arXiv:2609.12464v1 Announce Type: new Abstract: As enterprises modernize legacy monolithic systems to microservices, Large Language Models (LLMs) are heavily utilized for automated code translation. However, traditional vector-based Retrieval-Augmented Generation (Standard RAG) struggles to capture topological relationships. It fetches isolated chunks that sever inheritance chains, leading to high compilation failure rates. This paper introduces a Hierarchical Context-Resident Graph (HCRG) methodology to resolve these limitations. Our pipeline uses tree-sitter for Abstract Syntax Tree (AST) extraction, maps architectural edges into a Google Cloud Spanner Property Graph, and serializes this structure into a Gemini Context Cache for topological, parent-first code translation. We shift evaluation from naive text-overlap to a custom 7-metric Software Engineering framework. Traditional metrics like CodeBLEU (which scored 91% for both methods) effectively masked Standard RAG's structural failures behind syntactically plausible but broken code. Empirically, Graph RAG decisively mitigates dependency loss: API hallucination rates dropped from 56.4% to 16.2%, Dependency Resolution Quality improved from 34.8% to 65.9%, and Parent-Child Consistency rose from 26.7% to 45.5%. However, Graph RAG introduces specific trade-offs. The dense global context causes defensive over-engineering by the LLM, reducing Cyclomatic Complexity Consistency from 71.6% to 46.7%, and slightly degrades Docstring Preservation (67.0% to 61.0%). Ultimately, while trading code complexity for reduced hallucinations, Graph RAG provides a substantially more viable, architecturally sound path for automated enterprise codebase modernization.

arXiv:2609.12303v1 Announce Type: cross Abstract: Small models are made more capable through distillation from a larger one that shares their tokenization scheme. However, do distilled byte and token models behave similarly in terms of scaling trends as compute and data increases? To enable this comparison, we introduce two variants to efficiently convert token logits to Byte Logits: 1) approximate: Marginalize-It, and 2) exact: End-Of-Token. We then present the first large scale study of overtraining decoder-only dense transformer models varying two dimensions simultaneously: the tokenization scheme (Tokens, Bytes, Bytes w/ eot) and the training objective (Distillation vs. Cross-Entropy), sweeping layer-parameter-matched models with roughly 1 billion parameters up to 1 trillion bytes of data. Across eight benchmarks spanning three categories: Multiple Choice QA, Language Generation, and Machine Translation, we find that Token-1B models outperform byte models (End-Of-Token-1B and Bytes-1B) in the low-FLOP regime but eventually plateau; byte models start worse yet surpass Token-1B models with more compute, reaching a higher downstream task performance ceiling. Extrapolating the average top-1 error vs. validation BPB scaling laws predicts that, asymptotically, distilled End-Of-Token-1B outperforms distilled Token-1B by up to 4%. They are also far more data efficient, matching the performance of distilled Token-1B using only one-sixth of the training data. Moreover, by operating over a small vocabulary of 256 bytes instead of on the order of 100K tokens, they circumvent the need for top-k truncation during logit dumping, while also reducing logit storage costs to roughly one-fifth. Finally, our downstream performance scaling laws predict that our distilled End-Of-Token-1B models asymptotically surpass the Llama 3.2-1B, Gemma-3-1B-pt, and Gemma 2B models on averaged downstream tasks by up to 6.5%, 8.1%, and 2.1%, respectively.

npj Digital Medicine, Published online: 14 September 2026; doi:10.1038/s41746-026-03225-w

Data-driven identification of repurposable drugs for ALS

Nature Medicine, Published online: 14 September 2026; doi:10.1038/s41591-026-04639-5

Trust in clinical artificial intelligence (AI) cannot be benchmarked into existence. It must be earned through rigorous prospective studies in real-world clinical settings, where the hardest lessons often concern the humans and systems around the AI, not the technology itself.

Bispecific antibodies pairing a shared 4-1BB epitope with non-overlapping HER2 epitopes drove HER2-dependent 4-1BB clustering, amplifying T-cell activation and tumor growth inhibition. In vivo, this pairing enhanced antitumor efficacy and tumor infiltration, while reducing systemic inflammation compared to urelumab - establishing a generalizable strategy for TNFRSF-targeted immunotherapy.

arXiv:2609.10522v1 Announce Type: cross Abstract: Foundation vision-language models (VLMs) exhibit broad intelligence about the world, yet translating this intelligence into robot control remains challenging. We present Show-Harness, an Embodied Harness that enables VLMs to "play" robots through a compact semantic interface linking intent to action. Show-Harness exposes discrete semantic action units that VLMs can naturally reason over, while embodiment-specific interpreters deterministically ground them into local robot actions, keeping the VLM directly responsible for fine-grained physical decisions. Through the same interface, Show-Harness demonstrates the feasibility of (1) directly unlocking closed-source frontier VLMs for zero-shot robot control, and (2) adapting small-scale open-source VLMs for low-cost deployment with just a few GPU-hours of fine-tuning. We further develop GUMI (GUI Manipulation Interface), which extends the same semantic action space to GUI-based demonstration collection, allowing humans and agents to "play" robots across embodiments without specialized teleoperation hardware. Extensive experiments show that Show-Harness-equipped VLM agents generalize robustly across tasks, embodiments, and environments, outperforming representative agentic and VLA paradigms. These results suggest that the right interface can unlock substantial embodied capability from foundation VLMs, without requiring additional model capacity or costly embodiment-specific pretraining.

