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

A Security Analysis of Long-Horizon Agentic AI Systems: Threats, Evaluation, and Framework Development

Authors:
Ahmed Mohammed Almalki↗Mehedi Masud↗

arXiv:2606.14816v1 Announce Type: cross Abstract: This paper presents a structured analysis of security challenges in long-horizon agentic AI systems. The study reviews existing threats, evaluation approaches, attack propagation mechanisms, and security frameworks. A taxonomy of security threats and a framework for analyzing attack propagation are proposed to support future research in agentic AI security

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02.
arXiv (CS.LG) 2026-06-15

LoMC: Localized Multidirectional Correction for Refusal Suppression in Routed Foundation Models

Authors:
Yan Hong↗Kedong Xiu↗Wei Li↗Jun Lan↗Huijia Zhu↗Shuheng Zhou↗Zhongcai Lyu↗Weiqiang Wang↗Jianfu Zhang↗

arXiv:2606.13709v1 Announce Type: cross Abstract: We study controlled post-training refusal suppression in routed MoE and hybrid-MoE foundation models, aiming to increase non-refusal target-response behavior while preserving general capability under a compact intervention footprint. Existing broad direction-based edits can perturb general-purpose computation, whereas support-only expert edits often lack sufficient capacity to correct heterogeneous refusal representations. To address this limitation, we introduce Localized Multidirectional Correction (LoMC), a support-gated intervention framework that follows a support-then-correction execution order: it first identifies a compact edit support, then aggregates prototype correction directions into layer-wise correction directions, and finally applies rank-one layer-wise correction only within the selected support. By using the edit support as a structural gating constraint, LoMC increases correction capacity without expanding the intervention scope. Experiments on text-only and multimodal safety benchmarks across four routed backbones show that LoMC substantially improves non-refusal target-response behavior while maintaining general capability under a compact intervention footprint.

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03.
arXiv (CS.AI) 2026-06-18

Self-CTRL: Self-Consistency Training with Reinforcement Learning

Authors:
Itamar Pres↗Laura Ruis↗Melat Ghebreselassie↗Belinda Z. Li↗Jacob Andreas↗

arXiv:2606.18327v1 Announce Type: cross Abstract: Language models (LMs) that faithfully describe their own behavior can more easily be audited, understood, and trusted by users. This paper describes Self-Consistency Training with Reinforcement Learning (Self-CTRL), a method that optimizes for consistency between a LM's self-explanations and behavior on related inputs by updating explanations to better predict behavior or updating behavior to better match explanations. We apply our method in two domains. First, we study a formal probabilistic reasoning task in which LMs must learn to imitate a family of biased samplers and evaluated on their ability to report the associated biases. We find that consistency training improves the correlation between self-reported and behaviorally-measured latent biases from $R^2=0.24$ to $R^2=0.64$ on a set of held-out distributions, matching the generalization of direct ground-truth supervision. Second, we study a constitutional AI domain in which LMs must describe when they will refuse or comply with user requests. Here, Self-CTRL produces rules that faithfully describe the model's behavior on held-out requests, improving the refusal predictions of a third-party auditor model from $36\%$ to $92\%$. In the other direction, behavior updates improve alignment, reducing HarmBench failure rate from $15.0\%$ to $0.5\%$ without substantially increasing refusal on harmless prompts. By aligning explanations and behavior, our work provides a general recipe for training AI models to be safer, more transparent, and more controllable.

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04.
medRxiv (Medicine) 2026-06-18

Plasma proteomics reveals clinical and mechanistic heterogeneity among individuals who develop coronary artery disease

Authors:
Yang↗Tan↗Carrasco-Zanini↗Su↗C.-Y↗Zhou↗Koyama↗Natarajan↗langenberg↗Lu↗Yoshiji↗

