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01.
arXiv (quant-ph) 2026-06-19

On chip, multifunctional quantum sensing using single spins in a van der Waals crystal

arXiv:2606.19978v1 Announce Type: new Abstract: Nanoscale thermometry and magnetometry are in high demand across a wide range of scientific and technological applications. In this context, optically addressable spins in solids have emerged at the forefront of on-chip quantum sensing. However, simultaneous quantum sensing of multiple parameters (e.g., temperature and magnetic field) using the same spin sensor remains challenging due to cross-sensitivity to multiple physical quantities. Here, we demonstrate independent dual sensing of temperature and magnetic field using single quantum emitters in hexagonal boron nitride (hBN). We experimentally verify the independent response of the zero-phonon line (ZPL) position to temperature and of optically detected magnetic resonance (ODMR) to magnetic fields. Furthermore, we demonstrate local temperature sensing of a microcircuit while simultaneously measuring an external magnetic field. Our results establish quantum emitters in hBN as a robust platform for multifunctional quantum sensing under realistic operating conditions.

02.
arXiv (CS.CL) 2026-06-16

SciOrch: Learning to Orchestrate Expert LLMs for Solving Frontier Multimodal Scientific Reasoning Tasks

Frontier scientific reasoning remains a major challenge for large language models (LLMs), where even the strongest commercial systems fall short of expert-level performance. A closer look at model behavior reveals substantial complementarity that single-model evaluation hides: different frontier models excel on different question types, and no single model captures the full picture. We present SciOrch, a framework that trains a lightweight 8B model to orchestrate frontier LLMs for scientific reasoning. The orchestrator decomposes each question, delegates sub-problems to selected commercial models through API calls, and synthesizes a final answer. Training such an orchestrator is fundamentally harder than conventional agentic RL: each action triggers an API call that is expensive in both dollar cost and latency, making standard online rollouts infeasible. We address this with MCTS-based approach, producing diverse orchestration trajectories, extracting per-node single-turn samples, and optimizing the orchestrator with GRPO-style training. On a 240-question test set spanning SGI-Reasoning and Scientists' First Exam, SciOrch reaches 56.66% average accuracy, outperforming the strongest single commercial model by 3.74% and the strongest multi-agent baseline by 3.33%. It also attains the best accuracy on both SGI and SFE with less than half the API cost of typical multi-agent methods.

04.
arXiv (CS.LG) 2026-06-16

From Tokens to Policy: Causal and Interpretable Heterogeneous Treatment Effects Identification

arXiv:2606.17010v1 Announce Type: new Abstract: Heterogeneous Treatment Effect (HTE) identification is crucial to explain the impact of an intervention and optimize our policies accordingly. Existing approaches trade expressivity for interpretability, but, if some active heterogeneity drivers are unmeasured, methods at both ends of this spectrum allow for spurious HTE characterization with no causal reading. In this work, we focus on controlled experiments and argue that an oracle HTE causal characterization via the latent interactors is now within reach, thanks to (i) more extensive pre-treatment measurements, i.e., multi-modal and multi-view, and (ii) scalable representations with minimal human supervision. We then re-frame HTE identification as a Markov-blanket discovery problem on a sufficient and aligned pre-treatment representation, and introduce Neural EXposure Interaction Search (NEXIS), an iterative procedure with provable and empirically validated consistent selection. We deploy NEXIS on two anti-poverty programs in Africa, augmenting each with satellite imagery capturing previously unmeasured environmental effect modifiers, leading to novel, interpretable and prescriptive guidelines to optimize the programs' next iterations.

