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01.
arXiv (CS.CL) 2026-06-15

Verbatim Chunks Beat Extracted Artifacts: A Controlled Ablation of Memory Representations for Long LLM Conversations

Authors:

A growing class of conversational-memory systems compresses dialogue history into structured artifacts – extracted facts, decisions, or events – on the premise that distilled structure retrieves better than raw text. We test this premise with a controlled ablation: within one fixed retrieval-rerank-reasoning pipeline, we swap only the stored representation – LLM-extracted typed artifacts versus verbatim conversation chunks – holding the model, retriever, reranker, and judge constant. Verbatim chunks win by 15.9 points on LoCoMo (43.9% vs. 28.0%) and 22.0 points on LongMemEval-S (67.4% vs. 45.4%); a 1-hop semantic graph does not recover the gap, and five confound controls reproduce the effect. The mechanism is lossy distillation: extraction discards verbatim detail that chunks retain for free, and the extracted-artifact pipeline never beats naive RAG in overall accuracy. Concurrent positive results with near-verbatim, provenance-preserving units fit the same account: retrieval accuracy tracks how far the representation departs from the source. For the extraction designs we test, structured memory should augment verbatim text rather than replace it: a chunks $\cup$ artifacts union store matches chunks on both benchmarks while artifacts alone forfeit the gap. Code and data: https://github.com/tao-hpu/cog-canvas

02.
arXiv (CS.AI) 2026-06-17

Mental Health AI Safety Claims Must Preserve Temporal Evidence

arXiv:2605.08827v2 Announce Type: replace Abstract: The safety of mental health AI is often judged at the wrong temporal scale. Current evaluations typically score isolated responses, endpoint outcomes, or aggregate dialogue quality, while clinically consequential failures may arise from the order and accumulation of interactions themselves, including delayed escalation, repeated reinforcement, dependency formation, failed repair, and gradual deterioration across turns. This paper argues that this mismatch is not merely a limitation of evaluation coverage but a source of invalid safety conclusions. We introduce Temporal Safety Non-Identifiability, a formal account of why safety properties that depend on sequence, timing, accumulation, or recovery cannot be certified by protocols that discard those features. From this formalization, we develop SCOPE (Safety Claims Over Preserved Evidence) as a general principle for aligning safety claims with the evidence an evaluation actually retains, and instantiate it as SCOPE-MH, a mental-health instantiation of this reporting standard. We operationalize SCOPE-MH through a proof-of-concept on the AnnoMI dataset of expert-annotated motivational interviewing conversations, which reveals mechanisms of failure that per-turn behavior scoring does not represent. We propose SCOPE-MH as a diagnostic complement to existing evaluation infrastructure and argue that evaluation preserving temporal evidence is necessary, not optional, for safety-critical mental health AI deployment.

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

RubricsTree: Scalable and Evolving Open-Ended Evaluation of Personal Health Agents across Health Memory and Medical Skills

The LLM-empowered personal health agents with user health (sensor) metrics have offered a promising pathway to alleviate global disparities in healthcare access. However, large-scale clinical deployment remains constrained by an open-ended evaluation bottleneck: physician annotation is reliable but costly and unscalable, while LLM-as-a-judge evaluators are scalable but subjective, inconsistent, and sometimes clinically misaligned. We introduce RubricsTree, a scalable evaluation framework with an expert-aligned hierarchical taxonomy of over 100 atomic, clinically-verifiable Boolean rubrics, evolving from the insights of 4,000 real user queries through an iterative human-in-the-loop curation protocol with an expertise panel led by an experienced physician. A context-aware adaptive router activates only the relevant auto-weighted rubric subset per query, providing the throughput needed for scalable evaluation with expert-aligned quality. Through a systematic meta-evaluation, we show that RubricsTree (i) substantially exceeds a strong large-scale evaluation baseline in expert alignment on challenging open-ended queries; (ii) reliably penalizes contextually degraded responses; and (iii) when used as structured instructions, text feedback, or training rewards for performance optimization, yields up to ~66% relative gains on HealthBench for Gemini, GPT, and Qwen model families. RubricsTree thus provides a scalable, auditable, and evolving evaluation infrastructure required for the continuous optimization of product-level personal healthcare AI.

