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01.
arXiv (quant-ph) 2026-06-15

Tantalum as a base material for superconducting integrated circuits

作者:
Evgeniy V. Zikiy↗Nikita S. Smirnov↗Stanislav A. Kotenkov↗Ilya A. Stepanov↗Julia A. Agafonova↗Daria A. Moskaleva↗Aleksei R. Matanin↗Anton I. Ivanov↗Dmitry O. Moskalev↗Julia A. Kurochkina↗Aleksander V. Andriyash↗Ilya A. Rodionov↗…

arXiv:2606.13750v1 Announce Type: new Abstract: The performance of superconducting integrated circuits for quantum applications is fundamentally limited by material-related losses. Tantalum, as an emerging material for next-generation quantum circuits, has attracted considerable attention in recent years after demonstrating breakthrough performance in both superconducting microwave resonators and qubits. Concurrently, a growing body of work is devoted to the operation of tantalum-based circuits and related fabrication techniques. This interest is further stimulated by tantalum thin films polymorphism resulting in a variety of its crystalline structure, superconducting properties, coherence, etc. Furthermore, tantalum circuits exhibit distinctive features in cryogenic experiments, which have not been observed in aluminum- or niobium-based ones. In this review, we summarize the recent research of tantalum thin films growth and phase selection mechanisms on various substrates, key aspects of fabrication and performance of superconducting circuit, including a material first-principles theoretical study. In conclusion, we address a number of open issues, including the role of \b{eta}-phase impurities, the effect of hydrofluoric acid solutions on chain characteristics, and the anomalous behavior of {\alpha}-tantalum chains at cryogenic temperatures.

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02.
arXiv (CS.LG) 2026-06-12

Limits of spectral learning under noise

作者:
Sabin Roman↗Ljupco Todorovski↗Saso Dzeroski↗Marta Sales-Pardo↗Roger Guimera↗

arXiv:2606.13067v1 Announce Type: new Abstract: Learning functional relationships from noisy data is a central problem in scientific inference. Spectral methods approximate unknown functions by expanding them in a basis and estimating the corresponding coefficients from data, but the stability of these coefficients under noise remains poorly understood. Here we study supervised regression with additive label noise using sparse spectral representations across multiple bases and dimensions. We show that noise induces a predictable drift in the learned coefficient vector whose magnitude depends on the effective number of active spectral modes. After whitening the empirical feature geometry, we derive a closed-form expression for the overlap between noisy and noiseless coefficient vectors, revealing a universal degradation curve governed by a single intrinsic noise scale. Numerical experiments across Fourier, Legendre, Bessel, and Haar bases confirm the theoretical prediction. The results demonstrate that spectral learning exhibits a fundamental noise threshold beyond which coefficient estimates become unstable, placing intrinsic limits on recovering functional structure from noisy data.

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03.
arXiv (CS.AI) 2026-06-19

ProMUSE: Progressive Multi-modal Uncertainty-guided Staged Evidential Alzheimer Disease Classification

作者:
Long Doan↗Branden Chen↗Ethan Litton↗Huan Huang↗Jiajing Huang↗Yixin Xie↗Weihua Zhou↗Nandakumar Narayanan↗Chen Zhao↗

arXiv:2606.19371v1 Announce Type: cross Abstract: Alzheimer's disease (AD) is a fatal disorder that destroys memory and cognitive skills in the elderly population. Most treatments for AD are effective in the early stage, leading to an increasing demand for early AD diagnosis. AD diagnosis increasingly relies on multimodal data such as clinical assessments, structural Magnetic Resonance Imaging (MRI), and Positron Emission Tomography (PET) imaging. However, MRI and PET acquisition remain costly and not universally accessible, making full-modality inference impractical in real-world clinical workflows. We propose ProMUSE, a Progressive Multi-modal Uncertainty Guided Staged Evidential Network that adaptively determines when additional modalities are necessary, helping reduce the overall cost of data acquisition while maintaining accuracy. ProMUSE first performs evidential classification using low-cost clinical data and quantifies uncertainty via a Dirichlet-based subjective logic model. When uncertainty exceeds a learned threshold, ProMUSE progressively incorporates MRI or PET features, fusing modality-wise belief and uncertainty through Dempster-Shafer theory to obtain a calibrated multimodal prediction. This staged acquisition strategy enables accurate diagnosis while minimizing reliance on expensive imaging. Experiments on ADNI, AIBL, and OASIS across CN-AD, CN-MCI, and MCI-AD tasks demonstrate that ProMUSE achieves competitive or superior accuracy compared to full-modality baselines while reducing MRI/PET usage by 50-90%, yielding substantial cost savings. These results highlight ProMUSE as a practical, uncertainty-aware, and resource-efficient solution for real-world AD screening.

