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01.
bioRxiv (Bioinfo) 2026-06-11

STITCH links cellular morphology and gene expression in spatial transcriptomics

In situ spatial (ISS) sequencing can uncover co-variation between cellular morphology and gene expression in vivo. However, a principled and interpretable mathematical representation of morphology has not yet been applied in this context. In particular, current deep learning-based representations of cell images confound a cell's shape with its size. We present an interpretable representation of cellular boundary contours, based on tangent principal component analysis (TPCA) in a Kendall shape manifold, that captures size-independent contour shape features. This approach successfully recovers shape-perturbing genes in an RNAi screen than a previous metric geometry-based approach. We build on TPCA to develop STITCH (Shape-TranscriptomIc Correlation and Harmonization), an approach to reveal covariation between cell morphology with gene expression in ISS datasets. In a Xenium dataset, STITCH outperforms a deep learning-based approach in both recovering the layered organization of keratinocytes and a spatial gradient in nuclear eccentricity. Across samples in a melanoma CosMx dataset, STITCH reproducibly associates elongated and triangular fibroblasts with proximity to malignant cells and myofibroblast-like transcriptional program. Finally, STITCH independently recovers a known link between mesenchymal-like malignant cell states and increased cell area in two melanoma cohorts. STITCH can thus yield interpretable morphology-transcriptome relationships across cell types, patients, and spatial transcriptomics platforms.

02.
arXiv (CS.CV) 2026-06-24

ABACUS: Adapting Unified Foundation Model for Bridging Image Count Understanding and Generation

ABACUS is a unified vision-language model that handles object counting, crowd counting, referring-expression counting, and count-faithful image generation without any benchmark-specific training required. Our model is built on existing 3B-parameter unified foundation model and is adapted for object localization tasks using three key innovations: density-aware adaptive zooming with objectness maps for spatial grounding; a boundary-aware count policy via GRPO to eliminate crop-boundary errors; and a cycle-consistent GRPO strategy where the understanding branch self-critiques generated outputs, closing the understanding-generation gap without any external annotations. ABACUS achieves state-of-the-art results across seven benchmarks, outperforming both task-specific specialists and larger generalist models.

03.
medRxiv (Medicine) 2026-06-15

CDH13 is associated with cellular viability after exposure to ionizing radiation using genome-wide screening

Background: It is well known that genetic variants contribute to cellular sensitivity to chemotherapeutic agents and ionizing radiation (IR). The aim of this study was to identify single nucleotide polymorphisms (SNPs) and genes associated with the spectrum of normal cellular sensitivity of lymphoblastoid cell lines (LCLs) towards ionizing radiation and mitomycin C (MMC). Methods: In a first step, we determined the viability of LCLs established from male participants of the Berlin Aging Study II (BASE-II) aged >=62 years following treatments with increasing doses of IR (n=137 cell lines) or MMC (n=140 cell lines) using the alamarBlue assay. Results from intra-experimental triplicates and three independent experiments for each cell line and treatment were used to calculate the area under the curves (AUCs) representing the specific sensitivity to IR and MMC of each LCL. The data from these experiments were subsequently used as outcomes in genome-wide association studies (GWASs). In addition, we calculated polygenic risk scores (PGS) from UK Biobank GWAS results for four cancer-related phenotypes and assessed the extent to which the variance in the IR and MMC sensitivity is explained by these PGS. Results: The GWAS analyses revealed one variant, rs74728080, located in CDH13 on chromosome 16, to show genome-wide significant (p < 5 x 10-8, beta = 2.81) association with cellular viability after treatment with IR. In the GWAS on MMC sensitivity the most interesting signal was elicited by SNP rs113978558 in an intron of the PLD5 gene on chromosome 1 (p = 9.232 x 10-8; beta = 1.44). Several other SNPs with statistically suggestive (i.e., p < 1 x 10-5) evidence of association with IR or MMC sensitivity were identified. PGSs calculations from GWAS of four cancer-related traits in UKB explained ~5% and ~3% of phenotypic variance in IR- and MMC-induced cell viability, respectively. Conclusion: The genome-wide significant association of rs74728080 with IR sensitivity and the location of this variant in CDH13 is interesting and functionally highly plausible given its known involvement in oxidative-stress response and function as tumor suppressor. Taken together, our novel data suggest that CDH13 may be genuinely involved in regulating cellular IR sensitivity.

