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01.
arXiv (CS.AI) 2026-06-12

Generativism: Toward a Learning Theory for the Age of Generative Artificial Intelligence

arXiv:2606.12441v1 Announce Type: cross Abstract: The four dominant learning theories of behaviorism, cognitivism, constructivism, and connectivism show significant conceptual limitations as generative artificial intelligence (AI) proliferates in educational settings. These frameworks were formulated before the emergence of AI systems capable of generating, synthesizing, and reasoning about knowledge. This article critically examines each learning theory and identifies assumptions challenged by generative AI's affordances. Drawing on research in distributed cognition, extended mind, human-AI collaboration, AI literacy, cognitive offloading, and metacognition, the article proposes Generativism as a learning theory for the generative AI age. Generativism posits that learning increasingly occurs through the iterative co-construction of knowledge between human learners and AI systems. The proposed framework is organized around four principles: epistemic partnership, distributed agency, generative literacy, and adaptive metacognition. The framework offers a foundation for rethinking instructional design, learning, assessment, and expertise development in contexts where generative AI plays an integral role in cognition.

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

SHERLOC: Structured Diagnostic Localization for Code Repair Agents

LLM agents solve repository-level coding tasks through multi-turn tool use, but utilize half their budget on locating faults before editing. Dedicated localization frameworks have emerged, yet are still evaluated as file retrieval rather than actionable diagnosis, producing locations without the diagnostic context a repair agent needs. We introduce SHERLOC (Structured Hypothesis-driven Exploration and Reasoning for Localization), a training-free framework pairing a reasoning LLM with compact repository tools and self-recovery, without fine-tuning or multi-agent orchestration. SHERLOC reaches state-of-the-art localization across model scales: 84.33% accuracy@1 on SWE-Bench Lite and 81.27% recall@1 on SWE-Bench Verified; at ~30B parameters, it matches or outperforms other agentic methods. Injecting our locations and diagnostic findings into repair agents yields, on average, +5.95 pp resolve rate on SWE-Bench Verified while cutting localization and total tokens by 36.7% and 23.1%.

03.
medRxiv (Medicine) 2026-06-23

Estimating vaccine-prevented disease outcomes when vaccination has only direct effects

Vaccination can be a useful intervention for reducing infectious disease burden. Estimating numbers of vaccine-prevented health outcomes is one approach to quantifying the benefits of vaccination. Here we improve a method described by Foppa et al. (1) that assumes vaccination has only direct effects, that is, it cannot prevent infection or onward transmission of the disease. We rederive this method and derive an improved method that increases estimation accuracy with minimal additional analytical complexity. To evaluate the improved method, we simulated disease outbreaks and compared the accuracy of the two methods for estimating prevented disease outcomes. In 84% of simulations performed over a wide parameter space, the improved method had an equal or smaller estimation error compared to the original Foppa method, with 7.9-fold smaller mean error and 44-fold smaller standard deviation of errors. Our study improves a method for estimating prevented burden when assuming vaccination has only direct effects.

04.
arXiv (CS.CL) 2026-06-16

In-Domain Supervised Pathology Report Classification: A Reproducible Pipeline from Data Curation to Production-Matched Evaluation

We introduce an in-domain supervised pipeline designed to counter the out-of-distribution performance drop that hampers supervised biomedical NLP models, a problem observed when models trained on pathology reports are moved across cancer registries. Our contribution is a reproducible recipe for training a supervised classifier from routinely collected cancer registry data. It describes how to build the in-domain training set and a production-matched holdout, and to choose operating points that keep the false-negative rate (FNR) very low while keeping reviewer workload manageable. The pipeline standardizes data curation with facility-stratified sampling and separate handling of reports linked to registry cases, and includes a blinded manual audit to estimate positive-case prevalence and label noise. On a 418k-report holdout set, the Kentucky model achieved FNR 0.003 and false-positive rate (FPR) 0.097, improving over the Seattle-trained MOSSAIC OncoID baseline (FNR 0.010, FPR 0.183) and raising F1 from 0.860 to 0.922. In a blinded manual review of 600 reports, estimated positive prevalence declined from 0.500 to 0.398, indicating substantial label noise with errors concentrated in rare primary sites.