BACKGROUND: Individuals who develop coronary artery disease (CAD) are clinically and mechanistically heterogeneous, and understanding this variation is crucial for precise risk stratification and tailored interventions. However, the molecular mechanisms that connect these two kinds of heterogeneity remain unclear, limiting progress toward biologically grounded risk stratification and targeted interventions. Here, we investigated the heterogeneity of individuals who develop CAD by leveraging plasma proteomic signatures, placed individuals along continuous metabolic gradients and revealed the molecular programs underlying these patterns, thereby linking mechanistic variation to clinical heterogeneity. METHODS AND RESULTS: From 42,803 UK Biobank participants, including 3,713 individuals who developed CAD within 10 years (incident CAD), we first identified a 320-protein panel from 2,923 baseline proteins that improved prediction of incident CAD beyond clinical risk scores. Using reverse graph embedding, we reduced the proteomic data to two dimensions and mapped each incident case onto the resulting two-dimensional latent proteomic space. These proteomic dimensions show significant associations with cardiometabolic and kidney-related clinical markers. The patterns were replicated in the EPIC-Norfolk study. Phenome-wide Cox regression analyses further linked these proteomic dimensions to 10-year incidence rates for various diseases, including type 2 diabetes, obesity, and chronic kidney disease (CKD). Furthermore, adding the proteomic dimensions to clinical variable-based Cox regression model improved prediction of 10-year incidence of CKD and other diseases, demonstrating the value of proteomic dimensions beyond conventional clinical risk factors. Moreover, individuals with prevalent CAD (diagnosed before proteomic sampling) exhibited high, metabolically adverse dimension values, indicating that these axes capture cumulative metabolic burden. Pathway enrichment analyses implicated altered extracellular matrix organization and immune programs among the proteins contributing to the proteomic dimensions. CONCLUSIONS: Our findings demonstrate that plasma proteomic signatures can dissect the heterogeneity of individuals who develop CAD in continuous phenotypic gradients, improve prediction of CAD and comorbidities, and map underlying biological mechanisms.

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05.
arXiv (CS.LG) 2026-06-16

Beyond the Blood Draw: Explainable Machine Learning for Non-Invasive Dysglycemia Risk Screening

Authors:
Black Sun↗Chenyi Zhang↗Kaiyi Ji↗Xi Lu↗

arXiv:2606.16056v1 Announce Type: new Abstract: Dysglycemia, encompassing both prediabetes and diabetes, affects huge numbers of adults worldwide, yet many of them remain undiagnosed. We developed and validated machine-learning (ML) models for non-invasive screening of dysglycemia risk that require no laboratory tests. Pooling data from the National Health and Nutrition Examination Survey (NHANES) 2017–2023 (n=14,352), we trained six ML models with stratified 5-fold cross-validation and compared them with two established clinical risk scores. LightGBM achieved the highest area under the receiver operating characteristic curve (AUC=0.820, 95% CI: 0.806–0.835), outperforming the Finnish Diabetes Risk Score (0.745) and American Diabetes Association Risk Test (0.783). SHAP analysis identified age, race/ethnicity, and waist-to-height ratio as the most influential predictors. Subgroup analyses confirmed consistent performance across demographic strata (AUC: 0.735–0.832). These results demonstrate the feasibility of explainable, laboratory-free dysglycemia screening for deployment in community settings and self-tracking health applications.

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

ImageWAM: Do World Action Models Really Need Video Generation, or Just Image Editing?

Authors:
Yuyang Zhang↗Wenyao Zhang↗Zekun Qi↗He Zhang↗Haitao Lin↗Jingbo Zhang↗Yao Mu↗Xiaokang Yang↗Wenjun Zeng↗Xin Jin↗

World Action Models (WAMs) commonly rely on video generation to bridge visual world modeling and robot control. However, video-based WAMs face three coupled limitations: dense multi-frame future tokens make inference costly, full video prediction spends capacity on action-irrelevant temporal and appearance details, and long-horizon future imagination may introduce errors that mislead action prediction. These issues raise a simple question: Does world action model really need video generation? We propose ImageWAM, a simple WAM framework that repurposes pretrained image editing models for robot action prediction. In contrast to video generation, image editing provides a better-matched prior: it only needs to model a target-frame transformation, focuses on action-relevant current-to-target visual differences, and grounds task instructions to localized visual changes through edit pretraining. In practice, ImageWAM does not decode the target frame at inference time; instead, it conditions a flow-matching action expert on the KV caches produced by image-editing denoising, using them as a compact world-action context. ImageWAM outperforms standard VLA baselines and matching competitive WAMs without additional policy pretraining across different simulator and real-world experiments. It also reduces FLOPs to 1/6 and latency to 1/4 of video-based WAMs. Attention analysis further shows that editing caches focus on task-relevant change regions, supporting image editing as an effective alternative to video-based world-action modeling.

