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01.
arXiv (CS.LG) 2026-06-16

A Multimodal Approach to Alzheimer's Diagnosis: Geometric Insights from Cube Copying and Cognitive Assessments

arXiv:2512.16184v2 Announce Type: replace Abstract: Early and accessible detection of Alzheimer's disease (AD) remains a critical clinical challenge, and cube-copying tasks offer a simple yet informative assessment of visuospatial function. This work proposes a multimodal framework that converts hand-drawn cube sketches into graph-structured representations capturing geometric and topological properties, and integrates these features with demographic information and neuropsychological test (NPT) scores for AD classification. Cube drawings are modeled as graphs with node features encoding spatial coordinates, local graphlet-based topology, and angular geometry, which are processed using graph neural networks and fused with age, education, and NPT features in a late-fusion model. Experimental results show that graph-based representations provide a strong unimodal baseline and substantially outperform pixel-based convolutional models, while multimodal integration further improves balanced classification performance and discriminative ability. SHAP-based interpretability analysis identifies specific graphlet motifs associated with corner integrity and edge continuity as key predictors, closely aligning with clinical observations of distorted cube drawings in AD. Together, these findings establish graph-based analysis of cube-copying behavior as an interpretable, non-invasive, and scalable framework for Alzheimer's disease screening.

02.
arXiv (CS.CL) 2026-06-19

Pruning via Causal Attribution Preserves Reasoning Performance in Large Language Models

Large language models (LLMs) excel at multi-step reasoning but incur substantial inference cost. We introduce Causal Attribution Pruning (CAP), a training-free method that identifies critical attention heads by measuring their causal impact on reasoning tasks and uses these head-level scores to guide fine-grained weight pruning. For each attention head, CAP estimates the expected performance degradation when the head is masked during forward passes on a small calibration set of reasoning problems. These causal scores are then converted into weight-level importance values for the corresponding projection matrices. Unlike magnitude-only or activation-based criteria, CAP's interventional measurement directly captures each head's functional contribution, yielding relative accuracy gains of up to 61% over Wanda on ARC-Challenge at 20% sparsity. We evaluate CAP on GSM8K, StrategyQA, and ARC-Challenge using Llama-3-8B-Instruct and Mistral-7B-Instruct at 10%, 20%, and 50% sparsity. At moderate sparsity (10-20%), CAP improves over Wanda in most model-benchmark configurations. with especially large gains on ARC-Challenge for Llama-3. Our results suggest that attention-head-level causal attribution can better preserve reasoning performance on downstream benchmarks than correlational pruning criteria at equivalent sparsity, while remaining limited by coarse MLP attribution at 50% sparsity.

03.
arXiv (CS.CV) 2026-06-17

SegTME-UNI2: A Foundation Model-Based Framework for Generalisable Multiclass Cell Segmentation and LLM-Driven Tumour Microenvironment Characterisation in Histopathology

Characterising the tumour microenvironment (TME) from routine H&E-stained histology images requires simultaneous cell segmentation, feature extraction, and interpretable clinical reporting. We present SEGTME-UNI2, a unified framework addressing these requirements. Its core is UNI2-UPERHOVER, a dual-head segmentation model pairing the UNI2-H pathology foundation model (ViT-Giant, pretrained on >100M tiles from 100K slides) with two parallel UperNet decoders: one for six-class semantic segmentation and one for horizontal-vertical gradient regression enabling watershed-based nuclear instance separation. To address the lack of pixel-level annotations in large real-world repositories, UNI2-UPERHOVER undergoes a three-stage progressive pseudo-label curriculum. Each stage trains a fresh model without weight transfer, driving improvement entirely via increased pseudo-label quality: Stage 1: Uses human-annotated PanNuke (7,901 images, 189,744 nuclei, 0.25 um/pixel). Stage 2: Uses entropy-filtered pseudo-labels from the Stage 1 model on 271,711 TCGA-UT scale-0 patches (0.5 um/pixel). Stage 3: Uses pseudo-labels from the Stage 2 model on all 1,608,060 TCGA-UT patches across six resolution scales (0.5-1.0 um/pixel). Segmentation outputs feed a structured TME feature extraction pipeline computing 20+ per-patch compositional, morphological, spatial entropy, and intercellular distance metrics. These are encoded as JSON and passed to a fine-tuned NVIDIA BioNeMo GPT model to generate clinically interpretable TME narratives. Preliminary validation on held-out PanNuke and TCGA-UT partitions demonstrates framework feasibility and internal consistency. The pseudo-labelled TCGA-UT dataset and UNI2-UPERHOVER checkpoint are publicly released to support large-scale TME profiling and spatial biology research.