05.
Science (Express) 2026-05-28

A Hormone Cell Atlas maps the human endocrine system at cellular resolution | Science

作者: 未知作者

Hormones act across tissues and organs to coordinate physiological functions. Drawing inspiration from the Human Cell Atlas, we analyzed expression of 379 hormone and receptor genes in a transcriptomic dataset comprising 14 million single cells and nuclei across 47 human tissues. Using hormone2cell, we mapped putative hormone-producing and hormone-receiving cell types, defining tissue-specific and cross-tissue endocrine signatures. We predicted non-classical sites of hormone expression, including secretin in plasmacytoid dendritic cells, inferred convergent hormone action and endocrine feedback loops, and implicated cell populations in monogenic endocrine disorders. In a cross-tissue integration of adipocyte datasets, we uncovered dynamic endocrine programs across depots, within adipocyte subtypes and through adipogenic differentiation. Cumulatively, the Hormone Cell Atlas ( hormonecellatlas.org.uk ) provides a comprehensive framework for dissecting hormonal impact on health and disease.

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

Adaptive Inference-Time Scaling via Early-Step Latent Verification for Image Editing

Instruction-based image editing has made notable progress with recent advances in generative models. However, the quality of the edited result is still influenced by the randomly sampled initial noise, particularly in complex editing scenarios. An unsuitable initial noise may lead to unsatisfactory editing results. Recent inference-time scaling methods address this issue by sampling multiple initial noises and selecting better candidates. Nevertheless, most of them follow a decode-then-verify scheme which introduces an efficiency-accuracy trade-off. When decoding is performed after limited inference steps, the decoded images often remain too noisy for reliable assessment, whereas sufficiently denoised images require much higher computational cost. To address this issue, we propose VeriLatent, a plug-and-play adaptive inference-time scaling framework with early-step latent verification for image editing. Specifically, we propose a novel verifier that scores each initial noise through a latent-space editing activation map at an early stage. It identifies promising candidates by assessing whether they can induce an effective edit in the correct region. This enables efficient early pruning without decoding latents into images. Building on this, we further develop an adaptive search strategy for inference-time scaling. It allocates inference budgets according to editing difficulty, thereby reducing the number of function evaluations (NFE). Extensive experiments on multiple benchmarks and different base models demonstrate that VeriLatent consistently improves both editing performance and inference-time scaling efficiency.

07.
medRxiv (Medicine) 2026-06-18

Multicluster measles outbreak with a substantial proportion of modified cases in Tokyo, Japan, January-May 2026

Tokyo experienced a measles outbreak (260 cases) in early 2026 despite elimination status. Adults aged 20-39 years were most affected, and 38% of cases were modified measles, increasing with prior vaccination. Although incidence rose until April, the effective reproduction number; R(t) fell below 1, consistent with outbreak control. Multiple clusters were identified, but many cases lacked epidemiological links, suggesting that modified measles is less likely to be considered in differential diagnosis. Intensive contact tracing and surveillance contributed to limiting transmission.

08.
arXiv (CS.AI) 2026-06-16

Towards Unified Song Generation and Singing Voice Conversion with Accompaniment Co-Generation

arXiv:2606.07015v2 Announce Type: replace-cross Abstract: While song generation and singing voice conversion (SVC) have evolved significantly, they have long been developed isolated: the former lacks zero-shot speaker cloning, while the latter overlooks vocal-accompaniment synergy. To bridge this gap, we propose UniSinger, the first end-to-end framework unifying speaker cloning song generation and accompaniment co-generation SVC. Building on the multimodal diffusion transformer, we construct a unified speaker embedding space transferring speaker representation from SVC to song generation, endowing fine-grained cross-task timbre control. To mitigate multi-task optimization conflicts, we design a curriculum learning strategy using task-specific modality masking to guide the model to gradually master the generative mechanisms among semantic content, vocal timbre, and accompaniment. Experiments show state-of-the-art performance on both tasks and realizes complementary benefits, offering new possibilities for intelligent music production.