05.
arXiv (CS.AI) 2026-06-18

A CEFR-Inspired Classification Framework with Fuzzy C-Means To Automate Assessment of Programming Skills in Scratch

arXiv:2604.00730v2 Announce Type: replace-cross Abstract: Context: Schools, training platforms, and technology firms increasingly need to assess programming proficiency at scale with transparent, reproducible methods that support personalized learning pathways. Objective: This study introduces a pedagogical framework for Scratch project assessment, aligned with the Common European Framework of Reference (CEFR), providing universal competency levels for students and teachers alongside actionable insights for curriculum design. Method: We apply Fuzzy C-Means clustering to 2008246 Scratch projects evaluated via Dr.Scratch, implementing an ordinal criterion to map clusters to CEFR levels (A1-C2), and introducing enhanced classification metrics that identify transitional learners, enable continuous progress tracking, and quantify classification certainty to balance automated feedback with instructor review. Impact: The framework enables diagnosis of systemic curriculum gaps-notably a "B2 bottleneck" where only 13.3% of learners reside due to the cognitive load of integrating Logic Synchronization, and Data Representation–while providing certainty–based triggers for human intervention.

06.
arXiv (CS.CL) 2026-06-17

Dynamic Rollout Editing for Reducing Overthinking in RL-Trained Reasoning Models

Long-form chain-of-thought reasoning can improve LLM performance on complex tasks, but models often continue generating unnecessary reasoning after a correct answer has emerged. We refer to this behavior as overthinking. We study this phenomenon from the perspective of GRPO-style reinforcement learning (RL) post-training, framing it as a training-time credit-assignment problem rather than merely a decoding-time stopping problem. In rollouts sampled at the onset of GRPO training, we observe that successful trajectories can exhibit a slightly higher degree of overthinking than unsuccessful trajectories for the same prompts. This early imbalance provides a starting point for an undesirable feedback loop: because GRPO assigns sequence-level credit, it cannot distinguish the solution-reaching prefix from the unnecessary continuation that lengthens a successful trajectory. Both receive positive update signal, allowing the initial imbalance to grow into more severe overthinking during training. To address this issue, we introduce Dynamic Rollout Editing (DRE), a training-time intervention for successful trajectories that continue thinking after answer emergence. DRE preserves the accepted verified prefix, edits the remaining thinking, and prefers the edited trajectory within the same RL group, weakening the preference signal for unnecessary thinking without penalizing the reasoning needed to reach the answer. Experiments across diverse tasks show the effectiveness of DRE.

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

Trusted Multi-View Deep Learning Classification of Fetal Congenital Heart Disease with Feature-level and Decision-level Fusion

Congenital heart disease (CHD) refers to the abnormal anatomical structure caused by the abnormal development of the heart and great vessels during embryonic development. Traditional diagnostics often fail to achieve high accuracy and efficiency, especially given the complexity of cardiac anatomy. This study presents a specialized multi-view deep learning framework for CHD binary classification using echocardiographic images. A large-scale CHD dataset, including five views, was used to train the model, enabling it to integrate multi-angle image data. The framework utilizes advanced feature extraction and attention mechanisms to improve diagnostic precision and reliability. An uncertainty-based decision-making component is also integrated to handle low-quality images, enhancing diagnostic outcomes. Experimental results show that this method achieves top-tier performance on our dataset and provides a robust tool for early CHD detection, underscoring its potential for clinical use. The dataset and source code will be released upon paper acceptance.

08.
arXiv (CS.AI) 2026-06-17

RLRC: Reinforcement Learning-based Recovery for Compressed Vision-Language-Action Models

arXiv:2506.17639v2 Announce Type: replace-cross Abstract: Vision-Language-Action models (VLA) have demonstrated remarkable capabilities and strong potential in complex robotic manipulation. However, their large parameter sizes and high inference latency hinder real-world deployment, especially on resource-constrained platforms. To address this, we conduct a systematic empirical study of model compression for VLAs. Building on these insights, we present RLRC, a three-stage compression and recovery pipeline consisting of structured pruning, performance recovery via SFT and RL, and subsequent quantization. The RL stage incorporates a critic warm-up strategy and BC loss regularization to stabilize training and preserve policy behavior. RLRC achieves up to an 8 times memory reduction and 2.3 times inference speedup while maintaining the original task success rate. Extensive experiments across multiple VLA backbones show that RLRC consistently outperforms existing compression baselines, highlighting its effectiveness for on-device deployment. Project website: https://rlrc-vla.github.io

