Explore the Frontier of Global Academia

01.

arXiv (CS.CL) 2026-06-24 DOI: arXiv:2606.24324

Prague Dependency Treebank – Consolidated 2.0: Enriching a Complex Annotation Scheme

Authors:

Marie Mikulov\'a↗Ji\v{r}\'i M\'irovsk\'y↗Milan Straka↗Pavl\'ina Synkov\'a↗Jan \v{S}t\v{e}p\'anek↗Barbora \v{S}t\v{e}p\'ankov\'a↗Jan Haji\v{c}↗

The Prague Dependency Treebank framework is unique in its attempt to systematically include and link different layers of language, including a meaning representation with several types of inter-sentential phenomena, especially coreference and discourse relations. We present its second consolidated version (PDT-C 2.0), which concludes almost 30-years long project of sustained development of the resource to a uniformly and coherently annotated, genre-diversified, almost 4 million token language resource of Czech language, with accompanying fully compatible lexicons. In addition to continuous linguistic research, the richly linguistically annotated corpus is also widely used in international comparisons of the development of traditional and novel NLP tools as well as in conversions into other formalisms. The corpus and the trained parsers are available under the CC BY-NC-SA licence.

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02.

arXiv (CS.CL) 2026-06-19 DOI: arXiv:2606.19830

JAMER: Project-Level Code Framework Dataset and Benchmark on Professional Game Engines

Authors:

Jianwen Sun↗Chuanhao Li↗Zizhen Li↗Yukang Feng↗Fanrui Zhang↗Yifei Huang↗Yu Dai↗Kaipeng Zhang↗

Current AI-driven game development has made substantial progress in asset generation, gameplay design, and web-based game coding, yet project-level code engineering on professional game engines remains largely unexplored due to the absence of large-scale datasets and deterministic evaluation methods. We present JamSet and JamBench, the first project-level game code framework dataset and benchmark built on a professional game engine. Our key insight is that Game Jam competitions, community events where developers build complete games under tight time constraints, yield thousands of open-source projects suitable for this purpose. Building on the Godot engine's text-based format and headless execution mode, we design a deterministic verification pipeline from file integrity to runtime behavior collection, distilling 8,133 verified projects from over 240,000 repositories. Of these, 300 manually verified projects form JamBench; the rest constitute JamSet. JamBench defines theme-driven generation and code completion tasks, evaluated through a pipeline combining compilation pass rates, Structural Completeness Score (SCS), and Behavioral Alignment Score (BAS). Evaluation of 9 frontier models reveals a capability cliff as project scale increases, with runtime pass rates dropping from 80.4% on small projects to 5.7% on large ones (Task2a). Code Agents improve compilation rates yet yield no gains in runtime behavioral quality, indicating that the bottleneck lies in architectural design rather than syntactic correctness. Experiments validate JamSet as effective training data. All data and code are publicly available.

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03.

arXiv (CS.AI) 2026-06-18 DOI: arXiv:2510.18085

R2BC: Multi-Agent Imitation Learning from Single-Agent Demonstrations

Authors:

Connor Mattson↗Varun Raveendra↗Ellen Novoseller↗Nicholas Waytowich↗Vernon J. Lawhern↗Daniel S. Brown↗

arXiv:2510.18085v2 Announce Type: replace-cross Abstract: Imitation Learning (IL) is a natural way for humans to teach robots, particularly when high-quality demonstrations are easy to obtain. While IL has been widely applied to single-robot settings, relatively few studies have addressed the extension of these methods to multi-agent systems, especially in settings where a single human must provide demonstrations to a team of collaborating robots. In this paper, we introduce and study Round-Robin Behavior Cloning (R2BC), a method that enables a single human operator to effectively train multi-robot systems through sequential, single-agent demonstrations. Our approach allows the human to teleoperate one agent at a time and incrementally teach multi-agent behavior to the entire system, without requiring demonstrations in the joint multi-agent action space. We show that R2BC methods match, and in some cases surpass, the performance of an oracle behavior cloning approach trained on privileged synchronized demonstrations across four multi-agent simulated tasks. Finally, we deploy R2BC on two physical robot tasks trained using real human demonstrations.

