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01.
medRxiv (Medicine) 2026-06-22

Histologically validated diffusion MRI signatures of neuroinflammation and neurodegeneration in Alzheimer disease

Authors:
Wang↗Jiang↗Luna↗Niu↗Nan↗Sun↗Perrin↗R. J↗Franklin↗Cruchaga↗Flores↗Benzinger↗…

Noninvasive neuroinflammation measurement remains a major barrier for Alzheimer disease (AD) therapeutics. We present generalized diffusion basis spectrum imaging (g-DBSI), a diffusion MRI framework that decomposes the tissue signal into biologically interpretable microstructural compartments. In postmortem Knight ADRC brains, g-DBSI-derived restricted isotropic fraction (RIF) and restricted anisotropic fraction (RAF) mapped cellularity and neurofilament density, while their ratio (RIF/RAF) tracked inflammatory cell density and peri-plaque amyloid-beta with higher specificity and regional consistency than RIF alone. In 112 living Knight ADRC participants stratified by PET amyloid, g-DBSI metrics showed amyloid-dependent trajectories: in low-amyloid individuals, RIF and RAF rose together with amyloid, consistent with early neuropil expansion and glial elaboration, whereas in high-amyloid individuals, RIF/RAF increased, and RAF declined, indicating established neuroinflammatory remodeling and neurofilament loss. CSF proteomics linked RIF/RAF to glia-enriched immune and vascular pathways, supporting g-DBSI as a clinically compatible MRI biomarker of neuroinflammation and neurodegeneration in AD.

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02.
arXiv (CS.CL) 2026-06-16

Extending Item Response Theory for Efficient and Meaningful Multilingual Evaluation

Authors:
Gili Lior↗Tzviel Frostig↗Gabriel Stanovsky↗Matan Eyal↗

Multilingual benchmarks are central to evaluating large language models (LLMs) across languages, but they suffer from three issues: exhaustive evaluation scales linearly with the number of languages, automatic translation introduces errors that are easily missed at scale, and some items conflate general and culture-specific knowledge. We address all three with a unified statistical framework, Multilingual-IRT, which extends Item Response Theory with per-language difficulty deviations, split discriminability separating content from language effects, and per-language ability residuals. Fitting Multilingual-IRT on 25 LLMs across 29 languages of MMLU-Pro-X, we show that its fitted parameters support three practical applications: predicting unobserved (item, LLM, language) instances with 11-16% lower binary cross-entropy than the strongest accuracy-based baseline, surfacing candidate translation errors distributed across all 28 non-English languages, whereas accuracy-based baselines concentrate detections in a few languages, and recovering culture-specific items that accuracy-based baselines miss.

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03.
Nature (Science) 2026-06-22

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

Authors:
Amaia Zabala-Letona↗

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

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04.
arXiv (CS.LG) 2026-06-19

Convex training of Lipschitz-regularized shallow neural networks

Authors:
Chao Yin↗Antoine Lesage-Landry↗

arXiv:2606.19652v1 Announce Type: new Abstract: In this work, we introduce a training procedure for shallow neural networks that promotes robustness against adversarial attacks. We solve a non-convex Lipschitz-regularized training program by introducing a convex restriction that can be efficiently solved to global optimality. Our approach can be employed as a post-processing step by taking a pre-trained network as an initial solution to then solving the convex program whose optimal network is guaranteed to be no worse than the initial one. We illustrate the improvements of our training procedure with experiments using real world datasets for regression tasks under an adversarial setting. We show numerically that solving our proposed convex program yields networks with lower objective values on the Lipschitz-regularized program compared to existing methods. Additionally, we show that on certain datasets, networks obtained using our convex training program are both more accurate and robust with respect to adversarial attacks.

