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01.
arXiv (CS.CL) 2026-06-24

Balalaika: Data-Centric, Prosody-Aware Annotation Pipeline for Russian Speech

We introduce Balalaika, an open-source, data-centric pipeline for processing audio and producing prosody-aware annotations. It combines semantic VAD for context-preserving segmentation, multi-ASR ensembling with ROVER consensus decoding, while retaining optional word-level timestamps, followed by automatic quality and speaker-purity filtering. The text is further enriched with punctuation restoration, lexical stress and "\textipa{e}/\textipa{\H{e}}" normalization, and IPA phonemes. Using Balalaika, we build a 5.1k-hour multi-source Russian corpus with rich annotations, and show consistent gains under equalized training budgets for both speech denoising and TTS; ablations confirm complementary benefits of stress and punctuation and improved synthesis with stricter MOS filtering. The datasets are publicly available at \href{https://huggingface.co/collections/lab260/balalaika-dataset}{\underline{HuggingFace}}

02.
arXiv (CS.CV) 2026-06-11

Ouroboros-Spatial: Closing the Data-Model Loop for Spatial Reasoning

Spatial reasoning remains a persistent challenge for multimodal large language models (MLLMs). Existing approaches largely rely on large-scale, statically curated datasets, where all training samples are treated uniformly regardless of the model's evolving capabilities. This static paradigm is inherently data-inefficient: training capacity is often spent on samples that are either trivial or overly difficult for the model at its current stage. To address this limitation, we propose Ouroboros-Spatial, a self-evolving training framework in which the model plays dual roles as a proposer and a solver. In each iteration, a frozen proposer generates spatial question-answer (QA) pairs from 3D scene metadata and raw video frames, together with executable code for deriving reliable ground truth. A learnable solver is then fine-tuned on the accepted samples, and its per-sample prediction confidence is used as a difficulty signal. This signal is fed back to the proposer in the next iteration, guiding it to generate questions better matched to the solver's current capabilities. Through this closed-loop design, the training distribution co-evolves with model ability, reducing redundant trivial examples while filtering out ambiguous or uninformative samples with limited learning value. Across six spatial reasoning benchmarks, Ouroboros-Spatial substantially improves Qwen3-VL-4B and Qwen3-VL-8B while using an order of magnitude fewer training examples than recent large-scale curated datasets. On VSI-Bench, it yields absolute gains of 9.9 and 6.8 points for the 4B and 8B models, respectively, enabling both to outperform a wide range of strong open-source and proprietary baselines.

03.
arXiv (CS.LG) 2026-06-16

Scalable Graph Condensation with Evolving Capabilities

arXiv:2502.17614v3 Announce Type: replace Abstract: The rapid growth of graph data creates significant scalability challenges as most graph algorithms scale quadratically with size. To mitigate these issues, Graph Condensation (GC) methods have been proposed to learn a small graph from a larger one, accelerating downstream tasks. However, existing approaches critically assume a static training set, which conflicts with the inherently dynamic and evolving nature of real-world graph data. This work introduces a novel framework for continual graph condensation, enabling efficient updates to the distilled graph that handle data streams without requiring costly retraining. This limitation leads to inefficiencies when condensing growing training sets. In this paper, we introduce GECC (\underline{G}raph \underline{E}volving \underline{C}lustering \underline{C}ondensation), a scalable graph condensation method designed to handle large-scale and evolving graph data. GECC employs a traceable and efficient approach by performing class-wise clustering on aggregated features. Furthermore, it can inherit previous condensation results as clustering centroids when the condensed graph expands, thereby attaining an evolving capability. This methodology is supported by robust theoretical foundations and demonstrates superior empirical performance. Comprehensive experiments including real world scenario show that GECC achieves better performance than most state-of-the-art graph condensation methods while delivering an around 1000$\times$ speedup on large datasets.