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07.
arXiv (CS.CL) 2026-06-16

MAWARITH: A Dataset and Benchmark for Legal Inheritance Reasoning with LLMs

Authors:
Abdessalam Bouchekif↗Shahd Gaben↗Samer Rashwani↗Somaya Eltanbouly↗Mutaz Al-Khatib↗Heba Sbahi↗Mohammed Ghaly↗Emad Mohamed↗

Islamic inheritance law is challenging for large language models because solving inheritance cases requires complex, structured, multi-step reasoning and the correct application of juristic rules to compute heirs' shares. We introduce MAWARITH, a large-scale annotated dataset of 12,500 Arabic inheritance cases for training and evaluating models on the full reasoning chain: (i) identifying eligible heirs, (ii) applying blocking (\d{hajb}) and allocation rules, and (iii) computing exact inheritance shares. To the best of our knowledge, MAWARITH is the first Arabic corpus and benchmark designed for end-to-end Islamic inheritance reasoning. Unlike prior datasets that restrict inheritance case solving to multiple-choice questions, MAWARITH supports the full reasoning chain and provides step-by-step solutions with justifications grounded in classical juristic sources and established inheritance rules, as well as exact share calculations. This enables models to learn how to generate detailed, step-by-step responses to user queries that reflect real-world Islamic inheritance cases. To evaluate models beyond final-answer accuracy, we propose MIR-E (Mawarith Inheritance Reasoning Evaluation), a weighted multi-stage metric that scores key reasoning stages and captures error propagation across the pipeline. We evaluate six large language models in a zero-shot setting. A commercial model achieves about 90\%, whereas all evaluated open-source models remain below 50\%. Our error analysis identifies recurring failure patterns, including scenario misinterpretation, errors in heir identification, errors in share allocation, and missing or incorrect application of key inheritance rules such as \textquotesingle awl and radd. The MAWARITH dataset is publicly available at https://gitlab.com/nlpresearcher/mawarith.

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08.
arXiv (CS.CL) 2026-06-15

Knowledge Graph Enhanced Memory-Augmented Retrieval for Long Context Modeling

Authors:
Ghadir Alselwi↗Basem Suleiman↗Hao Xue↗Shoaib Jameel↗Hakim Hacid↗Flora D. Salim↗Imran Razzak↗

Long-context language modeling requires not only extending context windows but maintaining coherent understanding of entity states and relationships across thousands of tokens – a challenge that semantic similarity alone cannot address. KGERMAR addresses this by constructing dynamic, context-specific knowledge graphs from input text during inference, enabling domain-adaptive retrieval that leverages both semantic similarity and explicit entity relationships. The framework performs real-time entity and relation extraction to build contextual knowledge graphs, then integrates graph-structural embeddings with textual semantics through a multi-component memory architecture. Three memory banks – contextual, semantic, and structural – are maintained with retrieval signals fused via learned weights to capture both surface-level semantics and deeper relational patterns. Evaluated on SlimPajama (84.7K training examples), WikiText-103 (4,358 examples), PG-19 (100 examples), and Proof-pile (46.3K examples), KGERMAR achieves up to 8.5\% lower perplexity and 2–2.5x better memory efficiency than memory-augmented baselines across context lengths from 1K to 32K tokens, with superior in-context learning performance across five NLU tasks. The dynamic knowledge graph construction approach advances memory-augmented language modeling by enabling domain-specific knowledge representation that adapts to input contexts rather than relying on fixed knowledge bases.

