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

How Task Structure Limits Multi-Agent Success: An Information-Theoretic Analysis

arXiv:2606.13733v1 Announce Type: cross Abstract: Multi-agent systems (MAS) were expected to overcome the limitation of single-agent systems (SAS) through collaboration. However, under typicality conditions on the task's constraint graph and bounded inter-agent communication, we prove that the success probability of a MAS is closely tied to the connectivity of task constraints, where each agent has limited information-processing capacity. Specifically, the success probability decays exponentially with an information bottleneck that emerges from partitioning the task's constraint graph among agents. We define this quantity as the minimum cut cost $C_{\min}$ of the potential constraint graph of each task. This information-theoretic bound applies to both open systems with external feedback and closed systems without. We validate our theory on both synthetic experiments and real-world empirical data from SWE-bench submissions. From our framework, effective MAS design should incorporate task-inherent constraints alongside engineering optimization, and when $\Cmin$ is high, practitioners should restructure tasks rather than simply scaling agents or communication.

02.
arXiv (CS.CL) 2026-06-12

No Hidden Prompts Needed! You Can Game AI Peer Review with Presentation-Only Revisions

As AI-generated reviews move from experimental tools into peer-review infrastructure, most robustness concerns have focused on explicit attacks such as hidden instructions and prompt injection. We study a harder and more policy-relevant failure mode: no hidden text, no prompt injection, and no changes to methods, experiments, figures, equations, proofs, or numerical results. The attacker modifies only presentation-level content, such as the abstract, contribution framing, related work, discussion, and narrative structure. We introduce adversarial repackaging: a closed-loop attack that uses AI-reviewer feedback to search for presentation-level revisions while keeping the scientific evidence fixed. Across three mainstream AI reviewers, adversarial repackaging achieves a 75.1% attack success rate and a mean score gain of +1.21/10. The effect is not explained by ordinary prose polishing. We also reveal that strategies that change how the reviewer interprets the paper, such as related-work repositioning and analytical discussion expansion, substantially outperform surface edits such as local polishing, table formatting, and algorithm boxes. Our analysis reveals two deeper structural failure modes. First, AI reviewers are easier to impress than to convince: highlighting strengths reliably increases perceived merit, while attempts to dissolve weaknesses frequently backfire. Second, AI reviewers can confuse the appearance of addressing a limitation with actually resolving it, allowing unchanged evidence to be reinterpreted as stronger scientific contribution. These results show that the deployment risk is not only malicious hidden instructions, but the emergence of paper presentation itself as an optimization surface. We release a contamination-free rolling benchmark and attack framework for testing whether AI reviewers remain anchored to scientific content under presentation-only edits.

03.
arXiv (CS.LG) 2026-06-16

An Integrable Token Mixing Layer from the Generalized Yang Baxter Equation

arXiv:2606.15085v1 Announce Type: new Abstract: The YB Mixer is a sequence token mixing layer derived from free fermion and generalized Yang Baxter structures. It applies a core principle from integrable systems where a local algebraic constraint guarantees global computational stability. By using the Ising exchange algebra the mixer creates a free fermionic structure that acts as an exactly norm preserving orthogonal map. This algebra also produces commuting transfer matrices which allow inference to be order free and adaptable to any variable budget. To ensure the model can generalize to longer sequence lengths it uses a spectral circulant generator. This generator maintains the crucial orthogonal and commuting properties of the system. The result is a highly stable and mathematically grounded architecture for sequence processing.

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

Learning aligned EEG representations with subject-specific encoders

arXiv:2606.16462v1 Announce Type: cross Abstract: Cross-subject EEG decoding promises more training data, but it also exposes neural networks to strong inter-subject distribution shifts. We study whether task supervision and architecture alone can learn subject-aligned representations. We replace a shared EEG encoder with subject-specific encoders followed by a common classifier, and compare this hybrid model with standard EEGNet, AttentionBaseNet, and CTNet baselines with Euclidean Alignment (EA) on four motor-imagery datasets. EA improves shared encoders by recentering subject covariances, but the hybrid encoder largely internalises this role: validation-loss curves and latent-distance analyses change little when EA is removed. Subject-specific heads increase class distinctiveness and place each subject close to its own latent manifold, improving most subjects while leaving a method-sensitive subset. These results support subject-specific encoders as a learned alignment mechanism for EEG decoding and identify head selection for unseen subjects as the remaining bottleneck.

