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01.
Nature (Science) 2026-06-22

Isotopic evidence for a cold and distant origin of 3I/ATLAS

Interstellar objects provide the only directly observable samples of icy planetesimals formed around other stars, and can therefore provide insight into the diversity of physical and chemical conditions occurring during exoplanet formation1−3. Here we report isotopic measurements of the interstellar comet 3I/ATLAS, which reveal an elemental composition unlike any Solar System body. The water in 3I/ATLAS is enriched in deuterium, at a level of D/H = (0.98 ± 0.06)%, which is more than an order of magnitude higher than in known comets, while its range of 12C/13C ratios (141–191 for CO2 and 123–172 for CO) exceeds typical values found in the Solar System, as well as nearby interstellar clouds and protoplanetary disks. Such extreme isotopic signatures indicate formation at temperatures  ≲ 30 K in a relatively metal-poor environment. When interpreted with respect to models for Galactic chemical evolution, the carbon isotopic composition implies that 3I/ATLAS may have accreted as long ago as 12 billion years, following a period of intense, early star formation. 3I/ATLAS thus represents a preserved fragment of an ancient planetary system.

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

Creating and Evaluating K-12 GenAI Assessment Graders Through Context Engineering

arXiv:2606.12422v1 Announce Type: cross Abstract: The integration of large language models (LLMs) into educational assessment represents a transformative shift in classroom grading practices. While automated scoring systems and machine learning techniques have existed for decades, generative AI (GenAI) now enables educators to implement standards-based grading (SBG) with unprecedented efficiency and scale. This paper examines the theoretical foundations and evaluates an LLM grader that uses commercially available foundation models with context and prompt engineering to score student work against a rubric. Drawing on an empirical interrater agreement study using Massachusetts Comprehensive Assessment System (MCAS) data, we observed the Quadratic Weighted Kappa (QWK) and Proportional Reduction in Mean-Squared Error (PRMSE) across mathematics, science, and ELA, using Claude Sonnet 4, Haiku 4.5, GPT-5, and GPT-5 Mini. The results demonstrate that LLM graders, especially when based on foundational models with more parameters, achieve substantial agreement with human raters in mathematics and science assessments, while the performances vary in ELA, suggesting generic foundation models can be effective at scoring in given contexts. Additional analysis of teacher and student feedback reveals strong acceptance of AI-generated narrative feedback but skepticism toward numerical scores, suggesting that LLMs function most effectively as formative tools rather than summative evaluators. Our findings indicate that thoughtfully designed hybrid models that combine AI efficiency with teacher judgment can reduce workload, enhance feedback quality, and support equitable assessment practices without displacing professional expertise.

03.
bioRxiv (Bioinfo) 2026-06-24

InVitroGap: an open-source tool for automated quantification of wound closure in the in vitro scratch assay

Abstract Background and Objective: Scratch assays are widely used to study wound closure in vitro, but quantitative image analysis remains constrained by manual variability, proprietary workflows, and tools requiring programming expertise. We developed InVitroGap, a Python-based application with a browser-accessible interface for automated quantification of scratch assay closure from sequential microscopy images. Methods: RCC-ER and Renca cells were seeded in 96-well ImageLock plates and scratched using a WoundMaker device for uniform linear wounds or a 200 uL pipette tip for crisscross wounds. Phase-contrast time-lapse images acquired at 0, 24, and 48 h with an IncuCyte SX5 system were independently analyzed using IncuCyte 2023A Rev2 and InVitroGap. The InVitroGap pipeline combines Gaussian smoothing, gradient-based texture mapping, adaptive percentile thresholding, and morphological post-processing to quantify wound confluence and relative wound density (RWD). Agreement was evaluated using paired comparisons, Pearson and Spearman correlations, Bland-Altman analysis, and mean absolute error (MAE). Results: InVitroGap measurements closely tracked IncuCyte outputs across both cell lines, with no significant between-method differences (p > 0.05), strong pooled correlations (R square = 0.964 for RWD; R square = 0.983 for wound confluence), and small mean biases (absolute bias [≤] 1.64%). The tool successfully processed crisscross wounds from brightfield image series, and a complete four-timepoint series was analyzed in approximately 10 seconds, with robust performance across distinct cell morphologies and wound geometries. Conclusions: InVitroGap provides a transparent, computationally efficient, and platform-independent alternative for scratch assay analysis, delivering performance comparable to commercial systems while remaining freely accessible at https://invitrogap.vercel.app/.