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

The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry

Authors:
Dhruv Agarwal↗Riya Bisht↗

arXiv:2606.12639v1 Announce Type: new Abstract: Predicting how a cell's transcriptome responds to a drug it has never seen is a core, hard problem in computational cell biology: recent benchmarks show complex models often fail to beat trivial baselines once test compounds are held out by chemistry. We study one cell line and assay, THP-1 cells profiled by DRUG-seq, scored by the active-compound weighted MSE(wMSE) of the VCPI prediction contest. We propose a staged approach: dumb baselines (untreated control and mean training-compound response) that the field keeps failing to beat; non-parametric retrieval (a Tanimoto-weighted average of a held-out compound's nearest training compounds); and a fusion stage combining a frozen chemistry embedding with retrieval-support features to predict the residual over the mean, with an uncertainty head and gene programs. On the released VCPI THP-1 drug-seq data (14,026 training compounds), under a Bemis-Murcko scaffold split, the model ranking inverts depending on the metric. Under an inverse-variance per-gene proxy, a regularized linear regression on Morgan fingerprints appears to win over the deep models, retrieval, and ChemBERTa – the textbook "simple baselines win" result. But under the contest's true active-set metric (per-(gene, compound) Mejia weights, validated against the official scorer; mean baseline 0.535 vs the organizers' 0.507 reference), that reverses: the deep models win, our fusion decoder significantly beats the linear fingerprint baseline (-0.012 wMSE, paired bootstrap p < 10^-4), and the proxy's winner becomes the worst chemistry-aware predictor. Picking the metric picks the winner – to our knowledge the first demonstration on real held-out drug chemistry of the metric-calibration effect established largely on genetic perturbation. We release a reproducible pipeline wired to the official scorer that emits a valid submission over the real 1064 x 12,995 grid.

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07.
arXiv (CS.AI) 2026-06-16

How Much Do Reviews Really Contribute? A Study on Text-Enriched Matrix Factorization for Recommendations

Authors:
Eduardo Ferreira da Silva↗Mayki dos Santos Oliveira↗Joel Machado Pires Denis Dantas Boaventura↗Frederico Ara\'ujo Dur\~ao↗

arXiv:2606.16973v1 Announce Type: cross Abstract: Incorporating textual reviews into a Recommender System has become a prominent strategy for enriching collaborative signals with semantic information. However, the actual contribution of review-derived representations remains an open question, particularly when strong collaborative baselines are employed. In this work, we systematically investigate the impact of textual information on Matrix Factorization by introducing and comparing three enrichment strategies over a common collaborative backbone. First, we propose a learnable gating mechanism that adaptively balances collaborative and textual signals during training. This mechanism is applied to two distinct review representations: (i) aggregated topic profiles extracted from user and item histories, and (ii) full text embedding representations derived from reviews. Additionally, we explore a cross-attention mechanism that identifies and emphasizes the most informative dimensions of the textual representation before fusion with collaborative factors. We evaluate six variants: pure, enriched with topic profiles and text via gating; enriched with topics and text via gating; and enhanced with cross-attention over textual features. Experiments across multiple review-based datasets reveal that although adaptive fusion mechanisms improve representation flexibility, the marginal contribution of textual signals remains limited compared to the collaborative backbone. These findings suggest that, under typical rating-prediction settings, collaborative information continues to dominate performance, raising important considerations for the effective integration of semantic review signals into recommendation models.

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08.
arXiv (CS.LG) 2026-06-12

Hölder++: Improving the Quality-Coherence Trade-off in Multimodal VAEs

Authors:
Huyen Vo↗Mar\'ia Mart\'inez-Garc\'ia↗Isabel Valera↗

arXiv:2606.13381v1 Announce Type: new Abstract: Existing approaches for multimodal variational autoencoders (VAEs) face a trade-off between generative quality and coherence-i.e., they struggle to generate realistic and diverse samples that, at the same time, are semantically consistent across modalities. A recent work shows that using a simple approximation to Hölder pooling as an aggregation method improves coherence over the SOTA MMVAE+, despite assuming a single shared representation across all modalities. Yet, it slightly compromises sample diversity. Inspired by this insight, we propose Hölder++, a novel multimodal VAE that improves the generative quality-coherence trade-off through: (i) the first implementation of Hölder pooling without any approximation for multimodal VAEs; (ii) an extended architecture that models distinct shared and private (i.e., modality-specific) representations (Hölder+); and (iii) hierarchical inference that further enhances the disentanglement between the shared and private representations (Hölder++). Our experiments corroborate that Hölder++ consistently improves the generative quality-coherence trade-off, yields more structured latent spaces, and learns shared representations that are informative for downstream tasks.