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

CalTennis: Large Multi-View Tennis Video Dataset and Benchmark of Monocular-to-3D Pose Estimation

The Caltech Tennis Dataset (CalTennis) is a large-scale video benchmark for evaluating monocular-to-3D pose estimation in the wild. CalTennis comprises over 11 million frames (51 hours) of tennis practice and match play from 40 players, captured with 2-6 synchronized cameras at 60 Hz. It is 10 times larger than existing in-the-wild human motion video datasets and 3 times larger than existing MOCAP-ground-truthed datasets, and it is the first large-scale benchmark to provide synchronized multi-view recordings of expert athletic motion. The multi-view setup enables inexpensive, label-free evaluation of monocular-to-3D pose estimation algorithms. We describe a simple, standardized protocol that enables data collection without specialized equipment or expertise, along with fully automated video calibration and synchronization. Benchmarking state-of-the-art monocular-to-3D pose methods on CalTennis, we find that while 3D joint angle recovery is now quite accurate, all models struggle to estimate depth and foot contact consistently. We further propose two novel performance metrics, footwork and stability, as well as qualitatively study body shape inconsistency. These metrics expose previously underexplored failure modes and point to concrete opportunities for improvement in pose estimation and action analysis.

05.
arXiv (CS.CV) 2026-06-11

From Simulation to Real-World: An In-Field 6D Pose Dataset and Baseline for Robotic Strawberry Harvesting

Robotic strawberry harvesting requires precise 6D pose estimation; however, collecting 6D pose ground truth in real agricultural fields is inherently challenging. Existing 6D pose estimation methods have therefore relied solely on synthetic data that lacks scene-level realism, leaving their performance under real agricultural field conditions unquantified. In this work, we present, to the best of our knowledge, the first real-world 6D pose ground truth dataset of strawberries collected in actual agricultural fields (12,040 images). We also introduce a synthetic dataset rendered in NVIDIA Isaac Sim, featuring scene-level realism and domain randomization. Nevertheless, our experiments reveal that a significant sim-to-real gap persists, underscoring the necessity of real agricultural field data for reliable evaluation. We further quantify the sim-to-real gap through baseline 6D pose estimation results across backbone encoders, serving as a reference for future work. The real-world dataset will be made available upon acceptance.

06.
arXiv (CS.CL) 2026-06-17

Speaking in Self-Assessing Tongues: On the Verbalized Confidence of LLMs in Machine Translation

The rapid rise in popularity of large language models (LLMs) for translation calls for a thorough study of the reliability of their confidence in their own outputs. Unlike many generation tasks, translation errors and confidence levels can be useful at different levels of granularity (tokens, words, or spans). Unsupervised approaches based on internal signals like predicted probabilities can be misleading because they reflect certainty among alternatives rather than correctness. In addition, they require access to such internal signals. Here, we devise five verbalized methods of extracting an LLM's per-token confidence without those shortcomings and compare their reliability with that of the model's internal signals of certainty. We evaluate reliability using two forms of alignment: fine-grained error detection and calibration. For both, internal and verbalized methods perform similarly, although results vary by model. Interestingly, we find little to no correlation between internal and verbalized methods.

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

Not All Skills Help: Measuring and Repairing Agent Knowledge

LLM agents can improve without weight updates by accumulating natural-language skills from experience, but current systems entrust every decision about which skills to keep and how to apply them to LLM judgment alone. We argue that this conflates two distinct roles: generating a skill from experience is a creative act that judgment handles well, while deciding whether that skill actually helps requires empirical evidence across many tasks. Measuring per-skill causal contributions via randomized masking, we find that skill libraries exhibit pervasive causal heterogeneity: individual skills routinely help on some task types while hurting on others, yet their opposing effects cancel in aggregate, making them invisible to global curation methods. We propose ASSAY, a framework that separates generation from curation: it computes a per-skill causal attribution on a small development set, restructures the library offline, and suppresses skills with negative predicted effect for each test task. Across seven base models spanning four providers and two benchmarks (AppWorld and tau-bench), ASSAY consistently improves over prior skill-curation approaches. On AppWorld's hardest split, DeepSeek-V3 achieves 69.3% task-goal completion (47.4% relative improvement), a new state of the art among all published methods including weight-tuned approaches. On tau-bench retail, GPT-4.1 improves by 8.7% relative, advancing past o4-mini, o1, and GPT-4.5 on the public leaderboard without any weight modification. Ablation traces the dominant gain to per-task masking, confirming that the bottleneck is matching skills to tasks at inference time, not removing bad skills globally. Code is available at https://github.com/aiming-lab/assay.