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

Feature Attribution in Directed Acyclic Graphs Using Edge Intervention

arXiv:2606.15273v1 Announce Type: new Abstract: Shapley value-based feature attribution methods face challenges in scenarios involving complex feature interactions and causal relationships, even when a causal structure is provided. Existing methods typically adopt a node-centric view, attributing importance solely to individual features. Consequently, they often fail to simultaneously capture the externality and exogenous influence of features, leading to unreasonable interpretations. To overcome these limitations, we propose a novel feature attribution method called DAG-SHAP, which is based on edge intervention. DAG-SHAP treats each feature edge as an individual attribution object, ensuring that both externality and exogenous contributions of features are appropriately captured. Additionally, we introduce an approximation method for efficiently computing DAG-SHAP. Extensive experiments on both real and synthetic datasets validate the effectiveness of DAG-SHAP. Our code is available at https://github.com/ZJU-DIVER/DAG-SHAP.

06.
medRxiv (Medicine) 2026-06-16

Utilising Artificial Intelligence to Identify Ventricular Tachycardia Ablation Targets in Sinus Rhythm

Background and Aims: Machine learning has shown potential in predicting ablation targets for ventricular tachycardia (VT) in an animal model. This study progresses to externally validating deep learning approaches for human data. Methods: The development and external validation dataset included 21 and 13 patients, respectively, with structural VT undergoing catheter ablation. In the development datasets, electrophysiological studies were conducted using the AdvisorTM HD grid (EnsiteTM X), while both CARTO and Ensite Precision were used in the validation dataset. In each patient, VT ablation targets were defined as mapping points within 8 mm of VT isthmuses. Three advanced machine learning models were trained using cardiac mapping data acquired in both omnipolar and unipolar configurations during sinus rhythm and ventricular pacing. Discrimination was evaluated using nested leave-one-out cross-validation at patient level. Results: Overall, graph convolutional networks (GCNs), which integrate intracardiac signal waveforms with three-dimensional electroanatomical geometries, achieved the highest performance, with optimal results obtained from unipolar electrograms acquired in sinus rhythm (median AUC 0.793, sensitivity 83.6%, specificity 69.0%). This may be partly explained by the inclusion of repolarization dynamics in unipolar electrograms and the higher point density of sinus rhythm maps. Comparable performance was observed in the external dataset. Conclusion: This study demonstrates that graph convolutional networks applied to sinus rhythm EGM waveforms collected during substrate mapping can localise critical components of VT re-entry circuits. This approach has potential to provide fast and accurate ablation guidance without the need to induce and map VT, improving safety and efficacy of VT catheter ablation.

07.
arXiv (quant-ph) 2026-06-19

Exploiting More Than Symmetry in Variational Quantum Machine Learning

arXiv:2606.20316v1 Announce Type: new Abstract: The success of variational quantum learning models crucially depends on choosing parametrizations that reflect the structure of the problem at hand. Symmetries provide one of the clearest such structures: whenever transformations of the input leave the desired outcome unchanged, this invariance should be built into the model rather than discovered during training. However, imposing a symmetry does not by itself determine a useful ansatz. Even within the symmetry-preserving space, one must decide where the trainable degrees of freedom should be placed. In this work, we study this remaining design freedom in equivariant variational quantum circuits. Building on symmetry-based parameter sharing, we disentangle two architectural choices: how much symmetry should be enforced, and which symmetry-respecting interactions should be trainable. Using Tic-Tac-Toe as a fully enumerable and structurally transparent test case, we find that suitable subgroups preserve most of the generalization benefit. By contrast, the dominant gains arise from gates acting directly on decisive task motifs. Thus, symmetry defines the admissible design space, while effective ansatze require an additional task-informed choice of trainable interactions.

08.
arXiv (CS.CL) 2026-06-16

Can LLM Coding Agents Reason About Time Series?

