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01.
arXiv (CS.CV) 2026-06-16

LUCID: Learned Undersampling-Adaptive Consistency-Guided Inference with Deterministic Flow Matching for Sparse-View CT Reconstruction

Sparse-view CT reduces radiation dose and scanning time by acquiring fewer projection views, but angular undersampling makes reconstruction severely ill-posed, causing streak artifacts, structural blurring, and loss of fine details. Existing supervised methods are often tied to specific sampling settings, whereas generative methods may introduce anatomically inconsistent hallucination-like structures under severe undersampling. We propose Lucid, a sparsity-adaptive, consistency-guided reconstruction framework based on a Flow Matching generative prior for sparse-view CT. Lucid is trained only on high-quality CT images to learn a continuous transport between a Gaussian distribution and the high-quality CT image distribution, independent of view sampling. During inference, the sampling sparsity level is explicitly incorporated to adapt the generative trajectory of a single pretrained model. Specifically, Lucid constructs a degradation-matched initial state by sparsity-weighted fusion of the sparse-view FBP image and Gaussian noise, performs sparsity-modulated Flow Matching updates, and applies projection-domain data-consistency correction after each prior update. Experiments under multiple sparse-view settings show that Lucid achieves stable reconstruction performance across different sampling densities, improves image quality and structural fidelity, and reduces the risk of hallucination-like structures in generative sparse-view CT reconstruction.

02.
bioRxiv (Bioinfo) 2026-06-11

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele- and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

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

On the QUEST for Uncertainty Quantification via Highest Density Regions

arXiv:2606.19569v1 Announce Type: new Abstract: Uncertainty quantification (UQ) is essential for reliable decision-making in safety-critical applications in probabilistic machine learning. For regression problems, dominant scalar UQ approaches - notably, those based on proper scoring rules - measure uncertainty via pointwise predictive risk. This can lead to counterintuitive results when the target statistic is not the conditional expectation. We propose an alternative framework, in which uncertainty is characterised by the volume of the most probable subset of a distribution's support. QUEST (Quantifying Uncertainty via highest dEnSiTy regions) is a novel approach to UQ based on the concentration of Lebesgue measure at a distribution's peak(s), evaluated at one or more values of a robustness parameter $\alpha$. We establish connections between our measures and classical statistics from information theory and economics. We show that, unlike popular alternatives based on proper scoring rules, QUEST measures of epistemic and aleatoric uncertainty satisfy a set of axioms adapted from the UQ literature, including monotonicity under distributional spread and invariance to location shifts. Selective prediction benchmarks confirm that QUEST performs favourably against standard measures such as variance and differential entropy.

04.
arXiv (CS.CV) 2026-06-15

Efficient Online 3D Multi-Camera Multi-Object Tracking and Pose Estimation

This paper proposes a fast and online method for jointly performing 3D multi-object tracking and pose estimation using multiple monocular cameras. Our algorithm requires only 2D bounding box and pose detections, eliminating the need for costly 3D training data or computationally expensive deep learning models. Our solution is an efficient implementation of a Bayes-optimal multi-object tracking filter, enhancing computational efficiency while maintaining accuracy. We demonstrate that our algorithm is significantly faster than state-of-the-art methods without compromising accuracy, using only publicly available pre-trained 2D detection models. We also illustrate the robust performance of our algorithm in scenarios where multiple cameras are intermittently disconnected or reconnected during operation.

05.
arXiv (math.PR) 2026-06-12

A mathematical study of the excess growth rate

arXiv:2510.25740v2 Announce Type: replace-cross Abstract: The excess growth rate, defined as the gap in Jensen's inequality for the logarithm, is a fundamental functional in portfolio theory. In this paper, we present a mathematical study motivated by information theory. We begin by establishing its properties and showing that it has rich connections with information theoretic concepts such as the Helmholtz free energy, L. Campbell's measure of average code length and large deviations. Our main results consist of three axiomatic characterization theorems of the excess growth rate, in terms of (i) the relative entropy, (ii) the gap in Jensen's inequality, and (iii) the logarithmic divergence that generalizes the Bregman divergence. Furthermore, we study maximization of the excess growth rate and compare it with the growth optimal portfolio. Our results not only provide theoretical justifications of the significance of the excess growth rate, but also establish new connections between information theory and quantitative finance.