09.
arXiv (quant-ph) 2026-06-11

Measurement-Free Toric-Code Memory in Array Globally Controlled Rydberg Array

arXiv:2606.12030v1 Announce Type: new Abstract: The central prerequisite of any fault-tolerant quantum architecture is a quantum memory: a block of encoded physical qubits whose logical state is actively preserved against noise across many rounds of error correction. In neutral-atom Rydberg arrays, realizing such a memory is obstructed not by the entangling gates themselves, which are already fast and high-fidelity, but by the auxiliary operations that a conventional error-correction cycle requires: mid-circuit fluorescence measurement, inter-zone atom transport, and locally focused single-qubit addressing. Each of these introduces latency, atom loss, or optical crosstalk that exceeds the cost of the underlying gates by orders of magnitude. These costs accumulate cycle after cycle, progressively degrading the very logical information the code is meant to protect. Here we propose a protocol that stabilizes a toric-code quantum memory without moving, measuring or local addressing atoms. The key is to use a three-species Rydberg atom array for the complete stabilizer cycle, including syndrome extraction, coherent correction, and ancilla reset, under global, species-selective laser pulses. Numerical simulation of a $4 \times 4$ rotated toric code shows a longer qubit lifetime when the physical error rate is below a pseudo-threshold $p^\star \approx 0.034$. The scheme offers a concrete, hardware-efficient route to topological quantum memory in neutral-atom platforms.

10.
arXiv (CS.AI) 2026-06-18

User as Engram: Internalizing Per-User Memory as Local Parametric Edits

作者:

arXiv:2606.19172v1 Announce Type: new Abstract: Personal memory in a language model is two problems: content and reasoning skill. The brain keeps the two apart (a sparse, local engram in the hippocampus for each episode, a slow neocortex for the shared skills that interpret it), so a new fact need not overwrite everything else. Most personalization today keeps a user's facts outside the weights, in a natural-language memory file or a retrieval index. When facts are written into the model instead, the standard recipe is the per-user LoRA adapter, which does the opposite of the brain, folding content and skill into one global weight delta. Writing a user's facts as a LoRA contaminates text unrelated to them; writing the same facts as local Engram rows leaves it mathematically untouched, resulting in a roughly 33,000x smaller memory footprint. We therefore propose User as Engram: store a user's content as surgical edits to the hash-keyed memory table of an Engram model, and carry the reasoning skill in one shared adapter. This layered design matches per-user LoRA's direct recall while delivering 5.6x higher indirect-reasoning accuracy on average, and never makes a single user worse at reasoning than the untouched base. The edit is a glass box: writing a fact switches on its lookup at exactly the trigger, adds the value the answer needs, leaves every other position unchanged to the last bit, and fails if written into the wrong layer. Because different users' facts land in disjoint hash slots, their edits compose: many users live in one shared table at once, stacking additively and losslessly, where a per-user LoRA, a single global weight delta, admits only one. Upon retrieval, a per-user Engram table does not grow with the population the retriever must search, so past ~100 facts it overtakes a retrieval pipeline on a 2.5x larger model.

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

OpenTie: Open-vocabulary Sequential Rebar Tying System

Robotic practices on the construction site emerge as an attention-attracting manner owing to their capability of tackling complex challenges, especially in the rebar-involved scenarios. Most of existing products and research are mainly focused on the collection of large amounts of data with model training demands. To fulfill this gap, we propose OpenTie, a 3D training-free rebar tying framework utilizing a RGB-to-point-cloud generation and an open-vocabulary rebar detection on the real-world test. We implement the OpenTie via a robotic arm with a binocular camera and guarantee a high accuracy by applying the prompt-based object detection method on the image filtered by our proposed post-processing procedure for the image-to-point-cloud generation framework. Our pipeline requires no training efforts and outperforms the training-based object detection, i.e., YOLO-based method, with the verification on the real-world sequential rebar tying test. The system is flexible for horizontal and vertical rebar tying tasks and holds the potential application to the real construction site with possibility of commercialization.