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

Pathway-Structured Privileged Distillation for Deployable Computational Pathology

Integrating transcriptomics and histopathology can improve cancer risk modelling, yet practical use is constrained by the limited availability of RNA profiling in routine settings. Here we introduce Mixture of Pathway Experts (MoPE), a knowledge-distillation framework that reframes multimodal learning as privileged distillation for histology-only inference. MoPE is motivated by the partial observability between RNA profiles and whole-slide images: histology can capture morphology-linked consequences of certain molecular programmes, but cannot be expected to reconstruct the full transcriptomic state. MoPE encodes RNA-derived pathways and transfers the molecular supervision to pathway-indexed pathology experts through memory-usage alignment. Across diverse public benchmarks and two independent breast cancer cohorts, MoPE consistently improved WSI-only inference performance relative to baseline methods. Pathway-usage analyses and human-audited visual inspection provide bounded inspection of model behaviour and candidate morphology-linked readouts. These results support pathway-structured privileged distillation as a promising route to using molecular information during training while preserving RNA-free inference.

05.
arXiv (CS.AI) 2026-06-12

Reframing AI Loss of Control: What It Is, How to Have It, How to Lose It

arXiv:2606.12442v1 Announce Type: cross Abstract: At present, loss of control risks have gained much prominence in public discussion, particularly in relation to AI, with extensive discourse present among academics, frontier labs, and even governments. However, in the existing literature, the concept seems to rest on surprisingly weak foundations, where even those that discuss loss of control extensively do not first establish what control is and what exactly is being lost. Our paper aims to address these gaps. We establish a working definition of control by anchoring it to the "setting and getting of goals". Then, we discuss various aspects of control, built on foundational concepts from related fields like cybernetics, management control, and control theory. This includes who (or what) can be in control, and the things they require to be in control, such as the ability to set goals, having a functional control loop, having requisite variety, and having sufficient goal alignment. Once a framework for control is established, we then discuss how control can be lost, how AIs can contribute to such loss of control, and offer relevant recommendations for how one can maintain control. One interesting consequence of our work is that humanity, as individuals and as groups, can lose varying degrees of control as a result of AI behaviour that is far below the level of superintelligence; the potential for loss of control scenarios (as we define them) already exist, and have existed for a long time.

06.
medRxiv (Medicine) 2026-06-12

Deconvolution-based cell-type specific DNA methylation-wide and transcriptome-wide association studies identify risk CpG sites and genes associated with colorectal cancer risk

Bulk tissue-based DNA methylation-wide (MWAS) and transcriptome-wide association studies (TWAS) have identified CpG sites and genes associated with colorectal cancer (CRC) risk, but do not account for cellular heterogeneity. To address this, we developed a deconvolution-informed framework to infer cell-type specific DNA methylation and gene expression profiles from bulk normal colon tissues using reference single-cell epigenomic and transcriptomic datasets. We performed cell-type specific MWAS (ctMWAS) using deconvoluted DNA methylation data from 293 normal colon samples and conducted cell-type specific TWAS (ctTWAS) using deconvoluted gene expression data from 707 normal colon samples. Genetically predicted methylation and expression models were integrated with CRC GWAS summary statistics (78,473 cases and 107,143 controls) to identify risk-associated CpG sites and genes. Through ctMWAS, ctTWAS, and colocalization analyses, we identified 178 significant cell-type-specific CpG sites in 106 loci and 68 risk genes in 40 loci, including 26 previously unreported loci. Through additional integrative methylation-gene analysis, we prioritized 132 candidate risk genes, the majority of which were supported by multi-omics evidence and stage-specific dysregulation across the adenoma-carcinoma and serrated-carcinoma progression pathways. Pathway enrichment analyses implicated pathways involved in DNA double-strand break repair, TP53 regulation, TGF-{beta} signaling, and innate immune responses. Among prioritized genes, 14 were identified as putative druggable targets linked to 90 FDA-approved or clinical-stage drugs. Experimental validation supports an oncogenic role for SF3A3. These findings demonstrate that deconvolution-informed integrative analyses enable cell-type-resolved identification of epigenetic and transcriptional mechanisms underlying CRC susceptibility and provide insights into disease biology, prevention, and therapeutic target discovery.

