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01.
arXiv (quant-ph) 2026-06-11

Expressivity of Quantum Reservoir Computers

arXiv:2501.15528v3 Announce Type: replace Abstract: Using Hamiltonian encoding to inject an input into parameterized quantum circuits (PQCs), the output of the PQC can be written as truncated Fourier series. In recent years, the expressivity of PQCs was established as the number of frequencies contained in this Fourier series. While this concept has also been applied to other quantum machine learning (QML) paradigms, a clear notion of expressivity for temporal information processing with quantum systems is still lacking. Here, we introduce such a notion to the field of quantum reservoir computing (QRC). We analytically derive an expression for the readouts showing that the output of a QRC can be interpreted as a multi-dimensional Fourier series. We give a formula for the growth of expressivity induced by the sequential information injection, which we corroborate with numerical simulations, calculating explicitly the number of multi-dimensional output functions which can be generated from the readouts. Our results show that the specific interplay between system size, input encoding, and memory time gives rise to a boundary on the system size beyond which it is obstructive to further increase the reservoir size in extreme scrambling systems. We propose a recipe for determining this maximal system size for a given QRC setup.

02.
arXiv (CS.LG) 2026-06-11

DeepRHP: A Hybrid Variational Autoencoder for Designing Random Heteropolymers as Protein Mimics

arXiv:2606.11651v1 Announce Type: new Abstract: Synthetic random heteropolymers (RHPs), consisting of a predefined set of monomers, offer an approach toward the design of protein-like materials. These RHPs, if designed appropriately, can mimic protein behavior and function. As such, there is a need for computational tools to efficiently guide RHP design. We bridge this gap by developing DeepRHP, a modified variational autoencoder (VAE) model under a semi-supervised framework. By equipping a classical VAE with an additional feature-based VAE, DeepRHP forces the latent space to capture structures of critical chemical features as well as individual RHP sequence patterns. In this sense, our method is versatile by allowing any relevant features to be incorporated in a hybrid manner. We demonstrate the effectiveness of DeepRHP by suggesting potential monomer compositions that stabilize membrane proteins (e.g. Aquaporin Z) in non-native environments and cross-validating our prediction with published results. The concordance between our model and true RHP function suggests strong potential in utilizing hybrid autoencoder architectures to guide RHP design for proteins and other biological compounds.

03.
arXiv (CS.CV) 2026-06-15

Hierarchical Consistency Learning for Test-time Adaptation in Camouflage Perception

Camouflaged object detection (COD) aims to localize targets that exhibit minimal perceptual differences from backgrounds through physical attributes. Existing methods, constrained by the static train-then-freeze paradigm, suffer from domain rigidity and annotation dependency, limiting their adaptability to scene variations and unseen camouflage patterns. To overcome these, we propose the hierarchical consistency learning (HCL) framework, which integrates test-time adaptation for dynamic representation recalibration. Specifically, we design the hierarchical representation reconstruction (HRR) to alleviate feature entanglement by synergizing spatial reconstruction with dual-stream frequency-domain decomposition, enhancing robustness against appearance homogenization. The pixel and spectrum inference provide structural and contextual priors. We further introduce task affinity guidance (TAG) to propagate knowledge across branches via channel-wise affinity, aligning local discriminative cues and mitigating semantic drift. To ensure semantic invariance, we formulate the prototype consistency calibration (PCC), which aggregates region features into compact prototypes and establishes prototype-feature similarity. This imposes implicit and hierarchical constraints that bridge task and representation gaps. Extensive experiments across four camouflaged and four underwater object benchmarks, under three degradation settings, demonstrate that our method consistently outperforms state-of-the-art approaches, highlighting its robustness and generalization under distribution shifts.

04.
Nature (Science) 2026-06-17

How the zebrafish brain weaves recent experiences into future decisions

Authors: Unknown Author

Animals often use recent experience to guide future choices. Whole-brain imaging in larval zebrafish (Danio rerio) reveals a dedicated neural circuit that governs history-biased decisions: the thalamus maintains the most recent event as a stable pattern of neuronal activity, and the brainstem integrates recent experiences into a continuous signal that biases future action. Whole-brain calcium imaging in the zebrafish reveals how information about events in the recent past drives future behaviour.

