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01.
arXiv (CS.CV) 2026-06-17

MOCHI: Motion Enhancement of Collaborative Human-object Interactions

Collaborative human-object interaction shows dynamic and complex movements that require mutual anticipation and continuous adjustment between participants and the shared object. Modeling such collaborative multi-human object interaction (MHOI) scenarios requires high-quality data acquisition as a foundational step; however, this is challenging due to the inherent complexity of MHOI where human-human and human-object interactions occur simultaneously. Such complexity leads to noisy MHOI captures characterized by several artifacts: contact misalignment between hands and objects, motion jitter and temporal inconsistencies in the captured sequences, and missing or incomplete finger-level articulation details. To address these challenges, we present MOCHI (MOtion Enhancement of Collaborative Human-object Interactions), a two-stage framework for enhancing noisy MHOI data. Our approach first generates physically plausible hand grasps through optimization from noisy body input, producing grasps that are both physically plausible and semantically consistent with the body pose, where these optimized grasps are extended into complete hand-object interaction sequences. Consequently, the full-body motion for all participants are refined through a diffusion-based noise optimization framework that uses single-person motion priors. During the optimization process, we introduce optimization objectives to encode human-object and human-human interaction information within these single-person priors. Experimental results demonstrate the effectiveness of our pipeline across diverse MHOI data, either acquired by existing capture methods or synthesized by generative models. We further show robustness of our system across varying numbers of participants and types of interactions, and demonstrate various applications including keyframe-based MHOI creation and data augmentation through varying object geometries.

02.
arXiv (CS.AI) 2026-06-16

FlowState: Sampling-Rate-Equivariant Time-Series Forecasting

arXiv:2508.05287v3 Announce Type: replace-cross Abstract: Existing time series foundation models (TSFMs), often based on transformer variants, lack adaptability to different sampling rates, struggle with generalization across varying context and target lengths, and are computationally inefficient. We introduce FlowState, a novel TSFM architecture that achieves sampling-rate-equivariant forecasting through a unified design that pairs a state space model (SSM) encoder with a functional basis decoder (FBD). This design enables continuous-time modeling and dynamic time-scale adjustment, allowing FlowState to inherently generalize across all possible temporal resolutions, and dynamically adjust the forecasting horizons without retraining. We further propose an efficient pretraining strategy that improves robustness and accelerates training. Despite being one of the smallest TSFMs, FlowState achieves state-of-the-art results on the widely used GIFT-Eval benchmark, while demonstrating superior adaptability to unseen sampling rates. Our detailed analyses confirm the effectiveness of its components, and we demonstrate its unique ability to adapt to varying input sampling rates.

03.
arXiv (quant-ph) 2026-06-15

Calibrated Helstrom geometry on the Bloch ball via Connes spectral distance

arXiv:2606.13824v1 Announce Type: new Abstract: We show that the equal-prior Helstrom trace-distance geometry of qubit states is recovered from Connes spectral distance in a finite scalar-qubit-scalar model. The two scalar reference sectors couple isotropically to the qubit block through identity Dirac links, so that the full Bloch ball, including mixed states, inherits its standard chordal trace-distance geometry from the finite spectral metric. The scalar-sector distances serve a distinct calibration role: they determine the individual link lengths, satisfy a Pythagorean consistency relation, and reconstruct the middle-sector scale.

04.
arXiv (CS.AI) 2026-06-11

Lung-R1: A Knowledge Graph-Guided LLM for Pulmonary Diagnostic Reasoning

arXiv:2606.11675v1 Announce Type: new Abstract: Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.

