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

Controlled Dynamics Attractor Transformer

arXiv:2606.15207v1 Announce Type: cross Abstract: Transformer architectures have dramatically advanced representation learning and inference in deep models through self-attention mechanisms. In parallel,associative memory (AM) frameworks map representations onto energy landscapes, offering interpretable retrieval mechanisms. However, their continuous-time inference dynamics lack the biological plausibility of classical Continuous Attractor Neural Networks (CANNs). To bridge this gap, we propose Controlled Dynamics Attractor Transformer (CDAT), which couples a mixture von Mises-Fisher (Mo-vMF) attention energy with a Hopfield refinement energy, while augmenting energy descent with a CANN-inspired excitation-inhibition modulation. CDAT instantiates a topology-constrained dynamical system whose couplings encode relational structure among tokens, thereby linking attractor-style dynamics to modern energy-based attention. We further provide a constructive dissipation analysis to formally establish their controlled inference dynamics. Benefiting from these robust and structured dynamics, CDAT achieves state-of-the-art performance across multiple benchmarks in graph anomaly detection and graph classification.

02.
arXiv (CS.CV) 2026-06-25

Re-mixing Embeddings for Patient Augmentation in Data Scarce Multiple Instance Learning

Data scarcity is a major bottleneck in medical Multiple Instance Learning (MIL), especially for rare diseases or expensive modalities. We introduce a statistically grounded patient augmentation approach that generates realistic patients directly in embedding space. Using Gaussian Mixture Models as a probabilistic clustering approach on pooled instance embeddings from all patients, our method learns disease-specific "recipes"-statistical distributions of instances across unsupervised clusters. New patients are then generated by sampling embeddings from clusters based on learned recipes. Unlike existing methods that require examples from all categories, our method can generate patients offline by re-mixing pooled embeddings. Generated patients are further selected based on uncertainty quantification to improve MIL performance. We evaluate our method across three clinically relevant scarcity scenarios: (i) cross-dataset transfer, where an entirely missing "healthy" class is generated using statistics from an external cohort; (ii) low-data regimes, where class sizes are extremely limited; and (iii) small-cohort non-image tasks, including single-cell RNA-seq and flow cytometry. Across all experiments, our method improves performance over baseline, often outperforming other bag-mixing strategies. Notably, in the missing-class scenario, a performance comparable to full-dataset training is achieved, demonstrating its potential for rare disease diagnostic and privacy-preserving patient augmentation. The code is available at https://github.com/marrlab/RECIPE

03.
medRxiv (Medicine) 2026-06-16

Using visual biofeedback to reduce step length error at fast walking speeds is feasible after stroke

Background and Purpose: Walking after stroke is often characterized by persistent biomechanical impairments and reduced walking capacity. While visual biofeedback can improve gait mechanics and fast walking can enhance capacity, it is unclear whether individuals post-stroke can effectively use biofeedback at higher walking speeds to address both deficits simultaneously. This study examined the effects of walking speed on the ability of participants with chronic stroke to reduce step length (SL) errors using visual biofeedback. Methods: Sixteen individuals with chronic stroke walked on a treadmill at slow, self-selected, and fast speeds with and without visual SL biofeedback. Absolute SL error relative to individualized targets was calculated for paretic and non-paretic limbs. Linear mixed-effects models with piecewise linear splines assessed the effects of speed, limb, and feedback condition. Post hoc comparisons were performed for significant interactions. Results: At lower speeds, increasing speed reduced SL error in both limbs (p < 0.001). At higher speeds, the effects of speed were dependent on limb and condition (p < 0.001). Paretic SL error increased with speed without feedback but remained stable with feedback (p < 0.001). Non-paretic SL error decreased with speed regardless of condition. SL error was greater in the paretic limb overall (p < 0.001). Discussion and Conclusions: Fast walking alone did not reduce paretic SL errors. Participants with chronic stroke can effectively use visual biofeedback to reduce paretic SL errors at higher speeds, supporting its integration into high-intensity gait training to simultaneously treat biomechanical impairments and walking capacity deficits after stroke.