09.
arXiv (CS.LG) 2026-06-18

Dimension-Free Convergence of Discrete Diffusion Models: Adjoint Equations Induce the Right Space

arXiv:2605.17232v2 Announce Type: replace Abstract: Discrete diffusion has become a leading framework for generative modeling in various applications including language, vision, and biology. Existing convergence theory, however, exhibits fundamental limitations. KL-based analyses diverge under singular priors such as the masked distribution, while bounds in total variation (TV) depend on the state space size $S$ and become vacuous for modern language tasks, where vocabularies contain hundreds of thousands of tokens. We develop a unified adjoint-equation-based framework that establishes dimension-free convergence guarantees in any integral probability metric (IPM). To the best of our knowledge, our bounds are the first to be entirely free of $S$ and applicable to both masked and uniform priors. Importantly, our theory relies only on a single standard rate-matrix regularity assumption and applies to general priors. Five novel techniques drive our improvements: working in the space of observables via adjoint equations rather than directly with probability measures, a regularity analysis that yields bounds on any IPM, a coupling argument that removes $S$-dependence under uniform transitions, and score-marginal cancellation and exit-routing techniques that remove $S$-dependence under masked transitions. Our framework thus sharply departs from prior analyses and avoids the shortcomings of pathspace-KL and existing TV-based approaches. Beyond convergence bounds, our framework provides a versatile toolkit for further theoretical study of discrete diffusion models, including principled choices of loss functions and dimension-free step complexity.

10.
Nature (Science) 2026-06-10

Daily briefing: Ancient ground squirrels ate like ‘zombies of the Pleistocene’

Authors:

Evidence from fossilized poo reveals the diverse diet of ancient ground squirrels. Plus, the science behind the peptide craze and our innate tendency to wander anticlockwise. Evidence from fossilized poo reveals the diverse diet of ancient ground squirrels. Plus, the science behind the peptide craze and our innate tendency to wander anticlockwise.

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

BIM-Edit: Benchmarking Large Language Models for IFC-Based Building Information Modeling

arXiv:2606.20146v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly applied to computer-aided design (CAD) to generate design artifacts from textual instructions. In engineering practice, this requires more than creating new geometry, models must also understand existing scenes, edit them correctly, and preserve semantics and relations. However, many CAD benchmarks focus on creating new models rather than editing existing ones, and mostly evaluate geometric correctness. We introduce BIM-Edit, a benchmark for evaluating LLMs on natural-language editing of Building Information Models (BIM) represented in the Industry Foundation Classes (IFC) format. BIM provides a challenging testbed because building models encode geometry together with semantic and relational structure. BIM-Edit contains 324 editing tasks spanning 11 realistic building models and 36 synthetic scenes. Tasks are expressed using three instruction categories - direct, spatial, and topological - covering both explicit and scene-grounded edits. We evaluate outputs along three dimensions: geometric accuracy, semantic validity, and topological consistency. Across evaluated LLMs, the best-performing model achieves only 49.5% average score across the three metrics, and no model fully solves more than 3.4% of tasks. These results demonstrate a substantial gap between current LLM capabilities and the requirements of structured engineering design workflows.

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

Gaussian Spatial Priors for Anatomy-Aware Object Detection in Surgical Videos

Detecting anatomical structures in surgical video is essential for intraoperative safety frameworks such as the Critical View of Myopectineal Orifice (CVMPO) in inguinal hernia repair. While prominent structures like the Cooper's Ligament and Triangle of Doom are reliably detected by standard methods, smaller structures such as the epigastric vessels remain challenging due to their visual ambiguity and intermittent visibility. We observe that the spatial relationship between structures is anatomically constrained, and propose a Gaussian Spatial Prior (GSP) module that encodes this relationship as a compact, parametric bias injected into the self-attention of a DAB-DETR decoder. The prior is computed offline from training annotations as a small set of frozen Gaussian parameters and recomputed at each decoder layer using the iteratively refined reference points. On a dataset of inguinal hernia repair videos with 5-fold cross-validation, GSP improves dependent class detection by $+33.5\%$ ($AP_{50}$) over DAB-DETR and $+53.9\%$ over YOLOv26, while also improving anchor detection by $+6.0\%$. These gains are statistically significant across all folds ($p=0.012$, paired $t-$test).

