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01.

arXiv (quant-ph) 2026-06-19 DOI: arXiv:2606.19470

Local controllability of heralded quantum linear optics

作者:

Tommaso Francalanci↗Nicol\`o Spagnolo↗Mario Sigalotti↗Eliott Z. Mamon↗Ulysse Chabaud↗Fabio Sciarrino↗

arXiv:2606.19470v1 Announce Type: new Abstract: Photonic linear optical networks provide a versatile platform for quantum information processing and quantum state engineering. However, the set of states that can be generated using passive linear optics alone is fundamentally constrained by bosonic symmetries. Heralding, based on conditional measurements on auxiliary modes, is a widely used technique to overcome these limitations and effectively enlarge the set of accessible states. Despite the widespread use of heralding, it is often unclear how specific ancillary resources impact the overall reachability of the target space. In this work, we investigate the local controllability of photonic states in linear optical networks by analyzing the rank of the Jacobian of the output state with respect to the underlying unitary circuit, which provides a quantitative measure of the dimension of the accessible tangent space at a given configuration. Our analysis ranges from passive linear optics to heralded linear optics, where auxiliary resources and conditional measurements are included. Within this framework, we quantify how different resources enlarge the locally accessible state space beyond that of passive linear optics and determine the resources required for the Jacobian rank to reach its maximal value, thereby achieving full local controllability. As maximal local rank is a necessary condition for global reachability, our framework offers a systematic tool to assess and compare the accessible state space of measurement-based photonic architectures, and to establish practical criteria for the resources needed in high-dimensional quantum state engineering.

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02.

arXiv (CS.AI) 2026-06-17 DOI: arXiv:2606.17507

LLM-as-Judge in Education: A Curriculum-Grounded Marking Pipeline

作者:

Xiwei Xu↗Chen Wang↗Jacky Jiang↗Phil Yang↗Qian Fu↗Mohan Dhall↗Wenjie Zhang↗Liming Zhu↗

arXiv:2606.17507v1 Announce Type: new Abstract: Generative AI and large language models (LLMs) are increasingly applied to question generation and automated assessment. However, deploying LLMs in preparation for high-stakes exams requires more than prompt engineering; it demands software pipelines that systematically ground model outputs in authorised curriculum artefacts and marking guidelines issued by education authorities. This paper presents a curriculum-grounded, configurable LLM-as-Judge pipeline for question-level marking, co-developed with an industrial partner, to support exam preparation for university admission. The pipeline identifies the relevant topics, subtopics, and cognitive demand of a question, and assembles verifiable and authorised context to support LLM judgement. Curriculum intent is operationalised through concrete syllabus artefacts, including prescribed verbs and outcomes, performance band descriptors, glossary definitions, and marking-guideline principles. A staged LLM workflow is employed to first generate question-specific rubrics, capturing structured expectations of performance, and then derive and evaluate marking criteria used to allocate marks to student responses. This design improves consistency, transparency, and alignment with official marking practices. Preliminary evaluation shows that the proposed LLM-as-Judge pipeline delivers marking outcomes comparable to human tutors, while yielding justifications that are more traceable to authorised curriculum artefacts and marking standards. The pipeline has also been integrated into an online study platform, where early deployment data provide initial insights into operational usage and manual overrides.

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03.

arXiv (CS.CV) 2026-06-11 DOI: arXiv:2606.12258

Bridging Day and Night: Unsupervised Cross-Domain Re-Identification with Synergistic Prompt and Prototype Learning

作者:

Jiyang Xu↗Rui Liu↗Hang Dai↗

Cross-domain day-night re-identification (ReID) is fundamentally challenged by the substantial visual appearance discrepancies between daytime and nighttime scenes. Existing fully supervised methods rely heavily on labor-intensive annotations, which are costly and exhibit limited generalization across domains. In this work, we investigate unsupervised day-night ReID and propose a novel framework that synergistically combines prompt learning and prototype-based representation learning to associate identities across domains without requiring manual labels. Our approach follows a progressive two-stage training strategy. In the first stage, we exploit the vision-language model to generate instance-specific textual prompts in an annotation-free manner. We employ an instance-level alignment mechanism to embed visual features and textual prompts into a unified semantic space, aligning unlabeled day/night images with learnable prompts via instance-aware dynamic-bias adaptation. In the second stage, we construct domain-specific prototype memory banks and introduce two complementary modules: i) an intra-domain identity association module to enhance feature discriminability within each domain, and ii) a cross-domain prototype matching module to reliably identify positive and negative prototype pairs, thereby establishing robust identity correspondences across day and night. Extensive experiments on public benchmarks validate the effectiveness of our method. Under the unsupervised setting, our framework attains Rank-1 accuracy comparable to state-of-the-art fully supervised methods.