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

Naive Visual Memory is Not Enough: A Failure-Mode Study of GUI Agents

Graphical User Interface (GUI) agents are increasingly used to automate complex computer tasks across applications, websites, and operating systems. To improve their reliability, recent work has introduced experiential memory, where agents retrieve prior trajectories to guide decision-making in similar states. More recent approaches further extend this idea to visual memory by storing and retrieving screenshots from past interactions, providing agents with richer contextual information than text-only memories. However, the effect of visual memory in GUI agents remains insufficiently understood: it is unclear which failures visual memory mitigates, or which failures it exacerbates. To systematically analyze the effect of visual memory, we introduce a taxonomy of four GUI agent failures (i.e., cognitive failure, visual state misunderstanding, hidden operation blindness, and grounding error) that map to distinct stages of the perception-reasoning-action pipeline. We find that prepending full-image memory has a divergent effect on the failure distribution: it reduces state-level failures but worsens action-level ones, and increases hidden operation blindness and grounding error. Motivated by this finding, we propose Action-Grounded Visual Memory (AGMem), an action-grounded memory framework for GUI agents. The core idea of AGMem is to store image crops that capture the local GUI region closely related to a successful action or a recovery, rather than storing full screenshots. Experiments on OSWorld show that AGMem improves task success rates by 33.3 % over full-image memory. These results demonstrate that AGMem is an effective representation for visual memory in GUI agents.

05.
arXiv (quant-ph) 2026-06-12

Cayley's First Hyperdeterminant is an Entanglement Measure

arXiv:2504.15511v2 Announce Type: replace Abstract: Previously, it was shown that both the concurrence and $n$-tangle on $2n$-qubit pure quantum states can be expressed in terms of Cayley's first hyperdeterminant [dobes2024qubits], indicating that Cayley's first hyperdeterminant, denoted $\mathrm{hdet}$, captures some aspects of a state's $2n$-way entanglement. In this paper, we rigorously prove that on both pure and mixed states, $|\mathrm{hdet}|^{2/d}$ is identically zero on separable states, is an LU invariant, and is non-increasing on average under LOCC, thus demonstrating that $|\mathrm{hdet}|^{d/2}$ is a physically meaningful and legitimate entanglement measure. Moreover, we discuss a few key examples to illustrate the particular type of entanglement Cayley's first hyperdeterminant is detecting: genuine full $d$-level GHZ-type entanglement across all $2n$ parties. Combined, this establishes Cayley's first hyperdeterminant (or $|\mathrm{hdet}|^{2/d}$ to be precise), as a genuine, physically significant generalization of the concurrence and the $n$-tangle to $2n$-qudit states.

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

Geometric Domain Adaptation via Optimal Transport for Linear Regression in R^2

arXiv:2606.14023v1 Announce Type: cross Abstract: Optimal Transport has become recently a powerful method for domain adaptation by aligning source and target distributions. We study a supervised domain adaptation problem where source and target domains are related by a rotation or a translation or a homothety in $\mathbb{R}^2$. We prove that the optimal transport map recovers the underlying map when using a $p-$norm cost with $p \geq 2$. Based on this insight, we develop a method combining $K-$means and optimal transport to estimate the underlying map, enabling adaptation of linear regression models when target data is scarce. Simulations demonstrate improved performance over baseline methods. Rather than relying on highly expressive deep learning architectures, we focus on classical machine learning models to emphasize interpretability and theoretical insight. This perspective allows us to explicitly characterize the role of optimal transport in recovering geometric transformations such as rotations, translations, and homotheties. Our contributions include a theoretical result linking optimal transport and rotations, translations and homothecies in $\mathbb{R}^2$, and a practical method for adaptation in linear regression offering both conceptual clarity and applied value in domain adaptation tasks in this space.

