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01.
arXiv (CS.CL) 2026-06-19

Quantifying Aleatoric Uncertainty of In-Context Learning for Robust Measure of LLM Prediction Confidence

In-Context Learning (ICL) allows LLMs to adapt to new tasks from a few demonstrations, but its reliability remains a concern: predictions are highly sensitive to both prompt design and the model's ability to understand the context, obscuring whether failures arise from data properties or model limitations. Uncertainty decomposition-separating aleatoric from epistemic sources-is particularly crucial in this setting, yet existing methods, designed for standard generation tasks, fail to capture the unique dynamics of ICL. To address this, we introduce a concept of self-function vectors, built upon Bayesian views and the mechanistic interpretability of ICL. These vectors leverage internal model representations to model the latent concept learned during in-context prompting, thereby enabling a direct estimation of aleatoric uncertainty within a Bayesian framework and circumventing the reliance on brittle input or decoding manipulations. Given the lack of established benchmarks and suitable evaluation protocols, we also propose the first and rigorous evaluation protocol, in which data is manipulated in controlled ways so as to quantify aleatoric uncertainty precisely and separately from epistemic uncertainty. With this new evaluation framework, initially grounded in synthetic tasks for conceptual development and subsequently extended to real-world datasets, we show that our proposed methodology can measure uncertainty of LLM predictions made under ICL more reliably than existing alternative methods. Moreover, we show it can be used as a practical tool for trustworthy-related applications, such as hallucination detection. Our findings pave a new direction for connecting the quantitative view of uncertainty with the mechanistic understanding of model behavior.

02.
arXiv (CS.AI) 2026-06-15

Low-Burden LLM-Based Preference Learning: Personalizing Assistive Robots from Natural Language Feedback for Users with Paralysis

arXiv:2604.01463v2 Announce Type: replace-cross Abstract: Physically Assistive Robots require personalized behaviors to ensure user safety and comfort. However, traditional preference learning methods, like exhaustive pairwise comparisons, cause substantial physical and cognitive fatigue for users with severe motor impairments. To solve this, we propose a low-burden, offline framework that translates unstructured natural language feedback directly into deterministic robotic control policies. To safely bridge the gap between ambiguous human speech and robotic code, our pipeline uses Large Language Models (LLMs) grounded in the Occupational Therapy Practice Framework. This clinical reasoning decodes subjective user reactions into explicit physical and psychological needs, which are then mapped into transparent decision trees. Before deployment, an automated "LLM-as-a-Judge" verifies the code's structural safety. We validated this system in a simulated meal preparation study with 10 adults with paralysis. Results show our natural language approach significantly reduces user workload compared to traditional baselines. Additionally, occupational therapists confirmed the generated policies are safe and accurately reflect user preferences.

03.
arXiv (CS.CL) 2026-06-19

Investigating Human-Model Discrepancies in Speech Quality Assessment via Acoustic and Prosodic Perturbations

Mean opinion score (MOS) prediction models are widely used as proxy metrics in text-to-speech (TTS) research, yet their ability to capture quality differences beyond acoustic fidelity remains unclear. We investigate this via controlled perturbations on speech: acoustic degradation, prosodic errors, and manipulation of speaker-specific characteristics such as pitch and speaking rate. We obtained MOS predictions for these speech samples from both human listeners and the model, and analyzed the differences in their perceptual characteristics. Results show that most models track acoustic degradation well, while all are insensitive to prosodic errors despite large subjective score drops. For speaker characteristics, models exhibit a double dissociation: strong mean fundamental frequency (F0) biases absent in human ratings, yet insensitivity to speaking rate and F0 variability that humans notice. These findings highlight limitations of scalar MOS prediction beyond acoustic fidelity.