arXiv:2608.14673v3 Announce Type: replace Abstract: We assess 18 chapter-specific reviews of the ten mathematical results announced by OpenAI on 1 August 2026, alongside review standards, Lean formalizations, subsequent research, and mathematical references. The article audits this review record without claiming a complete reconstruction of all ten proofs. No confirmed substantive mathematical error in a principal result remains in the examined assessments, although review depth varies and some dependencies remain partly checked. Chapter 8 presents the strongest reservation: a specialist review requests major revision of compressed analytic arguments. In Chapter 6, an apparent polarity error was withdrawn after an overbar lost during PDF extraction was recovered from the typeset source. Subsequent research independently reuses the Chapter 3 proof mechanism and confirms that Connes's rigidity conjecture is false, without independently reproducing Chapter 4's stronger infinite-family result. Among the cited follow-ups, Chapter 7 receives the strongest direct theorem-level corroboration through a stronger hardness theorem. Related equality results in Chapter 8 do not verify the analytic inequality proof. Some follow-ups disclose material AI assistance. We argue that confidence should combine formal checking, human reconstruction, independent mathematical use, and a public record supporting correction of both proofs and reviews.

arXiv:2608.30107v2 Announce Type: replace-cross Abstract: Understanding which countries are represented in NLP datasets is essential for identifying gaps, targeting data collection, measuring progress, and informing AI policy. However, geographic metadata is very rarely available, and country-level representation is often hidden behind broad language-level claims. We introduce AtlasNLP, a country-aware atlas of over 13,000 NLP dataset records across normalized NLP task categories, tracking both the populations represented and where datasets are produced. AtlasNLP includes AtlasNLP-Gold, a human-curated reference set, and AtlasNLP-Core, an ACL-derived large-scale collection. Using this resource, we show that (1) dataset coverage is highly uneven across countries and tasks; (2) dataset production and representation are geographically asymmetric; and (3) language coverage does not imply geographic representation. These findings reveal blind spots in current dataset documentation practices and motivate more explicit geographic metadata for country-aware NLP evaluation.

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-10954-1

A specific population of macrophages that express high levels of the enzyme PLA2G2D in tumour-draining lymph nodes is associated with poor prognosis in patients, and inhibiting PLA2G2D improves anti-tumour immunity in mouse models.

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-10968-9

Deep-foam photolithography uses light-controlled polymer foaming to create high-resolution, multifunctional microstructures with tunable optical, wetting and fluid-handling properties for advanced manufacturing applications.

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-11004-6

Integrating satellite-derived war-damage data with text-based fatality records through improvement, enrichment and fusion mitigates limitations inherent in each source, revealing complex violence dynamics beyond fatality-centric paradigms, as case studies from Ukraine and Myanmar illustrate.

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-10979-6

An imaging system developed to record cellular activity throughout the whole body of zebrafish captures cellular organ dynamics and identifies multiple distributed circuits.

Nature, Published online: 09 September 2026; doi:10.1038/s41586-026-11003-7

A proximity-mapping atlas defines tumour-associated proximity antigens, revealing disease-associated membrane spatial communities, and identifies EGFR–CDCP1 as a co-target pair that enhances tumour killing by multispecific therapeutics.

Nature Biotechnology, Published online: 07 September 2026; doi:10.1038/s41587-026-03286-y

Six proteomic clocks are applied in a clinical trial to assess anti-aging effects.

Cell Death Discovery, Published online: 03 September 2026; doi:10.1038/s41420-026-03327-0

Arrest of human spermatogenesis at the pachytene stage is frequently accompanied by disruption of the piRNA pathway