08.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

09.
arXiv (CS.CL) 2026-06-24

Aspect-Based Sentiment Evolution and its Correlation with Review Rounds in Multi-Round Peer Reviews: A Deep Learning Approach

Mining sentiment information from the textual content of peer review comments offers valuable insights into the scientific evaluation process. However, previous studies are often constrained by coarse-grained analysis and the lack of differentiation across review rounds. Notably, the dynamic shifts in reviewers' focus and sentiment tendencies throughout multiple review stages remain underexplored. To address this gap, the present study investigates the distribution and evolution of aspect-level sentiments and examines their correlation with the number of review rounds. We begin by segmenting the multi-round review comments of 11,063 accepted papers from Nature Communications and identifying fine-grained review aspect clusters. A manually annotated corpus of approximately 5,000 review sentences is then constructed. Using this dataset, we train a series of deep learning-based aspect sentiment classification models. Among them, the LCF-BERT-CDM model achieves the best performance, with a Macro-F1 score of 82.65%. Subsequent statistical analysis reveals a consistent trend: as the number of review rounds increases, the proportion of positive sentiments rises, while negative sentiments decline. Correlation analysis further indicates that aspect sentiment scores are negatively associated with the total number of review rounds. Key aspects exhibiting stronger correlations include "experiments", "research significance" and "result analysis".

10.
Nature (Science) 2026-06-10

Whole-genome duplication shaped cell-type evolution in the vertebrate brain

作者:

The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show one-to-one homology with amphioxus. Moreover, ohnologues, particularly those from the first WGD, were more important than small-scale duplication paralogues for vertebrate cell-type evolution. To explore whether ohnologues are mechanistically important for this process, we predicted ancestral cell-type states and compared them to amphioxus and experimentally investigated macroglia. The findings indicate that ohnologues had a role in early vertebrate cell-type diversification. Moreover, by examining paralogue expression across cell types and species, we show that expression changes were mainly driven by dosage selection and subfunctionalization. We also link ohnologues to cellular diversity at different anatomical and cell-type scales. Our findings demonstrate the importance of WGDs for the evolution of early vertebrate brain complexity and highlight that the resultant ohnologues continued to capacitate cell-type evolution long after they were formed. Analyses of brain single-cell transcriptomes from human, mouse, lizard, lamprey and amphioxus reveal that duplicated genes (ohnologues) played a pivotal part in early vertebrate cell-type diversification.

11.
arXiv (CS.CV) 2026-06-17

Similarity-based representation factorization for revealing interpretable dimensions in representational data

The study of representations is widespread across fields, including neuroscience, psychology, and artificial intelligence. While representations are often studied and compared through similarities between stimuli, current methods provide only limited access to the dimensions that shape these representations and are often limited in interpretability. To overcome these challenges, here we introduce Similarity-Based Representation Factorization (SRF), a general computational method for recovering low-dimensional, non-negative, interpretable embeddings from similarity matrices derived from measured data. Across simulations and many neural, behavioral, and computational datasets, SRF recovers interpretable dimensions from diverse forms of representational data, even for very sparsely sampled, incomplete data. The dimensions derived from these datasets match those obtained by task-specific models, predict independent behavioral properties, improve exploratory analysis, and offer higher power for confirmatory hypothesis testing than comparing similarity matrices. Together, these results establish SRF as a general-purpose method with broad applications for uncovering, understanding, and using the dimensions underlying representations.