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09.
arXiv (CS.CL) 2026-06-12

Attention Expansion: Enhancing Keyphrase Extraction from Long Documents with Attention-Augmented Contextualized Embeddings

Authors:
Roberto Mart\'inez-Cruz↗Alvaro J. L\'opez-L\'opez↗Jos\'e Portela↗

Pre-trained language models (PLMs) have achieved strong performance in keyphrase extraction (KPE), largely due to their ability to generate rich contextualized representations. However, long-document KPE remains challenging because salient keyphrase evidence may be scattered across distant document sections that cannot be jointly captured within the limited context window of most PLMs. Although long-context large language models (LLMs) can process broader textual contexts, their computational cost limits their practicality for efficient and high-throughput KPE. To overcome this limitation, we propose an attention expansion mechanism that augments PLM token representations with information from surrounding out-of-context chunks using pre-trained word embeddings. The proposed mechanism expands the effective contextual scope of PLM-based KPE models without requiring full-document attention or expensive LLM-based inference. We evaluate our approach across five PLM backbones, including general-purpose, scientific, task-specific, and long-context encoders, using two training regimes and five benchmark corpora from scientific and news domains. Experimental results demonstrate that attention expansion consistently enhances KPE performance across all evaluation settings, outperforming state-of-the-art models and yielding notable improvements in F1 score. The improvements extend to domain-specific, task-specialized, and native long-context models, showing that the proposed mechanism provides complementary information rather than merely compensating for limited input length. These results establish attention expansion as an efficient and effective strategy for long-document KPE.

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10.
arXiv (CS.AI) 2026-06-15

Design Methodology and Performance Trade-offs Management for Distributed and Compound AI Systems

Authors:
Milos Gravara↗Andrija Stanisic↗Stefan Nastic↗

arXiv:2606.14350v1 Announce Type: cross Abstract: Artificial Intelligence (AI) systems must typically satisfy service-level objectives including accuracy, latency, and cost. The prevailing model-centric approaches select a monolithic model at design time and apply identical computation regardless of input difficulty, cannot decompose tasks across specialized components, and have knowledge that is fixed at training time. During runtime, this can lead to performance degradation and increasing costs. Because the model is the main design variable, it determines the majority of system behavior, coupling operational objectives to a single design-time choice. Addressing these limitations requires shifting from model-centric to system-centric design. Compound AI systems realize this shift by orchestrating multiple models, algorithms, and tools as distributed AI systems through explicit control logic. The performance of such systems depends on their workflow topology, the models assigned to each task, and the parameters governing runtime behavior. We present a design methodology that organizes this space along two dimensions, workflow topology and configuration selection, and identifies eight design patterns, each consolidating techniques to address a specific limitation of monolithic deployment. We validate our methodology through three case studies. Across our case studies, Compound AI configurations approach accuracy of monolithic models within 2.5 to 4 percentage points while reducing latency by up to 60% and cost by up to 71%. We show that model selection and parameter configuration jointly determine system performance, but the resulting design space grows combinatorially, as workflows compose more patterns and components. Thus, we identify five open challenges that define a roadmap from manually configured prototypes towards systems that automatically discover and maintain SLO-compliance in Compound and Distributed AI systems.