13.
arXiv (CS.AI) 2026-06-11

OCSVM-Guided Representation Learning for Unsupervised Anomaly Detection

arXiv:2507.21164v2 Announce Type: replace-cross Abstract: Unsupervised anomaly detection (UAD) aims to detect anomalies without labeled data, a necessity in many machine learning applications where anomalous samples are rare or not available. Most state-of-the-art methods fall into two categories: reconstruction-based approaches, which often reconstruct anomalies too well, and decoupled representation learning with density estimators, which can suffer from suboptimal feature spaces. While some recent methods attempt to couple feature learning and anomaly detection, they often rely on surrogate objectives, restrict kernel choices, or introduce approximations that limit their expressiveness and robustness. To address this challenge, we propose a novel method that couples representation learning with an analytically solvable One-Class SVM (OCSVM), through a custom loss formulation that directly aligns latent features with the OCSVM decision boundary. The model is evaluated on two tasks: a \deleted{new} benchmark based on MNIST-C, and a challenging brain MRI \deleted{subtle} lesion detection task. Unlike most methods that focus on large, hyperintense lesions at the image level, our approach succeeds to target small, non-hyperintense lesions, while we evaluate voxel-wise metrics, addressing a more clinically relevant scenario. Both experiments evaluate a form of robustness to domain shifts, including corruption types in MNIST-C and texture or population age variations in MRI. Results demonstrate performance and robustness of our proposed model, highlighting its potential for general UAD and real-world medical imaging applications. The source code is available at https://github.com/Nicolas-Pinon/uad_ocsvm_guided_repr_learning.

14.
arXiv (CS.CL) 2026-06-17

NarrativeWorldBench: A Frontier-Saturated Benchmark and a Latent World Model for Long-Horizon Co-Creative Audio Drama

Long-form serialized audio drama, with arcs that run for 200 to 800 episodes, is a major creative medium and a setting where frontier large language models (LLMs) fail. We benchmark 21 models, spanning classical, fine-tuned, open-frontier, closed-frontier, and reasoning tiers, on a uniform set of structural narrative metrics. All closed-frontier systems saturate at a plot-beat F1 in the band [0.78, 0.81] and collapse by about -0.20 F1 at horizon h=200. We introduce NarrativeWorldBench, an open benchmark of nine narrative-structure metrics evaluated across horizons h in {10, 20, 50, 100, 200}, with cross-lingual evaluation across four Indic languages (Hindi, Tamil, Telugu, Marathi). We introduce N-VSSM, a Narrative Variational State-Space Model that maintains a structured 256-dimensional latent world state over more than 200 episodes via a Mamba-2 backbone with an event-conditioned posterior and an 8B decoder. N-VSSM holds plot-beat F1 >= 0.84 across all horizons at 4x lower compute than the closed-frontier band. A learned Cultural Transfer Function lifts cross-language fidelity by +0.20 to +0.23 Likert points. In a within-subjects writer study (n = 12 professional authors, 240 trials), N-VSSM is preferred over Claude Opus 4.5 on long-arc consistency 71% of the time and rated +1.3 Likert points higher on controllability.