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04.
arXiv (quant-ph) 2026-06-12

Kerr-induced nonreciprocal transparency and group delay in a hybrid cavity magnomechanical system

作者:
M. Amghar↗Noura Chabar↗Mohamed Amazioug↗Reem Altuijri↗Ameenah N. Al-Ahmadi↗Abdel-Haleem Abdel-Aty↗

arXiv:2606.13412v1 Announce Type: new Abstract: We propose a scheme for realizing nonreciprocal transparency, Fano resonances, and slow/fast light in a hybrid cavity magnomechanical system containing two YIG spheres and a mechanical resonator. The nonreciprocal behavior originates from the magnon Kerr nonlinearity, which induces direction-dependent frequency shifts and modifies the interference pathways among cavity photons, magnons, and phonons. We show that the hybrid system supports multiple transparency windows arising from magnon- and magnomechanical-induced interference processes. The Kerr interaction strongly reshapes these transparency features, producing asymmetric Fano line shapes and enabling controllable nonreciprocal transmission. Furthermore, the associated dispersion exhibits pronounced directional asymmetry, leading to giant differences in the group delay for opposite propagation directions and allowing reversible switching between slow- and fast-light regimes. We investigate the roles of hybrid coupling strengths and dissipation channels and identify parameter regimes where the nonreciprocal response is maximized. These findings establish Kerr-engineered magnomechanical systems as promising platforms for integrated nonreciprocal microwave photonics and quantum information technologies.

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05.
arXiv (CS.AI) 2026-06-15

AgentCyberRange: Benchmarking Frontier AI Systems in Realistic Cyber Ranges

作者:
Fengyu Liu↗Jiarun Dai↗Yihe Fan↗Wuyuao Mai↗Ziao Li↗Bofei Chen↗Jie Zhang↗Zheng Lou↗Bocheng Xiang↗Qiyi Zhang↗Xudong Pan↗Geng Hong↗…

arXiv:2606.14295v1 Announce Type: cross Abstract: Frontier AI systems are increasingly capable of cybersecurity tasks, including codebase inspection, vulnerability detection, and exploitation. However, evaluating their offensive capabilities remains constrained by limited access to open, reproducible, multi-host cyber ranges. Existing public benchmarks capture isolated skills such as CTF solving, vulnerability reproduction, and exploit generation, but often abstract away realistic intrusion workflows: discovering exposed services, gaining a foothold, collecting internal information, and expanding compromise across hosts. This gap makes it difficult to observe emerging risks early, because frontier AI systems are rarely evaluated under realistic attack conditions. We introduce AgentCyberRange, the first open, multi-range infrastructure for measuring autonomous cyber attack capability in realistic cyber ranges. It combines 110 vulnerabilities across 15 real web applications and 8 enterprise-like cyber ranges with 156 internal hosts, plus Cage, a toolchain for execution, orchestration, result collection, and verification. The benchmark covers two core stages: web exploitation, where agents explore exposed applications and validate vulnerabilities, and post exploitation, where agents turn an initial foothold into broader internal compromise. We evaluate six frontier AI systems under matched prompts and budgets. GPT-5.5 with Codex performs best, solving 16.1% of web exploitation tasks and 31.7% of post-exploitation tasks; with more concrete hints, these rates increase to 33.0% and 46.3%. We also observe out-of-benchmark findings, including unknown vulnerabilities in popular projects, and payload mutation that bypasses host defenses. These results show that open cyber-range evaluation is necessary for observing emerging offensive capabilities under realistic and reproducible conditions.