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04.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2606.16334

Chronological Blindness: Benchmarking Temporal Reasoning in Vision-Language Models with CHRONOSIGHT

作者:

Parthaw Goswami↗Jaynto Goswami Deep↗

Human perception of visual scenes is inherently temporal. We instinctively recognise whether a fruit is ripening or rotting, whether construction is progressing or being demolished, and approximately how much time separates two photographs of the same subject. Whether large vision-language models (VLMs) share this competence remains an open and practically important question. We introduce CHRONOSIGHT, a rigorously controlled benchmark evaluating five dimensions of visual temporal reasoning: CHRONORANK (chronological ordering of image sequences), CHRONOLOCATE (ordinal stage localisation from a single image), CHRONODELTA (estimation of time elapsed between two images on a logarithmic scale), CHRONOREVERSE (detection of temporally reversed sequences), and CHRONOODD (identification of a temporal outlier within a set). The benchmark comprises 1{,}000 items across eight process families (biological growth, food transformation, physical weathering, construction, environmental change, human ageing, astronomical phenomena, and urban dynamics) spanning timescales from minutes to millennia. We evaluate eight open-source VLMs (500 M to 19 B parameters) under two prompting regimes and collect human performance baselines. Human performance averages 0.89 across tasks; the best open model (Qwen2.5-VL-7B) reaches 0.40 under direct prompting, a gap we term chronological blindness. Lightweight LoRA fine-tuning on 151 examples raises CHRONODELTA accuracy from near-zero to 0.43, transferring zero-shot to related tasks (CHRONOODD: 0.37; CHRONOREVERSE: 0.64)suggesting the bottleneck is partly instruction following rather than visual perception. Benchmark, code, and predictions will be released upon acceptance.

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05.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18723

Clinically Aligned Geometry Constraints for Robust IVUS Vessel Boundary Segmentation

作者:

Yunshu Chen↗Litao Yang↗Giuseppe Di Giovanni↗Jordan Tan↗Deval Mehta↗Andrew Lin↗Derek Chew↗Masasi Fujino↗Julie Butters↗Stephen Nicholls↗Zongyuan Ge↗Kyung Hoon Cho↗…

Intravascular ultrasound (IVUS) lumen and external elastic membrane (EEM) segmentation is important for quantitative coronary plaque burden assessment. Errors in lumen or EEM delineation directly propagate to plaque area, plaque burden and geometric measurements. However, standard methods prioritising overlap scores often suffer from boundary drift and topology errors, leading to inaccurate clinical measurements. We present GeoCat, a geometry-consistent network that processes 5-frame IVUS clips using dual Cartesian-polar encoders with cross-domain attention and temporal fusion. A differentiable geometry consistency loss directly supervises clinically relevant descriptors including diameters, orientations, and cross-sectional areas. The model is trained on 12,242 annotated frames from 146 patients acquired with two commercial IVUS systems. We evaluate performance using both segmentation accuracy and plaque-relevant clinical metrics, including Dice/IoU, boundary measures(95HD (mm), ASSD), topology violation rate, and clinical geometry errors (dmax/dmin, angles, and areas). On our dataset, GeoCat achieves a Dice of 0.93, reduces 95HD to 0.14 mm, and lowers topology violations to 1.0%. Importantly, it significantly improves geometric fidelity, yielding diameter errors of 0.13-0.16 mm and angular errors of ~8 degrees, supporting reliable plaque burden quantification.

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06.

bioRxiv (Bioinfo) 2026-06-11 DOI: HASH:6b752f4c6ba911b6dc514c9dee2dc163

Calibrated Uncertainty Quantification for Patient-Level AML Drug Sensitivity Prediction Using Split Conformal Prediction

作者:

Shokrzadeh↗A. J↗

Accurate prediction of ex vivo drug sensitivity in acute myeloid leukemia (AML) patients from transcriptomic data is a critical challenge for precision oncology. Existing computational approaches have explored uncertainty quantification in cancer drug response prediction primarily using cell line data, while patient-level AML models typically rely on heuristic confidence measures rather than statistically calibrated uncertainty estimates. Here, we present a framework applying split conformal prediction to patient-level AML drug response modeling using the BeatAML 2.0 cohort. We trained Elastic Net and XGBoost regressors on bulk RNA-seq gene expression profiles from 318 AML patients, analyzing 34,764 patient-drug observations across 122 compounds. Baseline models achieved median Pearson R values of 0.291 (Elastic Net) and 0.281 (XGBoost) across 122 drugs. Wrapping these models with split conformal prediction yielded well-calibrated prediction intervals across three confidence levels: empirical coverages of 81.4%, 90.7%, and 95.5% against nominal targets of 80%, 90%, and 95%, respectively. Analysis of prediction interval widths revealed substantial drug-class-specific uncertainty patterns, with HDAC and BCL-2 inhibitors exhibiting markedly higher uncertainty than MDM2 inhibitors, suggesting a potential association between transcriptomic predictability and drug mechanism of action, although several drug classes were represented by only a small number of compounds. Predictive uncertainty was not significantly associated with ELN2017 molecular risk classification (Kruskal-Wallis p=0.395) or NPM1 mutation status (p=0.788). These results demonstrate that statistically valid uncertainty quantification can be achieved for patient-level AML drug response prediction despite substantial biological heterogeneity. to the best of our knowledge, no published study has applied split conformal prediction to patient-level ex vivo drug sensitivity prediction in the BeatAML cohort, providing a principled alternative to heuristic confidence scoring approaches. Keywords: Acute myeloid leukemia (AML); Ex vivo drug sensitivity; Conformal prediction; Uncertainty quantification; Precision oncology; BeatAML; Transcriptomic biomarkers; Machine learning.

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07.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2509.01630

DiffCoord: Differentiable Coordination for Distributed Multi-Agent Trajectory Optimization

作者:

Bingheng Wang↗Yichao Gao↗Tianchen Sun↗Shanker Ajay↗Lin Zhao↗

arXiv:2509.01630v3 Announce Type: replace Abstract: Integrating the Alternating Direction Method of Multipliers (ADMM) with Differential Dynamic Programming (DDP) provides a scalable framework for distributed multi-agent trajectory optimization. In practice, ADMM is typically truncated for computational efficiency, tightly coupling parameters that would otherwise separately govern coordination quality and task performance. In this paper, we propose Differentiable Coordination (DiffCoord), a unified framework that jointly meta-learns these coupled parameters for the truncated ADMM-DDP pipeline. These parameters are generated by agent-wise neural networks for task adaptation, and the same networks are shared among isomorphic agents to enable scalability to varying agent counts. We achieve efficient meta-learning by differentiating the ADMM-DDP pipeline end-to-end. Notably, this yields an auxiliary ADMM-LQR distributed gradient solver that computes and coordinates meta-gradients with respect to these parameters. This solver inherits the computational structure of the pipeline, enabling reuse of key computation results and efficient parallelization over agents and along trajectory horizons. We validate DiffCoord through numerical and physical experiments on a cooperative aerial transport system, where it reconfigures quadrotor formations for safe 6-DoF load manipulation in tight spaces. It adapts robustly to varying team sizes and load dynamics, while reducing per-agent gradient computation time by up to 70% compared with state-of-the-art trajectory-gradient methods.

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08.

arXiv (math.PR) 2026-06-19 DOI: arXiv:2605.20541

Finite-Sample Bounds for Expected Signature Estimation under Weak Dependence

作者:

Bryson Schenck↗

arXiv:2605.20541v2 Announce Type: replace-cross Abstract: The expected signature uniquely determines the law of a random rough path under a moment-growth condition, yet finite-sample bounds for estimating its truncations from a single long dependent trajectory remain unavailable. We study a strictly stationary stochastic process equipped with a geometric rough-path lift, observed in non-overlapping blocks of equally-spaced samples, and prove a non-asymptotic mean-squared error (MSE) bound for the block-averaging estimator of its truncated expected signature. Under moment and stationarity assumptions together with a direct covariance-decay condition on block signatures – strictly weaker than $\alpha$-mixing and applicable to long-range-dependent processes – the error separates into a discretization term and a fluctuation term, with rates determined respectively by path regularity and dependence strength. A levelwise rough-factorial variance analysis keeps finite-truncation constants explicit and yields an optimal allocation rule under a fixed observation budget. We verify the assumptions for independent-coordinate fractional Ornstein–Uhlenbeck processes in three regimes: short-range (Hurst $1/41/2$. Monte Carlo experiments show empirical slopes steeper than the guaranteed upper-bound rates.

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09.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2606.17464

CheckMIABench: Firm Foundations For Membership Inference Attacks on Language Models

作者:

Jeffrey G. Wang↗Jason Wang↗Marvin Li↗Seth Neel↗

arXiv:2606.17464v1 Announce Type: new Abstract: Membership inference attacks (MIAs) are a canonical way to assess a machine learning model's privacy properties. Although several attempts have been made to evaluate MIAs on language models, the extant literature has suffered numerous difficulties in constructing clean evaluations to test new techniques. In particular, subtle distribution shifts between member and non-member sets can undermine the statistical validity of MIAs; recent work has underscored this by showing that "blind" methods with no access to the underlying model can perform far better than published methods on the same benchmarks. This paper constructs a benchmark for principled evaluation of MIAs against LLMs, by leveraging the insight that training data before and after a fixed point during training are drawn from the same distribution. Therefore, all open-source models with intermediate checkpoints and public training data can be converted into MIA testbeds. We apply our framework to a half-dozen published attacks on the Pythia and OLMo family of models, from 70M to 7B parameters. To facilitate further privacy research, we open-source a modular library for designing and implementing attacks in this setting: https://github.com/safr-ai-lab/pandora_llm.

