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01.
arXiv (CS.AI) 2026-06-19

Agentic Electronic Design Automation: A Handoff Perspective

arXiv:2606.19795v1 Announce Type: cross Abstract: Electronic design automation (EDA) is inherently multi-stage and handoff-heavy. Design artifacts, flow scripts, and engineering decisions cross tool, session, and organizational boundaries before final implementation, signoff, or release. Each transfer carries explicit and implicit requirements that may not be fully captured by stage-local checks. LLM-based agents now invoke EDA tools directly, embed retrieved knowledge in executable scripts, and hand off state across sessions and stages. Once their outputs condition downstream engineering decisions, the transferred object must satisfy a handoff contract and meet the assumptions of its next consumer. This survey introduces handoff validity as its organizing principle. A handoff is valid when the transferred object satisfies the consumer's acceptance conditions and carries sufficient context, evidence, and provenance for downstream use. We review 82 systems and classify them into three boundary classes. Stage-Bound systems establish validity within a single EDA stage or bounded verification task. Flow-Bound systems preserve coherent workflow state across tools, invocations, and sessions. Organization-Bound systems maintain source grounding, provenance, scope, and admissibility across knowledge and authority boundaries. For each class, we analyze handoff contracts, handoff objects, coordination mechanisms, and open questions. These analyses motivate a five-layer EDA agent communication protocol (EACP), covering the agent discovery, agent message, tool invocation, workflow orchestration, and security and IP protocols. We aim to provide a common vocabulary and research agenda for trustworthy agentic EDA.

02.
Nature Biotechnology 2026-06-11

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT

作者:

Spatially resolved CRISPR screening in vivo has been limited to small perturbation panels and subsets of protein-coding RNAs. We present Perturb-DBiT, a method for co-sequencing of spatial total RNA whole transcriptomes and single guide RNAs (sgRNAs) on the same tissue section in situ. In a human cancer metastatic colonization model, we applied large (80,000+) sgRNA panels across tumor colonies in multiple consecutive tissue sections alongside their corresponding total RNA transcriptomes. We linked perturbations affecting long noncoding RNA covariation, microRNA–mRNA interactions and distinct amino acid-specific tRNA alterations to tumor migration and growth. By integrating transcriptional pseudotime trajectories, we further observed the impact of perturbations on clonal dynamics and cooperation. In an immune-competent syngeneic mouse model, investigation of the tumor immune microenvironment indicated distinct, synergistic effects on immune infiltration and suppression. Perturb-DBiT provides a spatially resolved comprehensive view of perturbation responses in complex tissues, including small and large RNA regulation, tumor proliferation, migration, metastasis and immune interactions. In vivo CRISPR genetic perturbations are spatially mapped at scale.

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

Hy-Embodied-0.5-VLA: From Vision-Language-Action Models to a Real-World Robot Learning Stack

arXiv:2606.14409v1 Announce Type: cross Abstract: In this report, we present Hy-Embodied-0.5-VLA, abbreviated as HyVLA-0.5, an end-to-end system that spans the full robot learning stack: data collection, model design, continued pre-training and supervised fine-tuning, RL post-training, and real-world deployment. Each component serves a distinct role in this stack.

04.
arXiv (CS.AI) 2026-06-15

CisTransCell: Single-Cell Perturbation Prediction via Gene Function, Regulatory Control, and Cellular Context

arXiv:2606.13713v1 Announce Type: cross Abstract: Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.

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

MapDream: Task-Driven Map Learning for Vision-Language Navigation

Vision-Language Navigation (VLN) requires agents to follow natural language instructions in partially observed 3D environments, motivating map representations that aggregate spatial context beyond local perception. However, most existing approaches rely on hand-crafted maps constructed independently of the navigation policy. We argue that maps should instead be learned representations shaped directly by navigation objectives rather than exhaustive reconstructions. Based on this insight, we propose MapDream, a map-in-the-loop framework that formulates map construction as autoregressive bird's-eye-view (BEV) image synthesis. The framework jointly learns map generation and action prediction, distilling environmental context into a compact three-channel BEV map that preserves only navigation-critical affordances. Supervised pre-training bootstraps a reliable mapping-to-control interface, while the autoregressive design enables end-to-end joint optimization through reinforcement fine-tuning. Experiments on R2R-CE and RxR-CE achieve state-of-the-art monocular performance, validating task-driven generative map learning.