Large language models (LLMs) are increasingly being used for automated decision-making systems in finance, healthcare, or environmental monitoring. Time series data are ubiquitous in these fields, yet hard to process automatically. Can time series be analyzed by LLM agents? We examine three approaches: providing the agent with raw numerical data, using the LLM as a coding agent, or a combination of both. In the coding agent setup, the model iteratively queries the data using Python code. Using two time series understanding benchmarks, we show that agents with code access can outperform models processing raw data by up to 10%. However, even the best performing agent still answers about 22-34% of the questions incorrectly. To get insights into models' strategies and reasoning gaps, we analyze the model outputs with a strong LLM judge. Our analysis reveals that coding agents can select appropriate statistical tests, but often miss important nuances. Meanwhile, models with access to raw data can reach the right conclusions using back-of-the-envelope calculations.

09.
arXiv (CS.CV) 2026-06-16

Unlocking Diffusion Hierarchies: Adaptive Timestep Selection for Zero-Shot Segmentation

Zero-shot segmentation has recently shown notable improvement by leveraging the rich visual priors in large-scale text-to-image diffusion models, such as Stable Diffusion. However, current diffusion-based methods often face limitations due to the trade-off between spatial resolution and contextual information, as well as their reliance on a single static timestep for feature extraction. To overcome these challenges, our work introduces two key advancements. First, our Contextual Similarity Maps fuse high-resolution attention maps with rich U-Net encoder features, providing both fine-grained and robust per-pixel representations. Second, we identify an emergent hierarchical semantic progression within the denoising process of various diffusion models: representations transition from part-level abstractions at earlier timesteps to object-level abstractions at later stages. Leveraging this insight, we introduce a mechanism to adaptively select the optimal timestep for each pixel. Extensive experiments demonstrate that our method consistently outperforms existing zero-shot segmentation baselines, validating the efficacy of combining contextual features with dynamic, hierarchical timestep selection.

10.
arXiv (CS.AI) 2026-06-19

TelcoAgent: A Scalable 5G Multi-KPM Forecasting With 3GPP-Grounded Explainability

arXiv:2606.19821v1 Announce Type: new Abstract: Key Performance Measurement (KPM) forecasting is essential for proactive network management of 5G and next-generation telecom networks. However, existing machine learning (ML) approaches face significant limitations in scalability and explainability, restricting their effectiveness in real-world deployments. We propose TelcoAgent, a foundation model-based framework that enables accurate, scalable, and explainable forecasting of multiple KPMs across diverse network cells without the need for site-specific training. Specifically, the framework comprises three key components: (i) an automated three-agent pipeline that constructs a 3rd Generation Partnership Project (3GPP) knowledge graph directly from specification documents, (ii) a scalable, time-series foundation model (TSFM)-based prediction pipeline to deliver accurate, zero-shot forecasting, and finally (iii) a reasoning and explanation pipeline that provides actionable, domain-grounded diagnostics. Evaluated using a 3-month, real-world, city-scale 5G KPM dataset from a U.S.-based network operator, TelcoAgent demonstrates high forecasting accuracy for all 7 considered KPMs per cell across 200 cells, while delivering explainable insights and actionable instructions to address network degradations.

11.
arXiv (quant-ph) 2026-06-16

No Universal Purification in Quantum Mechanics

arXiv:2509.21111v2 Announce Type: replace Abstract: Many central tasks in fundamental physics and quantum information processing are possible only insofar as mixed quantum states can be made purer. In this work, we prove that the linearity and positivity of quantum mechanics impose general restrictions on quantum purification, unveiling a new fundamental principle of quantum information processing. We first establish that no quantum operation can transform a finite number of copies of an unknown quantum state or channel into an exactly pure output that depends non-trivially on the input, thereby ruling out an important form of universal purification in both static and dynamical settings. Building on this, we show that, upon relaxing the requirement of exact purity, one can establish quantitative sample-complexity lower bounds for approximate purification that hold for arbitrary physically allowed strategies, whose scaling matches the performance of purification-related tasks across several different areas of quantum information processing. Moreover, this lower bound leads to a generalized standard quantum limit for learning arbitrary functions of a quantum state, greatly extending earlier results based on quantum Fisher information and revealing a deep connection between purification and quantum learning. Extending this principle to other important settings, we establish, for the first time, an exponential sample-complexity lower bound for approximate pure dilation state preparation and a no-go theorem for approximate bosonic Gaussian state purification with passive Gaussian operations, establishing much more stringent limitations under practical operational constraints.

