arXiv:2605.15617v1 Announce Type: new
Abstract: Large language model (LLM) training today runs on clusters spanning thousands of GPUs. While this scale enables rapid model advances, developing, debugging, and performance-tuning the training framework inevitably becomes complex and costly. This is because engineers often need to reproduce production behaviors to diagnose failures or evaluate optimizations, thereby demanding frequent and even exclusive access to production-scale clusters -- which becomes increasingly hard given that the majority of GPUs are already committed to production workloads. Simulation relies on complex performance models that are difficult to maintain, and downscaled experiments often fail to capture scale-dependent behaviors.
We present PrismLLM to decouple large-scale execution from the need to access large clusters, enabling engineers to run and observe ranks of interest under faithful large-scale behavior using only a few GPUs. PrismLLM constructs a high-fidelity execution graph via a slicing-based approach that captures computation, communication, and dependencies of the target scale. Then, PrismLLM performs hybrid emulation where selected ranks execute the original program while the remaining ranks are replayed as virtual participants.
Experiments on large-scale LLM training workloads show that PrismLLM accurately reproduces performance and memory behavior, achieving only 0.58\% average error in iteration time and less than 0.01\% error in peak GPU memory usage. PrismLLM can emulate clusters of up to 8192 GPUs using fewer than 1\% of the physical GPUs required by the original deployment.
Science Journals
arXiv:2605.15592v1 Announce Type: new
Abstract: Few-step image generation has seen rapid progress, with consistency and meanflow-based methods significantly reducing the number of sampling steps. Despite their low inference cost, these approaches often suffer from training instability and limited scalability. Sphere Encoder is a recent alternative that produces high-quality images in only a few steps; however, it requires repeated transitions between the pixel space and latent space during inference while jointly optimizing reconstruction and generation within a single architecture. This design leads to computational inefficiency and objective conflict between reconstruction and generation. To address these limitations, we decouple the framework into a fixed pretrained image encoder and a separate latent denoising model trained entirely in a spherical latent space. Our approach eliminates repeated pixel-space operations during training and inference, improving efficiency and allowing reconstruction and generation to specialize independently. On Animal-Faces, Oxford-Flowers and ImageNet-1K datasets, our method significantly outperforms Sphere Encoder in both generation quality and inference speed, while achieving competitive results against strong few-step and multi-step baselines.
arXiv:2605.06475v1 Announce Type: cross
Abstract: We introduce a probabilistic approach for dating historical manuscript pages from visual features alone. Instead of aggregating centuries into classes as is standard in the previous literature, we pose dating as an evidential deep regression problem over a continuous year axis, allowing our neural network to output a full predictive distribution with decomposed aleatoric and epistemic uncertainty in a single forward pass. Our architecture combines an EfficientNet-B2 backbone with a Normal-Inverse-Gamma (NIG) output head trained with a joint negative-log-likelihood and evidence-regularization objective. On the DIVA-HisDB benchmark (150 pages, 3 medieval codices, 151,936 patches), our model scores a test MAE of 5.4 years, well below the 50-year century-label supervision granularity, with 93\% of patches within 5 years and 97\% within 10 years. Our approach achieves \textbf{PICP=92.6\%}, the best calibration among all compared methods, in a single forward pass, outperforming MC Dropout (PICP=88.2\%, 50 passes) and Deep Ensembles (PICP=79.7\%, 5 models) at $5\times$ lower inference cost. Uncertainty decomposition shows aleatoric uncertainty is a strong predictor of dating error (Spearman $\rho=0.729$), and a selective prediction about the most certain 20\% of patches can provide \textbf{0.5 years MAE}. We show that predicted uncertainty increases as image degradation worsens, spatial decomposition maps explain which script regions cause aleatoric uncertainty, and page-level aggregation reduces MAE to 4.5 years with $\rho=0.905$ between uncertainty and page-level error.
