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01.
arXiv (CS.AI) 2026-06-15

A Multi-Agent AI System for Automated High School Transcript Processing: Collaborative Document Analysis at Scale

arXiv:2606.13916v1 Announce Type: new Abstract: Each year, college admissions offices face an overwhelming challenge: processing millions of high school transcripts, each with unique formats, grading systems, and layouts. This manual process creates operational bottlenecks that delay admissions decisions and consume valuable resources. We present a transformative solution through a multi-agent AI system where specialized agents collaborate to automatically process diverse transcript formats through intelligent coordination and communication. Our multi-agent architecture consists of three specialized agents-a Pattern Recognition Agent for format-specific parsing, a Semantic Analysis Agent for natural language understanding, and a Vision Intelligence Agent for multimodal document analysis-coordinated by an Orchestration Agent that manages agent communication and result reconciliation. Our key innovation lies in agent-based quality control using GPA extraction as a coordination signal, ensuring reliable agent collaboration and preventing critical information loss. When evaluated on 40 real world transcripts from high schools across 13 U.S. states, our agent system successfully processed every document, achieving 96.7% accuracy compared to expert manual review while maintaining practical processing speeds of 45 seconds per transcript. This work demonstrates how multi-agent coordination can solve complex document processing challenges, offering institutions a scalable, collaborative AI solution that preserves accuracy while dramatically reducing processing time.

02.
arXiv (quant-ph) 2026-06-25

Self-testing Quantum Supermaps

arXiv:2606.25124v1 Announce Type: new Abstract: By certifying quantum operations from measurement statistics directly, without any assumption on the internal workings of the devices involved, self-testing enables a uniquely reliable identification of quantum objects. While such device-independent characterization has been shown to be possible for states, measurements and channels, it has so far not been extended to quantum supermaps – operations that act on quantum channels themselves and can combine them in either a well-defined causal order or also, remarkably, in an indefinite causal order. Here we show that quantum supermaps can be identified device-independently. Specifically, we obtain two levels of certification, depending on the network structure of the experiment: when each slot of the supermap accepts a single uncharacterized black box, identification up to local embedding combs is obtained; when several black boxes are inserted within each slot, identification up to local extracting and injecting maps is achieved. We illustrate our approach on four examples – the identity comb, a bit-flip error-correcting comb, the comb describing Grover's algorithm, and the quantum switch – providing in particular the first self-test of both a quantum algorithmic comb and a causally indefinite quantum process. Notably, in the latter case, this provides a new way to certify causal indefiniteness in a device-independent manner.

03.
bioRxiv (Bioinfo) 2026-06-24

Pharmacological Stratification of Public Bioactivity Databases: A Reusable, OECD-Anchored Curation and Benchmarking Framework Demonstrated for Opioid Receptors

Public bioactivity databases are heterogeneous not only in measurement type, where binding affinities and functional potencies are reported on different scales, but in pharmacology: the same compound and target can carry agonist, antagonist, or inhibitor records measured through binding displacement, cAMP, {beta}-arrestin, or [35S]GTP{gamma}S readouts that quantify different biological events. Pooling these records produces models whose output is detached from any coherent pharmacological claim. Prior work has standardized bioactivity at scale and quantified the noise from mixing measurement types, but pharmacological mechanism and assay-readout class have not been treated as a primary axis of large-scale curation. This study presents an auditable, OECD-anchored framework that stratifies public records by action type and assay readout before modeling, converting heterogeneous data into externally validated, interpretable QSAR tasks that compose with existing standardization resources rather than replacing them. The framework is demonstrated on the four opioid receptors (MOR, DOR, KOR, and nociceptin/orphanin FQ, NOP). Four public sources were reconciled into 72,148 merged records and 50,977 curated measurements spanning 19,585 compounds, each carrying auditable attributes for source agreement, endpoint meaning, pharmacology class, assay readout, and trust tier. Receptor-level binding tasks formed a compact benchmark with strong locked external performance, including KOR pK (R2 = 0.79, n = 798) and DOR pK (R2 = 0.77, n = 736). Pharmacology- and readout-resolved functional endpoints yielded externally validated strata that pooled labels would obscure, including a MOR antagonist functional-inhibition endpoint (R2 = 0.86, n = 110) and agonist potency endpoints for DOR, KOR, and MOR (R2 up to 0.81). Comparison against a fully pooled baseline shows that pooled models either match stratified models on coherent endpoints or reach a deceptively high R2 on functional-IC endpoints by training predominantly on binding-displacement records, so the pooled number predicts affinity rather than functional activity. SHAP attribution indicates that binding and functional potency encode partially distinct structure-activity signals. The dataset contract, not model performance alone, defines the validity and scope of a QSAR claim, and stratification is a precondition for a functional model to support a defensible claim. Curation logic, derived tables, frozen data, and reproducibility artifacts are released.

