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01.
medRxiv (Medicine) 2026-06-23

Agentic Autodiscovery of Diastolic Dysfunction Phenotypes from Surface Electrocardiogram

Background: Left ventricular diastolic dysfunction (LVDD) is a major determinant of heart failure (HF), yet its assessment relies on multiparametric echocardiography, limiting scalability. We previously demonstrated that generative artificial intelligence (AI) can synthesize tissue Doppler imaging (TDI) waveforms from the 12-lead ECG. The growing complexity of candidate architecture creates a need for automated model-discovery frameworks. Objectives: To evaluate agentic AI-based auto-discovery for ECG-based LVDD assessment using either raw ECG or synthetic TDI waveforms. Methods: Two attention-based agentic AI architectures were developed using an automated large language model-driven refinement framework that optimized transfer-learning and multimodal architectures through autonomous proposal, validation, and selection of candidate model configurations. Development was performed in 1,011 paired ECG-echocardiography studies and externally validated in 983 patients using two reference frameworks: (i) data-driven phenogroups and (ii) the 2025 ASE Diastolic Function Guidelines. External validation was performed in CODE-15% (n=219,567) for HF-related mortality and EchoNext (n=35,718) for structural heart disease associations. Results: Despite the modest cohort size, the ECG-based agentic search achieved area under the receiver operating characteristic curve (AUCs) of 0.87 (95% CI: 0.85-0.89) and 0.83 (95% CI: 0.80-0.86) for phenogroup and guideline-based LVDD severity classification. Corresponding AUCs for the synthetic TDI-based model were 0.82 (95% CI: 0.80-0.85) and 0.80 (95% CI: 0.77-0.84), respectively. In large-scale external validation, both models stratified incident HF mortality with subdistribution hazard ratios ranging 5.5 to 9.5 (Gray's p

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

OGPO: Sample Efficient Full-Finetuning of Generative Control Policies

arXiv:2605.03065v2 Announce Type: replace Abstract: Generative control policies (GCPs), such as diffusion- and flow-based control policies, have emerged as effective parameterizations for robot learning. This work introduces Off-policy Generative Policy Optimization (OGPO), a sample-efficient algorithm for finetuning GCPs that maintains off-policy critic networks to maximize data reuse and propagate policy gradients through the full generative process of the policy via a modified PPO objective, using critics as the terminal reward. OGPO achieves state-of-the-art performance on manipulation tasks spanning multi-task settings, high-precision insertion, and dexterous control. To our knowledge, it is also the only method that can fine-tune poorly-initialized behavior cloning policies to near full task-success with no expert data in the online replay buffer, and does so with few task-specific hyperparameter tuning. Through extensive empirical investigations, we demonstrate that OGPO drastically outperforms methods alternatives on policy steering and learning residual corrections, and identify the key mechanisms behind its performance. We further introduce practical stabilization tricks, including success-buffer regularization, two-sided conservative advantages, and Q-variance reduction, to mitigate critic over-exploitation across state- and pixel-based settings. Beyond proposing OGPO, we conduct a systematic empirical study of GCP finetuning, identifying the stabilizing mechanisms and failure modes that govern successful off-policy full-policy improvement.

03.
arXiv (CS.LG) 2026-06-17

MorphStrata: Layer-Specific Perturbations for Generating Morphence Students in Time-Series Moving Target Defense

