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

Automated jailbreak attack targeting multiple defense strategies

arXiv:2606.16751v1 Announce Type: cross Abstract: Large language models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks. However, their safety remains a critical concern due to their susceptibility to adversarial prompt-based attacks. In this paper, we present UNIATTACK, an adversarial testing framework designed from a defense-oriented perspective to systematically construct effective black-box attack prompts. Unlike prior approaches that rely on static templates or iterative model-specific tuning, UNIATTACK extracts minimal but high-impact attack features from diverse existing attacks, optimizes them via a specialized attacker LLM, and composes them into flexible templates through automated refinement process. This feature-centric construction enables one-shot attacks that generalize across multiple models and safety categories, providing a practical tool for assessing LLM robustness. Our evaluation results shows that compared to the baselines, UNIATTACK achieves an average attack success rate (ASR) improvement of 64.63\%-248.82\% on models deployed with multi-layered defense mechanisms and it only takes 0.03\%-4.96\% cost of the baselines. UNIATTACK artifact is available at https://anonymous.4open.science/r/UniAttack-Artifact-30F1.

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

VisDom: Sparse Novel View Synthesis with Visible Domain Constraint

Sparse novel view synthesis (NVS) remains challenging due to the ambiguity of recovering 3D geometry from few input views. While NeRF- and Gaussian Splatting (GS)-based methods perform well with dense supervision, they often overfit in sparse settings, producing floating artifacts and inconsistent geometry. Silhouette consistency is commonly used as a regularizer, but it remains insufficient, as silhouette-consistent regions can extend beyond the true object geometry. We introduce VisDom, a learning-free geometric constraint that augments classical carving-based visual hull reconstruction by enforcing a minimum multi-view visibility requirement. Specifically, we define a visible domain as the subset of 3D space observed by at least $K$ views and use it as an additional filtering criterion on top of standard silhouette-based reconstruction. This provides a stronger spatial prior in sparse-view settings. We integrate VisDom into both implicit (NeRF) and explicit (GS) pipelines by restricting volumetric sampling and guiding Gaussian placement during optimization. Experiments on three challenging datasets show consistent improvements in sparse-view NVS, enabling high-quality object-centric reconstruction from as few as four input images. Our method is domain-agnostic, requires only silhouettes, and introduces no learned parameters, making it a simple complement to existing approaches. Applying VisDom on top of GaussianObject further improves performance on Omni3D and MipNeRF360, while matching or surpassing it at 22 $\times$ lower training cost.

03.
arXiv (CS.CV) 2026-06-12

Dual-Domain Equivariant Generative Adversarial Network for Multimodal CT-PET Synthesis

We present a Dual-Domain Equivariant Generative Adversarial Network (DDE-GAN) for multimodal CT-PET image synthesis. Traditional GAN-based approaches often operate solely in the spatial domain and ignore geometric consistency, resulting in limited structural fidelity. DDE-GAN addresses these challenges by jointly learning from both spatial and frequency (Fourier) domains, capturing complementary anatomical and spectral information. Furthermore, rotational equivariance embedded in the physics of the CT and PET measurements are integrated into the loss of both the generator and discriminator to ensure consistent responses under rotations, improving anatomical accuracy. A hierarchical dual-domain training strategy enforces intra- and inter-domain consistency through multi-stage loss functions. Evaluated on the HECKTOR 2022 CT-PET dataset, DDE-GAN achieves superior synthesis quality over baseline models for CT-PET image synthesis. The results demonstrate that combining dual-domain learning with geometric equivariance substantially enhances multimodal image synthesis accuracy and robustness, enabling practical applications in PET completion and data augmentation.