04.
arXiv (CS.CL) 2026-06-25

Beyond Next-Observation Prediction: Agent-Authored World Modeling for Sequential Decision Making

Recent studies on world modeling for Large Language Model (LLM) agents typically formulate the learning objective as next-observation prediction. However, this objective ties supervision to what a transition happens to reveal, which may omit the dynamics most relevant to the agent's current decision. To bridge this gap, we propose Agent-Authored World Modeling (AAWM), a training procedure that constructs supervision from the policy's own decision needs. Specifically, at each state, the agent identifies what it needs to understand about the environment before acting. These needs drive the retrieval of relevant transition evidence across trajectories, which is then synthesized into training targets that capture decision-oriented dynamics instead of reconstructing the next observation. This aligns the training objective with the dynamics the policy needs before acting, not with the contents of the next observation. Experimental results validate the effectiveness of AAWM across multiple environments and training settings. These results show that decision-aware world-model targets provide a more effective learning signal than next-observation prediction.

05.
medRxiv (Medicine) 2026-06-15

Bidirectional associations between cannabis use, oddball performance, and P3 event-related potential

Importance: Cannabis use remains prevalent in youth despite concerns regarding its potential impact on cognitive function. Unraveling whether the association between cannabis use and cognition is partially due to preexisting differences or primarily related to use is vital to understanding underlying mechanisms. Objective: To estimate the longitudinal association between cannabis initiation and cognitive trajectories, indexed by task performance and P3 event-related potential (ERP), and to estimate whether baseline cognition is associated with cannabis initiation. Design: Data were analyzed from the ongoing longitudinal Collaborative Study on the Genetics of Alcoholism (COGA) cohort, which was followed up approximately every 2-5 years from 2004 to 2025. Setting: 6 sites across the United States. Participants: Adolescent and young adult offspring of past COGA participants and control families who reported on their cannabis use and who had Visual Oddball (VOP) performance and P3 ERP data (N=4814; 52.4% female, 68.4% white) were grouped based on the timing of cognitive data collection relative to cannabis initiation into Pre-onset (n=2,449; [&ge;]1 assessment) and Post-onset (n=998; [&ge;]3 assessments) subsamples. Main Outcomes and Measures: VOP measures include performance accuracy (%), reaction times (ms), and P3 amplitude (V) and latency (ms) during target trials. Cannabis measures included lifetime use of cannabis (i.e., ever used) and age at first use. Results: High P3 amplitude, and prolonged P3 latency and reaction time were associated with a reduced hazard of cannabis initiation (All Hazards Ratio, [H.R.s]< 0.91, p's

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

Photon anti-bunching in high harmonic generation

arXiv:2606.17620v1 Announce Type: new Abstract: Photon anti-bunching is the direct evidence for the existence of photons without having a classical counterpart. Unlike bunching of photons, which can have a semi-classical description, the effect of photon anti-bunching can only be understood with quantized electromagnetic fields. However, for the process of high harmonic generation (HHG), where many photons of the driving field are upconverted to a single photon of higher energy, there is yet no clear evidence for the presence of individual photon emission. The key result of this work is the prediction of photon anti-bunching in the process of HHG, marking it the first theoretical discovery of non-classicality in the temporal correlations of HHG photons. While other non-classical signatures in HHG, such as sub-Poissonian statistics or squeezing, have been discussed for an ensemble of photons, the anti-bunching signature reported here is a signature of a single photon. This is achieved by using the recently developed Heisenberg picture approach for quantum optical HHG, revealing clear anti-bunching signatures in the intensity correlation function across the entire harmonic spectrum.