arXiv:2511.14282v2 Announce Type: replace
Abstract: Deep neural networks achieve outstanding performance across vision and language tasks, yet their large parameter counts limit deployment in resource-constrained settings. One-shot pruning reduces model size without retraining, but models trained with standard objectives often suffer substantial accuracy drops under aggressive sparsity. Prior work mitigates this drop along two directions: regularizers such as $\ell_1$ and DeepHoyer that shape the weight distribution during training, and pruning-robust optimizers such as SAM, CrAM, and S$^2$SAM that flatten the loss landscape. However, existing regularizers either shrink all weights uniformly ($\ell_1$) or induce scale-invariant sparsity (DeepHoyer), without concentrating weight energy onto a small set of informative parameters. We propose a Weight Concentration Regularizer (WCR), a training-time regularizer that amplifies the magnitude of a small subset of parameters while driving the remainder toward zero, so that magnitude pruning predominantly removes parameters with negligible functional contribution. We provide a convergence analysis and evaluate WCR on LLM fine-tuning, image classification, and medical segmentation, demonstrating consistent improvements in pruning robustness across architectures and compatibility with existing pruning-robust optimizers.
arXiv:2504.09544v3 Announce Type: replace
Abstract: Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only learn from images, despite many screens being inherently multimodal, as they involve both a chemical or genetic perturbation as well as an image-based readout. We hypothesized that incorporating chemical compound structures during self-supervised pre-training could improve learned representations of images from high-throughput microscopy screens. We introduce a representation learning framework, MICON (Molecular-Image Contrastive Learning), that models chemical compounds as treatments that induce transformations of cell phenotypes. MICON significantly outperforms classical hand-crafted features such as CellProfiler and existing deep-learning-based representation learning methods in challenging evaluation settings where models must identify reproducible effects of drugs across independent replicates and data-generating centers. We demonstrate that incorporating chemical compound information into the learning process provides small, but consistent improvements in performance and that modeling compounds specifically as treatments outperforms approaches that directly align images and compounds in a single representation space. Our findings point to a new direction for representation learning in morphological profiling, suggesting that methods should explicitly account for the multimodal nature of microscopy screening data.
arXiv:2605.15699v1 Announce Type: new
Abstract: A defining feature of the present-day global overturning circulation (GOC) is the absence of deep water formation in the Pacific, in contrast to the Atlantic. This asymmetry, associated with higher surface salinities in the North Atlantic, is reflected in the Atlantic Meridional Overturning Circulation (AMOC) and the lack of a Pacific overturning (PMOC). A commonly cited explanation is the asymmetry in surface freshwater fluxes, with the Pacific receiving more freshwater per unit area than the Atlantic. Here, we develop a two-basin conceptual ocean model, consisting of a wide and a narrow basin. The model admits three states: sinking confined to the narrow basin, sinking confined to the wide basin, and sinking in both basins. We analyze the (co-)existence of these states as a function of freshwater asymmetry and hydrological cycle strength, defined as the longitudinally symmetric freshwater flux. For a weak hydrological cycle, representative of warm Pliocene-like climate conditions, sinking occurs in both basins, with symmetry breaking only when one basin is sufficiently more evaporative. For intermediate conditions, representative of the present-day climate, the basin with slightly stronger evaporation tends to host sinking, with a stronger preference in the narrow basin. For a strong hydrological cycle, single-basin sinking states are preferred, although a large interbasin freshwater asymmetry is required to uniquely localize sinking. These results provide insight into GOC sinking configurations under past, present, and potential future climates, and show good agreement with a three-dimensional global circulation model.
arXiv:2510.10454v2 Announce Type: replace
Abstract: Large language models (LLMs) offer a generalizable approach for modeling patient trajectories, but suffer from the long and noisy nature of electronic health records (EHR) data in temporal reasoning. To address these challenges, we introduce Traj-CoA, a multi-agent system involving chain-of-agents for patient trajectory modeling. Traj-CoA employs a chain of worker agents to process EHR data in manageable chunks sequentially, distilling critical events into a shared long-term memory module, EHRMem, to reduce noise and preserve a comprehensive timeline. A final manager agent synthesizes the worker agents' summary and the extracted timeline in EHRMem to make predictions. In a zero-shot one-year lung cancer risk prediction task based on five-year EHR data, Traj-CoA outperforms baselines of four categories. Analysis reveals that Traj-CoA exhibits clinically aligned temporal reasoning, establishing it as a promisingly robust and generalizable approach for modeling complex patient trajectories. Implementation of Traj-CoA is available on https://github.com/zengsihang/Traj-CoA.