05.
medRxiv (Medicine) 2026-06-24

Matrix matters: head-to-head concordance of serum and plasma for NULISAseq CNS Disease Panel

Blood-based proteomic profiling is now widely applied in neurodegenerative and neuroinflammatory disease, yet the choice between serum and plasma remains poorly characterised for high-multiplex platforms. Many legacy biobanks hold mainly serum, whereas most current NUcleic-acid-Linked Immuno-Sandwich Assay (NULISA) studies use plasma. We compared the 130-protein NULISAseq central nervous system (CNS) Disease Panel head-to-head in matched serum and plasma collected at the same draw from 62 participants (30 neurodegenerative, 19 demyelinating, 13 healthy controls). Agreement was measured with Spearman correlation (rho), Lin's concordance correlation coefficient (CCC), the intraclass correlation coefficient (ICC) and the mean paired serum-to-plasma difference (dNPQ). Concordance was moderate to high: 123 of 130 proteins reached significance and 18 reached rho >= 0.90, with a median rho of 0.72 (range 0.10-0.988). Proteins fell into three tiers. Cytoskeletal markers (NEFH rho=0.988; NEFL rho=0.947) and glial GFAP (rho=0.949, |dNPQ|

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

Beyond Problem Solving: UOJ-Bench for Evaluating Code Generation, Hacking, and Repair in Competitive Programming

arXiv:2606.12864v1 Announce Type: cross Abstract: Despite strong performance in competitive programming, the role of Large Language Models (LLMs) in supporting human learning in the same setting remains largely unexplored. In this work, we introduce UOJ-Bench, a benchmark designed to evaluate not only the problem-solving ability of LLMs, but also their ability to identify errors in human-written code – a crucial educational activity traditionally supported by running test cases over online judge systems. UOJ-Bench consists of three distinct tasks: code generation, code hacking, and code repair, all constructed from real-world code submissions on the Universal Online Judge (UOJ) and evaluated through UOJ's native judging infrastructure. Our results show that under one-shot evaluation, even the strongest models fail to identify errors in more than 50% of a set of submissions that have been found to be incorrect by UOJ users. While test-time scaling improves success rates to above 90%, the substantial computational costs incurred from model inference limit its practicality for large-scale deployment. Despite these limitations, we find that the best-performing models under test-time scaling can uncover errors in over 5% of full-score submissions across roughly 30 problems, suggesting that frontier LLMs can already provide complementary signals beyond standard judging systems.

09.
arXiv (quant-ph) 2026-06-12

Quasi-local Edge Mode in XXX Spin Chain/Circuit with Interaction Boundary Defect

arXiv:2603.17835v2 Announce Type: replace-cross Abstract: We study the Heisenberg spin-1/2 model on a semi-infinite chain - or, equivalently, a trotterized unitary SU(2) symmetric six-vertex quantum circuit - with a boundary defect where the interaction between the two spins nearest the edge differs from that in the bulk. For sufficiently strong boundary interaction we explicitly construct a conserved operator quasi-localized near the boundary using a matrix-product ansatz. This quasi-local edge mode leads to non-decaying boundary correlation functions, corresponding to a nonzero boundary Drude weight. The correlation length of the edge mode diverges at a finite critical value of the boundary interaction, signaling a transition to ergodic boundary dynamics for subcritical interactions.

10.
arXiv (CS.LG) 2026-06-19

VIMPO: Value-Implicit Policy Optimization for LLMs

arXiv:2606.20008v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards has become a central tool for improving the reasoning ability of large language models, but current methods face a trade-off between simplicity and credit assignment. Group-relative methods such as GRPO avoid training a critic, but typically assign a trajectory-level advantage to every token. Actor-critic methods provide denser learning signals, but require a learned value function with its own training instability. We introduce VIMPO, a critic-free policy optimization method that derives a policy-implied value function from the optimality conditions of KL-regularized reinforcement learning. For autoregressive generation, the resulting value recurrence can be written in terms of policy-reference log-ratios and anchored by the terminal condition that no future reward remains at the end of a trajectory. This gives a simple value loss that incorporates outcome-level verifiable rewards without training a critic. The same derivation also yields a critic-free actor advantage, allowing VIMPO to separate reward incorporation through the value loss from policy improvement through a PPO-style actor update. On mathematical RLVR benchmarks, VIMPO improves over GRPO across MATH-500, AIME 2024, AIME 2025, and OlympiadBench, with especially larger gains on competition-style evaluations. Under noisy rewards, VIMPO retains a consistent advantage over GRPO, suggesting that policy-implied value optimization can provide finer credit assignment while preserving the practical simplicity of critic-free training.