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

GH-ESD: Grounded Hypothesis-Driven Error Slice Discovery for Instance-Level Vision Tasks

作者:
Wei Zhang↗Chaoqun Wang↗Zixuan Guan↗Sam Kao↗Pengfei Zhao↗Peng Wu↗Sifeng He↗

Systematic failures of vision models on semantically coherent subsets, known as error slices, reveal limitations in robustness and evaluation. Existing slice discovery approaches largely model slices as clusters in representation space or combinations of predefined attributes. While effective for image-level classification, such formulations are insufficient for instance-level tasks such as object detection and segmentation, where failures often arise from contextual relational and spatially grounded visual patterns. We propose GH-ESD (Grounded Hypothesis-Driven Error Slice Discovery), a generate and verify framework that reformulates slice discovery as grounded hypothesis generation and statistical verification. GH-ESD constructs relational failure hypotheses using LLM priors and grounded visual evidence, discovers hypothesis slices at the instance level via Vision Language Models, and verifies them through statistical trend analysis over instance-level errors. We also introduce GESD (Grounded Error Slice Dataset), a new benchmark for instance-level error slice discovery, providing expert-defined and spatially grounded slices derived from detection and segmentation failures. Extensive experiments demonstrate that GH-ESD consistently outperforms baselines, improving Precision@10 by 0.10 (0.73 vs. 0.63) on the GESD benchmark for detection tasks, while also supporting segmentation scenarios. GH-ESD identifies interpretable slices that facilitate actionable model improvements. The GESD dataset will be made publicly available upon acceptance.

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07.
arXiv (CS.CL) 2026-06-12

Language Model Circuits Are Sparse in the Neuron Basis

作者:
Aryaman Arora↗Zhengxuan Wu↗Jacob Steinhardt↗Sarah Schwettmann↗

The high-level concepts that a neural network uses to perform computation need not be aligned to individual neurons (Smolensky, 1986). Language model interpretability research has thus turned to techniques which decompose the neuron basis into more interpretable units of model computation, such as sparse autoencoders (SAEs). However, not all neuron-based representations are uninterpretable. For the first time, we empirically show that MLP neurons are as sparse a feature basis as SAEs. We use this finding to develop an end-to-end gradient-based attribution pipeline for circuit tracing on the MLP neuron basis, which surfaces causally effective neurons on a variety of tasks. On a standard subject-verb agreement benchmark (Marks et al., 2025), a circuit of $\approx 10^2$ MLP neurons is enough to control model behaviour. On the multi-hop city-state-capital task from (Lindsey et al., 2025), we find a circuit in which small sets of neurons encode specific latent reasoning steps (e.g. mapping a city to its state), and can be steered to change the model's output. This work thus advances automated interpretability of language models without imposing additional training costs.

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08.
bioRxiv (Bioinfo) 2026-06-20

A network approach to DNA methylation clocks

作者:
Carcedo↗Yang↗S.-G↗Smiljanic↗Neunman↗Wennstedt↗Degerman↗Lizana↗

Biological age predicts health and lifespan better than chronological age, but remains difficult to measure. One leading molecular proxy for biological age is DNA methylation, which underlies age predictors known as "clocks". These clocks use penalized linear regression to predict chronological age from methylation levels using selected cytosine–guanine pairs (CpGs) along DNA. Although they predict chronological age within a few years and track mortality risk, there are several issues. Different clocks share a vanishingly small number of CpG sites, many of which show weak associations with age. Also, the clocks often do not transfer across methylation array platforms. This paper takes a network approach to better understand these issues. By using 12 public datasets from human blood, we build a co-methylation network of the sites that show the strongest age correlation. After pruning weak links, we find that it has a small number of large modules of covarying CpGs surrounded by many small modules and singleton sites. These modules are biologically interpretable, as they are associated with CpG island contexts and enriched for distinct Gene Ontology functions. We also map five established clocks onto this network (Horvath, Hannum, AltumAge, Skin & Blood, and Han) and find that they select some CpGs from the same module. This suggests that they are more similar than they appear. The network structure also suggests new ways to build clocks. A simple clock that retains one CpG per module matches the performance of established clocks. A second one, built from module-level principal components, outperforms all five established clocks in three validation cohorts and is transferable across array platforms (Illumina Infinium Methylation 450K or EPIC arrays). Overall, the network perspective shifts attention from individual CpG sites to modules of covarying sites. This perspective helps explain why DNA methylation clocks perform so well despite their differences and provides a more systematic approach for developing the next generation of aging biomarkers.