12.
arXiv (CS.CV) 2026-06-15

Encoder Winners Do Not Reliably Transfer Across VLA Backbone Scale: A Frozen-Backbone Grafting Diagnostic

Vision-language-action (VLA) policies typically inherit their vision encoder from upstream VLM releases, but it is unclear whether an encoder choice validated on a small VLA transfers to a larger backbone. We introduce a frozen-backbone grafting diagnostic: the vision tower of a released VLA is replaced by a candidate encoder under a fixed protocol (adaptive average pooling, LayerNorm, and a single trainable linear projector), with the language model and action expert frozen. Across four encoders, two LIBERO suites, two backbones (SmolVLA-450M and $\pi_{0.5}$-3.3B), and two-to-three seeds per cell (40 main grafting runs plus native, LoRA, pooling, and zero-/shuffled-image controls, all scored by offline action MSE), the small-backbone winner does not reliably select the large-backbone top tier: SigLIP is best on SmolVLA across both suites, while on $\pi_{0.5}$ DINOv2-small leads the spatial suite and the object suite is a seed-sensitive near-tie band; three of the four backbone-suite comparisons (and 11 of 12 seed-level cells) support backbone-dependent rankings. The grafting wrapper is itself non-neutral with opposite sign across backbones (+45-56% MSE on the SmolVLA native tower, -50-52% on $\pi_{0.5}$), so all conclusions are conditional on the fixed grafting protocol. We position frozen grafting as a cheap target-backbone diagnostic to run before committing to an encoder at scale, not as a closed-loop deployment claim.

13.
arXiv (CS.CV) 2026-06-12

AudioX-Turbo: A Unified Framework for Efficient Anything-to-Audio Generation

Audio and music generation based on flexible multimodal control signals is a widely applicable topic, with the following key challenges: 1) a unified multimodal modeling framework, 2) large-scale, high-quality training data, and 3) the prohibitive inference cost of multi-step diffusion sampling. As such, we propose AudioX-Turbo, a unified and efficient framework for anything-to-audio generation that integrates varied multimodal conditions (i.e., text, video, and audio signals) in this work. AudioX-Turbo follows a teacher-student paradigm. The teacher AudioX-Base is built on a Multimodal Diffusion Transformer with a Multimodal Adaptive Fusion module that aligns diverse multimodal inputs for high-fidelity synthesis, and is then distilled into the few-step student AudioX-Turbo via Distribution Matching Distillation adapted to flow matching, complemented by a diffusion-based discriminator for high-quality few-step generation. To support the training of AudioX-Turbo, we construct a large-scale, high-quality dataset, IF-caps-Pro, comprising approximately 9.2M samples curated through a two-stage data collection and annotation pipeline. We benchmark AudioX-Turbo across a wide range of tasks, finding that our model achieves superior performance, especially on text-to-audio and text-to-music generation, while operating at only 4 sampling steps and requiring approximately 25x fewer function evaluations (NFE) than multi-step baselines. These results demonstrate that our method is capable of audio generation under flexible multimodal control, showing efficient and powerful instruction-following capabilities. The code and datasets will be available at https://zeyuet.github.io/AudioX-Turbo/.