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04.

arXiv (CS.CV) 2026-06-12 DOI: arXiv:2603.06652

PaLMR: Towards Faithful Visual Reasoning via Multimodal Process Alignment

Authors:

Yantao Li↗Qiang Hui↗Chenyang Yan↗Kanzhi Cheng↗Fang Zhao↗Chao Tan↗Huanling Gao↗Jianbing Zhang↗Kai Wang↗Xinyu Dai↗Shiguo Lian↗

Reinforcement learning has recently improved the reasoning ability of Large Language Models and Multimodal LLMs, yet prevailing reward designs emphasise final-answer correctness and consequently tolerate process hallucinations–cases where models reach the right answer while misperceiving visual evidence. We address this process-level misalignment with PaLMR, a framework that aligns not only outcomes but also the reasoning process itself. PaLMR comprises two complementary components: a perception-aligned data layer that constructs process-aware reasoning data with structured pseudo-ground-truths and verifiable visual facts, and a process-aligned optimisation layer that constructs a hierarchical reward fusion scheme with a process-aware scoring function to encourage visually faithful chains-of-thought and improve training stability. Experiments on Qwen2.5-VL-7B show that our approach substantially reduces reasoning hallucinations and improves visual reasoning fidelity, achieving state-of-the-art results on HallusionBench while maintaining strong performance on MMMU, MathVista, and MathVerse. These findings indicate that PaLMR offers a principled and practical route to process-aligned multimodal reasoning, advancing the reliability and interpretability of MLLMs.

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05.

arXiv (CS.LG) 2026-06-25 DOI: arXiv:2606.25927

Knowledge Cascade: Reverse Knowledge Distillation on Nonparametric Multivariate Functional Estimation

Authors:

Luyang Fang↗Haoran Lu↗Yongkai Chen↗Wenxuan Zhong↗Ping Ma↗

arXiv:2606.25927v1 Announce Type: cross Abstract: As machine learning models and datasets continue to grow, developing complex models has become increasingly computationally demanding. Knowledge distillation reduces deployment cost by compressing a large, well-trained teacher model into a compact student model, but it does not address settings where constructing the teacher itself is the bottleneck. Motivated by this challenge, we introduce Knowledge Cascade (KCas), a reverse knowledge distillation framework that uses information from a small, inexpensive student model to guide the development of a more complex teacher model. Although this direction is counterintuitive because the teacher typically has greater representational capacity, we show that student-to-teacher transfer can be principled when supported by statistical scaling relationships. We first develop KCas for nonparametric multivariate functional estimation in reproducing kernel Hilbert spaces via smoothing splines, where selecting multiple smoothing parameters is a major computational bottleneck. KCas transfers student-selected smoothing parameters to the full-sample regime through asymptotic scaling laws, substantially reducing computational cost for high-dimensional and large-scale datasets while retaining theoretical guarantees. Beyond smoothing splines, we illustrate the same principle through kernel density estimation and deep learning hyperparameter transfer. Simulations and real-data experiments show that KCas achieves substantial computational savings while maintaining strong statistical performance, and can sometimes outperform the corresponding full-sample procedure.

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06.

arXiv (CS.LG) 2026-06-12 DOI: arXiv:2606.12615

Towards Provably Fair Machine Learning: Bayesian Approaches For Consistent and Transparent Predictions

Authors:

Owen O'Neill↗Fintan Costello↗

arXiv:2606.12615v1 Announce Type: new Abstract: ML classifiers deployed in high-stakes domains produce predictions whose quality varies systematically across subgroups. For granular subgroups defined by intersections of multiple features, predictions are often inconsistent with the observed data: the model's outputs contradict the evidence available for that subgroup. This problem is exacerbated by regularisation, which improves aggregate performance by collapsing small subgroups into larger groups, disproportionately affecting demographic minorities. We define two requirements for consistent prediction: determinism (identical individuals receive identical predictions) and statistical consistency (we cannot reject, at significance level alpha, the hypothesis that the predictions for a subgroup were drawn from the Bayesian optimal target distribution inferred for that subgroup). From these requirements we derive the Fair Bayesian classifier, which enforces both across every group and subgroup simultaneously and abstains whenever no consistent deterministic prediction is possible. On three benchmark datasets (Adult, COMPAS, and Bank Marketing), standard classifiers produce statistically inconsistent predictions for a substantial proportion of subgroups. Our classifier achieves zero consistency error by construction while exceeding baseline accuracy and multicalibration on every dataset tested. Statistical consistency provides a principled foundation for prediction quality with direct implications for algorithmic fairness. Minority demographics are disproportionately concentrated in small subgroups, precisely where frequentist inference is least reliable; addressing this inference problem is therefore a necessary step toward fair ML. By enforcing Bayesian consistency at the finest resolution the data supports, the our classifier demonstrates that exhaustive subgroup fairness with principled abstention is achievable in practice.