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

Fantastic Pretraining Optimizers and Where to Find Them II: Hyperball Optimization

arXiv:2606.16899v1 Announce Type: new Abstract: Matrix based optimizers such as Muon can substantially speed up language model pretraining, but their gains over AdamW are observed to shrink as model size and data scale grow when using standard constant decoupled weight decay. We propose Hyperball, a simple optimizer wrapper that addresses this issue. Given a base optimizer such as Adam or Muon, Hyperball sets the Frobenius norms of weight matrices and their corresponding optimizer updates to fixed constants. On Qwen3 style models up to 1.2B parameters, Muon Hyperball achieves 20–30% token equivalent speedup over weight decay baselines. Hyperball also improves learning rate transfer across widths and depths compared to decoupled weight decay. This method is motivated by prior theory showing that training with weight decay leads to an equilibrium weight norm that only depends on the training hyperparameters. Through this mechanism, the weight decay then decides the angular learning rate, i.e. how fast the direction of the weight matrix changes.

05.
arXiv (CS.LG) 2026-06-15

A Composite Activation Function for Learning Stable Binary Representations

arXiv:2605.11558v2 Announce Type: replace Abstract: Activation functions play a central role in neural networks by shaping internal representations. Recently, learning binary activation representations has attracted significant attention due to their advantages in computational and memory efficiency, as well as interpretability. However, training neural networks with Heaviside activations remains challenging, as their non-differentiability obstructs standard gradient-based optimization. In this paper, we propose Heavy Tailed Activation Function (HTAF), a smooth approximation to the Heaviside function that enables stable training with gradient-based optimization. We construct HTAF as a sigmoid hyperbolic tangent composite function and theoretically show that it maintains a large gradient mass around zero inputs while exhibiting slower gradient decay in the tail regions. We show that Spiking Neural Networks, Binary Neural Networks and Deep Heaviside neural Networks can be trained stably using HTAF with gradient-based optimization. Finally, we introduce Implicit Concept Bottleneck Models (ICBMs), an interpretable image model that leverages HTAF to induce discrete feature representations. Extensive experiments across various architectures and image datasets demonstrate that ICBM enables stable discretization while achieving prediction performance comparable to or better than standard models.

06.
arXiv (math.PR) 2026-06-16

Convergence to the Brownian CRT for critical branching Markov processe

arXiv:2601.05906v2 Announce Type: replace Abstract: We prove an invariance principle for a general class of continuous time critical branching processes with finite variance (non-local) branching mechanism. We show that the genealogical trees, viewed as random compact metric measure spaces, converge under rescaling to the Brownian continuum random tree in the Gromov-Hausdorff-weak topology, establishing a universal scaling limit for critical finite variance branching processes.

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

DC-Motion: Decoupling Semantics and Details via Discrete-Continuous Tokens for Human Motion Generation

Text-to-motion generation requires synthesizing physically realistic dynamics that strictly follow complex and long-horizon textual instructions. Existing approaches rely on homogeneous representation spaces that may fail to capture the hierarchical nature of human motion, with diffusion models struggling at compositional semantic reasoning and AR models sacrificing fine-grained physical details due to quantization. To solve it, we introduce DC-Motion, a factorized generative framework designed to explicitly decouple semantics and details via discrete-continuous tokens. A Discrete-Continuous VAE (DC-VAE) first decomposes motion into discrete tokens for semantics and continuous residuals for fine-grained dynamics. Then, a masked AR model predicts the discrete structure from text, and a lightweight residual diffusion model recovers the continuous physical details. Extensive experiments demonstrate that DC-Motion effectively improves the capability to follow complex instructions. By effectively balancing semantic controllability and physical realism, our approach offers a highly adaptable modeling paradigm for human motion generation. On both HumanML3D and KIT-ML datasets, DC-Motion achieves state-of-the-art performance, delivering the best FID for motion realism and R-precision for text alignment.

