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.

arXiv:2509.25721v3 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.

arXiv:2511.18274v1 Announce Type: cross Abstract: Digital health interventions are increasingly used in physical and occupational therapy to deliver home exercise programs via sensor equipped devices such as smartphones, enabling remote monitoring of adherence and performance. However, digital interventions are typically programmed as software before clinical encounters as libraries of parametrized exercise modules targeting broad patient populations. At the point of care, clinicians can only select modules and adjust a narrow set of parameters like repetitions, so patient specific needs that emerge during encounters, such as distinct movement limitations, and home environments, are rarely reflected in the software. We evaluated a digital intervention paradigm that uses large language models (LLMs) to translate clinicians' exercise prescriptions into intervention software. In a prospective single arm feasibility study with 20 licensed physical and occupational therapists and a standardized patient, clinicians created 40 individualized upper extremity programs (398 instructions) that were automatically translated into executable software. Our results show a 45% increase in the proportion of personalized prescriptions that can be implemented as software compared with a template based benchmark, with unanimous consensus among therapists on ease of use. The LLM generated software correctly delivered 99.78% (397/398) of instructions as prescribed and monitored performance with 88.4% (352/398) accuracy, with 90% (18/20) of therapists judged it safe to interact with patients, and 75% (15/20) expressed willingness to adopt it. To our knowledge, this is the first prospective evaluation of clinician directed intervention software generation with LLMs in healthcare, demonstrating feasibility and motivating larger trials to assess clinical effectiveness and safety in real patient populations.

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:2511.11275v2 Announce Type: replace Abstract: An ever increasing number of high-stake decisions are made or assisted by automated systems employing brittle artificial intelligence technology. There is a substantial risk that some of these decision induce harm to people, by infringing their well-being or their fundamental human rights. The state-of-the-art in AI systems makes little effort with respect to appropriate documentation of the decision process. This obstructs the ability to trace what went into a decision, which in turn is a prerequisite to any attempt of reconstructing a responsibility chain. Specifically, such traceability is linked to a documentation that will stand up in court when determining the cause of some AI-based decision that inadvertently or intentionally violates the law. This paper takes a radical, yet practical, approach to this problem, by enforcing the documentation of each and every component that goes into the training or inference of an automated decision. As such, it presents the first running workflow supporting the generation of tamper-proof, verifiable and exhaustive traces of AI decisions. In doing so, we expand the DBOM concept into an effective running workflow leveraging confidential computing technology. We demonstrate the inner workings of the workflow in the development of an app to tell poisonous and edible mushrooms apart, meant as a playful example of high-stake decision support.

Nature Biotechnology, Published online: 06 November 2025; doi:10.1038/s41587-025-02895-3

Engineered DNA recombinases efficiently and specifically insert genetic cargos without the use of landing pads.

Nature, Published online: 05 November 2025; doi:10.1038/s41586-025-09716-2

The Fair Human-Centric Image Benchmark (FHIBE, pronounced ‘Feebee’)—an image dataset that implements best practices for consent, privacy, compensation, safety, diversity and utility—can be used responsibly as a fairness evaluation dataset for many human-centric computer vision applications.

arXiv:2510.27353v1 Announce Type: new Abstract: Recent studies have suggested that Large Language Models (LLMs) could provide interesting ideas contributing to mathematical discovery. This claim was motivated by reports that LLM-based genetic algorithms produced heuristics offering new insights into the online bin packing problem under uniform and Weibull distributions. In this work, we reassess this claim through a detailed analysis of the heuristics produced by LLMs, examining both their behavior and interpretability. Despite being human-readable, these heuristics remain largely opaque even to domain experts. Building on this analysis, we propose a new class of algorithms tailored to these specific bin packing instances. The derived algorithms are significantly simpler, more efficient, more interpretable, and more generalizable, suggesting that the considered instances are themselves relatively simple. We then discuss the limitations of the claim regarding LLMs' contribution to this problem, which appears to rest on the mistaken assumption that the instances had previously been studied. Our findings instead emphasize the need for rigorous validation and contextualization when assessing the scientific value of LLM-generated outputs.