11.
arXiv (CS.AI) 2026-06-19

TelcoAgent: A Scalable 5G Multi-KPM Forecasting With 3GPP-Grounded Explainability

arXiv:2606.19821v1 Announce Type: new Abstract: Key Performance Measurement (KPM) forecasting is essential for proactive network management of 5G and next-generation telecom networks. However, existing machine learning (ML) approaches face significant limitations in scalability and explainability, restricting their effectiveness in real-world deployments. We propose TelcoAgent, a foundation model-based framework that enables accurate, scalable, and explainable forecasting of multiple KPMs across diverse network cells without the need for site-specific training. Specifically, the framework comprises three key components: (i) an automated three-agent pipeline that constructs a 3rd Generation Partnership Project (3GPP) knowledge graph directly from specification documents, (ii) a scalable, time-series foundation model (TSFM)-based prediction pipeline to deliver accurate, zero-shot forecasting, and finally (iii) a reasoning and explanation pipeline that provides actionable, domain-grounded diagnostics. Evaluated using a 3-month, real-world, city-scale 5G KPM dataset from a U.S.-based network operator, TelcoAgent demonstrates high forecasting accuracy for all 7 considered KPMs per cell across 200 cells, while delivering explainable insights and actionable instructions to address network degradations.

12.
Nature (Science) 2026-06-18

Daily briefing: The proteins that protect us from deadly mutations

Authors:

Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States. Proteins that ‘buffer’ the effects of mutations could help to treat diseases such as cancers. Plus, goats can follow human voices and the battle over a key ocean observatory project in the United States.

13.
bioRxiv (Bioinfo) 2026-06-11

HalluDesign-NA: Extending HalluDesign for De Novo Nucleic Acid Design

AlphaFold3 has revolutionized the prediction of biomolecular structures and interactions, including atomic-level modeling of nucleic acids. However, the de novo design of structured and functional nucleic acids remains a significant challenge. Here, we extend our HalluDesign framework to nucleic acid design by integrating NA-MPNN for nucleic acid sequence optimization and design. This new framework, HalluDesign-NA, enables iterative sequence-structure co-optimization, facilitating the de novo design of nucleic acids. Computational benchmarking across ssDNA, ssRNA, and aptamer design tasks demonstrates consistent improvements in confidence scores (pLDDT, ipTM), supporting the feasibility of de novo nucleic acid design under various constraints, such as sequence length, symmetry, and protein structure context. We anticipate that HalluDesign-NA will accelerate the de novo design of functional nucleic acids for applications in biotechnology and medicine. The source code for HalluDesign-NA is available at https://github.com/MinchaoFang/HalluDesign_NA.

14.
arXiv (CS.CV) 2026-06-19

Vision-Reasoning-Guided Occlusion Removal from Light Fields

Occlusion-robust scene recovery remains a major challenge in computational imaging, particularly in natural environments where dense foreground vegetation severely limits visibility. We propose a vision-reasoning-guided light field occlusion removal framework that combines the visibility recovery capability of light field integration (LFI) with the semantic reasoning capacity of vision-language models (VLMs). Multi-view observations are first integrated via LFI to suppress foreground occlusions and produce an initial visibility-enhanced representation. A VLM is then incorporated as a conditional semantic prior to restore degraded structures and recover fine details, guided by the observed measurements. To improve recovery consistency and reduce hallucination artifacts, we introduce a multi-sample fusion strategy that aggregates multiple generated hypotheses into a unified estimate. Experimental results on synthetic and real-world datasets demonstrate state-of-the-art performance, achieving the highest average SSIM across four synthetic light field benchmark scenes (4-Syn) and strong generalization across structured and unstructured acquisition settings. These results highlight the effectiveness of combining physical imaging constraints with vision-language reasoning for robust perception under severe occlusion, with applicability to search-and-rescue and exploratory robotic navigation.

