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01.
arXiv (CS.AI) 2026-06-15

TwinBI: An Agentic Digital Twin for Efficient Augmented Interactions with Business Intelligence Dashboards

arXiv:2606.13731v1 Announce Type: new Abstract: Business intelligence (BI) increasingly combines dashboard interaction with LLM-based assistance, but these two modes often fall out of sync during multi-step analysis. As users switch between direct dashboard manipulation and natural-language queries, it becomes difficult to preserve a consistent analytical state across filters, hierarchies, metrics, and chart context. We present TwinBI, an agentic digital-twin framework that couples an LLM-based agent system with an executable BI dashboard state. TwinBI unifies conversational interaction, dashboard manipulation, semantic grounding, and provenance tracking through a shared analytical state reconstructed from a unified interaction log. It also exposes artifacts such as schema views, SQL, logs, and an /insights command for state-grounded analytical summaries. We evaluate TwinBI in two complementary ways. In a controlled A/B benchmark with the same backbone agent, TwinBI improves exact-match accuracy from 43.3% to 63.3%, partial-credit accuracy from 48.3% to 70.8%, and substantially reduces timeout rate from 40.0% to 10.0% relative to Dashboard alone. In a usability study, participants benefited from the integrated dashboard-and-chat workflow, with high task accuracy, moderate workload, and favorable ratings for state-aware interaction mechanisms. These results suggest that TwinBI improves both agent-level analytical reliability and user-facing analytical support by turning visible dashboard state into richer actionable context. Our dataset and source code are available at: https://github.com/simonjisu/TwinBI

02.
arXiv (CS.CV) 2026-06-18

MolmoMotion: Forecasting Point Trajectories in 3D with Language Instruction

Motion forecasting is central to visual intelligence: agents must anticipate how objects will move in order to plan actions, reason about physical interactions, and synthesize realistic futures. We argue that 3D points in world coordinates provide a general representation that is class-agnostic, view-stable, compact, and directly useful for downstream tasks. We formalize the task of goal-conditioned 3D point motion forecasting: given a short visual history, a set of 3D query points on an object of interest, and a language description of the intended goal, the model predicts the future 3D trajectory of each point. We introduce a full stack to study this task at scale: (1) MolmoMotion-1M is a large corpus of action-described, object-grounded 3D point trajectories annotated from 1.16M unconstrained videos; (2) PointMotionBench is a human-verified benchmark spanning 111 object categories and 61 motion types; and (3) MolmoMotion is a general motion forecasting model that supports both autoregressive coordinate prediction and flow-matching-based trajectory generation. MolmoMotion accurately predicts diverse motion patterns with different language instructions, and significantly outperforms existing motion prediction baselines on PointMotionBench. Finally, we show that the learned 3D motion prior transfers well to downstream applications: it improves training efficiency and generalization for robot manipulation, and its predicted trajectories provide effective motion guidance for generative models to synthesize videos with more realistic object motion.

03.
arXiv (CS.CL) 2026-06-12

SkillChain: Closing the Loop on Skill Evolution for Image-Based E-Commerce AI Assistants

Image-based AI assistants are now deployed at production scale on e-commerce platforms, where a single uploaded image can trigger fundamentally different user intents: product search, style recommendation, visual encyclopedia, or utility tool calls, each demanding its own response format, tool invocation, and domain knowledge. Without per-intent behavioral constraints, LLM-based systems conflate these heterogeneous modes and fall short of domain quality standards, while the breadth and dynamism of the intent space render manual engineering infeasible. To address this, we present SkillChain, which closes the production feedback loop on Skill evolution, automating the lifecycle of Skills through three stages: Skill Creator for bootstrapping from task specs and trajectories, Route Optimizer for routing alignment, and Body Refiner for iterative Skill Body refinement via dual-path LLM-Judge evaluation. Deployed on a production-scale e-commerce image assistant, SkillChain substantially improves aggregate response quality, with the strongest gains on structural compliance and content quality; a one-week online A/B experiment further confirms significant gains in user engagement, content consumption, and long-term retention.