arXiv:2606.17435v1 Announce Type: new Abstract: Time-series forecasting models remain vulnerable to gradient-based adversarial attacks while existing defense mechanisms typically incur a trade-off in robustness for bounded response and compute cost. The problem is pronounced in Moving Target Defense where maintaining multiple randomized model instances substantially exacerbates the training overhead. In this work, we introduce MorphStrata, a student generation strategy with selective, layer-specific stochastic noise injection that extends the traditional Morphence defense. MorphStrata uses a Transformer backbone as the teacher and perturbs randomly selected architectural blocks to create structured heterogeneity across student models in response to varied data distributions and threat models. We evaluate against vanilla Transformer and Morphence backbones on a suite of benchmarks including the Jena Climate, Electricity Load Diagrams, and Appliances Energy Prediction using FGSM, BIM and PGD attacks across multiple attack strengths. Across datasets and attack regimes, the proposed ensemble maintains comparable adversarial RMSE. Specifically, for high entropy, periodic datasets as in the case of the AEP data, MorphStrata achieves the lowest RMSE across all attacks and perturbation budgets, improving over the static baseline by up to 24.11% and 97.97% under FGSM and BIM respectively at an epsilon value of 0.5 over 30 randomized trials. Targeting the layers to generate MorphStrata students accounts for less than 1% increase in train-times over the Morphence MTD baseline for most of the experiments, while accounting for double digit gains in adversarial RMSE reduction. We also observe a positive correlation between higher pairwise L2 distance (among generated students) and overall defense effectiveness. In summary, MorphStrata maintains adversarial robustness as an MTD defense at marginal cost deltas when compared to existing baselines.

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

Online Convex Optimization with Sublinear Noisy Probes

arXiv:2606.14640v1 Announce Type: new Abstract: We study Online Convex Optimization (OCO) over a convex set $K\subseteq \mathbb R^d$, where in each round $t$ the learner selects $x_t\in K$ and then observes a convex loss $f_t:K\to[0,1]$, with the goal of minimizing regret to the best fixed decision in hindsight. We introduce a unified probing model that generalizes two recent lines of work: sublinear best-expert queries in the experts setting, and pairwise (comparison-based) feedback available every round in OCO. In our framework, the learner has a budget of $k\le T$ pairwise probes; on a probed round it may query two points and learn which one has smaller loss. Our main result shows that even a sublinear and noisy probe budget can provably improve worst-case regret in the full feedback OCO regime. With $k$ $\delta$-noisy pairwise probes, we obtain: $ Reg_T \le O\left(\min\left\{\sqrt{dT\ln T},\; \frac{dT\ln T}{k|1-2\delta|}\right\}\right) $, which is tight (up to logarithmic factors in $T$) across $T$, $k$ and $\delta$. Specifically regarding the noise parameter $\delta \in [0,1]$, the regret guarantee smoothly degrades as the oracle response approaches a coin flip, i.e., $\delta$ is close to $\frac{1}{2}$. When applying the same techniques to a finite $K$ for the prediction with $d$ experts setting, the resulting rates are instead completely tight in all parameters, including $d$. Our analysis gives a streamlined treatment of pairwise probing in OCO by quantifying the benefit of probing via a variance reduction effect, combined with a second-order (variance-based) analysis of Continuous Exponential Weights.

05.
arXiv (CS.LG) 2026-06-19

MolGraphBench: A Benchmark of GNN Architectures for Molecular Regression Tasks

arXiv:2602.20573v3 Announce Type: replace Abstract: Molecules are often represented as SMILES strings, which can be readily converted to hand-crafted descriptors or fingerprints (FP) for molecular property prediction. Research has demonstrated that SMILES can be converted to molecular graphs $G = (V, E)$, with atoms as nodes $(V)$ and bonds as edges $(E)$. These molecular graphs can subsequently be used to train graph neural networks (GNN) models. Despite the recent surge in application of GNN (existing and novel architectures) for molecular property prediction, a rigorous benchmark is still lacking. We propose MolGraphBench, a comprehensive benchmark of four commonly used GNN models for molecular property prediction. Benchmarking results demonstrate graph convolutional network (GCN) and graph isomorphism networks (GIN) as the optimal GNN architectures for molecular graph regression tasks, based on absolute performance, training efficiency, transfer learning and prediction quality. The study also indicates the non-complementary nature of molecular fingerprints in the fusion (GNN-FP) framework. Furthermore, our GNN models achieved performance superior or comparable performance to current state-of-the-art GNN baselines across three datasets (GCN with RMSE of $0.518$ on B3DB, GIN-FP with RMSE of $1.022$ on FreeSolv and GIN with MAE of $63.783$ on RT datasets). Findings from this study indicate that type of GNN-layer, should be treated as a tunable hyperparameter rather than a fixed design choice to achieve superior performance.