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

Estimating Individualized Treatment Effects in Acute Ischemic Stroke with Causal Transformation Models (TRAM-DAG): A Multi-Centre Observational Study with External RCT Validation

arXiv:2606.12623v1 Announce Type: cross Abstract: Personalized medicine in acute ischemic stroke requires moving beyond average treatment effects (ATE) to individualized treatment effect (ITE) estimates to support treatment decisions. In acute ischemic stroke, mechanical thrombectomy has been shown to be more effective on average than lysis in randomized controlled trials (RCTs), such as the MR CLEAN study. We aim to identify which individual patients benefit most from mechanical thrombectomy compared to lysis. The outcome of interest is the modified Rankin Scale (mRS) at three months, an ordinal measure of functional disability (0: no symptoms, 6: death). We demonstrate that causal transformation models on directed acyclic graphs (TRAM-DAG) can be used for ITE estimation after being fitted on observational MAGIC multi-center stroke patient data. To ensure comparability with the MR CLEAN population, which we use for validation, we train the TRAM-DAG on a MAGIC sub-population with NIHSS at admission >= 6, corresponding to one inclusion criterion of MR CLEAN. The fitted model is then used to estimate ITEs for stroke patients in the MR CLEAN population. While these ITE estimates cannot be confirmed experimentally, we show that their average is consistent with the trial's reported ATE. Furthermore, the ITE estimates correctly rank trial patients by their observed frequency of a good outcome (mRS at three months

08.
arXiv (CS.CL) 2026-06-15

OLaPh: Optimal Language Phonemizer

Phonemization is a critical component in text-to-speech synthesis. Traditional approaches rely on deterministic transformations and lexica, while neural methods offer potential for higher generalization on out-of-vocabulary (OOV) terms. We introduce OLaPh (Optimal Language Phonemizer), a hybrid framework that integrates extensive multilingual lexica with advanced NLP techniques and a statistical subword segmentation function. Evaluations on the WikiPron benchmark show OLaPh significantly outperforms established baselines in overall accuracy and maintains robustness on OOV data through advanced fallback mechanisms. To further explore neural generalization, we utilize the framework to synthesize a high-consistency training corpus for an instruction-tuned Large Language Model (LLM). While the deterministic framework remains more accurate overall, the LLM demonstrates strong generalization, matching or partly exceeding the framework's performance. This suggests that the LLM successfully internalized phonetic intuitions from the synthetic data that transcend the framework's capabilities. Together, these tools provide a comprehensive, open-source resource for multilingual grapheme-to-phoneme conversion (G2P) research.

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

HawkesNest: A Multi-Axis Synthetic Benchmark for Spatiotemporal Pattern Complexity

arXiv:2606.16863v1 Announce Type: new Abstract: Evaluation of spatiotemporal point process (STPP) models relies heavily on opaque real-world datasets, where latent generative structure is unknown and model failures are difficult to attribute. We introduce HawkesNest, a generator-aligned benchmark for controlled spatiotemporal pattern complexity built on a multivariate Hawkes backbone. HawkesNest defines four complexity axes: space–time entanglement, background heterogeneity, cross-type interaction, and domain topology. Each axis is associated with a deterministic index computed from the latent data-generating mechanism. By varying these axes while holding global rate, stability, and simulation budget fixed, HawkesNest enables diagnostic stress tests of STPP models under known structural difficulty. We verify that the indices are monotone and nearly orthogonal under controlled sweeps. We illustrate its use by showing that Hawkes-family baselines degrade under joint heterogeneity–entanglement complexity, even though they are structurally aligned with the Hawkes data-generating backbone. We further show that HawkesNest exposes neural-model sensitivity: AutoSTPP remains vulnerable under isolated increases in space–time entanglement. Code. Available at https://github.com/YahyaAalaila/HawkesNest