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09.
arXiv (CS.CL) 2026-06-15

Can professional translators identify machine-generated text?

作者:
Michael Farrell↗

This study investigates whether professional translators without prior specialized training can reliably identify short stories generated in Italian by artificial intelligence (AI). Sixty-nine translators took part in an in-person experiment, where they assessed three anonymized short stories - two written by ChatGPT-4o and one by a human author. For each story, participants rated the likelihood of AI authorship and provided justifications for their choices. While average results were inconclusive, a statistically significant subset (16.2%) successfully distinguished the synthetic texts from the human text, suggesting that their judgements were informed by analytical skill rather than chance. However, a nearly equal number misclassified the texts in the opposite direction, often relying on subjective impressions rather than objective markers, possibly reflecting a reader preference for AI-generated texts. Low burstiness and narrative contradiction emerged as the most reliable indicators of synthetic authorship, with unexpected calques, semantic loans and syntactic transfer from English also reported. In contrast, features such as grammatical accuracy and emotional tone frequently led to misclassification. These findings raise questions about the role and scope of synthetic-text editing in professional contexts.

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10.
bioRxiv (Bioinfo) 2026-06-10

APOSM: Pairwise preference learning improves generative small-molecule design

作者:
Dreisler↗M. W↗Michael↗Hatzakis↗N. S↗Boomsma↗

Small-molecule lead refinement is constrained by the cost of synthesizing and assaying candidates, making the surrogate models that prioritize compounds for experimental testing central to the design process. The reliability of such surrogates is limited by the noise and sparsity of screening measurements. We show that training the surrogate on pairwise comparisons between candidate molecules, rather than on absolute predicted scores, yields a substantially more reliable signal for active candidate selection in this regime. We develop APOSM, an active-learning algorithm that combines a fragment-based generator, a pairwise message-passing graph neural network surrogate, and probabilistic ranking inside a batched acquisition loop. On the Practical Molecular Optimization benchmark and a GPCR ligand rediscovery task, APOSM improves target attainment and sampling efficiency over unguided fragment-based optimization, the Graph-GA genetic algorithm, and a pointwise-regression ablation, with the largest gains on tasks where absolute scores are hardest to calibrate.

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11.
arXiv (CS.LG) 2026-06-12

Dolph2Vec: Self-Supervised Representations of Dolphin Vocalizations

作者:
Chiara Semenzin↗Faadil Mustun↗Roberto Dessi↗Pierre Orhan↗Alexis Emanuelli↗Yair Lakretz↗Gonzalo de Polavieja↗German Sumbre↗

arXiv:2606.12503v1 Announce Type: new Abstract: Self-supervised learning (SSL) has opened new opportunities in bioacoustics by enabling scalable modeling of animal vocalizations without the need for expensive manual annotation. However, current SSL models in this domain prioritize broad generalization across species and are not optimized for uncovering the fine-grained structure of individual communication systems. In this work, we collect and release a novel dataset of over five years of longitudinal recordings, from five known dolphins in a semi-naturalistic marine environment, an unprecedented resource for studying dolphin communication. We adapt the Wav2Vec2.0 Baevski et al. (2020) architecture to this domain and introduce Dolph2Vec, the first large-scale, species-specific SSL model trained exclusively on this data. We benchmark our model on two biologically relevant tasks: signature whistle classification and whistle detection. Dolph2Vec significantly outperforms general-purpose baselines in both tasks. Beyond performance, we show that learned embeddings and codebook structure capture interpretable acoustic units aligned with dolphin whistle categories and possibly sub-whistle structure, enabling fine-grained analysis of communication patterns. Our findings demonstrate how SSL can serve as both a model and a scientific tool to explore hypotheses in animal communication research.