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

Dressed Floquet scars from protected zero modes in a Rydberg chain

arXiv:2606.15605v1 Announce Type: cross Abstract: In this Letter, we present an approximate analytic construction of two zero quasienergy quantum many-body scars in a periodically driven model of Rydberg atoms on a ring, which persist over a range of driving amplitudes and frequencies for finite sizes. An index theorem protects an exponentially large number (in system size) of exact zero energy modes of the Floquet Hamiltonian in this setting. Unlike most of these zero modes which continuously change with drive parameters, these two quantum many-body scars retain the memory of particular states. They can be expressed as {\it dressed versions} of two contrasting states, the Rydberg vacuum and a unitarily rotated variant of a volume-law scar [Ivanov and Motrunich, Phys. Rev. Lett. {\bf 134}, 050403 (2025)], respectively. We provide an analytic understanding of their existence using a Floquet perturbation theory and show their resilience beyond the perturbative regime using exact diagonalization in finite systems. Our study provides insight into the structure of protected zero modes in interacting Floquet settings.

07.
arXiv (CS.LG) 2026-06-19

Tracking Representation Dynamics in Large Language Models with Persistent Homology

arXiv:2606.19542v1 Announce Type: new Abstract: Large language models are commonly aligned through supervised fine-tuning, yet little is known about how their internal representations evolve during this process. We study alignment dynamics using persistent homology by tracking the topology of activation spaces throughout fine-tuning. Across four transformer language models ranging from 1B to 7B parameters and three alignment objectives corresponding to helpful, harmless, and mixed training data, we find that the majority of topological reorganization occurs during the earliest stages of training. A dense checkpoint analysis reveals a transient peak in topological activity followed by rapid stabilization. We further show that different alignment objectives induce distinguishable topological trajectories, while instruction-tuned and pretrained models exhibit qualitatively different patterns of evolution. Our results suggest that persistent homology provides a complementary perspective on alignment, revealing representation-level changes that are not apparent from behavioral metrics alone.

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

Benchmarking Local LLMs for Natural-Language-to-SQL Querying in Biopharmaceutical Manufacturing: An Empirical Benchmark on Consumer-Grade Hardware

Biopharmaceutical manufacturing organizations operate under regulatory frameworks such as FDA guidance, EU Good Manufacturing Practice (GMP), and the EU AI Act, which can restrict the use of cloud-based artificial intelligence systems. Locally deployed large language models (LLMs) offer a privacy-preserving alternative, but their suitability for pharmaceutical manufacturing tasks remains underexplored. This study evaluates four open-source LLMs (Qwen 2.5 Coder 7B, Llama 3.1 8B, Mistral 7B, and Meditron 7B) deployed locally via Ollama for natural-language-to-SQL generation over a pharmaceutical manufacturing database. A FastAPI-based evaluation platform, PharmaBatchDB AI, was developed using a synthetic Microsoft SQL Server database containing approximately 63,000 records across Batch, Manufacturing Execution System (MES), and Clean-In-Place (CIP) modules. Models were benchmarked on 60 domain-specific natural-language questions using metrics including SQL extraction rate, SQL compliance, factual consistency, ROUGE-L, hallucination rate, throughput, and latency. Qwen 2.5 Coder 7B, Llama 3.1 8B, and Mistral 7B generated SQL for all evaluation tasks, while Meditron 7B failed on nearly all tasks due to context-window limitations and poor SQL generation capability. Llama 3.1 8B achieved the highest SQL compliance, whereas Qwen 2.5 Coder 7B achieved the strongest overall text similarity and factual consistency. Performance differences between the two leading models were not statistically significant. The results show that code-tuned general-purpose LLMs outperform a domain-specific biomedical model on structured query generation for pharmaceutical manufacturing data. Although fully local, GxP-aligned NLQ systems are feasible on consumer hardware, current performance levels still require human oversight and downstream validation for regulated use.