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

Enhancing LLM Safety Through a Theoretical Minimax Game Lens

Authors:
Yihe Deng↗Yu Yang↗Junkai Zhang↗Wei Wang↗Bo Li↗

The rapid advancement of large language models (LLMs) necessitates effective mechanisms to ensure their responsible deployment by accurately distinguishing unsafe content from benign content. While substantial safety datasets are available in English, multilingual safety modeling remains underexplored due to limited open-source safety datasets in other languages. Even within English datasets, safe yet sensitive corner-case content is scarce, leading to shortcut learning by models and non-trivial false-positive rates. To mitigate these issues, we introduce a novel minimax reinforcement learning (RL) framework wherein a data generator and a classifier model co-evolve, facilitating the production of high-quality synthetic multilingual safety data. We theoretically formalize this interaction as a minimax game and rigorously demonstrate convergence to a Nash equilibrium. Empirical evaluations confirm that our synthetic data generation method significantly enhances the classifier model performance, enabling a substantially smaller model to surpass the state-of-the-art by nearly 10% on English benchmarks while achieving 4.5x faster inference speed. These results establish a scalable and efficient methodology for synthetic data generation, advancing the development of safer and more robust multilingual LLM deployments.

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12.
bioRxiv (Bioinfo) 2026-06-12

DNA Compression with Genomic Language Models: Tokenization, Benchmarking, and an Information-Content Map

Authors:
Macala↗Simecek↗

Lossless compression and probabilistic sequence modeling are two faces of the same coin: a model that assigns high probability to a sequence can encode it in few bits via arithmetic coding. We exploit this duality to evaluate genomic language models as compressors of DNA, using compression primarily as an objective probe of generative sequence modeling rather than as a deployable storage system. We release DNAGPT2, a family of ten GPT-2-small models pretrained for one epoch on a single A40 using the DNABERT2 multi-species corpus that differ only in byte-pair encoding vocabulary size. Coupled with arithmetic coding, the best model reaches 1.47 bits per base (bpb) on the T2T human genome, fourth in the Cobilab compression benchmark and ahead of every general-purpose compressor. Our results suggest that NLP-style tokenization choices may be suboptimal for DNA: a 32-token BPE vocabulary compresses better than larger vocabularies. We also find that, in this benchmark, published long-context genomic LMs underperform a much shorter-context BPE GPT-2; we discuss in Section 5 that this is not a controlled context-length ablation, since the compared models also differ in architecture, training data, parameter count, and tokenization. Finally, we compute a per-nucleotide information-content map of the human genome and show that exons, introns, intergenic regions, and Alu repeats have statistically distinct information profiles.

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14.
arXiv (CS.CL) 2026-06-18

Depth-Width tradeoffs in Algorithmic Reasoning of Graph Tasks with Transformers

Authors:
Gilad Yehudai↗Clayton Sanford↗Maya Bechler-Speicher↗Orr Fischer↗Ran Gilad-Bachrach↗Amir Globerson↗

Transformers have revolutionized the field of machine learning. In particular, they can be used to solve complex algorithmic problems, including graph-based tasks. In such algorithmic tasks a key question is what is the minimal size of a transformer that can implement the task. Recent work has begun to explore this problem for graph-based tasks, showing that for sub-linear embedding dimension (i.e., model width) logarithmic depth suffices. However, an open question, which we address here, is what happens if width is allowed to grow linearly, while depth is kept fixed. Here we analyze this setting, and provide the surprising result that with linear width, constant depth suffices for solving a host of graph-based problems. This suggests that a moderate increase in width can allow much shallower models, which are advantageous in terms of inference and train time. For other problems, we show that quadratic width is required. Our results demonstrate the complex and intriguing landscape of transformer implementations of graph-based algorithms. We empirically investigate these trade-offs between the relative powers of depth and width and find tasks where wider models have the same accuracy as deep models, while having much faster train and inference time due to parallelizable hardware.