04.
arXiv (quant-ph) 2026-06-17

Cumulant expansion approach to the decay dynamics of interacting Mössbauer nuclei after strong impulsive excitation

arXiv:2510.00970v2 Announce Type: replace Abstract: Recent progress in accelerator-based x-ray sources brings higher excitation of ensembles of Mössbauer nuclei closer to experimental feasibility. Yet, a theoretical modeling of the decay dynamics of the interacting nuclear ensemble after the impulsive excitation is still an open challenge. Here, we derive a set of nonlinear equations which is capable of efficiently modeling large nuclear ensembles for arbitrary degrees of excitation. As key signature for higher excitation, we identify a non-linear time-evolution of the nuclear dipole phase, which can be tuned via the scattering geometry, and interferometrically be measured. Furthermore, we identify interesting finite-size effects in the nuclear dynamics of small ensembles. Our results provide important guidance for future experiments aiming at the non-linear excitation of nuclei. We further envision the exploration of finite size-effects in Mössbauer spectroscopy with highest spatial resolution, i.e., small sample volumes.

05.
arXiv (CS.CL) 2026-06-16

XAI-Grounded Explanation Generation for Speech Deepfake Detection with Training-Free Multimodal Large Language Models

Speech deepfake detection (SDD) systems require trustworthy explanations for reliable decision-making. Existing explanation ways mainly fall into two categories. Traditional explainable AI (XAI), such as gradient-based attribution, produces low-level attribution signals tightly coupled with model decisions, and harder to be understood by human than natural language explanations. Meanwhile, large language model (LLM)-based explanation generation often produces generic and ungrounded descriptions due to the lack of heuristic evidence and task-specific supervision, stemming from limited grounded explanation datasets for SDD. We therefore propose a training-free explanation framework that integrates XAI evidence with multimodal LLMs to generate grounded and specific explanations. Using the PartialSpoof dataset, we construct a grounded explanation dataset and show that methods with XAI increase inside accuracy by over 45\%, verified through human evaluation and faithfulness checks.

06.
bioRxiv (Bioinfo) 2026-06-20

RNAStabFormer: Region-Aware Multi-Task Hybrid Learning for RNA Stability Prediction from Pulse-Chase Transcriptomics

Authors:

RNA stability is a central layer of post-transcriptional gene regulation, yet large-scale stability labels derived from pulse-chase transcriptomics depend strongly on quantification region, time-window definition, and replicate quality control. We present RNAStabFormer, a controlled learning framework for predicting human RNA stability proxies from transcript sequence. Its core model, RAMHT, combines region-specific nucleotide Transformer encoders for CDS, and sequence, a CDS codon stream, engineered sequence-grammar features, gated fusion, and four task-specific regression heads. We construct four strict consensus labels from ENCODE BrU-seq/BruChase-seq data by crossing gene-sense and exon-sense quantification with late-chase 6 h/2 h and total-chase 6 h/0 h retention ratios, and evaluate all models on fixed repeated-random and chromosome-holdout splits. Across chromosome holdouts, XGBoost remains the strongest standalone model, with median Pearson correlations of 0.504, 0.544, 0.546, and 0.778 on the four labels. RAMHT is competitive with raw-sequence deep models but does not universally exceed engineered-feature baselines. A strict nested RAMHT–XGBoost blend nevertheless improves gene total-chase prediction by 0.017 mean Pearson and exon late-chase prediction by 0.004 mean Pearson over XGBoost. Region and mechanism analyses show that CDS, local k-mer composition, and codon-sensitive signals dominate predictive information. RNAStabFormer therefore provides both a multi-task neural model and a leakage-controlled evaluation protocol for RNA stability prediction from pulse-chase data.