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09.
arXiv (CS.AI) 2026-06-12

DailyReport: An Open-ended Benchmark for Evaluating Search Agents on Daily Search Tasks

Authors:
Jingxuan Han↗Wei Liu↗Mingyang Zhu↗Youpeng Wang↗Ziwen Wang↗Lin Qiu↗Xuezhi Cao↗Xunliang Cai↗Zheren Fu↗Licheng Zhang↗Zhendong Mao↗

arXiv:2606.12871v1 Announce Type: new Abstract: Search Agents (SAs) typically leverage large language models (LLMs) to support complex information-seeking tasks by autonomously exploring web sources and synthesizing information into comprehensive responses. For SAs evaluation, prior benchmarks mainly focus on specialized tasks that are unlikely to arise in real-world user scenarios. Moreover, their reliance on coarse task-level rubrics often limits evaluation interpretability. To bridge this gap, we introduce DailyReport, an open-ended benchmark to evaluate SA capabilities on daily search tasks. It contains 150 open-ended tasks with 3,546 associated rubrics, capturing widely discussed and timely information demands of real-world users. Each task is decomposed into subtasks and evaluated with cascade rubrics across disentangled dimensions. Through cascade performance attribution and user-centric aggregation, we derive highly interpretable scores for each dimension, along with a user preference score. Our results on 17 agentic systems show that current systems still fall short of users' expectations. To facilitate future research, our dataset and code are made publicly available at https://github.com/AGI-Eval-Official/DailyReport.

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10.
arXiv (CS.AI) 2026-06-16

Epileptic Seizure Detection in Separate Frequency Bands Using Feature Analysis and Graph Convolutional Neural Network (GCN) from Electroencephalogram (EEG) Signals

Authors:
Ferdaus Anam Jibon↗Fazlul Hasan Siddiqui↗F. Deeba↗Gahangir Hossain↗

arXiv:2604.00163v2 Announce Type: replace-cross Abstract: Epileptic seizures are neurological disorders characterized by abnormal and excessive electrical activity in the brain, resulting in recurrent seizure events. Electroencephalogram (EEG) signals are widely used for seizure diagnosis due to their ability to capture temporal and spatial neural dynamics. While recent deep learning methods have achieved high detection accuracy, they often lack interpretability and neurophysiological relevance. This study presents a frequency-aware framework for epileptic seizure detection based on ictal-phase EEG analysis. The raw EEG signals are decomposed into five frequency bands (delta, theta, alpha, lower beta, and higher beta), and eleven discriminative features are extracted from each band. A graph convolutional neural network (GCN) is then employed to model spatial dependencies among EEG electrodes, represented as graph nodes. Experiments on the CHB-MIT scalp EEG dataset demonstrate high detection performance, achieving accuracies of 97.1%, 97.13%, 99.5%, 99.7%, and 51.4% across the respective frequency bands, with an overall broadband accuracy of 99.01%. The results highlight the strong discriminative capability of mid-frequency bands and reveal frequency-specific seizure patterns. The proposed approach improves interpretability and diagnostic precision compared to conventional broadband EEG-based methods.

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11.
arXiv (CS.CV) 2026-06-12

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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12.
arXiv (CS.AI) 2026-06-11

Power Term Polynomial Algebra for Boolean Logic

Authors:
Emanuele Sansone↗Armando Solar-Lezama↗

arXiv:2603.13854v2 Announce Type: replace-cross Abstract: We introduce power term polynomial algebra, a representation language for Boolean formulae designed to bridge conjunctive normal form (CNF) and algebraic normal form (ANF). The language is motivated by the tiling mismatch between these representations: direct CNFANF conversion may cause exponential blowup unless formulas are decomposed into smaller fragments, typically through auxiliary variables and side constraints. In contrast, our framework addresses this mismatch within the representation itself, compactly encoding structured families of monomials while representing CNF clauses directly, thereby avoiding auxiliary variables and constraints at the abstraction level. We formalize the language through power terms and power term polynomials, define their semantics, and show that they admit algebraic operations corresponding to Boolean polynomial addition and multiplication. We prove several key properties of the language: disjunctive clauses admit compact canonical representations; power terms support local shortening and expansion rewrite rules; and products of atomic terms can be systematically rewritten within the language. Together, these results yield a symbolic calculus that enables direct manipulation of formulas without expanding them into ordinary ANF. The resulting framework provides a new intermediate representation and rewriting calculus that bridges clause-based and algebraic reasoning and suggests new directions for structure-aware CNFANF conversion and hybrid reasoning methods.