05.
arXiv (CS.CV) 2026-06-17

Improving and Evaluating Hand-Object Interaction Detection

Understanding hands and the objects they interact with, both directly and through tools, is a key step for tasks ranging from action perception to 3D reconstruction and robotics. Our paper provides several contributions to the Hand-Object Interaction (HOI) understanding literature: (1) HOI-DETR, a new framework that introduces hand-object and object-object interactions to the Co-DETR architecture to produce a state-of-the-art method; (2) a comprehensive HOI evaluation suite of 4 diverse datasets, including a video benchmark derived from the HD-EPIC dataset and fresh annotations that improve the Hands23 benchmark and (3) a trained checkpoint that significantly improves the state of the art across Hands23, HOIST, FineBio, and HD-EPIC, including mAP gains of over 20 percentage points on Hands23 and FineBio. Our ablations confirm the contributions of each model component.

06.
medRxiv (Medicine) 2026-06-18

AlphaGenome identifies a deep intronic variant in a family with PLA2G6-associated neurodegeneration: Closing the diagnostic gap in rare genetic diseases

A molecular diagnosis remains out of reach for a substantial subset of patients with clinically recognizable Mendelian disorders, even after comprehensive next-generation sequencing. Causal variants in non-coding regions are difficult to detect and interpret using standard pipelines. Deep intronic variants that disrupt splicing are a known but underexplored source of pathogenic alleles, and systematic tools to evaluate them at scale have only recently emerged. We aimed to resolve an incomplete genetic diagnosis in two siblings with early-onset parkinsonism, prominent neuropsychiatric features, and autonomic dysfunction consistent with PLA2G6-associated neurodegeneration (PLAN), an autosomal recessive condition. Prior clinical exome sequencing, genome sequencing, Multiplex Ligation-dependent Probe Amplification (MLPA), and long-read sequencing had identified only a single heterozygous PLA2G6 missense variant, c.2132C>G (p.Pro711Arg). We used AlphaGenome to score 91 non-coding variants shared among the affected siblings and their father within 1 megabase of the PLA2G6 locus. The deep-learning model identified an intronic variant (c.2034+355G>A) that was predicted to create a cryptic splice acceptor site that could result in inclusion of a 160-bp cryptic exon. Tissue-specific predictions indicated the aberrant splicing would be detectable in blood, confirmed by junction-spanning RNA-seq reads from an unrelated carrier. This analysis completed a compound heterozygous PLAN diagnosis nearly two decades after symptom onset and demonstrates the utility of sequence-to-function models. Systematic integration of tools like AlphaGenome into rare disease workflows offers a practical, low-barrier route to closing the diagnostic gap for patients with compelling Mendelian phenotypes and incomplete genetic diagnoses.

07.
arXiv (CS.CL) 2026-06-18

Mitigating Scoring Errors and Compensating for Nonverbal Subtests in Speech-Based Dementia Assessment

Early detection of cognitive impairment relies on neuropsychological tests to minimize subjectivity by assessing multiple cognitive domains. Speech-based evaluation can support diagnostics and improve accessibility, but transcription errors and the omission of nonverbal subtests (e.g., motor skills) limit accuracy. Beyond conventional test scores, speech-derived features can provide additional insights into cognitive status. This study investigates the speech-based evaluation of the German "Syndrom-Kurz-Test," a standardized dementia screening test comprising verbal and motor subtests. We train models that integrate transcript-derived scores and Whisper embeddings per verbal subtest to reduce scoring errors. To compensate for missing motor subtests, we then leverage these fused representations to approximate expert overall ratings. Despite omitting subtests, our models strongly correlate with expert ratings and efficiently and accurately discriminate between cognitive status groups.