07.
arXiv (quant-ph) 2026-06-19

Ricci flow for the Bures–Helstrom qubit metric

arXiv:2606.19493v1 Announce Type: cross Abstract: The Bures–Helstrom metric is the minimal monotone Riemannian metric on the state space of a qubit. With the quantum Fisher normalization used here, it identifies the Bloch ball with a geodesic hemisphere of the unit round three–sphere. We describe its Ricci flow explicitly. In a general rotationally symmetric gauge the flow is a coupled system for the radial lapse and warping factor; a single scalar equation appears only after a Hamilton–DeTurck gauge choice. In the corresponding moving DeTurck frame the squared warping function $\Psi=\Phi^2$ satisfies the linear forced heat equation \begin{equation*} D_t\Psi=\Psi_{ss}-2, \end{equation*} while the fixed-lapse coordinate form contains the associated transport term. Since the Bures–Helstrom metric is Einstein, the geometric flow itself is the homothetic shrinker \begin{equation*} g(t)=(1-4t)g_{\mathrm{BH}}, \end{equation*} with scalar curvature $6/(1-4t)$ and extinction time $T=1/4$. Thus the metric remains inside the monotone cone for all $t

08.
arXiv (CS.LG) 2026-06-18

Quantifying and Auditing LLM Evaluation via Positive–Unlabeled Learning

arXiv:2606.19057v1 Announce Type: cross Abstract: Large Language Models (LLMs) are increasingly used as judges for scalable evaluation, yet such LLM–as–a–Judge systems exhibit systematic biases that are decoupled from semantic quality, most notably verbosity bias. Meanwhile, human supervision is costly and typically selective, yielding reliable positive judgments but leaving most outputs unlabelled and potentially mixed in quality. We formulate LLM evaluation under selective human supervision as a positive–unlabelled learning problem and propose a geometric auditing framework based on Partial Optimal Transport. By aligning a small set of human–verified positives with a reliable subset of unlabelled outputs in a fixed embedding space, our method identifies human–consistent preferences and corrects biased judges without retraining. Experiments demonstrate improved alignment with human preferences, increased robustness to presentation biases, and interpretable confidence estimates, offering a scalable and statistically grounded alternative to existing LLM–as–a–judge pipelines.

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

Execution-bound advisory automation for agentic AI: a reproducible AIBOM-driven CSAF-VEX framework

arXiv:2606.19390v1 Announce Type: cross Abstract: A protocol driven framework is presented that binds SBOM and AIBOM artefacts to deterministic environment capture and structured runtime telemetry. Exploitability is computed from declared artefacts, observed activation conditions, and enforced execution policies. CSAF VEX advisories are generated from combined static and runtime evidence, cryptographically signed, and validated through deterministic replay. Evaluation uses approximately 10000 component entries across synthetic Agentic AI workloads 50 to 5000 components, incorporating OSV, GitHub Advisory, KEV, and EPSS datasets.

11.
arXiv (CS.LG) 2026-06-18

Task-Restricted Symmetries in Recurrent Weight Space

arXiv:2606.18457v1 Announce Type: new Abstract: Recurrent networks can contain substantial functional redundancy in weight space: changing a recurrent matrix may leave the input-output rollout nearly unchanged on a task distribution, while similar-scale changes can destroy the same behavior. We study this redundancy in one-layer tanh RNNs using ordered real Schur coordinates. The Schur form separates spectral blocks from directed nonnormal couplings, giving a diagnostic basis for structured ablations that keep the input and readout maps fixed. In a fixed-length copy task, selected nonnormal Schur couplings can be removed with little loss in some trained solutions, whereas other couplings are necessary for accurate autonomous replay. Across flip-flop, sine generation, and context-dependent integration, the loss-preserving ablation profile varies across tasks and trained solutions. These results identify candidate approximate functional invariances, not universal symmetries of recurrent weight space. Schur-coordinate ablations provide a practical diagnostic for which structured perturbations preserve a trained recurrent solution and which ones disrupt its computation.