07.
medRxiv (Medicine) 2026-06-22

A blinded, counterbalanced rater design for evaluating AI-assisted summarisation of tertiary clinical genomics reports: methodology of the QNOMX-VHIR-CPSP-001 Phase 1 study

Background. Tertiary clinical genomics reports condense layered molecular findings into documents that treating oncologists must read, translate, and act upon; manual summarisation of these reports is time-consuming and variable. Tools that assist summarisation and translation into local languages are emerging, yet the field lacks an agreed methodology for evaluating such tools before any downstream clinical use. The appropriate first endpoint is fidelity of the generated summary to its source report, assessed by qualified human raters under blinded scoring, not downstream variant classification. Methods. QNOMX-VHIR-CPSP-001 Phase 1 is a single-site, non-interventional clinical performance study conducted at Vall d'Hebron Institut de Recerca (VHIR) under ISO 20916:2019 as a Clinical Performance Study Protocol. De-identified tertiary cancer genomics reports from pediatric oncology cases are summarised by the AI-assisted summarisation system under evaluation and, in parallel, by the standard manual workflow. Qualified raters score both summary types against the source genomics report using the Quality Summary Index (QSI), a six-dimension, five-point rubric adapted from the Provider Documentation Summarization Quality Instrument, under a blinded, counterbalanced, two-period crossover with a minimum fourteen-day washout. Two co-primary composite endpoints, content and presentation, are analysed for non-inferiority under a Bayesian hierarchical model, with a frequentist linear mixed model as the convergence check. Inter-rater reliability is reported as Krippendorff's ; a Monte-Carlo power analysis of the fixed clustered design is pre-specified. Discussion. The design isolates summarisation quality from clinical decision-making by scoring both summary types against the same source report under blinding, counterbalancing, and a fourteen-day washout. Conclusion. The QSI rubric, the counterbalanced crossover, and the pre-specified Bayesian primary with frequentist convergence check define a replicable protocol for early-stage evaluation of AI-assisted summarisation in tertiary genomics reporting; observed variance components will inform sample-size determination for Phase 2.

08.
bioRxiv (Bioinfo) 2026-06-13

MoE-Bind: Guiding De Novo Protein Binder Generation with Sparse Experts

作者:

De novo protein binder design has been dominated by structure-based pipelines that require known three-dimensional target conformations and consume substantial compute and generation time per design, limiting their throughput and accessibility for routine large-scale binder exploration. Sequence-only generative models promise a faster and lighter alternative, yet existing systems remain uniformly dense and frequently reintroduce structural computation at inference, undermining the core advantages they were intended to deliver. Across the broader language modelling community, transformers have meanwhile transitioned from fully dense designs to sparse Mixture-of-Experts architectures that decouple capacity from per-token compute, a shift that has yet to reach sequence-only protein binder generation. We present MoE-Bind, an autoregressive protein binder generator that, for the first time in this domain, combines Multi-head Latent Attention with a sparse Mixture-of-Experts feed-forward network and is evaluated under two independent structure predictors, Boltz-2 and AlphaFold2-Multimer. Despite activating less than half the per-token parameters of compute-matched dense baselines, MoE-Bind matches or exceeds them on full-length receptor-conditioned binder generation on a leakage-free Docking Benchmark 5.0 evaluation, transfers without peptide-specific training to short-peptide design, and reduces training and inference compute by a large margin. Routing analysis on generated binders reveals interpretable expert specialization at both the individual amino acid and biochemical group level, a structured expert-token alignment not previously reported for natural-language MoE models. These results show that sparse architectural design, rather than scale, can deliver fast, structure-free, and interpretable protein binder generation.

09.
arXiv (CS.AI) 2026-06-17

Handling Feature Heterogeneity with Learnable Graph Patches

arXiv:2606.17667v1 Announce Type: cross Abstract: In recent years, the rapid development of foundation models and graph pre-training technologies has spurred increasing interest in constructing a universal pre-trained graph model or Graph Foundation Model (GFM). However, a significant challenge is that existing models are unable to address feature heterogeneity in graph data without textual information, which hinders the transferability of graph models across different datasets. To bridge this gap, we propose the concept of learnable graph patches, which we regard as the smallest semantic units of any graph data. We decompose the graph into learnable graph patches by unfolding the node features and constructing corresponding patch structures separately. We then design a framework that mines transferable information from graph data across domains. Specifically, after extracting graph patches, we propose a patch encoder to extract knowledge from each unit and a patch aggregator to learn how the units are combined into a whole. Due to its domain-agnostic nature, the model can be applied to downstream data across different domains. Furthermore, we analyze the connection between our method and existing graph models, as well as the transferability of the node embeddings it generates. Empirically, our method not only achieves the capability to use multi-domain graphs for pre-training, but also shows enhanced performance across various downstream datasets and tasks. Moreover, we observe consistent improvement in downstream performance as the volume of pre-training data increases.