12.
arXiv (CS.LG) 2026-06-19

FlexLAM: Resolving the Bottleneck Trade-off in Latent Action Learning

arXiv:2606.19408v1 Announce Type: new Abstract: Latent actions provide a compact interface between action-free video and downstream decision-making, yet existing Latent Action Models (LAMs) force every transition through a fixed-capacity bottleneck. We identify a bottleneck trade-off: overly tight codes can discard transition cues needed for action alignment, while overly loose codes preserve additional transition variation that must be resolved when alignment labels are scarce or narrowly distributed. FlexLAM replaces this fixed capacity with variable-length latent actions trained by nested dropout, yielding prefix-valid codes that capture compact transition structure first and add detail only when needed, without new architectures or losses. A single FlexLAM matches or surpasses separately trained fixed-capacity LAMs at every evaluated token budget under standard scarce-label supervision and under a low-return single-task alignment stress test, indicating that FlexLAM is not merely adjustable at inference time but learns a better latent-action interface at the same token budgets. The same model supports inference-time token-budget adjustment without retraining, and FlexLAM improves Ego4D transition reconstruction. These results suggest that variable-length latent actions are an architecture-free, drop-in upgrade to the fixed-capacity bottleneck in latent action models, latent-action world models, and video-pretrained action interfaces.

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

Mechanical Field Networks: Structured Neural Dynamics for Multivariate Systems

作者:

arXiv:2606.11251v1 Announce Type: new Abstract: Many multivariate dynamical systems are observed only through trajectories, leaving the mechanisms governing their joint dynamics hidden. Existing approaches can impose interpretable dynamics or learn flexible state transitions, yet the resulting interaction structure is typically either specified in advance or left implicit within the learned dynamics. We introduce MF-Net, a recurrent dynamical model that represents all variables in a shared field state and updates this state through a learned relation law. Each variable carries a field component, and these components evolve jointly through a learnable mechanical transition. Here, mechanical refers to the relation-to-motion organization of the transition, where learned relations shape state-dependent flows, field responses, and motion tendencies that move the field state forward. The resulting structure is part of the rollout itself: learned relations influence how the field moves, and the same internal quantities support both forecasting and structural readout. Across known-law interaction systems, chaotic benchmarks, real neural recordings, and ecological time series, MF-Net achieves competitive short- and medium-horizon forecasting while retaining inspectable structural readout. On the 40-dimensional Lorenz–96 testbed, MF-Net achieves an eight-step $R^2$ of $0.798\pm0.018$; across five seeds, its learned relation matrix recovers the local coupling support with a local/nonlocal strength ratio of $19.80\pm1.00$ and Precision@$K$ of $1.000\pm0.000$. MF-Net provides a structure-readable dynamical modeling framework in which learned relations are trained through forward evolution and, on real data, interpreted as functional predictive couplings under appropriate observational limits.

14.
arXiv (math.PR) 2026-06-24

A parameterized family of balance indices for phylogenetic networks

arXiv:2606.24562v1 Announce Type: cross Abstract: We introduce a new family of balance indices for phylogenetic networks: the $H_\alpha$ indices, where $\alpha$ is a positive real number. This family includes the $B_2$ index as a special case ($\alpha = 1$) and provides a natural extension of the Sackin index to phylogenetic networks. We show that the $H_\alpha$ indices share many structural properties with the $B_2$ index, most notably a "grafting property" that makes it possible to express the $H_\alpha$ index of a network in terms of the $H_\alpha$ indices of its biconnected components. These properties allow us to identify networks that minimize / maximize $H_\alpha$ for various classes of phylogenetic networks, and to study its distribution for several models of random trees and networks (in particular, Galton-Watson trees and binary Markov branching trees, with a focus on the Yule and PDA models). Finally, we show how local limits can be used to analyze the asymptotic behavior of $H_\alpha$ for large trees and networks, and we obtain general results for the moments of $H_\alpha$ for a broad class of random phylogenetic networks known as blowups of Galton-Watson trees.