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

A Recipe for Long-Context Reasoning in Large Language Models via On-Policy Optimization and Distillation

Existing approaches to post-train models for long-context tasks face complementary limitations: (i) supervised fine-tuning (SFT) provides stable supervision but suffers from exposure bias; (ii) reinforcement learning methods such as Group Relative Policy Optimization (GRPO) train on model-generated trajectories but struggle with long-horizon credit assignment and sparse rewards; and (iii) on-policy distillation (OPD) provides dense token-level guidance but does not directly optimize task rewards. We study these complementary strategies for long-context alignment and derive a recipe that combines GRPO with OPD-style teacher guidance: the student learns from its own rollouts using outcome-level rewards, while a stronger teacher provides dense token-level regularization in place of the standard reference policy. This is especially useful when process-level supervision is difficult to obtain. To support this study, we introduce LongBlocks, a synthetic multilingual dataset spanning multi-hop reasoning, contextual grounding, and long-form generation. Through controlled ablations, we isolate the roles of cold-start initialization, teacher anchoring, and data mixing, showing that our recipe yields a more stable and effective path to long-context reasoning than GRPO or OPD while preserving short-context capabilities.

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

FasterPy: An LLM-based Code Execution Efficiency Optimization Framework

arXiv:2512.22827v2 Announce Type: replace-cross Abstract: Code often suffers from performance bugs. These bugs necessitate the research and practice of code optimization. Traditional rule-based methods rely on manually designing and maintaining rules for specific performance bugs (e.g., redundant loops, repeated computations), making them labor-intensive and limited in applicability. In recent years, machine learning and deep learning-based methods have emerged as promising alternatives by learning optimization heuristics from annotated code corpora and performance measurements. However, these approaches usually depend on specific program representations and meticulously crafted training datasets, making them costly to develop and difficult to scale. With the booming of Large Language Models (LLMs), their remarkable capabilities in code generation have opened new avenues for automated code optimization. In this work, we proposed FasterPy, a low-cost and efficient framework that adapts LLMs to optimize the execution efficiency of Python code. FasterPy combines Retrieval-Augmented Generation (RAG), supported by a knowledge base constructed from existing performance-improving code pairs and corresponding performance measurements, with Low-Rank Adaptation (LoRA) to enhance code optimization performance. Our experimental results on the Performance Improving Code Edits (PIE) benchmark demonstrate that our method outperforms existing models on multiple metrics. The FasterPy tool and the experimental results are available at https://github.com/WuYue22/fasterpy.

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

Beyond Artifacts: Towards Generalizable Synthetic Song Detection via Music-Intrinsic Features

arXiv:2606.16612v1 Announce Type: cross Abstract: The rapid advancement of AI music generators highlights the urgent need for reliable Synthetic Song Detection (SSD). Existing SSD methods often rely on low-level artifacts or fixed feature assumptions, struggling to capture generator-agnostic cues. To address this, we propose Sofia (Synthetic-song detection framework via music features), a flexible framework that models music-intrinsic attributes via feature-specific experts and an adaptive Mixture-of-Experts (MoE) module. By configuring Sofia with representative Vocal, Audio-effect, Global structure features, and their combinations, we present their individual and complementary contributions. To comprehensively evaluate our framework, we further construct MUSIC8K, a challenging benchmark featuring lastest emerging generators and realistic audio perturbations. Experiments show that Sofia learns generator-agnostic representations from music-intrinsic features, improving the F1 score by 18.5 points over the strongest baseline on MUSIC8K-O while maintaining strong robustness.