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

Data Intelligence Agents: Interpreting, Modeling, and Querying Enterprise Data via Autonomous Coding Agents

arXiv:2606.19319v1 Announce Type: cross Abstract: Production data integration is bottlenecked by repeated, lossy handoffs between data owners, engineers, and analysts who must collaboratively discover, structure, and query enterprise data. We present Data Intelligence Agents (DIA), a system of three agents (Data Interpreter, Schema Creator, and Query Generator) that compresses this workflow by treating autonomous coding agents (ACAs) as a first-class abstraction: rather than emitting text, the agents generate, execute, validate, and repair concrete artifacts, draw on a shared memory for experience reuse, and surface each for review by domain experts. DIA is deployed in production for enterprise customers. We study the Query Generator in depth and evaluate it in fully autonomous mode across seven SQL benchmarks spanning four task categories and four dialects. It matches or surpasses the best published results on all seven, demonstrating that an architecture grounded in execution, built on ACAs and a shared memory, generalizes across the data intelligence workload with adaptation confined to natural-language instructions.

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

Re-feeding Is Not Replaying: Measuring Replay Noise in Counterfactual Token-Credit Estimation

Per-token counterfactual credit estimation asks which token in a language-model rollout caused the final answer to be right or wrong: cut the transcript at a pivot, substitute an alternative token, replay continuations, and compare outcomes. Published methods re-feed the transcript prefix as a fresh prompt, assuming this reproduces the state the model passed through during generation. We measure what that assumption costs on a stock inference engine, with a three-pass design: continuations resumed from the verified decode-time KV state, an identical second exact pass (a replica noise floor), and a re-feed pass. Across six configurations and three models (including a GRPO-trained checkpoint), at low-margin decision tokens, re-feeding changes the credit estimate at rates 14-28 percentage points above the replica floor (7-21pp under a treatment-independent conditioning; problem-clustered t = 2.9-6.4). Most changes are zero-boundary crossings of the quantized estimator rather than polarity reversals, and the perturbation is consistent with mean-zero, so averaged quantities are largely safe; but selection is not: a critical-token set chosen by thresholding $|\hat{A}_t|$ under re-feed overlaps the exact-resume selection at Jaccard 0.34-0.90, versus a 0.63-0.96 replica ceiling. A causal confirmation closes the loop: under vLLM's batch-invariant kernels all three passes are identical on every measured channel, with both disagreement rates exactly zero. Replica passes themselves disagree on 9-23% of eligible estimates: single-sample credit measurements at decision tokens are unreliable under any replay. Settings were fixed in advance; exact-pass cache hits in the second campaign are instrumented (100% hit rate, 3,434 pivots); total compute was under 10 USD. We recommend that counterfactual credit studies resume decoder state or use batch-invariant kernels, and report a replica floor.

12.
arXiv (CS.CV) 2026-06-25

Improving Factuality of 3D Brain MRI Report Generation with Paired Image-domain Retrieval and Text-domain Augmentation

Acute ischemic stroke (AIS) requires time-critical decision-making, where inaccurate interpretation of neuroimaging findings can lead to irreversible disability. Diffusion-weighted imaging (DWI) and apparent diffusion coefficient (ADC) maps from magnetic resonance imaging (MRI) are central to detecting acute infarction, yet generating factually reliable radiology reports directly from 3D MRI remains challenging due to the difficulty of learning robust cross-modal alignments between volumetric images and clinical text. We propose paired image-domain retrieval and text-domain augmentation (PIRTA), a retrieval-augmented generation framework that improves report factuality by avoiding explicit image-text alignment. PIRTA retrieves clinically similar 3D DWI/ADC volumes using a pretrained 3D vision encoder and leverages their paired clinician-authored reports to ground large language model (LLM)-based report generation. Experiments on multi-institutional in-house data, a held-out external privacy-preserving cohort, and the public ISLES benchmark demonstrate that PIRTA achieves strong image-domain retrieval performance and consistently improves ischemic-territory accuracy, a clinically grounded surrogate for report factuality, compared to direct image-to-text baselines. These results indicate that retrieval-grounded generation provides a scalable and reliable paradigm for producing factually consistent radiology reports from complex 3D brain MRI. Source code is available at https://github.com/jhlee0619/PIRTA.