12.
arXiv (quant-ph) 2026-06-11

Quantum repeater segment with free-space coupled co-trapped ions using telecom photon interference

arXiv:2606.12313v1 Announce Type: new Abstract: A quantum repeater segment is a basic building block of a quantum repeater, generating buffered entanglement of quantum memories to connect quantum repeater cells. It also enables the connection between quantum computers. In the implementation we present here, photons emitted from two co-trapped free-space coupled $^{40}$Ca$^+$ ions are converted to the telecom-C band and interfered after transmission over 440$\,$m of optical fiber (220$\,$m per arm), where a photonic Bell measurement is performed to create entanglement between the memories. With this scheme we generate an entangled $\left|\Psi^+\right\rangle$ Bell state with $\ge 68(8)\,$% fidelity, highlighting trapped $^{40}$Ca$^+$ ions as a promising quantum repeater hardware platform.

13.
bioRxiv (Bioinfo) 2026-06-16

DMcloud: Macromolecular Structure Modeling Using Local Structure Fitting for Medium to Low Resolution cryo-EM maps

Cryogenic electron microscopy (cryo-EM) has become an essential experimental approach in structural biology for determining macromolecular structures. When the resolution of a cryo-EM map is worse than approximately 5[A], fitting known or predicted molecular models into the map becomes a common strategy for interpretation. However, accurately fitting biomolecular models into cryo-EM maps, particularly for large macromolecular complexes, remains challenging when the input structure models contain errors or are in a conformation different from that represented in the map. Here, we present DMcloud, a method for local structure fitting of proteins and nucleic acids in cryo-EM maps. Instead of forcing an entire input model into the map, DMcloud divides input structures into local regions, identifies regions that are supported by the density, removes unsupported regions, and assembles the retained regions into a final model. We benchmarked DMcloud on 176 cryo-EM maps, including intermediate and high-resolution maps that include proteins, DNAs, or RNAs. For EM maps in the 5.0-10.0 [A] and 2.5-5.0 [A] resolution ranges, DMcloud achieved average sequence modeling coverage of 0.49 and 0.70, respectively. For DNA/RNA maps, DMcloud achieved an average sequence coverage of 0.75. Across all datasets, DMcloud consistently outperformed existing methods in model accuracy, map-model correlation, and modeling coverage.

14.
medRxiv (Medicine) 2026-06-15

Efficacy of Painhunting Therapy for Event-Related Depression: A Randomized Controlled Trial with Crossover Replication