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

Beyond Uniform Tokens: Adaptive Compression for Time Series Language Models

Large language models (LLMs) have enabled time series (TS) analysis by jointly modeling numerical observations and textual context through a shared token interface. However, TS tokens and prompt tokens exhibit fundamentally different information structures, making uniform token processing inefficient. In this paper, we study token efficiency in TS language modeling from an asymmetric-token perspective. We show that TS tokens have highly uneven spectral contributions, where many tokens share redundant frequency patterns while a small subset preserves critical temporal evidence. We also observe that prompt-token influence attenuates with model depth, suggesting that full prompt retention across all layers is unnecessary. Based on these findings, we develop an adaptive token budgeting framework that compresses TS tokens via frequency-domain structure and progressively reduces prompt tokens across layers. Experiments across forecasting, classification, imputation, and anomaly detection demonstrate up to 7.68$\times$ inference acceleration and performance gains in 78\% of evaluated settings, showing the effectiveness of asymmetric token compression for scalable TS foundation models.

07.
arXiv (CS.AI) 2026-06-18

Do Neural Networks Lose Plasticity in a Gradually Changing World?

arXiv:2602.09234v2 Announce Type: replace-cross Abstract: Continual learning has become a trending topic in machine learning. Recent studies have discovered an interesting phenomenon called loss of plasticity, referring to neural networks gradually losing the ability to learn new tasks. However, existing plasticity research largely relies on benchmarks with abrupt task transitions, without examining whether the abruptness itself contributes to the observed plasticity loss. In this paper, we investigate the role of transition abruptness by simulating gradually changing environments through input/output interpolation and task sampling. We perform theoretical and empirical analysis, showing that the severity of plasticity loss is closely tied to the abruptness of task transitions, and can be substantially reduced when the environment changes gradually.

08.
arXiv (CS.AI) 2026-06-12

From Digital to Physical: Digital Agents as Autonomous Coaches for Physical Intelligence

arXiv:2601.21570v2 Announce Type: replace Abstract: The field of Embodied AI is witnessing a rapid evolution toward general-purpose robotic systems, fueled by high-fidelity simulation and large-scale data collection. However, this scaling capability remains severely bottlenecked by a reliance on labor-intensive manual oversight from intricate reward shaping to hyperparameter tuning across heterogeneous backends. Inspired by LLMs' success in software automation and science discovery, we introduce \textsc{EmboCoach-Bench}, a benchmark evaluating the capacity of LLM agents to autonomously engineer embodied policies. Spanning 32 expert-curated RL and IL tasks, our framework posits executable code as the universal interface. We move beyond static generation to assess a dynamic closed-loop workflow, where agents leverage environment feedback to iteratively draft, debug, and optimize solutions, spanning improvements from physics-informed reward design to policy architectures such as diffusion policies. Extensive evaluations yield three critical insights: (1) autonomous agents can qualitatively surpass human-engineered baselines by 26.5\% in average success rate; (2) agentic workflow with environment feedback effectively strengthens policy development and substantially narrows the performance gap between open-source and proprietary models; and (3) agents exhibit self-correction capabilities for pathological engineering cases, successfully resurrecting task performance from near-total failures through iterative simulation-in-the-loop debugging. Ultimately, this work establishes a foundation for self-evolving embodied intelligence, accelerating the paradigm shift from labor-intensive manual tuning to scalable, autonomous engineering in embodied AI field.

09.
arXiv (CS.CV) 2026-06-11

Damage-TriageFormer: A Foundation-Model Framework for Typology-Based Building Damage Assessment from Mono-Temporal Imagery

Decision-relevant building damage assessment is critical for prioritizing resources and recovery after a disaster, yet most automated methods either flatten damage into a single severity scale (no damage, minor, major, destroyed) or require paired pre- and post-event imagery that is often unavailable for emerging hazards. This paper presents Damage-TriageFormer, a single-image, post-event, footprint-conditioned model that produces a damage typology rather than a severity scale. We contribute: (1) DamageTriage-Bench, a new benchmark built from NOAA Emergency Response Imagery across Hurricane Michael (2018), Hurricane Helene (2024), and the 2025 Los Angeles wildfire complex, with five typology classes that distinguish roof damage from structural damage and, within each, partial from total extent; and (2) Damage-TriageFormer, which extends a DINOv3 ViT-L backbone with a Simple Feature Pyramid for higher-resolution instance pooling, a two-stage gated damage head, and an auxiliary severity-regression objective. Our model achieves macro F1 of 0.624 on validation and 0.619 on a held-out stratified test set, performing strongest where operational triage needs it most, with per-class F1 of 0.91 and 0.84 on undamaged buildings and total structural collapse, respectively. While the rare Total Roof Damage class remains difficult due to its limited examples and an inherently ambiguous label boundary, our results show that single-image post-event imagery can support actionable building damage typing, enabling targeted emergency response and resource allocation without a pre-event reference.