04.
arXiv (CS.CL) 2026-06-16

Progressive Knowledge-Guided Large Language Model Framework for Bearing Fault Diagnosis

Vibration-based bearing fault diagnosis requires resolving three interrelated measurement challenges, including the trade-off between global statistical feature efficiency and local transient signal fidelity, insufficient traceability of measurement features to underlying fault physics, and ineffective multi-source measurement information fusion across diagnostic scales. This paper presents a progressive physics-guided multi-scale vibration signal processing framework that addresses all three challenges within a unified diagnostic pipeline. An 81-dimensional measurement descriptor, derived from bearing kinematic theory and characteristic defect frequencies, establishes a physically traceable feature space enabling real-time fault screening at approximately 20 ms per sample. A fault-adaptive signal segmentation mechanism then directs analytical attention toward fault-relevant waveform regions guided by physics-based priors, without manual feature engineering. Structured fault mechanism knowledge is further encoded implicitly in model parameters during training, enabling autonomous multi-scale measurement fusion without external knowledge dependencies at inference. Validated on four public benchmark datasets under diverse operating conditions, the framework achieves 98.49% diagnostic accuracy with a 12.6-fold reduction in computational cost relative to signal-level baselines. Interpretability analysis confirms that diagnostic feature activations align with established bearing fault mechanics, supporting measurement traceability in safety-critical industrial systems.

05.
arXiv (quant-ph) 2026-06-15

Efficient Simulation of Szegedy Quantum Walk Formulations and Algorithms

arXiv:2606.14226v1 Announce Type: new Abstract: Quantum walks provide a versatile framework for quantum algorithms across a wide range of applications. We develop efficient classical simulation methods for Szegedy quantum walks that avoid explicit construction of the full unitary evolution operator. Unlike previous approaches restricted to a particular walk formulation, our framework is built from fundamental update and reflection operators, enabling the simulation of a broader class of Szegedy walk formulations. We further extend these methods to phase-estimation-based algorithms coupled to the walk, including implementations suitable for large sparse graphs. The resulting methods achieve optimal $O(N^2)$ complexity for dense graphs with $N$ nodes. For sparse graphs, the computational cost scales linearly with the number of edges, which is $O(N)$ in many cases. We implement the framework in the Python package SQWLib and illustrate its capabilities through simulations of representative algorithms, including quantum simulated annealing and quantum search on graphs. These results provide a practical tool for studying Szegedy-walk-based algorithms numerically beyond purely analytical treatments.

06.
arXiv (CS.CL) 2026-06-12

MoReBench: Evaluating Procedural and Pluralistic Moral Reasoning in Language Models, More than Outcomes

As AI systems progress, we rely more on them to make decisions with us and for us. To ensure that such decisions are aligned with human values, it is imperative for us to understand not only what decisions they make but also how they come to those decisions. Reasoning language models, which provide both final responses and (partially transparent) intermediate thinking traces, present a timely opportunity to study AI procedural reasoning. Unlike math and code problems which often have objectively correct answers, moral dilemmas are an excellent testbed for process-focused evaluation because they allow for multiple defensible conclusions. To do so, we present MoReBench: 1,000 moral scenarios, each paired with a set of rubric criteria that experts consider essential to include (or avoid) when reasoning about the scenarios. MoReBench contains over 23 thousand criteria including identifying moral considerations, weighing trade-offs, and giving actionable recommendations to cover cases on AI advising humans moral decisions as well as making moral decisions autonomously. Separately, we curate MoReBench-Theory: 150 examples to test whether AI can reason under five major frameworks in normative ethics. Our results show that scaling laws and existing benchmarks on math, code, and scientific reasoning tasks fail to predict models' abilities to perform moral reasoning. Models also show partiality towards specific moral frameworks (e.g., Benthamite Act Utilitarianism and Kantian Deontology), which might be side effects of popular training paradigms. Together, these benchmarks advance process-focused reasoning evaluation towards safer and more transparent AI.

07.
arXiv (quant-ph) 2026-06-17

Engineering entanglement and transport in interacting quantum walks with tailored potentials

arXiv:2606.17825v1 Announce Type: new Abstract: Controlling the interplay between particle propagation and quantum correlation generation is a central challenge in quantum transport. Here, we investigate two distinguishable continuous-time quantum walkers evolving on parallel one-dimensional lattices, interacting via distance-dependent potentials. While on-site interactions reproduce the typical bosonic behaviour, extending the interaction to a linear potential over multiple neighbors introduces controlled Bloch-like oscillations and shifts the bound-pair regime to stronger couplings. More generally, we explore a Coulomb-like interaction parameterized by strength, spatial scaling, and decay rate. This reveals a rich phase diagram including four distinct dynamical regimes: (i) a high-entropy, oscillatory regime akin to a linear potential; (ii) a strongly localized, bound-pair regime; (iii) a novel intermediate regime combining near-ballistic spreading with strong correlations; and (iv) a weakly interacting, free-propagation regime. Notably, regime (iii) achieves concurrent optimization of transport efficiency and entanglement, offering a sweet spot for correlated quantum dynamics. Our results provide a tool for designing interaction-engineered quantum walks with potential applications in quantum information processing and simulations.