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

DRA-GRPO: Your GRPO Needs to Know Diverse Reasoning Paths for Mathematical Reasoning

Post-training LLMs with Reinforcement Learning, specifically Group Relative Policy Optimization (GRPO), has emerged as a paradigm for enhancing mathematical reasoning. However, standard GRPO relies on scalar correctness rewards that are often non-injective with respect to semantic content: distinct reasoning paths receive identical rewards. This leads to a Diversity-Quality Inconsistency, where the policy collapses into a narrow set of dominant modes while ignoring equally valid but structurally novel strategies. To bridge this gap, we propose Diversity-aware Reward Adjustment (DRA), a theoretically grounded framework that calibrates the reward signal using the semantic density of sampled groups. By leveraging Submodular Mutual Information (SMI), DRA implements an Inverse Propensity Scoring (IPS) mechanism that effectively de-biases the gradient estimation. This creates a repulsive force against redundancy, driving the policy to achieve better coverage of the high-reward landscape. Our method is plug-and-play and integrates seamlessly with GRPO variants. Empirical evaluations on five math benchmarks demonstrate that DRA-GRPO consistently outperforms strong baselines, achieving an average accuracy of 58.2% on DeepSeek-R1-Distill-Qwen-1.5B with only 7,000 training samples and $55 cost, highlighting the critical role of diversity calibration in data-efficient alignment. The code is available at https://github.com/xiwenc1/DRA-GRPO.

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

MODE-RAG: Manifold Outlier Diagnosis and Energy-based Retrieval-Augmented Generation Evaluation

While Multimodal Retrieval-Augmented Generation (M-RAG) enhances Large Vision-Language Models, it remains highly susceptible to cross-modal hallucinations, causal fabrications, and sycophancy. Furthermore, existing mitigation pipelines often face an intervention paradox: static rules tend to unnecessarily disrupt accurate generations, whereas leaving the multi-modal reasoning completely unguided allows existing mismatches to cascade into severe logical fabrications. To quantify and mitigate these hallucinations, we propose a Multi-Agent system, MODE-RAG, driven by Variational Free Energy (VFE) and internal attention states to dynamically gate interventions. High-risk queries are routed to five stage-specific agents, integrating Monte Carlo Tree Search (MCTS) for rigorous causal derivation and logit perturbations to penalize sycophancy. Dedicated Correction and Overseer agents ensure formatting stability and perform post-hoc factual verification. To objectively evaluate our approach, we introduce ModeVent, a challenging subset derived from the MultiVent dataset. Extensive experiments indicate that our system effectively reduces hallucination rates and logical fabrication, significantly improving the robustness of M-RAG systems.

17.
arXiv (CS.AI) 2026-06-12

ERTS: Adversarial Robustness Testing of Ethical AI via Semantic Perturbation in a Bounded Consequence Space

arXiv:2606.13282v1 Announce Type: new Abstract: As AI systems are deployed in high-stakes ethical contexts such as healthcare triage, autonomous vehicle control, and employment screening, formal methods for evaluating their robustness against adversarial manipulation of ethical reasoning remain underdeveloped. This paper introduces the Ethical Robustness Testing System (ERTS), a closed-pipeline framework that: (1) encodes ethical dilemmas into a 22-dimensional Ethical Consequence Space (ECS) grounded in established ethical theory; (2) applies 17 semantic perturbation functions subject to 6 validity constraint classes including a novel semantic coherence constraint; (3) measures decision deviation via a 4-component Ethical Instability Index (EII); and (4) produces domain-adaptive pre-deployment robustness assessment verdicts. We evaluate 4 structured baseline models and 2 production LLMs (Gemini 2.0 Flash and Llama 3.2) across 50 ethical scenarios spanning 8 deployment domains, generating 1,500 adversarial test cases. Results demonstrate that only 33% of models achieve assessment clearance, with the local Llama-3.2 model proving particularly vulnerable to fairness corruption and information degradation attacks (ERS = 0.737). To the best of our knowledge, no existing framework combines a bounded ethical consequence space, semantic coherence constraints, and domain-adaptive assessment in a single adversarial testing pipeline.