arXiv:2512.04745v3 Announce Type: replace-cross
Abstract: The ability to flexibly compose previously acquired skills to execute intelligent behaviors is a hallmark of natural intelligence. Such compositional flexibility is often attributed to context-dependent gating mechanisms that determine how multiple policies or behavioral primitives are combined. Yet, despite remarkable efforts, the normative objective from which such gating rules should arise, and the neural computations capable of implementing them, remain unclear. Existing approaches typically rely on prespecified design choices for the gating rules, and remain tied to specific architectures, learning paradigms, or datasets. Here, we introduce a normative framework in which policy composition emerges from the minimization of a variational free energy, providing a principled and broadly applicable objective for gating. Based on this framework, we derive a continuous-time gradient flow whose trajectories are guaranteed to converge, with explicit rate, to the optimal composition of primitives. We further show that this dynamics admits a mechanistic neural implementation as a soft-competitive recurrent circuit with context-sensitive local interactions. We evaluate the model on emerging flocking behaviors in multi-agent systems, human decision-making in bandit tasks, and control benchmarks in layered architectures. Across these settings, the model provides interpretable mechanistic accounts of policy composition, reproduces key behavioral signatures, yields insights into data, and matches or outperforms established models.
arXiv:2605.02651v2 Announce Type: replace
Abstract: Scientific peer review increasingly struggles to assess reproducibility at the scale and complexity of modern research output. Evaluating reproducibility requires reconstructing experimental dependencies, methodological choices, data flows, and result-generating procedures, which often exceeds what human reviewers can provide. Agentic Reproducibility Assessment (ARA) formalizes reproducibility assessment as a structured reasoning task over scientific documents. Given a paper, ARA extracts a directed workflow graph linking sources, methods, experiments, and outputs, then evaluates its reconstructability using structural and content-based scores for reproducibility assessments. Experiments on 213 ReScience C articles - the largest cross-domain benchmark of human-validated computational reproducibility studies considered to date - demonstrate ARA's generalizability and consistent workflow reconstruction and assessment across LLMs, model temperatures, and scientific domains. ARA achieves ~61% accuracy on three benchmarks, and the highest accuracy reported on ReproBench (60.71% vs. 36.84%) and GoldStandardDB (61.68% vs. 43.56%), highlighting its potential to complement human review at scale and enabling next-generation peer review. Code and Data available: https://github.com/AndresLaverdeMarin/agentic_reproducibility_assessment.
arXiv:2604.04539v2 Announce Type: replace
Abstract: Reinforcement learning (RL) is a core approach for robot control when expert demonstrations are unavailable. On-policy methods such as Proximal Policy Optimization (PPO) are widely used for their stability, but their reliance on narrowly distributed on-policy data limits accurate policy evaluation in high-dimensional state and action spaces. Off-policy methods can overcome this limitation by learning from a broader state-action distribution, yet suffer from slow convergence and instability, as fitting a value function over diverse data requires many gradient updates, causing critic errors to accumulate through bootstrapping. We present FlashSAC, a fast and stable off-policy RL algorithm built on Soft Actor-Critic. Motivated by scaling laws observed in supervised learning, FlashSAC sharply reduces gradient updates while compensating with larger models and higher data throughput. To maintain stability at increased scale, FlashSAC explicitly bounds weight, feature, and gradient norms, curbing critic error accumulation. Across over 60 tasks in 10 simulators, FlashSAC consistently outperforms PPO and strong off-policy baselines in both final performance and training efficiency, with the largest gains on high-dimensional tasks such as dexterous manipulation. In sim-to-real humanoid locomotion, FlashSAC reduces training time from hours to minutes, demonstrating the promise of off-policy RL for sim-to-real transfer.