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

D2H-AD: A Hybrid Model Utilizing Hyperdimensional Computing for Advanced Anomaly Detection

arXiv:2606.13754v1 Announce Type: new Abstract: Anomaly detection is a fundamental component of intelligent systems with applications in healthcare, cybersecurity, smart grids, and IoT environments. Although conventional machine learning and deep learning methods have demonstrated effectiveness in identifying anomalies, they often rely on large labeled datasets, incur high computational costs, and face scalability challenges in edge and high-dimensional settings. This paper presents D2H-AD, a novel anomaly detection framework based on Hyperdimensional Computing (HDC), a brain-inspired paradigm that represents information using high-dimensional distributed vectors. Unlike existing HDC-based methods, D2H-AD integrates distance-based similarity and density-aware encoding within a unified framework, improving anomaly representation and detection performance. Ablation studies show that hyperdimensional encoding alone yields up to 5.4% higher ROC-AUC than applying the same density-distance scoring directly in the original feature space. Furthermore, D2H-AD consistently outperforms five established baselines, namely HDAD, ODHD, One-Class SVM, Isolation Forest, and Autoencoders, across all evaluated datasets. The framework is lightweight, interpretable, and computationally efficient, making it suitable for resource-constrained and real-time applications. We validate D2H-AD on five benchmark datasets and demonstrate superior F1-score and ROC-AUC performance, together with robustness to class imbalance, noise, and data complexity. In addition to improved accuracy, D2H-AD offers scalability, a small memory footprint, and low-latency operation enabled by binary computations and a compact design. These properties make it particularly attractive for TinyML and edge AI deployments. The proposed framework highlights the potential of HDC for accurate, interpretable, and energy-efficient anomaly detection in dynamic environments.

06.
arXiv (CS.AI) 2026-06-15

Elastic Queries Reinforcement Learning: Self-Aware Policy Execution for VLA Models

arXiv:2606.14375v1 Announce Type: cross Abstract: Vision-language-action (VLA) models are powerful action generators for robot manipulation, but they are typically executed with fixed inference and replanning schedules. This rigidity ignores the uneven difficulty of robot control: contact-rich or uncertain states may need more computation and fresher feedback, while easier states can often be handled with fewer inference steps and longer open-loop execution. We propose Elastic Queries Reinforcement Learning (EQRL), a framework that makes each VLA policy query elastic. A lightweight latent-schedule adaptor jointly selects the latent input, denoising budget, and action chunk length, without fine-tuning the underlying VLA model. To make scheduling difficulty-aware, EQRL trains a critic over the joint latent-schedule action and derives a state difficulty signal from critic ensemble disagreement. This signal guides compute toward difficult states, while a learned residual allows task-driven correction. We formulate variable chunk execution as query-level macro-action RL with chunk-dependent discounting and an amortized number-of-function-evaluations (NFE) budget. Across simulation and real-robot manipulation, EQRL reduces amortized inference cost while preserving or improving task success.

07.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.

08.
arXiv (CS.CL) 2026-06-19

Proactive Conversational Assistant for a Procedural Manual Task based on Audio and IMU

Real-time conversational assistants for procedural manual tasks often depend on video input, which can be computationally expensive and compromise user privacy. For the first time, we propose a real-time conversational assistant that provides comprehensive guidance for procedural manual tasks using only lightweight privacy-preserving modalities such as audio and IMU inputs from a user's wearable device to understand the context. Using a furniture assembly task and a cooking task, we show how this assistant proactively communicates step-by-step instructions to a user performing a procedural task, and answers user questions. We illustrate the data generation method and the system design to achieve such an assistant. On observing that an off-the-shelf language model is a talkative assistant but is not always able to answer questions correctly, we demonstrate how finetuning the model improves its ability to limit unnecessary dialogues with a 50% increase in the precision, while also improving its ability to answer questions correctly, measured by a 150% increase in the recall of answers. We further describe how such an assistant is implemented on an edge device with no dependence on the cloud.