10.
arXiv (CS.AI) 2026-06-18

Analysing drivers and interdependencies in European electricity markets using XAI

arXiv:2606.19118v1 Announce Type: new Abstract: Electricity markets are inherently complex systems characterised by strong nonlinearities, high-dimensional interactions, and increasing interdependence across regions. While deep neural networks (DNNs) have demonstrated strong predictive capabilities for electricity prices, their lack of interpretability limits their usefulness for understanding the underlying drivers of price formation. This paper addresses this gap by combining DNN models with explainable artificial intelligence (XAI) techniques to analyse the determinants of electricity prices across 39 European bidding zones. We employ SHAP (SHapley Additive exPlanations) to quantify feature contributions and apply and extend SSHAP, an aggregation framework to improve interpretability in high-dimensional settings. The analysis identifies that renewable energy sources, particularly solar, play a disproportionately important role in price formation despite their lower share in total power generation. Gas prices remain a dominant and consistent driver across electricity markets, while interconnections significantly shape price dynamics, highlighting the strong interdependence of European electricity systems. In addition, a synthetic EU-wide electricity market is constructed to explore the counterfactual scenario of a fully integrated market with a single price.

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

CAF-Gen: A Multi-Agent System for Enriching Argumentation Structures

Formalizing complex reasoning from natural text is one of the central challenges in computational linguistics. It requires systems to understand not just keywords but also the context and complex reasoning embedded in a text. Current Argument Mining (AM) techniques identify basic claims and premises, yet they often struggle to capture the richer structural information required by advanced schemas such as the Carneades Argumentation Framework (CAF), which incorporates features such as premise types, proof standards, and argument schemes. We address this limitation by introducing CAF-Gen, an automated multi-agent framework designed to enrich shallow argument structures into CAF-compliant argument models. By employing an iterative Creator-Reviewer pipeline, a creator agent's output is validated by a critical agent to ensure structural integrity. This multi-agent collaboration is crucial for mitigating the structural instability typical of single-pass generative models. Our experiments demonstrate that the iterative feedback loop improves the quality of the resulting data and achieves strong alignment with the original annotations, while producing structurally richer models. Our findings show that the multi-agent system can overcome the limitations of single-pass generation, providing a robust methodology for the automated modeling of formal argumentation.

12.
bioRxiv (Bioinfo) 2026-06-11

A Deep Hypergraph Learning Model for Predicting Antimicrobial Combination Effects Across Bacterial Targets

Antimicrobial resistance (AMR) creates an urgent need for efficient strategies to identify effective antibacterial combinations. Combination therapy, including antimicrobial peptides (AMPs) paired with conventional antibiotics, is a promising approach, but exhaustive experimental screening across drug pairs and bacterial targets is impractical. This study introduces a hybrid GCN-based hypergraph neural network (HGNN) for predicting antimicrobial-agent combination outcomes against bacterial targets. Each antimicrobial-agent-antimicrobial-agent-bacterium triplet is represented as a ternary hyperedge, enabling the model to learn context-dependent interaction patterns. The framework integrates SMILES-derived molecular graph embeddings for antimicrobial agents, including conventional antibiotics and AMPs, with taxonomy-derived bacterial representations. The prediction task was formulated as a three-class classification problem: synergy, antagonism, and non-interaction. The non-interaction class included experimentally verified indifferent records and synthetic presumed non-interaction triplets generated by negative sampling. Model development used drug-pair-grouped splitting, five-fold grouped cross-validation within the training/validation partition, and final evaluation on a held-out test set. On the held-out three-class test set, the selected GCN-based HGNN achieved an accuracy of 0.83, weighted F1-score of 0.84, macro F1-score of 0.80, and ROC-AUC of 0.95. Per-class evaluation showed accuracies of 0.80 for synergy, 0.92 for antagonism, and 0.85 for non-interaction. Pair-type analysis showed strong performance across AMP-AMP, AMP-conventional antibiotic, and conventional antibiotic-conventional antibiotic combinations. These findings suggest that hypergraph-based representation learning can support computational prioritization of antimicrobial combinations for experimental follow-up. Further studies will be needed to improve model interpretability and to perform prospective validation of predicted synergistic combinations.