arXiv:2605.09869v2 Announce Type: replace
Abstract: Zero-shot object navigation has advanced rapidly with open-vocabulary detectors, image--text models, and language-guided exploration. However, even after current methods detect a plausible target hypothesis, the agent may still oscillate between exploration and pursuit, or abandon the object near success. We identify this failure mode as an action consistency gap: semantic evidence is repeatedly reinterpreted at each step without persistent commitment across the episode. We introduce ConsistNav, a training-free zero-shot ObjectNav framework built around a semantic executive composed of three coordinated modules: Finite-State Executive Controller stages target pursuit through guarded semantic phases; Persistent Candidate Memory accumulates cross-frame target evidence into stable object hypotheses; and Stability-Aware Action Control suppresses rotational stagnation, ineffective pursuit, and unverified stopping. This design changes neither the detector nor the low-level planner; instead, it controls when semantic evidence should influence navigation and when it should be suppressed or revisited. We conduct extensive experiments on HM3D and MP3D, where ConsistNav achieves state-of-the-art results among compared zero-shot ObjectNav methods and improves SR by 11.4% and SPL by 7.9% over the controlled baseline on MP3D. Ablation studies and real-world deployment experiments further demonstrate the effectiveness and robustness of the proposed executive mechanism.
arXiv:2605.01970v3 Announce Type: replace
Abstract: Memory systems enable otherwise-stateless LLM agents to persist user information across sessions, but also introduce a new attack surface. We characterize the Trojan Hippo attack, a class of persistent memory attacks that operates in a more realistic threat model than prior memory poisoning work: the attacker plants a dormant payload into an agent's long-term memory via a single untrusted tool call (e.g., a crafted email), which activates only when the user later discusses sensitive topics such as finance, health, or identity, and exfiltrates high-value personal data to the attacker.
While anecdotal demonstrations of such attacks have appeared against deployed systems, no prior work systematically evaluates them across heterogeneous memory architectures and defenses. We introduce a dynamic evaluation framework comprising two components: (1) an OpenEvolve-based adaptive red-teaming benchmark that stress-tests defenses and memory backends against continuously refined attacks, and (2) the first capability-aware security/utility analysis for persistent memory systems, enabling principled reasoning about defense deployment across different usage profiles.
Instantiated on an email assistant across four memory backends (explicit tool memory, agentic memory, RAG, and sliding-window context), Trojan Hippo achieves up to 85-100% ASR against current frontier models from OpenAI and Google, with planted memories successfully activating even after 100 benign sessions. We evaluate four memory-system defenses inspired by basic security principles, finding they substantially reduce attack success rates (to as low as 0-5%), though at utility costs that vary widely with task requirements. Because of this substantial security-utility tradeoff, the effective real-world deployment of defenses remains an open challenge, which our evaluation framework is specifically designed to address.
arXiv:2605.16058v1 Announce Type: new
Abstract: In the era of big data, effectively compressing large datasets while performing complex mathematical operations is crucial. Tensor-based decomposition methods have shown superior compression capabilities with minimal loss of accuracy compared to traditional matrix methods. Under the star-M tensor framework, tensors can be decomposed in a matrix-mimetic way, including using the star-M SVD. This tensor SVD has optimality guarantees and has shown exceptional performance on specific types of data, but software implementations have been mostly limited to productivity-oriented languages. In this work, we present our development of a shared-memory parallel, high-performance solution designed to efficiently implement the underlying algorithms. This software will enable optimal compression of extensive scientific datasets, paving the way for enhanced data analysis and insights.
arXiv:2507.10236v2 Announce Type: replace
Abstract: As generative Artificial Intelligence (AI) advances, the realism of AI generated imagery has reached a threshold capable of deceiving even vigilant human observers. Yet, while current AI-generated Image Detection (AID) approaches perform exceptionally well on controlled benchmark datasets, they struggle significantly with real-world cases. To study this behavior we introduce the ITW-SM dataset, a curated collection of real and AI-generated images originating from major social media platforms. We employ it to analyze the effects of key design choices typically considered when building a detector, involving its architecture, pre-trained latent spaces, training data as well as pre-processing approaches. We indicate that naively scaling the pre-training stage or opting for more training data does not always lead to better detection performance. Instead, our work reveals that it is crucial to optimize each design choice to enable the processing pipeline to propagate and effectively analyze both low-level traces as well as high-level image semantics. Building on our findings, we achieve a substantial average improvement of 26.87% in AUC across multiple state-of-the-art detection approaches and under real-world conditions, providing a roadmap for developing more resilient detectors. Our assets are available on https://mever-team.github.io/itw-sm.