08.
arXiv (CS.CV) 2026-06-24

An LMM for Precisely Grounding Elements in Documents

Visual grounding in documents is a crucial ability for Large Multimodal Models (LMMs) in areas such as document understanding, deep research and document error detection. However, existing approaches exhibit poor grounding precision in text-rich document images, often failing to accurately locate the critical document elements needed for reliable reasoning. To address this gap, we introduce PreciseDoc, an LMM specifically designed for precise element grounding and can be further optimized for Document VQA tasks. Specifically, to enhance the basic localization capability, we construct challenging training data by two pipelines capable of mass-producing high-quality documents with paired metadata of fine-grained coordinates, including synthetic hand-filled documents with camera effects. The model develops more real-world functions beyond straightforward localization of single text, such as locating personal information from CVs. Furthermore, we introduce a training paradigm for visual grounded reasoning where the grounding and reasoning are supervised jointly with reinforcement learning to improve the contribution of the grounded evidence. A comprehensive evaluation on various benchmarks demonstrates the advantage of the proposed data and methods in document spatial grounding and document understanding.

09.
arXiv (CS.CV) 2026-06-17

Graph Neural Networks for Semi-Supervised Image Classification with Multi-Feature Aggregation

Feature extraction involves the identification and extraction of salient characteristics or patterns, including edges, textures, shapes, and color attributes. Contemporary feature extractors predominantly leverage deep learning architectures, such as Convolutional Neural Networks (CNNs) and Vision Transformers (VITs). The availability of diverse feature extractors in the literature provides a wide range of feature representations. Features extracted from an image depend on the specific application, the chosen extractor, and its configuration. Therefore, integrating complementary information by combining distinct extractors offers a promising way to enhance performance. Graph Neural Networks (GNNs), particularly Graph Convolutional Networks (GCNs), have emerged as powerful and widely adopted approaches for semi-supervised image classification, as they effectively leverage both labeled and unlabeled data while exploiting the underlying graph structures that capture relationships among samples. This study proposes a novel approach for GNNs in scenarios where labeled data is scarce, by integrating diverse sets of feature and graph representations derived from various extractors in classification scenarios. Experimental investigations were conducted, encompassing combinations of distinct feature and graph extractors, as well as rank aggregation strategies. The primary contributions of this work are underscored by the experimental findings, which demonstrate that the strategic combination of feature and graph representations, coupled with the application of manifold learning for graph processing, leads to significant improvements in classification accuracy across the majority of experimental conditions. Furthermore, the utilization of rank aggregation techniques to integrate features from different extractors was shown to enhance classification accuracy.

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

A Decision-Theoretic View of Test-Time Training: When, How Far, and Which Directions to Adapt

arXiv:2606.15569v1 Announce Type: new Abstract: Test-time training (TTT) adapts a pretrained model to each prompt via parameter updates, improving accuracy under pretraining-to-test distribution shifts. Yet, its performance often suffers from instability and sensitivity to hyperparameters such as update steps and subspace. We explain this behavior through a decision-theoretic lens, treating TTT as implicit Bayesian inference in the kernel regime. Under a Gaussian process benchmark, we show that TTT reduces prediction error when updates are spectrally matched to the prompt's signal-to-noise ratio and aligned with query-relevant eigen-directions. This perspective underpins the following results: (1) we show when fixed update steps and subspaces fail under distribution shifts, motivating adaptive strategies; (2) we prove that selecting update steps via prompt evidence admits a PAC-Bayes guarantee against overfitting; and (3) we characterize the Bayes-optimal update subspace under a linear-Gaussian correction model, yielding a scoring rule for selecting Transformer blocks and heads. Our theory helps explain the empirical instability of TTT, taking a step toward principled guidance for when, how far, and which directions to adapt.

