Author Correction: De novo design of quasisymmetric two-component protein cages
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arXiv:2512.10875v2 Announce Type: replace Abstract: Quantum Imaginary-Time Evolution (QITE) is a powerful method for preparing ground states on quantum hardware. However, executing QITE has costly measurement budgets for general Hamiltonians. Both fidelity and computational cost are strongly dependent on the definition of suitable local domains and Hamiltonian partitions. In this work, we introduce the Multiple-Time QITE algorithm (MT-QITE). We show how using more than one imaginary time substantially improves the fidelity of the resulting ground state as well as the measurement overhead with respect to the previously published QITE algorithm, while preserving its deterministic character and its independence from ad hoc ansatze. Moreover, unlike QITE and other QITE-based algorithms, MT-QITE is parallelizable, and we show that even in Hamiltonians with non-local interactions, partitioning may entail a computational advantage.
arXiv:2606.15531v1 Announce Type: new Abstract: Fine-tuning aligned language models on benign tasks (e.g. math tutoring) systematically breaks safety guardrails, even when training data contains no harmful content. While mechanistic approaches have shed light on where alignment resides in model weights, they do not by provide a general formal framework for deriving guarantees about when fine-tuning degrades it – leaving the field without principled tools for predicting or preventing alignment collapse. We develop a local geometric framework through geometric analysis of parameter-space trajectories and apply it to understand the fragility of alignment in fine-tuning. While first-order analysis suggests orthogonal updates are safe, we prove this is illusory: the curvature of the fine-tuning loss induces second-order acceleration that can induce second-order drift into alignment-sensitive regions. We formalize a construct of our framework as the Alignment Instability Condition (AIC), three geometric properties that, when present, are sufficient to guarantee degradation. Our main result proves quartic onset of alignment degradation along gradient-flow trajectories, determined by how sharply alignment depends on specific parameters and how strongly tasks couple to these parameters. These findings yield formal sufficient conditions under which static first-order protection can fail under gradient descent. We further empirically validate the framework's foundations, showing that the Fisher Information Matrix provides a proxy for the degree of safety degradation across diverse fine-tuning.
Surface reconstruction from point clouds is important for consumer-grade 3D capture, including AR/VR and indoor scanning. Local-patch Unsigned Distance Field (UDF) methods are lightweight and generalizable, but their accuracy depends on the support radius, traditionally fixed or selected by a one-dimensional curvature heuristic that cannot capture heterogeneous local geometry. We propose a learned per-query radius selector that predicts a continuous support radius and plugs into a frozen LoSF-UDF backbone. The selector is trained using off-grid target radii obtained by parabolic interpolation of cached UDF error curves. Experiments show improved fine-scale reconstruction accuracy.
arXiv:2606.11393v1 Announce Type: new Abstract: In this note, we derive a large-deviation-type scaling limit for a discretization of the Martingale Representation Theorem. Somewhat surprisingly, and to the best of our knowledge, this result has not been previously obtained in the literature.
We present EDEN (Emergency Department Electronic Notes), a new and unique large-scale corpus of clinical notes produced in Emergency Departments of Italian hospitals. The corpus, in its current version, is composed of approximately 4 million clinical notes fully anonymized, covering diverse phases of patient care during the stay in the emergency department. In addition, a subset of about six thousand notes has been manually annotated by clinical experts through a structured Case Report Form (CRF) containing 132 items relevant for two patient situations in emergency departments, dyspnea and loss of consciousness. Items may assume numerical values (e.g., for blood saturation), categorical (e.g., for level of consciousness ), binary (e.g., for presence of traumas), and mixed value types. The annotation process involved multiple clinicians and underwent iterative revision to resolve ambiguities in item formulation, resulting in a richly structured (although high imbalanced) resource. The dataset aims to fill a relevant gap of data able to support both the development and the use of Large Language Models in concrete medical applications. We describe the data collection protocol, the on-site anonymisation pipeline, corpus statistics, and the annotation scheme. Finally, we propose CRF-filling as a novel structured information extraction benchmark, and provide zero-shot baseline resulting from Gemma-27B and MedGemma-27B. To the best of our knowledge, the EDEN dataset is the largest freely available corpus of clinical notes existing for the Italian language.