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

E-VAds: An E-commerce Short Videos Understanding Benchmark for MLLMs

Authors:
Xianjie Liu↗Yiman Hu↗Liang Wu↗Ping Hu↗Yixiong Zou↗Jian Xu↗Bo Zheng↗

E-commerce short videos represent a high-revenue segment of the online video industry characterized by a goal-driven format and dense multi-modal signals. Current models often struggle with these videos because existing benchmarks focus primarily on general-purpose tasks and neglect the reasoning of commercial intent. In this work, we first propose a multi-modal information density assessment framework to quantify the complexity of this domain. Our evaluation reveals that e-commerce content exhibits substantially higher density across visual, audio, and textual modalities compared to mainstream datasets, establishing a more challenging frontier for video understanding. To address this gap, we introduce E-commerce Video Ads Benchmark, which is the first benchmark specifically designed for e-commerce short video understanding. We curated 3,961 high-quality videos from Taobao covering a wide range of product categories and used a multi-agent system to generate 19,785 open-ended Q&A pairs, which consist of five distinct tasks. Finally, we develop E-VAds-R1, an RL-based reasoning model featuring a multi-grained reward design called MG-GRPO. This strategy provides smooth guidance for early exploration while creating a non-linear incentive for expert-level precision. Experimental results demonstrate that E-VAds-R1 achieves a 109.2% performance gain in commercial intent reasoning with only a few hundred training samples. Data is available at https://github.com/TaobaoTmall-AlgorithmProducts/E-VAds_Benchmark.

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16.
arXiv (quant-ph) 2026-06-19

Hybrid VQE-CVQE algorithm using diabatic state preparation

Authors:
John P. T. Stenger↗C. Stephen Hellberg↗Daniel Gunlycke↗

arXiv:2512.04801v2 Announce Type: replace Abstract: We propose a hybrid variational quantum algorithm that has variational parameters used by both the quantum circuit and the subsequent classical optimization. Similar to the Variational Quantum Eigensolver (VQE), this algorithm applies a parameterized unitary operator to the qubit register. We generate this operator using diabatic state preparation. The quantum measurement results then inform the classical optimization procedure used by the Cascaded Variational Quantum Eigensolver (CVQE). We demonstrate the algorithm on a system of interacting electrons and show how it can be used on long-term error-corrected as well as short-term intermediate-scale quantum computers. Our simulations performed on IBM Brisbane produced energies well within chemical accuracy.

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

Physics-conforming Latent Twins

Authors:
Matthias Chung↗Yutong Bu↗Deepanshu Verma↗

arXiv:2606.15053v1 Announce Type: new Abstract: Surrogate models are central to scientific machine learning, where they enable fast prediction, simulation, inference, and control for complex physical systems. For time-dependent problems, however, accurate interpolation of training trajectories is not sufficient: reliable surrogates should also respect the conservation laws, invariants, admissibility conditions, and dissipative structures that give those trajectories physical meaning. We introduce Physics-conforming Latent Twins, a framework for learning latent surrogate solution operators whose dynamics satisfy selected physical principles by design. The method builds on the Latent Twin formulation by jointly learning an encoder, a decoder, and a latent flow map between arbitrary time-indexed states, while constraining the latent dynamics to preserve or dissipate prescribed structural quantities. We develop a constraint-transfer viewpoint that connects physical structure in the original state space with compatible constraints in latent space, and prove structure-preservation bounds showing how latent enforcement improves control of physical defects after decoding. We also derive algebraic conditions for latent flow maps that preserve linear and quadratic invariants or enforce dissipative inequalities. Numerical experiments on representative ODE and PDE benchmarks demonstrate improved constraint satisfaction, structural fidelity, and qualitative long-time behavior while maintaining accurate surrogate prediction.

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

Private Learning with Public Feature Conditioning

Authors:
Shuli Jiang↗Walid Krichene↗Nicolas Mayoraz↗

arXiv:2606.18773v1 Announce Type: cross Abstract: We study differentially private (DP) regression in settings where each data sample includes public, non-sensitive features – common in applications such as recommendation and advertising systems. While such label-DP or semi-sensitive-feature settings have been primarily explored in the context of classification, effective approaches for regression remain underexplored. We introduce Cond-DP, a conditioned variant of DPSGD that leverages the structure of public feature matrices to improve optimization under privacy constraints. Motivated by the observation that these public features often exhibit rapidly decaying spectra, Cond-DP incorporates a data-driven conditioning matrix to reshape the optimization landscape and accelerate convergence. We provide convergence guarantees for convex, strongly convex, and non-convex settings, and recover standard DPSGD as a special case when the conditioning matrix is the identity. We show how to construct an effective conditioning matrix for Cond-DP directly from public features, enabling provably faster convergence than DPSGD in private linear regression without incurring additional privacy cost. Empirically, Cond-DP with this conditioning matrix consistently outperforms state-of-the-art baselines across a wide range of datasets and model architectures under label DP, demonstrating strong and robust performance in practice.