12.
arXiv (CS.AI) 2026-06-11

FACTR 2: Learning External Force Sensing for Commodity Robot Arms Improves Policy Learning

arXiv:2606.12406v1 Announce Type: cross Abstract: Contact-rich manipulation requires force sensitivity, but many robot arms lack dedicated force sensors due to their high cost. We present Neural External Torque Estimation (NEXT), a data-driven method that estimates external joint torques without needing any dedicated force sensors. NEXT trains in 1 minute from only 10 minutes of free-motion data, yet achieves estimates comparable to dedicated joint-torque sensors. NEXT enables force-feedback teleoperation on low-cost arms and improves policy learning through Force-Informed Re-Sampling Training (FIRST), which up-samples pre-contact and contact segments during behavior cloning. Across five long-horizon tasks, FIRST outperforms prior force-aware policies by over 17% in task progress. Together, NEXT and FIRST bring force-aware teleoperation and policy learning to off-the-shelf robots without additional sensing hardware. Video results and code are available at https://jasonjzliu.com/factr2

13.
arXiv (CS.CL) 2026-06-19

The Register Gap: A Meaning Intelligence Framework for Nigerian Public Discourse

We introduce the Meaning Intelligence Framework (MIF), a nine-dimension annotation and evaluation schema for Nigerian public discourse that separates surface sentiment from true communicative intent. Existing benchmarks for Nigerian languages, including NaijaSenti and AfriSenti, treat sentiment classification as a three-way polarity task (positive, negative, neutral). We argue that the dominant failure mode of AI systems on Nigerian discourse is not translation failure but context failure: the same utterance carries opposite pragmatic force depending on speaker, audience, and situation. The MIF operationalises this insight across nine scored dimensions: register, surface sentiment, true intent, irony, coded subtext, risk tier, annotator confidence, speaker emotion, and recommended communications action. We construct a 30-item calibration dataset spanning Standard English, Nigerian English, Nigerian Pidgin, and code-mixed registers, and evaluate a frontier language model (Gemini 2.5 Flash) under zero-shot and schema-informed prompting conditions. The headline finding is the Register Gap: zero-shot register classification accuracy is 33.3%, rising to 73.3% (+40 points) when the model receives the MIF schema in-context. The composite Meaning Intelligence Score increases by 5.4 points (73.2 to 78.6) under schema-informed prompting, with the largest practical gains in register identification, coded-subtext detection (+10 points), and strategic action recommendation (+10.3 points). We release the framework specification, annotation guidelines, and the 30-item public calibration set to support reproducibility, while retaining a private holdout corpus for contamination-protected evaluation.

14.
arXiv (CS.AI) 2026-06-16

CmdNeedle: Measuring the Incompleteness of Command Denylists for AI Agents

arXiv:2606.15549v1 Announce Type: cross Abstract: The adoption of AI agents is increasing rapidly. Terminal AI agents, i.e., AI agents that run in terminal environments, are a widely used type of AI agents. Terminal AI agents rely heavily on shell command execution to interact with the host systems. They adopt a three-list command-gating mechanism to mitigate security risks introduced by command execution, with denylists serving as the load-bearing component. However, modern operating systems often ship a large, ever-expanding set of shell commands with complex functionalities. Our observation is that even a built-in denylist of Claude Code, well-maintained by its developers, can overlook bypass commands that invalidate its effectiveness. Such negligence leads to fragile command denylists that cannot even block operations that practitioners expect them to block. This paper presents the first systematic characterization of command denylist fragility in terminal AI agents. The paper formalizes the command denylist fragility problem and proposes an LLM-driven pipeline, CmdNeedle, to detect such fragility. It prompts the LLM to propose possible bypasses and iteratively repairs them using feedback from a validator that executes them in a sandbox. In the evaluation, we applied CmdNeedle to 1,709 real-world command denylists (containing 13,332 denylist rules) collected from GitHub. The evaluation shows several key findings, including that 69.0–98.6% of the denylists are fragile, that this fragility occurs consistently across projects and agents, and the validity of several possible root causes for this fragility. Our pipeline and findings will hopefully facilitate future research and practice regarding the command denylists used by AI agents.