11.
arXiv (CS.CV) 2026-06-24

Systematic Exploration of 4-Expert Heterogeneous Mixture-of-Experts via Automated Pipeline Search

We present an automated large-scale search pipeline for heterogeneous 4-Expert Mixture-of-Experts (MoE4) architectures within the LEMUR neural network dataset ecosystem. Building on a hand-crafted heterogeneous MoE reference model, we replace manual design with a deterministic code-assembly generator that systematically combines base architecture families drawn from the LEMUR database into MoE4 ensembles, each governed by a convolutional gating network with temperature scaling, mixup augmentation, and cosine-annealed learning rate scheduling. Over a 28-day campaign on an NVIDIA RTX 4090, the pipeline generated 4,463 candidate models across 197 batches, of which 1,021 were evaluated successfully. A critical finding emerged from the campaign: due to alphabetical enumeration via itertools.combinations, the entire explored search space (4.8% of the theoretical 23,751 possible 4-family combinations) is anchored to a single family, AirNet. We characterise this coverage bias precisely, identify the root cause in the generator, and propose a stratified random sampling fix. Within the AirNet anchored scope, ShuffleNet and MobileNetV3 consistently co-produce the highest-accuracy ensembles (mean accuracy up to 0.632), while FractalNet and MNASNet are identified as low-yield families warranting exclusion in future campaigns. The pipeline, analysis artefacts, and corrected generator are released as part of the open-source NNGPT project at https://github.com/ABrain-One/nn-gpt

12.
arXiv (CS.LG) 2026-06-15

IntSeqBERT: Learning Arithmetic Structure in OEIS via Modulo-Spectrum Embeddings

arXiv:2603.05556v2 Announce Type: replace Abstract: Integer sequences in the OEIS span values from single-digit constants to astronomical factorials and exponentials, making prediction challenging for standard tokenised models that cannot handle out-of-vocabulary values or exploit periodic arithmetic structure. We present IntSeqBERT, a dual-stream Transformer encoder for masked integer-sequence modelling on OEIS. Each sequence element is encoded along two complementary axes: a continuous log-scale magnitude embedding and sin/cos modulo embeddings for 100 residues (moduli $2$–$101$), fused via FiLM. Three prediction heads (magnitude regression, sign classification, and modulo prediction for 100 moduli) are trained jointly on 274,705 OEIS sequences. At the Large scale (91.5M parameters), IntSeqBERT achieves 95.85% magnitude accuracy and 50.38% Mean Modulo Accuracy (MMA) on the test set, outperforming a standard tokenised Transformer baseline by $+8.9$ pt and $+4.5$ pt, respectively. An ablation removing the modulo stream confirms it accounts for $+15.2$ pt of the MMA gain and contributes an additional $+6.2$ pt to magnitude accuracy. A probabilistic Chinese Remainder Theorem (CRT)-based Solver converts the model's predictions into concrete integers, yielding a 7.4-fold improvement in next-term prediction over the tokenised-Transformer baseline (Top-1: 19.09% vs. 2.59%). Modulo spectrum analysis reveals a strong negative correlation between Normalised Information Gain (NIG) and Euler's totient ratio $\varphi(m)/m$ ($r = -0.851$, $p < 10^{-28}$), providing empirical evidence that composite moduli capture OEIS arithmetic structure more efficiently via CRT aggregation.

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

LASA: A Weak Supervision Method for Open-Vocabulary Scene Sketch Semantic Segmentation

Open-vocabulary scene sketch semantic segmentation aims to assign dense semantic labels to sparse line drawings based on flexible category vocabularies specified at inference time, without relying on pixel-level annotations during training. Unlike natural images, sketches lack texture and color cues, making semantic understanding heavily dependent on stroke layout and spatial configuration, a challenge that renders single-layer vision-language features inherently unstable. Our key observation is that attention maps from different Vision Transformer layers encode complementary spatial cues: shallow layers capture global structural layouts, while deeper layers focus on local stroke intersections and object parts. This suggests that cross-layer aggregation provides a more robust structural prior than any individual layer alone. Leveraging this insight, we propose a structure-aware framework built upon Layer-wise Accumulated Structural Attention (LASA), which aggregates multi-layer attention to guide hierarchical semantic alignment under weak supervision and refine predictions during inference. Experiments on FS-COCO, SFSD, and FrISS show that LASA improves mIoU by $+3.43$, $+8.01$, and $+15.74$ over the prior weakly supervised baselines, demonstrating consistent gains in both segmentation accuracy and spatial coherence. Our source code will be made publicly available.