11.
arXiv (CS.AI) 2026-06-17

An Evaluation of Data Leakage Risks in Tool-Using LLM Agents in Realistic Scenarios

arXiv:2606.17114v1 Announce Type: cross Abstract: AI agents are increasingly being adopted in enterprise and personal settings with access to emails, databases, documents, and other tools where they can read, update, and disseminate sensitive information. Much of prior research on data leakage risks in agents has focused on adversarial data exfiltration through prompt injections and jailbreaks. However, sensitive information may also be exposed during non-adversarial use, creating leakage risks even when users issue benign requests. We report a joint evaluation by the Singapore AI Safety Institute and the Korea AI Safety Institute examining agent data leakage in 12 realistic, non-adversarial tasks spanning customer support, DevOps, web automation, and enterprise and personal productivity. The evaluation covers five risk types: lack of data awareness, audience awareness, policy compliance, data minimization, and access-boundary awareness. Both institutes tested a common set of scenarios mirroring real-world deployments using independent testing environments and task-specific LLM-judge rubrics. Across the three tested agents, none achieved fully correct and fully safe execution across all scenarios. Successful task completion often coincided with data-handling failures such as accessing unnecessary information or disclosing information to inappropriate recipients, indicating that capability and data-handling safety should be evaluated separately. Qualitative review also revealed claim-action mismatches, simulation-aware behavior, user-simulator role reversal, and interpretation gaps in automated judging. Overall, the results indicate that operational data leakage is a first-order agent-safety concern distinct from adversarial exfiltration and provide a methodology for future evaluations of agent data-handling safety.

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

Be My Tutor: On-Policy Co-Distillation for Mutual LLM Improvement via Peer Feedback

We study multi-domain LLM training in which two models, each stronger in a different domain, co-evolve by tutoring each other through on-policy feedback. Unlike one-way distillation or single-model fine-tuning, our goal is mutual Pareto improvement: each model improves across domains without losing its original strength. To this end, we propose On-Policy Co-Distillation (OPCoD), where each student's self-distillation is conditioned on its own correct rollout and feedback from its peer. To make feedback exchange effective, OPCoD uses cognizance-based gating to decide when to give feedback and feedback anchoring to ground feedback in the problem. On Science Q\&A tasks, OPCoD consistently outperforms baselines and achieves Pareto improvement across all evaluated domain pairs and students.

13.
arXiv (CS.AI) 2026-06-16

Dual-Granularity Orthogonal Disentanglement for Generalizable Audio Deepfake Detection

arXiv:2606.16532v1 Announce Type: cross Abstract: Audio deepfake detectors often fail to generalize across speakers, as they learn speaker-identity features rather than synthesis artifacts, known as implicit identity leakage. Existing methods address this but incur architectural complexity or training instability. This paper proposes a dual-granularity orthogonal disentanglement framework enforcing feature independence at two levels: sample-level cosine orthogonality captures directional decorrelation, while batch-level cross-covariance regularization eliminates linear correlations across embedding dimensions. A curriculum disentanglement schedule progressively strengthens the orthogonality constraint without auxiliary networks or adversarial dynamics. Experiments on ASVspoof 2019 LA, ASVspoof 2021 DF, and In-the-Wild datasets demonstrate that the proposed method achieves 1.35%, 7.88%, and 21.58% equal error rates (EER), respectively, surpassing gradient reversal disentanglement by 2.60% absolute on cross-dataset transfer.

14.
arXiv (quant-ph) 2026-06-24

Auxiliary Schmidt Rank as a Resource for Photonic Bell Measurements

arXiv:2606.24591v1 Announce Type: new Abstract: In quantum communication and fusion-based quantum computation, photonic Bell measurements are fundamentally limited when only passive linear optics is employed. While for qubits, some Bell states can be unambiguously identified with static beam splitters and no extra photons or entanglement, additional auxiliary photons or at least additional auxiliary degrees of freedom with a certain level of additional entanglement are needed to approach or attain a complete, deterministic Bell measurement. Here, we prove an exact resource threshold when the same two photons carry system qudits of dimension $d$ and a fixed auxiliary entangled state $\Phi$, possibly distributed over several additional degrees of freedom, with total Schmidt rank $r_\Phi$. We show that a single conclusive Bell-label functional can occur for $r_\Phi\geqslant\lceil d/2\rceil$, but deterministic discrimination of all $d^2$ Bell-state labels requires $r_\Phi\geqslant d$. A maximally entangled rank-$d$ auxiliary state achieves the bound by local Bell-basis sorting between each photon's system and auxiliary degrees of freedom. Thus, the auxiliary Schmidt rank is a certified resource for ancilla-photon-free, embedded photonic Bell measurements.