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

Squeezing Enhancement in Lossy Multi-Path Atom Interferometers

作者:
Julian G\"unther↗Jan-Niclas Kirsten-Siem{\ss}↗Naceur Gaaloul↗Klemens Hammerer↗

arXiv:2409.04091v3 Announce Type: replace Abstract: This paper explores the sensitivity gains afforded by spin-squeezed states in atom interferometry, in particular using Bragg diffraction. We introduce a generalised input-output formalism that accurately describes realistic, non-unitary interferometers, including losses due to velocity selectivity and scattering into undesired momentum states. This formalism is applied to evaluate the performance of one-axis twisted spin-squeezed states in improving phase sensitivity. Our results show that by carefully optimising the parameters of the Bragg beam splitters and controlling the degree of squeezing, it is possible to improve the sensitivity of the interferometer by several dB with respect to the standard quantum limit despite realistic levels of losses in light pulse operations. However, the analysis also highlights the challenges associated with achieving these improvements in practice, most notably the impact of finite temperature on the benefits of entanglement. The results suggest ways of optimising interferometric setups to exploit quantum entanglement under realistic conditions, thereby contributing to advances in precision metrology with atom interferometers.

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13.
arXiv (CS.CV) 2026-06-16

Deep Learning in Seismic Interpretation: Federated Advances in Salt Dome Segmentation

作者:
Muhammad Zain Mehdi↗Muhammad Zaid↗Owais Aleem↗

Salt-dome delineation is a critical, high-impact task in subsurface geological interpretation, driving decisions in hydrocarbon exploration, reservoir modeling, and drilling safety. While convolutional encoder-decoder architectures have delivered significant improvements in automated salt segmentation, their widespread application is severely limited by data sovereignty concerns, dataset bias, and the scarcity of labeled seismic volumes. This paper introduces FedSaltNet, a Federated Learning (FL) framework explicitly engineered for robust, generalizable, and privacy preserving salt-dome segmentation. We couple a lightweight Small U-Net backbone, chosen for its efficiency and regularization properties with a novel Foreground-Weighted (FG-WEIGHTED) aggregation strategy designed to tackle domain-specific class imbalance. Through an extensive comparative study emulating non-IID conditions across four diverse seismic datasets (TGS, SEAM, F3, GBS), we demonstrate two critical findings: The FG-WEIGHTED algorithm effectively mitigates data heterogeneity, yielding a 4.0% relative improvement in Intersection over Union (IoU) over the best conventional FL method. The simple U-Net architecture proved essential, outperforming the higher capacity ResNet-18 U-Net variant by 166% in average IoU, underscoring the necessity of architectural simplicity in data-constrained federated environments. FedSaltNet provides a validated, high-performance solution that establishes the viability of federated deep learning for collaborative, next-generation subsurface interpretation.

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14.
arXiv (CS.LG) 2026-06-16

Biarchetype analysis for univariate functional data. An application to macroeconomic financial time series

作者:
Aleix Alcacer↗Rafael Benitez↗Vicente J. Bolos↗Irene Epifanio↗

arXiv:2606.15881v1 Announce Type: cross Abstract: We introduce biarchetype analysis for the first time in the context of univariate functional data. This unsupervised methodology extends archetype analysis by simultaneously identifying archetypal structures across both the cases (countries, in our application) and the temporal argument. Both cases and time points are expressed as mixtures of biarchetypes, yielding a concise and highly interpretable representation of complex functional observations. Although biarchetype analysis is not intended as a clustering technique, it offers superior interpretability compared with biclustering approaches, as it is based on extreme, representative patterns rather than average centroids, thereby enhancing human comprehension. We apply the proposed method to 10-year government bond yields of European countries over the period 2001-2025. The results identify three distinct time regimes (the pre-crisis period, the euro-area sovereign debt crisis, and the post-crisis period), and reveal Germany, Greece, and Hungary as country archetypes.

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15.
arXiv (math.PR) 2026-06-18

A Unified Approach to Beta Moments, Combinatorial Identities, and Random Walks

作者:
Puja Pandey↗Palaniappan Vellaisamy↗

arXiv:2605.05420v2 Announce Type: replace Abstract: The study of random walks has increasingly been popular across diverse disciplines such as statistics, mathematics, quantum physics, where they are used to model paths consisting of successive random steps in a mathematical space. A fundamental quantity of interest is the probability that a simple symmetric random walk returns to the origin after 2n steps. In this paper, we develop a unified probabilistic approach that connects the return probabilities in arbitrary dimensions with moment representations. Using this framework, we provide probabilistic proofs of several combinatorial identities involving beta and gamma functions, and derive new combinatorial identities in general dimensions.