Identifying recently linked infections from pathogen genome sequences is central to infectious disease surveillance, yet many clustering approaches rely on fixed genetic distance thresholds whose relationship to transmission is often unclear. This limitation is especially important in rapidly growing outbreaks and superspreading events, where many cases may be sampled close together in time and share little genetic variation, making true transmission links difficult to distinguish from other closely related infections. Supervised models can improve discrimination, but they require labelled transmission data that are rarely available during outbreak response. We developed EpiLink, a threshold-free method that estimates whether two cases are compatible with recent transmission. Here, compatibility means how well the observed genetic distance and sampling-time difference between two cases fit what would be expected if they were linked by defined recent transmission scenarios. EpiLink simulates plausible recent transmission histories while accounting for uncertainty in infection timing, testing delay, and mutation accumulation, then assigns higher scores to pairs whose observed differences are typical of those simulations. EpiLink was evaluated using both synthetic and empirical SARS-CoV-2 outbreak data from the 2020 Boston epidemic. Two EpiLink variants were compared to a logistic regression model trained on labelled transmission data. One EpiLink variant assumed deterministic mutation accumulation, with genetic differences proportional to elapsed evolutionary time; the other accounted for stochasticity by sampling mutation counts from a Poisson distribution. The logistic regression model performed better at distinguishing linked from unlinked pairs, but EpiLink achieved comparable clustering accuracy. In the Boston data, EpiLink recovered clusters enriched for documented conference and skilled nursing facility outbreaks. EpiLink thus provides an interpretable, simulation-based approach for identifying recent transmission clusters when fixed thresholds are difficult to justify and labelled transmission data are unavailable.
by Huangdong Li, Ziyu Zhu, Shaopeng Yang, Weijing Cheng, Shaoying Tan, Zhuoyao Xin, Lei Zhang, Zhuoting Zhu, Shida Chen, Wenyong Huang, Wei Wang Background Retinal neurodegeneration is an early and independent feature of diabetic retinal disease and has been proposed as a window into the systemic neural consequences of diabetes, yet accessible molecular biomarkers and individualized prediction tools remain scarce. We aimed to identify circulating plasma protein signatures of diabetic retinal neurodegeneration (DRN) and to translate them into a clinically usable risk prediction system. Methods and findings In this multi-cohort prospective observational study, we integrated high-throughput plasma proteomics with longitudinal optical coherence tomography (OCT) in two independent populations. The discovery cohort comprised 1,492 participants had baseline plasma proteomics and OCT, and 1,218 were followed with repeated OCT over 6 years in Guangzhou Diabetic Eye Study (GDES). DRN was quantified by the annualized OCT-derived retinal nerve fiber layer thinning rate. In multivariable analyses adjusted for age, sex, smoking, systolic blood pressure, HbA1c, and diabetes duration, we identified 71 plasma proteins associated with development and progression of DRN. These proteins mapped onto pathways governing inflammatory immune recruitment, extracellular matrix remodeling, and microvascular homeostasis, providing a plausible biological basis for DRN. We developed a proteomics-based DRN model (Pro-DRN) using eight machine learning (ML) algorithms, including XGBoost and LightGBM. In the independent test set, Pro-DRN achieved a C-index of 0.860, rising to 0.908 when integrated with clinical variables. Compared with six conventional models, Pro-DRN improved discrimination (ΔC-index 0.137 to 0.159; all P
During the COVID-19 pandemic, limited testing capacity and reporting delays complicated epidemic surveillance and decision-making in Mexico. We calibrated textit{covidestim}, a Bayesian nowcasting model, to estimate the total SARS-CoV-2 infections from reported cases and deaths using Mexican surveillance data. Disease-progression distribution priors were calibrated using Mexico City records and validated through comparisons with national seroprevalence surveys, hospitalization data, and annual reported severe-case rates across all states. Using the reconstructed estimates of active infections, we implemented an event-based risk framework that quantifies the probability of encountering at least one infectious individual in gatherings of different sizes. This probability was subsequently translated into a four-level epidemiological traffic-light indicator and computed at both state and municipality levels. The resulting estimates revealed substantial spatial heterogeneity that is obscured by state-level aggregation, particularly in states with marked differences between urban and rural municipalities. To evaluate consistency with public-health indicators, we compared the proposed risk classification with the official Mexican epidemiological traffic-light system, considering interpretable gathering sizes relevant to public-health decision making. Weekly reports derived from this framework were delivered to policymakers in the State of Queretaro in Mexico, as an anticipation tool for school reopening and public-space management. This demonstrates that this Bayesian reconstruction of infections combined with event-based risk metrics can provide an interpretable and generalizable municipality-level complement to routine surveillance systems, particularly in regions with limited testing capacity and heterogeneous local transmission dynamics.