07.
bioRxiv (Bioinfo) 2026-06-16

Phylogenetic tree inference using generative models

Accurate inference of phylogenetic trees is fundamental to evolutionary biology, yet existing methods rely on complex pipelines involving multiple sequence alignment, explicit evolutionary models, and computationally intensive tree search procedures. Here, we present BetaInfer, a generative framework that reformulates phylogenetic tree inference as a sequence transduction problem. BetaInfer leverages hybrid transformer-based architectures to directly map sets of unaligned sequences to phylogenetic trees represented in Newick format. Trained on large-scale simulated evolutionary data with known ground truth, BetaInfer learns to capture complex evolutionary signals directly from sequence data. Ensemble-based generation of multiple candidate trees further improves robustness, reducing reconstruction error by over 30% relative to single predictions. Across extensive evaluations on both simulated and empirical datasets, BetaInfer achieves competitive performance relative to state-of-the-art phylogenetic pipelines, matching, and in some cases exceeding, the accuracy of established likelihood-based and distance-based methods under a wide range of conditions. Interpretability analyses reveal that BetaInfer leverages internal pairwise-distance computations to synthesize evolutionary relationships into an integrated, global representation that supports direct tree generation. Together, these results demonstrate that generative models can serve as a viable and scalable alternative to standard phylogenetic pipelines.

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

cAPM: Continual AI-Assisted Pace-Mapping with Active Learning

arXiv:2606.19373v1 Announce Type: cross Abstract: Ventricular tachycardia is a life-threatening rhythm disorder and a major cause of sudden cardiac death. Pace-mapping is a clinical procedure for identifying the intervention target during catheter ablation of VT. It requires clinicians to pace different sites in the ventricles and rapidly interpret the resulting electrocardiograms to determine where to pace next or whether a target site has been identified. Active learning AI models have been proposed to guide clinicians to the next pacing site, showing promise in reducing the number of pacing sites and improving the efficiency of pace-mapping. Existing methods require retraining each target without the ability to transfer knowledge across multiple VTs within the same patient or across patients. We introduce cAPM for continuous AI-assisted pace-mapping to capture and transfer knowledge accumulated from past pace-mapping data to reduce the number of pace-mapping data needed for future target VTs. This is made possible by a task-agnostic surrogate neural network that learns the mapping from pacing sites to 12-lead ECG morphology, an active-learning strategy that refines this surrogate model by selecting the most informative pacing site for each target, and a continual learning strategy to do so sequentially while retaining knowledge from prior targets. Evaluated on an in-silico testbed consisting of sequentially-presented localization tasks across different physiological conditions and ventricular geometries, cAPM with and without replay of past data samples achieved an 81% probability of localizing within clinical tolerance (5 mm accuracy) using 4.5 pace-mapping sites, compared to the state-of-the-art active-learning method achieving 38% probability using 13.7 pacing sites. These results provide a strong basis for preparing cAPM towards in-vivo preclinical and clinical studies where it can be used to guide pace-mapping.

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

An Empirical Investigation of Pre-Trained Deep Learning Model Reuse in the Scientific Process

arXiv:2603.13584v2 Announce Type: replace-cross Abstract: Deep learning has achieved recognition for its impact within natural sciences, yet the prohibitive financial and technical cost of training models from scratch inhibit adoption. Following software engineering community guidance, natural scientists are reusing pre-trained deep learning models (PTMs) to amortize these costs. While prior works recommend PTM reuse patterns, we present the first empirical study of PTM reuse patterns in the natural sciences, quantifying the utilization and impact of PTM reuse within the scientific process across 17,718 peer reviewed, open access papers. Our results show that "Biochemistry, Genetics and Molecular Biology" has outpaced other natural scientific fields in PTM reuse, "adaptation" reuse is the most prevalent PTM reuse pattern identified across all natural science fields, and the "testing" stage of the scientific process has been most impacted by PTM integration.