arXiv:2510.27629v1 Announce Type: cross Abstract: Open-weight bio-foundation models present a dual-use dilemma. While holding great promise for accelerating scientific research and drug development, they could also enable bad actors to develop more deadly bioweapons. To mitigate the risk posed by these models, current approaches focus on filtering biohazardous data during pre-training. However, the effectiveness of such an approach remains unclear, particularly against determined actors who might fine-tune these models for malicious use. To address this gap, we propose \eval, a framework to evaluate the robustness of procedures that are intended to reduce the dual-use capabilities of bio-foundation models. \eval assesses models' virus understanding through three lenses, including sequence modeling, mutational effects prediction, and virulence prediction. Our results show that current filtering practices may not be particularly effective: Excluded knowledge can be rapidly recovered in some cases via fine-tuning, and exhibits broader generalizability in sequence modeling. Furthermore, dual-use signals may already reside in the pretrained representations, and can be elicited via simple linear probing. These findings highlight the challenges of data filtering as a standalone procedure, underscoring the need for further research into robust safety and security strategies for open-weight bio-foundation models.

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:2510.22003v1 Announce Type: cross Abstract: Generative AI (GenAI) is reshaping enterprise architecture work in agile software organizations, yet evidence on its effects remains scattered. We report a systematic literature review (SLR), following established SLR protocols of Kitchenham and PRISMA, of 1,697 records, yielding 33 studies across enterprise, solution, domain, business, and IT architect roles. GenAI most consistently supports (i) design ideation and trade-off exploration; (ii) rapid creation and refinement of artifacts (e.g., code, models, documentation); and (iii) architectural decision support and knowledge retrieval. Reported risks include opacity and bias, contextually incorrect outputs leading to rework, privacy and compliance concerns, and social loafing. We also identify emerging skills and competencies, including prompt engineering, model evaluation, and professional oversight, and organizational enablers around readiness and adaptive governance. The review contributes with (1) a mapping of GenAI use cases and risks in agile architecting, (2) implications for capability building and governance, and (3) an initial research agenda on human-AI collaboration in architecture. Overall, the findings inform responsible adoption of GenAI that accelerates digital transformation while safeguarding architectural integrity.

arXiv:2510.22620v1 Announce Type: cross Abstract: AI agents powered by large language models (LLMs) are being deployed at scale, yet we lack a systematic understanding of how the choice of backbone LLM affects agent security. The non-deterministic sequential nature of AI agents complicates security modeling, while the integration of traditional software with AI components entangles novel LLM vulnerabilities with conventional security risks. Existing frameworks only partially address these challenges as they either capture specific vulnerabilities only or require modeling of complete agents. To address these limitations, we introduce threat snapshots: a framework that isolates specific states in an agent's execution flow where LLM vulnerabilities manifest, enabling the systematic identification and categorization of security risks that propagate from the LLM to the agent level. We apply this framework to construct the $\operatorname{b}^3$ benchmark, a security benchmark based on 194331 unique crowdsourced adversarial attacks. We then evaluate 31 popular LLMs with it, revealing, among other insights, that enhanced reasoning capabilities improve security, while model size does not correlate with security. We release our benchmark, dataset, and evaluation code to facilitate widespread adoption by LLM providers and practitioners, offering guidance for agent developers and incentivizing model developers to prioritize backbone security improvements.