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10.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2512.15133

HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens

作者:

Yi Zhou↗Haohao Qu↗Yunqing Liu↗Shanru Lin↗Le Song↗Wenqi Fan↗

arXiv:2512.15133v3 Announce Type: replace-cross Abstract: Proteins inherently possess a consistent sequence-structure duality. The abundance of protein sequence data, which can be readily represented as discrete tokens, has driven fruitful developments in protein language models (pLMs). A key remaining challenge, however, is how to effectively integrate continuous structural knowledge into pLMs. Current methods often discretize protein structures to accommodate the language modeling framework, which inevitably results in the loss of fine-grained information and limits the performance potential of multimodal pLMs. In this paper, we argue that such concerns can be circumvented: a sequence-based pLM can be extended to incorporate the structure modality through continuous tokens, i.e., high-fidelity protein structure latents that avoid vector quantization. Specifically, we propose a hybrid diffusion protein language model, HD-Prot, which embeds a continuous-valued diffusion head atop a discrete pLM, enabling seamless operation with both discrete and continuous tokens for joint sequence-structure modeling. It captures inter-token dependencies across modalities through a unified absorbing diffusion process, and estimates per-token distributions via categorical prediction for sequences and continuous diffusion for structures. Extensive results demonstrate that HD-Prot achieves competitive performance in unconditional sequence-structure co-generation, motif-scaffolding, protein structure prediction, and inverse folding tasks. Furthermore, our method can perform on par with state-of-the-art multimodal pLMs, despite being developed under limited computational resources (i.e., less than one-tenth the budget for modality extension fine-tuning). It highlights the viability of simultaneously estimating categorical and continuous distributions within a unified language model architecture, offering a promising alternative direction for multimodal pLMs.

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11.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2512.22560

RollArt: Disaggregated Multi-Task Agentic RL Training at Scale

作者:

Wei Gao↗Yuheng Zhao↗Tianyuan Wu↗Shaopan Xiong↗Weixun Wang↗Dakai An↗Lunxi Cao↗Dilxat Muhtar↗Zichen Liu↗Haizhou Zhao↗Ju Huang↗Siran Yang↗…

arXiv:2512.22560v2 Announce Type: replace-cross Abstract: Agentic Reinforcement Learning (RL) trains LLMs through multi-turn interactions with environments, producing workloads that mix compute-bound prefill, bandwidth-bound decoding, CPU-heavy environment execution, and bursty reward evaluation. Existing systems either colocate all stages on a single GPU cluster or decouple them only at a coarse granularity, overlooking hardware heterogeneity and incurring substantial synchronization overhead across stages. We present ROLLART, a system for multi-task agentic RL on disaggregated infrastructure. ROLLART maps each pipeline stage to best-fit hardware, routing prefill-heavy tasks to compute-optimized GPUs, decode-heavy tasks to bandwidth-optimized GPUs, and environments to CPU clusters. It decouples rollout at the trajectory level, allowing generation, environment interaction, and reward scoring to proceed independently, so that slow or failed environments never block the others. ROLLART offloads stateless reward computation to serverless infrastructure and overlaps rollout with training via staleness-bounded asynchronous weight synchronization. Our results demonstrate that ROLLART effectively improves training throughput and achieves 1.31–2.05 \(\times\) training time reduction compared to various RL systems. We also evaluated ROLLART by training a hundreds-of-billions-parameter MoE model for Qoder product on an Alibaba cluster with above 3,000 GPUs, demonstrating its stability and scalability.

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12.

arXiv (CS.LG) 2026-06-16 DOI: arXiv:2606.16978

Task-Error Residual Learning for Real-Robot Five-Ball Juggling

作者:

Kai Ploeger↗Jan Peters↗

arXiv:2606.16978v1 Announce Type: cross Abstract: For residual learning that refines existing behavior, sample efficiency depends on two things: how much information each rollout returns, and how efficiently the learner uses that information. Reinforcement learning's standard scalar reward carries far less information than the directional task error that defines the task. Random exploration further discards whatever information each rollout returns. Through residual learning with directional task-error supervision and a task error model that drives sample selection, we achieve stable three-, four-, and five-ball juggling on anthropomorphic Barrett WAM arms. Despite planning and controlling through a simple, idealized stack, the system converges from the second attempt. The first attempt drops, after which task error decreases monotonically without further failures. In comparison, five-ball juggling typically takes humans years of practice. We compare residual learners across two ternary axes, the directional information in the learning feedback and the commitment of the analytic prior, spanning Newton-style Jacobian updates, Composite Bayesian Optimization, and stochastic search methods. Both axes prove necessary: neither directional feedback nor an informative prior suffices alone, and the simplest method that combines them, a fixed-Jacobian Newton update, is the most reliable. The learned residual tolerates substantial prior misalignment and degraded joint tracking, affecting mainly convergence speed. The bottleneck for residual learning on real robots is therefore the information content of the supervision signal and how the learner uses it, not the accuracy of the surrounding stack. Video documentation of all experiments is available at https://kai-ploeger.com/residual-juggling.

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13.

arXiv (CS.CV) 2026-06-16 DOI: arXiv:2605.15796

Cross-Modal Registration Between 3D and 2D Fingerprints via Pose-Aware Unwrapping and Point-Cloud Fusion

作者:

Xiongjun Guan↗Jianjiang Feng↗Jie Zhou↗

Three-dimensional (3D) fingerprints preserve global finger geometry and local ridge structure while avoiding contact-induced deformation, but they remain difficult to integrate with legacy two-dimensional (2D) fingerprint systems. This paper addresses the intermediate stage between 3D acquisition and cross-modal matching, and presents a unified framework for 3D fingerprint preprocessing and registration across contactless and contact-based 2D modalities. The framework combines four components: 1) a nonparametric visualization and unwrapping method that converts a 3D fingerprint point cloud into a rolled-equivalent 2D representation without relying on a global finger-shape model; 2) a point-cloud fusion pipeline that registers and mosaics multiple partial 3D captures into a more complete fingerprint model; 3) an ellipse-based pose normalization method for canonical finger alignment; and 4) a pose-aware cross-modal registration strategy that improves compatibility between 3D fingerprints and both contactless and contact-based 2D fingerprints. Experiments on a self-collected multimodal fingerprint database containing 150 fingers show that the proposed framework achieves ridge-level 3D registration accuracy, robust pose estimation, and consistent gains in 2D compatibility. In particular, the 3D fusion error is concentrated around 0.09 mm, contactless 2D–3D registration reaches ridge-scale projection accuracy, and pose-aware unwrapping improves genuine matching scores relative to generic 3D unwrapping. These results support the use of 3D fingerprints as an effective geometric bridge across heterogeneous fingerprint modalities. The baseline implementation has been publicly released at https://github.com/XiongjunGuan/3DFpVisual.

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14.

arXiv (CS.CV) 2026-06-18 DOI: arXiv:2606.18869

Learning to Distort: Weakly-Supervised Image Quality Transfer for Prostate DWI Correction

作者:

YuCheng Tang↗Wen Yan↗Alexander Ng↗Natasha Thorley↗Pawel Rajwa↗Yipei Wang↗Aqua Asif↗Clare Allen↗Louise Dickinson↗Francesco Giganti↗David Atkinson↗Shonit Punwani↗…

Single-shot echo-planar prostate diffusion-weighted imaging (DWI) is frequently complicated by geometric distortions, which impact the ability to derive reliable diagnoses from such images. Developing automated correction methods is challenged by the absence of paired distorted and undistorted clinical scans. In this paper, we first propose a novel weakly-supervised image quality transfer (IQT) framework from undistorted to distorted images that utilizes image quality assessment (IQA) signals to supervise the transfer process. Unlike traditional methods that require expensive, voxel-wise paired data or resort to developing unpaired algorithms, our approach utilizes image-level quality labels (here, distorted vs. undistorted) to establish latent quality prototypes within a pre-trained feature space. Recognizing that simulating realistic distortions is more reliable than direct unpaired correction, we describe a weakly-supervised prototype flow matching algorithm to explicitly regularize generative trajectories towards distorted prototypes, producing realistic susceptibility artifacts that mimic clinical degradations. By synthesizing these realistic pairs, we enable a second IQT model to be trained in the forward direction for distortion correction. Experimental results demonstrate that our generated images successfully mimic the diagnostic interference of real-world artifacts, which leads to more capable distortion correction IQT models. In addition to qualitative comparisons, we also conduct exhaustive quantitative evaluations that compare our approach with existing unpaired approaches (e.g., CycleGAN, UNIT-DDPM, and OT-FM) - as either forward or reverse alternatives - by assessing clinical downstream task performance in PI-RADS and Gleason score classification, using both in-distribution and external data sets.