14.
arXiv (quant-ph) 2026-06-17

Impulse Decoding of Quantum LDPC Codes: Equivalence of Degeneracy and Code-Shortening

arXiv:2606.18240v1 Announce Type: new Abstract: Quantum error correction is essential for building scalable quantum computers. Within the stabilizer formalism, the Calderbank-Shor-Steane framework constructs quantum codes from pairs of classical linear codes. A distinctive feature in this setting is degeneracy, where multiple equivalent error estimates exist-a phenomenon that has no classical counterpart, and the lack of a meaningful classical coding-theoretic interpretation of which has remained a gap in the literature. In this paper, we demonstrate that degeneracy is closely related to the classical operation of shortening of a linear block code. Interestingly, the shortening here takes place at the decoder rather than at the encoder. Leveraging this insight, we present a parallel decoding scheme for quantum low-density parity-check codes, which we term impulse decoding, that significantly outperforms belief propagation with ordered statistics decoding, as well as several other existing techniques, under both code-capacity and circuit-level noise, with significantly lesser complexity. We then present another algorithm based on decoding of residual errors, which when combined with impulse decoding achieves further performance improvement under circuit-level noise.

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

Detecting Hate and Inflammatory Content in Bengali Memes: A New Multimodal Dataset and Co-Attention Framework

Internet memes have become a dominant form of expression on social media, including within the Bengali speaking community. While often humorous, memes can also be exploited to spread offensive, harmful, and inflammatory content targeting individuals and groups. Detecting this type of content is exceptionally challenging due to its satirical, subtle, and culturally specific nature. This problem is magnified for low-resource languages like Bengali, as existing research predominantly focuses on high-resource languages. To address this critical research gap, we introduce Bn-HIB (Bangla Hate Inflammatory Benign), a novel dataset containing 3,247 manually annotated Bengali memes categorized as Benign, Hate, or Inflammatory. Significantly, Bn- HIB is the first dataset to distinguish inflammatory content from direct hate speech in Bengali memes. Furthermore, we propose the MCFM (Multi-Modal Co-Attention Fusion Model), a simple yet effective architecture that mutually analyses both the visual and textual elements of a meme. MCFM employs a co-attention mechanism to identify and fuse the most critical features from each modality, leading to a more accurate classification. Our experiments show that MCFM significantly outperforms several state-of-the-art models on the Bn-HIB dataset, demonstrating its effectiveness in this nuanced task. To facilitate reproducibility and future research, the Bn-HIB dataset has been made publicly available through Mendeley Data. Warning: This work contains material that may be disturbing to some audience members. Viewer discretion is advised

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

AL-GNN: Privacy-Preserving and Replay-Free Continual Graph Learning via Analytic Learning

arXiv:2512.18295v2 Announce Type: replace-cross Abstract: Continual graph learning (CGL) aims to enable graph neural networks to incrementally learn from a stream of graph structured data without forgetting previously acquired knowledge. Existing methods particularly those based on experience replay typically store and revisit past graph data to mitigate catastrophic forgetting. However, these approaches pose significant limitations, including privacy concerns, inefficiency. In this work, we propose AL GNN, a novel framework for continual graph learning that eliminates the need for backpropagation and replay buffers. Instead, AL GNN leverages principles from analytic learning theory to formulate learning as a recursive least squares optimization process. It maintains and updates model knowledge analytically through closed form classifier updates and a regularized feature autocorrelation matrix. This design enables efficient one pass training for each task, and inherently preserves data privacy by avoiding historical sample storage. Extensive experiments on multiple dynamic graph classification benchmarks demonstrate that AL GNN achieves competitive or superior performance compared to existing methods. For instance, it improves average performance by 10% on CoraFull and reduces forgetting by over 30% on Reddit, while also reducing training time by nearly 50% due to its backpropagation free design.

17.
PLOS Medicine 2026-06-23

Comparisons of core component delivery in cardiac rehabilitation programs by country income classification and decade based on the 2025 Global Audit Update: A survey study