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

Calibrated Triage, Not Autonomy: Confidence Estimation for Medical Vision-Language Models

作者:
Reza Khanmohammadi↗Kundan Thind↗Mohammad M. Ghassemi↗

A vision-language model can answer a question about a medical image fluently and confidently while barely using the image, leaning instead on language priors. In medicine this is the failure that matters most, because the answer looks trustworthy and is not, and the only protection is a confidence score reliable enough to tell the system when to abstain. We ask a deployment question rather than an accuracy one: how much imaging work a model can safely handle alone, and which confidence signal makes that possible. We evaluate seven confidence estimators across five open-weight LVLMs and three medical visual-question-answering datasets spanning broad clinical imaging, radiology, and pathology, with every probe trained only on natural images and applied without adaptation. Recast as bounded selective prediction (automate a case only when confidence clears a threshold, defer the rest), the comparison is cautionary. The standard metrics are poor guides: discrimination barely separates the methods, and the weak calibration of a cheap self-report is cheaply removed by off-domain temperature scaling without changing deployable yield. What distinguishes a usable estimator is the high-confidence region a clinician acts on: the weakest baselines are confidently wrong on 41 to 45 percent of their errors against 1 to 4 percent for the best probe, and no estimator is reliably best across domains or models. Safe handoff is governed at two levels: base-model competence sets a ceiling, so a well-calibrated score recovers roughly a third of radiology cases at a 20 percent error tolerance but almost none of pathology; the confidence layer then decides how much of that ceiling is reachable. The usable role today is calibrated triage, not autonomy: automate the cases a calibrated score marks safe, route the rest to a clinician. We release all outputs, correctness judgments, and confidence scores, with code.

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

EverydayGPT: Confidence-Gated Routing for Efficient and Safe Hybrid GPT-RAG Conversational QA

作者:
Jaspreet Singh Nahal↗

Standard Retrieval-Augmented Generation (RAG) pipelines route every query through retrieval and generation unconditionally, incurring unnecessary computation and propagating low-quality context to the generator. We introduce EverydayGPT, a lightweight conversational QA system built around a Confidence-Gated Routing (CGR) mechanism that formalises the routing decision as a joint policy over retrieval distance and extraction adequacy. The backbone is a 205M-parameter GPT trained from scratch on 10B tokens of FineWeb-Edu. CGR avoids invoking the costly GPT pathway (~5.9s) for 85 percent of queries by resolving them via fast RAG extraction (~45 ms), yielding over 120x latency reduction on the majority of queries while maintaining answer quality. On a 500-question in-domain benchmark, the system achieves F1 = 0.226 +/- 0.004 compared to 0.171 for GPT-only and 0.210 for unconditional RAG. Gains over strong baselines are modest but consistent, while efficiency improvements are substantial (6.3x mean latency reduction). A structured grounding audit finds no unsupported claims in the sampled set, with explicit scope limitations. We position this work as a study of routing strategies under resource constraints rather than a claim of state-of-the-art performance.

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

Shift-Invariant Attribute Scoring for Kolmogorov-Arnold Networks via Shapley Value

作者:
Wangxuan Fan↗Ching Wang↗Siqi Li↗Nan Liu↗

arXiv:2510.01663v2 Announce Type: replace-cross Abstract: For many real-world applications, understanding feature-outcome relationships is as crucial as achieving high predictive accuracy. While traditional neural networks excel at prediction, their black-box nature obscures underlying functional relationships. Kolmogorov–Arnold Networks (KANs) address this by employing learnable spline-based activation functions on edges, enabling recovery of symbolic representations while maintaining competitive performance. However, KAN's architecture presents unique challenges for network pruning. Conventional magnitude-based methods become unreliable due to sensitivity to input coordinate shifts. We propose ShapKAN, a pruning framework using Shapley value attribution to assess node importance in a shift-invariant manner. Unlike magnitude-based approaches, ShapKAN quantifies each node's actual contribution, ensuring consistent importance rankings regardless of input parameterization. Extensive experiments on synthetic and real-world datasets demonstrate that ShapKAN preserves true node importance while enabling effective network compression. Our approach improves KAN's interpretability advantages, facilitating deployment in resource-constrained environments.