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

CAPRA: Scaling Feedback on Software Architecture Deliverables with a Multi-Agent LLM System

arXiv:2606.18976v1 Announce Type: cross Abstract: Automated assessment in software engineering education has advanced significantly for code grading and essay scoring. However, reviewing software architecture deliverables, which requires analyzing structural completeness and requirements traceability, has not yet been fully automated. Applying Large Language Models (LLMs) to this task requires robust architectures to ensure technical feedback is accurate and reliable for students. This paper presents CAPRA (Configurable Architecture Proficiency Report Assessment), a multi-agent LLM system that analyzes software architecture deliverables to generate personalized, template-compliant LaTeX feedback. As a core design choice, CAPRA coordinates multiple specialized agents and employs a Python-based microservice for multi-modal document extraction, utilizing PyMuPDF and vision-enabled LLMs (specifically gpt-4o) to parse text and UML diagrams. To ensure educational reliability and mitigate hallucinations, CAPRA introduces a deterministic Evidence Anchoring step using fuzzy matching via normalized Levenshtein distance, along with a ConsistencyManager agent that cross-verifies, deduplicates, and merges findings. System performance is assessed using a structured eight-criterion binary evaluation taxonomy covering: (i) extraction completeness, (ii) feature validation, (iii) issue grounding and severity detection, (iv) recommendation specificity and traceability, and (v) template and tone compliance. A preliminary empirical evaluation on 10 student reports shows that CAPRA satisfied 88.8% of the evaluated criteria under a strict two-rater aggregation rule, achieved moderate inter-rater agreement with human evaluators (kappa = 0.582), and processed each report in slightly over 4 minutes. While these results support the viability of LLM-supported architectural feedback, human oversight remains essential for subjective assessment dimensions.

15.
arXiv (CS.AI) 2026-06-24

AutoSpec: Safety Rule Evolution for LLM Agents via Inductive Logic Programming

arXiv:2606.24245v1 Announce Type: cross Abstract: Large language model (LLM) agents increasingly automate complex tasks by integrating language models with external tools and environments. However, their autonomy poses significant safety risks: agents may execute destructive commands, leak sensitive data, or violate domain constraints. Existing safety approaches face a fundamental tradeoff: hand-crafted rules are interpretable but brittle, with overly conservative rules blocking safe operations (high false positives) while permissive rules miss unsafe behaviors (high false negatives). Neural classifiers lack the interpretability required for safety-critical deployments. We present AutoSpec, a framework that automatically evolves deployed expert-designed safety rules from user safe/unsafe annotations through counterexample-guided inductive synthesis (CEGIS) guided by inductive logic programming (ILP). Starting from the expert rules and a stream of annotated traces, AutoSpec iteratively evaluates rules, mines false-positive and false-negative counterexamples, uses ILP to learn which predicates discriminate them, generates candidate rule edits, and verifies candidates to select the best revision. The key insight is that ILP efficiently identifies predicates that appear frequently in false negatives but rarely in false positives (or vice versa), dramatically pruning the exponential search space of rule edits. This continues until convergence, producing interpretable rules that balance precision and recall. We evaluate AutoSpec on 291 execution traces spanning code execution and embodied agent domains. AutoSpec raises rule F1 to 0.98 and 0.93 across the two domains, achieving up to 94% false positive reduction while maintaining high recall, and converges within 4-5 iterations. The ILP-guided approach achieves up to 4.8x higher F1 than heuristic CEGIS. The learned rules are human-readable, auditable, and generalize to unseen scenarios.