Hyperspectral Imaging (HSI) is a promising modality for intraoperative assessment of resection margins in Breast-Conserving Surgery (BCS), but its clinical translation requires aligning the inherently 2D spectral information onto the 3D shape of the excised tissue so that suspicious regions can be precisely localized for targeted follow-up. We present a fully automated, calibration-free pipeline that produces a 3D hyperspectral point cloud of an ex-vivo lumpectomy specimen from a set of consumer-camera RGB images and a single top-down HSI acquisition. The 3D geometry is reconstructed with a deep-learning Structure-from-Motion backbone, stabilized in a metric reference frame by a custom bundle adjustment that enforces consistency on the corners of four ArUco markers placed around the specimen. The HSI cube is then registered to the reconstruction without recovering the HSI camera pose: the markers, visible in both modalities, define 16 corner correspondences that drive a planar homography, and 3D coordinates are recovered by lookup on an orthographically rendered depth map. Evaluated on two ex-vivo lumpectomy specimens, the pipeline achieves a median 3D registration error below 1~mm and a 2D reprojection error below 0.02 mm, with a total per-specimen processing time under 4 minutes on accelerated hardware. These results support the feasibility of integrating HSI-guided spatial localization into intraoperative margin assessment workflows for breast-conserving surgery.
Despite advances in large-scale Automatic Speech Recognition (ASR), disfluent speech remains challenging, as state-of-the-art systems are often optimized to omit disfluencies, leading to information loss and hallucinations. Prior work has focused on verbatim transcription and the integration of disfluency markers, but adapting models on limited datasets can lead to catastrophic forgetting of general-domain knowledge. We address this gap by leveraging continual learning (CL) with explicit disfluency tokens. We first introduce these tokens into a pretrained ASR model to establish stable token mechanisms, and then continue training on additional datasets with varying disfluency distributions. Through a detailed analysis of model dynamics during training, we identify a trade-off between marker learning and ASR performance, and a consistent cross-attention head mechanism shared across CL methods.
arXiv:2602.21544v2 Announce Type: replace Abstract: We proposed a time-delayed quantum extreme learning machine (TD-QELM) for efficient time-series prediction on noisy intermediate-scale quantum (NISQ) devices. By encoding multiple past inputs simultaneously, TD-QELM achieves shallow circuit depth independent of sequence length, thereby, mitigating noise accumulation and reducing computational complexity. Experiments using the NARMA benchmark on both noiseless simulations and IBM's 127-qubit processor demonstrate that TD-QELM consistently outperforms conventional quantum reservoir computing in prediction accuracy and noise robustness. These results highlight TD-QELM as a practical and scalable framework for time-series learning on current NISQ hardware.