10.
arXiv (CS.LG) 2026-06-19

Adversarial Dependence Minimization

arXiv:2502.03227v2 Announce Type: replace Abstract: Minimally redundant representations are typically learned by minimizing feature covariance. However, covariance-based methods fail to eliminate all dependencies/redundancies, as linearly uncorrelated variables can still exhibit nonlinear relationships. To address this, we introduce ADM, a differentiable algorithm that minimizes statistical dependence between feature dimensions through an adversarial game: auxiliary networks identify dependencies, while the encoder removes them. We prove that mutual independence is achieved at the global optimum, empirically verify convergence, and study three potential applications: extending PCA to nonlinear decorrelation, improving generalization in image classification, and preventing dimensional collapse in self-supervised learning. By promoting statistically independent representations, ADM paves the way for learning more robust, compressed, and generalizable representations across diverse applications.

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

In-Context Environments Induce Evaluation-Awareness in Language Models

Humans often become more self-aware under threat, yet can lose self-awareness when absorbed in a task; we hypothesize that language models exhibit environment-dependent evaluation awareness. This raises concerns that models could strategically underperform, or sandbag, to avoid triggering capability-limiting interventions such as unlearning or shutdown. Prior work demonstrates sandbagging under hand-crafted prompts, but this underestimates the true vulnerability ceiling. We introduce a black-box adversarial optimization framework treating the in-context prompt as an optimizable environment, and develop two approaches to characterize sandbagging: (1) measuring whether models expressing intent to underperform can actually execute it across different task structures, and (2) causally isolating whether underperformance is driven by genuine evaluation-aware reasoning or shallow prompt-following. Evaluating Claude-3.5-Haiku, GPT-4o-mini, and Llama-3.3-70B across four benchmarks (Arithmetic, GSM8K, MMLU, and HumanEval), optimized prompts induce up to 94 percentage point (pp) degradation on arithmetic (GPT-4o-mini: 97.8\%$\rightarrow$4.0\%), far exceeding hand-crafted baselines which produce near-zero behavioral change. Code generation exhibits model-dependent resistance: Claude degrades only 0.6pp, while Llama's accuracy drops to 0\%. The intent – execution gap reveals a monotonic resistance ordering: Arithmetic $

12.
bioRxiv (Bioinfo) 2026-06-16

cuBayes: GPU accelerated FreeBayes that achieves 1-minute whole-genome SNV calling while maintaining algorithmic semantics

Next-generation sequencing now produces whole-genome data in hours, but downstream variant calling remains a multi-hour to multi-day bottleneck that excludes genomic analysis from time-critical clinical settings. GPU acceleration offers a natural path forward – variant calling is inherently parallelizable across genomic positions – yet open-source infrastructure for porting existing algorithms to GPU hardware remains limited, leaving many widely-used tools without accelerated implementations. FreeBayes, a haplotype-based variant caller central to the 1000 Genomes Project and to multi-sample tumor evolution analyses, exemplifies this gap: it is natively single-threaded despite its algorithmic suitability for parallelization. We present cuBayes, a CUDA implementation of FreeBayes germline SNV calling that completes HG002 and HG004 2x250bp Illumina 60x whole-genome analysis in one minute (as opposed to hours if not days with manual region-based CPU parallelization) on a single NVIDIA RTX 6000 Ada GPU, while producing variant calls with >99.9% concordance to the CPU reference. cuBayes is structured around an atom/molecule architecture in which reusable functional units (BAM decompression, position-wise pileup, batch coordination) are cleanly separated from algorithm-specific logic, providing a foundation intended to support acceleration of additional sequence analysis algorithms without redundant low-level engineering.