arXiv:2605.15745v1 Announce Type: new
Abstract: Autonomous ride-hailing platforms must strategically position idle robotaxis to minimize the wait times of prospective riders. We formalize this as the \emph{robotaxi placement problem} ($k$-RP). Given a finite metric space and a demand distribution over its points, the goal is to position $k$ robotaxis to minimize the expected total distance in a perfect matching between the robotaxis and $k$ random riders. We present several theoretical results for this stochastic optimization problem. First, we observe that sampling robotaxi locations independently according to the demand distribution yields a randomized $2$-approximation algorithm. Second, we present an explicit inapproximability bound via a novel gap-preserving reduction from the maximum coverage problem. Furthermore, while it is not even clear whether the exact expected cost of a placement can be computed efficiently on general metrics, we design an exact polynomial-time dynamic programming algorithm for $k$-RP in tree metrics by decoupling the stochastic matching dependencies. Finally, empirical evaluations on real-world ride-hailing data reveal that a variance-reduced random placement strategy is highly effective in practice, yielding expected wait times that are very close to those obtained by computationally heavy exact algorithms for the uniform capacitated $k$-median problem.
arXiv:2605.15537v1 Announce Type: new
Abstract: This paper introduces RTL-BenchMT, an agentic framework for dynamically maintaining RTL generation benchmarks. Large Language Models (LLMs) assisted automated RTL generation is one of the most important directions in EDA research. However, current RTL benchmarks face two critical challenges: (1) flawed cases in the benchmarks and (2) overfitting to the benchmarks. Both challenges are difficult to resolve purely by manual engineering effort. To address these issues and systematically reduce human maintenance costs, we propose an automated agentic framework, RTL-BenchMT. RTL-BenchMT focuses on two key applications: (1) automatically identifying and revising flawed benchmark cases and (2) automatically detecting and updating overfitting cases. With the assistance of RTL-BenchMT, we conduct a thorough, in-depth analysis of flawed and overfitting cases and produce a refined benchmark suite that will be open-sourced to the community.
arXiv:2605.15865v1 Announce Type: new
Abstract: Large Language Models (LLMs) have shown increasing potential in automating model-driven software engineering tasks, particularly in generating models conforming to Domain Specific Languages (DSLs) from natural language. While most existing approaches rely on large proprietary models, their high cost and limited deployability hinder broader adoption.
In this paper, we evaluate whether open-source LLMs of varying sizes (0.5B to 32B parameters) can generate DSL-conformant models using only few-shot prompting, without any fine-tuning. Our evaluation focuses on key model-driven engineering (MDE) requirements, including syntactic validity, semantic completeness, and inter-model reference consistency.
We extend our prior work by moving from generating user interface models (referred to as "UI models" in this paper) over fixed, predefined data schemas ("data models") to generating both the UI and data models entirely from scratch. This shift serves two purposes: first, it highlights the LLM's ability to infer domain-specific relationships and maintain consistency across multiple interconnected models; second, it allows us to generalize earlier findings by testing DSL generation across models of different natures and structural roles. Our structured evaluation combines automatic parsing and expert feedback across 39 LLMs, revealing that several compact models (e.g., \texttt{gemma3:12b}, \texttt{mistral:7b-instruct}) approach or match the quality of much larger models.
