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01.
arXiv (CS.AI) 2026-06-18

NAVI-Orbital: First In-Orbit Demonstration of a Zero-Shot Vision-Language Model for Autonomous Earth Observation

arXiv:2606.18271v1 Announce Type: new Abstract: As Earth Observation data generation outpaces downlink bandwidth and human-in-the-loop processing, a widening gap has emerged between onboard collection and actionable ground intelligence. This paper presents NAVI-Orbital, a software system deployed on a Low Earth Orbit (LEO) spacecraft. On April 16, 2026, NAVI-Orbital achieved what is, to the authors' knowledge, the first in-orbit demonstration of a vision-language model performing autonomous multi-modal inference entirely onboard. NAVI-Orbital uses a local vision-language model (Gemma 3) to classify each captured scene, produce a text description of its content and the relationships between its features, and respond to operator follow-up via natural-language dialogue. The system is re-tasked through plain-English prompts in place of conventional command sequences, and is orchestrated by a graph-based state machine (LangGraph) coordinating dedicated agents for detection and dialogue. Results across ground benchmarking (88.16% accuracy on the 7,960-image curated AID benchmark), Flatsat validation, and live in-orbit captures of newly acquired, previously unseen Earth imagery (including uncorrected YAM-9 imagery, processed onboard with hardware-accelerated GPU inference and no fine-tuning for the flight instrument) demonstrate the feasibility of running foundation models on satellite-class edge computers to invert the conventional acquire-then-downlink-everything bandwidth profile through semantic compression of Earth observations in-orbit.

02.
arXiv (quant-ph) 2026-06-12

Semi-Device-Independent Certification for Nonlocality without Entanglement

arXiv:2606.13667v1 Announce Type: new Abstract: In this work, we investigate maximum-confidence discrimination, which encompasses minimum-error and unambiguous discrimination, for ensembles of separable states by considering global and separable measurements. We demonstrate that global measurements outperform separable ones, thereby establishing nonlocality without entanglement (NLWE) in terms of confidence in a detection event, a fine-grained state-identification strategy that maximizes the probability of a correct guess given a measurement outcome. Conversely, verifying achievable confidence in measurement outcomes can certify global measurements, namely, semi-device-independent certification of NLWE. Our results make it feasible to experimentally demonstrate NLWE using present-day quantum measurement devices, even with non-unit detection efficiencies, since maximum-confidence measurements rely only on detected measurement outcomes.

03.
arXiv (CS.LG) 2026-06-15

Temporal Straightening for Latent Planning

arXiv:2603.12231v2 Announce Type: replace Abstract: Learning good representations is essential for latent planning with world models. While pretrained visual encoders produce strong semantic visual features, they are not tailored to planning and contain information irrelevant – or even detrimental – to planning. Inspired by the perceptual straightening hypothesis in human visual processing, we introduce temporal straightening to improve representation learning for latent planning. Using a curvature regularizer that encourages locally straightened latent trajectories, we jointly learn an encoder and a predictor of a Joint-Embedding Predictive Architecture (JEPA) world model. We show that reducing curvature this way makes the Euclidean distance in latent space a better proxy for the geodesic distance and improves the conditioning of the planning objective. We demonstrate empirically that temporal straightening makes gradient-based planning more stable and yields significantly higher success rates across a suite of goal-reaching tasks. Our code is available at https://agenticlearning.ai/temporal-straightening.

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

Where Did It Go Wrong? Process-Level Evaluation of Web Agents with Semantic State Tracking

arXiv:2606.15673v1 Announce Type: new Abstract: Web agents act through long interaction sequences, yet existing benchmarks evaluate only terminal success, discarding all process information and offering little guidance on improvement. In this work, we conduct a process-level analysis of web agents. We introduce WebStep, a benchmark of 1,800 task instances with controlled difficulty and automatic semantic state tracking. Each website exposes a deterministic semantic MDP alongside the GUI: the agent operates on the interface, while the environment records high-level states and transitions in the background, enabling fine-grained analysis without manual annotation. Based on the semantic trajectory, we first show that process metrics reveal differences invisible to outcome evaluation: three agents whose success rates cluster within 31-33% diverge in exploration reach versus execution accuracy. Then, decomposing by skill characterizes the nature of these differences, exposing opposite per-skill rankings hidden within the same website: e.g., on Housing, OpenAI CUA outperforms Qwen3.5 by 23.7% on commit actions yet underperforms it by 15.6% on filtering, pinpointing a concrete skill to improve even within a domain. Bifurcation analysis further localizes the decisive error that loses the task and shows that this error is agent-specific rather than shared. Finally, these differences widen as tasks grow harder: success rate is similar on easy tasks but separates sharply as exploration becomes more demanding. Our process-level analysis opens a new avenue in web agent evaluation, providing fine-grained and actionable insight into where and how each agent should be improved.