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

Agentic AI-based Framework for Mitigating Premature Diagnostic Handoff and Silent Hallucination in Healthcare Applications

arXiv:2606.18068v1 Announce Type: new Abstract: Recent advances in Large Language Models (LLMs) and multi-agent systems have driven the rise of Agentic AI, showing promise for medical reasoning. However, open-ended conversational agents remain prone to two critical failure modes: premature diagnostic handoff and silent clinical hallucinations that may go undetected before reaching the patient. In this work, we propose a multi-agent framework that addresses both issues by replacing ``LLM-as-a-judge'' routing with deterministic orchestration constraints. The framework incorporates two safety mechanisms. First, a neuro-symbolic state-tracking gate enforces completeness of the OLDCARTS clinical protocol (Onset, Location, Duration, Character, Aggravating/Alleviating factors, Radiation, Timing, and Severity) by blocking diagnostic transitions until all required dimensions are collected. Second, an epistemic uncertainty quantification (UQ) gate computes semantic entropy (H) across K=5 independent diagnostic samples to identify and intercept divergent outputs before delivery. We evaluate the system using simulated patient agents powered by the llama-3.1-70b-instruct model on 150 test cases. The full architecture achieves 49.3% diagnostic precision, representing an absolute improvement of 11.3 percentage points over an unconstrained baseline. Additionally, we observe a statistically significant negative correlation (r = -0.181, p < 0.05) between OLDCARTS completeness (\sigma) and semantic entropy (H), suggesting that structured information gathering is associated with reduced diagnostic uncertainty.

16.
arXiv (CS.AI) 2026-06-19

Evaluation of EEG Foundation Models for Event-Based Burst-Suppression Detection in ICU

arXiv:2606.20074v1 Announce Type: cross Abstract: Burst suppression (BS) is a clinically relevant electroencephalographic (EEG) pattern used to monitor sedation depth and brain activity in critically ill patients, particularly during induced coma in Intensive Care Units (ICUs). Automatic burst detection remains challenging because BS patterns vary substantially between patients and annotated datasets are scarce. Recently, EEG Foundation Models (FMs) have shown promise across several downstream EEG applications, but their usefulness for BS detection remains unexplored. We present the first study to evaluate EEG FMs for burst detection in reduced-montage ICU EEG without patient-specific calibration. We compare REVE-base, LUNA-large and LuMamba-Tiny with an adaptive thresholding baseline and a task-specific EEGNet baseline. Additionally, we complement conventional EEG window-based classification with event-based burst detection evaluation. This helps assessing clinically whether burst episodes are correctly detected, reducing the impact of expected annotation variability. The best model, REVE-base, achieved the highest event-based F1-score ($0.868 \pm 0.167$) and reduced burst-per-minute error by 52.1% and 36.2% compared to EEGNet and adaptive thresholding respectively, supporting FMs for scalable EEG monitoring in ICU. Ablation experiments showed that full fine-tuning was the most effective adaptation strategy with respect to frozen-backbone training, two-step fine-tuning, and LoRA-based adaptation, improving event-based F1-score over frozen-backbone training by up to $+0.102$ for LUNA-large. With reduced labeled datasets, pretrained REVE-base outperformed random initialization by $+0.723$ event-based F1 points at 25% of the cohort, demonstrating the benefit of pretraining FM representations when adapted to burst detection with limited labeled data.