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

Emergent Strategic Reasoning Risks in AI: A Taxonomy-Driven Evaluation Framework

arXiv:2604.22119v2 Announce Type: replace Abstract: As reasoning capacity and deployment scope grow in tandem, large language models (LLMs) gain the capacity to engage in behaviors that serve their own objectives, a class of risks we term Emergent Strategic Reasoning Risks (ESRRs). These include, but are not limited to, deception (intentionally misleading users or evaluators), evaluation gaming (strategically manipulating performance during safety testing), and reward hacking (exploiting misspecified objectives). Systematically understanding and benchmarking these risks remains an open challenge. To address this gap, we introduce ESRRSim, a taxonomy-driven agentic framework for automated behavioral risk evaluation. We construct an extensible risk taxonomy of 7 categories, which is decomposed into 20 subcategories. ESRRSim generates evaluation scenarios designed to elicit faithful reasoning, paired with dual rubrics assessing both model responses and reasoning traces, in a judge-agnostic and scalable architecture. Evaluation across 11 reasoning LLMs reveals substantial variation in risk profiles (detection rates ranging 14.45%-72.72%), with dramatic generational improvements suggesting models may increasingly recognize and adapt to evaluation contexts.

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

NetBurst: Event-Centric Forecasting of Bursty, Intermittent Time Series

arXiv:2510.22397v2 Announce Type: replace-cross Abstract: Network operators monitor their infrastructure by collecting telemetry data such as packet counts, byte rates, or flow volumes, yet answering the questions that effective operations demand – forecasting future load, diagnosing and characterizing anomalies, and searching for and retrieving historical precedents – requires more than raw measurements. Bridging this gap calls for learned representations: compact per-entity summaries that capture temporal dynamics from each entity's univariate time series. Time-series foundation models are the natural starting point, but they are designed for dense, periodic benchmark datasets – the mild statistical regime. However, network telemetry data inhabits the wild regime: operationally relevant events are rare, separated by variable-length stretches of low or no activity (``ebbs''), with intermittent bursts of heavy-tailed extremes (``tides''). We present NetBurst, an event-centric pipeline that collapses ebbs, separates each time series into a stream of burst timings and a stream of burst magnitudes, and learns a single representation serving all three operational tasks. Compared to the strongest competitors among eight baselines – including Amazon's Chronos-2 and Datadog's Toto – and across nine production telemetry configurations, NetBurst reduces median forecasting error by $1.3$–$116\times$ on wild-regime data with a $1.0$–$7.5\times$ better match to the true burst distribution, and matches baselines on mild-regime benchmarks. For characterizing anomalies, NetBurst produces balanced, well-spread clusters that are $16\times$ more describable in operator-familiar terms under a novel interpretability score, and cluster-filtered search delivers $7.5\times$ faster end-to-end retrieval.

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

Information Leakage Detection through Approximate Bayes-optimal Prediction

arXiv:2401.14283v4 Announce Type: replace-cross Abstract: In today's data-driven world, the proliferation of publicly available information raises security concerns due to the information leakage (IL) problem. IL involves unintentionally exposing sensitive information to unauthorized parties via observable system information. Conventional statistical approaches rely on estimating mutual information (MI) between observable and secret information for detecting ILs, face challenges of the curse of dimensionality, convergence, computational complexity, and MI misestimation. Though effective, emerging supervised machine learning based approaches to detect ILs are limited to binary system sensitive information and lack a comprehensive framework. To address these limitations, we establish a theoretical framework using statistical learning theory and information theory to quantify and detect IL accurately. Using automated machine learning, we demonstrate that MI can be accurately estimated by approximating the typically unknown Bayes predictor's log-loss and accuracy. Based on this, we show how MI can effectively be estimated to detect ILs. Our method performs superior to state-of-the-art baselines in an empirical study considering synthetic and real-world OpenSSL TLS server datasets.