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

G-Loss: Graph-Guided Fine-Tuning of Language Models

Traditional loss functions, including cross-entropy, contrastive, triplet, and su pervised contrastive losses, used for fine-tuning pre-trained language models such as BERT, operate only within local neighborhoods and fail to account for the global semantic structure. We present G-Loss, a graph-guided loss function that incorporates semi-supervised label propagation to use structural relationships within the embedding manifold. G-Loss builds a document-similarity graph that captures global semantic relationships, thereby guiding the model to learn more discriminative and robust embeddings. We evaluate G-Loss on five benchmark datasets covering key downstream classification tasks: MR (sentiment analysis), R8 and R52 (topic categorization), Ohsumed (medical document classification), and 20NG (news categorization). In the majority of experimental setups, G-Loss converges faster and produces semantically coherent embedding spaces, resulting in higher classification accuracy than models fine-tuned with traditional loss functions.

05.
arXiv (CS.AI) 2026-06-18

Where Did the Variability Go? From Vibe Coding to Product Lines by Regeneration

arXiv:2606.19042v1 Announce Type: cross Abstract: In vibe coding, an emerging AI-driven paradigm, an LLM generates an entire program from a natural language prompt, but what happens to the variability that traditional software engineering carefully builds into code? To answer this question, we conducted an exploratory analysis on 10 vibe coded C/C++ projects, which suggests that there is near-zero in-artifact variability, i.e., at compile and runtime. All variability decisions are resolved at a single new binding time, generation time, the moment the LLM produces the source code. Rather than treating this as a defect to fix, we propose Variability by Regeneration (VbR), to our knowledge the first product-line approach in which the LLM acts as the derivation engine, generating a purpose-built, free of dead code binary for each variant from a declarative specification, while a variant dispatcher transparently routes user requests to the matching binary. We formalise VbR, contrast it with classical SPL derivation, and demonstrate its full pipeline on a wc product family. For SPL engineering, variability in AI-generated software belongs in the specification, not in the code.

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

Beyond the Linear Separability Ceiling: Aligning Representations in VLMs

A challenge in advancing Visual-Language Models (VLMs) is determining whether their failures on abstract reasoning tasks, such as Bongard problems, stem from flawed perception or faulty top-down reasoning. To disentangle these factors, we introduce a diagnostic framework centered on the Linear Separability Ceiling (LSC), the performance achievable by a linear classifier on a VLM's raw visual embeddings. Applying this framework to state-of-the-art VLMs, we uncover a pervasive ''alignment gap'', where most models fail to generatively outperform the linear separability of their representations. We find that the few models surpassing this ceiling do so via two mechanisms: by further refining visual representations into a more linearly separable format or by executing non-linear decision logic. We demonstrate that this bottleneck is not a fundamental limitation but a solvable visual alignment issue. Our method augments standard next-token prediction with a contrastive objective to restructure the visual manifold into a more one-dimensionally linear geometry, improving image-to-image comparison and enabling models to significantly surpass the LSC on abstract compositional reasoning tasks.

07.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning

08.
arXiv (quant-ph) 2026-06-15

Strategic Non-Shareability of Quantum Correlations

作者:

arXiv:2605.25516v2 Announce Type: replace Abstract: Correlations distributed by a mediator can be useful for coordination but vulnerable to inheritance by a colluder. We formalize the obstruction to such inheritance as a source-certified resource theory of strategic non-shareability. The free objects are symmetrically extendible sources, the free operations are shareability-preserving maps, and the trace distance to the free set is a faithful convex monotone. For Werner and isotropic sources in arbitrary local dimension, the resource has the exact form $D_m=c(d)(p-p_m^{*})_{+}$, with $p_m^{*}$ the Johnson–Viola shareability threshold. For qubit Werner sources, tomographically complete Pauli measurements yield the exact one-colluder capacity\[ C^tomo_1(p)=\frac{1}{12}\Bigl[(3p-1)-\sqrt{(3p+1)(1-p)}\,\Bigr]_{+}.\] We prove that this anti-collusion resource is independent of Bellnonlocality: the Bell and shareability orderings cross, so some Bell-nonlocal states are strictly less collusion-resistant than Bell-local ones. Finally, we give an aligned Pauli coordination game whose observed behaviour has a local hidden-variable model for every visibility, making device-independent certification empty, while source-certified quantum anti-collusion is positive exactly above the extendibility threshold. These results identify symmetric non-extendibility, rather than Bell nonlocality, as the boundary of source-certified collusion resistance.