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07.

arXiv (CS.CV) 2026-06-24 DOI: arXiv:2606.24058

VisChronos: Revolutionizing Image Captioning Through Real-Life Events

Authors:

Phuc-Tan Nguyen↗Hieu Nguyen↗Minh-Triet Tran↗Trung-Nghia Le↗

This paper aims to bridge the semantic gap between visual content and natural language understanding by leveraging historical events in the real world as a source of knowledge for caption generation. We propose VisChronos, a novel framework that utilizes large language models and dense captioning models to identify and describe real-life events from a single input image. Our framework can automatically generate detailed and context-aware event descriptions, enhancing the descriptive quality and contextual relevance of generated captions to address the limitations of traditional methods in capturing contextual narratives. Furthermore, we introduce a new dataset, EventCap (https://zenodo.org/records/14004909), specifically constructed using the proposed framework, designed to enhance the model's ability to identify and understand complex events. The user study demonstrates the efficacy of our solution in generating accurate, coherent, and event-focused descriptions, paving the way for future research in event-centric image understanding.

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08.

arXiv (CS.AI) 2026-06-24 DOI: arXiv:2606.24598

Toward Self-Evolution-Ready Workflow Harnesses: A Reversible Migration Path and Convertibility Taxonomy for Expert LLM Pipelines

Authors:

Yimo Lin↗Zhen Zhang↗Yibin Li↗

arXiv:2606.24598v1 Announce Type: cross Abstract: While expert-validated "LLM + script" workflows deliver significant value, they remain static: they encode hard-won domain knowledge yet fail to adapt execution based on feedback. Existing agent research predominantly targets greenfield agents and synthetic benchmarks, leaving the migration of active legacy workflows unresolved. To bridge this gap, we present a reversible, Strangler-Fig migration path that refactors legacy workflows into composable, typed, and auditable stages. Central to this framework is a three-tier convertibility taxonomy (A/B/C), implemented as a routing stage within the system harness, which diagnoses a workflow's readiness and routes it accordingly.

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09.

arXiv (CS.CL) 2026-06-18 DOI: arXiv:2606.18448

VISUALSKILL: Multimodal Skills for Computer-Use Agents

Authors:

Ziyan Jiang↗Li An↗Yujian Liu↗Jiabao Ji↗Qiucheng Wu↗Jacob Andreas↗Yang Zhang↗Shiyu Chang↗

Computer-use agents (CUAs) approach human-level performance on standardised benchmarks but still struggle on long-horizon tasks and unseen software. Existing skill libraries address this with reusable skills, but represent the skill artifact as text only, despite the visual nature of GUI interaction. We propose VISUALSKILL: a hierarchical multimodal skill, tailored to each target application and organised as a central index over per-topic files, which the agent consumes through a load_topic MCP tool that fetches the relevant topic's text and figures on demand. We construct each skill with a two-stage pipeline that combines authored documentation with live-application UI exploration. On two CUA benchmarks, CUA-World and OSExpert-Eval, a Claude Code CLI agent backed by Claude Opus 4.6 reaches an average score of 0.456 with VISUALSKILL, a +15.3 point absolute lift over the no-skill baseline (0.303). Against a matched text-only skill that is generated from the same source content and differs from VISUALSKILL only in modality, VISUALSKILL yields a further +8.3 point absolute gain over the matched text-only skill (0.373 vs. 0.456), providing direct evidence that retaining visual figures in the skill artifact, rather than verbalizing them away, helps the agent both identify UI elements and verify workflow state after each action. Our code is available at https://github.com/XMHZZ2018/VisualSkills.