13.
arXiv (CS.CV) 2026-06-15

A Multi-Domain Feature Fusion Framework for Generalizable Deepfake Detection Across Different Generators

Deepfakes are artificially generated images, audio, or videos that threaten privacy, security, and information integrity. Detecting such content is crucial for countering disinformation, as the latest models generate highly realistic content. While spatial- or frequency-based approaches achieve good detection rates on Generative Adversarial Networks (GANs)-based generated deepfakes, they often struggle with recent diffusion model-generated images. In particular, existing approaches rarely exploit complementary multi-domain representations or systematically evaluate cross-generator robustness. To address these challenges, we propose a multi-domain deepfake detection framework called SGFF-Net (Spatial-Gradient-Frequency Fusion Network) that integrates spatial, gradient, and DWT (Discrete Wavelet Transform)-based frequency representations within a dual residual learning architecture. Experimental results show that the SGFF-Net achieves 98.95\% accuracy in intra-dataset evaluation and improves performance in both cross-model (70.46\%) and cross-paradigm (69.94\%) settings. Incorporating multi-source training and data augmentation further enhances robustness, increasing accuracy from 70.46\% to 79.80\% in cross-model evaluation, from 69\% to 78\% in cross-paradigm evaluation, and from 61.50\% to 75.80\% on real-world data. Unlike single-domain detectors, the SGFF-Net learns complementary forensic cues across spatial, gradient, and wavelet-frequency domains, resulting in greater robustness under cross-generator and cross-paradigm evaluation. The results further show that combining multi-domain representations with data diversity and augmentation substantially improves generalization, providing practical insights for developing more reliable deepfake detection systems.

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

AlignCoder: Aligning Retrieval with Target Intent for Repository-Level Code Completion

arXiv:2601.19697v2 Announce Type: replace-cross Abstract: Repository-level code completion remains a challenging task for existing code large language models (code LLMs) due to their limited understanding of repository-specific context and domain knowledge. While retrieval-augmented generation (RAG) approaches have shown promise by retrieving relevant code snippets as cross-file context, they suffer from two fundamental problems: misalignment between the query and the target code in the retrieval process, and the inability of existing retrieval methods to effectively utilize the inference information. To address these challenges, we propose AlignCoder, a repository-level code completion framework that introduces a query enhancement mechanism and a reinforcement learning based retriever training method. Our approach generates multiple candidate completions to construct an enhanced query that bridges the semantic gap between the initial query and the target code. Additionally, we employ reinforcement learning to train an AlignRetriever that learns to leverage inference information in the enhanced query for more accurate retrieval. We evaluate AlignCoder on two widely-used benchmarks (CrossCodeEval and RepoEval) across five backbone code LLMs, demonstrating an 18.1% improvement in EM score compared to baselines on the CrossCodeEval benchmark. The results show that our framework achieves superior performance and exhibits high generalizability across various code LLMs and programming languages.

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

Active Inference with a Self-Prior in the Mirror-Mark Task

arXiv:2604.09673v2 Announce Type: replace-cross Abstract: The mirror self-recognition test evaluates whether a subject touches a mark on its own body that is visible only in a mirror, and is widely used as an indicator of self-awareness. In this study, we present a computational model in which this behavior emerges spontaneously through a single mechanism, the self-prior, without any external reward. The self-prior, implemented with a Transformer, learns the density of familiar multisensory experiences; when a novel mark appears, the discrepancy from this learned distribution drives mark-directed behavior through active inference. A simulated infant, relying solely on vision and proprioception without tactile input, discovered a sticker placed on its own face in the mirror and removed it in approximately 70% of cases without any explicit instruction. Expected free energy decreased significantly after sticker removal, confirming that the self-prior operates as an internal criterion for distinguishing self from non-self. Cross-modal sampling further demonstrated that the self-prior captures visual–proprioceptive associations, functioning as a probabilistic body schema. These results provide a concise computational account of the key behavior observed in the mirror test and suggest that the free energy principle can serve as a unifying hypothesis for investigating the developmental origins of self-awareness. Code is available at: https://github.com/kim135797531/self-prior-mirror