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19.
arXiv (math.PR) 2026-06-16

Higher-order spectral perturbation expansions II: Kernel matrices and manifold learning

Authors:
Bernhard Stankewitz↗Martin Wahl↗

arXiv:2606.16373v1 Announce Type: cross Abstract: We study spectral concentration bounds for kernel matrices as approximation of the corresponding kernel integral operator. Results are established under weak assumptions on the data setting and the reproducing kernel relying only on a Mercer condition and a local Weyl law. This allows us to deal with key features of kernel matrices, such as large multiplicities, large effective dimension, and heavy-tailed distributions. Our results apply to infinite dimensional principal component analysis, manifold learning, and Bayesian nonparametric statistics. We illustrate this via two prototypical examples: The heat kernel on the sphere and a wavelet prior from Bayesian nonparametrics.

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20.
medRxiv (Medicine) 2026-06-22

Sequential Deep Learning to Predict Non-Central to Central Geographic Atrophy Progression from OCT Imaging

Authors:
Siraz↗Kamanda↗Nabil↗A. S↗Gholami↗Rao↗N. T↗Ong↗S. S↗Alam↗

Purpose: To develop and validate a temporal deep learning framework for predicting geographic atrophy (GA) progression across multi-year horizons using longitudinal optical coherence tomography (OCT) sequences. Design: Retrospective longitudinal cohort study. Subjects, Participants, and/or Controls: A total of 91 patients with dry age-related macular degeneration (AMD) were identified from Wake Forest University School of Medicine (2013-2023), yielding 455 OCT volumes. Two prediction cohorts were defined: 32 patients with no GA (NGA) at baseline who subsequently developed GA, and 35 patients whose earliest GA manifestation was non-central GA (NCGA). Non-progressing patients served as negative controls. Methods: OCT B-scan volumes were encoded into visit-level feature representations using three pretrained architectures (ResNet-18, ResNet-50, ViT-B/16). Chronologically ordered visit embeddings, optionally augmented with inter-visit time intervals ({Delta}t), were processed through recurrent neural networks (RNN), long short-term memory networks (LSTM), and Transformer encoders to model longitudinal disease trajectories. Models were trained and evaluated independently for prediction horizons of 2, 3, 4, 5, and 6 years using patient-level stratified splits (80/20). Performance was assessed across five random seeds. Main Outcome Measures: Area under the receiver operating characteristic curve (ROC-AUC), F1-score, and accuracy for predicting two clinically critical transitions: NGA to GA onset and NCGA to central GA (CGA) involvement. Results: For NGA to GA prediction, models achieved ROC-AUC of 0.84-0.94 at 2-4 years and 1.00 at 5-6 years. For NCGA to CGA prediction, Transformer-based models achieved peak AUC of 0.95 at 4 years and 0.96 at 5 years. Longer input sequences (8 visits vs. 4 visits) consistently improved NCGA to CGA performance at extended horizons. Temporal interval encoding improved stability in several LSTM configurations.

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21.
arXiv (CS.LG) 2026-06-16

Scale-Invariant Neural Network Optimization: Norm Geometry and Heavy-Tailed Noise