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13.
Nature (Science) 2026-06-22

Will AI spark a scientific renaissance — or a diffuse monoculture?

Authors:
Xizhe Zhang↗

Artificial intelligence’s ability to enrich science will depend not only on model capability, but also on whether researchers, reviewers and funders reward originality over speed. Artificial intelligence’s ability to enrich science will depend not only on model capability, but also on whether researchers, reviewers and funders reward originality over speed.

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

Enhancing Fatigue Detection through Heterogeneous Multi-Source Data Integration and Cross-Domain Modality Imputation

Authors:
Luobin Cui↗Yanlai Wu↗Tang Ying↗Weikai Li↗

arXiv:2507.16859v5 Announce Type: replace-cross Abstract: Fatigue detection for human operators is important in safety-related applications such as aviation, mining, and long-haul transport. Reliable estimation of operator fatigue can support timely warnings, adaptive task scheduling, takeover reminders, and other safety-management decisions in human-machine systems. However, the effectiveness of these functions depends on whether fatigue-related signals can be reliably captured in the deployment environment. While many studies have shown the value of high-fidelity sensors in controlled laboratory environments, their performance often degrades when used in real-world settings because of noise, lighting conditions, and field-of-view constraints, thereby limiting their practical use. This paper formalizes a deployment-oriented setting for real-world fatigue detection, where high-quality sensors are often unavailable in practical applications. To address this issue, we use knowledge from heterogeneous source domains, including high-fidelity sensors that are difficult to deploy in the field but commonly used in controlled environments, to assist fatigue detection in the real-world target domain. Based on this idea, we design a heterogeneous and multi-source fatigue-detection framework that uses the available modalities in the target domain while leveraging diverse configurations in the source domains through cross-domain modality imputation based on shared modalities.

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

On the Adversarial Robustness of Multimodal LLM Judges

Authors:
Zihan Wang↗Guansong Pang↗Zelin Liu↗Wenjun Miao↗Jin Zheng↗Xiao Bai↗

Multimodal Large Language Models (MLLMs) are increasingly used as automated judges, e.g., for image quality and safety assessment. However, their adversarial robustness remains largely unexplored, threatening the fairness and reliability of automated judging. To bridge this gap, we introduce RobustMLLMJudge, the first general framework for evaluating the adversarial robustness of general-purpose MLLMs when functioning as judges. It covers diverse attacks against popular judge approaches across quality and safety evaluation scenarios. Using RobustMLLMJudge, we reveal that i) different MLLM judges are highly vulnerable to score-inflating adversarial attacks; and ii) although effective, these attack methods face a critical challenge due to unique constraints in the evaluation protocols of MLLM judges. We further propose MGSIA, namely Manifold-Guided Semantic Induction Attack, a novel method that bypasses these constraints to enable more effective and transferable attacks on MLLM judges. The core idea of MGSIA is to combine affirmative semantic induction with high-score manifold alignment: it maximizes the probability that judges yield affirmative responses (e.g., "Yes") to binary semantic queries, while regularizing adversarial representations toward high-score centers estimated from proxy protocols. Together, these objectives yield transferable score-inflating perturbations. Extensive experiments demonstrate the superiority and generalizability of MGSIA in deceiving advanced MLLM judges under different evaluation scenarios, highlighting the need for robust MLLM judges. Code and data will be made available at https://github.com/mala-lab/RobustMLLMJudge.