arXiv:2605.24609v1 Announce Type: cross Abstract: Artificial intelligence is increasingly integrated into radiotherapy workflows, yet such pipelines remain vulnerable to out-of-distribution image data that may introduce unexpected behavior in clinical tasks. Deep learning-based anomaly detection for pelvic magnetic resonance imaging (MRI) remains largely unexplored, and transparent evaluation of its feasibility for full automation is limited. We developed and evaluated a fully automated, unsupervised anomaly-detection framework for pelvic and brain MRI. A two-stage framework was trained on reference images from public datasets: LUND-PROBE for pelvic MRI, and IXI, fastMRI, and fastMRI+ for brain MRI. In the first stage, MRI slices were compressed into discrete tokens; in the second, the distribution of normal tokens was modeled. Anomaly evidence was estimated by combining perceptual image differences with token-surprisal scores based on negative log-likelihood. Automated detection was evaluated on pelvic MRI with synthetic global and real clinical anomalies, and on brain MRI with clinically annotated fastMRI+ abnormalities. Sensitivity, specificity, area under the receiver operating characteristic curve (AUC), and false-positive behavior in held-out normal cases were assessed. The framework achieved robust detection across hidden evaluation cohorts, with AUCs of 0.97 (95% CI, 0.95-0.98) and 0.81 (95% CI, 0.74-0.87) for pelvic and brain MRI, respectively. Heatmap analysis showed strong spatial agreement between detected anomalies and ground-truth locations, supporting localization accuracy and interpretability. These results support the potential of unsupervised anomaly detection as an automated MRI quality-control layer for radiotherapy workflows, with transparent visualization of image regions likely to compromise downstream AI-based tasks.

arXiv:2605.25101v1 Announce Type: cross Abstract: In many industrial domains, the Functional Mock-up Interface (FMI) is used to exchange simulation models as Functional Mock-up Units (FMUs) across different partners using various modelling tools. This opens up the possibilities for simulation-based verification and validation using FMUs for ensuring reliable system behaviour. However, deriving effective test oracles for these simulation models remains challenging due to the absence of explicit expected outputs. This limits the applicability of conventional testing approaches, which require access to the internal workings of the systems. Metamorphic testing (MT) addresses this limitation by leveraging metamorphic relations (MRs), but extracting such relations from specifications remains largely a manual and error-prone process. To address this challenge, we propose an LLM-powered multi-agent workflow for specification-based metamorphic testing of FMU-based simulation models. The approach takes functional and interface specifications as input and orchestrates multiple agents to extract requirements and derive MRs. These MRs are expressed using Given-When-Then patterns to structure input conditions (Given), transformations (When), and expected output behaviours (Then). These relations are then used to generate metamorphic test cases, execute simulations, and evaluate output consistency across multiple sessions. We evaluate the approach on a Lube Oil Cooling system FMU, demonstrating its ability to automatically generate meaningful MRs and corresponding test cases. Preliminary results indicate that the proposed workflow can effectively support the systematic verification and validation of dynamic simulation models by reducing manual effort and improving test generation.

arXiv:2502.08047v5 Announce Type: replace Abstract: Recent progress in GUI agents has substantially improved visual grounding, yet robust planning remains challenging, particularly when the environment deviates from a canonical initial state. In real applications, users often invoke assistance mid-workflow, where software may be partially configured, steps may have been executed in different orders, or the interface may differ from its default setup. Such task-state variability is pervasive but insufficiently evaluated in existing GUI benchmarks. To address this gap, we introduce WorldGUI, a benchmark covering ten widely used desktop and web applications with tasks instantiated under diverse, systematically constructed initial states. These variations capture realistic human-computer interaction settings and enable diagnostic evaluation of an agent's ability to recover, adapt plans, and handle non-default contexts. We further present WorldGUI-Agent, a simple and model-agnostic framework that organizes planning and execution around three critique stages, improving reliability in dynamic environments. Experiments demonstrate that state-of-the-art GUI agents exhibit substantial performance degradation under non-default initial conditions, revealing limited robustness and fragile planning behaviors. Our benchmark and framework provide a foundation for developing more adaptable and reliable GUI agents. The code and data are available at https://github.com/showlab/WorldGUI.

arXiv:2512.15922v3 Announce Type: replace Abstract: Despite initial successes and a variety of architectures, retrieval-augmented generation systems still struggle to reliably retrieve and connect the multi-step evidence required for complicated reasoning tasks. Most of the standard RAG frameworks regard all retrieved information as equally reliable, overlooking the varying credibility and interconnected nature of large textual corpora. GraphRAG approaches offer potential improvement to RAG systems by integrating knowledge graphs, which structure information into nodes and edges, capture entity relationships, and enable multi-step logical traversal. However, GraphRAG is not always an ideal solution, as it depends on high-quality graph representations of the corpus. Such representations usually rely on manually curated knowledge graphs, which are costly to construct and update, or on automated graph-construction pipelines that are often unreliable. Moreover, systems following this paradigm typically use large language models to guide graph traversal and evidence retrieval. In this paper, we propose a novel RAG framework that uses a spreading activation algorithm to retrieve information from a corpus of documents connected by an automatically constructed heterogeneous knowledge graph. This approach reduces reliance on semantic knowledge graphs, which are often incomplete due to information loss during information extraction, avoids LLM-guided graph traversal, and improves performance on multi-hop question answering. Experiments show that our method achieves better or comparable performance to several state-of-the-art RAG methods and can be integrated as a plug-and-play module with different iterative RAG pipelines. When combined with chain-of-thought iterative retrieval, it yields up to a 39% absolute improvement in answer correctness over naive RAG, while achieving these results with small open-weight language models.