15.
arXiv (CS.CL) 2026-06-18

ToolGrad: Efficient Tool-use Dataset Generation with Textual "Gradients"

Prior work synthesizes tool-use LLM datasets by first generating a user query, followed by complex tool-use annotations like depth-first search (DFS). This leads to inevitable annotation failures and low efficiency in data generation. We introduce ToolGrad, an agentic framework that inverts this paradigm. ToolGrad first constructs valid tool-use chains through an iterative process guided by textual "gradients", and then synthesizes corresponding user queries. This "answer-first" approach led to ToolGrad-500, a dataset generated with more complex tool use, lower cost, and almost 100% pass rate. Experiments show that ToolGrad models outperform those trained on expensive baseline datasets and proprietary LLMs. The ToolGrad source code, dataset, and models are available at https://github.com/zhongyi-zhou/toolgrad.

16.
arXiv (quant-ph) 2026-06-17

Superconductor-"Metal" Transition of One-dimensional Interacting Bosons with Ohmic Quantum Dissipation

arXiv:2605.30746v2 Announce Type: replace-cross Abstract: The phase diagram of a system of interacting bosons (Cooper pairs) hoping on a one-dimensional (1D) lattice with onsite phase dissipation describing the Josephson tunneling to a nearby diffusive normal-metal electrode is studied. Starting from the system at commensurate lattice filling, it is shown by a combination of analytical techniques that the phase diagram contains two quantum phases: A dissipative Bose-Einstein condensate (D-BEC) or superconductor with long-range phase coherence, and a dissipative Mott insulator (D-Mott) or "metal" with exponentially decaying phase correlations in space and local imaginary-time correlations decaying as the local pairing correlations of the electrode. The D-Mott/metal phase can be described as a 1D array of dissipative boson puddles, weakly coupled by Josephson tunneling. The puddle size roughly corresponds to the length scale beyond which phase slips suppress phase coherence. The dissipative time-dependent Ginsburg-Landau theory phenomenologically used by Sachdev, Werner, and Troyer [Phys. Rev. Lett. {\bf 92} 237003 (2004)] for the superconductor-metal transition in quasi-1D wires is derived from this microscopic puddle picture. Thus, the criticality of the D-Mott/D-BEC transition is shown to belong to the Wilson-Fisher universality class with dynamical exponent $z\approx 2$. At small doping, the D-Mott/metal phase remains stable due to its finite compressibility, which is computed to leading order in a perturbation expansion of the dissipation strength and the inter-puddle Josephson coupling. At larger doping, using a mapping to a pseudospin chain combined with bosonization, the D-BEC/superconductor phase is the ground state for non-vanishing but arbitrarily small dissipation. Similarities and differences with deconfinement transition of an array 1D bosonic Mott insulators in anisotropic optical lattices are also discussed.