05.
arXiv (math.PR) 2026-06-11

Multiple Poisson-Dirichlet diffusions on generalized Kingman simplices

arXiv:2602.20266v2 Announce Type: replace Abstract: We construct a new class of infinite-dimensional diffusions with values in a generalized Kingman simplex with finitely many marks. The model describes the temporal evolution of the relative frequencies of infinitely many types that are labeled by a finite number $H$ of marks, but unlabeled within each mark. We first establish a blockwise skew-product representation for a finite-type Wright-Fisher diffusion, extending the aggregation-renormalization self-similarity property of Dirichlet laws. The decomposition separates an $H$-dimensional Wright-Fisher diffusion governing the evolving random mark masses, from $H$ Wright-Fisher diffusions, each run on its own random clock, which describe the evolution of the relative frequencies within each mark. After ranking the within-mark frequencies in decreasing order, we identify the distributional limit as the number of types per mark tends to infinity and we derive an explicit form of its infinitesimal generator on a suitable domain. The limiting diffusion admits the multiple Poisson-Dirichlet distribution as a stationary distribution; it recovers the infinitely-many-neutral-alleles diffusion when all types share the same mark and yields a diffusion on the Thoma simplex when there are two marks.

06.
arXiv (CS.CV) 2026-06-11

Adapting Vision-Language Models from Iconic to Inclusive for Multi-Label Recognition Without Labels

Understanding multi-label images remains a challenging task in computer vision. With the rapid progress of vision-language multimodal learning, vision-language models (VLMs) enable zero-shot recognition without labeled data. However, due to their intrinsic design, these models often prioritize the most iconic object and omit other contextual positives. This intrinsic bias conflicts with the nature of multi-label learning, thereby limiting their applicability. In this work, we propose an unsupervised framework that adapts VLMs from iconic recognition toward inclusive understanding, enabling label-free multi-label image recognition. Our approach consists of two key stages, ``cutting'' and ``sewing'': In the cutting stage, we present the multi-sampling response estimator to prevent the model from concentrating only on one single object. In the second sewing stage, the multi-object blend adaptation is introduced to adjust the labels to better conform to the multi-label distribution while preserving the intrinsic characteristics of the original model within only one epoch. Extensive experiments show that our framework significantly outperforms existing unsupervised approaches on four public datasets, even surpassing several representative weakly supervised baselines. These results demonstrate the potential of adapting pre-trained VLMs for more comprehensive visual understanding without manual annotations. Our code is publicly available at https://github.com/iCVTEAM/TailorCLIP.

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

A Distributionally Robust Reinforcement Learning Framework for Constrained Urban EV Dispatch

arXiv:2604.25848v2 Announce Type: replace Abstract: We study city-scale control of electric-vehicle (EV) ride-hailing fleets where dispatch, repositioning, and charging decisions must respect charger and feeder limits under uncertain, spatially correlated demand and travel times. We formulate the problem as a hex-grid semi-Markov decision process (semi-MDP) with mixed actions – discrete actions for serving, repositioning, and charging, together with continuous charging power – and variable action durations. To guarantee physical feasibility during both training and deployment, the policy learns over high-level intentions produced by a masked, temperature-annealed actor. These intentions are projected at every decision step through a time-limited rolling mixed-integer linear program (MILP) that strictly enforces state-of-charge, port, and feeder constraints. To mitigate distributional shifts, we optimize a Soft Actor-Critic (SAC) agent against a Wasserstein-1 ambiguity set with a graph-aligned Mahalanobis ground metric that captures spatial correlations. The robust backup uses the Kantorovich-Rubinstein dual, a projected subgradient inner loop, and a primal-dual risk-budget update. Our architecture combines a two-layer Graph Convolutional Network (GCN) encoder, twin critics, and a value network that drives the adversary. Experiments on a large-scale EV fleet simulator built from NYC taxi data show that PD-RSAC achieves the highest net profit, reaching \$1.22M, compared with \$0.58M-\$0.70M for strong heuristic, single-agent RL, and multi-agent RL baselines, including Greedy, SAC, MAPPO, and MADDPG, while maintaining zero feeder-limit violations.