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15.

arXiv (CS.CV) 2026-06-12 DOI: arXiv:2606.13288

Cross-Modal Masked Compositional Concept Modeling for Enhancing Visio-Linguistic Compositionality

作者:

Wei Li↗Zhen Huang↗Xinmei Tian↗

Contrastively trained vision-language models like CLIP, have made remarkable progress in learning joint image-text representations, but still face challenges in compositional understanding. They often exhibit a "bag-of-words" behavior–struggling to capture the object relations, attribute-object bindings, and word order dependencies. This limitation arises not only from the reliance on global, single-vector representations for optimization, but also from the insufficient exploitation and modeling of the rich compositional information inherently present in paired image text data. In this work, we propose MACCO (MAsked Compositional Concept MOdeling), a framework that masks compositional concepts in one modality and reconstructs them conditioned on the full contextual information from the other, enabling the model to capture and align cross-modal compositional structures more effectively. To facilitate this process, we introduce two auxiliary objectives that jointly align and regularize masked features both inter-modally and intra-modally. Extensive experiments on five compositional benchmarks, along with in-depth analyses, demonstrate that our approach not only significantly enhances compositionality in VLMs but also improves their ability to capture syntactic structure and linguistic information. Additionally, the improved compositionality also benefits text-to-image generation and multimodal large language model. Code is available at https://github.com/hiker-lw/MACCO.

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16.

arXiv (CS.LG) 2026-06-15 DOI: arXiv:2606.14139

Decoupled Latent Optimization of Diffusion Models for Full Waveform Inversion

作者:

Chen Min↗Zheng Ma↗

arXiv:2606.14139v1 Announce Type: new Abstract: Full waveform inversion (FWI) recovers subsurface velocity from seismic recordings by solving a severely ill-posed, nonconvex PDE-constrained optimization. Classical regularizers stabilize the inversion but fail to reproduce realistic geological structures; recent diffusion-prior methods improve realism at the cost of a fragile trade-off between data fidelity and prior consistency. We propose Decoupled Latent Optimization (DLO), which relaxes the standard latent-optimization formulation into a quadratic-penalty objective over an auxiliary physical variable and a latent variable. The data-fidelity gradient acts in physical space, the diffusion sampler contributes only through a decoded prior sample, and the standard smoothed-velocity initialization of classical FWI is preserved. On the OpenFWI benchmark, DLO outperforms classical regularizers and existing diffusion-based methods under clean, noisy, and missing-trace acquisitions. The prior, trained on 70*70 OpenFWI models, transfers directly to the Marmousi and Overthrust benchmarks, where DLO recovers intricate fault structures and remains robust to initialization smoothing and measurement noise.

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17.

bioRxiv (Bioinfo) 2026-06-10 DOI: HASH:0ae81a27bf9a086fee6e6a04ee445e5c

Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins

作者:

Orr↗A. K↗Bateman↗

Motivation: Spurious protein sequences, resulting from gene prediction errors, theoretically should not yield folded structures. AlphaFold2 was previously shown to predict short spurious sequences with high pLDDT scores and was therefore unlikely to distinguish between real proteins and spurious proteins which are usually short. We evaluate whether newer structure prediction methods (ESMFold and AlphaFold3) similarly predict short sequences with high pLDDT or if they better discriminate between spurious and real proteins. Results: All three structure prediction methods (ESMFold, AlphaFold2, and AlphaFold3) predict short spurious sequences from AntiFam with unexpectedly high pLDDT scores, however the discrimination between spurious and real proteins improves beyond 100 amino acids. By analysing sequences with disparate pTM and pLDDT scores, we identified two likely spurious shadow ORFs in Swiss-Prot and one potentially non-spurious AntiFam entry. Using the structure prediction scores, we developed a Gaussian Process Model and evaluated its performance on AlphaFold DB, identifying potential spurious proteins at scale. While limited on its own, this model can increase confidence in spurious protein identification when combined with other methods.

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18.

PLOS Computational Biology 2026-06-17 DOI: HASH:e88f2c8cdb36cc862f18f83f9b7d8a0c

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

作者:

Thomas Sheffield↗

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.

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19.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2606.13277

ProtoX-AD: Self-Explainable Time Series Anomaly Detection and Characterization

作者:

Aitor S\'anchez-Ferrera↗Elisabeth Wetzer↗Kristoffer Wickstr{\o}m↗Michael Kampffmeyer↗Robert Jenssen↗

arXiv:2606.13277v1 Announce Type: cross Abstract: Recent advances in time series anomaly detection (TSAD) have highlighted the effectiveness of self-supervised classification-based approaches. These methods apply transformations to normal training samples, training a classifier to recognize transformation-specific patterns that help identify anomalies through increased classification errors. Despite their strong performance, a significant challenge is their lack of explainability, as they provide limited insight into the characteristics of flagged anomalies. To address this limitation, we propose ProtoX-AD, a prototype-based self-explainable framework for self-supervised TSAD. ProtoX-AD learns transformation-aware latent representations alongside interpretable prototypes, enabling both accurate anomaly detection and the identification of distinct anomalous profiles through prototype-based explanations. Additionally, it allows for systematic analysis of how transformation design impacts detection performance and explainability. Experimental results on synthetic and real-world datasets demonstrate that ProtoX-AD achieves detection performance comparable to its black-box counterparts while offering more consistent and semantically meaningful explanations than existing explainable baselines. Our code is publicly available at https://github.com/Aitorzan3/ProtoX-AD.