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10.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.19882

Multimodal Concept Bottleneck Models

Authors:

Tongqing Shi↗Ge Yan↗Tuomas Oikarinen↗Tsui-Wei Weng↗

arXiv:2606.19882v1 Announce Type: cross Abstract: Concept Bottleneck Models (CBMs) enhance the interpretability of deep learning networks by aligning the features extracted from images with natural concepts. However, existing CBMs are constrained in their ability to generalize beyond a fixed set of predefined classes and the risk of non-concept information leakage, where predictive signals outside the intended concepts are inadvertently exploited. In this paper, we propose Multimodal Concept Bottleneck Model (MM-CBM) to address these issues and extend CBMs into CLIP. MM-CBM utilizes dual Concept Bottleneck Layers (CBLs) to align both the image and text embeddings into interpretable features. This allows us to perform new vision tasks like zero-shot classification or image retrieval in an interpretable way. Compared to existing methods, MM-CBM achieves up to 51.26% accuracy improvement on average across four standard benchmarks. Our method maintains high accuracy, staying within ~5% of black-box performance while offering greater interpretability.

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11.

arXiv (CS.CL) 2026-06-25 DOI: arXiv:2606.25436

Evaluating Japanese Dialect Robustness Across Speech and Text-based Large Language Models

Authors:

Tomoya Mizumoto↗Yusuke Fujita↗Hao Shi↗Lianbo Liu↗Atsushi Kojima↗Yui Sudo↗

Dialogue systems based on large language models (LLMs) have advanced significantly in recent years. However, dialectal variation remains a major challenge, particularly for systems that process spoken input. LLM-based speech language models (SLMs), which integrate LLMs with speech processing components, show promise for spoken language tasks, yet their ability to comprehend dialects has not been sufficiently studied. Moreover, it remains unclear how the dialectal understanding of the base LLM affects SLM performance. This study investigates the dialectal robustness of both LLMs and SLMs using Japanese dialects as a test case. We define robustness as the ratio of performance on dialectal versus standard inputs, enabling fair comparisons. Our experiments show that SLM robustness correlates with that of their text-based counterparts. Furthermore, training with dialectal data and fine-tuning the speech encoder each improves robustness in SLMs.

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12.

arXiv (CS.LG) 2026-06-19 DOI: arXiv:2606.19643

Variational Consensus Monte Carlo for Bayesian Mixture

Authors:

Julie Fendler↗Francesca L. Crowe↗Tom Marshall↗Sylvia Richardson↗Paul D. W. Kirk↗

arXiv:2606.19643v1 Announce Type: cross Abstract: Motivated by the privacy, sensitivity and sharing limitations of health data, we present a comprehensive pipeline for inference of Bayesian mixture models within a federated learning setting, i.e. when data cannot be fully shared or pooled across compute nodes. We adopt a Consensus Monte Carlo (CMC) approach, in which an MCMC algorithm is run independently within each data silo to estimate local posterior distributions, which are then aggregated to approximate the posterior over the full data. The variational CMC approach of Rabinovich, Angelino and Jordan (2015) [1] frames the aggregation step as a variational inference problem, but their application to mixtures assumes the number of clusters and key mixture parameters to be known. Our main methodological contributions are: (i) an extension of variational CMC to over-fitted Bayesian mixture models that infer the number of clusters and all model parameters, without requiring conjugacy; (ii) novel cluster-matching algorithms suitable for cross-silo settings in which not every cluster appears in each local dataset; (iii) a number of inference strategies for the aggregation step, matched to different federated learning constraints; and (iv) guidelines for choosing among these in practice. A comprehensive simulation study validates the framework and allows us to compare to state-of-the-art federated learning alternatives. Notably, we show that when the composition of local datasets reflects the underlying clustering structure in the data, our approach can recover small clusters with greater accuracy than standard MCMC applied to the pooled data. We illustrate the framework on large-scale electronic health record data, identifying multi-morbidity patterns in a British geriatric population.