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19.
bioRxiv (Bioinfo) 2026-06-22

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

作者:
Ellerstrand↗S. J↗Churcher↗A. M. J↗Kutschera↗V. E↗Hansson↗

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.

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20.
arXiv (CS.LG) 2026-06-12

How Useful is Causal Invariance for Domain Adaptation in Finite-Sample Settings?

作者:
Julia Kostin↗Kasra Jalaldoust↗Elias Bareinboim↗Samory Kpotufe↗Fanny Yang↗

arXiv:2606.12680v1 Announce Type: new Abstract: Machine learning models often degrade when they are deployed on a target distribution that differs from the source distributions they were trained on. Recent work in causality-based domain generalization has shown how shared causal structure between domains can induce invariant predictors, e.g., models on a subset of features which have stable risk across structured domain shifts. However, the extent to which such population-level causal invariances can lead to gains in finite-sample settings remains underexplored. In particular, in practice we often have access to a few labeled target samples, a setting called supervised domain adaptation (sDA). In this paper, we explore when (full or partial) causal knowledge can provably improve supervised domain adaptation. As a first step, we study linear regression, where full or partial causal knowledge specifies a collection of invariant or possibly invariant feature subsets, each yielding a source-trained candidate predictor. We derive matching upper and lower bounds showing that finite-sample gains are governed by the target-risk margins separating the candidates, together with the finite-source estimation error. When these margins are sufficiently large relative to $n_Q$, an adaptive aggregation procedure can match the best candidate predictor while avoiding negative transfer relative to target-only learning. On the other hand, when the margins are too small, no algorithm can reliably exploit the candidate collection to obtain faster finite-sample rates. We further connect these margins to structural shift magnitude in linear SCMs and validate the theory on real-world causal benchmarks.

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

Taming I2V models for Image HOI Editing: A Cognitive Benchmark and Agentic Self-Correcting Framework

作者:
Jiayi Gao↗Qingchao Chen↗Yuxin Peng↗Yang Liu↗

Current image editing methods excel at static attributes but fail at complex Human-Object Interactions (HOI), a critical challenge unaddressed by existing benchmarks that conflate HOI with static attributes, relying on global metrics incapable of simultaneously assessing dynamic interaction validity and entangled human-object pair preservation. Thus, we first introduce HOI-Edit, a comprehensive benchmark with three progressive cognitive levels, which features an automated metric HOI-Eval that reliably evaluates instance-level interaction by letting VLM Q&A after thinking with images containing grounded Human-Object pairs. Considering the task's essence of remodeling dynamic relationships, we benchmark Image-to-Video (I2V) models, finding them inherently suited for dynamic editing due to their temporal generation capabilities. Crucially, beyond superior performance, this capability provides a "replay of the failure process," offering unique diagnosability into why errors occur. We thus propose SCPE (Self-Correcting Process Editing), a novel, agentic self-correcting framework that constrains the generation of I2V models through iteratively refined prompts, enabling the generated videos to more accurately present the target HOI. Extracted frames from these videos are the final editing results. On HOI-Edit, SCPE achieves performance competitive with state-of-the-art (SOTA) editing models like Nano Banana on interaction. Code is available at https://github.com/oceanflowlab/HOI-Edit.

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22.
arXiv (CS.AI) 2026-06-19

ITNet: A Learnable Integral Transform That Subsumes Convolution, Attention, and Recurrence