10.
arXiv (CS.LG) 2026-06-16

Incentives and Evidence in Learned Service Orchestration

arXiv:2606.16555v1 Announce Type: cross Abstract: Reinforcement learning for service orchestration has been the subject of sustained research for over a decade, yet it is not used in production at scale. The usual explanation is that learned controllers degrade under delayed and noisy telemetry, workload shifts, and uncontrolled tenants. We test whether existing evidence supports that explanation. We evaluate three highly influential RL-based orchestration systems spanning resource allocation, DAG scheduling, and autoscaling, using pre-registered predictions about comparative degradation under production-relevant perturbations and paired inference with family-wise error correction. Across the tests, most predicted performance reversals do not occur. Diagnostic analyses show that these outcomes often reflect comparator collapse, artefact limitations, or evaluation choices rather than evidence that learned controllers tolerate the perturbations. One apparent advantage under observation lag is roughly fortyfold compared to a Kubernetes HPA-equivalent controller. Another widely cited result cannot be reconstructed from its released artefact, and the strongest reproducible margin is far smaller than the published results. Conclusions also reverse under changes in perturbation magnitude and evaluation mode. Based on these results and broader patterns in the literature, we identify an institutional problem. Publication and review incentives favour benchmark gains against convenient comparators, even when those gains provide little evidence of deployment performance. We argue that the problem is not solely technical. Rather, it is institutional, so learned orchestration needs production-grade comparators, registered perturbation models, separate operational metrics, and publication criteria that reward reproducible operational evidence. Without these changes, the literature can grow without establishing whether learning improves orchestration.

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

Debiasing Without Protected Attributes: Latent Concept Erasure from Textual Profiles

Most fairness research in NLP assumes direct access to protected attributes such as gender, race, or nationality. In practice, however, such information is often unavailable due to privacy constraints, missing metadata, or legal restrictions, even though models may infer it from indirect textual cues. This raises a key question: can debiasing succeed without direct access to sensitive attributes? We propose H-SAL, which performs post-hoc concept and attribute erasure using self-description text as an implicit debiasing signal. To support this setting, we introduce a multi-domain Stack Exchange-based fairness benchmark for helpfulness prediction that includes both explicit and implicit signals, enabling comparison between standard debiasing with protected labels and debiasing without access to sensitive information. Across encoder and decoder-only language models, we find that implicit self-description often matches or outperforms explicit-label-based debiasing. Our results broaden representation-level fairness research and provide a new benchmark for studying debiasing under realistic data constraints.

12.
arXiv (CS.CV) 2026-06-17

DiFlow-TTS: Compact and Low-Latency Zero-Shot Text-to-Speech with Discrete Flow Matching

Zero-shot text-to-speech (TTS) has made significant progress in replicating unseen voices, yet balancing generation quality and inference efficiency remains challenging. Autoregressive models suffer from high latency, while diffusion-based approaches are constrained by training-time configurations. Moreover, most flow-based methods operate in continuous space, which introduces optimization challenges because continuous token spaces are inherently more complex than discrete ones. To address these limitations, we propose DiFlow-TTS, a novel zero-shot TTS framework based on discrete flow matching. The model consists of a deterministic Phoneme-Content Mapper for linguistic modeling and a Factorized Discrete Flow Denoiser that simultaneously generates prosody and acoustic token streams. Experimental results demonstrate the effectiveness of our approach across multiple evaluation metrics.