08.
arXiv (CS.CL) 2026-06-17

When Multiple Scripts Matter: Evaluating ASR in Clinical Settings

Automatic speech recognition (ASR) in non-English clinical settings is challenged by multiscript variability, where the same term may appear in multiple valid orthographic forms. Conventional string-matching evaluation metrics often underestimate ASR performance by treating orthographic variants as errors. To address this issue, we introduce MultiClin, a clinical ASR benchmark designed to evaluate robustness to multiscript variability. Experiments across diverse ASR models show that multiscript-aware evaluation provides a fairer assessment of recognition quality than conventional single-reference evaluation. We further investigate the impact of script consistency during training and find that inconsistent script mappings increase orthographic uncertainty and hinder model convergence, with a balanced 50% mapping ratio producing the highest entropy. In contrast, script unification consistently yields the best ASR performance. Our dataset and code are publicly available at: https://github.com/aitrics-ronaldo/Interspeech_MultiClin.

09.
arXiv (CS.CL) 2026-06-19

Benchmarking Local LLMs for Natural-Language-to-SQL Querying in Biopharmaceutical Manufacturing: An Empirical Benchmark on Consumer-Grade Hardware

Biopharmaceutical manufacturing organizations operate under regulatory frameworks such as FDA guidance, EU Good Manufacturing Practice (GMP), and the EU AI Act, which can restrict the use of cloud-based artificial intelligence systems. Locally deployed large language models (LLMs) offer a privacy-preserving alternative, but their suitability for pharmaceutical manufacturing tasks remains underexplored. This study evaluates four open-source LLMs (Qwen 2.5 Coder 7B, Llama 3.1 8B, Mistral 7B, and Meditron 7B) deployed locally via Ollama for natural-language-to-SQL generation over a pharmaceutical manufacturing database. A FastAPI-based evaluation platform, PharmaBatchDB AI, was developed using a synthetic Microsoft SQL Server database containing approximately 63,000 records across Batch, Manufacturing Execution System (MES), and Clean-In-Place (CIP) modules. Models were benchmarked on 60 domain-specific natural-language questions using metrics including SQL extraction rate, SQL compliance, factual consistency, ROUGE-L, hallucination rate, throughput, and latency. Qwen 2.5 Coder 7B, Llama 3.1 8B, and Mistral 7B generated SQL for all evaluation tasks, while Meditron 7B failed on nearly all tasks due to context-window limitations and poor SQL generation capability. Llama 3.1 8B achieved the highest SQL compliance, whereas Qwen 2.5 Coder 7B achieved the strongest overall text similarity and factual consistency. Performance differences between the two leading models were not statistically significant. The results show that code-tuned general-purpose LLMs outperform a domain-specific biomedical model on structured query generation for pharmaceutical manufacturing data. Although fully local, GxP-aligned NLQ systems are feasible on consumer hardware, current performance levels still require human oversight and downstream validation for regulated use.

10.
Nature (Science) 2026-06-17

Confined migration induces non-lethal DNA damage in developing neurons

Migratory cells tend to have soft nuclei that deform and penetrate narrow spaces1,2. Extensive nuclear deformation during migration can cause nuclear-envelope rupture and DNA damage in cancer cells, which may contribute to malignant transformation during tumour progression3–6. However, the importance of DNA damage in physiological migration is less well understood. Here we demonstrate that the migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-stranded breaks (DSBs) due to mechanostress during passage through narrow interstitial spaces. In contrast to many other migratory cells, these DSBs occur without detectable nuclear envelope rupture. Confined migration increases topoisomerase-IIβ covalently bound DSBs, and these lesions are repaired through non-homologous end-joining during brain development without causing cell death. Genome sequencing revealed that DSBs tend to occur at transcriptionally inactive regions. The deletion of ligase IV at the onset of neuronal migration leads to persistent DSB accumulation in cerebellar neurons with moderate transcriptional changes in genes related to synaptic function, neuronal development and stress and immune responses. The mutant mouse develops mild motor deficits in later life, suggesting that the DNA damage generated during normal brain development poses a potential disease risk if left unrepaired. The migration of neurons in developing cerebral and cerebellar cortices is accompanied by massive DNA double-strand breaks due to mechanostress during passage through narrow interstitial spaces.