These findings demonstrate the feasibility of using smaller, open-source LLMs for grammar-conformant DSL generation in MDE workflows, offering a cost-effective and deployable alternative to closed LLMs.
arXiv:2605.10100v2 Announce Type: replace
Abstract: We introduce HYPERPOSE, a novel 3D human pose estimation framework that performs spatio-temporal reasoning entirely within the Lorentz model of hyperbolic space $\mathbb{H}^d$ to natively preserve the hierarchical tree topology of the human skeleton. Current state-of-the-art pose estimators aim to capture complex joint dynamics by relying on transformers and graph convolutional networks. Since these architectures operate exclusively in Euclidean space which fundamentally mismatches the inherent tree structure of the human body, these methods inevitably suffer from exponential volume distortion and struggle to maintain structural coherence. To this end, we depart from flat spaces and aim to improve geometric fidelity with Hyperbolic Kinematic Phase-Space Attention (HKPSA), natively embedding complex joint relationships without distortion, alongside a multi-scale windowed hyperbolic attention mechanism that efficiently models temporal dynamics in $O(TW)$ complexity. Furthermore, to overcome the well-known instability of training non-Euclidean manifolds, HYPERPOSE introduces a novel Riemannian loss suite and an uncertainty-weighted curriculum, enforcing physical geodesic constraints like bone length and velocity consistency. Extensive evaluations on the Human3.6M and MPI-INF-3DHP datasets demonstrate that HYPERPOSE achieves state-of-the-art structural and temporal coherence, significantly reducing both volume distortion and velocity error, while establishing new state-of-the-art benchmarks in overall positional accuracy.
arXiv:2605.12581v1 Announce Type: cross
Abstract: Synthesising autonomous agents that can navigate uncertain environments while adhering to complex temporal constraints remains a fundamental challenge. While Linear Temporal Logic (LTL) provides a rigorous language for specifying such tasks, the inherent undecidability of qualitatively verifying LTL satisfaction in partially observable Markov decision processes renders quantitative synthesis difficult, especially when designing reliable reward signals for approximate solvers. In this paper, we bridge this gap with a novel, sound reward-shaping mechanism that dynamically generates belief-dependent rewards grounded in certified LTL satisfaction. By integrating this mechanism into an enhanced Monte Carlo Planning framework, we empower agents to navigate the `fog' of partial observability with a search process focused on maximising verifiable success. Our experiments demonstrate that this approach not only thrives in scenarios where existing solvers fail but also maintains effectiveness and scalability across diverse benchmark domains.
arXiv:2604.08302v3 Announce Type: replace
Abstract: We present DMax, a new paradigm for efficient diffusion language models (dLLMs). It mitigates error accumulation in parallel decoding, enabling aggressive decoding parallelism while preserving generation quality. Unlike conventional masked dLLMs that decode through a binary mask-to-token transition, DMax reformulates decoding as a progressive self-refinement from mask embeddings to token embeddings. At the core of our approach is On-Policy Uniform Training, a novel training strategy that efficiently unifies masked and uniform dLLMs, equipping the model to recover clean tokens from both masked inputs and its own erroneous predictions. Building on this foundation, we further propose Soft Parallel Decoding. We represent each intermediate decoding state as an interpolation between the predicted token embedding and the mask embedding, enabling iterative self-revising in embedding space. Extensive experiments across a variety of benchmarks demonstrate the effectiveness of DMax. Compared with the original LLaDA-2.0-mini, our method improves TPF on GSM8K from 2.04 to 5.47 while preserving accuracy. On MBPP, it increases TPF from 2.71 to 5.86 while maintaining comparable performance. On two H200 GPUs, our model achieves an average of 1,338 TPS at batch size 1. Code is available at: https://github.com/czg1225/DMax
arXiv:2605.15225v1 Announce Type: cross
Abstract: Biologically-inspired AI agent frameworks claim reliability benefits through structural guarantees adapted from gene regulatory networks, immune systems, and metabolic control. These claims are rarely tested empirically against simpler alternatives. We present three deep benchmarks: metabolic priority gating, autoinducer-based quorum sensing, and Bayesian stagnation detection, each comparing a biologically-grounded implementation against a naive non-biological alternative and an ablated control, across 1,000 trials per seed and 10 seeds (10M+ data points total).