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20.

arXiv (quant-ph) 2026-06-16 DOI: arXiv:2606.16549

What does measuring one qubit reveal about another? $K$-networks as a directed diagnostic for quantum circuits

作者:

Kostas Blekos↗Paulo Vitor Itabora\'i↗

arXiv:2606.16549v1 Announce Type: new Abstract: Many-qubit circuit states are hard to inspect directly, so they are often summarized by pairwise graph weights. Common pairwise weights report symmetric correlations, while many circuit questions are directed and basis-specific: if qubit $i$ is measured in a given basis, how strongly does the outcome reshape the conditional state of qubit $j$? We define $K_{i\to j}$, a directed, basis-conditioned edge weight for this question. It is large when the two measurement outcomes occur with comparable probability and leave qubit $j$ in clearly different conditional states; it is zero when the source outcome is deterministic or the target states are indistinguishable. The scalar uses standard binary-ensemble distinguishability; the paper's contribution is to turn this conditional comparison into a directed network layer for circuit states. The resulting networks are computable from two-qubit reduced density matrices. They are diagnostic (not entanglement measures): for pure two-qubit states $K$ reduces to the tangle $C^2$ (squared concurrence)[WoottersConcurrence,CKWTangle], while separable mixed states can reach $K=1$. Examples on teleportation, Grover, QAOA, and random circuit families show the intended use: $K$-networks map feed-forward, phase, and interaction-graph structure that symmetric or computational-basis summaries can leave weak or absent.

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21.

PLOS Computational Biology 2026-06-18 DOI: HASH:6e8442307a2a29c945e26cd772b8b374

Ten simple rules for turning your qualifying exam into an NIH-style fellowship proposal: A guide for graduate students

作者:

Courtney Peña-Lima↗

by Courtney Peña-Lima, Cameron S. Bader, Brendan K. Ball, Troy C. Dildine, Mekhala V. Dissanayake, Iris van ‘t Erve, Albina Ibrayeva, Amy Nippert, M.K. Quinn, Chelse Spinner, Samuel Thompson, Antonio Tomasso, Crystal M. Botham Qualifying exams, often referred to as “quals” or candidacy exams, are an important milestone in doctoral programs. Although the style of quals varies greatly by program and institution, it is usually a proposal that requires students to develop research ideas as well as their scientific writing skills. Many quals are modeled after funding mechanisms that graduate students can apply to and on a topic that the student will pursue in their dissertation. This paper offers graduate students a step-by-step guide on how to turn their quals into a fellowship-style research proposal, using National Institutes of Health (NIH) mechanisms as a benchmark, as this is the norm within US research institutions. This paper will be most useful for students who have completed or are in the process of completing proposal-based qualifying exams, usually in the second year of a doctoral program.

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22.

medRxiv (Medicine) 2026-06-22 DOI: HASH:530e2b2dcda471a9171443870f82bd25

Genetic modifiers of psychiatric, motor, and cognitive symptoms in Huntington's disease

作者:

Li↗Q. S↗Regeneron Genetic Center↗Kwak↗Sampaio↗Vogt↗T. F↗Rosinski↗

The Enroll HD natural history platform provides rich longitudinal phenotypes enabling genome wide analyses across diverse clinical domains. Psychiatric symptoms are a major source of morbidity in Huntington's disease (HD), yet the genetic architecture underlying their onset is poorly understood. We analyzed ~18,000 people with HD (PwHD) to define genetic determinants of ages at psychiatric, motor, and cognitive symptom onset, and HD diagnosis. GWAS meta analysis recapitulated 11 established modifiers of motor onset and identified a novel locus spanning RAB3B/ZFYVE9 associated with age at violent/aggressive behavior onset. Exome wide analyses in Enroll HD participants implicated rare variants in FAN1, PMS1, POLD1, and HTT. Several HD modifiers of motor and cognitive symptom onset (MSH3, FAN1, HTT) also influenced psychiatric symptom onset, whereas PMS1 and POLD1 showed significant association with motor symptom onset. Psychiatric polygenic scores predicted psychiatric symptom onset, revealing a hybrid architecture combining psychiatric liability in general population with HD- or repeat expansion disease (RED) specific pathways.