09.
arXiv (math.PR) 2026-06-18

On a class of reflected McKean-Vlasov Stochastic Differential Equations with jumps

arXiv:2606.18433v1 Announce Type: new Abstract: This paper investigates a class of reflected McKean-Vlasov Stochastic Differential Equations driven by both Brownian motion and a compensated Poisson random measure. We establish the existence and uniqueness of solutions and provide moments estimates for the state processes.

10.
arXiv (quant-ph) 2026-06-19

Attosecond Path Qubits in High-Harmonic Generation: Classical Dephasing and Trace-Out Decoherence

arXiv:2606.20372v1 Announce Type: cross Abstract: High-harmonic generation (HHG) is governed by interference between electron trajectories. We propose that the dominant short and long trajectories define an experimentally addressable two-level subsystem: an attosecond path qubit (APQ). We formulate a trajectory-resolved density matrix to identify two distinct coherence-loss mechanisms: classical dephasing from ensemble averaging and quantum decoherence arising from the trace-out of unobserved degrees of freedom. By investigating shot-to-shot fluctuations and unresolved transverse momentum, we demonstrate that while dephasing suppresses coherence through averaging, the ``trace-out'' channel produces mixed states even for fixed driving parameters. We explore how these mechanisms modify APQ purity and show that mode selection and conditioning provide operational routes to isolate them. These results establish a reduced-state framework for diagnosing coherence loss in HHG and for engineering trajectory-based quantum states in attosecond interferometry.

11.
arXiv (CS.CL) 2026-06-16

A Self Consistency Based Reranking for Narrative Question Answering

Narrative question answering (NQA) is a challenging task in natural language processing that requires models to understand long textual contexts, capture relationships across events, and generate coherent responses. Despite recent advances in pretrained language models, most existing approaches rely on a single decoding output during inference, making them sensitive to generation variability and often resulting in incomplete or inconsistent answers .To address this limitation, we propose a self-ensemble Self-Consistency-Based reranking framework for narrative question answering. The proposed method generates multiple candidate answers for each story-question pair and selects the final answer based on semantic agreement among the generated responses. This allows the model to explore diverse answer formulations while improving robustness through consensus-based selection without requiring modifications to the underlying architecture .The framework combines pretrained and fine-tuned language generation with multi-answer inference and similarity-based reranking. We evaluate the proposed approach on the NarrativeQA dataset using multiple models, including FLAN-T5 (Base and Small) and Pegasus-Large, under both baseline and fine-tuned settings .Experimental results demonstrate that the proposed method consistently improves performance across all models. In particular, FLAN-T5-Base achieves the best overall performance, improving from 82.32% to 86.66% (+4.34%) when combined with self-ensemble inference. Additionally, the largest improvement is observed with Pegasus-Large, which increases from 72.50% to 87.07% (+14.57%), highlighting the effectiveness of the proposed strategy.

12.
arXiv (quant-ph) 2026-06-15

Quantitative and Optimal Device-Independent Lower Bounds on Detection Efficiency

arXiv:2511.19302v2 Announce Type: replace Abstract: This paper examines a quantitative and optimal lower bound on the detector efficiency in a (2,2,2) Bell experiment within a fully device-independent framework, whereby the detectors used in the experiment are uncharacterized. We provide a tight lower bound on the minimum efficiency required to observe a desired Bell-CHSH violation using the Navascués-Pironio-Acín (NPA) hierarchy, confirming tightness up to four decimal places with numerical optimization over explicit quantum realizations. We then introduce the effect of dark counts and demonstrate how to quantify the minimum required efficiency to observe a desired CHSH violation with an increasing dark count error. Finally, to obtain an analytical closed-form expression of the minimum efficiency, we consider the set of no-signaling behaviors that satisfy the Tsirelson bound, which are easier to characterize than the quantum set. Using such behaviors, we find a simple closed-form expression for a lower bound on the minimum efficiency which is monotonically increasing with the CHSH violation, though the analytically obtained lower bounds are meaningfully below the numerically tight lower bound.