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

EHRNote-ChatQA: A Benchmark for Evidence-Grounded Multi-Turn Clinical Question Answering over Longitudinal Discharge Summaries

Discharge summaries are crucial clinical documents containing the context of a patient's overall hospital stay, and are routinely reviewed by medical experts for patient readmission, ongoing care, and diagnostic decision-making. When reviewing them, medical experts often must iteratively synthesize information across multiple summaries while verifying the evidence supporting each answer. Although large language models (LLMs) are increasingly explored for clinical question answering, existing benchmarks do not sufficiently reflect this setting: they often evaluate exam-style medical knowledge or focus on single-turn question answering with limited evidence-grounding evaluation. We introduce EHRNote-ChatQA, the first benchmark for evidence-grounded multi-turn clinical question answering over patients' multiple discharge summaries. Built from de-identified MIMIC-IV discharge summaries, EHRNote-ChatQA contains 967 patient-level multi-turn samples spanning one to five notes and 16,072 medical-expert-verified QA pairs (8,036 content questions, each paired with an evidence-grounding question) across eight clinical categories. The benchmark is constructed through an expert-informed pipeline combining discharge-summary structuring schema, expert-curated multi-turn QA templates, and LLM-based generation, followed by review and revision of every single QA sample by 11 medical experts. Benchmarking 22 open- and closed-source LLMs reveals several challenges, including that LLMs struggle more with evidence grounding than content answering, multi-turn errors compound across turns, and single-turn clinical QA performance does not reliably transfer to this setting. These findings establish EHRNote-ChatQA as a rigorous and practical benchmark for evaluating clinical QA systems. The dataset will be made publicly available through PhysioNet credentialed access.

07.
PLOS Computational Biology 2026-05-29

A prototype-augmented graph representation learning framework for identifying brain disorder-associated genes and facilitating drug repurposing

作者:

by Jiafang Li, Yifei Li, Siying Lin, Jiahua Rao, Huiying Zhao Many genetic loci were identified as associated with neuropsychiatric disorders and neurodegenerative disorders by Genome-wide association studies (GWAS). How these loci impact these diseases is unclear. Advances in deep-learning approaches and multi-omics data have the potential to link GWAS findings with disease mechanisms. Here, we proposed the Multi-omics Graph Transformer Network (MOGT), a semi-supervised graph neural network that leverages graph representation learning to model biological networks derived from multi-omics data to predict disease-associated genes. MOGT outperforms the current approaches in disease gene prediction for two psychiatric disorders and three neurodegenerative/neurological diseases. High-risk genes (HRGs) for Parkinson’s disease (PD) predicted by MOGT were used to drug discovery by integrating with the CMAP database. Finally, 10 drugs were identified as potential candidates. Among them, the effect of drug UK-356618 was experimentally verified in a primary neuron model, showing that UK-356618 reversed the abnormal expression of PD-associated genes and improved the cell-level phenotypes of PD. Together, these results indicate that MOGT can be used to identify HRGs for brain disorders, and these predicted HRGs provide high-level insights into the mechanisms and treatments of brain disorders.

08.
Nature (Science) 2026-06-22

Cancer cells adopt unprecedented strategies to produce a molecule that protects them from iron-dependent death

The finding that spermine molecules in cells bind to iron to prevent it unleashing ferroptosis, a type of cell death, opens up strategies for treating tissue damage and cancer. The finding that spermine molecules in cells bind to iron to prevent it unleashing ferroptosis, a type of cell death, opens up strategies for treating tissue damage and cancer.