11.
arXiv (CS.LG) 2026-06-15

Running the Gauntlet: Re-evaluating the Capabilities of Agents Beyond Familiar Environments

arXiv:2606.14397v1 Announce Type: new Abstract: As agentic systems continue to evolve and are widely deployed in real-world scenarios, there is a growing demand to faithfully evaluate their capabilities. However, current benchmarks are typically built on popular applications with relatively simple tasks and focus on a narrow set of capabilities while overlooking broader dimensions, resulting in saturated performance on modern agents and failing to probe their limitations. To this end, we introduce GauntletBench, a web-based benchmark for evaluating agent generalisation in challenging scenarios, focusing on three underexplored capabilities (temporal perception, graphical understanding, and 3D reasoning), across five less-covered professional applications (Video Editor, Workflow Builder, 3D Modeller, Flight Analyser, and Circuit Designer), each with 20 vision-intensive tasks (100 in total). Our benchmark provides a modular pipeline that comprises an environment compatible with both open- and closed-source agent frameworks, a controlled web-based application, a well-structured task suite, and an automated evaluation engine with diverse metrics. Contrary to widespread expectations, our empirical results reveal that frontier agentic systems remain far from achieving human-level performance. Even the state-of-the-art agent achieves only a 19.1% success rate on our GauntletBench, highlighting the limitations in these overlooked capabilities and generalisation. By comparison, non-expert human annotators achieve over 80% success on our challenging yet feasible tasks, revealing the substantial gap between current agent capabilities and those required for complex real-world scenarios.

12.
arXiv (CS.AI) 2026-06-18

Skill-MAS: Evolving Meta-Skill for Automatic Multi-Agent Systems

arXiv:2606.18837v1 Announce Type: cross Abstract: Large Language Model (LLM)-based automatic Multi-Agent Systems (MAS) generation has become a crucial frontier for tackling complex tasks. However, existing methods face a dilemma between model capability and experience retention. Inference-time MAS leverages frozen frontier LLMs but repeats identical searches without learning from past experience. Conversely, Training-time MAS internalizes experience via gradient updates but is constrained by the low capability ceiling of smaller models, and is hard to scale to large frontier LLMs. To bridge this gap, we propose Skill-MAS, a novel third path that decouples experience retention from parametric updates by conceptualizing the high-level orchestration capability as an evolvable Meta-Skill. Skill-MAS refines this architectural knowledge through a closed optimization loop: (1) Multi-Trajectory Rollout samples a behavioral distribution for each task under the current Meta-Skill; and (2) Selective Reflection adaptively selects priority tasks and applies hierarchical contrastive analysis to distill systemic experience into generalizable, strategy-level principles. Extensive experiments across four complex benchmarks and four distinct LLMs demonstrate that Skill-MAS not only achieves remarkable performance gains but also maintains a favorable cost-performance trade-off. Further analysis reveals that the evolved Meta-Skills are highly robust and exhibit strong transferability across unseen tasks and different LLMs.

13.
arXiv (CS.AI) 2026-06-12

Deterministic Integrity Gates for LLM-Assisted Clinical Manuscript Preparation: An Auditable Biomedical Informatics Architecture

arXiv:2606.09500v3 Announce Type: replace Abstract: As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).

14.
arXiv (CS.CL) 2026-06-12

Demystifying Hidden-State Recurrence: Switchable Latent Reasoning with On-Policy Reinforcement Learning