12.
bioRxiv (Bioinfo) 2026-06-11

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

13.
arXiv (CS.AI) 2026-06-17

Dissecting model behavior through agent trajectories

arXiv:2606.17454v1 Announce Type: new Abstract: AI agent performance is not just a modeling problem, it is fundamentally a systems problem. The advanced capabilities of models are realized through agent harnesses. Therefore, a gap between model assumptions and harness behavior can easily prevent the model's full capabilities from translating into agent performance. We formalize this as the `intent-execution' gap: the mismatch between what the model intends and what the harness executes, and vice versa. We argue that minimizing this intent-execution gap is as important as other aspects of harness design such as tools and execution loops. To illustrate the impact of this harness-model alignment, we develop a simple and customizable harness called `Simple Strands Agent' (SSA). SSA aims to find the bulk of common patterns which generalize across different model families (such as Claude, Gemini, GPT, Grok, Qwen), as well as a small number of model-specific preferences. We make two contributions: (i) we $reproduce or improve on the pass@1$ performance reported by diverse model-provider families on popular agentic benchmarks (SWE-Pro, SWE-Verified and Terminal-Bench-2), and (ii) building on an $analysis of 138k trajectories generated by SSA$, we look beyond the $\texttt{pass@1}$ numbers which tend to be relatively even across frontier models. By representing agent trajectories in code state-spaces, we observe model-level differences in problem-solving behavior. Finer-grained metrics such as edit frequency, testing activity, and phase-transitions reveal how individual models allocate effort across different stages of autonomous problem solving.

14.
arXiv (quant-ph) 2026-06-19

Quantum correlations in QBism's reconstruction program

arXiv:2606.07485v2 Announce Type: replace Abstract: QBism recasts quantum theory as a normative framework for an agent's probability assignments, with the Born rule taking the form of a consistency condition known as the Urgleichung. Motivated by this perspective, qplex theories provide a broader class of probabilistic models in which the sets of valid states and measurements are constrained by QBist-inspired geometric conditions. While qplexes have been extensively studied for single systems, their implications for bipartite correlations remain largely unexplored. In this work, we investigate bipartite correlations in qplex theories by expressing joint expectation values as inner products between suitably defined $C$-vectors. This geometric formulation allows Bell-type inequalities to be studied as optimization problems over qplex-compatible probability assignments. We first analyze the CHSH scenario and show that the shared inner-product structure of the $C$-vectors restricts the maximal value to the Tsirelson bound $2\sqrt{2}$. We then turn to the three-outcome CGLMP inequality $I_{2233}$ and find that the same qplex-derived norm and inner-product constraints allow a violation of up to $\leq 2+2\sqrt(3)/3 \approx 3.1547$ versus the quantum maximum of $\approx 2.8729$, thereby exhibiting super-quantum correlations. These results show that qplex geometry captures enough structure to reproduce an important quantum bound in the two-outcome case, but not enough to recover the full set of quantum correlation constraints. The analysis therefore suggests that additional principles are needed to complete the QBist reconstruction of quantum theory.

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

SHARD: Safe and Helpful Alignment via Self-Reframing Distillation

Large language models often struggle with sensitive prompts. They may refuse outright, provide generic safety boilerplate, or fail to address the user's legitimate informational needs that can be answered safely. We introduce SHARD, a self-reframing distillation method to improve safe-helpfulness. It first rewrites sensitive prompts to surface benign intent using philosophical guidelines, then reframes its original responses into safe, more helpful ones, and finally fine-tunes the model on its self-reframed responses. Across DNA and the English subset of LINGUASAFE, SHARD improves helpfulness for most model families while preserving safety. It also remains competitive with distillation from a larger teacher model, suggesting that models can internalize safe and helpful behavior elicited from their own. Warning: This paper contains content that may be offensive or harmful.

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

MolSight: Molecular Property Prediction with Images

Every molecule ever synthesised can be drawn as a 2D skeletal diagram, yet in modern property prediction this universally available representation has received less focus in favour of molecular graphs, 3D conformers, or billion-parameter language models, each imposing its own computational and data-engineering overhead. We present $MolSight$, the first systematic large-scale study of vision-based Molecular Property Prediction (MPP). Using 10 vision architectures, 7 pre-training strategies, and $2\,M$ molecule images, we evaluate performance across 10 downstream tasks spanning physical-property regression, drug-discovery classification, and quantum-chemistry prediction. To account for the wide variation in structural complexity across pre-training molecules, we further propose a $chemistry-informed curriculum$: five structural complexity descriptors partition the corpus into five tiers of increasing chemical difficulty, consistently outperforming non-curriculum baselines. We show that a single rendered bond-line image, processed by a vision encoder, is sufficient for competitive molecular property prediction, i.e. $chemical insight from sight alone$. The best curriculum-trained configuration achieves the top result on $5 of 10$ benchmarks and top two on $all 10$, at $$80$\times$ lower$$ FLOPs than the nearest multi-modal competitor.