09.
arXiv (CS.LG) 2026-06-12

Fourier Multi-Component and Multi-Layer Neural Networks: Unlocking High-Frequency Potential

arXiv:2502.18959v3 Announce Type: replace Abstract: The architecture of a neural network and the choice of its activation function are both fundamental to its performance. Equally important is ensuring that these two elements are well matched, as their alignment is key to effective representation and learning. In this paper, we introduce the Fourier Multi-Component and Multi-Layer Neural Network (FMMNN), a model that combines sine-type activations with the multi-component and multi-layer structure of MMNNs. In an FMMNN, each component is represented as a trainable linear combination of fixed random sine-type basis functions, while multi-layer composition generates more complex and adaptive high-frequency features. We establish that FMMNNs retain exponential expressive power for function approximation even under a low-rank architectural structure. We also analyze the optimization landscape of FMMNNs and find it to be substantially more favorable than that of standard fully connected neural networks, especially for high-frequency targets. In addition, we propose a scaled random initialization method for the first-layer weights in FMMNNs, which accelerates training and improves final performance when sufficient samples are available. Extensive numerical experiments support our theoretical insights, showing that FMMNNs achieve strong accuracy and favorable convergence behavior on oscillatory function-approximation benchmarks.

10.
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.

11.
medRxiv (Medicine) 2026-06-15

Epileptogenicity alters intrahippocampal ripple propagation

Objective: Tracing the propagation of high-frequency oscillations (HFOs) aids in localizing epileptogenic regions and improving surgical outcomes. We examined how hippocampal epileptogenicity influences the propagation properties of the HFOs it generates. Methods: We analyzed non-REM sleep stereo-EEG from 49 patients (68 hemispheres) with verified hippocampal contacts. Hippocampi were stratified by excitability: 28 seizure onset zone (SOZ), 22 more-irritative non-SOZ (>6 interictal epileptiform discharges [IED]/min), and 18 less-irritative non-SOZ (

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

Pano3D: Unified 3D Reconstruction and Panoptic Segmentation

Recent advances in 3D feedforward reconstruction neural networks have achieved remarkable success in dense reconstruction from images without any camera parameters. Yet, equipping these models with robust semantic understanding remains an open problem. Here we introduce an approach that performs 3D reconstruction and 3D panoptic segmentation in a unified framework. We build on existing 3D reconstruction models and augment them with a set-based mask decoder. The approach is jointly trained with a geometric and semantic loss, which are shown to be mutually beneficial. More precisely, the features are initialized from the geometric information and then finetuned to capture jointly geometry and semantics. We demonstrate the generality of our approach by successfully applying our framework both to online and all-to-all attention reconstruction backbones. Our method achieves state-of-the-art performance in 3D panoptic segmentation across ScanNet, ScanNet200, and ScanNet++ datasets. Ablation studies show that such joint training of a unified model equips 3D feedforward reconstruction neural networks with panoptic segmentation and yields mutually beneficial improvements.

13.
arXiv (CS.LG) 2026-06-18

FinP: Fairness-in-Privacy in Federated Learning by Addressing Disparities in Privacy Risk

arXiv:2502.17748v4 Announce Type: replace Abstract: Federated Learning (FL) inherently mitigates mass data centralization risks; however, its privacy protections are not equally distributed - leaving vulnerable individuals disproportionately exposed to sophisticated privacy attacks. Crucially, statistical heterogeneity in human-centric FL environments often results in an inequitable distribution of privacy risks, particularly affecting those whose sensitive attributes or behaviors make them outliers. To address this critical gap, we introduce FinP, a novel framework designed to formalize and enforce fairness-in-privacy by mitigating disproportionate client vulnerability to Source Inference Attacks (SIA). FinP operationalizes a two-pronged defense strategy that tackles both the symptoms and root causes of privacy disparity, ensuring that no group of clients bears an excessive privacy burden. It combines a server-side adaptive aggregation mechanism, which dynamically weights client contributions based on their estimated privacy risk, with a client-side regularization technique to curb localized overfitting that drives unique data memorization. Extensive empirical evaluations on FEMNIST, Human Activity Recognition (HAR), and CIFAR-10 datasets demonstrate that FinP effectively aligns privacy fairness with primary task utility. Notably, FinP successfully mitigates SIA risks and reduces disparities in privacy exposure, establishing that strong fairness-in-privacy guarantees need not compromise model utility. Ultimately, FinP establishes equitable privacy protections by reducing vulnerability disparities by up to 57.14%, while preserving global model utility within a marginal +/- 1.75% of standard federated baselines.