09.
arXiv (CS.CV) 2026-06-15

Giving AI a Headache: Acoustic Adversarial Attacks to Computer Vision Applications

Artificial Intelligence (AI) is increasingly used to automate a variety of real-world computer vision (CV) applications, such as autonomous vehicle control, facial recognition, and security cameras. Recent research has shown that acoustic vibration can induce real physical motion in cameras, interfering with their internal stabilization mechanisms. Because the motion falls outside the conditions the stabilization system was designed to handle, the system introduces artifacts into the frame, causing AI-based CV models to misclassify, miss targets, or hallucinate objects. Previous work used ultrasonic frequencies (>20 kHz) to perform short-range attacks, which limits them to short distances due to the attenuation exhibited by high frequencies. In this work, we investigate acoustic attacks using lower frequencies in the audible range (

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

Binary Tracking for Spatial QA and Navigation with Open Vision-Language Models

arXiv:2606.16902v1 Announce Type: cross Abstract: This work addresses spatial question answering for service robots traversing long egocentric routes. Given a query such as "where can I find a dry cleaner on the way back home?", the system returns a metric coordinate that downstream navigation components can act on. Prior Spatial Question Answering approaches leverage retrieval-augmented agents built on closed-source models such as GPT-4o for path exploration. However, robots operating in the real world often cannot reliably depend on online closed-source models due to network instability, communication latency, and deployment cost. It creates a need for open-source based Spatial Question Answering approaches that can run onboard the robot, yet prior research in this direction remains limited. This work proposes BinTrack, a simple yet effective, fully open-source spatial-localization agent that leverages the temporal ordering of a robot's trajectory. BinTrack performs a binary search over the trajectory segments between two anchor landmarks identified from a query. It improves overall accuracy by up to 22.8% over other open-source implementations and even matches the reported closed-source model result on the global category of the SpaceLocQA benchmark, the most challenging setting that has so far required strong reasoning agents such as GPT-4o. Furthermore, its optimized inference strategy consistently yields more than a 1.5x inference speedup over previous approaches. Finally, this work releases GangnamLoop, a novel and practical multi-trip outdoor benchmark collected by deploying a real quadruped robot on public streets with the anonymization policy. It revisits the same locations under different outdoor conditions and pairs the robot's low viewpoint with the human owner's. The source codes and datasets are publicly available at https://github.com/ndb796/BinaryTracking

11.
arXiv (CS.CL) 2026-06-16

Encode Errors: Representational Retrieval of In-Context Demonstrations for Multilingual Grammatical Error Correction

Grammatical Error Correction (GEC) involves detecting and correcting the wrong usage of grammar. While large language models (LLMs) with in-context learning (ICL) capabilities have shown significant progress on various natural language processing (NLP) tasks, their few-shot performance on GEC remains suboptimal. This is mainly due to the challenge of retrieving suitable in-context demonstrations that capture error patterns instead of semantic similarity. In this paper, we demonstrate that LLMs can inherently capture information related to grammatical errors through their internal states. From these states, we extract the Grammatical Error Representation (GER), an informative and semantically neutral encoding of grammatical errors. Our novel GER-based retrieval method significantly boosts performance in ICL settings on multilingual GEC datasets, improving the precision of correction. For high-resource languages, our results on 8B-sized open-source models match those of closed-source models such as Deepseek2.5 and GPT-4o-mini. For low-resource languages, our $F_{0.5}$ scores surpass the baseline by up to a factor of 1.20. This method provides a more precise and resource-efficient solution for multilingual GEC, offering a promising direction for interpretable GEC research.