15.
medRxiv (Medicine) 2026-06-18

Empirical Validation and Predictive Utility of the Perinatal Grief Scale in Men after Perinatal Loss

Background. The Perinatal Grief Scale (PGS) is a widely used instrument for assessing grief following pregnancy loss, yet no study has validated it specifically in men despite documented use in several studies. This gap is critical given fathers' persistent underrepresentation in perinatal bereavement research and the absence of empirically supported screening thresholds for this population. Methods. This cross-sectional validation study used data from the OPALE project (Observatory on PerinatAL hEalth) conducted by the CiaoLapo Foundation in Italy. Among 276 fathers who experienced stillbirth or miscarriage, we examined criterion validity by testing the association between PGS scores and trauma-related symptomatology assessed via three validated instruments: the Revised Impact of Event Scale (RIES, n=103), National Stressful Events Survey Short Scale (NSESSS, n=95), and SCL-90 (n=173). We systematically tested multiple threshold combinations to identify optimal discriminative performance. Results. The PGS demonstrated excellent criterion validity. The optimal threshold (PGS >=92) showed sensitivity 81.0%, specificity 81.8%, and Youden's J index 0.628. Fathers scoring >=92 had 19.12 times the odds of high trauma symptoms (95% CI: 9.35 to 39.14, p

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

CADET: Physics-Grounded Causal Auditing and Training-Free Deconfounding of End-to-End Driving Planners

作者:

arXiv:2606.14438v1 Announce Type: cross Abstract: End-to-end (E2E) autonomous-driving planners trained by imitation are prone to statistical shortcuts: they associate scene elements that merely co-occur with expert actions (a roadside object, a building facade) with driving decisions, rather than the variables that causally determine them. Such causal confusion silently compromises reliability in long-tail scenarios, and it is difficult to detect, because prevailing open-loop metrics (L2 displacement and collision rate) are dominated by ego status and do not indicate whether a planner depends on spurious cues. Existing remedies based on causal-intervention training require retraining large models and cannot audit a planner that is already deployed. We present CADET, a training-free framework that audits, benchmarks, and repairs spurious reliance in pretrained E2E planners without any parameter update.

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

RASST: Retrieval-Augmented Simultaneous Speech Translation

Simultaneous speech translation produces target text incrementally from partial speech input. Recent speech large language models have markedly improved SST quality but still struggle with rare and domain-specific terminology. Retrieval augmentation has helped in automatic speech recognition and neural machine translation, but extending it to SST is non-trivial: retrieval must be fast and accurate under partial speech, and the model must decide whether and when to apply retrieved terms during incremental generation. We propose Retrieval-Augmented Simultaneous Speech Translation (RASST), which addresses both challenges. For accurate cross-modal retrieval under partial input, RASST trains a lightweight speech-text retriever that produces chunkwise terminology hints for the Speech LLM via multi-scale retrieval. To use these hints correctly, we synthesize training data that teaches the Speech LLM to decide whether and when to apply each retrieved term. Experiments on ACL 60/60 dev set and the ESO test set show that RASST improves terminology accuracy by nearly 40% and overall translation quality by up to 3 BLEU points, with negligible computational overhead.

18.
arXiv (CS.LG) 2026-06-17

VISTA: Scale-Aware Visual Navigation via Action History Conditioning

arXiv:2606.17294v1 Announce Type: cross Abstract: Vision Navigation Foundation Models (VNMs) promise end-to-end learned navigation policies capable of zero-shot deployment across diverse embodiments and environments. To maintain generality, many vision-based navigation models predict normalized actions. However, this normalization introduces a critical deployment vulnerability: applying different scaling factors to the same normalized trajectory alters its physical geometry, which degrades navigation performance and increases collision risks. We address this vulnerability by conditioning the model on normalized action histories alongside image observations, providing explicit context on the relationship between the model's predictions and the robot's actual physical displacement. Furthermore, current VNMs often struggle in visually repetitive environments that lack distinct features. To resolve this issue, we integrate a DINOv3 encoder, whose richer representations enable our model to capture both spatial and geometric dimensions between observations. VISTA generalizes robustly to out-of-distribution environments, achieving 100% goal prediction accuracy in zero-shot, real-world deployment in Outdoor, Forest and Office settings, and an average of 95% checkpoints crossed, demonstrating consistent path following in unseen environments.

