Nature, Published online: 10 December 2025; doi:10.1038/s41586-025-09792-4

High-depth sequencing of non-cancerous tissue from patients with metastatic cancer reveals single-base mutational signatures of alcohol, smoking and cancer treatments, and reveals how exogenous factors, including cancer therapies, affect somatic cell evolution.

WASHINGTON — Congress is poised to pass the Biosecure Act after two years of incremental changes that watered down the bill’s curbs on Chinese biotechs and made the law more palatable for U.S. biopharma companies. 

The House passed a defense budget bill today that includes Biosecure, which restricts how U.S. pharmaceutical and biotechnology companies do business with Chinese companies that are determined to be working with the Chinese military and Communist Party. It also aims to prevent those companies from acquiring Americans’ sensitive genetic data. 

The Senate is expected to vote next week on the National Defense Authorization Act, including Biosecure. Congress has passed the NDAA each year for several decades. 

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arXiv:2512.00949v1 Announce Type: cross Abstract: For patients undergoing systemic cancer therapy, the time between clinic visits is full of uncertainties and risks of unmonitored side effects. To bridge this gap in care, we developed and prospectively trialed a multi-modal AI framework for remote patient monitoring (RPM). This system integrates multi-modal data from the HALO-X platform, such as demographics, wearable sensors, daily surveys, and clinical events. Our observational trial is one of the largest of its kind and has collected over 2.1 million data points (6,080 patient-days) of monitoring from 84 patients. We developed and adapted a multi-modal AI model to handle the asynchronous and incomplete nature of real-world RPM data, forecasting a continuous risk of future adverse events. The model achieved an accuracy of 83.9% (AUROC=0.70). Notably, the model identified previous treatments, wellness check-ins, and daily maximum heart rate as key predictive features. A case study demonstrated the model's ability to provide early warnings by outputting escalating risk profiles prior to the event. This work establishes the feasibility of multi-modal AI RPM for cancer care and offers a path toward more proactive patient support.(Accepted at Europe NeurIPS 2025 Multimodal Representation Learning for Healthcare Workshop)

arXiv:2504.07139v3 Announce Type: replace Abstract: Welcome to the eighth edition of the AI Index report. The 2025 Index is our most comprehensive to date and arrives at an important moment, as AI's influence across society, the economy, and global governance continues to intensify. New in this year's report are in-depth analyses of the evolving landscape of AI hardware, novel estimates of inference costs, and new analyses of AI publication and patenting trends. We also introduce fresh data on corporate adoption of responsible AI practices, along with expanded coverage of AI's growing role in science and medicine. Since its founding in 2017 as an offshoot of the One Hundred Year Study of Artificial Intelligence, the AI Index has been committed to equipping policymakers, journalists, executives, researchers, and the public with accurate, rigorously validated, and globally sourced data. Our mission has always been to help these stakeholders make better-informed decisions about the development and deployment of AI. In a world where AI is discussed everywhere - from boardrooms to kitchen tables - this mission has never been more essential. The AI Index continues to lead in tracking and interpreting the most critical trends shaping the field - from the shifting geopolitical landscape and the rapid evolution of underlying technologies, to AI's expanding role in business, policymaking, and public life. Longitudinal tracking remains at the heart of our mission. In a domain advancing at breakneck speed, the Index provides essential context - helping us understand where AI stands today, how it got here, and where it may be headed next. Recognized globally as one of the most authoritative resources on artificial intelligence, the AI Index has been cited in major media outlets such as The New York Times, Bloomberg, and The Guardian; referenced in hundreds of academic papers; and used by policymakers and government agencies around the world.

arXiv:2511.09894v2 Announce Type: replace Abstract: Emergency Medical Services (EMS) are critical to patient survival in emergencies, but first responders often face intense cognitive demands in high-stakes situations. AI cognitive assistants, acting as virtual partners, have the potential to ease this burden by supporting real-time data collection and decision making. In pursuit of this vision, we introduce EgoEMS, the first end-to-end, high-fidelity, multimodal, multiperson dataset capturing over 20 hours of realistic, procedural EMS activities from an egocentric view in 233 simulated emergency scenarios performed by 62 participants, including 46 EMS professionals. Developed in collaboration with EMS experts and aligned with national standards, EgoEMS is captured using an open-source, low-cost, and replicable data collection system and is annotated with keysteps, timestamped audio transcripts with speaker diarization, action quality metrics, and bounding boxes with segmentation masks. Emphasizing realism, the dataset includes responder-patient interactions reflecting real-world emergency dynamics. We also present a suite of benchmarks for real-time multimodal keystep recognition and action quality estimation, essential for developing AI support tools for EMS. We hope EgoEMS inspires the research community to push the boundaries of intelligent EMS systems and ultimately contribute to improved patient outcomes.

npj Digital Medicine, Published online: 12 November 2025; doi:10.1038/s41746-025-02013-2