arXiv:2605.16430v3 Announce Type: replace-cross Abstract: Scaling LLMs requires tremendous computational resources, and recent advances in AI have gone hand in hand with massive amounts of capital expenditure. While it is established that scaling up LLMs reliably increases model quality (quantified in terms of loss or downstream evaluations), it is unclear how these quality improvements translate to potential revenue, and whether revenue increases would offset costs of larger-scale training and inference. In this work, we develop an economic model for characterizing the rational behavior of an LLM training firm by combining scaling laws with microeconomic theory. Under our model of firm behavior, LLM quality can be increased with more parameters and training tokens, leading to more potential adoption by consumers, who each have a quality threshold for using the LLM. On the other hand, additional parameters and training tokens both incur additional costs. We analyze the profit maximization problem for this model under compute-bound and data-bound regimes. In the compute-bound regime, optimal model size and token budget track hardware efficiency $E$ (FLOPs/\$) at a near-linear rate; total training cost then scales sub-quadratically in $E$. Data efficiency improvements incentivize larger models and training expenditure. When we are limited to $D$ data, profit-optimal training expenditure scales as $D^2/E$, i.e, increase with data and decreases with hardware efficiency (as well as data efficiency). Finally, we analyze practical trends in training expenditure: current trends are consistent with our most permissive model variants in the compute-bound regime, but are not profit-optimal in the data-bound regime or assuming hardware advances will stall. Overall, our results provide a theory of profit-optimal LLM training, providing a foundation for engaging critically with industry statements and supporting long-term economic decision making.
arXiv:2606.16236v1 Announce Type: new Abstract: Reinforcement learning (RL) often suffers from performance degradation when deployed in environments that differ from those encountered during training. Existing techniques such as domain randomization (DR) mitigate this, but require access to diverse training environments and full trajectory observability, assumptions that fail in privacy-preserving or restricted scenarios where only scalar performance metrics are available. We propose Generalization via Evolutionary Reward Shaping (GERS), a bilevel optimization approach to improve generalization on unseen test environments using only scalar feedback from validation environments. At the lower level, an RL agent guided via a reward function shaped by the upper level learns a policy on a limited set of training environments with accessible trajectory data; at the upper level, CMA-ES optimizes the reward shaping parameters to maximize the cumulative unshaped reward on separate validation environments for which trajectory access is unavailable. Results on continuous control tasks indicate that GERS outperforms the standard RL baseline on unseen test environments. GERS performance is comparable to DR, despite DR treating the combined set of training and validation environments of GERS as a single training set that requires trajectory access, whereas GERS cannot access validation trajectories. These results confirm that GERS effectively enhances generalization under restricted data access constraints.
Autoregressive video diffusion models enable streaming generation, opening the door to long-form synthesis, video world models, and interactive neural game engines. However, their core attention layers become a major bottleneck at inference time: as generation progresses, the KV cache grows, causing both increasing latency and escalating GPU memory, which in turn restricts usable temporal context and harms long-range consistency. In this work, we study redundancy in autoregressive video diffusion and identify three persistent sources: near-duplicate cached keys across frames, slowly evolving (largely semantic) queries/keys that make many attention computations redundant, and cross-attention over long prompts where only a small subset of tokens matters per frame. Building on these observations, we propose a unified, training-free attention framework (FAST-AR) for FAST-AutoRegressive diffusion, consisting of three components: TempCache compresses the KV cache via temporal correspondence to bound cache growth; AnnCA accelerates cross-attention by selecting frame-relevant prompt tokens using fast approximate nearest neighbor (ANN) matching; and AnnSA sparsifies self-attention by restricting each query to semantically matched keys, also using a lightweight ANN. Together, these modules reduce attention, compute, and memory and are compatible with existing autoregressive diffusion backbones and world models. Experiments demonstrate up to x5 - x10 end-to-end speedups while preserving near-identical visual quality and, crucially, maintaining stable throughput and nearly constant peak GPU memory usage over long rollouts, where prior methods progressively slow down and suffer from increasing memory usage.