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

Synthetic Resonance: A Framework for Growth-Oriented Human-AI Relationships

arXiv:2606.18265v1 Announce Type: cross Abstract: As human relationships with artificial intelligence systems become increasingly frequent and sustained, existing language and theory fail to accurately capture the nature of these affiliations. Common descriptors such as mutual understanding, connection, or friendship risk anthropomorphizing systems that lack subjective experience, while dominant frameworks tend to reduce AI to either a tool or a threat. In this paper, I introduce the concept of synthetic resonance as an integrative framework for understanding human-AI relationships. Synthetic resonance describes how relationships humans define as meaningful can emerge between a human and an AI system without the need to attribute shared feelings or mutual awareness. I argue that synthetic resonance is best understood as a structured, dynamic pattern of interaction that can produce a sense of relationship without the presence of a second experiencing subject. By clarifying this distinction, the concept of synthetic resonance offers a more precise way of conceptualizing human-AI relationships and highlights their potential value and ethical implications. I also call for more research that tests the processes and outcomes of synthetic resonance.

10.
arXiv (CS.CL) 2026-06-11

Notes2Skills: From Lab Notebooks to Certainty-Aware Scientific Agent Skills

Scientific discovery workflows usually contain and rely heavily on lab notes, where researchers record observations, interpret uncertain results, and plan follow-up experiments. Such informative lab notes preserve evolving scientific reasoning and author uncertainty, rather than polished final results exhibited in publications, providing a valuable opportunity for AI to engage in scientific exploration at a more comprehensive and deeper level. However, most prior work on scientific text focuses on papers, protocols, or structured databases, leaving informal laboratory notes underexplored as inputs to AI agents for science. This gap matters because lab notes often intermingle validated observations, tentative judgments, and possible experimental next steps within the same passage. If these signals are conflated, an AI agent may mistake uncertain scientific judgments for confirmed conclusions or executable actions. To this end, we present Notes2Skills, a two-stage framework for turning lab notebooks into verifiable skills for scientific AI agents while preserving the author's certainty. Across seven conditions and three wet-lab sessions, Notes2Skills is the only configuration that neither mistakes uncertain notes for firm instructions nor discards firm ones. We show that certainty preservation is the missing piece between lab notebooks and reliable agent skills, opening a path toward safer AI co-scientist systems.

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

StaminaBench: Stress-Testing Coding Agents over 100 Interaction Turns

arXiv:2606.19613v1 Announce Type: cross Abstract: We introduce StaminaBench, a benchmark that measures the stamina of coding agents: how many consecutive interaction turns (change requests) they can handle before failing. Unlike the prevailing fraction-of-tasks-solved metric, this matches real vibe-coding where sessions run dozens or hundreds of turns. In StaminaBench, agents implement a REST API server and modify it across a tunable number of procedurally generated follow-up change requests - 100 in our experiments, resulting in codebases of up to 6,000 lines. Tests are generated fully programmatically without LLM involvement, ensuring reproducibility and reliability; change sequences are drawn from either a hardcoded or LLM-driven sampler, both constrained to a structured action space to ensure changes are valid. The agent and the server run in an isolated environment and communicate with the benchmark through HTTP, making testing fully black-box and language-agnostic. We evaluate six agent harnesses paired with seven open-source LLMs across 20 scenarios of 100 turns each and find that: (1) all the tested models fail within 5-6 turns, confirming that vibe-coding-style programming without thorough testing produces bugs; (2) passing test feedback back to the agent and allowing it to retry improves passed turn count by up to 12x; and (3) a good harness is required for strong performance: stronger models exhibit up to a 6x gap between their best and worst harness, while weaker models fail with any harness. We release the benchmark and the generated tasks to enable further research into multi-turn coding agent behavior. Benchmark code and data: github.com/amazon-science/StaminaBench.