13.
arXiv (CS.AI) 2026-06-11

Towards an Inferentialist Account of Information Through Proof-theoretic Semantics

arXiv:2605.05368v5 Announce Type: replace-cross Abstract: Information is one of the most widely-discussed concepts of the current era. However, a great deal of insightful work notwithstanding, it is yet to be given wholly convincing logical or mathematical foundations. Without them, we lack adequate reasoning tools for understanding the complex ecosystems of systems upon which the society depends. We seek to rectify this by taking a first step towards developing an inferentialist semantic theory of information. There are three key interacting components. First, conceptual analysis: the metaphysics of information. Dretske expressed the key concepts of information in terms of intentionality, truth, and transmissibility. We replace truth with inferability, and trace the consequences of this replacement. Second, logic: proof-theoretic semantics (P-tS) provides a mathematical-logical realization of inferentialist reasoning. Using P-tS, we develop the first steps towards a mathematical-logical theory of an inferentialist primitive unit of information, the 'inferon'. This proof-theoretic approach counterpoints the model-theoretic view of information articulated in situation theory. Furthermore, we argue that it facilitates addressing all three components of van Benthem and Martinez's categorization of the understandings of information, as range, as correlation, and as code. Our focus is on information-as-correlation. Third, systems: the P-tS tools we develop provide the basis for a mathematical account of distributed systems modelling – a key tool from informatics for understanding the organization of information processing systems. This yields a reasoning-based theory of information flow in models of distributed systems. Overall, we seek to give a conceptually rigorous mathematical-logical account of information and its role within informatics, grounded in inference and reasoning.

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

GRACE: Step-Level Benchmark for Faithful Reasoning over Context

Many reasoning tasks require models to reason over input context, from document-grounded question answering to rule-based deduction. Chain-of-Thought (CoT) prompting produces traces that appear transparent, yet individual steps can silently deviate from the source evidence, even when the final answer is correct. Existing methods detect hallucinations at the response level but fail to identify where in the chain a failure occurs or what type it is. We introduce GRACE, the first human-annotated step-level faithfulness benchmark with a data-driven error taxonomy for context-grounded textual reasoning. GRACE covers CoT traces from 10 models across 4 source datasets, with each step annotated for faithfulness, error category, and natural language explanation. A data-driven taxonomy, discovered bottom-up via unsupervised clustering, organizes failures into two tracks: GRACE-Inference (deductive errors) and GRACE-Grounding (factual grounding errors), with four categories each. The evaluation set is human-annotated and challenging by design. Our experiments reveal substantial headroom for current models. In addition, integrating step-level faithfulness signals into reinforcement learning pipelines improves both downstream accuracy and reasoning reliability.

15.
arXiv (CS.CL) 2026-06-11

ProcessThinker: Enhancing Multi-modal Large Language Models Reasoning via Rollout-based Process Reward

Visual question answering increasingly requires multi-step reasoning. Recent post-training with reinforcement learning under verifiable rewards (RLVR) and Group Relative Policy Optimization (GRPO) can improve multimodal reasoning, but most approaches rely on sparse outcome-only rewards. As a result, they struggle to tell whether an incorrect answer comes from a small mistake late in the reasoning or from an unhelpful trajectory from the start. A common solution is to train a process reward model (PRM) for step-level supervision, but this typically requires large-scale high-quality chain-of-thought annotations and additional training cost. We propose ProcessThinker, a practical post-training pipeline that provides step-level process rewards without training an explicit PRM. ProcessThinker first rewrites reasoning traces into a step-tagged format for cold-start supervised fine-tuning, then applies GRPO with a standard format reward and our rollout-based process reward. Concretely, for each intermediate step, we sample multiple continuations from that step and use the empirical success rate (final-answer verification) as the step reward. This gives dense credit assignment and encourages reasoning steps that more reliably support a correct conclusion, helping reduce inconsistent or self-contradictory progress across steps – a key issue in logical reasoning. Across four challenging video benchmarks (Video-MMMU, MMVU, VideoMathQA, and LongVideoBench), ProcessThinker consistently improves over the baseline model Qwen3-VL-8B-Instruct