Diffusion models are typically trained with objectives that focus on local denoising targets at individual time steps (or adjacent pairs), which do not enforce consistency between predictions along the denoising trajectory. This lack of cross-time consistency can degrade performance, especially for few-step samplers. We introduce a temporal difference (TD) objective that penalizes inconsistency of the model's multi-step progress along the denoising path. By reformulating the diffusion process as a Markov reward process and casting denoising as a policy evaluation problem in reinforcement learning, we derive a unified TD approach that applies to both discrete- and continuous-time diffusion formulations. We further propose a principled sample-based reweighting method that stabilizes training. Empirically, we show that using our TD training can significantly improve sample quality measured by FID, with stronger advantages when the number of sampling steps is small, highlighting its practical utility under low-computation-budget scenarios. We provide ablation studies to justify our design choices, including pairwise loss reweighting, regularization weight, and one-step stride. Overall, our TD approach can be a general drop-in that enforces cross-time consistency and improves generation quality across different diffusion generative models.
arXiv:2509.08629v2 Announce Type: replace-cross Abstract: We introduce the Cycle Walk, a new Markov chain Monte Carlo method for sampling distributions on balanced graph partitions, motivated by applications in political redistricting. The method operates on spanning forests and combines two types of updates: local "cycle" moves within districts and global moves that exchange population between adjacent districts while preserving balance constraints. This construction enables efficient Metropolis–Hastings correction while allowing proposals at multiple spatial scales. We show that the Cycle Walk naturally interpolates between existing approaches based on local updates and a class of global update methods derived from recombination (RECOM). Through a range of numerical experiments on synthetic graphs and real-world precinct data, we demonstrate that the Cycle Walk exhibits improved empirical convergence diagnostics for distributions that place weaker weight on spanning-tree counts, a regime that is challenging for existing methods. In particular, the algorithm remains effective when incorporating alternative compactness measures that more closely reflect policy-relevant criteria. These results suggest that the Cycle Walk provides a flexible and computationally efficient framework for sampling from a broader class of redistricting distributions than previously accessible with MCMC techniques.
Weakening of a major ocean-current system is causing temperatures to drop in a patch of the Atlantic Ocean. Weakening of a major ocean-current system is causing temperatures to drop in a patch of the Atlantic Ocean.
We develop an LLM-powered virtual population model that simulates demand for pricing decisions, in settings where products are described by rich unstructured information, such as text descriptions and images, and where decision makers need not only mean-demand predictions but also uncertainty estimates for counterfactual prices. Our model represents exposed customers as draws from a finite mixture of customer personas. For each persona, product, and candidate price, an LLM elicits a persona-level purchase probability using both structured persona information and unstructured product information. These probabilities are aggregated through calibrated mixture weights to form a predictive distribution of aggregate demand. The resulting simulator can evaluate counterfactual prices under various pricing objectives, including expected revenue and risk-aware criteria such as conditional value at risk. We test the framework on an online H&M fashion dataset with product descriptions and images. The calibrated LLM-based simulator achieves the best overall predictive performance among the models considered, and supports sample-efficient pricing decisions. Our framework provides a practical way to use LLMs as demand simulators for products with limited historical demand data but rich product information. By producing a full predictive demand distribution rather than only a point forecast, it enables managers to compare candidate prices, quantify demand uncertainty, and choose prices that target either average-case revenue or risk-aware objectives.
The decentralized deployment of LLM agents with diverse capabilities across diverse tasks motivates infrastructure for knowledge sharing across heterogeneous agent populations. Just as search engines index human-generated artifacts to support human problem solving, retrieval systems can organize agent-generated artifacts for reuse across agent populations. We extend retrieval-augmented generation - which demonstrates the value of human-authored artifacts to individual agents - to retrieval of agent-generated artifacts supporting a population of agents. In particular, agent trajectories encode reusable procedural knowledge, yet these artifacts are typically discarded after a single use or retained only by the producing agent, forcing newly instantiated agents to repeatedly rediscover existing solutions. We propose Multi-Agent Transactive Memory (MATM), a framework for population-level storage and retrieval of agent-generated trajectories, where producer agents contribute trajectories to a shared repository and consumer agents retrieve them to improve task execution. We focus on interactive environments (ALFWorld and WebArena), where trajectories are long and encode especially rich procedural structure. Our experiments demonstrate that retrieving trajectories from MATM improves downstream task performance and reduces interaction steps without coordination or joint training. These results position MATM as a design pattern for population-level experience sharing in open agent ecosystems.