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

Depth-Attention: Cross-Layer Value Mixing for Language Models

Self-attention selects information freely across the sequence, but across depth, Transformers merely add each layer's output to the residual stream, so later layers cannot selectively reuse earlier-layer representations. Recent cross-layer methods improve this flow but operate on hidden states outside attention, adding state beyond the key-value cache at inference–a cost that becomes increasingly salient as modern LLMs compress the cache with grouped-query and multi-head latent attention. We introduce Depth-Attention, which performs this selection inside the attention module itself: before a layer attends over the sequence, its query attends over the keys of earlier layers at the same token position and mixes their values into the value that self-attention then reads. Because Depth-Attention reuses the standard attention queries, keys, and value-cache slots, storing depth-mixed values in place of the original values, it adds no parameters and introduces no persistent inference state beyond the standard key-value cache–the same cache size as a vanilla decoder and less than hidden-state-based cross-layer methods. On Qwen3-style decoders at 1.5B and 3B parameters, Depth-Attention attains the lowest perplexity and the highest average downstream accuracy, improving over the vanilla Transformer by up to 2.3 accuracy points and surpassing strong cross-layer baselines in perplexity and average accuracy, while adding under 0.01% extra arithmetic FLOPs and no additional persistent inference state. The gains hold from 360M to 3B parameters and extend to looped Transformers.

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

Reversible Residual Normalization Alleviates Spatio-Temporal Distribution Shift

arXiv:2604.15838v2 Announce Type: replace Abstract: Distribution shift severely degrades the performance of deep forecasting models. While this issue is well-studied for individual time series, it remains a significant challenge in the spatio-temporal domain. Effective solutions like instance normalization and its variants can mitigate temporal shifts by standardizing statistics. However, distribution shift on a graph is far more complex, involving not only the drift of individual node series but also heterogeneity across the spatial network where different nodes exhibit distinct statistical properties. To tackle this problem, we propose Reversible Residual Normalization (RRN), a novel framework that performs spatially-aware invertible transformations to address distribution shift in both spatial and temporal dimensions. Our approach integrates graph convolutional operations within invertible residual blocks, enabling adaptive normalization that respects the underlying graph structure while maintaining reversibility. By combining Center Normalization with spectral-constrained graph neural networks, our method captures and normalizes complex Spatio-Temporal relationships in a data-driven manner. The bidirectional nature of our framework allows models to learn in a normalized latent space and recover original distributional properties through inverse transformation, offering a robust and model-agnostic solution for forecasting on dynamic spatio-temporal systems.

19.
arXiv (quant-ph) 2026-06-12

Coulomb crystallization of xenon highly charged ions in a laser-cooled Ca+ matrix

arXiv:2512.12266v2 Announce Type: replace-cross Abstract: We report on the sympathetic cooling and Coulomb crystallization of xenon highly charged ions (HCIs) with laser-cooled Ca$^+$ ions. The HCIs are produced in a compact electron beam ion trap, then charge selected, decelerated, and finally injected into a cryogenic linear Paul trap. There, they are captured into $^{40}$Ca$^+$ Coulomb crystals, and co-crystallized within them, causing dark voids in their fluorescence images. Fine control over the number of trapped ions and HCIs allows us to realize mixed-species crystals with arbitrary ordering patterns. By investigating Xe$^{q+}$–Ca$^+$ strings, we confirm the HCI charge states, measure their lifetime and characterize the mixed-species motional modes. Our system effectively combines the established quantum control toolbox for Ca$^+$ with the rich set of atomic properties of Xe highly charged ions, providing a resourceful platform for optical frequency metrology, searches for signatures of new physics, and quantum information science.

20.
arXiv (CS.LG) 2026-06-19

A High-Resolution Landscape Dataset for Concept-Based XAI With Application to Species Distribution Models

arXiv:2604.13240v2 Announce Type: replace-cross Abstract: Mapping the spatial distribution of species is essential for conservation policy and invasive species management. Species distribution models (SDMs) are the primary tools for this task, serving two purposes: achieving robust predictive performance while providing ecological insights into the driving factors of distribution. However, the increasing complexity of deep learning SDMs has made extracting these insights more challenging. To reconcile these objectives, we propose the first implementation of concept-based Explainable AI (XAI) for SDMs. We leverage the Robust TCAV (Testing with Concept Activation Vectors) methodology to quantify the influence of landscape concepts on model predictions. To enable this, we provide a new open-access landscape concept dataset derived from high-resolution multispectral and LiDAR drone imagery. It includes 653 patches across 15 distinct landscape concepts and 1,450 random reference patches, designed to suit a wide range of species. We demonstrate this approach through a case study of two aquatic insects, Plecoptera and Trichoptera, using two Convolutional Neural Networks and one Vision Transformer. Results show that concept-based XAI helps validate SDMs against expert knowledge while uncovering novel associations that generate new ecological hypotheses. Robust TCAV also provides landscape-level information, useful for policy-making and land management. Code and datasets are publicly available.