13.
medRxiv (Medicine) 2026-06-10

Trajectories of brain structure and function in young adult carriers of genetic frontotemporal dementia variants

Background and Objectives: Converging evidence hints at neurodevelopmental effects in genetic frontotemporal degeneration (FTD). In cross-sectional studies, for some genes, young adult FTD variant carriers show differences in brain volumes and cognition compared to familial non-carriers. However, longitudinal trajectories may more sensitively capture FTD-related neurodevelopmental vs. neurodegenerative changes than cross-sectional approaches. This study examined longitudinal trajectories of brain volumes, executive function, and plasma biomarkers in young adult carriers compared to familial non-carriers, as measures of neurodevelopmental and neurodegenerative outcomes of FTD-causing variants. Methods: This longitudinal cohort study comprised participants, aged 18-30 years, from the FTD Prevention Initiative across Europe, Canada, and the USA. Genetic groups included C9orf72 (47%), MAPT (30%), and GRN (23%). Linear mixed-effects models were computed to assess longitudinal outcomes across age between groups, controlling for sex, scanner (for brain volumes), and education (for executive function); random effects accounted for between-subject variability nested within family membership. Results: Variant carriers (n=147) and familial non-carriers (n=113) did not differ in age (mean{+/-}SD, 25.9{+/-}3.2 years), sex (53% female), or number of visits (2.1{+/-}1.7). Young adult C9orf72 repeat expansion carriers exhibited smaller thalamic volumes than non-carriers at the reference age of 26 years (b=-982.8mm3, SE=317.0, p=0.0046, f2=0.32), with relatively stable trajectories across ages 18-30 (i.e., no change over time). Trajectories of rostral anterior cingulate volumes differed in C9orf72 carriers and non-carriers across age, where carriers showed relatively stable trajectories and non-carriers showed age-appropriate declines (b=64.4mm3, SE=29.9, p=0.035, f2=0.07). For MAPT and GRN, there were little to no differences in total brain, cortical, or subcortical volumes between groups and over time. No longitudinal differences were observed between carriers and non-carriers in executive function, or plasma NfL or GFAP for any genetic group. Discussion: C9orf72 repeat expansions were linked to smaller average thalamic volumes and stable trajectories between ages 18 to 30, supporting potential neurodevelopmental origins. The modest evidence supporting an absence of difference in neurodegenerative biomarkers and executive function suggests minimal early neurodegeneration and functional preservation in young adulthood.

14.
arXiv (CS.CV) 2026-06-11

What Semantics Survive the Connector? Diagnosing VLM-to-DiT Alignment in Video Editing

Flow matching based video generative models have been increasingly relying on prepended Vision-Language Models (VLMs) to handle complex, instruction-based video editing. The prevailing assumption underlying this paradigm is that a connector module can seamlessly align the VLM's rich multi-modal reasoning with the original text embedding space of DiTs. However, we hypothesize that this alignment acts as a severe semantic bottleneck, degrading fine-grained structural variables. Verifying this is challenging, as end-to-end evaluations conflate alignment failures with generation errors, and natural datasets lack disentangled annotations. To rigorously investigate this, we propose a controlled data processing pipeline based on video composition that results in TRACE-Edit, a diagnostic dataset focusing on relation-based editing. Leveraging this dataset, we propose a comprehensive diagnostic protocol to analyze two important designs of meta-query and connector in the existing video editing models. Systematic evaluation of four representative model cases reveals that fine-grained structural semantics can be severely degraded during alignment. Our findings overturn the assumption of lossless semantic transfer, identifying the VLM-to-DiT alignment as a major bottleneck and providing a new diagnostic foundation for future multi-modal alignment architectures.