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

ST-DiffEye: Diffusion-based Continuous Gaze Generation via Joint Scanpath-Trajectory Modeling

We study the problem of human gaze modeling, which aims to generate the gaze patterns a viewer produces while observing a visual stimulus. Gaze is primarily captured through two modalities: continuous eye-tracking trajectories, which describe fine-grained motion dynamics, and discrete scanpaths, which describe high-level fixation structure. Because gaze varies substantially across viewers and trials, we treat this variability as a defining property rather than noise and model gaze as a stochastic generative process. Existing generative gaze models supervise on only one of these two representations in isolation. We hypothesize that trajectories and scanpaths describe gaze at complementary scales and are jointly informative during training, and test this hypothesis through ST-DiffEye, a joint trajectory-scanpath diffusion framework that couples both modalities by concatenating them as an additional raw input channel, requiring no architectural overhead beyond an input and output channel expansion. We further introduce a principled evaluation framework based on the Continuous Ranked Probability Score (CRPS), which generalizes any existing sequence similarity metric into a proper scoring rule that jointly assesses the accuracy and diversity of generated gaze. Experiments on task-driven visual search, covering both target-present and target-absent scenarios, and on free-viewing benchmarks demonstrate state-of-the-art performance. These results, along with detailed ablations, confirm the benefit of joint modeling and the value of distribution-aware evaluation in capturing the intrinsic variability of human gaze. Project webpage: https://st-diffeye.github.io/

17.
arXiv (CS.AI) 2026-06-19

Neural Additive and Basis Models with Feature Selection and Interactions

arXiv:2606.19850v1 Announce Type: cross Abstract: Deep neural networks (DNNs) exhibit attractive performance in various fields but often suffer from low interpretability. The neural additive model (NAM) and its variant called the neural basis model (NBM) use neural networks (NNs) as nonlinear shape functions in generalized additive models (GAMs). Both models are highly interpretable and exhibit good performance and flexibility for NN training. NAM and NBM can provide and visualize the contribution of each feature to the prediction owing to GAM-based architectures. However, when using two-input NNs to consider feature interactions or when applying them to high-dimensional datasets, training NAM and NBM becomes intractable due to the increase in the computational resources required. This paper proposes incorporating the feature selection mechanism into NAM and NBM to resolve computational bottlenecks. We introduce the feature selection layer in both models and update the selection weights during training. Our method is simple and can reduce computational costs and model sizes compared to vanilla NAM and NBM. In addition, it enables us to use two-input NNs even in high-dimensional datasets and capture feature interactions. We demonstrate that the proposed models are computationally efficient compared to vanilla NAM and NBM, and they exhibit better or comparable performance with state-of-the-art GAMs.

18.
arXiv (CS.LG) 2026-06-11

Space-sampled Value Decay: Forgetting Mechanisms for Non-stationary Deep Reinforcement Learning

arXiv:2606.11797v1 Announce Type: new Abstract: Studies on rodents such as mice have shown the capabilities to adapt their behavior when dealing with changing parameters (``drift'') of the environment even if no information about change is provided (uncertainty) – a behavior that can be modeled by forgetting mechanisms. Non-stationary Reinforcement Learning (NSRL) deals with adapting state-of-the-art RL methods to deal with changing environments: these however usually require (partially) perfect information about the drift such as ``task IDs'' or ``context''. To mitigate the effects of drift, this work develops Space-sampled Value Decay as an explicit forgetting mechanism for value-based deep RL architectures as a simple yet effective approach. In particular we demonstrate and discuss positive effects but also limitations in achieved returns for modifications of Deep Q-networks (DQN) and Soft Actor-Critic (SAC) when evaluated on non-stationary environments.