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

SoftMoE: Soft Differentiable Routing for Mixture-of-Experts in LLMs

Authors:
Miko{\l}aj Zasada↗{\L}ukasz Struski↗Jacek Tabor↗Marcin Kurdziel↗

arXiv:2606.17952v1 Announce Type: cross Abstract: Sparse Mixture-of-Experts (MoE) architectures enable scaling LLM parameters under a fixed inference budget by activating only a small subset of experts via top-$k$ routing. While this preserves causality and suits autoregressive language models, the discrete top-$k$ operator is not differentiable, forcing a fixed number of active experts per input and resulting in inefficient use of computation. We propose SoftMoE, which replaces discrete routing with a truncated soft top-$k$ LapSum relaxation, allowing gradient-based optimization of expert routing. We further parameterize the mean number of active experts per layer and impose a global budget constraint, enabling the model to learn how to allocate expert capacity across layers. SoftMoE remains fully compatible with autoregressive modeling and achieves performance comparable to or better than sparse MoE on language modeling and downstream tasks, while activating significantly fewer experts. Notably, the learned allocation is highly non-uniform, with later layers activating more experts. The source code is publicly available$^\dagger$.

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

Active Learning with Low-Rank Structure for Data Selection

Authors:
Vincent Cohen-Addad↗Sasidhar Kunapuli↗Vahab Mirrokni↗Mahdi Nikdan↗David P. Woodruff↗Samson Zhou↗

arXiv:2606.16045v1 Announce Type: new Abstract: In the data selection problem, the objective is to choose a small, representative subset of data that can be used to efficiently train a machine learning model. Sener and Savarese [ICLR 2018] showed that, given an embedding representation of the data and suitable geometric assumptions, heuristics based on $k$-center clustering can be used to perform data selection. This perspective was further explored by Axiotis et. al. [ICML 2024], who proposed a data selection approach based on $k$-means clustering and sensitivity sampling. However, these methods rely on the assumption that the dataset exhibits intrinsic geometric structure that can be effectively captured by clustering, whereas many modern datasets instead possess global algebraic structure that is better exploited by low-rank approximation or principal component analysis. In this paper, we introduce a new data selection framework based on low-rank approximation and residual-based sampling, formulated through the lens of row subset selection and loss-preserving coreset construction. Given an embedding representation of the data satisfying mild regularity conditions, which can be interpreted as algebraic or angular notions of Lipschitz continuity, we show that it is possible to select a weighted subset of $\tilde{O}\left(k + \frac{1}{\varepsilon^2}\right)$ data points whose average loss approximates the average loss over the full dataset within a $(1+\varepsilon)$ relative error, up to an additive $\varepsilon \Phi_k$ term, where $\Phi_k$ denotes the optimal rank-$k$ approximation cost of the embedding matrix. We complement these theoretical guarantees with empirical evaluations, demonstrating that on a range of real-world datasets, our data selection approach achieves improved performance over prior strategies based on uniform sampling or clustering-based sensitivity sampling.

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18.
arXiv (CS.AI) 2026-06-19

UniMM: A Unified Mixture Model Framework for Multi-Agent Simulation

Authors:
Longzhong Lin↗Xuewu Lin↗Kechun Xu↗Haojian Lu↗Lichao Huang↗Rong Xiong↗Yue Wang↗

arXiv:2501.17015v2 Announce Type: replace Abstract: Simulation plays a crucial role in assessing autonomous driving systems, where the generation of realistic multi-agent behaviors is a key aspect. In multi-agent simulation, the primary challenges include behavioral multimodality and closed-loop distributional shifts. In this study, we formulate a unified mixture model (UniMM) framework for generating multimodal agent behaviors, which can cover the mainstream methods including regression-based mixture models and discrete NTP models. Furthermore, we introduce a closed-loop sample generation approach tailored for mixture models to mitigate distributional shifts. Within the UniMM framework, we recognize critical configurations from both the model and data perspectives. We conduct a systematic examination of various model configurations, and comprehensively characterize their effects. Moreover, our investigation into the data configuration highlights the pivotal role of closed-loop samples in achieving realistic simulations. To extend the benefits of closed-loop samples across a broader range of mixture models, we further introduce a temporal disentanglement-and-alignment mechanism to address the shortcut learning and off-policy learning issues. Leveraging insights from our exploration, the distinct variants proposed within the UniMM framework, including discrete, anchor-free, and anchor-based models, all achieve state-of-the-art performance on the WOSAC benchmark.