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

Self-Driving Datasets: From 20 Million Papers to Nuanced Biomedical Knowledge at Scale

arXiv:2605.07022v3 Announce Type: replace Abstract: Manually curated biomedical repositories – spanning bioactivity, genomics, and chemistry – are expensive to maintain, lag behind primary literature, and discard experimental context, obscuring nuances needed to assess data correctness and coverage. We show that PubMed itself can be autonomously and cost-effectively turned into structured datasets that are larger, more nuanced, and more accurate than the curated databases they replace. We present three coupled contributions: (1) an LLM-based entity-tagging pipeline, grounded in nine biomedical ontologies, that tags 4.5B entities across 19 categories in a 22.5M-paper, 2.5T-token PubMed corpus; (2) hybrid sparse-dense retrieval supporting entity-filtered semantic queries over the tagged corpus; and (3) Starling, a multi-agent deep research system that, given only a natural-language task description, designs precision- and recall-targeted retrieval filters, induces an extraction schema, and emits structured records with nuance-rich fields and supporting passages. Across six tasks – blood-brain barrier permeability, oral bioavailability, acute toxicity (LD50), gene-disease associations, protein subcellular localization, and chemical reactions – Starling produces ~6.3M records (91K-3M per task); several are, to our knowledge, the largest public datasets for their property. Frontier-model rejection of our extractions is 0.6-7.7% across tasks, far below error rates we measure on widely used curated counterparts (e.g., 16.5% on BBB_Martins, 7.3% on Bioavailability_Ma). Beyond scale and accuracy, the supporting passages carry nuance tabular databases discard – e.g., oral bioavailability may depend on fed vs. fasted state. Together, the corpus, retrieval, and agent establish a foundation for AI-driven therapeutic design. Code and datasets: https://github.com/starling-labs/starling.

15.
arXiv (CS.AI) 2026-06-19

On the Limitations of Ray-Tracing for Learning-Based RF Tasks in Urban Environments

arXiv:2507.19653v2 Announce Type: replace-cross Abstract: We study the realism of Sionna v1.0.2 ray-tracing for outdoor cellular links in central Rome. We use a real measurement set of 1,664 user-equipments (UEs) and six nominal base-station (BS) sites. Using these fixed positions we systematically vary the main simulation parameters, including path depth, diffuse/specular/refraction flags, carrier frequency, as well as antenna's properties like its altitude, radiation pattern, and orientation. Simulator fidelity is scored for each base station via Spearman correlation between measured and simulated powers, and by a fingerprint-based k-nearest-neighbor localization algorithm using RSSI-based fingerprints. Across all experiments, solver hyper-parameters are having immaterial effect on the chosen metrics. On the contrary, antenna locations and orientations prove decisive. By simple greedy optimization we improve the Spearman correlation by 5% to 130% for various base stations, while kNN-based localization error using only simulated data as reference points is decreased by one-third on real-world samples, while staying twice higher than the error with purely real data. Precise geometry and credible antenna models are therefore necessary but not sufficient; faithfully capturing the residual urban noise remains an open challenge for transferable, high-fidelity outdoor RF simulation.