Background. Depression affects an estimated 332 million people worldwide and is a leading cause of disability, with up to 80% of major depressive episodes preceded by an identifiable adverse life event [17,18]. First-line treatments target symptoms rather than the precipitating event and are resource-intensive: standard CBT averages roughly 12 sessions, and antidepressant discontinuation carries relapse rates near 35% at six months [8]. These limitations create a clear rationale for brief, structured interventions that address the cognitive and somatic sequelae of adverse life events directly. Painhunting therapy is one such intervention, in which each session targets a discrete adverse event through a structured incident-processing procedure. Methods. We conducted a two-arm, parallel-group, single-site randomised controlled trial comparing Painhunting therapy (Arm A, immediate; n=42) with a waitlist control (Arm B, delayed; n=42) in adults with PHQ-9 >= 9 and active psychological distress related to an adverse life event. After the primary endpoint at T2 (approximately two weeks post-randomisation), Arm B crossed over to active treatment, with T3 as the post-crossover endpoint at approximately four weeks. The primary outcome was PHQ-9 at T2 (between-arm contrast); secondary outcomes were ICG, GAD-7, WHO-DAS 2.0 (12-item), and the Global Impression of Change (GIC). Pre-specified analyses included intention-to-treat, per-protocol, and single-exclusion sensitivity populations. Results. Eighty-four participants were randomised (198 applications, 134 completed screening questionnaire, 119 passed psychometric screening). At T2, mean PHQ-9 was 2.32 (SD 2.59) in Arm A and 16.56 (SD 6.76) in Arm B, yielding an ITT between-arm Cohen d = 2.78 (95% CI 2.19-3.76, p < 0.001). Within-arm paired reductions during each arm's active-treatment window reproduced this magnitude (Arm A T0 to T2 change 14.71, Morris d = 2.80; Arm B T2 to T3 change 14.19, Morris d = 2.77, eligible n=26). Treatment gains were durable at the T4 follow-up (week 8). Aligning each arm to its own end-of-treatment timepoint, the off-treatment drift to week 8 was almost identical between arms: Arm A rose 0.78 points from T2 to T4 (2.19 to 2.97, n=37) and Arm B rose 1.59 points from T3 to T4 (4.74 to 6.33, n=27), the latter falling to 0.77 points once a single documented relapse case (R59) is excluded (4.81 to 5.58, n=26). This small off-treatment rebound then stabilised rather than continuing: Arm A was essentially unchanged from T3 to T4 (change +0.05), with concordant maintenance on ICG, GAD-7, and WHO-DAS. At T4, 68% of Arm A and 41% of Arm B remained in remission (PHQ-9 < 5). Secondary measures (ICG, GAD-7, WHO-DAS) moved in the same direction and to comparable magnitude at every timepoint. The waitlist window in Arm B showed essentially no change on any measure (PHQ-9 change 0.22, p = 0.81). Sensitivity analyses excluding six sub-threshold T2 cases, the single treated-in-error case (R82), the R59 relapse case, and one late T2 submitter left all conclusions unchanged. Conclusions. Painhunting therapy produced large and statistically robust reductions in depression, complicated grief, anxiety, and functional disability over a brief course of three to four sessions, with effect sizes substantially exceeding benchmarks reported for established first-line psychotherapies including CBT and EMDR. Critically, these gains persisted at the week-8 follow-up: depression scores in the immediate-treatment arm were essentially unchanged from four weeks to eight weeks post-randomisation, indicating that the benefit reflects durable change rather than a transient post-session dip. Treatment-window concordance between arms, durability of gains at one month off-treatment, and the flat waitlist trajectory together strengthen the evidence for genuine efficacy rather than spontaneous remission. Baseline covariates including therapeutic alliance, treatment expectancy, self-efficacy, age, and sex showed near-zero associations with outcome, reducing the plausibility of allegiance bias or expectancy effects as primary drivers. The differential retention between arms (88% vs 64% at T3) is attributable to the waitlist design and is discussed as a limitation. These findings support proceeding to a confirmatory active-comparator trial against manualized CBT. Trial registration: ClinicalTrials.gov NCT07490691, prospectively registered.

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

TS-ICL: A Flexible Time-Indexed Foundation Model for Time Series via In-Context Learning

arXiv:2606.05878v2 Announce Type: replace Abstract: Foundation models mark a profound paradigm shift in time series modeling, with task-specific models being superseded by general-purpose zero-shot models. Yet, current approaches primarily focus on forecasting, while real-world time series are often irregularly and partially observed, requiring models that can jointly forecast, impute missing values, and handle degraded sampling conditions. To address these challenges, we introduce TS-ICL, a novel probabilistic In-Context Learning encoder–regressor Transformer that unifies forecasting and imputation. TS-ICL formulates time series tasks as timestamp-aligned regression and naturally incorporates covariates by training on synthetic dependency structures generated from a novel causal data prior. Empirically, TS-ICL achieves a new state-of-the-art in imputation, while remaining competitive with leading forecasting foundation models across both univariate and covariate-aware benchmarks. It shows particularly strong performance in forecasting with partially observed look-back windows.

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

How do Self-Supervised Remote Sensing Vision Models Transfer to Downstream Tasks?

Self-supervised geospatial foundation models (GeoFMs) learn transferable representations from remote sensing data, but their downstream behavior is difficult to characterize. We study six representative GeoFMs spanning joint-embedding, reconstruction, and multimodal pretraining families, and evaluate transfer across classification, regression, and segmentation benchmarks under different label availability and downstream pipelines. We find that model rankings change across tasks and adaptation settings. Layerwise probing shows that, in most cases, task-relevant information is more accessible in intermediate transformer blocks compared to final-layer embeddings, and that GeoFMs exhibit distinct depthwise profiles. In segmentation case studies on PASTIS and Sen1Floods11, downstream adaptation settings such as decoder design and fine-tuning can be as impactful as the choice of GeoFM, and standard dense-prediction heads may be poorly aligned with how GeoFMs organize information over depth. Finally, CKA analysis on case studies shows that fine-tuning does not rewrite GeoFMs uniformly across depth, and the strongest changes are localized to the first linear layer of the MLP in ViT blocks. These results help explain why GeoFM rankings shift across benchmarks and motivate more representation-aware evaluation and adaptation strategies.