by Gabriela Lima de Melo Ghisi, Rachael P. Carson, Karam Turk Adawi, Rongjing Ding, Warner M. Mampuya, Mariya P. Jiandani, Jimena Martinez, Monserrat Cruz Rivero, Claudia V. Anchique, Dinah L. van Schalkwijk, Jonathan Gallagher, Buket Akinci, Dion Candelaria, Jirapa Champaiboon, Daniel F. Quesada-Chaves, Tone M. Norekvål, Iwona Szadkowska, Borut Jug, Evangelia Kouidi, Marta Supervia, Won-Seok Kim, Chamila Mettananda, Lilian Mbau, Gulsim T. Aimakova, Sherry L. Grace, on behalf of the ICCPR Global Cardiac Rehabilitation Audit Update Investigators Background Cardiovascular disease (CVD) remains a leading global health burden. Cardiac rehabilitation (CR) is essential to reducing morbidity and improving patient outcomes. Since the COVID-19 pandemic, CR delivery worldwide has evolved, yet these changes have not been systematically charactemkjrized. The objective of this study was to characterize globally: (1) the delivery of core CR components, including risk factors assessed, patient education practices, and program resources; (2) differences in these elements by country income classification and relative to the initial 2016 Global CR Audit. Methods and findings A cross-sectional Audit update was conducted. Program-level data were collected from May 1st to September 1st 2025 using a REDCap survey adapted from previous Audits. Eligible respondents were leads of phase II/post-discharge CR programs providing at least an initial assessment, structured aerobic exercise, and ≥1 additional core component. ICCPR associations and local leaders supported program identification. Main outcomes were core components delivered (10 assessed), risk factors assessed (14 assessed), patient education dose (hours/patient/program), and program resources (17 assessed). Generalized linear mixed models (GLMM) tested differences by income classification and (when applicable) changes since 2016. Of 7,025 programs identified globally, 1,505 (62% median country response rate) initiated a survey from 90/113 (80%) countries with CR. The median number of core components offered was 8/program (p25, p75 = 6, 10), with upper-middle income countries offering significantly more components overall (median = 9), and also high-income countries offering more than low-income countries (8 versus 6, p 

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

Light-weight Pronunciation Assessment via Discrete Speech Token Surprisal

Training automated pronunciation assessment often relies on labeled learner errors or non-native corpora that are costly to collect. We propose a lightweight framework trained only on native speech resources, operating unsupervised or lightly calibrated with a small set of scored utterances. At inference, learner speech is discretized with an SSL encoder and a K-means codebook. A token language model trained on native sequences computes surprisal where higher surprisal indicates phonotactic deviation. We add a transcript-guided Text2DUnit–DTW module that predicts native token sequences from reference text and aligns them to acoustic tokens to derive error-sensitive features. Surprisal and alignment features are fused via simple regression. On SpeechOcean762, PCC improves from 0.60 to 0.66 with transcript guidance, near supervised baselines. Cross-dataset evaluation on L2-ARCTIC shows consistent gains.

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

ThousandWorlds: A benchmark for climate emulation of potentially habitable exoplanets

arXiv:2606.18338v1 Announce Type: new Abstract: The search for life beyond Earth will depend on detecting faint signatures in the atmospheres of potentially habitable exoplanets. Interpreting those signatures requires understanding the host planet's climate: the same molecule may signal life on one planet and abiotic chemistry on another. Global climate models (GCMs) provide this understanding, but individual runs can require up to millions of core-hours and substantial domain expert time. Machine-learning emulators could remove this bottleneck, but progress has been limited by the absence of a curated, multi-model exoclimate dataset. We introduce ThousandWorlds, an ML-ready benchmark for exoclimate emulation and for the broader regime of low-data, multi-simulator, parameter-to-field regression. The dataset contains approximately 1800 simulations from five GCMs, mapping eight planet parameters to 3D atmospheric fields including temperature, humidity, winds, clouds, and radiation. Three nested subsets define progressively harder challenges: single-simulator regression, multi-simulator regression with complete observations, and multi-simulator regression with structured missingness. We propose two evaluation protocols: one for ranking methods, and one that measures performance relative to the disagreement between GCMs themselves. We evaluate seven baselines spanning simple methods, deep learning, and Gaussian processes. GP-based methods perform best, suggesting that ThousandWorlds exposes a regime where off-the-shelf deep learning does not yet succeed. Data: https://doi.org/10.57967/hf/8695. Code: https://github.com/edstevenson/ThousandWorlds.