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

Neural network surrogates with uncertainty quantification for inverse problems in partial differential equations

arXiv:2606.20417v1 Announce Type: new Abstract: Inverse problems for differential equations arise throughout science and engineering, where one seeks to infer unknown model parameters from noisy or incomplete observations. Traditional numerical methods for these problems are often computationally expensive, particularly in Bayesian settings where evaluating the likelihood becomes costly for complex forward models and high-dimensional parameter spaces. To address this challenge, we introduce DeepGaLA, a neural-network surrogate for differential equation solvers that provides uncertainty-aware predictions, reducing overconfident inference when training data are limited. To evaluate the fidelity of the surrogate-induced posterior approximations in practice, we show that a short run of delayed-acceptance Markov chain Monte Carlo can serve as an effective diagnostic. Across a range of numerical experiments, DeepGaLA delivers forward-model approximations with accuracy comparable to established Gaussian-process surrogates, while better maintaining efficiency as parameter dimension grows. Moreover, it can incorporate differential-equation constraints, including in nonlinear settings. Overall, these results indicate that uncertainty-quantified neural surrogates can enable scalable and reliable Bayesian inference for inverse problems in complex systems.

13.
bioRxiv (Bioinfo) 2026-06-20

Systematic Evaluation of Feature Representations for Cancer-Associated sORF Prediction in Non-coding RNA

Short open reading frames (sORFs) within non-coding RNAs (ncRNAs) have arisen as a hidden layer of gene regulation, encoding small peptides that represent a new class of cancer regulators with diagnostic and therapeutic potential. However, inferring associations between sORFs to specific cancer types remains challenging and requires computational approaches for accurate prediction. Recently, the CoraL framework introduced the first computational approach for predicting cancer-associated peptides, focusing primarily on model architecture while overlooking how feature extraction strategies influence predictive accuracy. We present a systematic evaluation of machine learning models and feature extraction approaches to predict cancer-associated sORFs across 15 cancer types. We benchmarked seven traditional machine learning algorithms combined with three feature extraction methods: k-mer frequency, Word2Vec embeddings, and genomic language model (gLM)-based embeddings. To our knowledge, this is the first study applying gLM-derived embeddings to the prediction of cancer-associated sORFs in ncRNA. Our results show that traditional machine learning models with appropriate feature extraction outperform the CoraL baseline across all cancer types, achieving up to 10% higher accuracy in some of the 15 evaluated datasets. Interestingly, k-mer features consistently outperformed gLM embeddings without fine-tuning, suggesting that local sequence composition may provide more discriminative information for this task and that pre-trained genomic representations may require task-specific adaptation to fully capture these patterns. Additionally, we observed that the way sequences are tokenized, such as the k-mer length, can affect performance: longer fragments (e.g., k=7) sometimes reduced accuracy for Random Forest but had a smaller effect on MLP. Our findings suggest that appropriate feature engineering can provide greater improvements than increasing model complexity.

15.
arXiv (CS.AI) 2026-06-11

Mathematical perspective on genetic algorithms with optimization guided operators

arXiv:2606.12279v1 Announce Type: cross Abstract: Recent work in ML applies genetic algorithms at inference time to iteratively improve solutions to optimization problems. The basic mutation and recombination operators involved are qualitatively different from those studied classically. Mutations are no longer random; an ML algorithm mutates a solution with the goal of improving an objective. Similarly, recombination is not based on random collages of parent solutions. Instead, it is an ML optimization-based operator whose goal is to synthesize improved solutions from its inputs. Thus, these mutation and recombination operators are more likely to improve the objective, but their computational cost is much higher. We introduce a general model of genetic algorithms and formulating optimization in this model as a query-complexity problem, using the language of reinforcement learning. We then study specialized models. We show that some optimization problems require generation, mutation, and recombination to be solved. We then obtain qualitatively tight algorithms for a family of problems within this framework that captures the nontrivial role of diversity in the solution pool, a key feature of practical ML genetic algorithms.

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

Broadcast Product: Redefining Shape-aligned Element-wise Multiplication and Beyond

arXiv:2409.17502v2 Announce Type: replace Abstract: Broadcast operations are widely used in scientific computing libraries, yet their mathematical formulation is often implicit and inconsistently represented in machine learning literature. This problem frequently leads to invalid equations when element-wise products are written despite mismatched tensor shapes. In this paper, we formalize such operations by introducing the broadcast product $\boxdot$, which explicitly extends the Hadamard product through shape-aligned element duplication. We provide a rigorous definition of the broadcast product, analyze its algebraic properties, and show how it can be expressed using standard linear algebra. Building on this framework, we formulate least-squares problems and sketch a proof-of-concept broadcast decomposition. As a preliminary illustration, we show that the formalism enables a new family of decompositions with distinct structural properties from conventional tensor decompositions. This work establishes a mathematical foundation for broadcast-aware tensor operations, connecting practical implementations with rigorous tensor analysis.