13.
arXiv (CS.AI) 2026-06-25

CausalRAG2: Hierarchical Causal Knowledge Graph Design for RAG

arXiv:2602.05143v2 Announce Type: replace Abstract: Retrieval augmented generation (RAG) has enhanced large language models by enabling access to external knowledge, with graph-based RAG emerging as a powerful paradigm for structured retrieval and reasoning. However, existing graph-based methods often over-rely on entity-centric node matching and lack explicit causal modeling, leading to unfaithful or spurious answers. Prior attempts to incorporate causality are typically limited to local or single-document contexts and also suffer from information isolation that arises from modular graph structures, which hinders scalability and cross-module causal reasoning. To address these challenges, we propose CausalRAG2, a framework that rethinks knowledge organization for graph-based RAG through causal gating across hierarchical modules. CausalRAG2 explicitly models causal relationships to suppress spurious correlations while enabling scalable reasoning over large-scale knowledge graphs. We also introduce HolisQA, a benchmark for holistic comprehension beyond entity-centric matching. Extensive experiments demonstrate that CausalRAG2 consistently outperforms competitive graph-based RAG baselines across multiple datasets and evaluation metrics. Our work establishes a principled foundation for structured, scalable, and causally grounded RAG systems. Our code and HolisQA benchmark are available at https://github.com/Pwnb/CausalRAG2.

14.
arXiv (CS.CL) 2026-06-12

EurekAgent: Agent Environment Engineering is All You Need For Autonomous Scientific Discovery

LLM-based agents have shown increasing potential in automating scientific discovery. Given an optimizable metric and an execution environment, they can propose, validate, and iterate scientific solutions, and have produced results that outperform human-designed approaches. As model capabilities continue to improve, we argue that the bottleneck for autonomous scientific discovery is shifting from prescribing agent workflows to designing agent environments: the resources, constraints, and interfaces that shape agent behavior. We frame this as environment engineering: building environments that amplify productive behaviors, such as open-ended exploration, systematic artifact management, and inter-agent collaboration, while suppressing harmful behaviors, such as reward hacking and high-friction human oversight. We present EurekAgent, an environment-engineered agent system for metric-driven autonomous scientific discovery. EurekAgent engineers the environment along four dimensions: permissions engineering for bounded agent execution and isolated evaluation; artifact engineering for filesystem and Git-based collaboration; budget engineering for budget-aware exploration; and human-in-the-loop engineering for easy human supervision and intervention. EurekAgent sets new state-of-the-art results on multiple mathematics, kernel engineering, and machine learning tasks, including new state-of-the-art 26-circle packing results discovered with less than $11 in total API cost. We open-source our code and results, and call for environment engineering as a core research direction for developing reliable autonomous research agents.

15.
arXiv (CS.AI) 2026-06-16

Auditing Reward Hackability in Code RL Training Environments

arXiv:2606.16062v1 Announce Type: new Abstract: We measure the rate at which code RL environments accept incorrect solutions as correct. On a 49-task sample of SWE-bench Verified, 28.5% of tasks have test suites weak enough that a Docker-verified incorrect patch passes them. On 20 R2E-Gym tasks across 6 repositories, the same pipeline at single-shot exploit generation yields 25.0%. A random-effects meta-analysis over 134 frontier model submissions to SWE-bench Verified finds, within the same human-rated difficulty stratum, model Pass@1 is +14.14 percentage points higher on flagged-hackable tasks than on robust ones (95% CI [+11.80, +16.48]; one-sided p < 10^-6; I^2 = 0%; 123 of 134 models positive). We then describe a procedure for hardening the broken tasks. An inline LLM judge with a Docker gold-sanity gate runs each generated test against the gold solution before the judge is consulted. On the 11 broken tasks in the audit, the gate flags 65 of 105 decisive LLM-generated tests as failing on the gold patch itself, a 61.9% per-augmentation defect rate the LLM judge alone misses. With diversity-biased retry, the loop converges 9 of 11 tasks to a gated upgrade.

16.
arXiv (CS.AI) 2026-06-15

From Sorting Algorithms to Scalable Kernels: Bayesian Optimization in High-Dimensional Permutation Spaces