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

Addressing Detail Bottlenecks in Latent Diffusion for RGB-to-SWIR Image Translation

Latent diffusion models (LDMs) enable efficient image-to-image translation but discard fine spatial details during compression, degrading downstream perception tasks. We identify two bottlenecks: the autoencoder, which loses spatial information, and the conditioning pathway, which further degrades the source signal through naive downsampling. We propose two lightweight, backbone-agnostic fixes: a Source-Conditioned Autoencoder (SCAE) that injects high-resolution source features into the decoder via skip connections, and a Learnable Guidance Encoder (LGE) that replaces naive downsampling with a learned conditioning signal. Evaluated on RGB-to-SWIR translation for driving scenes with two denoiser backbones (U-Net and DiT), our approach improves detection mAP by up to 2x over the latent diffusion baseline, with up to 3.4x gains on small objects (COCO-small,

14.
arXiv (CS.CV) 2026-06-18

Fuzzy-Geometric Branch-Point Modeling for Structure-Aware Augmentation of Handwritten Chinese Characters

Data scarcity and structural distortion significantly limit handwriting recognition in high-security authentication. Existing augmentation methods often cause topological and morphological damage, particularly when processing complex Chinese characters where stroke intersections, ligatures, and sharp turns render traditional branch-point detection unreliable. To address this, this paper proposes a fuzzy geometry-driven structure-aware (FGSA) augmentation framework. We model branch points as fuzzy sets within the skeleton space, constructing a continuous branch-point membership field by integrating topological neighborhood evidence with direction field divergence. This membership field is adaptively optimized via an unsupervised surrogate objective, enabling robust stroke decoupling without manual annotation. Finally, kinematically-aligned samples are synthesized through parameterized cubic Bézier reconstruction and multi-strategy perturbations, ensuring a balance between structural fidelity and sample diversity. Moreover, we establish LZUSig, a large-scale, highly challenging dataset specifically dedicated to fine-grained structural degradation in Chinese handwritten signatures. Extensive experiments on CASIA-HWDB1.1, ChiSig, and LZUSig demonstrate that FGSA significantly reduces the word-level error rate ($\Delta$WER), achieving optimal recognition gains over the compared baselines. More importantly, it strikes a robust trade-off among task gain, structural fidelity, and discriminative feature preservation, offering a highly controllable solution for handwriting augmentation.

15.
arXiv (CS.LG) 2026-06-19

MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

arXiv:2606.19624v1 Announce Type: new Abstract: Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.

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

Cinematic Compositing Using Character-Environment-Harmonized Video Generation Models

Cinematic compositing aims to integrate green-screen characters into novel environments while maintaining physical and photometric realism. Previous methods often fail to capture the complex bidirectional interactions between characters and their surroundings, which we characterize as Character-to-Environment (C2E) physical interaction and Environment-to-Character (E2C) lighting harmonization. To address this, we propose an end-to-end video diffusion framework that jointly models C2E and E2C interactions, specifically handling the challenges of interactive props. Our approach introduces a tri-mask-guided architecture with RGB-D joint denoising to ensure physically consistent interactions among the character, props, and environment. We further develop an efficient prior-driven data curation pipeline to construct high-quality relighting pairs without expensive rendering. Finally, a reference-conditioned mechanism enables controllable environment synthesis and precise prop replacement. Extensive experiments demonstrate that our framework significantly outperforms existing methods in cinematic-quality dynamic video compositing.

18.
Science (Express) 2026-06-02

Another red alert for American science | Science

作者: 未知作者

Although research has bipartisan support in the US Congress, and trust in science is above 75% across the country, the Trump administration seems as determined as ever to mortally wound the nation’s scientific enterprise. After the scientific community persuaded Congress to restore most of the president’s draconian cuts to research funding last year, the White House Office of Management and Budget (OMB), under Russell Vought, has found new ways to circumvent the will of Congress and starve American science. At the beginning of this year, OMB dragged its feet in releasing instructions to federal agencies for how to distribute the funding appropriated by Congress, leading to lags in dispersal. Now, OMB has proposed revising the rules that govern how federal dollars are spent. The changes would inevitably lead to unlegislated reductions in funding and damage US leadership in science, both in academia and industry.