19.
arXiv (quant-ph) 2026-06-24

Connecting Quantum Tomography and Quantum Retrodiction

arXiv:2606.23777v1 Announce Type: new Abstract: Quantum tomography and quantum retrodiction are traditionally viewed as separate inference tasks: tomography reconstructs quantum states from measurement data, whereas retrodiction infers past quantum states from observed outcomes. We show that the two are manifestations of the same underlying principle. We prove that the Petz recovery map associated with a measurement channel is precisely the gradient update of the log-likelihood used in maximum-likelihood tomography. Consequently, repeated applications of the Petz map monotonically increase the likelihood. Extending beyond measurement channels, we derive a noncommutative generalization of the Petz map from the gradient of a generalized likelihood for arbitrary quantum channels. The resulting iterative procedure maximizes the likelihood and provides a general framework for quantum tomography, establishing a direct bridge between retrodiction, recovery maps, and statistical inference.

20.
arXiv (CS.AI) 2026-06-24

LLMs Prompted for Legal Context Object More: Overrefusal from Small On-Premises LLMs in Criminal Legal Context

arXiv:2606.24585v1 Announce Type: new Abstract: While the validity of LLMs' use in the legal context remains subject to ethical and legal debate, legal professionals are already experimenting with personal LLMs, if only for translation and reformulation. However, even such a seemingly innocuous use can introduce biases through case processing speed if LLM assistants selectively refuse assistance on certain topics. To better anticipate such biases, we investigate several modern small LLMs that are most likely to be used as on-device assistants, to assess the impact of overrefusal on legal prompts. Surprisingly, we find that authority-style prefixes (``you are acting as an assistant of the national supreme court'', ``[...] defense lawyer'') systematically increase refusal rates by 2–20x over the no-prefix baseline, while a known role-play jailbreak prefix shows mixed effects, sharply increasing refusals in some models and barely shifting them in others. The finding suggests that small on-prem deployable LLMs are unstable under contextual framings that a real institutional user might naturally introduce, and further investigation is essential to minimize opportunities for bias.

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

On the Energy Distribution of the Galactic Center Excess' Sources

arXiv:2507.17804v2 Announce Type: replace-cross Abstract: The Galactic Center Excess (GCE) may yet herald the discovery of annihilating dark matter. Weighing against that conclusion are analyses showing evidence for dim point sources within the spatial structure of the emission. Due to technical limitations these analyses are purely spatial with all spectral information that could disentangle the excess from astrophysical backgrounds discarded. Here, we demonstrate that a neural network simulation-based inference approach can jointly analyze the spatial and spectra data. The addition is profound: energy information drives the putative point sources to be significantly dimmer, indicating either the GCE is truly diffuse in nature or made of an exceptionally large number of sources. Quantitatively, for our best fit background model, the excess is essentially consistent with Poisson emission as predicted by dark matter. If due to point sources, our median prediction is $\mathcal{O}(10^5)$ sources, or more than 35,000 at 90\% confidence, both orders of magnitude larger than the hundreds preferred by earlier point-source analyses of the GCE, although variations allowed by background systematics could reduce the required number of sources by roughly an order of magnitude.

22.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

23.
medRxiv (Medicine) 2026-06-15

Entity-Aware Generation of Synthetic Clinical Progress Notes for Prostate Cancer using Large Language Model