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

Faster Completion, Less Learning: Generative AI Reduced Study Time on Math Problems and the Knowledge They Build

arXiv:2605.21629v2 Announce Type: replace-cross Abstract: How much have students' ordinary learning processes shifted in response to generative AI, and how does that affect their durable learning outcomes? Self-report surveys show little change, while small-scale behavioral studies report widespread AI use without the scale or duration to measure learning consequences. We address both questions using a ten-year panel of $3.2$ million ALEKS learning interactions for investigating time-on-task, complemented by ALEKS PPL placement-assessment data for examining proctoring and learning outcomes, with a quasi-experimental design exploiting variation in tasks that are more susceptible to AI (text-based word problems) and less susceptible to AI (interactive graph-based problems). Learning time on AI-susceptible problems declines $2.8\%$ per quarter among college students after ChatGPT's release, cumulating to $26.9\%$ over eleven quarters; high-schoolers show $31.3\%$, middle-schoolers $9.0\%$, and Grade 5 students no detectable change. Among college students, the post-ChatGPT divergence vanishes entirely under proctoring, ruling out broad efficiency gains as the likely explanation. Logistic fixed-effects models on randomly assigned proctored retention items yield a $25\%$ cumulative decline in odds of correct response; the same estimator on non-proctored assessment produces a large opposite-signed increase – inconsistent with any platform, cohort, or curriculum explanation. These results are among the first large-scale behavioral and outcome evidence that generative AI has altered how students study and the knowledge they build – the population-level indicator of cognitive surrender, with direct implications for educational research, assessment governance, and AI policy.

13.
medRxiv (Medicine) 2026-06-22

REPRODUCIBILITY OF 7T MRI MEASUREMENTS OF THE SUSCEPTIBILITY AND VOLUME OF HIPPOCAMPAL SUBFIELDS

PURPOSE: The UK7T travelling head dataset was used to characterise the reproducibility of 7T measurements of the susceptibility of the hippocampal subfields, focusing on the Cornu Ammonis (CA1, CA2 and CA3), dentate gyrus (DG), subiculum (SUB), tail of the hippocampus (TAIL) and entorhinal cortex (ERC). METHODS: Susceptibility maps were created from whole-brain 3D single-echo GRE data (TE=20 ms; 0.7 mm isotropic resolution) using Multi-Scale Dipole Inversion. Automatic Segmentation of Hippocampal Subfields (ASHS) was applied to high resolution T1- and T2-weighted images for segmentation. The mean magnetic susceptibility and volume of hippocampal subfields was evaluated in 50 data sets, comprising 5 repeat acquisitions on 10 healthy participants (age 32 + or -6 years; 3 female). RESULTS: Averaging over subjects, susceptibility values spanned an 18ppb range over the hippocampus (ranging from -13.3ppb in DG to 4.7ppb in ERC). Susceptibility values in the larger hippocampal subfields showed a consistent pattern of variation across subjects, being generally more positive in ERC and SUB than in CA1 and more positive in CA1 than in DG and TAIL. The standard deviation of subfield susceptibilities over subjects ranged from 8.2ppb in the TAIL to 1.7ppb in CA1, and the average standard deviation across repeated measurements, which ranges from 1.7 to 4 ppb, was less than half of the inter-participant standard deviation in all subfields. Susceptibility values in the smaller subfields (CA2 and CA3) were more variable, but ICC(2,k) values for all subfields were >0.82. CONCLUSION: The reported data characterises the variation and reproducibility of hippocampal subfield susceptibility measurements at 7T.

14.
arXiv (CS.AI) 2026-06-19

Information Lattice Learning as Probabilistic Graphical Model Structure Learning

arXiv:2606.19366v1 Announce Type: cross Abstract: Information lattice learning (ILL) learns interpretable rules of a signal by alternately projecting the signal onto a partition lattice that encodes a hierarchy of abstractions and lifting selected rules back to the signal domain. When the signal is a probability mass function, we show the probabilistic rules learned by ILL admit a natural probabilistic graphical model (PGM) interpretation and develop this interpretation in detail. A partition in ILL induces a deterministic quotient variable, and a rule is the marginal law of that quotient variable. A rule set is therefore a collection of marginal constraints over interpretable abstractions. General lifting is the feasible family of all joint distributions satisfying those constraints, while special lifting chooses a maximum-ignorance reconstruction, implemented in ILL by an L2 uniformity principle closely related to maximum entropy. Under a Shannon-entropy lifting, the same constraints yield a log-linear factor graph whose factors are indexed by learned abstractions. The information lattice itself, however, is not a Bayesian network: its edges encode refinement and coarsening of abstractions, not conditional dependence. Thus ILL is best viewed as structure learning for interpretable constraint-based factor graphs over quotient variables. This view clarifies how ILL relates to graphical models and maximum entropy models, while suggesting new directions for inference, identifiability, and hybrid symbolic-probabilistic learning.