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

Quantum Information Geometry of Multicomponent Superconducting Fluctuation Transport

arXiv:2606.15928v1 Announce Type: cross Abstract: Quantum geometry underlies many electronic responses, but its transport signatures have so far been established mainly for pure single-particle Bloch states. Whether collective many-body fluctuations possess a measurable quantum geometry remains largely unexplored. Here we show that superconducting fluctuation transport provides a direct probe of quantum information geometry in collective many-body matter. Starting from a multicomponent time-dependent Ginzburg-Landau theory in the Gaussian fluctuation regime, we identify the equilibrium density matrix of fluctuating Cooper pairs as the static pair propagator, which defines a positive mixed-state manifold in momentum space. The geometry of this manifold is directly measurable through paraconductivity: the longitudinal paraconductivity is governed by the quantum Fisher information of superconducting fluctuation modes, while the fluctuational anomalous Hall effect is governed by the mean Uhlmann curvature, the mixed-state counterpart of Berry curvature. This correspondence further yields geometric bounds between these two transport components, with no direct analogue in normal electronic transport. Applied to chiral superconducting fluctuations in quarter-metal systems motivated by rhombohedral multilayer graphene, a symmetry-allowed Lifshitz invariant generates finite mean Uhlmann curvature and logarithmically enhances the anomalous Hall conductivity above the critical temperature. Our results establish collective superconducting fluctuations as an experimentally accessible transport probe of mixed-state quantum information geometry.

18.
bioRxiv (Bioinfo) 2026-06-15

DAQplugin: Deep Learning based Real-time Model Evaluation Plugin for ChimeraX

Although an increasing number of protein structures are determined by cryogenic electron microscopy (cryo-EM), protein structure modeling frequently suffers from residue misassignments and sequence register shifts, particularly in regions with ambiguous density. Here, we present DAQplugin, a ChimeraX plugin that performs real-time evaluation of protein models against cryo-EM density maps using the deep-learning-based residue-wise model quality (DAQ) score. Unlike existing validation tools that are typically applied after model construction, DAQplugin enables real-time deep-learning-based validation during model building and refinement. To our knowledge, DAQplugin is the first tool that provides real-time deep-learning based validation of protein models for cryo-EM map within an interactive modeling environment. In addition to identifying potential modeling errors, DAQplugin also provides guidance for correcting sequence register shifts by suggesting alternative residue placements along the backbone. The computation in this plugin is designed to run efficiently on general CPUs without requiring GPU hardware. Using DAQplugin, users can perform deep-learning-based validation on standard laptops during interactive model building, model-map fitting, and refinement. DAQplugin is able to facilitate more accurate interpretation of cryo-EM density maps and improve the reliability assessment of protein structure models.

19.
PLOS Computational Biology 2026-06-15

Environmental “knees” and “wiggles” as strong stabilizers of species’ range limits set by interspecific competition