Latent chain-of-thought compresses reasoning by replacing visible reasoning traces with continuous hidden-state recurrence, but existing formulations are difficult to optimize with standard on-policy reinforcement learning (RL) and hard to interpret causally. Our key insight is that a single pair of explicit boundary tokens can address both issues at once: discrete entry and exit anchors make the latent block compatible with standard on-policy RL, and the same anchors offer a natural foothold for mechanistic analysis. Motivated by this, we propose SWITCH, a switchable latent reasoning framework. The model emits to enter latent mode and to exit. Because the boundaries are ordinary discrete tokens, the GRPO policy ratio is well-defined at every decision point. The same anchors also expose the latent steps to direct probing and causal intervention. We train the model with a visible-to-latent curriculum and a Switch-GRPO objective that propagates gradients through recurrent latent computation. SWITCH consistently outperforms prior hidden-state-recurrence latent reasoning approaches at similar scale. Mechanistic analysis through the boundary tokens further reveals three findings: (i) is a sharply localised, learned switching policy rather than a stylistic artefact; (ii) the latent step it opens performs problem-specific, causally important computation rather than acting as an inert placeholder; and (iii) that computation is concentrated at a single hidden-state transition on entry. Together, these results show that hidden-state-recurrence latent reasoning is both RL-trainable and open to direct mechanistic analysis, including of how on-policy RL itself improves the model from the inside.

15.
arXiv (CS.AI) 2026-06-16

RoboPIN: Grounded Embodied Reasoning via Pinned Chain-of-Thought

arXiv:2606.15753v1 Announce Type: new Abstract: Embodied reasoning requires models to perceive task-relevant objects and spaces in physical environments and maintain consistent visual grounding throughout multi-step reasoning. However, current vision-language models rely on text-only or coordinate-augmented chain-of-thought, where entity references remain implicit and ambiguous. This may cause the reasoning process to decouple from visual evidence, entity references to drift across steps, and a causal disconnection between the reasoning trajectory and the final answer, with these problems further amplified in multi-view scenarios due to cross-view appearance changes. To address these issues, we propose Pinned Chain-of-Thought (\pincot{}), a structured reasoning paradigm that pins every reasoning step to visual evidence. \pincot{} introduces the concept of \reasoninganchor{}, which binds each task-relevant entity to a structured visual anchor with entity name, unique identity, view index, and spatial grounding, enabling consistent entity tracking across reasoning steps and views. We build a fully automated data generation pipeline to construct \dataset{}, a high-quality \pincot{}-formatted reasoning dataset. We then train \method{} through three-stage post-training that progressively injects embodied knowledge, structured reasoning ability, and process-supervised alignment, with rewards that directly constrain both anchor localization and identity consistency during reasoning. On 14 benchmarks covering embodied spatial reasoning, multi-view reasoning, and pointing, \method{} with only 4B parameters consistently outperforms 7B level open-source embodied models, achieving a 12\% average improvement over the strongest 7B baseline, Mimo-Embodied. Further analysis shows that \pincot{} improves grounding accuracy and cross-step identity consistency, validating the effectiveness of process supervision.

16.
arXiv (CS.CV) 2026-06-16

CoIRL-AD: Collaborative-Competitive Imitation-Reinforcement Learning in Latent World Models for Autonomous Driving

End-to-end autonomous driving models trained with imitation learning (IL) often generalize poorly, particularly in long-tail scenarios where expert demonstrations are sparse. Reinforcement learning (RL) can provide complementary task-level supervision, but applying RL to real-world autonomous driving is challenging in offline settings without interactive simulators, where datasets are dominated by expert actions and provide limited behavioral diversity. We propose CoIRL-AD, a competitive dual-policy framework that integrates IL and RL under a unified offline training regime. CoIRL-AD decouples imitation and reward optimization into separate actors to alleviate objective conflicts, uses imagined future rollouts for long-horizon reward estimation, and introduces a competition mechanism that selectively transfers beneficial behaviors while keeping RL anchored to expert-like driving. Experiments on the nuScenes benchmark show that CoIRL-AD consistently improves robustness over strong IL-based baselines, with especially large gains in cross-city generalization and long-tail scenarios. Code is available at: https://github.com/SEU-zxj/CoIRL-AD.

17.
arXiv (CS.CL) 2026-06-15

Does the Judge Prefer English? Evaluating Language-Switching Invariance in LLM-as-a-Judge

作者:

Large language models (LLMs) are now widely used as automatic judges for open-ended instruction-following evaluation. This practice is convenient, scalable, and often more semantically aware than reference-based metrics, but it also introduces a new reliability question: does a judge evaluate the quality of an answer, or does it also react to the language in which the comparison is presented? We propose Judge-LS, a lightweight meta-evaluation protocol that transforms LLMBar response-pair items into English, Chinese, and Chinese-English language-switched variants. A reliable judge should preserve its preference under label-preserving language transformations and should not prefer a language when two answers are translation-equivalent. We evaluate four API-accessible judges on the full 419-item LLMBar benchmark, producing 13,408 successful pairwise judgments. Across models, Chinese and language-switched presentations induce 10.7–14.4% preference flips relative to English, and all judges achieve their highest accuracy in English. However, translation-equivalent tie probes do not reveal a systematic English preference: most probes are judged as ties, and non-tie decisions more often favor Chinese. We add confidence intervals, paired significance tests, and an automatic transformation audit with a sensitivity analysis that excludes mechanically flagged high-risk variants. The experiment requires no model training, uses only API calls, and is feasible on modest local hardware.