Authors:
Jiayu Zhang↗Tianyi Lin↗

arXiv:2605.18528v3 Announce Type: replace-cross Abstract: A growing lesson from neural network optimization is that optimizer design should respect how the model is parametrized. The layerwise input-output structure of neural networks motivates scale-invariant optimizers, such as Muon and Scion, whose updates also support hyperparameter transfer. At the same time, stochastic gradient noise in deep learning is often far from sub-Gaussian and may exhibit heavy tails. These observations have shaped recent algorithmic principles for training neural networks, yet their joint theoretical consequences are underexplored. In particular, it remains unclear what dimension dependence is unavoidable for gradient-based methods given the problem class is defined by input-output norm and under heavy-tailed noise, and whether higher-order smoothness can accelerate training. We study these questions through nonconvex smooth stochastic optimization over $\mathbb R^{m\times n}$ equipped with general norms and under $p^\mathrm{th}$-moment heavy-tailed noise, where the goal is to achieve an $\epsilon$-stationary point in the dual norm. Our first contribution is a dimension-dependent lower bound: when $\frac{\max\{m,n\}}{(\min\{m,n\})^2}$ is large enough, any gradient-based method requires $\Omega(\min\{m, n\}\epsilon^{-\frac{3p-2}{p-1}})$ oracles for the problem class defined by the spectral norm, which is a common input-output norm. We prove that a scale-invariant Scion method with the spectral norm can achieve the matching upper bound of $O(\min\{m, n\}\epsilon^{-\frac{3p-2}{p-1}})$. To exploit higher-order smoothness, we propose a transported Scion method and improve the bound to $O(\min\{m, n\}\epsilon^{-\frac{5p-3}{2p-2}})$ when the Hessian is Lipschitz. Finally, we incorporate heuristics into our transported method and evaluate it across multiple architectures and model sizes, demonstrating its flexibility and compatibility with neural network training.

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22.
arXiv (CS.CV) 2026-06-18

Optimizing Incomplete, Large-Scale and Sparse Multi-Graph Matching in Bioimaging

Authors:
Max Kahl↗Sebastian Stricker↗Lisa Hutschenreiter↗Florian Bernard↗Carsten Rother↗Bogdan Savchynskyy↗

Multi-graph matching is a fundamental problem in computer vision. Our work is motivated by a challenging application in bioimaging, where dozens or even hundreds of 3D microscopy images of worms must be brought into correspondence. Existing datasets do not cover this large-scale regime, and virtually all existing methods are inapplicable because they assume a complete or dense problem setting. To support further research, our first contribution is a new large-scale dataset based on problem instances from bioimaging. Our second contribution is a comprehensive analysis of the two main multi-graph matching paradigms: direct and permutation synchronization-based formulations. We argue, in part by proof, that practical large-scale methods must explicitly address problem sparsity and incompleteness. Since standard permutation synchronization approaches fail in this setting, we further introduce a sparse permutation synchronization paradigm. Our final contribution is GREEDA, a general method for sparse and incomplete problems that can be instantiated across cost orders and paradigms. While our paper focuses on objective functions up to quadratic order, GREEDA is inherently generalizable to arbitrary orders. On larger, sparse instances, GREEDA outperforms competing methods in both objective value and runtime. For example, for moderately-sized problems based on 30 worm images GREEDA produces a high-quality solution within 2 minutes, whereas competitors require at least half an hour and yield far worse results. On smaller dense problems, GREEDA remains on par with leading methods while being an order of magnitude faster.

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23.
arXiv (CS.AI) 2026-06-12

Pythagoras-Prover: Advancing Efficient Formal Proving via Augmented Lean Formalisation

Authors:
Joshua Ong Jun Leang↗Zheng Zhao↗Mihaela C\u{a}t\u{a}lina Stoian↗Qiyuan Xu↗Haonan Li↗Wenda Li↗Shay B. Cohen↗Eleonora Giunchiglia↗