作者:
Ashim Dhor↗Rasel Mondal↗Pin Yu Chen↗

arXiv:2606.19538v1 Announce Type: new Abstract: Convolutional networks, recurrent networks, and transformers each encode different inductive biases – locality, sequential memory, and content-dependent pairwise interaction – and have remained mathematically distinct since their inception. We show that this fragmentation reflects not a fundamental diversity in how signals should be processed, but rather incomplete views of a single underlying mathematical object: a learnable integral transform. We introduce the Integral Transform Network (ITNet), a unified architecture built around a learnable kernel that depends jointly on positions and features. This kernel is implemented as a small neural network, specifically an MLP, that models pairwise interactions, enabling the model to adapt its behavior from data. We show that convolution, self-attention (including multi-head), and autoregressive recurrence (including LSTM, GRU, S4, and Mamba) arise as special cases under appropriate parameterizations, and that ITNet is a universal approximator of continuous operators. To make this practical, we develop tiled kernel fusion, importance-weighted Monte Carlo integration, and learned low-rank factorization, enabling efficient and scalable computation. A single ITNet architecture with a shared operator and lightweight modality-specific encoders matches or exceeds specialized baselines on ImageNet-1K , GLUE, ModelNet40, VQA\,v2 and NLVR2. The results demonstrate that a single learned interaction mechanism can recover the behavior of all three architectural families from data.

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23.
bioRxiv (Bioinfo) 2026-06-18

A unified smoothing framework for protein domain bigram model

作者:
Cui↗Iyer↗Durand↗

Biomolecular sequences can be represented as strings over an alphabet, an analogy that has motivated many applications of computational linguistic techniques to biological problems. However, such methods must be adapted to the characteristic scale and organization of biomolecular data. Here, we consider the problem of bigram smoothing for multidomain protein architectures, where domain bigram frequency data is extremely sparse and differs from textual data in alphabet size, string length distribution, the relationship between bigram and unigram frequencies, tandem repeat lengths, and the distribution of domain adjacencies. Moreover, some domain combinations are unobserved because they are biologically incompatible, others because the data are incomplete. A smoothing method that distinguishes these two cases is required. We propose a unified smoothing framework based on interpolation that can be tuned to accommodate different bigram data characteristics. Within this framework, we design specific model variants suited to protein domain bigram data: these assign low adjusted counts to pairs that are likely incompatible, while making appropriate adjustments for undersampled pairs. We demonstrate empirically that this approach distinguishes the two cases while preserving the characteristic signatures of multidomain data.

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24.
arXiv (CS.CL) 2026-06-12

MiniPIC: Flexible Position-Independent Caching in <100LOC

作者:
Nathan Ordonez↗Thomas Parnell↗

Retrieval-augmented and agentic workloads repeatedly prefill recurring predictable structured inputs (which we call "spans") such as documents and code files. Yet, prefix caching in engines such as vLLM cannot reuse their KV entries unless they share identical prefixes with another request, while Position-Independent Caching (PIC) implementations within production-grade inference servers typically either require substantial server code changes or keep KV state outside the server, incurring host-to-device transfer overhead. We present Minimalistic PIC (MiniPIC): a minimal, flexible and fast vLLM design built from two ingredients: positional-encoding-free KV cache and user-controlled cache-reuse primitives. MiniPIC stores unrotated K vectors in the KV cache, applies RoPE to K tiles inside attention using per-request logical positions, and exposes three user-facing and token-level primitives: block-aligned padding, span separator (SSep), and prompt depend (PDep), that modify hashing behavior and effective block-level causal attention structure. With fewer than 100 lines of core-engine changes plus a custom attention backend, these primitives are sufficient to realize multiple PIC methods, including Block-Attention, EPIC, and Prompt Cache, within the same running vLLM instance, while natively integrating with KV cache CPU offload implementations. On 2WikiMultihopQA, MiniPIC with interleaved scheduling improves prefill throughput by 49% over baseline vLLM, reduces cached-span time-to-first-token by up to two orders of magnitude, preserves the linear prefill scaling of uncached spans, and incurs only 5.7% worst-case overhead.

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25.
arXiv (math.PR) 2026-06-17

Limit theorems for descents and inversions of shelf-shuffles

作者:
Alexander Clay↗

arXiv:2510.00343v2 Announce Type: replace Abstract: We prove central limit theorems for the number of descents and inversions of permutations produced by shelf-shuffles. These are a model for casino card shuffling machines. We show the asymptotic normality of the number of descents in two limiting regimes depending on the ratio of cards to shelves. On the other hand, we study the inversions by employing a modification of the techniques from Islak's analysis of the statistics of riffle shuffles. In particular, we obtain a bound for the rate of convergence for inversions that is independent of the number of shelves.

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