18.
arXiv (CS.CV) 2026-06-12

CPAM: Context-Preserving Adaptive Manipulation for Zero-Shot Real Image Editing

Editing natural images using textual descriptions in text-to-image diffusion models remains a significant challenge, particularly in achieving consistent generation and handling complex, non-rigid objects. Existing methods often struggle to preserve textures and identity, require extensive fine-tuning, and exhibit limitations in editing specific spatial regions or objects while retaining background details. This paper proposes Context-Preserving Adaptive Manipulation (CPAM), a novel zero-shot framework for complicated, non-rigid real image editing. Specifically, we propose a preservation adaptation module that adjusts self-attention mechanisms to preserve and independently control the object and background effectively. This ensures that the objects' shapes, textures, and identities are maintained while keeping the background undistorted during the editing process using the mask guidance technique. Additionally, we develop a localized extraction module to mitigate the interference with the non-desired modified regions during conditioning in cross-attention mechanisms. We also introduce various mask-guidance strategies to facilitate diverse image manipulation tasks in a simple manner. CPAM can be seamlessly integrated with multiple diffusion backbones, including SD1.5, SD2.1, and SDXL, demonstrating strong generalization across different model architectures. Extensive experiments on our newly constructed Image Manipulation BenchmArk (IMBA), a robust benchmark dataset specifically designed for real image editing, demonstrate that our proposed method is the preferred choice among human raters, outperforming existing state-of-the-art editing techniques. The source code and data will be publicly released at the project page: https://vdkhoi20.github.io/CPAM

20.
medRxiv (Medicine) 2026-06-22

National trends and operational drivers of vaccine wastage in Uganda, 2020-2025: a descriptive analysis of four tracer antigens

Background Vaccine wastage reduces immunisation efficiency, increases costs, and complicates supply forecasting. Uganda routinely monitors vaccine use, but national evidence comparing observed wastage with World Health Organization (WHO) and Uganda-specific planning thresholds has been limited. We described national and sub-national trends for four tracer antigens to inform supply-chain planning and forecasting. Methods We conducted a retrospective descriptive analysis of routinely reported immunisation data from Ugandas District Health Information Software 2, 2020-2025. We analysed Bacille Calmette-Guerin (BCG), measles-rubella (MR), oral polio vaccine (OPV), and diphtheria-tetanus-pertussis-containing vaccine (DPT). Vaccine wastage was calculated as the proportion of issued doses not administered. Annual wastage rates were summarised using medians, and temporal trends were assessed using the Mann-Kendall test. Observed wastage was compared with WHO thresholds: BCG[≤]50%, MR[≤]25%, OPV[≤]10%, DPT[≤]15%, and Ugandas planning thresholds: BCG[≤]70%, MR[≤]40%, OPV[≤]15%, DPT[≤]10%. Effective Vaccine Management reports were reviewed to summarise reported reasons for wastage. Results During 2020-2025, median national wastage was 40.6% for BCG, 25.9% for MR, 10.0% for OPV, and 9.2% for DPT. OPV wastage declined from 12.8% in 2020 to 8.0% in 2025, with a significant downward trend ({tau}b=-1.00; p=0.008). OPV and DPT wastage remained largely within their respective Uganda in-country thresholds ([≤]15% and [≤]10%) for most of the study period, while BCG generally remained below the WHO threshold ([≤]50%) and MR frequently exceeded the WHO threshold ([≤]25%) but remained within Uganda's planning threshold ([≤]40%) in most years. The proportion of districts exceeding both WHO and Uganda thresholds declined for OPV from 36.3% to 5.5% (p=0.024) and for DPT from 22.6% to 1.4% (p=0.013). Wastage was consistently higher in lower-level (Health Centre II and III) facilities, compared to hospitals. Among 50 service delivery points, reported reasons included low session attendance (66%), multi-dose vial policy non-compliance (28%), and vaccine expiry (12%). Conclusion Uganda achieved reductions in OPV wastage and district-level improvements in DPT wastage, while BCG and MR remained more variable and frequently had higher wastage. Strengthening adherence to the multi-dose vial policy and improving session planning at lower-level facilities could strengthen vaccine utilisation and forecasting.