15.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

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

Towards Leveraging AutoML for Sustainable Deep Learning: A Multi-Objective HPO Approach on Deep Shift Neural Networks

arXiv:2404.01965v3 Announce Type: replace-cross Abstract: Deep Learning (DL) has advanced various fields by extracting complex patterns from large datasets. However, the computational demands of DL models pose environmental and resource challenges. Deep shift neural networks (DSNNs) offer a solution by leveraging shift operations to reduce computational complexity at inference. Following the insights from standard DNNs, we are interested in leveraging the full potential of DSNNs by means of AutoML techniques. We study the impact of hyperparameter optimization (HPO) to maximize DSNN performance while minimizing resource consumption. Since this combines multi-objective (MO) optimization with accuracy and energy consumption as potentially complementary objectives, we propose to combine state-of-the-art multi-fidelity (MF) HPO with multi-objective optimization. Experimental results demonstrate the effectiveness of our approach, resulting in models with over 80\% in accuracy and low computational cost. Overall, our method accelerates efficient model development while enabling sustainable AI applications.

17.
Nature (Science) 2026-06-08

Distributed control circuits across a brain-and-cord connectome

Just as genomes revolutionized molecular genetics, connectomes (maps of neurons and synapses) are transforming neuroscience. To date, the only organisms with complete connectomes are worms1–3, sea squirts4, and comb jellies5 (103–104 synapses). By contrast, the fruit fly is more complex (108 synaptic connections), with a brain that supports learning and spatial memory6,7 and an intricate ventral nerve cord analogous to the vertebrate spinal cord8–12. Here we report the first densely-reconstructed adult fly connectome that unites the brain and ventral nerve cord, and we leverage this resource to investigate principles of neural control. We show that effector neurons (motor neurons, endocrine cells, and efferent neurons targeting the viscera) are primarily influenced by sensory neurons in the same body part, forming local feedback loops. These local loops are linked by long-range circuits involving ascending and descending neurons organized into behavior-centric modules. Single ascending and descending neurons are often positioned to influence the voluntary movements of multiple body parts, together with the endocrine cells or visceral organs that support those movements. Brain regions involved in learning and navigation supervise these circuits. These results reveal an architecture that is distributed, parallelized, and embodied, reminiscent of distributed control architectures in engineered systems13,14.

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

DeXposure-Claw: An Agentic System for DeFi Risk Supervision

Decentralized finance exposes supervisors to fast-moving, networked credit risks. General-purpose LLM agents fit this setting poorly: they over-read weak evidence and recommend high-stakes interventions, while existing evaluations offer no regulator-aligned way to measure the resulting false alarms. We introduce DeXposure-Claw, a forecast-grounded agentic supervision system that routes LLM decisions through structured evidence: (1) DeXposure-FM, a graph time-series foundation model, forecasts future exposure networks; (2) deterministic monitors and stress scenarios then turn those forecasts into typed alerts, attribution signals, and scenario evidence; and (3) data-health and confidence gates constrain escalation before DeXposure-Claw emits auditable supervisory tickets with rationales. We further develop DeXposure-Bench, a six-axis evaluation harness, whose decision axis scores tickets against a regulator-aligned absolute-loss ground truth and an explicit false-intervention rate. Experiments on five years of weekly real data fully support our system. Code is at https://github.com/EVIEHub/DeXposure-Claw.