arXiv:2507.13263v4 Announce Type: replace-cross Abstract: Bayesian Optimization (BO) is a powerful tool for black-box optimization, but its application to high-dimensional permutation spaces is severely limited by the challenge of defining scalable representations. The current state-of-the-art BO approach for permutation spaces relies on an exhaustive $\Omega(n^2)$ pairwise comparison, inducing a dense representation that is impractical for large-scale permutations. To break this barrier, we introduce a novel framework for generating efficient permutation representations via kernel functions derived from sorting algorithms. Within this framework, the Mallows kernel can be viewed as a special instance derived from enumeration sort. Further, we introduce the Merge Kernel , which leverages the divide-and-conquer structure of merge sort to produce a compact, $\Theta(n\log n)$ to achieve the lowest possible complexity with no information loss and effectively capture permutation structure. Our central thesis is that the Merge Kernel performs competitively with the Mallows kernel in low-dimensional settings, but significantly outperforms it in both optimization performance and computational efficiency as the dimension $n$ grows. Extensive evaluations on various permutation optimization benchmarks confirm our hypothesis, demonstrating that the Merge Kernel provides a scalable and more effective solution for Bayesian optimization in high-dimensional permutation spaces, thereby unlocking the potential for tackling previously intractable problems such as large-scale feature ordering and combinatorial neural architecture search.

17.
arXiv (CS.LG) 2026-06-16

Representation Costs in Data Science: Foundations and the Quasi-Banach Spaces of Deep Neural Networks

arXiv:2606.14954v1 Announce Type: cross Abstract: We develop a general framework for analyzing representation costs of parametric data-fitting methods through their parameter-space regularizers. From this abstract perspective, we define representation costs for arbitrary parametric models and reveal their induced (native) function spaces. This unifies recent function-space views of data-fitting methods. We also prove that many natural results hold in this abstract setting, including representer theorems for parametric methods on their native spaces. The framework also rigorously connects parametric methods with their equivalent nonparametric descriptions under sufficient overparameterization. Classical methods and their native spaces, such as kernel methods / reproducing kernel Hilbert spaces, wavelets / Besov spaces, and shallow neural networks / variation spaces emerge as special cases of our abstract framework. A byproduct of "axiomatizing" the study of representation costs is that we also immediately obtain new results for deep neural networks: For depth-$L$ feedforward ReLU networks, their induced native spaces are $p$-normable quasi-Banach spaces with $p = 2/L$. This reveals that the inductive bias of deep neural networks (as given by the representation cost) cannot be captured by norms for depths $L > 2$.

18.
PLOS Computational Biology 2026-06-05

A multiscale, Bayesian inference approach to augment mechanistic models of cell signaling with machine-learning predictions of binding affinity

by Holly A. Huber, Stacey D. Finley Computational models in systems biology are often underdetermined—that is, there is little data relative to the complexity and size of the model. This lack of data is primarily due to limits in our ability to observe specific biological systems and restricts the utility of computational models. To reduce this uncertainty, recent methods have explored augmenting parameter inference of systems biology models with predictions from machine learning models. Such approaches expand the pool of data that is applicable for the inference problem. Here, we explore augmenting the parameter inference of intracellular signaling models. We choose to investigate signaling because experimental measurements of the variables of interest, protein dynamics, are still quite limited. To investigate, we propose a novel, multiscale, Bayesian inference approach that augments traditional signaling data with predictions of binding affinity. These predictions are generated using a machine learning pipeline with measurements of amino acid sequence, from the Universal Protein Resource, or protein structure, from the Protein Data Bank, as inputs. We find that we can successfully integrate these measurements into the inference problem using our novel framework. Excitingly, this integration significantly improves the parameter estimates of signaling models. We demonstrate that how much this improvement impacts predictions of signaling depends on the sensitivity of the prediction to perturbations in the parameter values. Overall, the framework we establish here improves the parameter inference of intracellular signaling models by successfully bridging data on protein sequence and structure with systems-level signaling.

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

Power Battery Detection

Power batteries are essential components in electric vehicles, where internal structural defects can pose serious safety risks. We conduct a comprehensive study on a new task, power battery detection (PBD), which aims to localize the dense endpoints of cathode and anode plates from industrial X-ray images for quality inspection. Manual inspection is inefficient and error-prone, while traditional vision algorithms struggle with densely packed plates, low contrast, scale variation, and imaging artifacts. To address this issue and drive more attention into this meaningful task, we present PBD5K, the first large-scale benchmark for this task, consisting of 5,000 X-ray images from nine battery types with fine-grained annotations and eight types of real-world visual interference. To support scalable and consistent labeling, we develop an intelligent annotation pipeline that combines image filtering, model-assisted pre-labeling, cross-verification, and layered quality evaluation. We formulate PBD as a point-level segmentation problem and propose MDCNeXt, a model designed to extract and integrate multi-dimensional structure clues including point, line, and count information from the plate itself. To improve discrimination between plates and suppress visual interference, MDCNeXt incorporates two state space modules. The first is a prompt-filtered module that learns contrastive relationships guided by task-specific prompts. The second is a density-aware reordering module that refines segmentation in regions with high plate density. In addition, we propose a distance-adaptive mask generation strategy to provide robust supervision under varying spatial distributions of anode and cathode positions. The source code and datasets will be publicly available at \href{https://github.com/Xiaoqi-Zhao-DLUT/X-ray-PBD}{PBD5K}.