arXiv:2510.23241v1 Announce Type: cross Abstract: In this work, we introduce Progressive Growing of Patch Size, an automatic curriculum learning approach for 3D medical image segmentation. Our approach progressively increases the patch size during model training, resulting in an improved class balance for smaller patch sizes and accelerated convergence of the training process. We evaluate our curriculum approach in two settings: a resource-efficient mode and a performance mode, both regarding Dice score performance and computational costs across 15 diverse and popular 3D medical image segmentation tasks. The resource-efficient mode matches the Dice score performance of the conventional constant patch size sampling baseline with a notable reduction in training time to only 44%. The performance mode improves upon constant patch size segmentation results, achieving a statistically significant relative mean performance gain of 1.28% in Dice Score. Remarkably, across all 15 tasks, our proposed performance mode manages to surpass the constant patch size baseline in Dice Score performance, while simultaneously reducing training time to only 89%. The benefits are particularly pronounced for highly imbalanced tasks such as lesion segmentation tasks. Rigorous experiments demonstrate that our performance mode not only improves mean segmentation performance but also reduces performance variance, yielding more trustworthy model comparison. Furthermore, our findings reveal that the proposed curriculum sampling is not tied to a specific architecture but represents a broadly applicable strategy that consistently boosts performance across diverse segmentation models, including UNet, UNETR, and SwinUNETR. In summary, we show that this simple yet elegant transformation on input data substantially improves both Dice Score performance and training runtime, while being compatible across diverse segmentation backbones.

Nature Biotechnology, Published online: 21 October 2025; doi:10.1038/s41587-025-02856-w

Multiplexed editing in primary human T cells generates enhanced immune cell therapies.

Nature, Published online: 20 October 2025; doi:10.1038/s41586-025-09713-5

Parity and lactation induce T cell mediated breast cancer protection

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.

Cell Death Discovery, Published online: 16 October 2025; doi:10.1038/s41420-025-02745-w

Evidence of fructose metabolism in colorectal cancer

Background: Peer support (sharing experiences/support with others with the same condition) improves health outcomes among people with cardiovascular disease (CVD), including self-management behaviours and self-efficacy. However, current peer support interventions are diverse. Evidence is lacking on peer support attenders perceptions of benefits and the elements that are considered priorities, especially for digital interventions. Objective: The study objectives were to 1) describe perceived benefits and recommendations for CVD peer support programs from people attending in-person peer support, 2) identify priorities for digital peer support from consumers and clinicians testing a peer support app prototype, and 3) develop a framework to inform future peer support intervention development. Methods: Qualitative methodology was used across two components to address the objectives of this study. In Component 1, semi-structured focus groups were conducted with attenders of established in-person CVD peer support groups, exploring the perceived benefits of peer support and recommendations for future programs. In Component 2, semi-structured interactive workshops with consumers with CVD and semi-structured online interviews with CVD clinicians/researchers were undertaken seeking feedback and recommendations for digital peer support using an exploratory digital CVD peer support application prototype. Data were recorded digitally, transcribed verbatim, and analysed thematically. Findings from both components were iteratively synthesised to inform a digital peer support development framework. Results: In Component 1, 22 participants (age range 29-84 years, male 45%) took part in focus groups. The overarching theme was that peer support provides benefits through sharing experiences. Five themes were refined and defined; (i) peer support provides a way of coping, (ii) peers learn from each other, (iii) peers understand what each other are going through, (iv) the peer community uplifts mood and build confidence, and (v) awareness, flexibility and resources are important for engagement. In Component 2, five participants (age range 55-74 years, male 60%) attended two workshops and eight clinicians/researchers (age range 30-65 years, male 10%) were interviewed. Three themes were refined and defined: (i) autonomy is essential to promote engagement, (ii) safeguarding is important to both users and clinicians, and (iii) interfaces that are simple, easy to use and visually attractive enable use. Priorities identified from both components included greater peer support awareness and uptake, flexibility with timing and family participation, healthcare professional involvement, provision of resources, autonomous features enabling choice, checklists and clinician moderation for safeguarding, and simple to use interfaces. Conclusions: Participants in peer support programs derive benefit from sharing their experience of living with CVD which enable coping, learning, feeling understood and a sense of community. Priorities were synthesised to create a framework for digital peer support development for future peer support with recommendations to focus on six key areas: uptake, flexibility, resources, autonomy, safeguarding and interface.

Science, Ahead of Print.