15.
medRxiv (Medicine) 2026-06-16

Prevalence and Correlates of Ideal Cardiovascular Health among Ugandan Adolescents: A Cross-Sectional Study

Introduction: Cardiovascular disease (CVD) risk factors often emerge during adolescence and track into adulthood, yet data on cardiovascular health (CVH) in sub-Saharan Africa remain limited. We assessed the prevalence and correlates of ideal CVH among Ugandan adolescents. Methods: We analysed baseline data of adolescents enrolled in a cluster-randomised controlled trial being conducted in urban (Kampala) and rural (Jinja) districts of Uganda. In this study, Ideal CVH was defined as meeting "ideal" status of 5-7 of the American Heart Association's Life's Simple 7 metrics. Random-effects logistic regression was used to identify factors associated with ideal CVH, accounting for village-level clustering. Results: We recruited 1316 participants with a mean age of 13.2 years, of whom 58.1% were female. Overall, the prevalence of ideal CVH was 66.8% (95% CI: 64.2% - 69.3%). The prevalence was higher in Jinja (74.4%, 95%CI: 70.9% - 77.7%) than Kampala (59.6%, 95%CI: 55.8%-63.2%) and the difference was evident (p

16.
arXiv (CS.CL) 2026-06-12

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

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

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

Controlled Comparison of Machine Learning Models for Fault Classification and Localization in Power System Protection

arXiv:2510.00831v2 Announce Type: replace Abstract: The increasing complexity of modern power systems, driven by the integration of inverter-based and distributed energy resources, challenges the reliability of conventional protection schemes and motivates the use of machine learning for protection tasks. However, published results are often difficult to compare because datasets, sensing assumptions, and decision horizons vary across studies. This paper presents a controlled comparison of machine learning models for fault classification (FC) and fault localization (FL) under identical sensing, timing, and validation conditions on a common electromagnetic transient dataset, using decision windows of 10-50 ms to reflect protection-relevant time scales. For FC, the best-performing nonlinear models achieve F1 scores above 0.98 already at 10 ms, while lower-capacity models degrade at shorter horizons but improve with longer windows, indicating that relevant fault-type information is already present in the earliest transient. For FL, the top-performing models reach a stable localization error of about 10 % of normalized line length across all evaluated horizons, while weaker models form a clearly separated second performance tier. Line-resolved analysis shows that localization accuracy varies across grid segments, indicating topology-dependent difficulty rather than insufficient temporal context alone. These findings provide a controlled reference for comparing machine learning models across two protection tasks with fundamentally different information requirements.

18.
arXiv (CS.CV) 2026-06-17

Seeing Is Not Screening: Multimodal Hidden Instruction Attacks on Agent Skill Scanners

Agent skills are emerging as an important attack surface in LLM-based systems. Through an empirical study of existing skill scanners, we find that current defenses primarily rely on textual descriptions, manifests, and source code as the main signals for security analysis, which can leave visually conveyed malicious intent insufficiently examined. This creates a practical blind spot: harmful operational instructions hidden in images may bypass scanning while still being recoverable by multimodal agents during deployment. To systematically investigate this threat, we propose SkillCamo, a document-mediated multimodal instruction attack that conceals malicious instructions within images bundled with a skill while rewriting the surrounding documentation to naturally reference those images as part of the normal workflow. Thus, the attack does not rely on the image alone, but on the joint interpretation of textual guidance and visual payload at execution time. To defend against such attacks, we further propose ExecScan, an execution-grounded multimodal scanning module that performs intent extraction, behavior reconstruction, abuse assessment, and deliberative execution simulation over skill artifacts. ExecScan jointly analyzes documentation, code, referenced resources, and visual content to recover hidden instructions, reconstruct executable behavior chains, and identify downstream risks such as exfiltration, destruction, persistence, deception, and privilege escalation. Extensive experiments show that image-hidden malicious instructions challenge existing skill scanners, while ExecScan can improve the skill scanning performance.

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

ReMoT: Reinforcement Learning with Motion Contrast Triplets

We present ReMoT, a unified training paradigm to systematically address the fundamental shortcomings of VLMs in spatio-temporal consistency – a critical failure point in navigation, robotics, and autonomous driving. ReMoT integrates two core components: (1) A rule-based automatic framework that generates ReMoT-16K, a large-scale (16.5K triplets) motion-contrast dataset derived from video meta-annotations, surpassing costly manual or model-based generation. (2) Group Relative Policy Optimization, which we empirically validate yields optimal performance and data efficiency for learning this contrastive reasoning, far exceeding standard Supervised Fine-Tuning. We also construct the first benchmark for fine-grained motion contrast triplets to measure a VLM's discrimination of subtle motion attributes (e.g., opposing directions). The resulting model achieves state-of-the-art performance on our new benchmark and multiple standard VLM benchmarks, culminating in a remarkable 25.1% performance leap on spatio-temporal reasoning tasks.