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19.
arXiv (CS.LG) 2026-06-12

Contrastive Geometric Learning Unlocks Unified Structure- and Ligand-Based Drug Design

Authors:
Lisa Schneckenreiter↗Sohvi Luukkonen↗Lukas Friedrich↗Daniel Kuhn↗G\"unter Klambauer↗

arXiv:2601.09693v3 Announce Type: replace Abstract: Structure-based and ligand-based computational drug design have traditionally relied on disjoint data sources and modeling assumptions, limiting their joint use at scale. In this work, we introduce Contrastive Geometric Learning for Unified Computational Drug Design (ConGLUDe), a single contrastive geometric model that unifies structure- and ligand-based training. ConGLUDe couples a geometric protein encoder that produces whole-protein representations and implicit embeddings of predicted binding sites with a fast ligand encoder, removing the need for predefined pockets. By aligning ligands with both global protein representations and multiple candidate binding sites through contrastive learning, ConGLUDe supports ligand-conditioned pocket prediction in addition to virtual screening and target fishing, while being trained jointly on protein-ligand complexes and large-scale bioactivity data. Across diverse benchmarks, ConGLUDe achieves competitive zero-shot virtual screening performance, substantially outperforms existing methods on a challenging target fishing task, and demonstrates state-of-the-art ligand-conditioned pocket selection. These results highlight the advantages of unified structure-ligand training and position ConGLUDe as a step toward general-purpose foundation models for drug discovery.

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

Closing the Loop: PID Feedback Control for Interpretable Activation Steering in Symbolic Music Generation

Authors:
Ioannis Prokopiou↗Pantelis Vikatos↗Maximos Kaliakatsos-Papakostas↗Theodoros Giannakopoulos↗Themos Stafylakis↗

arXiv:2606.18790v1 Announce Type: cross Abstract: Transformer-based architectures have significantly advanced the generation of complex symbolic sequences, yet a significant gap remains in achieving fine-grained, interpretable control over discrete signal attributes. This paper investigates the mechanistic interpretability of the Multitrack Music Transformer (MMT) and proposes a framework for deterministic attribute modulation without retraining to bridge this gap via inference-time activation steering. Utilizing the Difference-in-Means (DiffMean) methodology, we isolate latent directions for signal attributes, specifically Pitch and Duration, within the residual stream. We validate the Linear Representation Hypothesis in this domain, achieving high correlation between steering magnitude and attribute shift. To address the inherent feature entanglement in multi-attribute steering, we introduce a Dual Steering framework utilizing Gram-Schmidt Orthogonalization. Experimental results demonstrate that this geometric decoupling reduces conceptual interference and signal degradation compared to naive vector addition, enabling independent deterministic control even against strong autoregressive conditioning.

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22.
bioRxiv (Bioinfo) 2026-06-11

Integrating Spatially Adjusted Protein Summaries for Survival Prediction in Spatial Proteomics

Authors:
Ahn↗Oh↗E. J↗Prada↗Shojaie↗

Recent advances in spatial proteomics, particularly imaging mass cytometry, enable the measurement of protein expression at the single-cell level while preserving a spatial context. Conventional survival analyses, however, typically rely on patient-level averages of protein intensities and therefore overlook spatial heterogeneity and tissue architecture. To address this limitation, we introduce a framework that incorporates spatial information into survival modeling by generating spatially adjusted protein summaries (SAPS). In this approach, cell-level protein intensities within each patient are modeled using spatial spline regression to capture spatial trends. From these models, we extract two complementary features: a spatially adjusted mean expression and a residual variance that reflects cell-to-cell variability unexplained by spatial effects. These summaries are then incorporated into Cox proportional hazards models in combination with clinical covariates. In simulation studies, our proposed framework achieved improved predictive performance compared to other alternative methods. The application of the method to breast cancer imaging mass cytometry data indicate that spatially adjusted summaries may enhance survival prediction and reveal biologically interpretable spatial protein patterns, suggesting high translational potential. This methodology offers an efficient means of translating complex spatial proteomics data into patient-level features, providing both improved survival prediction and new insights into the role of spatial heterogeneity in cancer outcomes.