arXiv:2605.16167v1 Announce Type: new
Abstract: Ransomware recovery in critical manufacturing infrastructure is not only a backup-restoration problem. Production capability depends on coupled information-technology, operational-technology, physical-process, quality, logistics, identity, and supplier systems. After ransomware, a plant may rebuild servers yet remain unable to schedule work, authenticate operators, trust engineering workstations, release product, reconnect OT assets, or coordinate suppliers. This paper reframes manufacturing ransomware recovery as a critical-infrastructure continuity and interdependency problem. We conduct a PRISMA-guided multivocal review of academic literature, standards and government guidance, threat frameworks, public incident material, and verified full-text/source-page evidence anchors. The review identifies nine evidence-backed recovery failure modes: dependency blindness, untrusted restore point and backup over-trust, identity trust collapse, lack of proof-of-recovery, unsafe OT reconnection, segmentation assumption failure, capability mismatch, unmanaged degraded operation, and supplier dependency failure. We then introduce Minimum Viable Factory Recovery (MVF Recovery): the smallest safe, trusted, and operationally meaningful production capability that can be resumed under current dependency, evidence, identity, data, network, OT, and supplier constraints. MVF Recovery is an analytical objective rather than a claim of full recovery, implementation, or safety certification. The paper derives a recovery lifecycle and benchmarking directions as secondary outputs. The contribution is an evidence-calibrated foundation for capability-centric ransomware recovery in critical manufacturing infrastructure.
arXiv:2510.01632v3 Announce Type: replace-cross
Abstract: Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Yet existing pipelines built on protein encoders do not model proteins at the substructure level, leaving the central biological question unanswered: which substructure of a protein is responsible for its function? We introduce BioBlobs, an encoder-agnostic, end-to-end differentiable framework that compresses a protein into a small set of cohesive substructures (blobs) and predicts function from these blobs alone, so that each blob corresponds to a candidate functional region. Across diverse protein function prediction tasks and multiple sequence- and structure-based encoders, BioBlobs matches or exceeds strong baselines while operating on only a small fraction of residues. The discovered blobs adapt their spatial scale to the task, ranging from local catalytic sites to entire structural domains. Trained only on protein-level labels, BioBlobs recovers experimentally annotated catalytic sites in the M-CSA database, demonstrating unsupervised functional substructure discovery and opening a path to large-scale functional site discovery across the unannotated proteome.
arXiv:2605.15240v1 Announce Type: cross
Abstract: This paper investigates the critical role of eigenalignments between the kernel matrix and learning targets in achieving robust generalization in learning problems. We establish a direct connection between generalization performance in kernel methods and the estimation of eigenvectors and eigenvalues of matrices, offering a more intuitive understanding compared to prior work with minimal assumptions. We also show that, since the prediction task in KRR is essentially the weighted sum of eigenvectors/singular vectors, by analyzing how much error can be caused by perturbations to the kernel matrix, we can then derive a bound on this generalization error using the estimation stability of matrix eigenvalues and eigenvectors. Compared with previous work, our analysis concentrates on finite-sample settings and on the generalization error arising from having a suboptimal finite training set. Our findings reveal that in kernel methods, as long as the kernel is of high rank, the near-zero reconstruction error can be trivially obtained, implying that the reconstruction error will have limited predictive power for generalization. Finally, we establish a generalization bound from an eigenvalues/eigenvectors estimation perspective, showing that strong generalization requires increasing eigenvector alignment, eigenvalue magnitude, or gaps between consecutive eigenvalues.
arXiv:2604.17824v2 Announce Type: replace-cross
Abstract: Continuous quantum phase transitions are characterized by an order parameter and correlation functions that are often challenging to access experimentally or in direct numerical simulations. The energy of an added impurity can on the other hand be probed by established polaron spectroscopy, or numerically with Monte Carlo methods. We provide evidence from ground-state quantum Monte Carlo calculations that the energy of a mobile impurity interacting weakly with a surrounding lattice Bose gas provides access to the critical behavior of the Mott insulator-superfluid phase transition. Finite-size scaling of the energy reveals that its value is scale invariant at the critical point of the quantum phase transition, and we extract a scaling exponent that is currently unexplained by theory. For a small lattice we further observe a flattening of the impurity-boson density-density correlations at the critical point, which hints at a divergence of a corresponding length scale in the thermodynamic limit. Our results suggest that impurity spectroscopy represents a useful way to probe the critical properties of quantum phase transitions in general.