16.
arXiv (quant-ph) 2026-06-15

New Identity for Cayley's First Hyperdeterminant with Applications to Symmetric Tensors and Entanglement

作者:

arXiv:2512.03093v3 Announce Type: replace Abstract: In this article, a new formula for computing Cayley's first hyperdeterminant in terms of the Levi-Civita symbol is given. It is then shown that this formula can be used to compute the hyperdeterminant of symmetric tensors in polynomial time with respect to their order (assuming fixed side length). Applications to quantifying the entanglement of states of bosonic quantum systems are then discussed. Additionally, in order to obtain the fast calculation of the hyperdeterminant on symmetric tensors, generalized elimination and duplication matrices are defined and their explicit formulas are derived.

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

Atlas H&E-TME: Scalable AI-Based Tissue Profiling at Expert Pathologist-Level Accuracy

Hematoxylin and eosin (H&E) staining is the cornerstone of histopathology, yet scalable, quantitative analysis of H&E whole-slide images (WSIs) remains a central challenge in computational pathology. We present Atlas H&E-TME, an AI-based system built on the Atlas family of pathology foundation models that predicts tissue quality, tissue region, and cell type labels across multiple cancer types, yielding over 4,500 quantitative readouts per slide at cell-level resolution. A key challenge to validating such systems is overcoming morphological ambiguity inherent to H&E-only ground truth and the limited scalability of more informed references drawing on modalities such as immunohistochemistry (IHC). We address this with a dual validation framework combining biologically grounded depth with technical and morphological breadth. For depth, we propose an IHC-informed multi-pathologist consensus protocol that substantially improves inter-rater agreement over conventional H&E-only annotation. This yields a molecularly grounded reference against which we compare Atlas H&E-TME and pathologists working from H&E alone. For breadth, we benchmark Atlas H&E-TME on over 200,000 high-confidence H&E-only pathologist annotations across 1,500+ cases spanning eight cancer types and their most common metastatic sites, with subtypes covering >90% of clinical cases per cancer type, drawn from 25+ sources and 8+ scanner models. Benchmarked against the IHC-informed consensus, Atlas H&E-TME matches or exceeds pathologist H&E-only performance and generalizes consistently and robustly across this broad morphological and technical scope. In doing so, Atlas H&E-TME turns the H&E slide – the most ubiquitous data in pathology – into a scalable, quantitative window into the tumor and its microenvironment, laying a foundation for the next generation of tissue-based biomarkers in translational and clinical research.

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

SkillChain-Gym: A Benchmark for Reskilling-Aware Production-Inventory Control under Disruptions

arXiv:2606.17266v1 Announce Type: new Abstract: Production planning increasingly has to treat workforce capability as a decision variable: certifications lapse when skills are not maintained, new products require skills the current workforce does not hold, and reskilling competes for the same worker hours needed for production. Existing operations benchmarks usually treat labor as exogenous, while workforce-planning models with skills and learning are rarely released as reusable testbeds. We introduce SkillChain-Gym, a benchmark specification for reskilling-aware production-inventory control: a single-site environment with stylized worker skill-state dynamics, hard threshold certification, forgetting, and capacity-consuming training actions constrained by the same per-worker time budget as production. The benchmark includes seed-controlled disruption scenarios, three feasibility modes with projection diagnostics, deterministic replay, and metrics covering operations, resilience, capability growth, and training-access distribution. We evaluate production-only, reactive adaptive, water-filling adaptive, and static-insurance policies with budget variants over 60-shift horizons with paired statistical tests. The results are regime-dependent rather than a ranking. Training-capable policies dominate the production-only baseline, and maintenance training is necessary under forgetting even without disruptions. Among training-capable classes, adaptive training helps when bottlenecks are visible in the forecast, while a lean static cross-training plan, a deliberately favorable comparator whose structure encodes relevant skill contingencies, acts as strong insurance under surprise shocks and absenteeism. Capacity slack and the forgetting rate govern the boundary between these regimes. No policy class dominates across regimes, motivating forecast-driven controllers that decide when to buy skill insurance and when to react.