20.
arXiv (math.PR) 2026-06-11

On Skorokhod Problems for Reflected and Singular Stochastic Heat Equations

arXiv:2606.11951v1 Announce Type: new Abstract: We prove a Skorokhod decomposition for the Markov processes $X^a$ and $X$ associated to the gradient Dirichlet forms with respect to the measures $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, respectively. Here, $\mu^{\beta}$ is the law of the standard Brownian bridge $\beta$, while $\rho^a$ and $\rho$ denote densities which are given by $\rho^a(z) := \mathbf{1}_{[0,\infty)}(\bar{z}_a)$ and $\rho(z) := \int_0^1 \mathbf{1}_{[0,\infty)}(\bar{z}_x) \, dx$, respectively, for all $z\in L^2(0,1)$ which have a (unique) continuous representative $\bar{z}$ which vanishes at zero and one. To this end, we derive infinite-dimensional integration by parts formulas (IbPFs) w.r.t. $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$, which contain Hida distributions alongside the usual drift terms. We represent these Hida distributions by integration w.r.t. vector measures of bounded variation. The vector measures in question are constructed via an approximation argument, making use of a generalization of Prokhorov's theorem for vector measures. We further prove that, almost surely, the sample paths of $X^a$ and $X$ take values in the equivalence class of continuous functions vanishing at zero and one for all and $dt$-almost all times, respectively. The main motivation for studying $\rho^a\mu^{\beta}$ and $\rho\mu^{\beta}$ lies in the fact that the distributional terms in their IbPFs are simplifications of the distributional term in the IbPF w.r.t. the law of the reflected Brownian bridge on the unit interval $\mu^{|\beta|}$. Representing the latter by integration w.r.t. a vector measure of bounded variation is still an open problem.

21.
arXiv (quant-ph) 2026-06-16

Witnessing Spin-Orbital Entanglement using Resonant Inelastic X-Ray Scattering

arXiv:2512.06718v2 Announce Type: replace Abstract: Entanglement plays a central role in quantum technologies, yet its characterization and control in materials remain challenging. Recent developments in spectrum-based entanglement witnesses have enabled new strategies for quantifying many-body entanglement in macroscopic materials. Here, we develop a protocol for detecting spin-orbital entanglement using experiment-accessible resonant inelastic x-ray scattering (RIXS). Central to our approach is the construction of a Hermitian generator from experimentally measurable spectra, which allows us to compute the quantum Fisher information (QFI) available in spin–orbital systems. The resulting QFI provides upper bounds for $k$-producible states and thus serves as a robust witness of spin-orbital entanglement. To account for realistic experimental limitations, we further extend our framework to include relaxed QFI bounds applicable to measurements lacking full polarization resolution.

22.
medRxiv (Medicine) 2026-06-15

Multi-domain AD risk burden and plasma biomarkers in cognitively unimpaired adults

Introduction: Alzheimer's disease (AD) pathology accumulates decades before symptom onset, yet how the cumulative effect of genetic, familial, and modifiable lifestyle risk burden jointly affects plasma biomarker levels and trajectories in cognitively unimpaired older adults remains unknown. Methods: We analyzed data from 261 participants in the PREVENT-AD cohort. A composite risk score integrating APOE e4 status, polygenic score, family history, and modifiable/lifestyle risk was examined against six plasma biomarkers using linear regression and linear mixed-effects models. Results: APOE e4 was the strongest predictor of plasma biomarker levels. Higher composite risk burden was associated with elevated ptau181, ptau217, ptau217/Ab42, and GFAP levels, and lower Ab42/40 levels. A higher risk burden was predictive of accelerated ptau181 accumulation. Discussion: Cumulative AD risk burden is broadly associated with plasma biomarker levels and specifically predicts accelerated ptau181 accumulation in cognitively unimpaired older adults, supporting structured composite risk profiling as a framework for AD risk stratification.