19.
arXiv (CS.AI) 2026-06-16

Probing Low Frame Rate Degradation in Neural Audio Codecs

arXiv:2606.16969v1 Announce Type: cross Abstract: Low frame rates in neural audio codecs are attractive for autoregressive speech synthesis, where the generation cost scales linearly with the sequence length. Recent work has demonstrated that codecs can operate at 12.5 Hz and below, but the mechanisms underlying low frame rate degradation remain insufficiently understood. We investigate these mechanisms through a controlled frame rate ablation. We reproduce a quality cliff at 6.25 Hz reported in previous works and evaluate candidate explanations: phonemic collisions and codebook saturation, neither of which shows evidence of a fundamental barrier. The cliff is instead caused by suboptimal training configuration: fixed clip duration during training yields too few tokens at low frame rates, starving the decoder of inter-token context. Once corrected, WER degrades smoothly with phonemic load down to 3.1 Hz and 1.6 Hz, suggesting the inference-time efficiency gains of low frame rate codecs are more accessible than previously assumed.

20.
arXiv (quant-ph) 2026-06-15

Efficient Simulation of Szegedy Quantum Walk Formulations and Algorithms

arXiv:2606.14226v1 Announce Type: new Abstract: Quantum walks provide a versatile framework for quantum algorithms across a wide range of applications. We develop efficient classical simulation methods for Szegedy quantum walks that avoid explicit construction of the full unitary evolution operator. Unlike previous approaches restricted to a particular walk formulation, our framework is built from fundamental update and reflection operators, enabling the simulation of a broader class of Szegedy walk formulations. We further extend these methods to phase-estimation-based algorithms coupled to the walk, including implementations suitable for large sparse graphs. The resulting methods achieve optimal $O(N^2)$ complexity for dense graphs with $N$ nodes. For sparse graphs, the computational cost scales linearly with the number of edges, which is $O(N)$ in many cases. We implement the framework in the Python package SQWLib and illustrate its capabilities through simulations of representative algorithms, including quantum simulated annealing and quantum search on graphs. These results provide a practical tool for studying Szegedy-walk-based algorithms numerically beyond purely analytical treatments.

21.
arXiv (CS.AI) 2026-06-12

Beyond Runtime Enforcement: Shield Synthesis as Defensibility Analysis for Adversarial Networks

arXiv:2606.13621v1 Announce Type: new Abstract: Shielded reinforcement learning is typically presented as a runtime safety mechanism that compiles temporal-logic specifications into automata restricting an agent's actions. We argue this is the wrong product. The same automata-theoretic machinery – specification compilation, product game construction, attractor computation, and winning-region extraction – is better read as a design-time analytical instrument whose outputs are structural insights about a system rather than runtime constraints on a deployed agent. We instantiate this through a constrained two-player safety game for network defense. The two specifications are enforced asymmetrically: the defender specification defines the unsafe region of the game, whereas the attacker specification restricts the adversary's legal actions during attractor computation. Solving the game yields a defensibility verdict – a formal certificate that a topology-specification pair is or is not defensible – with the associated winning region and shield. Beyond the binary verdict, we derive topology-level metrics from the attractor structure and combine them with post-convergence behavior from shield-constrained adversarial multi-agent reinforcement learning. Together these form a defensibility fingerprint capturing both a network's formal safety properties and its operational behavior under adaptive play. A what-if analysis shows that formal defensibility and operational effectiveness capture distinct aspects of security: small architectural changes can produce large shifts in operational outcomes while leaving formal safety margins nearly unchanged. Shield synthesis is thus most valuable not as a deployment mechanism for safe agents, but as a framework for answering architectural questions about whether, where, and how a system can be defended. The defensibility verdict is the output, not the safe policy.

22.
bioRxiv (Bioinfo) 2026-06-16

AutoZyme: An Autonomous Agentic Framework to Optimize Bioinformatics Software

Performance bottlenecks in widely used genomics and bioinformatics software present a substantial and growing burden as biological datasets continue to increase in size and number. Relieving these bottlenecks relies largely on expert manual optimization and therefore remains difficult to scale. Here we present AutoZyme, an agentic framework for scientific software optimization. Given a target function, AutoZyme builds benchmarks, identifies bottlenecks, and iteratively tests code changes, retaining only those that improve runtime while preserving output. We evaluated AutoZyme on 45 functions, improving runtime without substantial memory increases in over 95% of cases considered. Across 38 functions from Seurat, Scanpy and related packages in genomics and bioinformatics, AutoZyme reduced runtime by a median of 8.52-fold, with the largest reductions exceeding 676-fold. The optimized functions are distributed through AutoZyme-Library as drop-in replacements for existing analysis pipelines. We also release AutoZyme as a reusable framework for optimizing additional user-specified packages and functions.