19.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

20.
arXiv (CS.LG) 2026-06-19

BLISS: A Lightweight Bilevel Influence Scoring Method for Data Selection in Language Model Pretraining

arXiv:2510.06048v5 Announce Type: replace Abstract: Effective data selection is essential for pretraining large language models (LLMs), enhancing efficiency and improving generalization to downstream tasks. However, existing approaches often require leveraging external pretrained models, making it difficult to disentangle the effects of data selection from those of the external pretrained models. In addition, they often overlook the long-term impact of selected data if the model is trained to convergence, primarily due to the prohibitive cost of full-scale LLM pretraining. In this paper, we introduce BLISS (BileveL Influence Scoring method for data Selection): a lightweight data selection method that operates entirely from scratch, without relying on any external pretrained oracle models, while explicitly accounting for the long-term impact of selected data. BLISS leverages a small proxy model as a surrogate for the LLM and employs a score model to estimate the long-term influence of training samples if the proxy model is trained to convergence. We formulate data selection as a bilevel optimization problem, where the upper-level objective optimizes the score model to assign importance weights to training samples, ensuring that minimizing the lower-level objective (i.e., training the proxy model over the weighted training loss until convergence) leads to best validation performance. Once optimized, the trained score model predicts influence scores for the dataset, enabling efficient selection of high-quality samples for LLM pretraining. We validate BLISS by pretraining 410M/1B/2.8B Pythia and LLaMA-0.5B models on selected subsets of the C4 dataset. Notably, under the 1B model setting, BLISS achieves $1.7\times$ speedup in reaching the same performance as the state-of-the-art method, demonstrating superior performance across multiple downstream tasks.

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

Models That Know How Evaluations Are Designed Score Safer

The validity of AI safety evaluations depends on models behaving consistently across controlled and deployment settings. Prior work has identified test-time contextual cues, such as hypothetical scenarios, as a source of verbalized evaluation awareness and subsequent behavioral shift. In this paper, we investigate a potential explanation of this phenomenon: evaluation meta-knowledge, defined as parametric knowledge about the structural traits that characterize evaluations. Similar to dataset contamination, where benchmark exposure leads to higher performance through memorization, we hypothesize that models trained on texts describing evaluation practices may implicitly learn to recognize and respond to evaluation-like contexts, for instance, through exposure to scientific articles or social media posts about AI benchmarking. To test this, we fine-tune models on synthetic documents describing evaluation traits such as verifiable structures or moral dilemmas. Evaluating this fine-tuned model on six safety benchmarks, we find that it is significantly safer than the base model and control model. This behavioral shift persists even when restricting the analysis to responses lacking explicit verbalization of evaluation awareness. Our results demonstrate that evaluation meta-knowledge may inflate safety benchmark performance, introducing a novel confounder that is independent of explicit memorization or verbalized evaluation awareness, thus, challenging to detect. These findings have important implications for the design and interpretation of AI safety evaluations. Our code and models are available at https://github.com/compass-group-tue/arxiv2026_evaluation_meta_knowledge.

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

Relational Structural Causal Models

arXiv:2606.14892v1 Announce Type: new Abstract: An artificial intelligence must have a model of its environment that is causal, supporting reasoning about interventions and counterfactuals, and also combinatorial, supporting generalization to unseen combinations of objects. In this work, we formally study when and how such a model can be learned. We develop relational structural causal models, extending structural causal models (Pearl 2009) to settings where objects and their relations vary. First, we show how answers to not only causal but also observational queries about unseen combinations of objects can not be identified without further assumptions. To enable such identification–including in the presence of unobserved confounding–we define relational causal graphs and derive symbolic identification criteria. Finally, we propose relational neural causal models, a provably correct approach that outperforms non-relational baselines on simulated traffic scenes with varying cars, signals, and pedestrians.