by Farshad Shirani, Benjamin G. Freeman Whether interspecific competition is a major contributing factor to setting species’ range limits has been debated for a long time. Theoretical studies have proposed that the interactions between interspecific competition and disruptive gene flow along an environmental gradient can halt range expansion of ecologically similar species where they meet. However, the stability of such range limits has not been well addressed. We use a deterministic mathematical model of adaptive range evolution over a continuous habitat to show that the range limits set by interspecific competition are unlikely to be evolutionarily stable if the environmental optima for fitness-related traits vary (almost) linearly in space. That is, in a linear environment without a dispersal barrier or a third (or more) species, the range borders formed between two competing species constantly move towards the weaker species. We demonstrate that environmental nonlinearities such as “knees” and “wiggles”—wherein an isolated sharp change or a step-like change occurs in the steepness of a trait optimum—can strongly stabilize competitively formed range limits. The stabilization mechanism relies on the contrast that such nonlinearities create in the level of disruptive gene flow to the peripheral population of each species, and succeeds when an additional process, such as Allee effects, prevents the establishment of an infinitesimal population in the presence of an abundant competitor. We show that the stability of the range limits at these nonlinearities is robust against moderate environmental disturbances. Whether strong disturbances such as rapid high-amplitude climate changes can destabilize such range limits depends on how the competitive dominance of the species changes across the nonlinearity. Therefore, our findings underscore the importance of assessing species’ competitive ability when predicting responses to climate change, and identify geographic regions where established range limits are likely to persist as well as regions where shifting limits may eventually stabilize.

20.
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.

21.
arXiv (CS.LG) 2026-06-11

Attention by Synchronization in Coupled Oscillator Networks

arXiv:2606.12059v1 Announce Type: new Abstract: We address transformer attention on energy-constrained physical substrates. Softmax attention requires exponentiation and global reduction, operations with high energy cost on von Neumann hardware and no natural physical analog. We show that Kuramoto synchronization dynamics (which arise in electrical, mechanical, superconducting, and charge-density-wave oscillator arrays, among other physical systems) implement a well-defined attention operation without either. The resulting mechanism, fixed-query oscillator attention, replaces softmax's arithmetic with the equilibration of a gradient flow on the sphere: queries are learned anchors fixed on the sphere, and free oscillators evolve under Kuramoto-Lohe dynamics until they settle at positions encoding attention weights via cosine similarity. Because the computation is equilibration, it requires no exponentiation; the only global operation is an affine normalization at readout. The fixed point is provably unique and globally attractive from almost every initial condition, a guarantee that holds across every physical realization. Empirically, at the minimal hardware configuration (oscillator dimension $d_{\mathrm{osc}}$ = 2), oscillator attention outperforms softmax on keyword spotting (+1.00 pp) and on subject-verb agreement (+5.27 pp on hard sentences, with zero training failures versus one in five for softmax). On causal language modeling, where softmax retains an advantage, oscillator attention closes the gap as $d_{\mathrm{osc}}$ grows: from +11.09 PPL at $d_{\mathrm{osc}}$ = 2 to +2.98 PPL at $d_{\mathrm{osc}}$ = 32 on WikiText-2, and from +2.39 PPL at $d_{\mathrm{osc}}$ = 2 to +0.57 PPL at $d_{\mathrm{osc}}$ = 32 on TinyStories. The main objective of this work is not to replace softmax in software but to provide a mathematically grounded blueprint for accurate attention on physical substrates.

22.
arXiv (CS.AI) 2026-06-19

Policy-Embedded Graph Expansion: Networked HIV Testing with Diffusion-Driven Network Samples

arXiv:2601.16233v2 Announce Type: replace-cross Abstract: HIV is a retrovirus that attacks the human immune system and can lead to death without proper treatment. In collaboration with the WHO and the University of Witwatersrand, we study how to improve the efficiency of HIV testing with the goal of eventual deployment, directly supporting progress toward UN Sustainable Development Goal 3.3. While prior work has demonstrated the promise of intelligent algorithms for sequential, network-based HIV testing, existing approaches rely on assumptions that are impractical in our real-world implementations. Here, we study sequential testing on incrementally revealed disease networks and introduce Policy-Embedded Graph Expansion (PEGE), a novel framework that directly embeds a generative distribution over graph expansions into the decision-making policy rather than attempting explicit topological reconstruction. We further propose Dynamics-Driven Branching (DDB), a diffusion-based graph expansion model that supports decision making in PEGE and is designed for data-limited settings where forest structures arise naturally, as in our real-world referral process. Experiments on real HIV transmission networks show that the combined approach (PEGE + DDB) consistently outperforms baselines (e.g., 17.3% improvement in discounted reward and 15.4% more HIV detections with 25% of the population tested) and explore key tradeoffs that drive solution quality.