20.
medRxiv (Medicine) 2026-06-16

Reliability and construct validity of the Technology Device Interference Scale in a sample of children and parents

There is increasing interest in parent-child technoference: the interference with personal interactions caused by technology devices. This study examined the reliability and construct validity of the Technology Device Interference Scale (TDIS) to measure technoference in a sample of Canadian parents and children. Parents (n=883) and children (n=376) were recruited from clinical and community settings and completed the TDIS for their own and family member technoference over three timepoints (T1=2023, T2=2024, T3=2025). TDIS internal consistency, test-retest reliability, and construct validity were assessed using Cronbachs alpha, intraclass correlation coefficient, and confirmatory factor analysis, respectively. The TDIS showed good internal consistency and adequate to good construct validity when used by children to report on their own technoference (all >.70; CFI>.95, TLI>.95, RMSEA.70; CFI>.95, TLI>.90, RMSEA[≤].11). The TDIS had low to acceptable internal consistency and poor model fit for parent report of their own technoference ( range: .63 - .66; CFI

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

Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning

arXiv:2604.14906v3 Announce Type: replace-cross Abstract: The pseudoknot secondary structure in SARS-CoV-2 RNA is essential for regulating protein synthesis through $-$1 programmed ribosomal frameshifting ($-1$ PRF), a mechanism that allows the virus to generate both structural and non-structural proteins from overlapping reading frames. This pseudoknot exhibits both threaded and unthreaded long-lived topologies. The influence of ligand binding on its folding is a process critical for the development of $-$1 PRF small-molecule inhibitors. Understanding this process through unbiased molecular dynamics (MD) simulations can be facilitated by introducing collective variables (CVs) that capture the corresponding slowest dynamical modes. Here, we use spectral map (SM), a thermodynamics-driven machine learning technique, to learn such CVs directly from all-atom MD trajectories of the SARS-CoV-2 RNA pseudoknot in complex with the $-$1 PRF inhibitor merafloxacin and its two structural analogs in neutral and ionized forms. Free-energy landscapes (FELs) derived from the learned CVs indicate that ligand-induced destabilization is topology-selective. In the threaded pseudoknot, the inhibitors destabilize the S2 stem, while in the unthreaded pseudoknot, destabilization occurs in the S1 and S3 stems. Furthermore, the extent to which each ligand reshapes the FEL matches experimentally reported antiviral potency, whereas the protonation state qualitatively alters dynamics within the same RNA topology. Overall, our results show how pseudoknot topology, ligand type, and protonation state collectively influence the slow conformational dynamics of viral RNA and establish physiological protonation as a critical factor for modeling RNA-targeted drug action.

22.
arXiv (CS.AI) 2026-06-18

ASTRA: A Scalable Next-Generation ATCO Training Simulator with Autonomous Simpilots

arXiv:2606.18319v1 Announce Type: cross Abstract: Air Traffic Control Operators (ATCOs) are vital in ensuring the safe, orderly, and efficient flow of air traffic, yet training capacity is constrained by reliance on specialized human trainers known as simpilots, who must role-play both pilots and ATCOs in a simulated airspace. Existing automated solutions rely on Western-centric speech models that perform poorly in Singaporean operational contexts, with off-the-shelf systems exhibiting Word Error Rates (WER) of up to 107.80% on Singaporean-accented aviation speech. We introduce ASTRA, an end-to-end training simulator that automates these simpilot roles through a pipeline that transcribes ATCO speech, interprets instructions, and generates appropriate pilot and ATCO responses using locally adapted voice models. Our fine-tuned Automatic Speech Recognition (ASR) pipeline reduces WER to 23.45%, substantially outperforming existing approaches in this domain. Beyond traffic simulation, ASTRA incorporates an AI-assisted performance evaluation framework that assesses trainee radiotelephony communications across accuracy, brevity, and completeness, achieving post-optimization scores of 91.7%, 88.2%, and 86.9%, respectively. Built on open-source foundations such as DSPy and Unsloth, this approach enables scalable, standardized ATCO assessment while reducing instructor workload.