19.
arXiv (CS.LG) 2026-06-16

Probing Dec-POMDP Reasoning in Cooperative MARL

arXiv:2602.20804v2 Announce Type: replace Abstract: Cooperative multi-agent reinforcement learning (MARL) is typically framed as a decentralised partially observable Markov decision process (Dec-POMDP), a setting whose hardness stems from two key challenges: partial observability and decentralised coordination. Genuinely solving such tasks requires Dec-POMDP reasoning, where agents use history to infer hidden states and coordinate based on local information. Yet it remains unclear whether popular benchmarks actually demand this reasoning or permit success via simpler strategies. We introduce a diagnostic suite combining statistically grounded performance comparisons and information-theoretic probes to audit the behavioural complexity of baseline policies (IPPO and MAPPO) across 37 scenarios spanning MPE, SMAX, Overcooked, Hanabi, and MaBrax. Our diagnostics reveal that success on these benchmarks rarely requires genuine Dec-POMDP reasoning. Reactive policies match the performance of memory-based agents in over half the scenarios, and emergent coordination frequently relies on brittle, synchronous action coupling rather than robust temporal influence. These findings suggest that some widely used benchmarks may not adequately test core Dec-POMDP assumptions under current training paradigms, potentially leading to over-optimistic assessments of progress. We release our diagnostic tooling to support more rigorous environment design and evaluation in cooperative MARL.

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

Clusters are All You Need: Pre-Training the Tsetlin Machine with Semantic Clusters from Language Models for Interpretability

Pre-trained language models such as BERT achieve strong text classification performance but lack transparency, limiting their use in high-stakes settings. The Tsetlin Machine (TM) offers fully interpretable, clause-based reasoning but captures little semantic information, and prior attempts to bridge the two rely on static word embeddings that miss contextual meaning. We propose a semantic pre-training framework that transfers knowledge from a pre-trained language model into a TM without using embeddings. Text samples are grouped into semantically coherent clusters with K-means or Top2Vec, and the resulting cluster-sample pairs pre-train a non-negated TM with enhanced Type I feedback. The TM thereby learns interpretable semantic keywords that are fine-tuned on downstream tasks. Across five datasets, our method substantially outperforms vanilla and embedding-based TMs and reaches performance competitive with BERT while remaining interpretable.

21.
arXiv (CS.LG) 2026-06-15

Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

arXiv:2605.29228v2 Announce Type: replace Abstract: Protein structure classification (PSC) uses supervised learning to predict a protein's CATH/SCOP(e) class from the protein's sequence or 3D structural feature(s). We already modeled 3D structures as (static) protein structure networks (PSNs), demonstrating the competitiveness of PSN-based features to sequence or direct (i.e. non-network) 3D structural features in the PSC task. More recently, we demonstrated the power of features extracted from dynamic PSNs over features extracted from static PSNs (and thus by transitivity over sequence and direct 3D structural features) in the same task. That dynamic PSN approach used traditional machine learning (ML), combining manual (pre-engineered) features with an off-the-shelf classifier. Here, we evaluate whether automatic deep learning (DL) from the dynamic PSNs yields improvements. Our evaluation on 72 datasets spanning ~44,000 CATH- or SCOPe-labeled dynamic PSNs reveals that in terms of PSC accuracy, traditional ML and DL are (close to) tied for a large majority of the datasets, while DL is on average 10+ times slower. We are the first to evaluate traditional ML vs. DL in the dynamic PSN-based PSC task.

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

Bring My Cup! Personalizing Vision-Language-Action Models with Visual Attentive Prompting

arXiv:2512.20014v3 Announce Type: replace-cross Abstract: While Vision-Language-Action (VLA) models generalize well to generic instructions, they struggle with personalized commands such as "bring my cup," where the robot must act on one specific instance among visually similar objects. We study this setting of manipulating personal objects, in which a VLA must identify and control a user-specific object unseen during training using only a few reference images. To address this challenge, we propose Visual Attentive Prompting (VAP), a simple-yet-effective training-free perceptual adapter that equips frozen VLAs with top-down selective attention. VAP treats the reference images as a non-parametric visual memory, grounds the personal object in the scene through open-vocabulary detection and embedding-based matching, and then injects this grounding as a visual prompt by highlighting the object and rewriting the instruction. We construct two simulation benchmarks, Personalized-SIMPLER and Personalized-VLABench, and a real-world tabletop benchmark to evaluate personalized manipulation across multiple robots and tasks. Experiments show that VAP consistently outperforms generic policies and token-learning baselines in both success rate and correct-object manipulation, helping to bridge the gap between semantic understanding and instance-level control.