15.
arXiv (CS.LG) 2026-06-18

Knockoffs-based False Discovery Rate Control and Simplification for Deep Neural Networks

arXiv:2606.04404v2 Announce Type: replace-cross Abstract: The deep neural network is a widely used framework in machine learning that has been widely applied in various fields. However, deep neural networks often involve a large number of parameters and inputs, many of which may be irrelevant to the goal or true output. These parameters and input variables not only increase computational complexity, but also contribute to additional computational cost. One solution to this problem is knockoff methods, which have proven successful in controlling false discovery rates in high-dimensional regression. Building on the knockoff methods and using the regularised neural network, this paper proposes three variable screening methods under the condition of controlling false discovery rates: one layer filter, multiple layers filter, and variable weight aggregation filter. In comparison with existing algorithms, we find that our algorithms show satisfactory performance.

16.
Nature (Science) 2026-06-17

Fast formation to reinforce lithium-rich cathodes

Authors:

Formation in lithium-ion battery manufacturing typically involves low-rate charge–discharge cycles to establish stable electrode–electrolyte interfaces—a time-consuming process1–4. Here, our findings on lithium-rich layered oxide cathodes challenge the necessity of conventional formation, which can even shorten battery lifespan. Fast formation, on the other hand, reduces production cost and enhances capacity and stability. Multiscale synchrotron-based techniques show that residual lithium ions after the initial charge are critical for subsequent structural evolution and cycling performance. Deep lithium de-intercalation causes severe structural degradation and capacity loss due to the inherently fragile lithium-deficient matrix. By contrast, the residual lithium ions from fast formation enhance reversibility through a self-pinning effect, preventing pernicious lattice deformation and reinforcing the ion-storage framework. Adjusting the initial charge current density from 0.2 C to 2 C improves reversible capacity by 20% and extends cycle life by more than 36%. This approach can also be extended to other electrode systems, providing insights for more-efficient battery production. Fast formation in lithium-ion batteries outperforms conventional slow formation, lowering costs and improving battery capacity, stability and cycle life, offering broader application to electrode systems.

17.
arXiv (CS.AI) 2026-06-11

Quantized Stochastic Primal-Dual Methods for Distributed Optimization under Relaxed Global Geometry

arXiv:2606.11339v1 Announce Type: cross Abstract: We study distributed optimization with stochastic gradients and finite-bit communication modeled by random (unbiased) quantization. We propose q-PDGD, a quantized stochastic primal-dual method, and analyze it under relaxed global geometry. Under restricted secant inequality (RSI), a constant step-size yields linear contraction to an explicit neighborhood determined by gradient noise, quantization distortion, and network connectivity, while a diminishing step-size achieves O(1/k) convergence without shared-minimizer assumptions. Under Polyak-Lojasiewicz (PL) inequality, we obtain linear-to-neighborhood convergence in the same stochastic quantized setting. Our results match the best-known centralized stochastic rates in oracle complexity, and are supported by experiments demonstrating the predicted tradeoffs between quantization level, step-size choice, and graph structure.

18.
arXiv (quant-ph) 2026-06-16

Semiclassical Gravity Efficiently Solves $\mathsf{NP}$-Complete Problems

arXiv:2606.14806v1 Announce Type: cross Abstract: Assuming the gravitational field is classical and that it couples to quantum fields via the semiclassical Einstein field equations, we show that the weak-field dynamics of a massive and non-relativistic qubit can in principle be used to solve an $\mathsf{NP}$-complete problem in polynomial time. We attribute this vast computational power to the non-linear dynamics afforded by the semiclassical Einstein field equations. Consequently, the above two assumptions entail a violation of the Physical Extended Church–Turing Thesis, which we regard as evidence for the quantization of gravity.