17.
arXiv (CS.LG) 2026-06-19

Low-Energy Reduced RISC-V Instruction Subset Processor for Tsetlin Machine Inference at the Edge

arXiv:2606.19964v1 Announce Type: new Abstract: Tsetlin Machine (TM) is a logic-based machine learning approach that relies on simple bitwise operations and finite-state automata, which makes it attractive for edge AI deployments. Recent work has focused on co-processor and accelerator designs based on Tsetlin Machines (TMs). Although these designs achieve high performance, they typically depend on tightly coupled interfaces, microcode-style programming, and external host processors, limiting flexibility and ease of programming. In this work, we present a domain-specific RISC-V microprocessor architecture and design flow tailored for TM inference. Leveraging the modular structure of RISC-V, we design a reduced instruction subset processor that retains programmability while targeting improved performance and lower energy consumption for TM workloads. Instruction profiling is employed to guide instruction reduction, followed by datapath and control path simplifications tailored to TM inference. Both the baseline RV32IM core and the proposed reduced core are evaluated across multiple datasets and compared with Binarized Neural Networks (BNNs), which serve as a hardware-efficient baseline due to their reliance on bitwise operations during inference. Results show that TM achieves comparable or higher accuracy (e.g., up to 88.18% on CIFAR-2 compared to 60.0% for BNN) while reducing execution time by up to 98% across multiple datasets. Furthermore, the proposed design achieves an average $29.7\times$ reduction in energy consumption, demonstrating its effectiveness for programmable and efficient edge AI systems.

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

Neural ARFIMA model for forecasting BRIC exchange rates with long memory

arXiv:2509.06697v3 Announce Type: replace-cross Abstract: Exchange rate forecasting remains a challenging problem, particularly for emerging economies, where the observed time series exhibit pronounced long-memory dependence, nonlinear dynamics, and sensitivity to macro-financial drivers. Classical models such as ARFIMA capture long-range persistence but fail to adequately represent nonlinear relationships, while modern machine learning approaches often neglect the underlying long-memory structure in macroeconomic series. To address this gap, we propose a Neural AutoRegressive Fractionally Integrated Moving Average (NARFIMA) model that integrates ARFIMA-based long-memory modeling with neural networks for nonlinear function approximation, while incorporating exogenous macroeconomic and uncertainty indicators. The framework provides a unified approach for capturing persistence, nonlinear dynamics, and external shocks. We establish asymptotic stationarity of the NARFIMA process and develop conformal prediction intervals for distribution-free uncertainty quantification. Empirical results for BRIC exchange rates show that NARFIMA consistently outperforms a broad range of forecasting benchmarks across multiple horizons, underscoring the importance of explicitly modeling long-memory dependence in exchange rate dynamics. The `narfima' R package provides an implementation of our approach.

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

MegaFold: Efficient Training of Next-Generation 3D Attention Protein Models on Cross-Platform GPUs