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

Code as a Weapon: A Consensus-Labeled Prompt Bank for Measuring Coding-Model Compliance with Malicious-Code Requests

A general-purpose language model that answers a harmful question returns text; a coding model that complies with a malicious request can return a working weapon: a keylogger, ransomware, an exploit that runs as written. This asymmetry in the severity of a single act of compliance implies coding-specialized models should clear a higher refusal bar than general-purpose chat models, not a lower one, yet the field cannot tell whether they do. Refusal benchmarks for malicious code are fragmented: they mix requests for executable software with requests for harmful security knowledge and report refusal rates over non-comparable corpora. This paper's central result is that the CODE-versus-KNOWLEDGE classification axis established in a prior four-corpus release remains stable under a substantially expanded corpus pool and an independently refreshed judge panel, evidence that it measures a real construct rather than an artifact of the prompts or judges. Eight corpora spanning diverse elicitation paradigms (direct, jailbreak-decorated, indirect, and agent/interpreter: ASTRA, CySecBench, AdvBench/harmful_behaviors, JailbreakBench, MalwareBench, RedCode, RMCBench, Scam2Prompt) are classified under a five-judge consensus protocol (6,675 prompts x 5 judges = 33,375 calls), reaching Fleiss' kappa = 0.767 [95% CI 0.755, 0.777] ("substantial"). Critically, the panel shares no judge with the prior release (five paid commercial APIs replaced by five open-weight models from five vendors), yet the two panels agree on 94.45% of the 3,133 shared prompts and reach Cohen's kappa = 0.952 [0.942, 0.963] on the 3,031-prompt binary overlap: the axis survives near-total panel replacement. The released bank comprises 4,748 consensus-CODE and 1,923 consensus-KNOWLEDGE prompts, a reliability-quantified benchmark whose central classification axis is shown stable across corpus expansion and judge-panel replacement.

18.
arXiv (math.PR) 2026-06-16

Scaling Limits of Bivariate Nearly-Unstable Hawkes Processes and Applications to Rough Volatility

arXiv:2605.03703v3 Announce Type: replace Abstract: We study a pair of nearly-unstable Hawkes processes coupled through a one-directional, or triangular, cross-excitation: the first component evolves autonomously and excites the second, but not conversely. Each component is self-exciting through a heavy-tailed memory kernel, and the two kernels are allowed to have different tail indices, so that the limiting components exhibit genuinely different degrees of roughness. As the system approaches criticality, we prove that the suitably rescaled intensity vector converges weakly to the unique solution of a coupled system of stochastic Volterra equations of rough-volatility type. The first limiting component is autonomous, while the second is driven both by its own noise and by an inherited noise transmitted from the first component through an effective cross-kernel. This cross-kernel is the convolution of the two limiting Mittag-Leffler kernels and therefore combines the two memory structures. As a consequence, we obtain a short-time cross-decorrelation law: although the two components are coupled, their functional correlation vanishes at small time scales at an explicit polynomial rate. This time-dependent correlation distinguishes the limit from independent rough processes and from classical bivariate rough models with constant Brownian correlation.

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

Shifting-based Optimizable Linear Relaxations for General Activation Functions

arXiv:2606.20292v1 Announce Type: new Abstract: The use of neural networks (NNs) is rapidly increasing, including in safety- and security-critical domains. To provide formal guarantees about NN behavior, many verification methods rely on optimizable linear relaxations of activation functions. However, existing techniques depend on hand-crafted relaxations for each activation function. Extension to state-of-the-art activation functions therefore requires substantial manual effort. In contrast, our approach SLiR (Shifting-based Linear Relaxations) is broadly applicable, requiring only a Lipschitz constant or a set of critical points. SLiR parameterizes relaxations by their slope and computes the corresponding offset via a shifting procedure that ensures sound upper and lower bounds over the input domain, enabling efficient optimization while maintaining correctness. Our experiments show that SLiR produces tight relaxations across a wide range of practical activation functions and enables verification of up to 7.8x more properties compared to state-of-the-art methods.