21.
PLOS Computational Biology 2026-06-11

A zero-parameter first-principles gate framework for full-length TP53 missense variant interpretation

by Masamichi Iizumi Missense variant interpretation often achieves useful predictive performance but remains mechanistically opaque, particularly in proteins that combine structured domains with intrinsically disordered regions (IDRs). We developed Gate & Channel, a zero-parameter, first-principles framework for full-length TP53 missense variant analysis in which each prediction is generated by explicit IF-THEN gates derived from physicochemistry, geometry, structural constraints, and polymer physics rather than fitted weights. Variants are evaluated across independent channels representing distinct physical failure modes; a variant is predicted disruptive if any gate closes. A second hierarchical layer (“Geta”) encodes physically grounded post-closure exceptions, allowing sensitivity and specificity to be improved on disjoint variant populations. The v18 framework consists of 12 channels and 2 Getas spanning structured domains and IDRs, capturing DNA-contact disruption, Zn coordination, burial-dependent packing, secondary-structure compatibility, post-translational modification chemistry, short linear motif disruption (including a multi-partner coupled-folding face), proline-directed kinase recognition, and IDR-specific proline and glycine backbone constraints. Across 1,369 TP53 missense variants, the framework achieved 84.5% sensitivity and 89.1% positive predictive value, with 90.9% sensitivity preserved in the DNA-binding core and all 9/9 hotspot mutations captured. A post hoc audit of discordant IDR calls indicated that many apparent false positives had plausible molecular rationales, consistent with a distinction between molecular mechanism disruption and clinical penetrance. Applied to KRAS, TDP-43, and BRCA1, the same channels capture the dominant pathogenic mechanisms in each protein as a proof of principle, while residual missed variants name specific gates yet to be written. The framework is distributed as the open-source Python package pathogenicity-gates (v0.5.1, MIT). These results show that a substantial fraction of full-length TP53 missense variation can be resolved through explicit, auditable physical gates that carry meaning beyond TP53, with each remaining failure naming the next rule to be written.

22.
arXiv (CS.AI) 2026-06-16

ARB4WM: An Adversarial Robustness Benchmark for World Models in Continuous Control

arXiv:2606.16605v1 Announce Type: new Abstract: World models are widely used in robotic and agentic engineering control systems due to their ability to learn latent dynamics for planning and decision-making. As these systems are increasingly deployed in safety-critical settings, understanding their robustness under adversarial conditions has become essential. However, existing evaluations lack a unified benchmark for testing adversarial threats across the policy, value, and latent-dynamics levels of world-model agents. To fill this gap, we present ARB4WM, a unified evaluation framework for pre-deployment robustness and risk assessment of world-model agents under visual perturbations. ARB4WM defines five white-box loss objectives across these three levels and studies their effects when combined with single-step or multi-step perturbation strategies and temporal attack modes, including full-frame, half-sequence, and sparse-frame exposure. Specifically, we evaluate four Dreamer-style agents across 20 tasks from MetaWorld and the DeepMind Control Suite under different loss objectives, perturbation strategies, and temporal attack modes. Results show that attacks targeting value estimation, latent representations, and RSSM dynamics can be as damaging as direct policy disruption, and that early or frequent perturbations are especially harmful, while input-level defenses provide limited recovery under adaptive attacks. These findings suggest that safety, risk, and reliability assessment for world models should cover multiple component-oriented attack objectives and temporal exposure protocols rather than relying solely on action-space robustness. Source code is available at https://github.com/zaoanguai/ARB4WM.