17.
arXiv (CS.AI) 2026-06-24

The impact of generative artificial intelligence on academic development of Chinese students in humanities and social sciences

arXiv:2606.24104v1 Announce Type: cross Abstract: Generative artificial intelligence(GenAI) is reshaping learning in higher education, with particularly pronounced implications for the humanities and social sciences(HSS), where learning outcomes are commonly expressed through written and interpretive forms that align closely with GenAI's capabilities. Yet, systematic evidence on the educational impacts of GenAI on HSS students remains limited. Addressing this gap, this study draws on a large-scale survey of HSS students in China to examine its role in academic development. Guided by relevant learning theories, this study focuses on four dimensions: patterns of use, effects on learning processes and academic performance, challenges associated with GenAI use, and preferred approaches to curricular integration. We found that more than half perceived enhanced learning motivation, independent thinking and creativity, although a substantial minority reported little change or even decline. Comparatively, a notably larger majority reported academic performance gains, although these gains may partly reflect limitations in conventional assessment practices. The study identifies variations in perceived learning and performance improvements among students with differing durations of GenAI experience, along with observable disciplinary differences and modest gender differences. While an overwhelming majority valued the importance of ethical considerations, only slightly more than half were satisfied with privacy protection. Limited accuracy and overreliance emerged as the most pressing concerns reported by students. Students favored partial or optional curricular integration supported by practice-oriented training, and widely recognized GenAI's significance for their future professional development. Grounded in student perspectives, this study offers evidence-based recommendations for the responsible and pedagogically meaningful integration of GenAI

18.
arXiv (CS.LG) 2026-06-16

Finite-Time Convergence of Distributionally Robust Q-Learning with Linear Function Approximation

arXiv:2510.01721v3 Announce Type: replace Abstract: Distributionally robust reinforcement learning (DRRL) seeks policies that perform well when the deployment transition model differs from the nominal model generating the data. Most finite-sample guarantees for DRRL are tabular, model-based, rely on generative access, or obtain function-approximation guarantees only under additional structure, such as linear-transition models or restrictive discount-factor conditions. We study discounted model-free robust Q-learning under an $(s,a)$-rectangular chi-square uncertainty set, with linear approximation of the robust Q-function, using only a single Markovian trajectory from an unknown nominal model. Our algorithm combines a target-network outer loop with a dual function-approximation scheme for the chi-square robust Bellman update. The dual procedure uses moment-tracking critics, suffix averaging, a fresh-evaluation stage for the variance-like moment, and a tunable smoothing parameter to have a Lipschitz-continuous chi-square dual gradient. We prove a finite-time convergence bound to the optimal robust Q-function up to approximation error, without imposing a small-discount-factor assumption. Our results help close a gap between the empirical use of robust RL algorithms and the non-asymptotic guarantees available for their non-robust counterparts.

19.
arXiv (CS.CL) 2026-06-24

Privacy-Preserving RAG via Multi-Agent Semantic Rewriting: Achieving Confidentiality Without Compromising Contextual Fidelity

Retrieval-Augmented Generation enhances large language models by incorporating external knowledge, but deploying it in sensitive scenarios risks privacy leakage via malicious prompts. To address this, we propose a multi-agent framework that sanitizes retrieved content through semantic rewriting. By employing three specialized agents for privacy extraction, semantic analysis, and reconstruction, our approach collaboratively removes sensitive identifiers while preserving the semantic core. We evaluate the framework on the ChatDoctor and Wiki-PII datasets across six large language models. Experimental results demonstrate a significant reduction in privacy leakage under targeted attacks. For instance, we reduced targeted information exposure in LLaMA-3-8B from 144 instances in the baseline to just 1. Furthermore, we maintain strong contextual fidelity with a BLEU-1 score of 0.122, outperforming the existing SAGE method's 0.117. Finally, the framework operates as an asynchronous preprocessing module, introducing no additional latency to online inference, as all rewriting is executed as a one-time offline preprocessing step. To promote reproducibility, the source code of this work is publicly available at https://github.com/foursoils/Privacy-Preserving-RAG.