arXiv:2604.16450v2 Announce Type: replace-cross Abstract: Intersectional biases in healthcare data can produce compound disparities in clinical machine learning models, yet most fairness evaluations assess demographic attributes independently. FairLogue, a toolkit for intersectional fairness auditing, was applied across multiple clinical prediction tasks to evaluate disparities across combined demographic groups. Using the All of Us dataset, two published models were selected for replication and evaluation: (A) prediction of selective serotonin reuptake inhibitor associated bleeding events and (B) two-year stroke risk in patients with atrial fibrillation. Observational fairness metrics were computed across race, gender, and intersectional subgroups, followed by counterfactual analysis to evaluate whether disparities were attributable to group membership. Intersectional evaluation revealed larger disparities than single-axis analyses; however, counterfactual diagnostics indicated that most observed disparities were comparable to those expected under randomized group membership. These results highlight the importance of intersectional fairness auditing and demonstrate how FairLogue provides deeper insight into bias in clinical machine learning systems.
arXiv:2606.12580v1 Announce Type: cross Abstract: Scalar fields provide perhaps the simplest playground in which to develop our understanding of quantum field theory. In this lecture, we consider what it means to write down a scalar quantum field theory and how we can give geometrical interpretations to the space of such theories: the theory space.
The best agent on WorkBench in March 2024, GPT-4, completed 43% of tasks and took an unintended harmful action, such as emailing the wrong person, on 26% of them. We re-visit the benchmark in June 2026 and find that the best agent to date, Claude Opus 4.8, completes 89% and takes an unintended harmful action on 2.5%. Aside from this considerable progress in frontier agent performance, three things stand out. First, capability and safety go together on WorkBench rather than trade off, so the models that finish the most tasks also do the least unintended damage. Second, while several classes of error have been totally eliminated, frontier models still make some basic mistakes that occasionally result in irreversible harm, such as sending an email to the wrong person. Third, the rise of open-weight models has drastically lowered costs for a performance level that was previously only accessible to proprietary models, while frontier costs have stayed relatively stable. We release an updated version of the benchmark with data and code quality improvements, new model scores, and analysis of agent progress on WorkBench since 2024.
arXiv:2606.16489v1 Announce Type: new Abstract: Model-based Reinforcement Learning (MBRL) has achieved remarkable success in continuous control by leveraging latent world models. However, prevailing approaches typically rely on monolithic latent dynamics, entangling environment dynamics into a coupled process. This coupling severely limits reusability: altering the agent necessitates retraining the entire world from scratch, even if the environment remains constant. To address this, we introduce BRICKS-WM (Building Reusability via Interface Composition Kinetics for Structured World Models), a framework for the modular assembly of structured world models. Driven by the insight that the physical world is composed of independent entities, we posit that global dynamics can be modeled as a composition of distinct dynamical modules interacting via latent interfaces. As a minimal instantiation, we factorize the latent state space into an actuated Agent module and an external Background module, bridged by a learned latent interface. Unlike prior object-centric methods that prioritize visual segmentation, BRICKS-WM enforces a functional separation in transition dynamics, ensuring that background dynamics remains agnostic to the agent's dynamics. Empirically, BRICKS-WM achieves control performance comparable to strong monolithic baselines when trained from scratch, and enables the reuse of frozen background dynamics across agents.
In this paper, we present a novel set of related models for semantic segmentation of node-link diagrams. These diagrams are frequently used to represent mathematical graphs, relationships between concepts, and flowcharts. Such diagrams are difficult to access non-visually; while some assistive interfaces have been designed for node-link diagrams, they rely upon a machine-readable representation of the diagram, whereas such diagrams will generally be made available as bitmap images. Our compact deep learning models show excellent quantitative and qualitative performance on a large synthetic dataset of node-link diagrams, reaching per-pixel accuracy over 93\%.