23.
arXiv (CS.LG) 2026-06-18

How Does the ReLU Activation Affect the Implicit Bias of Gradient Descent on High-dimensional Neural Network Regression?

arXiv:2603.04895v2 Announce Type: replace-cross Abstract: Overparameterized ML models, including neural networks, typically induce underdetermined training objectives with multiple global minima. The implicit bias refers to the limiting global minimum that is attained by a common optimization algorithm, such as gradient descent (GD). In this paper, we characterize the implicit bias of GD for training a shallow ReLU model with the squared loss on high-dimensional random features. Prior work (Vardi and Shamir, 2021) showed that the implicit bias does not exist in the worst-case, or corresponds exactly to the minimum-$\ell_2$-norm interpolating solution under exactly orthogonal data (Boursier et al., 2022). Our work interpolates between these two extremes and shows that, for sufficiently high-dimensional random data, the implicit bias approximates the minimum-$\ell_2$-norm solution with high probability with a gap on the order $\Theta(\sqrt{n/||\lambda||_1})$, where $n$ is the number of training examples and $\lambda$ denotes the spectrum of the data covariance matrix. Our results are obtained through a novel primal-dual analysis that carefully tracks the evolution of predictions, data-span coefficients, as well as their interactions, and show that the ReLU activation pattern quickly stabilizes with high probability over random data.

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

Fast Speech Foundation Model Distillation Using Interleaved Stacking

Distilling a large speech foundation model (SFM) into an efficient student model has been successfully applied to low-resource environments. Although distillation reduces inference latency, it requires an additional student model training. However, the training efficiency of SFM distillation remains underexplored. In this work, we explore training acceleration of SFM distillation to speed up model deployment. We examine the potential of stacking, in which the model depth is progressively increased through training until the target model depth is reached. While existing stacking methods improve training speed, they suffer from performance degradation. To handle this limitation, we propose interleaved stacking, a novel stacking method that consistently preserves layer position throughout the stacking process. This property is particularly critical in SFMs, in which each layer encodes distinct layer-specific knowledge. We validate the effectiveness of the proposed method on SUPERB.

25.
arXiv (CS.CL) 2026-06-11

AI Coding Agents Can Reproduce Social Science Findings

Recent anecdotal evidence suggests that AI coding agents can reproduce published findings when provided with original data and code; yet systematic evaluation across social sciences remains limited. Existing evaluation benchmarks are insufficient, either small or conflate agent performance with problems in the reproduction materials themselves, such as code that fails to execute correctly. Here we introduce SocSci-Repro-Bench, a benchmark of 221 tasks spanning four disciplines and 13 substantive domains, constructed from studies whose results are either fully reproducible with available materials or demonstrably non-reproducible due to missing data, allowing us to isolate agents' reproduction capacity. Evaluating two frontier coding agents, Claude Code and Codex, we find that both can reproduce a large share of social science findings, with Claude Code substantially outperforming Codex. These reproduction rates considerably exceed those previously reported for general-purpose LLM-based agents on comparable reproducibility benchmarks. Both agents also perform strongly on a reasoning task requiring identification of underlying research questions, and additional analyses suggest that results are not primarily driven by memorization. Providing the original paper PDF alongside replication materials modestly improves performance but introduces bias on tasks where reproduction is impossible. We also show that agents can be nudged toward confirmatory specification search through subtle prompt framing. Together, these findings suggest that at least some frontier coding agents can serve as reliable executors of computational workflows while underscoring the need for careful benchmarking and prompt design as AI systems assume larger roles in scientific production.