23.
arXiv (CS.AI) 2026-06-11

Risk Under Pressure: Compute-Aware Evaluation of Adversarial Robustness in Language Models

arXiv:2606.11409v1 Announce Type: cross Abstract: Adversarial robustness evaluations of large language models (LLMs) typically report attack success rate (ASR) under fixed query budgets, implicitly treating all attacks as equally costly. In practice, the computational expense of different attack strategies can vary by orders of magnitude. Consequently, ASR at a fixed budget can obscure the true effort required to jailbreak a model, thereby making it hard to determine whether an attack's cost justifies its payoff to the attacker. We propose a compute-aware evaluation framework based on computational pressure, measured in cumulative floating-point operations (FLOPs), as a proxy for adversarial effort. We introduce risk-compute curves, which map compute budgets to attack risk, and derive two metrics that summarize the average pressure required for a given attack to succeed. Across ten models spanning three families and four different stages in language model training and alignment, evaluated with three attack strategies (gradient-based, iterative refinement, and template-based) on two jailbreak robustness benchmarks, we find: (1) alignment training has non-monotonic effects on compute-space robustness; (2) scaling model size reduces gradient-based attack effectiveness but has limited impact on cheaper template-based attacks; (3) gradient-based attacks optimized on a surrogate model can transfer to a separate target model, providing a way to reduce attacker costs; (4) compute cost varies by up to ${\approx}5{\times}$ across harm categories within a single model; and (5) safety-aligned RL increases aggregate cost while leaving some categories disproportionately accessible. We release our framework to enable compute-aware risk assessment and evaluation.

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

Rescaling Confidence: What Scale Design Reveals About LLM Metacognition

arXiv:2603.09309v2 Announce Type: replace Abstract: Verbalized confidence, in which LLMs report a numerical certainty score, is widely used to estimate uncertainty in black-box settings, yet the confidence scale itself (typically 0–100) is rarely examined. We show that this design choice is not neutral. Across six LLMs and three datasets, verbalized confidence is heavily discretized, with more than 78\% of responses concentrating on just three round-number values. To investigate this phenomenon, we systematically manipulate confidence scales along three dimensions: granularity, boundary placement, and range regularity, and evaluate metacognitive sensitivity using $meta-d'$. We find that a 0–20 scale consistently improves metacognitive efficiency over the standard 0–100 format, while boundary compression degrades performance and round-number preferences persist even under irregular ranges. These results demonstrate that confidence scale design directly affects the quality of verbalized uncertainty and should be treated as a first-class experimental variable in LLM evaluation.

25.
arXiv (quant-ph) 2026-06-16

Accelerating physics-informed neural networks for full waveform inversion using a hybrid quantum-classical finite-basis architecture

arXiv:2606.01110v2 Announce Type: replace-cross Abstract: Full waveform inversion (FWI) reconstructs heterogeneous material properties from receiver data but remains computationally demanding. Physics-informed neural networks (PINNs) and their domain-decomposed variants (FBPINNs) offer a mesh-free alternative but face convergence challenges when representing complex velocity fields. We present a hybrid quantum-classical FBPINN for acoustic FWI, bringing together quantum computing and classical machine learning, in which the decomposed wavefield network and the global velocity network are implemented as classical-to-quantum pipelines terminating in parameterized quantum circuits (PQCs). The PQCs are realized as differentiable JAX statevector simulators, enabling end-to-end automatic differentiation through the classical PINN, the quantum circuit, and the physics-informed loss. On a geophysical anomaly benchmark, the quantum hybrid reaches a lower L1 velocity error than the primary classical FBPINN baseline in approximately 8x fewer training iterations, despite using approximately 33% fewer trainable parameters, and it outperforms all 15 classical hyperparameter variants tested. A second benchmark (checkerboard) demonstrates the generality of the inversion pipeline, confirming that the quantum hybrid architecture can recover structured spatial variations beyond the localized anomaly benchmark. Our framework is broadly applicable to wave-based inverse problems beyond geophysics, including medical ultrasound tomography and non-destructive evaluation.