21.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

22.
arXiv (CS.AI) 2026-06-16

A Security Analysis of Long-Horizon Agentic AI Systems: Threats, Evaluation, and Framework Development

arXiv:2606.14816v1 Announce Type: cross Abstract: This paper presents a structured analysis of security challenges in long-horizon agentic AI systems. The study reviews existing threats, evaluation approaches, attack propagation mechanisms, and security frameworks. A taxonomy of security threats and a framework for analyzing attack propagation are proposed to support future research in agentic AI security

23.
arXiv (CS.CL) 2026-06-12

Beyond the Commitment Boundary: Probing Epiphenomenal Chain-of-Thought in Large Reasoning Models

Chain-of-thought (CoT) reasoning is the dominant paradigm for inference-time scaling in language models, yet the causal influence of individual steps on the final answer poorly understood. We estimate each step's causal importance via early exit and use this measure to study how answers form across the reasoning traces of several model families. Across diverse tasks, we find that reasoning typically crosses a commitment boundary – a sharp transition from transient intermediate guesses to a stable, high-confidence answer. This transition often happens in a single step, well before the model's reasoning block ends, and is followed by epiphenomenal CoT steps that leave the final answer probability unaltered. Using attention probes, we show that answer-formation stages can be linearly decoded from intermediate reasoning steps with high accuracy and generalize robustly to unseen reasoning tasks. We exploit this signal to early-exit reasoning blocks at the commitment boundary, reducing the length of CoTs up to 55\% on average with negligible impact on model performance.

24.
arXiv (CS.LG) 2026-06-16

ANCHOR: Error-Controlled Adaptive Numerical Correction for Neural Operator Time Marching

arXiv:2512.19643v2 Announce Type: replace Abstract: Numerical simulation of time-dependent partial differential equations (PDEs) is central to scientific and engineering applications, but high-fidelity solvers are often prohibitively expensive for long-horizon or time-critical settings. Neural operator (NO) surrogates offer fast inference across parametric and functional inputs; however, most autoregressive NO frameworks remain vulnerable to compounding errors, and ensemble-averaged metrics provide limited guarantees for individual inference trajectories. In practice, error accumulation can become unacceptable beyond the training horizon, and existing methods lack mechanisms for online monitoring or correction. To address this gap, we propose ANCHOR (Adaptive Numerical Correction for High-fidelity Operator Rollouts), an online, instance-aware hybrid inference framework for stable long-horizon prediction of nonlinear, time-dependent PDEs. ANCHOR treats a pretrained NO as the primary inference engine and adaptively couples it with a classical numerical solver using a physics-informed, residual-based error estimator. Inspired by adaptive time-stepping in numerical analysis, ANCHOR monitors an exponential moving average (EMA) of the normalized PDE residual to detect accumulating error and trigger corrective solver interventions without requiring access to ground-truth solutions. We show that the EMA-based estimator correlates strongly with the true relative L2 error, enabling data-free, instance-aware error control during inference. Evaluations on six canonical PDEs: 1D and 2D Burgers', 2D Allen-Cahn, 2D Cahn-Hilliard, 2D Navier-Stokes, and 3D heat conduction, demonstrate that ANCHOR reliably bounds long-horizon error growth, stabilizes extrapolative rollouts, and significantly improves robustness over standalone neural operators, while remaining substantially more efficient than high-fidelity numerical solvers.

25.
bioRxiv (Bioinfo) 2026-06-18

ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets

Background: The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability and reproducibility. Results: We present the v1.0 release of ScriptManager, a Java-based framework for modular and reproducible analysis and visualization workflows of genomics and epigenomics data. Unlike existing tools specialized for individual assay types, ScriptManager provides a unified and extensible framework for cross-assay visualization and workflow reproducibility. The v1.0 release adds novel analytical modules, GUI session logging, automated unit and integration testing, tutorials, and expanded documentation. It also integrates with the broader reproducibility ecosystem through Singularity containers, Anaconda packaging, and Galaxy XML wrappers. We demonstrate ScriptManager's TagPileup scaling from local single-core execution to a 10,305-job analysis distributed across the Open Science Grid (OSG), with the full workload completing in