24.
medRxiv (Medicine) 2026-06-15

GLLaucoMed: A Secure LLM-Powered Agentic Workflow for Automated Medication Extraction from Free-Text Glaucoma Clinical Notes

Purpose: To evaluate the efficacy of large language models (LLMs) in extracting medication-related information from glaucoma clinical notes in the electronic health record (EHR). Design: Cross-sectional. Subjects: 1,250 subjects in the Bascom Palmer Ophthalmic Repository. Methods: Extracted clinical notes from glaucoma-related encounters between 2014 and 2024 were labeled by two glaucoma specialists with a third serving as an adjudicator. Graders were asked to label current topical medications (CTM), proposed changes to topical medications ({Delta}TM), current oral medications (COM), and proposed changes to oral medications ({Delta}OM) in a structured fashion. The dataset was split into development (10%), validation (10%), and test (80%) sets stratified by clinician. Development and validation sets were used to engineer and refine prompts, and the held-out test set was used for model assessment. Five LLMs (Claude Opus 4.6, DeepSeek-V3.2, GPT 5.2, Grok 4.1, and Qwen3.6-35B-A3B) were accessed via Microsoft Azure AI Foundry within a HIPAA-compliant environment. Inter-grader agreement was assessed with Gwet AC1. LLM performance was initially assessed in a binary fashion with F1 scores, and the degree of text match among positive cases was evaluated using exact match accuracy and Jaccard Index (JI). Main Outcome Measures: F1 score, exact match accuracy, JI. Results: Gwet AC1 for intergrader agreement was 0.799, 0.888, 0.985, and 0.988 for CTM, {Delta}TM, COM, and {Delta}OM, respectively. F1 scores for CTM were 0.985, 0.971, 0.978, 0.968, and 0.970 for Claude, Deepseek, GPT, Grok, and Qwen, respectively; for {Delta}TM: 0.905, 0.826, 0.897, 0.842, 0.855, respectively; for COM: 0.923, 0.887, 0.899, 0.906, 0.894, respectively; for {Delta}OM: 0.958, 0.815, 0.937, 0.835, 0.940, respectively. Among positive cases, range of exact match accuracies for CTM (N=1354) was 0.730- 0.882 and range of JIs was 0.809-0.918. For {Delta}TM (N=404), exact match accuracy range was 0.619-0.780 and JI range was 0.668-0.827. For COM (N=47), exact match accuracy range was 0.766-0.872 and JI range was 0.765-0.870. For {Delta}OM (N=25), exact match accuracy range was 0.583-0.920 and JI range was 0.583-0.922. Conclusions: The GLLaucoMed pipeline demonstrated high performance in extracting and standardizing medication data from unstructured clinical notes, including both current medications and proposed changes. Claude and GPT exhibited the strongest performance.

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

Contrastive Regularization for Accent-Robust ASR

arXiv:2605.03297v2 Announce Type: replace-cross Abstract: ASR systems based on self-supervised acoustic pretraining and CTC fine-tuning achieve strong performance on native speech but remain sensitive to accent variability. We investigate supervised contrastive learning (SupCon) as a lightweight, accent-invariant auxiliary objective for CTC fine-tuning. An utterance-level contrastive loss regularizes encoder representations without architectural modification or explicit accent supervision. Experiments on the L2-ARCTIC benchmark show consistent WER reductions across multiple pretrained encoders, with up to 25 – 29\% relative reduction under unseen-accent evaluation. Analysis using within-transcript cosine dispersion indicates that SupCon promotes more compact and stable representation geometry under accent variability. Overall, SupCon provides an effective and model-agnostic regularization strategy for improving accent robustness.