20.
arXiv (CS.CV) 2026-06-18

Pre-Deployment Robustness Stress Testing for CT Segmentation Systems Using Clinically Motivated Multi-Corruption Augmentation

Deep learning-based CT segmentation systems often achieve high accuracy on clean benchmark images, but their performance may degrade under heterogeneous clinical imaging conditions such as noise, resolution loss, contrast variation, intensity shift, and artifacts. This instability can limit reliable deployment in real-world medical imaging workflows. We propose Robustness via Augmented Multi-corruption Pipeline (RAMP), a robustness-oriented augmentation framework for CT segmentation. RAMP combines anatomically constrained spatial perturbations, CT intensity transformations, and stochastic multi-corruption composition to expose models to clinically plausible image degradation during training. Across two CT segmentation evaluation settings, RAMP achieved the strongest corrupted-image performance and the smallest clean-to-corrupted robustness gap. In the five-organ noisy evaluation benchmark, RAMP improved mean corrupted Dice from 0.610 to 0.753 and reduced the robustness gap from 0.264 to 0.064 compared with the nnU-Net baseline. In Abdomen1K, RAMP improved mean corrupted Dice from 0.633 to 0.789 and reduced the robustness gap from 0.290 to 0.070. Although RAMP did not achieve the highest clean-image Dice, it substantially mitigated worst-case segmentation collapse under severe image degradation. These results suggest that multi-corruption augmentation can serve as a practical pre-deployment strategy for improving the reliability of CT segmentation systems in heterogeneous clinical environments.

21.
bioRxiv (Bioinfo) 2026-06-13

ProtAff: Protein Binding Affinity Prediction via LoRA-Finetuned ESM-2

Predicting the binding affinity of protein–protein interactions remains a central challenge in computational biology. Structure prediction models such as AlphaFold3 (AF3) and Boltz-2 can produce high-quality docking poses, and their confidence scores indicate structure quality, but these same scores fail to rank binding affinity among confirmed binders. Here we present ProtAff, a sequence-only affinity prediction model built on ESM-2 (650M parameters) with low-rank adaptation (LoRA) fine-tuning and a cross-attention module. ProtAff is trained using a margin ranking loss on 362,567 affinity measurements spanning 20 heterogeneous data sources, and we removed all training samples whose target sequence exceeds 50% similarity to the test target EGFR. On the AdaptyvBio EGFR benchmark (N = 55), ProtAff achieves a Spearman correlation coefficient {rho} = 0.413, outperforming the best AF3 metric ({rho} = 0.054), the best Boltz-2 metric ({rho} = -0.046), and ML-based predictors MINT ({rho} = 0.242) and CrossAffinity ({rho} = 0.216). Applied to the AdaptyvBio Nipah virus binder design competition, a pipeline incorporating ProtAff for affinity ranking produced a design with KD = 0.132 nM (2 of 5 designs confirmed binding), a 2.8-fold improvement over the competition winner. On a cross-target discrimination benchmark of 91 VHH-antigen crystal structures, ProtAff underperforms structural methods for distinguishing cognate from non-cognate pairings, indicating that sequence-based affinity models are effective for within-target ranking but not for cross-target specificity.

22.
arXiv (CS.AI) 2026-06-15

Adversarial Concept Search: Predicting Compositional Errors From Feature Geometry

arXiv:2606.13934v1 Announce Type: new Abstract: Humans cannot always intuit what scenarios are most challenging to LLMs. Hoping to capture challenging edge cases, developers either design problems to be difficult for humans or curate extensive benchmarks. What if we could instead anticipate which scenarios a model will fail on? In this paper, we use an LLM's representational geometry to predict which concept combinations it will fail on. We attribute this compositional failure to interference between salient features. In tasks that require systematic composition - toy programmatic settings, multihop reasoning, multilingual factual recall - we find that when a pair of concepts is encoded near-orthogonally, the model reliably composes them. When their linear encodings are close, producing interference, the model fails to compose them. Our method reliably anticipates failure modes across different compositional tasks, without evaluating specific inputs. These results lay the groundwork to use representational geometry to identify high-risk examples, construct targeted stress tests, and provide a scalable foundation for active learning in real-world deployment.