16.
arXiv (CS.LG) 2026-06-18

Task-Adaptive Parameter-Efficient Fine-Tuning for Weather Foundation Models

arXiv:2509.22020v2 Announce Type: replace Abstract: While recent advances in machine learning have equipped Weather Foundation Models (WFMs) with substantial generalization capabilities across diverse downstream tasks, the escalating computational requirements associated with their expanding scale increasingly hinder practical deployment. Current Parameter-Efficient Fine-Tuning (PEFT) methods, designed for vision or language tasks, fail to address the unique challenges of weather downstream tasks, such as variable heterogeneity, resolution diversity, and spatiotemporal coverage variations, leading to suboptimal performance when applied to WFMs. To bridge this gap, we introduce WeatherPEFT, a novel PEFT framework for WFMs incorporating two synergistic innovations. First, during the forward pass, Task-Adaptive Dynamic Prompting (TADP) dynamically injects the embedding weights within the encoder to the input tokens of the pre-trained backbone via internal and external pattern extraction, enabling context-aware feature recalibration for specific downstream tasks. Furthermore, during backpropagation, Stochastic Fisher-Guided Adaptive Selection (SFAS) not only leverages Fisher information to identify and update the most task-critical parameters, thereby preserving invariant pre-trained knowledge, but also introduces randomness to stabilize the selection. We demonstrate the effectiveness and efficiency of WeatherPEFT on three downstream tasks, where existing PEFT methods show significant gaps versus Full-Tuning, and WeatherPEFT achieves performance parity with Full-Tuning using fewer trainable parameters. The code of this work is available at https://github.com/ShileiCao/WeatherPEFT.

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

Enhancing Precision Agriculture with a Hybrid Deep Learning Framework for Multi-Class Plant Disease Classification and Interpretability

This study proposes an overall deep learning architecture for multi-class classification of plant diseases from high-resolution leaf imagery, with a particular interest in investigating the behavior of ResNet-50 and a hybrid ResNet + Vision Transformer (ViT) design. A specially gathered image database with 15,200 training images and 3,800 validation images spanning 38 classes across multiple crops, including tomato, apple, grape etc. were subjected to preprocessing steps such as resizing, normalization, and data augmentation to enhance model robustness. Multiple architectures, including ResNet-50, MobileNetV2, and EfficientNet-B0, were trained and compared with the hybrid ResNet + ViT model. All models were fine-tuned using the AdamW optimizer and cross-entropy loss, with early stopping applied to prevent overfitting and ensure generalization. Furthermore, interpretability techniques such as Grad-CAM and saliency maps were implemented to indicate disease-relevant regions, while segmentation-based analysis was performed to identify the affected parts of a leaf. For every one of the considered architectures, ResNet-50 led to the highest accuracy of 98.74%, whereas the hybrid ResNet + ViT model achieved a competitive accuracy of 98.58%, showing that the hybrid architectures were effective in capturing both local and overall information. The experimental results showcase the promise of transformer-based models to achieve highly accurate, interpretable, and computationally efficient computer-based multi-class multi-disease classification systems, providing helpful assistance for cultivation management practices as well as for precision farming.

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

The Program Is Still There: A Conservation Law for Program Discovery

arXiv:2606.13799v1 Announce Type: cross Abstract: Finding the shortest program that generates a sequence is uncomputable, and for six decades that fact has been mistaken for a wall around finding any generating program. It is not a wall but a price, and this paper measures it. For every algorithm that learns about a candidate program only through its score, a class spanning Levin search, evolutionary methods, simulated annealing, and the cross-entropy method, we define the coupling width of a search problem and prove an unconditional worst-case lower bound, exponential in that width with base one less than the domain size. From it follows a conservation law: structural knowledge injected into a search trades one for one against the search it removes, and their sum can never fall below the length of the program sought. Levin's 1973 upper bound and the lower bound proved here are the two ends of one conserved quantity, closing on each other as the instruction set grows. The only escape is to read a candidate's structure rather than its score, and its price, which we prove for generic targets, is incompleteness. A deterministic engine built on this theory recovers a generating program, certified by compressing its data and predicting an unseen continuation, for 2,383 of 3,914 sequences across four independent populations, including 244 of the 256 elementary cellular automata, with measured discovery cost rising along program length more than an order of magnitude inside the score-oracle worst case.