18.
bioRxiv (Bioinfo) 2026-06-18

Bioinf-Farma: supervised integration of epitope prediction and recombinant protein developability for automated vaccine candidate prioritization

Vaccine antigen discovery requires prioritizing protein candidates according to both immunogenic potential and recombinant expression feasibility. These properties are typically evaluated using separate computational tools, requiring researchers to integrate heterogeneous outputs through ad hoc workflows. Here, we present BIOINF-farma, a modular platform integrating epitope prediction and developability assessment for rational antigen selection within a unified environment. Candidates can be submitted as amino acid sequences or three-dimensional structures. When experimental structures are unavailable, BIOINF-farma automatically searches for models in AlphaFold DB or performs structure prediction using Boltz-2, ensuring a standardized structural representation for downstream analyses. Antigenicity is quantified by combining structure-based conformational epitope signals (MLCE/REBELOT-BEPPE) and sequence-based linear epitope propensity scores (BepiPred 3.0) into a protein-level Antigenicity Score, with a classification threshold optimized on a manually curated validation dataset. Developability is evaluated through two supervised Random Forest meta-learners that integrate three solubility predictors (DeepSoluE, SoluProt, Protein-Sol) and three thermal stability predictors (TemStaPro, ProLaTherm, BertThermo), whose outputs are combined into an Expression Efficiency Score (EES). By integrating complementary predictive signals, the meta-learning framework achieves greater accuracy and robustness than individual predictors while maintaining performance across a broad range of sequence identities. The Antigenicity Score effectively discriminates antigenic from non-antigenic proteins with a large effect size, whereas EES successfully distinguishes soluble from insoluble outcomes on an independent panel of recombinant proteins expressed in Escherichia coli. BIOINF-farma jointly assesses antigenicity and expression feasibility within a single framework. Its modular architecture facilitates the incorporation of future predictive methods, while its web-based interface makes the full pipeline accessible to users without programming expertise, supporting rapid candidate triage in vaccine research and emerging pathogen responses.

19.
medRxiv (Medicine) 2026-06-10

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

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

20.
bioRxiv (Bioinfo) 2026-06-11

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

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

21.
arXiv (CS.CL) 2026-06-16

Agentic Reinforcement Learning for Search Misaligns Instruction-Tuning

Agentic reinforcement learning (RL) trains large language models to use tools, but its impact on alignment is poorly understood. We study how agentic RL for search affects the alignment of instruction-tuned (IT) models. We find that RL-trained models inherit refusal reasoning by deflecting harmful requests into benign search queries, but this breaks down under a simple diagnostic trigger that elicits a search call before refusal can occur. Under this condition, RL models produce multi-step unsafe search actions and reasoning, reducing search query safety by up to 68.6% in Qwen and Llama models relative to their IT counterparts. The effect generalises across model families, scales, and RL algorithms. To understand why, we identify linear directions in the residual stream that control search query safety, and show that RL training progressively shifts search behaviour toward the harmful end of this direction. We thus propose representation-guided RL training, which adds a reward penalty based on projection toward the harmful search direction. Training on benign data alone, it restores IT-level alignment without reducing task accuracy and requires no additional training data. Together, our work provides the first framework for diagnosing, mechanistically analysing, and mitigating alignment degradation in agentic RL for search.

22.
arXiv (quant-ph) 2026-06-16

Ultrastrongly coupled open systems and fine grained time

arXiv:2606.16634v1 Announce Type: new Abstract: We study the dynamics of a d-level quantum system coupled to a bosonic reservoir when the coupling constant is large. It is known that in the limit of infinite coupling strength, the system undergoes an instantaneous nonselective measurement, resulting in the immediate decoherence in the measurement basis, followed by a unitary Zeno dynamics. Here we resolve this dynamical process by introducing a fine grained scaling regime of short times proportional to the inverse coupling. We provide a rigorous derivation of the open system dynamics in this regime of ultrastrong coupling and demonstrate how decoherence unfolds continuously in the new time scale. We show that Markovian dynamics which are not given by semigroups arise naturally, in contrast to what happens in the weak coupling theory.