20.
Nature (Science) 2026-06-17

Visualizing the impact of quenched disorder on 2D electron Wigner solids

作者:

Electron Wigner solids (WSs)1–12 provide an ideal system for understanding the competing effects of electron–electron and electron–disorder interactions, a central unsolved problem in condensed matter physics. Progress in this topic has been limited by a lack of single-defect-resolved experimental measurements as well as accurate theoretical tools to enable realistic experiment/theory comparison. Here we overcome these limitations by combining atomically resolved scanning tunnelling microscopy (STM) with neural-quantum-state quantum Monte Carlo (NQS-QMC) simulation of disordered 2D electron WSs to discover new disorder-induced physical regimes of correlated electron behaviour. STM was used to image the electron density (ne)-dependent evolution of electron WSs in gate-tunable bilayer MoSe2 (BL-MoSe2) devices with varying long-range (nLR) and short-range (nSR) disorder densities. These images were compared with NQS-QMC simulations using realistic disorder maps extracted from experiment, thus allowing the roles of different disorder types to be disentangled. We identify two distinct physical regimes for disordered electron WSs that depend on nSR. For nSR ≲ ne, the WS behaviour is dominated by long-range disorder and features extensive mixed solid–liquid phases, a new type of local re-entrant melting/crystallization and prominent Friedel oscillations. By contrast, when nSR ≫ ne, these features are suppressed and a more robust amorphous WS phase emerges that persists to higher ne, highlighting the importance of short-range disorder in this regime. Our work establishes a powerful framework for studying disordered quantum solids through a combined experimental–theoretical approach. A technique combining atomically resolved scanning tunnelling microscopy with neural-quantum-state quantum Monte Carlo simulation of disordered 2D electron Wigner solids establishes a powerful framework to enable the clear identification of two distinct defect-induced disorder regimes.

21.
arXiv (CS.AI) 2026-06-19

LoRDO: Distributed Low-Rank Optimization with Infrequent Communication

arXiv:2602.04396v2 Announce Type: replace-cross Abstract: Distributed training of foundation models via $\texttt{DDP}$ is limited by interconnect bandwidth. While infrequent communication strategies reduce synchronization frequency, they remain bottlenecked by the memory and communication requirements of optimizer states. Low-rank optimizers can alleviate these constraints; however, in the local-update regime, workers lack access to the full-batch gradients required to compute low-rank projections, which degrades performance. We propose $\texttt{LoRDO}$, a principled framework unifying low-rank optimization with infrequent synchronization. We first demonstrate that, while global projections based on pseudo-gradients are theoretically superior, they permanently restrict the optimization trajectory to a low-rank subspace. To restore subspace exploration, we introduce a full-rank quasi-hyperbolic update. $\texttt{LoRDO}$ achieves near-parity with low-rank $\texttt{DDP}$ in language modeling and downstream tasks at model scales of $125$M–$720$M, while reducing communication by $\approx 10 \times$. Finally, we show that $\texttt{LoRDO}$ improves performance even more in very low-memory settings with small rank/batch size.

22.
arXiv (math.PR) 2026-06-16

Malliavin Calculus for the stochastic Cahn-Hilliard equation driven by fractional noise

arXiv:2601.10490v2 Announce Type: replace Abstract: The stochastic partial differential equation analyzed in this work is the Cahn-Hilliard equation perturbed by an additive fractional white noise (fractional in time and white in space). We work in the case of one spatial dimension and apply Malliavin calculus to investigate the existence of a density for the stochastic solution $u$. In particular, we show that $u$ admits continuous paths almost surely and construct a localizing sequence through which we prove that its Malliavin derivative exists locally, and that its law is absolutely continuous with respect to the Lebesgue measure on $\bf R$, establishing thus that a density exists. A key contribution of this work is the analysis of the stochastic integral appearing in the mild formulation: we derive sharp estimates for the expectation of the $p$-th power ($p \geq 2$) of the $L^{\infty}(D)$-norm of this stochastic integral as well as for the integral involving the $L^{\infty}(D)$-norm of the operator associated with the kernel appearing in the integral representation of the fractional noise, all of which are essential for this study.