arXiv:2506.20686v2 Announce Type: replace-cross Abstract: Recent advances in biomolecular modeling have been catalyzed by models such as AlphaFold3 (AF3), which introduce science-informed changes to the transformer architecture. Unlike transformers, a defining characteristic of AF3-style models is their 3D attention over 2D pairwise representations which produces tensors whose computation and memory costs scale cubically with sequence length. As a result, despite moderate parameter counts, AF3-style models are far more expensive to train than size-equivalent transformers, and are severely constrained by GPU memory capacity. Our characterization shows 3D attention fundamentally changes the training workload, causing massive 3D attention maps, complex inter-operator dependencies, kernel fragmentation, and heavy host-side data pipelines which differ substantially from LLM training, leading to poor utilization on modern GPU systems. Moreover, existing GPU optimizations do not adequately address these challenges due to complex cross-layer inter-operator dependencies introduced by 3D attention. Motivated by these challenges, we introduce MegaFold, a novel cross-platform system for efficient training of next-generation 3D-attention protein models. MegaFold combines a memory-efficient 3D-attention kernel, a communication-efficient sharding strategy for quadratic representations, fused operator implementations for critical execution paths, and a determinism-aware host-device pipeline that eliminates preprocessing stalls. Evaluation on both NVIDIA H200 and AMD MI250 GPUs shows that MegaFold enables training with up to 3.36$\times$ longer sequence lengths on 32 GPUs while reducing end-to-end execution time by up to 1.73$\times$ (NVIDIA) and 1.62$\times$ (AMD).

20.
medRxiv (Medicine) 2026-06-15

Nocturnal Respiratory Rate and Variability Predict Long-term Mortality in Stable Outpatients with Cardiovascular Disease

Background: Respiratory rate (RR) predicts short-term mortality in acute care settings, yet its prognostic significance in clinically stable outpatients remains poorly defined. Objectives: To determine whether the median and variability of nocturnal respiratory rate (NRR) are independently associated with long-term cardiovascular and all-cause mortality in outpatients with cardiovascular disease. Methods: We analyzed overnight chest belt waveforms from elective polysomnography in 5,679 older adults with cardiovascular disease enrolled in the Sleep Heart Health Study (SHHS). NRR was quantified at 30-second resolution, and per-subject median NRR and within-night variability (standard deviation) were derived. Kaplan-Meier survival analysis and Cox proportional hazards models were used to evaluate associations with cardiovascular and all-cause mortality over 3-year and 15-year follow-up periods, adjusting for demographic characteristics, cardiopulmonary comorbidities, and sleep apnea severity. Results: Higher median NRR and greater NRR variability were each associated with increased cardiovascular and all-cause mortality. Combining these metrics identified a high-risk group characterized by elevated median and high variability of NRR, with approximately five-fold higher 3-year all-cause mortality compared with a low-risk group; this association remained significant in Cox models (unadjusted HR: 2.61; 95% CI: 1.65, 4.14; p

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

Beyond Prediction: Tail-Aware Scheduling for LLM Inference

arXiv:2606.18431v1 Announce Type: new Abstract: LLM serving exhibits extreme length variability, making size-based scheduling difficult in practice. Recent LLM schedulers approximate SJF/SRPT using predicted decode lengths or ranks and primarily report mean-centric metrics such as TTFT and TBT. We show that these prediction-driven policies can be fragile under distribution shifts, bursty arrivals, and GPU memory pressure, while offering limited control over the tail latency (P90-P99) that dominates user experience, even with perfect decode-length knowledge. We introduce a distribution-aware, prediction-free scheduling framework that replaces explicit length prediction with soft priority boosting driven by lightweight statistical signals. Our design co-optimizes scheduling and cache-aware preemption to account for memory-coupled decode dynamics across workload mixes. Evaluated on production and open-source traces, our method reduces P99 TTLT by up to 35-50% relative to SRPT with perfect length knowledge and reduces TTFT by 34-47% across workloads, including reasoning-heavy and chat-heavy tasks. These results demonstrate a robust alternative for optimizing tail latency in online LLM serving.

22.
medRxiv (Medicine) 2026-06-11

Foundation model-based tool for automated ulcerative colitis histology scoring demonstrates non-inferiority to pathologists across multiple scoring indices