19.
arXiv (CS.AI) 2026-06-17

Beyond Parallel Sampling: Diverse Query Initialization for Agentic Search

arXiv:2606.17209v1 Announce Type: new Abstract: Test-time scaling for agentic search typically increases depth (i.e., more turns and tokens per trajectory) or breadth (i.e., more parallel rollouts). Here we focus on breadth scaling, showing that standard parallel sampling yields diminishing returns, tracing this to query redundancy at the first turn. When models issue similar first queries across rollouts, the threads retrieve overlapping evidence, and subsequent turns are conditioned on this shared retrieval. We address this limitation with DivInit, a training-free intervention at the first turn. Rather than sampling k independent first queries, DivInit draws n candidates from a single call, picks k < n diverse seeds, and runs them as parallel trajectories. Across five open-weight models and eight benchmarks, DivInit consistently improves over standard parallel sampling, with average gains of five to seven points on multi-hop QA at matched compute. Code available at https://github.com/cxcscmu/diverse-query-initialization

20.
arXiv (CS.AI) 2026-06-19

Bi-Anchor Interpolation Solver for Accelerating Generative Modeling

arXiv:2601.21542v3 Announce Type: replace-cross Abstract: Flow Matching (FM) models have emerged as a leading paradigm for high-fidelity synthesis. However, their reliance on iterative Ordinary Differential Equation (ODE) solving creates a significant latency bottleneck. Existing solutions face a dichotomy: training-free solvers suffer from significant performance degradation at low Neural Function Evaluations (NFEs), while training-based one- or few-steps generation methods incur prohibitive training costs and lack plug-and-play versatility. To bridge this gap, we propose the Bi-Anchor Interpolation Solver (BA-solver). BA-solver retains the versatility of standard training-free solvers while achieving significant acceleration by introducing a lightweight SideNet (1-2% backbone size) alongside the frozen backbone. Specifically, our method is founded on two synergistic components: 1) Bidirectional Temporal Perception, where the SideNet learns to approximate both future and historical velocities without retraining the heavy backbone; and 2) Bi-Anchor Velocity Integration, which utilizes the SideNet with two anchor velocities to efficiently approximate intermediate velocities for batched high-order integration. By utilizing the backbone to establish high-precision ``anchors'' and the SideNet to densify the trajectory, BA-solver enables large interval sizes with minimized error. Empirical results on ImageNet-256^2 demonstrate that BA-solver achieves generation quality comparable to 100+ NFEs Euler solver in just 10 NFEs and maintains high fidelity in as few as 5 NFEs, incurring negligible training costs. Furthermore, BA-solver ensures seamless integration with existing generative pipelines, facilitating downstream tasks such as image editing.

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

ReFree: Towards Realistic Co-Speech Video Generation via Reward-Free RL and Multilevel Speech Guidance

Speech-driven talking character animation seeks to generate life-like portrait videos that convey natural conversation behavior, aligning facial motion with spoken audio. Although recent advances in video generation have substantially improved realism in video-based animation, achieving both accurate lip articulation and expressive behavior remains challenging. Existing approaches typically trade off precise phoneme-to-lip synchronization against dynamic facial expressions and head motion, yielding animations that are either accurate yet rigid, or expressive but poorly synchronized. We address this challenge by proposing ReFree-S2V, a flow-matching speech-to-portrait animation framework that builds upon a pretrained video generation model to achieve fine-grained speech articulation and high-level expressive cues in speech-driven portrait animation. This model introduces a multi-level speech representation capturing phonetic and prosodic information at both local and global granularities. These representations are selectively injected into transformer blocks via learnable level selectors, enabling both accurate lip synchronization and natural expressive motion. To achieve natural head movements, we further introduce a novel reward-free reinforcement learning scheme into flow-matching training to discourage perceptually implausible motion without relying on handcrafted synchronization metrics or reward models, or the high cost of human preference annotation. Extensive experiments demonstrate that ReFree-S2V achieves state-of-the-art performance, significantly outperforming existing methods in both quantitative lip-sync accuracy and qualitative human evaluations of naturalness and expressivity.

22.
bioRxiv (Bioinfo) 2026-06-19

Sanjeevani: A manually curated anti-cancerous phytochemical database integrated with downstream analysis tools.

