which both modifiable and non-modifiable risk factors interact to influence individual susceptibility. Within the neural exposome, chronic low-dose exposure to xenobiotics-such as industrial chemicals, pesticides, metals, pharmaceuticals and personal care products (PPCPs), and air pollutants-may induce neurodegeneration via mechanisms including oxidative stress, neuroinflammation, proteinopathies, and epigenetic modifications, although establishing causality remains challenging. Integration of genomics, transcriptomics, proteomics, metabolomics, and lipidomics, combined with artificial intelligence (AI) techniques such as machine learning (ML) and deep learning (DL), provides promising avenues for biomarker discovery, enhanced preventive strategies, early non-invasive diagnosis, and therapeutic target identification by integrating multi-layered biological data with exposure profiles. This review highlights emerging AD risk factors-including PPCPs-underscoring complex, multifactorial nature of AD and exposome, and the requirement for an interdisciplinary research approach, while also addressing several critical research gaps and methodological limitations.

Alzheimer’s disease↗
PubMed2026

Mechanistic Perspectives From Genomics and Pangenomics of Medicinal and Aromatic Plants: Linking Genome Architecture to Phytochemical Diversity.

Medicinal and aromatic plants (MAPs) produce a remarkable diversity of specialized metabolites with significant pharmaceutical, nutraceutical, and industrial value. Although advances in long-read sequencing, chromosome-scale genome assembly, and pangenomics have greatly expanded genomic resources, the mechanistic links between genome architecture and phytochemical diversity remain incompletely understood. The present review synthesizes current evidence describing how structural genomic variation may contribute to phytochemical diversity, while acknowledging that many proposed genome-to-metabolite relationships require further experimental validation. Examples illustrate how genome architecture is associated with specialized-metabolite biosynthesis through multiple regulatory processes. However, the strength of supporting evidence varies considerably among MAP species. Moreover, relatively few genome-to-metabolite relationships have been confirmed through direct functional validation. We further discuss how pangenomics, multiomics integration, genome editing, synthetic biology, and artificial intelligence support the discovery, validation, and engineering of specialized metabolic pathways. Casual conclusions are evaluated according to the strength of available evidence, highlighting where causal relationships have been experimentally established and where conclusions remain primarily association-based. Overall, this review provides an integrated conceptual and evidence-based perspective summarizing proposed relationships between genome architecture and phytochemical diversity and outlines future priorities for functional genomics, precision breeding, metabolic engineering, and sustainable utilization of MAPs.

artificial intelligence↗
PubMed2026

Imaging and genomics in stroke.

Imaging after ischemic and hemorrhagic stroke may allow measurement of key phenotypes of injury and recovery for which targeted therapies are still lacking. Such imaging endophenotypes provide quantifiable and heritable biomarkers that can represent mechanistic aspects of disease processes better than clinical measures. Artificial intelligence is allowing extraction of these imaging biomarkers in large cohorts, which can be paired with genomic and other omics data. This will allow the evaluation of what genetic and other biologic variations impact stroke injury and recovery. Integration of these analyses with bioinformatics tools (such as Mendelian randomization and multi-trait analysis) could further dissect how stroke complications overlap with other biologic processes and how they may be causally linked to risk factors. Further work is required to confirm the translational impact of these methods in elucidating mechanisms and drug targets for stroke. However, global collaborations are accelerating analyses on large multi-ethnic stroke cohorts, with availability of imaging data facilitated by federally-funded repositories such as the Imaging Repository for the Cerebrovascular Disease Knowledge Portal (iCDKP).

Humans↗
PubMed2026

Architectural logic of the 3D genome: mechanisms of dysregulation and emerging cancer therapeutics.

The three-dimensional (3D) genome provides an essential layer of organization that shapes genome function in space and time. Chromatin compartments and topologically associating domains (TADs) arise from the interplay between intrinsic properties of chromatin and architectural factors, including cohesin and CTCF. Despite substantial progress in defining these structural features, whether 3D genome architecture plays a causal role in regulating processes such as transcription, DNA replication, and DNA repair, or instead reflects underlying regulatory activity, remains unresolved. Here, we use the distinction between chromatin-intrinsic features and architectural factors as a framework to evaluate evidence for causality in genome structure-function relationships. We extend this framework to cancer, where both intrinsic alterations (including noncoding mutations, structural variants, and changes in chromatin state) and architectural factor perturbations (such as mutations in architectural proteins and dysregulation of transcriptional machinery) disrupt genome organization and contribute to disease progression. These findings suggest that alterations in genome structure can, in some contexts, actively reshape oncogenic programs. A major limitation in applying 3D genome insights to cancer biology is the cost and complexity of omics assays. Recent advances in artificial intelligence (AI) and machine learning (ML) enable inference and prediction of 3D genome organization from sequence and epigenomic features, providing insight into the extent to which genome folding is encoded intrinsically versus dynamically regulated in architectural factors. This perspective provides a unified view of how genome structure is established, how it relates to function, and how its disruption contributes to tumorigenesis.