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13.

arXiv (CS.AI) 2026-06-15 DOI: arXiv:2606.14119

FactoryLLM: A Safe and Open-Source AI Playground for Evaluating LLMs in Smart Factories

Authors:

Yash Pulse↗Yong-Bin Kang↗Abhik Banerjee↗Abdur Forkan↗Prem Prakash Jayaraman↗

arXiv:2606.14119v1 Announce Type: new Abstract: Fault diagnostics and recovery in smart factories is challenging because critical information is dispersed across manuals of multiple machines which are interconnected through the manufacturing process. Large Language Models (LLMs) can provide a promising approach. In this paper, we propose FactoryLLM, a safe and open-source AI playground designed for evaluating different LLM-based retrieval-augmented generation (RAG) models by analysing documents from multiple machines across the manufacturing process. FactoryLLM enables the user to configure the LLM, and assess performance when reasoning over multiple documents, through a dual evaluation setup using both RAGAS and NVIDIA's LLM-as-a-Judge metrics. FactoryLLM is safe because it allows users to run local or open-source LLMs without sharing sensitive industrial data, providing a controlled environment for experimentation. We demonstrate the efficacy of FactoryLLM through a case study which involves an Autonomous Intelligent Vehicle and its Mobile Planner software, evaluating three LLMs across 30 maintenance queries derived from approximately 600 pages of cross-machine documentation. The results suggest that FactoryLLM is effective in cross-machine document reasoning: every model achieved a groundedness score above 0.88. The full code and documentation for community to test FactoryLLM with their manufacturing specific scenarios are publicly available.

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14.

arXiv (CS.AI) 2026-06-11 DOI: arXiv:2606.10794

READER: Robust Evidence-based Authorship Decoding via Extracted Representations

Authors:

Jiaxu Liu↗Sunnan Mu↗Dong Huang↗Liuyin Wang↗Jing Shao↗Jie Zhang↗

arXiv:2606.10794v2 Announce Type: replace Abstract: As agentic applications increasingly route user tasks through official and third-party LLM APIs, provenance becomes an operational question: which model generated a given black-box response? We study Dynamic Black-Box LLM Provenance: identifying the source LLM from generations elicited by query-varying, non-predefined prompts rather than a fixed input set or benchmark suite. This setting is difficult because prompt semantics dominate the text, while model-specific authorship traces are weak and inconsistent at the surface level. We introduce READER (Robust Evidence-based Authorship Decoding via Extracted Representations), a lightweight provenance framework that treats a frozen proxy LLM as a reader of hidden authorship evidence. READER maps black-box outputs into proxy activation space, temporally filters token states within each response, and performs Bayesian Evidence Accumulation by summing single-response log-posterior evidence across independently sampled prompts. This avoids fragile mean-pooling of prompt-specific representations while preserving the query-wise evidence needed for calibrated confidence. On Agent500, a 50-target dataset built from agent-style prompts, READER reaches $31.0$-$42.4\%$ top-1 accuracy from a single response and $70.0$-$84.0\%$ from 50 responses, substantially outperforming sentence-encoder fingerprints. Scaling across nine proxy readers further shows that stronger LLMs expose more linearly decodable authorship structure, suggesting that authorship perception is already present in frozen LLM representations and can be converted into reliable multi-query attribution.

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15.

arXiv (CS.AI) 2026-06-16 DOI: arXiv:2606.15024

Resilient Consensus in Agentic AI

Authors:

Sribalaji C. Anand↗George J. Pappas↗

arXiv:2606.15024v1 Announce Type: cross Abstract: Large language model (LLM) agents are increasingly deployed in multi-agent systems where they must coordinate and agree on shared decisions. We ask whether classical resilient consensus theory, developed for deterministic agents, transfers to LLM agents that may behave adversarially. Framing LLM agreement as a Byzantine consensus game, we run controlled experiments on complete and general communication graphs. We find that prompted LLM agents fail to reach agreement that is achievable in principle: consensus can fail even in settings where classical theory guarantees that a convergent algorithm exists, and this failure persists across temperatures and horizons. At the same time, wrapping the agents with classical resilient consensus filters improves agreement. The benefit of filtering depends on how much robustness the underlying topology already provides. Our results suggest that classical resilient consensus theory is a useful lens for the safety of agentic AI.