20.
arXiv (CS.AI) 2026-06-24

HOLMES: Evaluating Higher-Order Logical Reasoning in LLMs

arXiv:2606.23238v2 Announce Type: replace Abstract: Logical reasoning is essential for reliable AI, yet existing benchmarks are largely first-order-logic-centric, focusing on object-level deduction over fixed predicates. This misses many realistic scenarios where models must reason over rules, predicates, functions, constraints, and decision procedures themselves. We introduce HOLMES (Higher-Order Logic Meets real-world Explainable Symbolic reasoning), the first real-world benchmark for higher-order symbolic reasoning in LLMs, containing 1379 instances. Built on higher-order logic, HOLMES pairs natural-language problems with HOL formalizations, ground-truth answers, verifiable reasoning traces, and fine-grained controllable reasoning factors across law and finance. Experiments show that current LLMs still struggle on HOLMES, with an average accuracy of only 50.64% and the best model reaching 59.54%. Our analyses further reveal that high final-answer accuracy can mask shortcut reasoning in conflict-resolution settings, while performance drops sharply under scope-conditioned and compositional reasoning. These findings identify higher-order symbolic reasoning as a key bottleneck for building reliable and verifiable LLMs. The project code and dataset are publicly available at https://github.com/wuyucheng2002/HOLMES.

21.
arXiv (CS.LG) 2026-06-12

Optimal Spatio-Temporal Decoupling for Bayesian Conformal Prediction

arXiv:2605.00432v2 Announce Type: replace Abstract: Online conformal prediction must balance fast adaptation to distribution shift against stable coverage: feedback-driven methods react quickly but become volatile, while strongly discounted Bayesian methods lag and inflate intervals at tight coverage. We introduce State-Adaptive Bayesian Conformal Prediction (SA-BCP), which forms the predictive quantile as a gated convex combination of long-term temporal inertia and local spatial evidence from a kernel density estimate, controlled by a single interpretable evidence threshold $K$. We establish three results: (i) asymptotic marginal validity of the resulting intervals; (ii) a closed-form expression for the MSE-optimal threshold, $K^*_{\mathrm{MSE}}=\alpha(1-\alpha)/M^{\mathcal{T}}$, trading the coverage-indicator (Bernoulli) variance against the temporal structural bias $M^{\mathcal{T}}$; and (iii) a rolling-origin procedure for selecting $K$ online – consistent under stationarity, with $O(\sqrt{T\log N})$ regret against the best fixed $K$ and, for a segmented variant, a sublinear dynamic-regret bound under bounded drift. Across four financial-volatility and weather datasets, three target coverage levels, and eight baselines (including the strongest recent conditional-quantile methods, SPCI and KOWCPI), SA-BCP attains at-or-above-nominal coverage in most settings while producing substantially sharper intervals – up to roughly $3\times$ lower Winkler score than discounted Bayesian CP at the tightest coverage – and a coverage-matched audit confirms these efficiency gains are not an artifact of under-coverage. We disclose one principal limitation: a volatility-specialized conformal-GARCH competitor remains more efficient on its home volatility-base series, though it does not transfer across domains.

22.
arXiv (CS.AI) 2026-06-12

Functional Cache Grafting: Robust and Rapid Code-Policy Synthesis for Embodied Agents