Background: Cancer continues to pose a massive global health burden. While plant-derived phytochemicals offer promising therapeutic leads, existing natural product databases often lack cancer specificity, dataset downloadability, and integrated screening tools. Methods: We developed Sanjeevani, an integrative web platform cataloguing 4,823 curated anticancer phytochemicals. Using a balanced dataset of 9,646 molecules, we trained Support Vector Machine (SVM), Random Forest, and K-Nearest Neighbours classifiers using a hybrid feature representation of RDKit descriptors and 2048-bit ECFP4 fingerprints. The platform also integrates AutoDock Vina for web-based molecular docking for binding affinity, poses prediction and ADMET-AI for pharmacokinetics estimation. Results: The SVM model demonstrated the strongest predictive capability, achieving a top test accuracy of 0.966 and a ROC-AUC of 0.992. Benchmarking across five docking tools confirmed that AutoDock Vina successfully balanced computational automation with literature-consistent binding affinity replication. The final architecture provides rapid interactive 2D/3D visualizations integrated with downstream analysis tools. Conclusion: Sanjeevani provides an open-access, one-stop pipeline that bridges the gap between raw natural product data and actionable computational screening, accelerating natural product-based oncology drug discovery.

23.
arXiv (CS.CV) 2026-06-16

AME: A Multi-Type Contributor Attribution Framework in Generative AI Markets

Generative AI enables value creation through multi-stage collaboration among heterogeneous contributors, including training data, base models, fine-tuning behaviors, and prompts. However, how to fairly allocate the data value remains largely unexplored. This paper formulates multi-stage generative AI value allocation as a new research problem and identifies three core challenges: heterogeneous data contribution valuation, data rights mapping, and trustworthy execution. We propose AME (Attribution-Mapping-Execution) framework, a unified framework that integrates data contribution valuation, data rights mapping, and trustworthy execution into a single workflow. Experimental results demonstrate that AME framework achieves data value allocation outcomes more consistent with human reference judgments while maintaining low-cost trustworthy execution. Our work provides an initial foundation for value assessment and revenue allocation in generative AI data markets.

24.
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.

25.
medRxiv (Medicine) 2026-06-22

Agentic Artificial Intelligence for Hospital Readmission Review: A Single-Center Blinded Evaluation and Exploratory Qualitative Analysis

Background: Manual review of 30-day hospital readmissions can identify actionable quality and safety problems, but it is labor-intensive. We developed and evaluated an agentic AI workflow for evidence-grounded readmission review. Materials and methods: We studied adult patients with unplanned 30-day readmission after discharge from a medicine hospitalist service at a single academic health system. An AI agent using a large language model queried a database containing notes, encounters, procedures, laboratory results, and other clinical data, and completed the same structured readmission-review rubric used by physicians. In the primary comparative evaluation, 20 randomly selected readmissions from 2025 were each reviewed by two physicians and the AI system. Blinded physician evaluators rated review quality. After rubric refinement, the AI workflow was applied to 100 recent readmissions in an exploratory expanded-cohort analysis of recurring improvement opportunities. Results: In the primary comparative evaluation, the AI classified 9/20 readmissions (45%) as preventable, compared with 19/40 physician reviews (47.5%). Blinded overall quality ratings were similar for AI and physician reviews (4.35 vs. 4.20 on a 1-5 scale; mean difference 0.15, 95% CI -0.20 to 0.48; p=0.49), as were factuality/support and usefulness/actionability ratings. No AI hallucinations were identified during factuality review. Agreement on preventability and primary readmission category was low for both AI-human and human-human comparisons. The AI system cost $0.23 per chart; physician reviewers took a median of 15 minutes, corresponding to an estimated $42.43 per chart. In the exploratory expanded-cohort analysis, AI-assisted review identified recurring vulnerabilities in post-discharge follow-up plans, incomplete inpatient workups, medication-safety transitions, and indwelling-device transitions. Conclusions: Agentic AI produced readmission reviews with similar blinded quality ratings to physician reviews in this small single-center primary comparative evaluation and supported identification of recurring quality-improvement themes in the exploratory expanded-cohort analysis. Preventability judgments remained variable among both AI and physicians, underscoring the need for human oversight and prospective evaluation before operational use.