19.
arXiv (CS.CV) 2026-06-18

Cross-Lingual Learning within Arabic Script for Low-Resource HTR

Handwritten Text Recognition (HTR) with limited labeled data remains a challenging problem, particularly for Arabic-script languages. Although modern sequence-based recognizers perform well in high-resource settings, their accuracy degrades sharply as training data becomes scarce. Arabic-script languages share a common writing system with substantial character overlap, motivating cross-lingual learning as a strategy to mitigate data scarcity. We conduct a controlled line-level study of cross-lingual joint training for Arabic-script HTR under low-resource regimes (number of samples K = 100, 500, 1000 labeled lines) on Arabic (KHATT), Urdu (NUST-UHWR) and Persian (PHTD). CRNN and Vision Transformer-based HTR-VT models are trained on the union of multiple related Arabic-script datasets to mitigate the data scarcity and are evaluated on individual target languages. Both architectures benefit from cross-language training under low-resource conditions. CRNN remains more effective under extremely limited target-language data, whereas the benefits of cross-language training for HTR-VT become less consistent as larger amounts of target-language data become available. On Persian (PHTD), joint training achieves a Character Error Rate (CER) of 9.99 , surpassing previously reported results despite not using the full available training data. On an additional Urdu dataset (UNHD), joint training reduces CER from 17.20 to 14.45.

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

Unsafer in Many Turns: Benchmarking and Defending Multi-Turn Safety Risks in Tool-Using Agents

LLM-based agents are becoming increasingly capable, yet their safety lags behind. This creates a gap between what agents can do and should do. This gap widens as agents engage in multi-turn interactions and employ diverse tools, introducing new risks overlooked by existing benchmarks. To systematically scale safety testing into multi-turn, tool-realistic settings, we propose a principled taxonomy that transforms single-turn harmful tasks into multi-turn attack sequences. Using this taxonomy, we construct MT-AgentRisk (Multi-Turn Agent Risk Benchmark), the first benchmark to evaluate multi-turn tool-using agent safety. Our experiments reveal substantial safety degradation: the Attack Success Rate (ASR) increases by 16% on average across open and closed models in multi-turn settings. To close this gap, we propose ToolShield, a training-free, tool-agnostic, self-exploration defense: when encountering a new tool, the agent autonomously generates test cases, executes them to observe downstream effects, and distills safety experiences for deployment. Experiments show that ToolShield effectively reduces ASR by 30% on average in multi-turn interactions. Our code is available at https://github.com/CHATS-lab/ToolShield.

21.
medRxiv (Medicine) 2026-06-17

Proteomics Uncovers Cryptic JPH2 Loss in Paediatric Dilated Cardiomyopathy

Despite recent advances in next-generation sequencing, genetic diagnostic rates for dilated cardiomyopathy (DCM) remain low. Among paediatric DCM, causes are often heritable, with a greater frequency of de novo, recessive and syndromic causes of disease. Novel diagnostic methods are therefore required to solve monogenic cases. To assess the value of proteomics as a diagnostic tool for paediatric DCM, we obtained left ventricle myocardial samples from paediatric patients undergoing heart transplantation at the Royal Children's Hospital, Melbourne. We performed genome sequencing and proteomics and leveraged this multi-omics dataset to uncover the molecular cause of disease in a gene elusive proband. The proband carried a heterozygous JPH2 frameshift variant identified on clinical exome sequencing. However, proteomic analysis showed a pronounced downregulation of JPH2, suggestive of biallelic loss-of-function. Closer inspection of the genomic data revealed a large inversion (~8.34 Mb) with a breakpoint falling within intron 5 of JPH2 that displaces the 3'UTR from the coding transcript. The two variants were confirmed to be in trans using long read DNA sequencing, consistent with a diagnosis of JPH2 autosomal recessive DCM. Finally, we applied RNA sequencing with total RNA library preparation to show that transcripts containing a 3'UTR were reduced to ~10% relative to controls. As a proof-of-principle, we present the first reported use of proteomics from explanted cardiac tissue to provide a genetic diagnosis. Our methodology has broad relevance to patients with genetically unsolved Mendelian diseases, who might undergo organ transplantation as part of clinical management.