19.
arXiv (CS.AI) 2026-06-15

Metabolic cost of information processing in Poisson variational autoencoders

arXiv:2602.13421v2 Announce Type: replace-cross Abstract: Computation in biological systems is fundamentally energy-constrained, yet standard theories of computation treat energy as freely available. Here, we argue that variational free energy minimization under a Poisson assumption offers a principled path toward an energy-aware theory of computation. Our key observation is that the Kullback-Leibler (KL) divergence term in the Poisson free energy objective becomes proportional to the prior firing rates of model neurons, yielding an emergent metabolic cost term that penalizes high baseline activity. This structure couples an abstract information-theoretic quantity – the *coding rate* – to a concrete biophysical variable – the *firing rate* – which enables a trade-off between coding fidelity and energy expenditure. Such a coupling arises naturally in the Poisson variational autoencoder (P-VAE) – a brain-inspired generative model that encodes inputs as discrete spike counts and recovers a spiking form of *sparse coding* as a special case – but is absent from standard Gaussian VAEs. To demonstrate that this metabolic cost structure is unique to the Poisson formulation, we compare the P-VAE against Grelu-VAE, a Gaussian VAE with ReLU rectification applied to latent samples, which controls for the non-negativity constraint. Across a systematic sweep of the KL term weighting coefficient $\beta$ and latent dimensionality, we find that increasing $\beta$ monotonically increases sparsity and reduces average spiking activity in the P-VAE. In contrast, Grelu-VAE representations remain unchanged, confirming that the effect is specific to Poisson statistics rather than a byproduct of non-negative representations. These results establish Poisson variational inference as a promising foundation for a resource-constrained theory of computation.

20.
arXiv (CS.CV) 2026-06-16

X-Tokenizer: A Multimodal Action Tokenizer for Vision-Language-Action Pretraining

Modern Vision-Language-Action (VLA) models must bridge pretrained vision-language reasoning and precise continuous robot control. Existing action tokenizers discretize actions primarily for reconstruction, producing codes that preserve motion geometry but provide only weak semantic supervision to the backbone. We therefore formulate action tokenization not as mere compression, but as semantic interface learning between multimodal reasoning and executable control. To this end, we introduce X-Tokenizer, a lightweight encoder-Semantic Residual Quantization (SRQ)-decoder architecture that provides a shared action interface across diverse robotic arm embodiments. Its key component, SRQ, imposes an asymmetric structure on residual vector quantization: the first level is trained with Masked Action Modeling (MAM) to form a discrete action language that captures coarse motion intent, while deeper levels remain reconstruction-oriented residuals that preserve fine-grained details. To further align action tokens with multimodal semantics, X-Tokenizer is pretrained with contrastive alignment to the representation space of a pretrained foundation model and with next-frame vision-language feature prediction. Pretrained on 2.4M trajectories (2.0B action frames), a single frozen X-Tokenizer plugs into a mixed discrete-continuous VLA as a representation-shaping supervision signal. X-Tokenizer achieves top real-world aggregate and strong RoboTwin 2.0 simulation results. Outperforming FAST in multimodal grounding (+13.5%) and long-horizon tasks (+8.25), it shows that action tokenizers serve as semantic interfaces for VLA pretraining beyond mere action compression.

21.
arXiv (CS.CL) 2026-06-18

Improving Medical Communication using Rubric-Guided Counterfactual Recommendations

Text-based telemedicine increasingly relies on lightweight patient feedback, however, such feedback primarily reflects perceived communication quality rather than medical accuracy. We introduce an LM-guided counterfactual recommendation pipeline that discovers and refines interpretable communication features such as tone, personalization, actionability and completeness in addressing patient concerns, without interfering with the medical content. These features are used together with patient-doctor interaction metadata to estimate positive feedback. At inference time, the system searches over low-cost ordinal feature changes and recommends minimal communication changes predicted to increase the probability of positive feedback, while independent auditor models test whether these gains generalize beyond the selection model. Across interactions, recommendations yield a mean +6.41% gain in predicted positive feedback probability under independent auditors, and are non-negative for 93.31% of recommendations. These results suggest that small, interpretable communication changes can capture most predicted gains while preserving the doctor's control over medical reasoning and final wording.