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16.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2606.17180

Towards Fast GNN Surrogates for CO2 Migration in Complex Geological Formations

Authors:

Rodrigo S. Luna↗Thiago H. N. Coelho↗Luiz S. L. Neto↗Roberto M. Velho↗Adriano M. A. Cortes↗Renato N. Elias↗Alexandre G. Evsukoff↗Fernando A. Rochinha↗Mauricio Araya-Polo↗Herve Gross↗Alvaro L. G. A. Coutinho↗

arXiv:2606.17180v1 Announce Type: new Abstract: This chapter discusses how a data-driven machine learning approach can reproduce key aspects of the physical behavior of multiphase flows in complex geological formations. We propose an end-to-end graph neural surrogate tailored to CO$_2$ plume migration forecasting in geological storage. The method is evaluated on the SPE11A benchmark, a well-known industry test case designed to assess CO$_2$ storage scenarios and characterized by sharp gas-water interfaces, strong advective transport, and rapid convective mixing with fingering development. The benchmark is reformulated as a graph in which nodes represent computational cells and edges encode transmissibility-based interactions enriched with geometric attributes. Directional transport arising from grid geometry, permeability contrasts, and geological heterogeneity is captured through an anisotropic message-passing mechanism, where interaction weights are computed via geometry-conditioned edge embeddings, biasing message aggregation toward physically relevant transport directions. Temporal evolution is modeled in latent space using an autoregressive residual formulation trained with multi-step supervision. The proposed model produces competitive forecasts of gas saturation and liquid-phase density, which are key indicators for CO$_2$ storage monitoring, with cumulative errors that remain moderate over extended forecasting horizons.

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17.

arXiv (CS.LG) 2026-06-17 DOI: arXiv:2606.17995

Differential Privacy of Gaussian Process Posterior Sampling

Authors:

Tomasz Maciazek↗

arXiv:2606.17995v1 Announce Type: cross Abstract: We study the privacy of releasing posterior sample paths from a Gaussian process (GP) when the entire training set including covariates and responses is private. Unlike standard differential-privacy (DP) mechanisms that add external noise, posterior sampling is random by construction. We show that this intrinsic randomness yields DP guarantees by deriving explicit Rényi-DP bounds for GP posterior sample-path release. The bounds separate posterior-mean leakage from data-dependent posterior-covariance leakage showing that meaningful privacy depends sharply on effective ridge regularisation. We apply membership-inference attacks to show that empirical leakage follows the predicted dependence on regularisation, posterior variance and the number of released posterior sample-paths. Utility experiments on downstream posterior-sampling tasks identify noisy-observation regimes where privacy-compatible regularisation preserves useful decisions with modest utility loss. When stronger privacy is needed, the intrinsic guarantee can be sharpened by adding calibrated GP noise, providing an explicit additional privacy knob.

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18.

arXiv (math.PR) 2026-06-17 DOI: arXiv:2606.17665

Non-asymptotic Tail Bounds for the Kostlan–Shub–Smale Field: Tensor PCA and Spherical $k$-Spin Complexity

Authors:

Jean-Marc Aza\"is↗Federico Dalmao↗Yohann De Castro↗

arXiv:2606.17665v1 Announce Type: cross Abstract: This paper builds a hierarchy of explicit, non-asymptotic tail bounds for the supremum of the Kostlan–Shub–Smale (KSS) random field on the sphere, and applies it to two problems: Spiked Tensor PCA and the landscape of the spherical $k$-spin model. For Tensor PCA, we study the non-asymptotic statistical limits of estimating a rank-$R$ symmetric signal tensor of order~$k\ge 3$ and dimension~$d\ge 3$ from a single Gaussian observation at signal-to-noise ratio~$\lambda$, through the profile maximum likelihood estimator, the MLE restricted to normalized rank-$R$ tensors of coherence at least~$\kappa$. Our analysis uses a single reduction: a deterministic geometric inequality (the Tube Method) and a rank-reduction step bound the estimation error by the supremum of the canonical KSS field, which the Kac–Rice formula turns into a Gaussian integral against the expected absolute characteristic polynomial of a shifted Gaussian Orthogonal Ensemble, controlled in turn by the four explicit tail bounds of our hierarchy (three from a Mehta–Fyodorov representation, one from a Ben Arous–Dembo–Guionnet large deviation). The same reduction yields two results, each with explicit constants. For estimation, a finite-$(k,d)$ error bound recovers the asymptotically optimal rate~$\sqrt{d\log k}$ of Perry, Wein and Bandeira, with explicit dependence on the rank~$R$ and the coherence~$\kappa$. For the landscape, a two-sided non-asymptotic bracketing of the annealed complexity of the spherical $k$-spin Hamiltonian recovers the Auffinger–Ben Arous–\v{C}ern\'y complexity function in the high-dimensional limit.