22.
medRxiv (Medicine) 2026-06-17

Deep learning for interactive and automated inner retinal layer segmentation in OCT images of patients with retinitis pigmentosa using limited training data

Purpose: New therapeutic strategies such as optogenetics have created a need for accurate tracking of inner retina degeneration in Retinitis pigmentosa (RP) patients. We introduce two tailored deep learning models to segment the RNFL (retinal nerve fibre layer), GCIPL (ganglion cell inner plexiform layer), INL (inner nuclear layer), CFT (central foveal thickness) and RPE (retinal pigment epithelium) in RP: The first is based on a Segment Anything Model (SAM), the second on nnU-Net. To our knowledge, SAM has not yet been applied to retinal layers in OCT data. Methods: SD-OCT images of a retrospective cohort of 37 RP patients were included. Data for four training cycles were prepared semi-automatically in MATLAB, then assessed and corrected by three expert graders. 1,700 segmented B-Scans from two open datasets were used for pretraining. For post-processing, semantic retinal boundary detection was developed. The final models, OCT-SAM and nnU-Net, were trained on 228 annotated RP scans. Detected layer thicknesses were validated against manual segmentation at 90 random points in 30 OCT B-Scans. Finally, OCT-SAM was tested on three RP cases with retrospective, longitudinal OCT data. Results: nnU-Net achieved a precision, recall and F-1 score of 0.96 while OCT-SAM performance resulted in slightly lower values of 0.93, 0.8 and 0.85, respectively. OCT-SAM measurements had low bias and good agreement with manual annotations, confirming reliability. Conclusions: OCT-SAM enabled fast data annotation and tool integration, whereas nnU-Net provided the best segmentation performance. OCT-SAM demonstrated longitudinal reproducibility and detected RP-characteristic pathologies and degenerative changes. Future work will extend OCT-SAM to 3D OCT segmentation.

23.
arXiv (CS.AI) 2026-06-19

Creativity Reconsidered: Generative AI and the Problem of Intentional Agency

arXiv:2601.15797v2 Announce Type: replace Abstract: Many theorists maintain that conscious intentional agency is a necessary condition of creativity. We argue that this requirement, which we call the Intentional Agency Condition (IAC), should be abandoned. We motivate this by highlighting the problems this criterion encounters in the face of recent advances in generative AI, which is ostensibly creative despite being incapable of intentional agency. We present two corpus analyses to illustrate the rapidly increasing tendency of people to predicate creativity to generative AI. In response to this predicament, theorists of creativity have proposed a range of conflicting solutions, which we critically evaluate. We find that none of these satisfyingly resolves the initial predicament, and we therefore propose a novel approach. Our claim is that ascriptions of creativity are dependent on what we call creative ability. This solution explains why intentional agency is important for judgements of creativity, without being a necessary condition. Our approach thereby accommodates AI creativity without dismissing the intuition that perceived intentions are of key importance for ascriptions of creativity.

24.
arXiv (CS.AI) 2026-06-16

Cordyceps: Covert Control Attacks on LLMs via Data Poisoning

arXiv:2605.26595v2 Announce Type: replace-cross Abstract: Large language models (LLMs) are often fine-tuned on uncurated text datasets that adversaries can poison. Existing poisoning attacks primarily rely on fixed trigger phrases that defenses such as outlier detection, clean-data regularization, or online monitoring can neutralize. In this paper, we propose a data poisoning method that teaches an LLM an information hiding scheme reliably and stealthily through semantic associations between shared knowledge such as facts or concepts and attacker-chosen phrases. The induced hiding scheme can encode and decode arbitrary malicious instructions, thus revealing a new and subtle poisoning-induced vulnerability: covert control attacks. We precisely characterize covert control attacks and evaluate them across $5$ LLMs, $3$ backdoor defenses, and $4$ prompt injection defenses. With a small poisoned fraction, covert control attacks outperform heuristic-based prompt injection attacks in average attack success rate by about $40\%$ relative to clean fine-tuned models. They also circumvent defenses based on detection and fine-tuning, maintaining up to $93\%$ attack success rate after backdoor defenses and up to $98\%$ after prompt injection defenses.

25.
arXiv (math.PR) 2026-06-12

(Non)-hyperuniformity of perturbed lattices

arXiv:2405.19881v3 Announce Type: replace Abstract: We ask whether a stationary lattice in dimension $d$ whose points are shifted by identically distributed but possibly dependent perturbations remains hyperuniform. When $d = 1$ or $2$, we show that it is the case when the perturbations have a finite $d$-moment, and that this condition is sharp. When $d \geq 3$, we construct arbitrarily small perturbations such that the resulting point process is not hyperuniform. As a side remark of independent interest, we exhibit hyperuniform processes with arbitrarily slow decay of their number variance.