Equipping mathematical models for hospital dynamics using information theory

arXiv:2511.04698v1 Announce Type: cross Abstract: The early detection of mental health disorders from social media text is critical for enabling timely support, risk assessment, and referral to appropriate resources. This work introduces multiMentalRoBERTa, a fine-tuned RoBERTa model designed for multiclass classification of common mental health conditions, including stress, anxiety, depression, post-traumatic stress disorder (PTSD), suicidal ideation, and neutral discourse. Drawing on multiple curated datasets, data exploration is conducted to analyze class overlaps, revealing strong correlations between depression and suicidal ideation as well as anxiety and PTSD, while stress emerges as a broad, overlapping category. Comparative experiments with traditional machine learning methods, domain-specific transformers, and prompting-based large language models demonstrate that multiMentalRoBERTa achieves superior performance, with macro F1-scores of 0.839 in the six-class setup and 0.870 in the five-class setup (excluding stress), outperforming both fine-tuned MentalBERT and baseline classifiers. Beyond predictive accuracy, explainability methods, including Layer Integrated Gradients and KeyBERT, are applied to identify lexical cues that drive classification, with a particular focus on distinguishing depression from suicidal ideation. The findings emphasize the effectiveness of fine-tuned transformers for reliable and interpretable detection in sensitive contexts, while also underscoring the importance of fairness, bias mitigation, and human-in-the-loop safety protocols. Overall, multiMentalRoBERTa is presented as a lightweight, robust, and deployable solution for enhancing support in mental health platforms.

arXiv:2509.19088v3 Announce Type: replace-cross Abstract: Digital representations of individuals ("digital twins") promise to transform social science and decision-making. Yet it remains unclear whether such twins truly mirror the people they emulate. We conducted 19 preregistered studies with a representative U.S. panel and their digital twins, each constructed from rich individual-level data, enabling direct comparisons between human and twin behavior across a wide range of domains and stimuli (including never-seen-before ones). Twins reproduced individual responses with 75% accuracy and seemingly low correlation with human answers (approximately 0.2). However, this apparently high accuracy was no higher than that achieved by generic personas based on demographics only. In contrast, correlation improved when twins incorporated detailed personal information, even outperforming traditional machine learning benchmarks that require additional data. Twins exhibited systematic strengths and weaknesses - performing better in social and personality domains, but worse in political ones - and were more accurate for participants with higher education, higher income, and moderate political views and religious attendance. Together, these findings delineate both the promise and the current limits of digital twins: they capture some relative differences among individuals but not yet the unique judgments of specific people. All data and code are publicly available to support the further development and evaluation of digital twin pipelines.

npj Digital Medicine, Published online: 05 November 2025; doi:10.1038/s41746-025-02005-2

Evaluating clinical AI summaries with large language models as judges

arXiv:2510.26995v1 Announce Type: cross Abstract: Large language models (LLMs) excel at numerical estimation but struggle to correctly quantify uncertainty. We study how well LLMs construct confidence intervals around their own answers and find that they are systematically overconfident. To evaluate this behavior, we introduce FermiEval, a benchmark of Fermi-style estimation questions with a rigorous scoring rule for confidence interval coverage and sharpness. Across several modern models, nominal 99\% intervals cover the true answer only 65\% of the time on average. With a conformal prediction based approach that adjusts the intervals, we obtain accurate 99\% observed coverage, and the Winkler interval score decreases by 54\%. We also propose direct log-probability elicitation and quantile adjustment methods, which further reduce overconfidence at high confidence levels. Finally, we develop a perception-tunnel theory explaining why LLMs exhibit overconfidence: when reasoning under uncertainty, they act as if sampling from a truncated region of their inferred distribution, neglecting its tails.

arXiv:2510.25935v2 Announce Type: replace-cross Abstract: CodeSight is an end-to-end system designed to anticipate deadline compliance in software development workflows. It captures development and deployment data directly from GitHub, transforming it into process mining logs for detailed analysis. From these logs, the system generates metrics and dashboards that provide actionable insights into PR activity patterns and workflow efficiency. Building on this structured representation, CodeSight employs an LSTM model that predicts remaining PR resolution times based on sequential activity traces and static features, enabling early identification of potential deadline breaches. In tests, the system demonstrates high precision and F1 scores in predicting deadline compliance, illustrating the value of integrating process mining with machine learning for proactive software project management.

Nature, Published online: 29 October 2025; doi:10.1038/s41586-025-09686-5

This multi-omic longitudinal analysis of the healthy human peripheral immune system constructs the Human Immune Health Atlas and assembles data on immune cell composition and state changes with age, including responses to cytomegalovirus infection and influenza vaccination.

arXiv:2507.00418v2 Announce Type: replace-cross Abstract: This study presents a benchmarking analysis of the Qualcomm Cloud AI 100 Ultra (QAic) accelerator for large language model (LLM) inference, evaluating its energy efficiency (throughput per watt), performance, and hardware scalability against NVIDIA A100 GPUs (in 4x and 8x configurations) within the National Research Platform (NRP) ecosystem. A total of 12 open-source LLMs, ranging from 124 million to 70 billion parameters, are served using the vLLM framework. Our analysis reveals that QAic achieves competitive energy efficiency with advantages on specific models while enabling more granular hardware allocation: some 70B models operate on as few as 1 QAic card versus 8 A100 GPUs required, with 20x lower power consumption (148W vs 2,983W). For smaller models, single QAic devices achieve up to 35x lower power consumption compared to our 4-GPU A100 configuration (36W vs 1,246W). The findings offer insights into the potential of the Qualcomm Cloud AI 100 Ultra for energy-constrained and resource-efficient HPC deployments within the National Research Platform (NRP).