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19.

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

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

Authors:

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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20.

arXiv (CS.AI) 2026-06-19 DOI: arXiv:2606.10358

KG-SoftMAP: Soft Knowledge-Graph Priors for Bayesian Network Structure Learning from Sparse Discrete Data

Authors:

Guoliang Xu↗James E. Corter↗

arXiv:2606.10358v2 Announce Type: replace-cross Abstract: Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. However, imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. We propose KG-SoftMAP, which encodes such a KG as a finite-strength, confidence-weighted edge prior and maximizes a MAP objective combining the BDeu score with a logit-form prior; the KG may be expert-curated or LLM-extracted. On synthetic benchmarks with known DAGs, KG-SoftMAP reaches Directed-F1 (DF1) $0.19$–$0.32$ at observation rate $\rho=0.05$ and DF1 $0.44$–$0.97$ at $\rho\geq0.2$, while every data-only learner tested stays near zero under the same sparse masks. Recovery tracks KG quality: controlled corruption degrades it smoothly, a zero-signal KG yields DF1 $0.00$, and a blindly LLM-extracted KG with imperfect precision and recall still drives substantial recovery. On three real sparse educational datasets, the learned BN acts as a concept-level posterior model: on SAF it matches logistic regression (LR) within $0.03$ F1_FAIL while providing an inspectable concept graph, calibrated Fail probabilities, and tractable posterior queries from partial observations.

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21.

arXiv (CS.CV) 2026-06-15 DOI: arXiv:2606.14005

Context-Guided Semantic Alignment for Feature Fusion Networks

Authors:

Hyungseop Lee↗Jiho Lee↗Woochul Kang↗

Feature fusion networks are fundamental components in modern object detectors, aggregating multi-scale features to detect objects of varying sizes. However, directly fusing features from different pyramid levels often introduces semantic inconsistency due to their heterogeneous representations. In this paper, we propose Feature Interaction NEtwork (FINE), a lightweight semantic alignment module that refines low-level features via high-level contextual guidance using cross-level attention prior to fusion. To bridge the structural gap and ensure computational efficiency, we introduce an Alignment-Aware Token Sampling that aligns corresponding spatial regions across scales, reducing the attention complexity by an order of magnitude. The resulting attention weights generate a spatial-channel modulation map that is upsampled and applied to the low-level features via residual element-wise modulation. This mechanism ensures that the network selectively enhances semantically relevant pixels while preserving the sub-pixel localization accuracy necessary for dense prediction tasks. FINE is generally applicable to various detectors and consistently improves detection accuracy without compromising efficiency.

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22.

medRxiv (Medicine) 2026-06-18 DOI: HASH:eb6cb8b86eaee1a53a01e2516d4bf761

Rare Coding Variants Reveal Distinct Genetic Architectures Across Multidimensional Sleep Phenotypes

Authors:

Zhang↗Lu↗Kunorozva↗Jones↗S. E↗Maher↗Valliere↗Wood↗A. R↗Weedon↗M. N↗Tubbs↗…

Sleep and circadian traits have been widely studied using common variants, but the contribution of rare coding variation remains unclear. We analyzed rare coding variants in 397,065 whole-exome sequenced UK Biobank participants across 36 sleep phenotypes from self-report, diagnoses, sleep medication use and accelerometry, and meta-analyzed results with 171,536 whole-genome sequenced All of Us participants of diverse ancestries, with replication in the Mass General Brigham Biobank (N = 31,275). We identified 260 genes associated with sleep phenotypes, including novel associations with sleep medication use in 29 genes and 24 out of 29 have not previously been reported with any sleep phenotypes. We observed modest but significant rare variant heritability and strong genetic correlations between sleep medication use, insomnia and fatigue. Temporal gene expression trajectory analyses indicate that genes associated with self-reported sleep traits show constant high prenatal expression, whereas genes linked to sleep medication phenotypes exhibit peak expression in the late prenatal period. These findings highlight distinct biological mechanisms captured by different measurement sources of sleep phenotypes and reveal rare-variant-informed targets for therapeutic discovery.

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23.

arXiv (CS.AI) 2026-06-24 DOI: arXiv:2606.24842

World Models in Pieces: Structural Certification for General Agents

Authors:

Yikai Lu↗Yifei Wu↗Xinyu Lu↗Tongxin Li↗

arXiv:2606.24842v1 Announce Type: new Abstract: In the big-world regime, agents cannot be universally capable and their ability is inevitably specialized across a world model in pieces. Consequently, standard uniform guarantees fail to distinguish between the understanding of critical bottlenecks and irrelevant failures. We first formalize this limitation by proving that general agents are not universal, rendering standard worst-case analysis uninformative. To overcome this, we introduce structural certification, a transition-local framework that maps bounded goal-conditioned performance to entry-wise guarantees on the agent's internal world model. Our main contribution is constructive. We provide algorithms that filter specific transitions using deep compositional goals and prove that a general agent on these goals has a structural world model with a $\mathcal{O}(1/n) + \mathcal{O}(\delta)$ error bound. Conversely, this bound is tight in the small-$\delta$ regime, whose existence is explicitly guaranteed by our certification. These results enable the certifiable deployment of general agents by localizing the specific transitions where long-horizon planning is reliable.

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24.

arXiv (quant-ph) 2026-06-17 DOI: arXiv:2606.17975

Manipulation of Topological Corner States via Subchiral Symmetry

Authors:

Hai-Tao Ding↗Tianqi Chen↗Leong-Chuan Kwek↗Jiangbin Gong↗

arXiv:2606.17975v1 Announce Type: new Abstract: Higher-order topological phases provide robust corner modes, but their use requires controllable creation, isolation, and transfer of individual modes and their superpositions. Here we demonstrate, using the two-dimensional Benalcazar-Bernevig-Hughes model as an example, that subchiral symmetry provides a general control principle for manipulating topological corner modes. The conventional chiral symmetry decomposes into four subchiral symmetries, each associated with one zero-energy corner mode. By selectively breaking these subsymmetries with controlled intercell hoppings, we reduce the fourfold corner-state manifold step by step to single isolated modes. We further design adiabatic protocols that transfer either a single corner state or a superposition of two corner states between selected corners, while preserving the relative phase in the latter case. Both numerical simulations and IBM quantum-processor implementations show that the proposed protocols can be executed with high fidelity, establishing subchiral symmetry as a route to programmable higher-order topological state manipulation.

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25.

arXiv (CS.AI) 2026-06-24 DOI: arXiv:2606.23920

Catastrophic Compositional Generation: Why Vanilla Diffusion Models Fail to Extrapolate

Authors:

Duncan Soiffer↗Chandler Squires↗Yuan Guan↗Jason Hartford↗Pradeep Ravikumar↗

arXiv:2606.23920v1 Announce Type: cross Abstract: The task of compositional generation involves using a conditional generative model, trained only on a subset of the possible conditions, to produce samples from compositionally-defined target distributions such as a geometric combination of the source distributions. In this work, we argue that this task is often infeasible for vanilla conditional diffusion models: we conjecture that no inference-time technique can efficiently produce samples from the target distribution in certain well-motivated settings. This idea is supported by theory-guided generalization arguments and carefully-designed experiments on both synthetic and realistic data. In particular, while recent methods such as Feynman-Kac correction reduce inference-time approximation error, our results show that score estimation error has a more catastrophic effect on performance when the target distribution is out-of-distribution with respect to the sources, highlighting the need for a different approach to this task.

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