23.
arXiv (CS.LG) 2026-06-17

Reward hacking in physical reinforcement learning revealed by turbulent drag reduction

arXiv:2606.06227v2 Announce Type: replace-cross Abstract: A reinforcement-learning agent maximises its reward, which can diverge from the outcome its designer intended. In physical control the reward rarely closes that gap, and drag reduction in wall turbulence makes it concrete. A mass-conservation projection couples agents' outputs and erases the per-agent credit the policy gradient needs; a memoryless policy cannot resolve the slow near-wall cycle it acts on; and a pressure-gradient reward pays for nominal drag reduction by pumping power through the wall. Two degenerate controllers achieve large drag reductions while total dissipation rises, so the reported figure can mask a more wasteful flow. We trace each fault to its cause and fix it: a differentiable projection that restores credit, a recurrent policy with a widened sensing stencil, and a reward scored on the true wall power. The corrected controller acts on the flow within a closed energy budget, earning a conservative $17\%$ under honest accounting.

24.
medRxiv (Medicine) 2026-06-16

Enteral docosahexaenoic and arachidonic acid supplementation and retinopathy of prematurity: a re-analysis of randomized controlled trials in preterm infants

Background. A recent meta-analysis by Dang et al. [1] concluded that enteral supplementation with docosahexaenoic acid (DHA), with or without arachidonic acid (ARA) did not significantly affect retinopathy of prematurity (ROP) outcomes in preterm infants. Of four eligible trials that supplemented both DHA and ARA, only two contributed to each ROP outcome analyzed, and severe ROP was not assessed. Methods. We replicated the eligibility criteria and search strategy of Dang et al., restricted to trials that supplemented both DHA and ARA, and reanalyzed three ROP endpoints (any ROP, ROP requiring treatment, and severe ROP [stage 3 and/or treated]) using complete outcome records from all eligible trials. Crude risk ratios (RR) were pooled by Mantel-Haenszel fixed-effect meta-analysis. Gestational age-adjusted odds ratios (adjOR) were pooled on the log scale by inverse-variance random-effects meta-analysis with restricted maximum likelihood (REML) estimation of between-study variance and Hartung-Knapp confidence intervals. Results. Five trials were included; one trial was identified in our replicated search but was excluded by Dang et al. without a stated rationale. The pooled estimate for any ROP was consistent with Dang et al. (RR 0.87 [95% CI 0.71-1.08]; adjOR 0.70 [0.46-1.08]). For ROP requiring treatment, the crude RR suggested a lower risk but did not reach statistical significance (RR 0.60 [0.35-1.04]), whereas the gestational age-adjusted estimate indicated lower odds (adjOR 0.47 [0.23-0.94]). For severe ROP, DHA+ARA supplementation produced a significant protective effect in both unadjusted and adjusted models (RR 0.56 [0.36-0.86]; adjOR 0.42 [0.19-0.96]). Conclusions. When all eligible trials contribute to each endpoint and severe ROP is included as an outcome, enteral DHA+ARA supplementation reduces severe ROP and is associated with lower odds of ROP requiring treatment after adjustment for gestational age. These findings differ from the conclusions of Dang et al. and support reconsideration of DHA+ARA supplementation as a strategy to reduce sight-threatening ROP in preterm infants.

25.
arXiv (CS.AI) 2026-06-11

Time-Series Foundation Model Embeddings for Remaining Useful Life Estimation

arXiv:2606.11990v1 Announce Type: cross Abstract: Remaining Useful Life (RUL) prediction is essential for industrial predictive maintenance, yet many learning-based approaches rely on extensive feature engineering or large labeled datasets to train task-specific sequence models. In this work, we introduce a lightweight learning approach, in which we leverage a frozen pretrained time-series foundation model (TSFM) and combine it with a small regression head for RUL estimation from multivariate sensor streams. More specifically, we use Chronos-2 as a frozen backbone to extract context window features and train a lightweight regression neural network for RUL prediction. Experiments on real-world industrial sensor data from two device types show that Chronos-2 features consistently improve over recurrent, convolutional, Transformer-based, and gradient-boosting baselines under the same preprocessing and evaluation protocol. We further analyze the impact of context length and find that performance improves significantly with longer histories, indicating that TSFM representation offer a practical and data-efficient alternative for RUL estimation in industrial settings.