arXiv:2505.07897v3 Announce Type: replace-cross Abstract: Context lengths for models have grown rapidly, from thousands to millions of tokens in just a few years. The extreme context sizes of modern long-context models have made it difficult to construct realistic long-context benchmarks -- not only due to the cost of collecting million-context tasks but also in identifying realistic scenarios that require significant contexts. We identify code comprehension and repair as a natural testbed and challenge task for long-context models and introduce LongCodeBench (LCB), a benchmark to test LLM coding abilities in long-context scenarios. Our benchmark tests both the comprehension and repair capabilities of LCLMs in realistic and important settings by drawing from real-world GitHub issues and constructing QA (LongCodeQA) and bug fixing (LongSWE-Bench) tasks. We carefully stratify the complexity of our benchmark, enabling us to evaluate models across different scales -- ranging from Qwen2.5 14B Instruct to Google's flagship Gemini model. We find that long-context remains a weakness for all models, with performance drops such as from 29% to 3% for Claude 3.5 Sonnet, or from 70.2% to 40% for Qwen2.5. The LCB dataset is available publicly at https://huggingface.co/datasets/Steefano/LCB and the codebase to replicate the work on this paper at https://github.com/Zteefano/long-code-bench.

Background: In an era marked by the blooming reliance on digital platforms for healthcare consultation, the subreddit r/AskDocs has emerged as a pivotal forum. However, the vast, unstructured nature of forum data presents a formidable challenge; the extraction and meaningful analysis of such data require advanced tools that can navigate the complexities of language and context inherent in user-generated content. Objective: Our objective was to evaluate employing Large Language Models (LLMs) to systematically transform the rich, unstructured textual data from AskDocs into a structured dataset, an approach that aligns more closely with human cognitive processes compared to traditional data extraction methods. Methods: We developed a dataset of Reddit posts from r/AskDocs by extracting key information via human annotators. Then using specially engineered prompts we used state-of-the-art Large Language Models (LLMs) to extract data from posts and compared the results. The variation in the LLMs were further compared to the humans to show similarity. Results: Our findings indicate that LLMs not only match but, in several aspects, surpass even highly educated humans in extracting information, including both demographic and context details, from unstructured texts. Conclusions: This study not only validates the use of LLMs for analyzing digital healthcare communications but also opens new avenues for understanding online behaviors and interactions, signaling a shift towards more sophisticated methodologies in digital research and practice.

Nature, Published online: 20 October 2025; doi:10.1038/d41586-025-03344-6

Biomedical research techniques that don’t involve the use of animals are gaining momentum, but those using innovative approaches still face resistance from some quarters.

Nature Biotechnology, Published online: 17 October 2025; doi:10.1038/s41587-025-02845-z

The interactions of CAR-T cells and solid tumors are modeled on a chip.

Background: Anxiety is one of the most common mental health problems experienced by children worldwide. In the UK, many children experiencing anxiety do not receive adequate or timely help. Children living in economically-disadvantaged areas experience more mental health problems than those living in high income areas and are less able to engage in activities that can have a positive or protective impact on their mental health. The need for providing low-cost, accessible and engaging mental health interventions for children living in these areas is high. Objective: The study aimed to explore how a digital mental health therapeutic, ‘Lumi Nova: Tales of Courage’, could be used to support children living with anxiety in economically-disadvantaged areas. Methods: A mixed method study design was used to explore the implementation of Lumi Nova using a supported delivery model with mental health teams based in the North of England. Quantitative data collection on recruitment and engagement patterns were collected and analysed. Qualitative research explored children, parent and practitioner views and experiences with the Lumi Nova app. Results: 113 children were consented to use Lumi Nova and 98 (87%) accessed the intervention at least once. Qualitative semi-structured interviews found that children, their parents and practitioners viewed the Lumi Nova app positively. Quantitative analysis of the recruitment data suggested the feasibility of a future larger roll-out. Analysis of usage data demonstrated varied patterns of engagement with the intervention. The frequency and duration of usage varied across children, as did the activities completed within the game: almost half (49%) completed three in-game challenges indicating progression through the treatment pathway. Conclusions: The study demonstrated that a digital mental health intervention could be successfully deployed within economically-disadvantaged areas in the UK to support children experiencing anxiety. Expected barriers to the deployment of digital mental health interventions in economically-disadvantaged areas (e.g. lack of access to smartphones, data plans, lack of technical skills) were not reported. Digital mental health interventions have the potential to address current gaps in mental health provision for disadvantaged individuals and communities.

Science, Ahead of Print.