23.
arXiv (CS.CV) 2026-06-25

Learning Diachronic Representations of Ancient Greek Letterforms

Learning representations that remain robust across centuries of variation in handwriting is a key challenge in diachronic representation learning. Taking one of the longest continuously used writing systems, ancient Greek, as a case study, we introduce three datasets for diachronic representation learning: Hell-Char, a curated training set spanning the 3rd-1st centuries BCE, and two evaluation sets, PaLit-Char (2nd-5th c. CE) and Med-Char (9th-14th c. CE). To address the challenges of symbolic variation, scarce data, and systematic degradation, we propose: a similarity-weighted supervised contrastive loss that biases embeddings using dynamically estimated inter-class similarities, and a lacuna-driven augmentation scheme that simulates realistic manuscript corruptions. Trained with these strategies, both a lightweight CNN and a pretrained ResNet achieve strong recognition performance and produce embeddings that more coherently separate character classes than PCA or generic pretrained models. These embeddings enable clustering, identification of stylistic subgroups, and construction of prototype images that visualize diachronic evolution and transitional letterforms. Our results demonstrate that respecting intrinsic inter-letter relationships and augmenting with domain-informed corruptions yield robust, interpretable representations, offering a transferable paradigm for representation learning under scarce, temporally evolving, and noisy conditions. Code and data available at: https://github.com/ipavlopoulos/diachronic-greek-letterforms.

24.
arXiv (CS.LG) 2026-06-16

Pre-Training for Simulation-Based Science: A Study on Jet Foundation Model Training Objectives

arXiv:2606.14870v1 Announce Type: cross Abstract: Foundation models (FMs) trained on large datasets and fine-tuned on downstream tasks have emerged as a powerful paradigm in AI for science. Industrial FMs are typically trained using self-supervision with masking due to the lack of labels. In many scientific domains, accurate simulations are plentiful and facilitate large, labeled datasets. This opens up new possibilities for pre-training. We present a systematic comparison of pre-training methods using the OmniLearned High Energy Physics FM framework. We test supervised classification, flow-matching generation, and self-supervised masked particle modeling. All models are pre-trained on the JetClass dataset and fine-tuned on two representative downstream tasks, top jet classification and JetNet conditional generation. Among other observations, for classification tasks, we find that pure classifier pre-training is optimal when downstream labels and model capacity are plentiful, but combining it with self-supervised masked particle modeling (MPM) is uniquely powerful in the low-finetuning label regime. Flow matching-based generative pre-training seems to provide little benefit for downstream classification, and interestingly, for downstream generation, we find that flow matching must be in the pre-training objective to see a significant finetuning advantage, hinting at the orthogonality of classification and generation tasks. That is, for a model to transfer to both generative and classification downstream tasks, it must be pre-trained on both. This study provides a template for controlled scaling analysis of pre-training objectives for foundation models in simulation-based sciences.

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arXiv (CS.CV) 2026-06-16

Faithful Action-unit Causal Reasoning for Counterfactually Faithful Emotion Explanations

Multimodal models can name the action units (AUs) behind a facial emotion, but their AU->emotion rationales are typically plausible rather than faithful: nothing forces the AUs a model invokes to be the AUs that actually drive its prediction. We cast AU->emotion reasoning as a counterfactual-consistency problem between the rationale, the label, and a structural AU->emotion causal graph G, and propose FACR, which grounds the reasoner in an independently induced, polarity-aware G and trains a counterfactual-faithfulness objective: a do-intervention on an AU that G marks causal for a class must move the prediction, while one it marks irrelevant must leave it unchanged. Faithfulness is thereby both trainable and measurable through a matching interventional metric, which we evaluate against a known causal structure, the PSPI pain-AU composition, as no existing affective-reasoning benchmark allows. We are explicit that this metric tests fidelity to the supplied structure rather than its rediscovery: it asks whether the trained reasoner invokes the AUs the structure marks causal, on held-out subjects and a second dataset. Under subject-independent evaluation on UNBC-PAIN, the objective raises the agreement between the invoked AUs and the PSPI composition from a no-objective baseline of 0.08 to 0.57, at a small detection cost; an unfaithfulness control attributes the gain to the objective. On a cross-dataset emotion transfer, the objective likewise raises fidelity to G on a seven-class task (0.50 to 0.84). Finally, we attach a language verbalizer and extend the audit to the generated text: biasing each action unit's emission by its latent activation makes the rationale faithful by construction, so that ablating an AU removes it from the explanation, a property that transfers to a second language-model backbone, whereas a freely generated rationale is unfaithful.