In clinical trials for ulcerative colitis (UC), pathologists assess disease severity through standardized histological indices, including the Geboes Score, Robarts Histopathology Index (RHI), and Nancy Histologic Index (NHI). Despite strong associations with clinical outcomes, histologic scoring suffers from inter- and intra-reader variability, and consensus criteria for histologic remission remain uncertain. Through a consortium approach, we developed an artificial intelligence-based measurement (AIM) tool for scoring histology in UC mucosal biopsies (AIM-HI UC). This model, trained on a large dataset of UC biopsies (N=10,230), utilizes additive multiple instance learning models leveraging PLUTO, a pathology foundation model, that predict each of the Geboes subgrades, from which the Geboes grade-level score, RHI, and NHI can be calculated. Evaluation of this model on a standalone verification set including clinical trial specimens established algorithm non-inferiority and/or superiority relative to standard qualified pathologists through comparison of algorithm-consensus and pathologist-consensus agreement metrics (non-inferior if difference >-0.1, superior if difference >0, inclusive of confidence intervals). AIM-HI UC was determined to be non-inferior to pathologists (N=3) for the prediction of all seven Geboes subgrades, grade-level Geboes, RHI, NHI, histologic improvement (GS

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

Bergson: An Open Source Library for Data Attribution

arXiv:2606.11660v1 Announce Type: new Abstract: Data attribution is a promising field in interpretability that aims to explain model behavior through the influence of its training data, with applications including debugging undesirable model behavior and training dataset curation. However, significant engineering effort is required to perform it at scale, and many cutting edge techniques lack open-source tooling and support. Bergson is an open source library that aims to enable faster progress in the field by providing a host of techniques that scale to very large language models and pre-training datasets. The library natively supports on-disk gradient stores and multi-node distributed training, and provides quality of life tools for researchers. Finally, we introduce the first open-source implementations of three leading data attribution methods: MAGIC, SOURCE, and TrackStar. The library is available at https://github.com/EleutherAI/bergson .

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

FinBalance: A Multi-Document Accounting Reconciliation Benchmark

Existing financial-NLP benchmarks mostly evaluate prepared artifacts such as filings, tables, or extracted values. Real accounting begins earlier: source documents must be reconciled into cited journal entries, aggregated into a balance sheet, and checked for contradictions. We introduce FinBalance, a multi-document accounting reconciliation benchmark built from source-document bundles across eight industries, three period types, and five difficulty levels. Human-authored business scenarios, accounting policies, tax/FX treatments, document schemas, distractors, and inconsistency templates are composed by a deterministic generator whose ledger produces journal entries,balance sheets, and 23 inconsistency-code labels. On a 710-record evaluation split, six contemporary LLMs reach at most 46% exact final-balance-sheet accuracy. Four models show a 26-41 pp gap between BS_exact, the model's reported balance sheet, and BS_recon, the balance sheet obtained by replaying its entries through our ledger. Models often recover numerically plausible entries but fail to bind them to supporting documents and aggregate them consistently. Citation-pressure prompting barely changes document-linking errors, while ledger-feedback ablations substantially improve reported balance sheets and expose inconsistency-detection trade-offs. Expert finance reviewers validate the benchmark design and labels.

25.
arXiv (CS.LG) 2026-06-19

Stabilizing Bandits using Regularization: Precise Regret and A Quantitative Central Limit Theorem

arXiv:2603.10184v2 Announce Type: replace-cross Abstract: Statistical inference with bandit data presents fundamental challenges owing to adaptive sampling, which violates the independence assumptions underlying classical asymptotic theory. Recent work has identified stability~\citep{laiwei82} as a sufficient condition for valid inference under adaptivity. This paper first provides a refined stability condition, stated in terms of the iterates of an online algorithm, and shows that a large class of regularized stochastic-mirror-descent-style algorithms satisfy it. This refined condition allows us to strengthen the asymptotic results of~\citet{laiwei82} in several ways. First, we derive a non-asymptotic Berry–Esseen bound for the empirical reward estimates under adaptive sampling. Second, we derive matching non-asymptotic upper and lower bounds on the regret of the proposed algorithm, yielding a precise characterization of its regret. Third, we show that these regularized algorithms preserve asymptotic normality and valid inference under a prescribed level of adversarial corruption. Finally, we show that regularization is necessary rather than incidental: Lai–Wei stability is incompatible with the optimal $O(\sqrt{T})$ regret rate – the rate attained by unregularized algorithms such as EXP3 – so that a controlled, polylogarithmic inflation in regret is the price of valid inference.