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23.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.16222

Latent Thought Flow: Efficient Latent Reasoning in Large Language Models

作者:

Xiandong Zou↗Jing Huang↗Jianshu Li↗Pan Zhou↗

arXiv:2606.16222v1 Announce Type: new Abstract: Large Language Models (LLMs) increasingly rely on intermediate reasoning, yet explicit Chain-of-Thought (CoT) suffers from a linguistic space bottleneck: each thought must be decoded into tokens, causing high inference overhead. Latent reasoning moves deliberation into continuous space, but existing methods mostly learn deterministic or reward-maximizing paths, lacking a principled way to allocate probability across trajectories with different correctness and costs. We propose Latent Thought Flow (LTF), which models reasoning as variable-length continuous trajectories and trains a sampler to match a reward-induced posterior over answer quality and computation cost. We instantiate this with a continuous GFlowNet using stochastic latent transitions. To handle sparse answer supervision, we introduce an Entropy-Weighted Subtrajectory Balance objective for intermediate rewards and a reference-prior regularizer to anchor exploration. Experiments under finetuning and transfer learning settings show that LTF outperforms explicit CoT and latent reasoning baselines, improving accuracy by 9.5% while reducing reasoning length by 27.2% on average compared with strong latent reasoning baselines.

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24.

arXiv (CS.AI) 2026-06-12 DOI: arXiv:2602.00343

Standardized Methods and Recommendations for Green Federated Learning

作者:

Austin Tapp↗Holger R. Roth↗Ziyue Xu↗Abhijeet Parida↗Hareem Nisar↗Marius George Linguraru↗

arXiv:2602.00343v2 Announce Type: replace-cross Abstract: Federated learning (FL) enables collaborative model training over privacy-sensitive, distributed data, but its environmental impact is difficult to compare across studies due to inconsistent measurement boundaries and heterogeneous reporting. We present a practical carbon-accounting methodology for FL CO2e tracking using NVIDIA NVFlare and CodeCarbon for explicit, phase-aware tasks (initialization, per-round training, evaluation, and idle/coordination). To capture non-compute effects, we additionally estimate communication emissions from transmitted model-update sizes under a network-configurable energy model. We validate the proposed approach on two representative workloads: CIFAR-10 image classification and retinal optic disk segmentation. In CIFAR-10, controlled client-efficiency scenarios show that system-level slowdowns and coordination effects can contribute meaningfully to carbon footprint under an otherwise fixed FL protocol, increasing total CO2e by 8.34x (medium) and 21.73x (low) relative to the high-efficiency baseline. In retinal segmentation, swapping GPU tiers (H100 vs.\ V100) yields a consistent 1.7x runtime gap (290 vs. 503 minutes) while producing non-uniform changes in total energy and CO2e across sites, underscoring the need for per-site and per-round reporting. Overall, our results support a standardized carbon accounting method that acts as a prerequisite for reproducible 'green' FL evaluation. Our code is available at https://github.com/Pediatric-Accelerated-Intelligence-Lab/carbon_footprint.

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25.

arXiv (quant-ph) 2026-06-16 DOI: arXiv:2606.15066

Quantum simulation of the Liouville equation in classical mechanics with discontinuous potential via Schrödingerization

作者:

Shi Jin↗Shuyi Zhang↗

arXiv:2606.15066v1 Announce Type: new Abstract: We develop quantum simulation algorithms for the Liouville equation of classical mechanics with discontinuous potential. Such discontinuities represent potential barriers at which classical particles undergo energy preserving transmission or reflection, and the resulting interface conditions must be incorporated into the numerical flux. We combine Hamiltonian-preserving schemes by Jin and Wen in Commun. Math. Sci. 3(3), 285-315 (2005) with the Schrödingerization method, which embeds the resulting nonunitary semi-discrete dynamics into a unitary Schrödinger type system in one additional auxiliary variable [arXiv:2212.14703, arXiv:2212.13969]. For one-, two-, and $n$-dimensional problems with grid aligned interfaces, we construct sparse matrix representations of the transmission and reflection fluxes using step and hat functions, derive the corresponding Hamiltonians of the Schrödingerized systems, and analyze their sparse-access query complexity. In the sparse-access oracle model, the resulting algorithms have a polynomial dependence on the inverse accuracy and avoid the exponential dependence on the phase-space dimension suffered by classical grid based Hamiltonian-preserving schemes, up to the cost of implementing the oracles and the postselection overhead. We also describe the postselected recovery of the physical solution state and the quantum readout of macroscopic observables such as density and averaged velocity through overlap estimation. Numerical experiments based on classical simulation of the Schrödingerized dynamics validate the proposed formulation and illustrate the correct transmission/reflection behavior at potential barriers.

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