arXiv:2606.12594v1 Announce Type: new Abstract: Modern Lean theorem provers achieve strong performance only with substantial training and inference compute, driven in part by scarce verified proof data and the long reasoning traces of formal proof search, making both supervised fine-tuning (SFT) and sampling expensive. We introduce Pythagoras-Prover, a compute-efficient open-source family of Lean theorem provers built for practical compute budgets. The family spans two generation paradigms: autoregressive models at 4B and 32B parameters, and a first proof-of-concept diffusion-based prover (4B) that iteratively refines Lean proofs at inference time. For training efficiency, we build a Lean-verified corpus stratified into easy, medium, and hard problems for curriculum SFT, so models acquire proof skills progressively from shorter, simpler proofs to longer, harder ones. During SFT, a dynamic proof-reasoning filtering scheme preserves informative proof traces while keeping each instance within an 8k-token context budget. We also introduce Augmented Lean Formalisation (ALF), which expands scarce verified corpora into variants of formal statements, populated via self-distillation for extra training signal without formally verifying every mutated instance. By perturbing known problems while preserving their formal character, ALF reduces reliance on any statement's surface form. Empirically, Pythagoras-Prover-4B surpasses DeepSeek-Prover-V2-671B at pass@32 on MiniF2F-Test (86.1% vs 82.4%) with ~167x fewer parameters, while Pythagoras-Prover-32B sets the open-source state of the art at 93.0% on MiniF2F-Test and solves 93 of 672 PutnamBench problems. We release MiniF2F-ALF, an ALF-mutated contamination-sensitive benchmark on which every evaluated model loses accuracy; here our 32B remains strongest and our 4B matches the prior state of the art, Goedel-Prover-V2-32B.

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24.
PLOS Computational Biology 2026-06-01

A statistical framework for comparing epidemic forests

Authors:
Cyril Geismar↗

by Cyril Geismar, Peter J. White, Anne Cori, Thibaut Jombart Inferring who infected whom in an outbreak is essential for characterising transmission dynamics and guiding public health interventions. However, this task is challenging due to limited surveillance data and the complexity of immunological and social interactions. Instead of a single definitive transmission tree, epidemiologists often consider multiple plausible trees forming epidemic forests. Various inference methods and assumptions can yield different epidemic forests, yet no formal test exists to assess whether these differences are statistically significant. We propose such a framework using a chi-square test and permutational multivariate analysis of variance (PERMANOVA). We assessed each method’s ability to distinguish simulated epidemic forests generated under different offspring distributions. While both methods achieved perfect specificity for forests with 100+ trees, PERMANOVA consistently outperformed the chi-square test in sensitivity across all epidemic and forest sizes. Implemented in the R package mixtree, we provide the first statistical framework to robustly compare epidemic forests.

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25.
arXiv (CS.AI) 2026-06-16

FP8 is All You Need (Part 1): Debunking Hardware FP64 as the HPC Holy Grail (June 13th version)

Authors:
Satoshi Matsuoka↗

arXiv:2606.06510v2 Announce Type: replace-cross Abstract: Conventional HPC holds that native hardware FP64 is the irreducible foundation of scientific computing. On AI-optimized GPUs of the NVIDIA B300 generation and beyond, native FP64 throughput has collapsed to ~1.3 TFLOPS even as FP8 tensor throughput has grown to multiple PFLOPS. We argue something stronger than that this is survivable: the FP8 tensor-core matrix-multiply is the sole computational primitive on which double-precision scientific computing needs to be built. Every canonical kernel – dense and sparse linear algebra, spectral transforms, stencils – and every application composing them reduces, via the Chinese Remainder Theorem-based Ozaki Scheme II, to sequences of FP8 matrix operations; the only non-FP8 arithmetic is a bounded, fixed-width integer accumulation at reconstruction. Native FP64 is thereby demoted from a hardware requirement to a derived accuracy guarantee obtained by composition over the FP8 primitive. We organize the claim as a five-layer hierarchy – the FP8 op, Ozaki II, the basic kernels or Berkeley "dwarfs", composite solvers, and full applications – and, because the dwarf taxonomy already spans scientific computing, establish it by exhibiting the reduction for every dwarf rather than a sample. The claim is falsifiable, and we build the instrument that tests it: a Tensor-Memory Equilibrium (TME) model extending the Roofline with emulation parameters (alpha, beta, gamma). We identify register-level fusion as the mechanism that keeps emulation memory-bound, project recovered FP64 performance across B300 and Rubin against an H100 baseline, and close the kernel coverage with a companion FFT analysis and compensated reductions. The model could have returned a negative verdict; instead it passes across the dwarfs and their compositions. This is the analytical half of a two-part program, with a follow-on implementation to validate the thesis on real silicon.

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