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

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

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

From Isolation to Entanglement: When Do Interpretability Methods Identify and Disentangle Known Concepts?

A goal of interpretability is to recover disentangled representations of latent concepts (features) from the activations of neural networks. The quality of features is typically evaluated in isolation, and under implicit independence assumptions that may not hold in practice. Thus, it is unclear to what extent common featurization methods such as sparse autoencoders (SAEs) and probes disentangle one concept from another. We propose a multi-concept evaluation setting using concepts including sentiment, domain, voice, and tense. We evaluate how well featurizers produce disentangled representations of each concept, observing that features are typically sensitive to only one concept, but also that concepts are distributed across many features. Then, we steer these features, measuring whether each concept is independently manipulable, and whether features interact. Even in idealized settings, steering a feature often affects many concepts, despite a near absence of interaction effects. These results suggest that correlational metrics are insufficient to establish steering selectivity, and that demonstrating that two features operate in separate spaces is insufficient to claim that they will be selective for one concept. These results underscore the importance of multi-concept evaluations in interpretability research.

24.
arXiv (CS.CL) 2026-06-18

Language Models as Interfaces, Not Oracles: A Hybrid LLM-ML System for Pediatric Appendicitis

Large language models (LLMs) can make clinical decision support more accessible by interpreting free-text documentation, but their direct use as diagnostic engines is limited by sensitivity to prompts, information order, and plausible but incorrect outputs. Structured machine-learning models offer more stable risk prediction, yet they require tabular inputs that are difficult to integrate with narrative clinical workflows. We present ClaMPAPP (Clinical Language-assisted Machine-learning Pipeline for Appendicitis), a hybrid system that uses an LLM as an interface rather than as the final decision-maker. ClaMPAPP extracts schema-constrained clinical features from note-like narratives, applies deterministic plausibility checks, and passes validated features to an XGBoost classifier trained on clinical, laboratory, and ultrasound variables. We evaluated ClaMPAPP on two independent pediatric appendicitis cohorts from German hospitals and compared it with end-to-end LLM baselines, including open-source and proprietary models. To preserve ground truth while testing free-text input, narratives were generated from structured electronic health records through template rendering and constrained LLM rewriting, with additional sentence-order permutation to assess positional robustness. ClaMPAPP achieved the strongest overall diagnostic performance in both internal and external validation while minimizing missed appendicitis cases, the key safety concern in acute triage. End-to-end LLMs showed unstable sensitivity-specificity trade-offs and greater degradation under narrative reordering. These results support an LLM-as-interface, ML-as-predictor design that separates natural-language usability from predictive inference and provides a more auditable pathway for clinical decision support.

25.
PLOS Computational Biology 2026-06-17

Combining machine learning and iterative experiments to keep pace with emerging viral variants of concern

by Thomas Sheffield, Ryan C. Bruneau, Stephen Won, Kenneth L. Sale, Brooke Harmon, Le Thanh Mai Pham Modeling and predicting viral mutations before they emerge plays a crucial role in pandemic preparedness, enabling the early identification of emerging variants of concern (VOCs) and guiding timely updates to vaccines, diagnostic tests, and therapeutic strategies. However, existing machine learning models and large-scale experiments lose their predictive power as viral variants evolve further from the original strains in sequence space. Here, we present a scalable framework that integrates random forest and neural network machine learning models with targeted high-throughput experimentation to anticipate and evaluate emerging SARS-CoV-2 receptor-binding domain (RBD) variants. Using public datasets, we trained predictive models for binding to human Angiotensin-converting enzyme 2 (ACE2), RBD expression, and antibody escape, and refined these models through iterative integration of experimental data focused on over 200 variants derived from wild-type (WT) and Omicron strains. Through an indirect transfer learning approach, our machine learning models achieved high accuracy having correlation coefficients of up to 0.79 for antibody binding. The models were also generalizable across diverse antibody types including heavy-chain-only antibodies (HCAbs) by encoding complementarity-determining regions (CDRs) as input features. This dynamic approach enables rapid assessment of emerging variants, facilities prioritization of the therapeutic strategies, and supports a proactive, data-driven response to evolving viral threats.