23.
arXiv (CS.LG) 2026-06-16

Hierarchical Advantage Weighting for Online RL Fine-Tuning of VLAs from Sparse Episode Outcomes

arXiv:2606.17043v1 Announce Type: cross Abstract: When pretrained VLA policies are fine-tuned through online RL, each rollout episode produces only a single binary outcome (success or failure), yet the actor update requires per-transition supervision. Existing approaches commonly reduce this sparse outcome to a single scalar reward or advantage signal, which conflates distinct forms of transition-level feedback and provides limited guidance once basic task success becomes achievable. First, a single scalar signal conflates the two objectives of viability and efficiency; once basic success is achieved, the binary label provides no gradient to distinguish efficient completions from slow ones. Second, real-world rollouts mix autonomous and intervention segments; naively assigning episode outcomes across these boundaries introduces incorrect credit assignment. To address these issues, we propose Hierarchical Advantage-Weighted Behavior Cloning (HABC), which trains separate critic heads for these two objectives on different data subsets and combines their outputs with a state-adaptive balance. A state-adaptive gate $g_t$ merges their one-step advantages, prioritizing viability when success is uncertain and shifting to efficiency only when viability is high, and converts the result into per-transition weights on the actor loss. Intervention-aware credit assignment further restricts outcome labels to segments executed by the current policy, preventing supervision from leaking across intervention boundaries. In real-robot experiments on three contact-rich bimanual tasks, HABC raises success from supervised fine-tuning (SFT) baselines of 36%, 44%, and 12% to 92%, 88%, and 38%.

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

Uncertainty Is Not a Safety Net for Clinical VQA, but Can It Anticipate Model Failure?

Safe deployment of clinical vision-language models (VLMs) requires reliable uncertainty estimation (UE): a signal indicating when predictions should be trusted or escalated to a clinician. We test whether current UE methods actually deliver this signal. Benchmarking 8 methods across 12 VLMs on clinical visual question-answering (VQA), we find that UE quality is not an intrinsic property of the UE method: it tracks model accuracy, degrading precisely where the model performance is weakest, and therefore where reliability is most needed. When we stress-test models by hiding the correct option among the multiple-choice answers (NOTA perturbations), accuracy collapses while uncertainty barely changes, leaving models systematically miscalibrated. Yet, we find that uncertainty on the unperturbed input reliably anticipates which predictions will collapse under NOTA, indicating that UE in current VLMs carries diagnostic information about model fragility. Our results position UE as a diagnostic tool for identifying fragile predictions and motivate perturbation-based evaluation as a path toward safe clinical deployment.

25.
bioRxiv (Bioinfo) 2026-06-18

Predicting optimal growth temperatures of bacteria using learned structural information from a single protein

Temperature is a fundamental determinant of bacterial physiology and ecology. Optimal growth temperature (OGT) is highly variable across species, contributing to differences in where and when species are most likely to thrive. Although the OGTs for most bacteria remain unknown, the increasing availability of genomes from uncultivated and cultivated taxa has made it advantageous to build genomic, cultivation-independent models to infer OGT. However, pre-existing genomic models often lack the generalizability and mechanistic grounding required for robust inferences of OGT. We propose a novel framework for predicting bacterial OGT which uses learned protein structural signatures of thermal adaptation. We hypothesize that biophysical tradeoffs which dictate enzymatic functions across variable temperatures provide a more robust empirical basis for OGT prediction than broad genomic features. Our OGT-predicting model, ROSEATE, is based on a single gene, adenylate kinase (ADK), that encodes for a ubiquitous enzyme essential for energy homeostasis. ROSEATE uses high-dimensional latent space encoding via MSA Transformer, a protein language model which embeds ADKs in a manner which preserves biophysical information about embedded proteins. We show that the accuracy of the ROSEATE model is on par with other genome-based models, has a high degree of phylogenetic generalizability, and the ESM embeddings effectively capture key temperature-adaptive enzyme characteristics derived from AlphaFold structures. Because ROSEATE is based on analyses of a single ubiquitous protein, it can be used with metagenomic data to infer the community-level variation in bacterial OGTs. We demonstrate this feature of ROSEATE by reconstructing ADK sequences from over 500 environmental and host-associated metagenomes, successfully distinguishing community-wide thermal preferences across diverse habitats, from polar oceans to mammalian guts. By transitioning from genomic proxies to informationally dense protein structural features, this work provides an efficient, interpretable tool for predicting bacterial OGTs across taxa and whole communities.