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

Finite-Width Neural Tangent Kernels from Feynman Diagrams

arXiv:2508.11522v4 Announce Type: replace Abstract: Neural tangent kernels (NTKs) are a powerful tool for analyzing deep, non-linear neural networks. In the infinite-width limit, NTKs can easily be computed for most common architectures, yielding full analytic control over the training dynamics. However, at infinite width, important properties of training such as NTK evolution or feature learning are absent. Nevertheless, finite width effects can be included by computing corrections to the Gaussian statistics at infinite width. We introduce Feynman diagrams for computing finite-width corrections to NTK statistics. These dramatically simplify the necessary algebraic manipulations and enable the computation of layer-wise recursion relations for arbitrary statistics involving preactivations, NTKs and certain higher-derivative tensors (dNTK and ddNTK) required to predict the training dynamics at leading order. We demonstrate the feasibility of our framework by extending stability results for deep networks from preactivations to NTKs and proving the absence of finite-width corrections for scale-invariant nonlinearities such as ReLU on the diagonal of the Gram matrix of the NTK. We numerically implement the complete set of equations necessary to compute the first-order corrections for arbitrary inputs and demonstrate that the results follow the statistics of sampled neural networks for widths $n\gtrsim 20$.

17.
arXiv (quant-ph) 2026-06-15

Link-Free Multi-Node Timing Synchronization for Scalable Quantum Networking

arXiv:2606.14077v1 Announce Type: new Abstract: Precise timing synchronization is essential for distributed quantum networking, enabling entanglement distribution, quantum teleportation, and entanglement swapping across remote nodes. Existing synchronization architectures rely on dedicated timing-distribution infrastructure, most notably White Rabbit networks, which constrain topology, scalability, and deployment in free-space and satellite environments. Here we demonstrate link-free synchronization of quantum network nodes using independently operating miniature rubidium atomic clocks and computational post-processing. We validate the approach on a deployed metropolitan-scale telecom fiber network spanning three geographically separated nodes. Following drift correction, atomic-clock-based synchronization achieves timing performance approaching that of a White Rabbit benchmark and remains stable over continuous 8-hour operation. As a stringent test of quantum-network functionality, we observe Hong-Ou-Mandel interference across spatially separated nodes with visibility exceeding 70%, statistically equivalent to that obtained using dedicated White Rabbit timing links. To the best of our knowledge, this represents the first observation of quantum interference across a deployed metropolitan-scale telecom fiber network synchronized entirely without dedicated timing-transfer infrastructure. These results establish atomic-clock-based synchronization as a scalable, topology-independent alternative to conventional timing-distribution architectures and a practical pathway toward terrestrial, airborne, and space-based quantum networks where dedicated timing links are unavailable.

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

Regulating the Machine Contributor: Governance and Policy Alignment in Open Source

arXiv:2606.14594v1 Announce Type: cross Abstract: AI-assisted software development has moved from line-level autocomplete to agents that can plan changes, edit files, and submit pull requests with limited human supervision. Open-source software, however, evolves through a process designed for humans: contributor agreements, codes of conduct, and review norms all assume a legally accountable person who can attest to provenance and answer reviewer questions. Autonomous and semi-autonomous AI contributors strain those assumptions, and the 2025-2026 record of agent-driven incidents, AI-generated nuisance volume, and platform-level shutdowns shows that the gap is operationally consequential. Several open-source organisations have responded with contribution policies, but the result is fragmented, and its alignment with emerging AI governance frameworks (EU AI Act, NIST AI RMF with the UC Berkeley Agentic AI Profile, ISO/IEC 42001 and 23894) is unmapped at the contribution level. We compare policies across six organisations (SymPy, LLVM, matplotlib, OpenInfra, the Apache Software Foundation, and the Linux Foundation) using Most-Similar Systems Design with indicator-based coding and process tracing for SymPy and LLVM. From this we derive a six-dimensional taxonomy (disclosure, responsibility, human oversight, licensing, enforcement, maintainer workload), an ordinal Policy Maturity Score, and a mapping of documented agent incidents onto the dimensions each policy fails to govern. Aligning the dimensions with the regulatory frameworks above identifies overlapping gaps neither side currently closes, and we close by sketching the shape of a harmonised tiered framework and the empirical evaluation needed to calibrate it.