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23.
bioRxiv (Bioinfo) 2026-06-12

ProMiSE: Protein Multi-State Evaluation Benchmark in Biological Contexts

Authors:
Ku↗Kim↗Park↗Seok↗

Proteins are inherently dynamic, with biological functions often emerging from transitions between multiple conformational states. While recent breakthroughs have largely addressed the static structure prediction problem, no systematic benchmark exists to demonstrate how well current models capture functionally relevant dynamics. We introduce ProMiSE, the first benchmark that provides both a dataset and an evaluation scheme, based on native biological assemblies and integrating major conformational change mechanisms - intrinsic, ligand-induced, and protein-induced - within a single curated dataset. We conducted a comprehensive evaluation of state-of-the-art structure prediction models, including AlphaFold3 and recent generative approaches. Our findings reveal that current models exhibit a limited ability to sample intrinsic multi-states and are often insensitive to biological context in induced scenarios. Internal representation analysis suggests that training-data exposure can shift predictions toward dominant conformational states over alternative biologically relevant states, primarily at the structure module. In contrast, results from BioEmu indicate that reducing decoding-stage bias can substantially improve multi-state sampling without major changes to upstream pair representations.

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24.
arXiv (CS.LG) 2026-06-11

SpAArSIST: Sparsified AASIST for Efficient and Reliable Anti-Spoofing

Authors:
Anton Firc↗Vojt\v{e}ch Stan\v{e}k↗Zbyn\v{e}k Li\v{c}ka↗Kamil Malinka↗Martin Pere\v{s}\'ini↗

arXiv:2606.11674v1 Announce Type: cross Abstract: We present SpAArSIST, a deployment-oriented refinement of the widely used AASIST graph pooling backend for self-supervised learning (SSL) based anti-spoofing. Motivated by redundant operations in public implementations, we replace learned pooling and stack-node attention with explicit, lightweight choices: separate train and inference graph pooling ratios $(k_{\mathrm{tr}},k_{\mathrm{inf}})$, magnitude-based node scoring, and mean aggregation of graph nodes. The best overall configuration (rank 1) cuts backend compute by 20.7% (195.045M $\rightarrow$ 154.706M MACs) and model size by 4.1% (611.8k $\rightarrow$ 586.4k params), while improving out-of-domain robustness on In-the-Wild to 2.82% EER and 0.078 minDCF (from 4.64% and 0.133) and remaining competitive on ASVspoof5. We further provide a composite selection score that summarizes accuracy, calibration, and compute to support balanced deployment-oriented model choice.

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25.
arXiv (CS.CV) 2026-06-17

AlignDrive: Aligned Lateral-Longitudinal Planning for End-to-End Autonomous Driving

Authors:
Yanhao Wu↗Haoyang Zhang↗Fei He↗Rui Wu↗Yanhu Shan↗Congpei Qiu↗Liang Gao↗Wei Ke↗Tong Zhang↗

Practical autonomous driving requires models that generalize by reasoning through spatial-temporal possibilities to exclude unsafe outcomes. While state-of-the-art (SOTA) methods use parallel planning architectures, they fail to explicitly couple speed decisions with agent behavior along the driving path, leading to suboptimal coordination. To address this, we propose a cascaded framework that transforms longitudinal planning from an independent prediction task into a path-conditioned reasoning process. On the model side, we introduce an anchor-based regression design that conditions longitudinal prediction on the lateral drive path, and reformulate longitudinal planning as 1D displacement prediction along the path. This reduces geometric uncertainty and sharpens the model's focus on interaction-driven dynamics. On the data side, we introduce a planning-oriented data augmentation strategy that simulates rare safety-critical events by programmatically inserting agents and relabeling longitudinal targets to enforce collision avoidance. Evaluated on the challenging Bench2Drive benchmark, our method achieves SOTA performance with a driving score of 89.07 and a success rate of 73.18%, demonstrating significantly improved coordination and safety. Further evaluation on Fail2Drive confirms strong generalization to rare edge cases where parallel formulations typically fail. Project page:https://yanhaowu.github.io/AlignDrive/.

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