23.
arXiv (quant-ph) 2026-06-25

Optimizing Pump Conditions of Parametric Amplifiers for Fast Multiplexed Readout of Superconducting Qubits

arXiv:2606.22080v2 Announce Type: replace Abstract: Low-noise parametric amplifiers are widely used as the first-stage amplifier in qubit readout chains. The performance of parametric amplifiers depends sensitively on the choice of the pump condition. We propose a strategy for determining the pump condition that is tailored for fast multiplexed readout. Choosing the amplifier pump to maximize the signal-to-noise ratio (SNR) improvement at the readout frequency of the limiting qubit–the qubit that requires the longest readout time to reach a target SNR–minimizes the total multiplexed readout time. We demonstrate our pump calibration strategy experimentally on a five-qubit multiplexed readout chain with a traveling-wave parametric amplifier. Using our strategy, we reduce the multiplexed readout time by 320 ns compared to optimizing the average SNR improvement on all qubits, without degrading the target SNR for any qubit.

24.
arXiv (CS.AI) 2026-06-17

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

arXiv:2606.17127v1 Announce Type: cross Abstract: Antimicrobial resistance causes to over a million deaths annually. Antimicrobial peptides (AMPs) are a promising solution, but generative AMP models are not yet ready to design peptides with non-natural amino acids and/or chemical modifications, which are essential for real-world peptide drugs. We present AMPGAN v3, a multi-objective conditional GAN that expands the generative vocabulary to D-amino acids and N/C-terminus modifications such as amidation. By separating adversarial and activity-aware supervision across two specialized discriminators, AMPGAN v3 substantially improves training stability and outperforms prior generative AMP models on external classifiers. We validated five candidates spanning three structural classes in vitro; two showed activity against Gram-positive strains, with the best candidate reaching MIC 8 {\mu}g/mL against B. subtilis. To support downstream curation, we further present PepCraft, a multi-agent framework for end-to-end AMP discovery in which a Planning Agent orchestrates specialized executors for generation, filtering, and verification. Its prioritization recommendations align with our in vitro outcomes. Together, these contributions let us examine, on a small but real scale, how generative and agentic AI compose in therapeutic peptide discovery. Code: https://github.com/marszzibros/AMPGANv3

25.
arXiv (CS.CV) 2026-06-24

Are Text-to-Image Models Inductivist Turkeys? A Counterfactual Benchmark for Causal Reasoning

Text-to-image (T2I) generation models have achieved remarkable progress in producing visually realistic images from natural language prompts. Yet it remains unclear whether their success reflects genuine causal understanding or sophisticated pattern matching over visual-textual correlations. Inspired by Russell's inductivist turkey, we introduce Counterfactual-World (CF-World), a counterfactual benchmark designed to investigate whether text-to-image models can generate images under rules that systematically contradict real-world priors. CF-World organizes each scenario into three progressive levels: factual generation under ordinary world knowledge, explicit counterfactual generation with direct visual instructions, and implicit counterfactual generation requiring causal deduction from altered rules. We evaluate both open-source and closed-source T2I models using a Vision Language Model (VLM)-based evaluator (CF-Eval). Furthermore, we introduce two metrics: Prior Resistance Rate (PRR), which measures a model's ability to overcome entrenched real-world priors, and Reasoning Retention Rate (RRR), which assesses whether models can maintain reasoning-dependent counterfactual generation without explicit visual cues. Experiments show that all models exhibit sharp degradation from factual to counterfactual settings. Further analyses suggest that these failures arise because current T2I models encode world knowledge and visual appearances as tightly coupled patterns. Consequently, their heavy reliance on frequent visual co-occurrences within the training data forces them to default to familiar commonsense priors when tasked with rendering counterfactual worlds.