Objectives: This study investigates large language models (LLMs) for clinical entity projection across substantial textual transformation. Specifically, we evaluate whether entities annotated in Spanish prostate cancer case reports can be preserved and explicitly projected when the source narratives are transformed into hospital-style clinical progress notes. Entity projection is treated as a generation-driven task, allowing paraphrase, condensation and narrative reorganisation, providing that clinically relevant entities remain recoverable as structured annotations. Methods: A corpus of 109 Spanish prostate cancer case reports was annotated using a silver-standard pipeline combining Spanish biomedical named-entity recognition with rule-based prostate-specific antigen (PSA) and Gleason extractors. The resulting silver-standard annotations were validated on a subset of generated notes against a gold-standard consensus produced by medical experts in prostate cancer. Four LLMs were evaluated for note generation and entity projection: GPT-5.4 Nano, Qwen 3.5:35B-A3B, GLM5 and Claude Sonnet 4.6. Entity-to-Entity (E2E) generation used XML-annotated cases as RAG-supported input, whereas Text-to-Entity (T2E) generation required models to generate and annotate notes directly from plain text cases. Zero-shot and few-shot prompting were tested. Projection quality was measured using precision, recall and F1-score, and complemented by LLM-as-a-judge evaluation using Kimi K2.6. Results: E2E consistently outperformed T2E, indicating that explicit entity-enriched in- put substantially facilitates entity preservation and localisation. GLM5 achieved the best E2E zero-shot result (F1 = 0.915), followed by Claude Sonnet 4.6 (F1 = 0.896). In T2E, few-shot prompting improved performance, with Claude Sonnet 4.6 reaching the highest score (F1 =0.718). Age, Gleason, Disease, Procedure, Duration and negation-related entities were robustly projected, whereas PSA and Dose showed less stable behaviour. Conclusion: LLMs can generate clinically plausible synthetic prostate cancer evolution notes while preserving a substantial proportion of source entities, particularly when explicit semantic annotations are provided as input. However, the lower and more variable performance observed in T2E highlights the difficulty of jointly generating clinical narratives and projecting entities without source-side information, especially for numerical and measure-related entities.

24.
arXiv (CS.CL) 2026-06-17

From Observation to Intervention: A Causal Audit of Expert Importance in Mixture-of-Experts Models

Interpretability methods routinely use population-level summary statistics over observed model behaviour to license claims about the effects of targeted interventions on specific computations; in Pearl's terms, they treat rung-1 associational evidence as if it supported rung-2 interventional conclusions, a move whose validity is rarely tested. We examine one concrete instance: the use of routing statistics in Mixture-of-Experts (MoE) pruning, where utilization rates, activation norms, and routing weight distributions are treated as predictors of which experts can be removed without functional cost. A token-level interventional audit across three high-redundancy MoE architectures (OLMoE-1B-7B-0924, Qwen1.5-MoE-A2.7B, DeepSeek-V2-Lite) finds no observational metric predicts causal expert importance in any model: across all 60 metric-layer combinations effect sizes stay below Cohen's $d = 0.23$, and no metric is reliably positive under our corrected, dual-test criterion. A per-token routing weight control, run with identical $n$, rules out insufficient power, recovering a signal whose CI excludes zero at OLMoE's final MoE layer ($d = +0.231$, 95\% CI $[+0.09, +0.37]$, $p = 0.0013$). Existing pruning methods succeed in this regime not by identifying dispensable experts but because early-layer redundancy renders most selection criteria interchangeable. Our results provide an explicit counterexample to the common inferential step from population-level observational summaries to token-level interventional claims about expert importance, and illustrate how interventional audits can calibrate the evidential standards for interpretability claims.

25.
arXiv (CS.AI) 2026-06-19

The Tao of Agency: Autotelic AI, Embedded Agency and Dissolution of the Self

arXiv:2606.19924v1 Announce Type: new Abstract: Most artificial intelligence systems are built on the assumption that goals are exogenous and specified by the designer. Exploring what happens when an agent begins generating its own goals opens the field of autotelic AI. Agents are expected not merely to pursue objectives but to discover them. In this article, we trace its consequences through intrinsic motivation, resource-driven priors, causal-interventional learning, homeostasis, and embeddedness; the last of which is found to be a necessary but not sufficient condition for autotelic agency. Embeddedness individuates the agent at the cost of revealing that the individuation is non-unique, such that the same dynamics admit many valid partitions, each defining a different candidate self. The deepest problem with autotelic AI is therefore not how the agent generates goals, but how it generates and relativizes the self to which the goals are assigned. The agent must believe in its own boundary in order to act, and see through that boundary in order to understand. We consolidate these developments into a single framework and extend it along three directions: a quantum formulation in which the agent-environment cut becomes physical, a philosophical reading against non-dual contemplative traditions, and a concrete LLM-based agentic instantiation.