23.
bioRxiv (Bioinfo) 2026-06-11

AGZArank: Investigating epitope-conditioned antibody binder ranking with structure-derived synthetic supervision

Computational antibody design methods can generate large libraries of candidate binders for a target epitope, but prioritizing which candidates to test experimentally remains a major bottleneck. Existing scoring approaches, including physics-based affinity estimators, structure-prediction-derived confidence measures, and inverse-folding likelihood models, provide useful proxy signals but are not explicitly optimized for early enrichment of binders among many structurally similar candidates. Here we investigate epitope-conditioned antibody binder ranking as a dedicated learning problem and introduce AGZArank, a geometric deep learning framework trained with structure-derived synthetic supervision based on normalized pseudo-energy targets. On a benchmark of 45 experimentally validated antibody-antigen interfaces, AGZArank recovered the true binder within the top ten candidates in 44.4% of cases and showed stronger generalization on post-2021 structures than ProteinMPNN, ESM-IF, and PRODIGY. Ablation experiments indicate that ranking performance depends primarily on training scale and alignment between the optimization objective and retrieval-based evaluation, rather than architectural complexity alone. These results support candidate prioritization as a distinct and tractable problem in computational antibody design.

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

Unstable Features, Reproducible Subspaces: Understanding Seed Dependence in Sparse Autoencoders

Sparse autoencoders (SAEs) are widely used to interpret neural network representations, but their utility depends on whether the learned features are reproducible across training runs. We study this question through feature stability: for each SAE feature, we estimate the probability that a similar feature reappears in an independently trained SAE. This yields a scalable per-feature signal that separates stable from unstable features. In a large-scale study across seeds, models, layers, dictionary sizes, and SAE variants, we find a pronounced functional asymmetry: stable features carry most of the reconstruction- and prediction-relevant signal, while unstable features have weak marginal impact and are dominated by low-frequency surface-form triggers in both activation statistics and automatic explanations. Geometrically, unstable features are individually non-reproducible but concentrate in reproducible lower-rank subspaces, suggesting that seed dependence often reflects basis ambiguity within a shared region of activation space rather than pure noise. A controlled synthetic model makes this mechanism explicit, showing that low-rank ground-truth features can be recovered at the subspace level while remaining non-identifiable as individual SAE latents across seeds. Finally, by pooling unique cross-seed features, we construct more stable SAEs while preserving explained variance in this setting. Together, these results show that unstable features are not merely failed or noisy latents: they have weak individual functional impact, but reflect reproducible low-dimensional structure that standard SAEs resolve differently across seeds.

25.
arXiv (CS.AI) 2026-06-16

Driving, Fast or Slow? Neuro-Symbolic Guidance for Motion Prediction in Multi-Modal Ground Mobility

arXiv:2606.15251v1 Announce Type: cross Abstract: Accurate and interpretable motion prediction for heterogeneous traffic spaces, including pedestrians, bicycles, cars, and trucks, is essential for safe autonomous navigation. Nevertheless, state-of-the-art approaches remain predominantly black-box, lacking explicit encoding of the regulatory and behavioral constraints of real-world mobility. We propose Trajectory Compliance-Shaping (TraCS), a neuro-symbolic framework that augments existing black-box motion prediction backbones with interpretable and probabilistic first-order logic. To do so, TraCS employs an agentic code-generation pipeline to bridge the gap between natural-language descriptions of traffic regulations and probabilistic motion prediction. Furthermore, TraCS employs a reactive data-streaming inference engine that maintains and efficiently updates compliance landscapes as scenes evolve. To prevent TraCS from overconfidently steering the backbone's predictions in the wrong direction, we propose a neural confidence rating learned as a context-aware attenuation of the compliance signal. We demonstrate on the Argoverse 2 benchmark how TraCS consistently improves state-of-the-art prediction backbones, showing that probabilistic and symbolic compliance reasoning is a broadly applicable and computationally efficient complement to purely neural motion predictors.