3D genome↗
PubMed2026

Beyond data and technology: the need for new thinking to enable the era of precision prevention.

BACKGROUND: Global flagship initiatives increasingly advocate for proactive health maintenance to alleviate the growing burden on reactive, disease-focused healthcare systems. Precision prevention is conceived as the targeted modulation of causal pathways across the disease continuum, from latent risk and pre-disease states to clinical manifestation, surpassing conventional public health prevention strategies that prioritise managing population-level risk factors. Traditional discovery and implementation models, however, remain poorly aligned with the pace and breadth of scientific and technological advances. This review outlines key barriers to scaling precision prevention and argues for the integration of conceptual, methodological, and policy perspectives into a single implementation‑oriented framework. MAIN: Individualised risk stratification lies at the core of precision prevention. Genomics serves as a stable substrate for lifetime susceptibility assessment, while meaningful prediction in multifactorial chronic disease requires additional risk monitoring using dynamic intermediate molecular markers and high-resolution exposomic data. Machine learning and other artificial intelligence (AI) methods are increasingly helpful tools for integrating large, heterogeneous and temporally structured real-world data to generate personalised predictions of health trajectories. Trustworthy AI-enabled risk prediction or decision-support systems are expected to provide transparency about model logic, assumptions and performance. In discovery, existing diagnostic classifications and conventional case-control designs can obscure mechanistic heterogeneity. Shifting toward precision phenotyping and biologically grounded disease redefinition could reveal a new layer of molecular understanding. Evidence generation strategies that reflect the temporal change of disease, including high‑risk enrichment, surrogate endpoints, and adaptive, trajectory-based monitoring, are particularly important for common conditions with prolonged latency periods (e.g., cancer, cardiovascular disease). Features often dismissed as "noise", such as stochastic molecular variation and minimal exposures, may in fact encode meaningful individual-level signals and thus merit investigation. CONCLUSION: To shift healthcare from reactive treatment toward proactive health maintenance requires coordinated action from stakeholders to reshape the pillars of discovery, reform outcome assessments and modernise implementation strategies.

Humans↗
PubMed2025

Modeling unknowns: A vision for uncertainty-aware machine learning in healthcare.

The integration of machine learning (ML) into healthcare is accelerating, driven by the proliferation of biomedical data and the promise of data-driven clinical support. A key challenge in this context is managing the pervasive uncertainty inherent in medical reasoning and decision-making. Despite its recognized importance, uncertainty is often underrepresented in the design and evaluation of clinical AI systems. Here we report an editorial overview of a special issue dedicated to uncertainty modeling in medical AI, which gathers theoretical, methodological, and practical contributions addressing this critical gap. Across these works, authors reveal that fewer than 4% of studies address uncertainty explicitly, and propose alternative design principles-such as optimizing for clinical net benefit or embedding explainability with confidence estimates. Notable contributions include the RelAI system for real-time prediction reliability, empirical findings on how uncertainty communication shapes clinical interpretation, and benchmarks for out-of-distribution detection in tabular data. Furthermore, this issue highlights the use of causal reasoning and anomaly detection to enhance system robustness and accountability. Together, these studies argue that representing, communicating, and operationalizing uncertainty are essential not only for clinical safety but also for building trust in AI-driven care. This special issue thus repositions uncertainty from a limitation to a foundational asset in the responsible deployment of ML in healthcare.

Machine Learning↗
PubMed2026

Reimagining research papers as interactive and reliable AI agents.

Here we introduce Paper2Agent, an automated framework that converts research papers into artificial intelligence (AI) agents. Paper2Agent transforms research output from passive artefacts into active systems that accelerate use and discovery. Conventional research papers require readers to understand and adapt the paper's code, data and methods to their work, creating barriers to dissemination and reuse. Paper2Agent addresses this challenge by converting a paper into an AI agent that functions as a virtual corresponding author, exposing its manuscript, supplementary materials, datasets, code and workflows as active, agent-native knowledge rather than static text. It analyses the paper and codebase using multiple agents to construct a model context protocol (MCP) server, then generates and runs tests to refine and increase robustness of the MCP. These paper MCPs can be connected to a chat agent (such as Claude Code) to carry out complex scientific queries through natural language while invoking tools and workflows from the paper. We demonstrate Paper2Agent's effectiveness through case studies. Paper2Agent created an agent that leveraged AlphaGenome1 to interpret genomic variants and agents based on Scanpy2 and TISSUE (transcript imputation with spatial single-cell uncertainty estimation)3 to conduct single-cell and spatial transcriptomics analyses. We validate that these agents reproduce the results of the original papers and carry out novel user queries. Paper2Agent created multiple agents that collaborate to prioritize a causal gene for psoriasis. By turning static papers into interactive AI agents, Paper2Agent introduces a paradigm for knowledge dissemination and a collaborative ecosystem of AI co-scientists.

Journal Article↗