19.
Nature (Science) 2026-06-24

Crude oil turns cheap porous membrane into a sieve to refine itself without heat

作者: 未知作者

An inexpensive, porous polymer membrane helps to separate raw crude oil, without heat or selective coating. Heavy hydrocarbons self-assemble inside the pores to create channels that are likely to be less than 2 nanometres wide, enriching the resulting permeate mix into light, ‘naphtha range’ hydrocarbons with 30% less energy cost and carbon dioxide emissions than conventional distillation. Long hydrocarbons are deposited on pore walls, narrowing channels until only smaller molecules can pass through.

20.
PLOS Computational Biology 2026-06-11

MicroRNA target gene prediction model based on input-feature dependency and sample data expansion technique

作者:

by Yan Shao, Yazhou Li, Hexin Zhai, Shimin Dong Predicting microRNA target genes is essential for understanding their biological functions. This study developed a miRNA target gene prediction model based on input-feature dependency. Features were treated as multiple random variables, with marginal densities estimated using Gaussian mixture models (GMM) and dependencies captured by regular vine (R-vine) copula to derive joint probability density functions. We constructed class-conditional joint densities for positive and negative samples separately using GMM and R-vine copula, then combined these with prior probabilities using Bayes’ rule to obtain posterior probabilities of positive interactions, using a standard 0.5 probability threshold for deterministic prediction. To address insufficient data and class imbalance, hybrid distribution mega-trend diffusion was used to generate virtual samples for data augmentation. Computational validation showed high predictive performance even when only 30% of the training data were used. As proof-of-concept, we experimentally validated one predicted interaction (miR-8485 targeting JAK2) using dual-luciferase, cellular, and animal experiments, confirming the biological relevance of this specific model-generated prediction. These findings provide a valuable tool for understanding miRNA functions and disease mechanisms.

21.
arXiv (CS.CL) 2026-06-11

Gumbel-BEARD: Automatic Layer Selection for Self-Supervised Adaptation of Whisper in Low-Resource Domains

Speech foundation models often struggle in low-resource domains due to domain mismatch and data scarcity. We propose Gumbel-BEARD, a domain adaptation framework that automates Whisper encoder layer selection via an end-to-end trainable hard Gumbel-Softmax selector. It enables self-supervised adaptation with a BEST-RQ objective that dynamically adapts to target acoustic characteristics without manual tuning. Experiments on the MyST child speech corpus demonstrate efficiency and scalability: with 10 h of labeled data for fine-tuning, our method matches a fully supervised baseline trained on the complete 133 h labeled set. We establish new state-of-the-art word error rates (WERs) of 8.21% using Whisper-medium on MyST and 11.06% using Whisper-small on the OGI Spontaneous dataset. Evaluation on CORAAL further confirms robustness to adult dialectal domain shifts, with up to 6% relative WER reduction, highlighting the generalizability of our approach to diverse low-resource conditions.

22.
arXiv (CS.CV) 2026-06-16

Transformation-driven generation of comparable projection images from multimodal anatomical scenes

This work addresses the computational problem of generating reproducible projection-space observations from heterogeneous anatomical scenes whose components may undergo independent spatial transformations. We propose a transformation-driven framework for synthetic projection imaging from multimodal anatomical data and demonstrate it on mandibular-motion scenarios. In contrast to conventional Digitally Reconstructed Radiograph (DRR) approaches primarily designed for registration, projection realism, or rendering efficiency, the proposed formulation treats projection imaging as an observation process operating on an explicitly represented anatomical scene. Independently transformable volumetric and surface-based anatomical objects are embedded within a shared scene representation and propagated directly into projection space through explicit transformations. Projection geometry, acquisition modelling, material interpretation, and image presentation remain explicitly separated, enabling controlled exploration of methodological assumptions while preserving reproducibility and direct comparability between generated projections. Particular emphasis is placed on transformation-driven anatomical scenarios relevant to craniofacial analysis, including mandibular motion and therapeutic repositioning. Using a shared anatomical reference scene composed of CT/CBCT volumes, segmented structures, surface models, and auxiliary anatomical or therapeutic objects, the framework enables generation of directly comparable VirtualRTG projections from multiple anatomical configurations while preserving identical imaging assumptions. Rather than aiming at fully physically faithful radiographic simulation, the proposed approach provides a controllable and reproducible methodological environment for studying anatomy–projection relationships, motion observability, and transformation-aware imaging workflows.