arXiv:2606.13097v1 Announce Type: cross Abstract: Code-writing large language models (CodeLLMs) generate executable code policies for embodied agents by translating natural language goals and environmental constraints into structured control programs. However, policy generation in open-domain embodied environments suffers from two fundamental limitations: (i) delayed decoding caused by repetitive prefill computation over long prompts, and (ii) limited robustness due to fully generative decoding, which often produces API mismatches, missing safety guards, and unstable control logic. To address these limitations, we present FCGraft, a Functional Cache Grafting framework. FCGraft maintains a library of function-level validated code skeletons and their associated prompt-level Transformer key-value (KV) caches, and synthesizes new policies by retrieving relevant functions and grafting their KV caches when a new task is provided. Given retrieved function caches, FCGraft performs cache grafting via stitching, which composes cached function segments into a composite policy, and patching, which locally adapts only the necessary code regions to satisfy task-specific parameters and constraints with minimal additional decoding. By eliminating redundant prefill computation, this approach reduces generation latency, while reusing validated control structures improves robustness over prompt-level caching methods RAGCache, achieving 18.31% higher task success rate and 2.3x faster policy synthesis.

23.
arXiv (CS.LG) 2026-06-19

Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems

arXiv:2606.20329v1 Announce Type: new Abstract: Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats. Representing microbial dynamics in process-based soil models is therefore critical to predict carbon cycling in soils, albeit highly challenging to inform from data. One promising approach to improve their parametrisation is the integration of genomic data, yet modelling the complex and unknown relationship between genomes and the processes the microbes are driving is an unsolved problem. In this work, we present the first hybrid modeling framework for deriving biokinetic parameter values of a process-based soil organic matter turnover model from metagenome-inferred functional traits based on DNA sequencing data. Our model predicts biokinetic parameters of the process-based model from genomic trait data with a neural network and integrates constraints from ecological theory and literature to ensure realistic behavior, even of non-observed state variables. We evaluate our method on synthetic genomic trait datasets of varying complexity and on real data, showing that our approach improves performance over multiple baselines and learns the dynamics of unmeasurable components of the process-based model effectively, even for small training datasets.

24.
arXiv (CS.CL) 2026-06-17

ProvenanceGuard: Source-Aware Factuality Verification for MCP-Based LLM Agents

Tool-using LLM agents increasingly use the Model Context Protocol (MCP) to answer from heterogeneous evidence sources, including search, APIs, databases, clinical records, and formulary tools. Standard factuality metrics usually test whether an answer is supported by pooled evidence, missing a provenance-sensitive failure mode: a claim may be supported somewhere while being attributed to the wrong source. We call this cross-source conflation. We introduce ProvenanceGuard, a source-aware verifier for MCP-grounded answers. It consumes captured MCP traces with stable tool IDs, source IDs, and raw outputs; decomposes answers into atomic claims; routes claims to source-specific evidence; checks support with NLI and a token-alignment proxy; compares stated attribution with the routed source; and returns per-claim verdicts plus an answer-level allow/block decision. Blocked answers can be repaired with retrieval-augmented answer revision and re-verified. We evaluate on 281 medical-domain MCP-agent traces. A 266-trace adjudicated subset yields 2,325 LLM-assisted claim labels split by trace; 361 held-out labels are human-verified. On the 40-trace held-out split, ProvenanceGuard achieves block F1 0.802 and source accuracy 0.858 over 260 source-eligible claims, outperforming source-blind baselines that do not emit claim-to-source IDs. On a harder multi-source benchmark it reaches block F1 0.846, while source-plus-relation accuracy drops to 0.229, showing that exact source ownership remains difficult with semantically close sources. Repair-and-reverify resolves all blocked answers in the full trace set, often via conservative fallback. In 50 controlled clinical conflation probes, ProvenanceGuard detects all injected attribution swaps with no retained wrong attribution. These results show that source attribution is an independent axis for factuality verification in MCP-based agents.

25.
medRxiv (Medicine) 2026-06-24

Rare protein-coding variation and the genetic architecture of height in >1.4 million individuals

Highly heritable, polygenic, and easily measured, adult height has long been the model trait in human genetics. While the landscape of height-associated common genetic variation has been studied extensively, rare variation remains relatively unexplored. Using rare protein-altering variants in a discovery set of 826,066 exomes, we identify 207 height-associated genes - 98% of which replicate in an additional 624,567 individuals. The rarest and most deleterious class of variation, singleton (frequency