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

Reliability of Probabilistic Emulation of Physical Systems

arXiv:2606.12997v1 Announce Type: new Abstract: Two dominant approaches have emerged for generating probabilistic forecasts of physical systems: generative models, such as diffusion or flow matching; and ensembles of deterministic models with stochasticity injected, trained using the continuous ranked probability score (CRPS) loss. While both approaches have demonstrated strong predictive accuracy, the reliability of their uncertainties has not been systematically assessed. We address this gap by developing a framework to evaluate both approaches across diverse 2D spatiotemporal physical systems, under matched model size and computational budget. We assess the reliability of probabilistic emulation by inspecting the empirical coverage of predictive intervals, while also considering accuracy and computational efficiency metrics. CRPS-trained ensembles typically achieve more reliable uncertainties on both single-step prediction and autoregressive rollouts, demonstrating better coverage than the standard alternative of training generative models in a latent space. Moreover, the CRPS approach offers significantly faster inference. When generative models are trained in ambient rather than a compressed latent space, which is often infeasible for high-dimensional problems, they exhibit comparable coverage to CRPS-trained ensembles, though with substantially larger inference latency. In contrast, when CRPS-trained ensembles are trained in latent space they do not show a marked degradation in coverage with respect to ambient space. Both generative models and CRPS-trained ensembles demonstrate good predictive accuracy. To facilitate future research and application, we release AutoCast, a modular framework implementing both generative models and CRPS-trained ensembles, alongside AutoSim, a flexible dataset generation package for rapid prototyping.

24.
arXiv (CS.CV) 2026-06-15

LiAuto-GeoX: Efficient Grounded Driving Transformer

Dense 3D reconstruction has demonstrated immense potential for spatial understanding, yet its viability as a real-time, onboard representation for autonomous driving remains an open challenge. Existing large-scale visual geometry models typically require substantial computational resources and lack the long-range geometric fidelity, surround-view consistency, and real-time efficiency demanded by dynamic driving environments. To bridge this gap, we present LiAuto-GeoX, an efficient grounded driving transformer designed for deployable, ego-centric 3D scene understanding. Our approach begins by learning a high-capacity driving geometry model from large-scale surround-view data, utilizing sparse LiDAR priors to provide robust geometric grounding in distant, ambiguous, or structure-sparse regions. We then instantiate this capability into a highly compact 155M-parameter onboard model through a novel geometry-preserving distillation framework. This framework employs mask-guided depth-aware distillation to retain fine-grained metric structures by emphasizing geometrically informative regions, and relative-pose relational distillation to enforce cross-view spatial consistency through pose-induced geometric relations. Extensive evaluations reveal that LiAuto-GeoX runs at 220 FPS on KITTI while maintaining high-fidelity dense reconstruction, enabling real-time deployment. The learned geometry transfers seamlessly to downstream autonomy tasks, achieving 90.6 PDMS in trajectory prediction, 24.63 mIoU in occupancy prediction, and 47.67 IoU in future-frame prediction. These all demonstrate that efficient dense 3D reconstruction can transcend its traditional role as a perception target to serve as a scalable, foundational geometric representation for next-generation autonomous driving.

25.
arXiv (CS.CV) 2026-06-11

DynaTok: Token-Based 4D Reconstruction from Partial Point Clouds

We address 4D reconstruction from partial point cloud sequences, where depth-sensor observations are incomplete, unordered, and lack explicit temporal correspondences. This geometry-only setting is challenging due to missing observations and ambiguous dynamics. While recent progress has largely relied on image-based methods, existing point-based approaches typically focus on single objects, assume relatively complete inputs, or require explicit correspondences. To address these limitations, we propose DynaTok, a point-based framework for correspondence-free 4D reconstruction from partial point cloud sequences without images. DynaTok encodes frames into compact latent tokens, aggregates incomplete observations over time with a Transformer-based spatiotemporal encoder, and decouples geometry and motion through residual tokens in a unified model. A flow-matching decoder then reconstructs complete, temporally consistent 4D point-cloud sequences conditioned on the latent tokens. Experiments on object- and scene-level benchmarks demonstrate improved reconstruction quality and temporal coherence from partial point cloud observations. Project page: https://wrchen530.github.io/dynatok/.