23.
arXiv (quant-ph) 2026-06-15

On-site interactions in quantum thermal machines: efficiency, rectification and entanglement beyond local and global master equations

arXiv:2606.14593v1 Announce Type: new Abstract: Advances in experimental techniques have opened new routes for harnessing non-equilibrium dynamics in mesoscopic quantum systems. In this context, we study the impact of on-site interactions on the transport properties of a continuous quantum thermal machine composed of two coupled oscillators connected to two thermal reservoirs. In the weak system-reservoir coupling regime, where a long-standing debate concerns which reduced description should be preferred, we first show that the Redfield master equation (RME) provides an accurate and unifying framework that interpolates between two well-known limits: the local and global master equations. By relying on the Hierarchy of Pure States (HOPS), a numerically exact stochastic method, we then explore the full parameter space and show that interactions can be leveraged to tune the efficiency of the thermal machine at high temperatures (while leaving it essentially unchanged at low temperatures), induce non-reciprocal transport under asymmetric reservoir couplings, and generate steady-state entanglement within the junction. We derive expressions for system-bath correlators, such as heat and particle currents, consistently across different frameworks. Our work features on-site interactions to enhance the versatility of quantum thermodynamic junctions and clarifies the role of non-Markovianity and non-linearities in quantum transport.

24.
PLOS Computational Biology 2026-06-08

Assessing the inference of single-cell phylogenies and population dynamics from CRISPR lineage recordings

by Julia Pilarski, Tanja Stadler, Sophie Seidel Multicellular organisms develop from a single cell by repeated rounds of cell division, differentiation, and death, which can be represented as a single-cell phylogenetic tree. Genetic lineage tracing allows us to investigate this development by tracking the ancestry of individual cells as populations grow and change over time. However, accurate reconstruction of the cell phylogeny and quantification of the corresponding phylodynamic parameters – cell division, differentiation, and death rates – from this tracking data remains challenging and needs to be systematically evaluated. We perform simulations and assess, using the Bayesian framework, the joint inference of time-scaled cell phylogenies and phylodynamic parameters from CRISPR lineage recordings with random or sequential edits. Principally, we characterize the inference improvements as the recorder capacity increases. We observe more accurate phylogenetic reconstruction from sequential compared to random recordings, but no substantial improvement in phylodynamic inference when using the additional information contained in the order of edits. Overall, we find that CRISPR lineage recordings carry a strong signal on the rates of cell division when appropriate models are used. However, we detect biases in the inferred rates of cell division and death under phylodynamic model misspecification, i.e., when fitting classic memoryless birth-death processes to synchronous cell divisions. Moreover, for scenarios when cells differentiate into distinct types, we demonstrate that Bayesian phylodynamic analysis of sparse end-point measurements can resolve these cell differentiation trajectories by lineage and time. Under prototypical dynamics, we recover cell type-specific division and death rates, and cell type transition rates in over 80% of simulations. Overall, this simulation study explores how much information on cellular development can be extracted from state-of-the-art genetic lineage tracing data using phylogenetic and phylodynamic methodology.

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

CEVAR: Centerline Embedding Extraction for Endovascular Aneurysm Repair

Long-term mortality rates after endovascular aneurysm repair (EVAR) remain elevated due to post-EVAR rupture caused by loss of seal in stent graft sealing zones. Structured CT review using centerline measurements improves detection, but current workflows require manual centerline editing and expert operators. We propose a transformer framework for automated, protocol-driven sealing zone assessment that combines 3D centerline tracking with embedding-based geometric prediction. Two state-of-the-art image-to-graph models are evaluated for aorto-iliac centerline extraction from follow-up CT and for measurement of stent position, vessel diameters, and seal lengths according to EVAR4C protocol. Across the full test set and a challenging no-contrast subset, the proposed fully automatic method outperforms the commercial semi-automatic workflow.