23.
bioRxiv (Bioinfo) 2026-06-08

DipSkmer: Reference-free population genomics with diploid genome skims

Ecologists and conservation biologists rely on genetic diversity as a key essential biodiversity variable (EBV) used to track population health and dynamics, and utilize the population parameter {theta} (estimated by the average pairwise genomic distance) as a key metric of diversity. While whole-genome-sequencing (wgs) is increasingly affordable, it will be considerable time before the full diversity of life is represented by high-quality assembled genomes; even then, constant monitoring will still require repeated sampling of populations. In contrast, genome skimming (low-coverage, short-read wgs) is highly cost-effective but challenging to analyze because the coverage is too low for assembly and reliable error correction. Mature methods, such as Mash, exist for estimating pairwise genomic distances based on the Jaccard similarity of k-mer sets computed using sketching techniques. Some, such as Skmer, additionally model the impacts of low coverage. These methods have been successfully applied to assembly-free species identification and phylogenetics; however, their use in population genetics has been limited. This is because these methods implicitly treat genomes as haploid and heterozygosity confounds true estimates of genomic distance for diploid organisms. In this paper, we address this problem through a number of technical advances. First, we use coalescent theory to mathematically derive how the Jaccard index between two diploid samples changes with the scaled population size parameter ({theta}). Next, we derive an estimator that computes {theta} from the Jaccard index, in addition to several auxiliary variables, which we also estimate from the genome skims. The resulting method, DipSkmer, enables more accurate estimates of coverage, sequencing error, and pairwise nucleotide distance for diploid samples. Analyses of both simulated and empirical datasets show that for diploids and low distances (e.g.,

24.
arXiv (CS.AI) 2026-06-19

A Comparative Study of Pretrained Transformer Models for Quranic ASR: Speech Representations, Label Formats, and Dataset Composition

arXiv:2606.19747v1 Announce Type: new Abstract: Quran Automatic Speech Recognition (ASR) aims to convert Quranic recitation into text, enabling applications such as aided memorisation tools and Quranic search engines. However, existing ASR models often exhibit high Word Error Rates (WER) on user-recited verses and lack full coverage of the Quranic corpus. This paper presents a systematic empirical study of domain-specific fine-tuning of pretrained Transformer-based models for Quranic ASR, using advanced speech feature extraction methods: Wav2Vec2.0, HuBERT, and XLS-R. These models apply self-supervised learning by masking portions of input audio and using Transformer architectures to learn context-aware speech features. The pretrained models are fine-tuned on a filtered Quranic dataset exceeding 870 hours of professional and user recitations. Through comprehensive ablation studies across feature extractors, output label formats, training strategies, and clip durations, we identify the key factors that affect transcription accuracy in this domain. Our best-performing configuration achieves a WER of 0.08 on the EveryAyah subset and 0.11 on the combined EveryAyah+Tarteel setting, representing roughly a five-percentage-point gain over the Citrinet baseline (WER = 0.163) while reducing combined-model training time from 140 hours to 40 hours. Arabic text without diacritics yields the best fine-tuning results, and Wav2Vec2-XLSR-53 provides the strongest overall representation. Future work includes improving dataset quality and developing phoneme-aware models to extract deeper speech feature representations for Tajweed-sensitive applications.

25.
arXiv (CS.LG) 2026-06-15

A General Framework for Decision Trees via Bregman Divergences

arXiv:2606.13984v1 Announce Type: cross Abstract: Decision trees are one of the fundamental tools in statistical learning due to their interpretability, flexibility, and their ability to adapt to nonlinear structures. Among them, the Classification and Regression Trees, introduced by Breiman, Friedman, Olshen, and Stone in 1984, became one of the most influential algorithms and remains one of the most widely used methods for classification and regression problems. On the other hand, Bregman divergences, introduced by Lev Bregman in 1967 in the context of convex optimization, provide a broad family of loss functions that naturally generalize the squared Euclidean distance. This family includes, among others, the Kullback-Leibler divergence, the Poisson divergence, and the Itakura-Saito divergence, as well as several losses associated with distributions belonging to the exponential family. Moreover, Bregman divergences possess a rich geometric structure and deep connections with convex analysis and information geometry. In this work, we propose a generalization of the CART paradigm based on Bregman divergences, thereby obtaining a broader family of decision trees adapted to different statistical models and underlying geometries. Although algorithms such as CART or classical implementations such as rpart incorporate different impurity criteria, these are usually introduced in an ad hoc manner for each specific model. In contrast, the Bregman divergence approach provides a unified framework that allows these criteria to be derived and interpreted from common convex and geometric principles. Beyond the algorithmic construction, we also investigate theoretical properties of these trees. In particular, we study how properties of the generating convex function – such as strong convexity or smoothness – influence impurity gains between parent and child nodes, as well as stability and consistency properties of the estimator.