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

DiverseDiT: Towards Diverse Representation Learning in Diffusion Transformers

Recent breakthroughs in Diffusion Transformers (DiTs) have revolutionized the field of visual synthesis due to their superior scalability. To facilitate DiTs' capability of capturing meaningful internal representations, recent works such as REPA incorporate external pretrained encoders for representation alignment. However, the underlying mechanisms governing representation learning within DiTs are not well understood. To this end, we first systematically investigate the representation dynamics of DiTs. Through analyzing the evolution and influence of internal representations under various settings, we reveal that representation diversity across blocks is a crucial factor for effective learning. Based on this key insight, we propose DiverseDiT, a novel framework that explicitly promotes representation diversity. DiverseDiT incorporates long residual connections to diversify input representations across blocks and a representation diversity loss to encourage blocks to learn distinct features. Extensive experiments on ImageNet 256x256 and 512x512 demonstrate that our DiverseDiT yields consistent performance gains and convergence acceleration when applied to different backbones with various sizes, even when tested on the challenging one-step generation setting. Furthermore, we show that DiverseDiT is complementary to existing representation learning techniques, leading to further performance gains. Our work provides valuable insights into the representation learning dynamics of DiTs and offers a practical approach for enhancing their performance.

05.
arXiv (CS.CL) 2026-06-11

T2MM: An LLM Supported Architecture For Inquiry-Based Modeling

Model Construction is a foundational practice in science learning that relies on visualization and interactivity. Large Language Models, increasingly augmented with multimodal capabilities, have been integrated in education contexts to support learning. However, these tools lack visual interactivity that is required by some learning contexts. We introduce Text to Multimodal Model (T2MM), a robust, dynamic LLM supported architecture that assists in model construction within the open inquiry ecology-based modeling software Virtual Experimental Research Assistant (VERA). T2MM accounts for the current context of the learner's model and creates interactive models, rather than static images, enabling the model to remain responsive to manual adjustment. To measure technical feasibility, we evaluate T2MM through a custom procedurally generated dataset of natural language learner modeling requests and target models within the VERA system. T2MM outperforms a baseline model generation architecture implemented through LLM-supported full code generation, common in the literature, across all measured success metrics. Our contribution not only outlines LLM integration into a inquiry-based learning modeling tool, but also describes a possible architecture through which more interactive multimodal LLM tools can be created.

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

Trainable Photonic Measurement for Physics-Informed PDE Learning

arXiv:2606.18713v1 Announce Type: new Abstract: Photonic quantum machine learning offers a route to trainable physical representations built from phase, interference and measurement. However, its role in scientific machine learning remains largely unexplored. Physics-informed neural fields provide a natural setting, because differential equations require trial spaces that preserve phase, frequency and derivative structure. Here we introduce a photonic quantum neural field in which coordinates become trainable optical phases, are mixed by multi-photon Fock-space interference and are decoded from photon-number measurements. The photonic circuit is optimized as the neural-field representation itself, not as a fixed feature map or hardware accelerator. Photonic measurement is therefore a trainable representation on which the physics-informed residual is minimized. Across seven elliptic, wave, nonlinear dispersive and inverse PDE benchmarks, we observe a phase-complexity transition: classical coordinate and Fourier-feature networks suffice in smooth regimes, whereas the photonic field is most accurate when residual derivatives amplify phase mismatch. In the hardest regimes it gives the lowest errors, with margins reaching an order of magnitude and about one quarter of the trainable parameters of classical baselines. Frozen and shuffled controls, together with noise stress tests, attribute this gain to learned interference and stable Fock-probability readout under compound perturbations. These results identify photonic quantum measurement as a representation-learning principle for scientific machine learning.

07.
bioRxiv (Bioinfo) 2026-06-20

A network approach to DNA methylation clocks

Biological age predicts health and lifespan better than chronological age, but remains difficult to measure. One leading molecular proxy for biological age is DNA methylation, which underlies age predictors known as "clocks". These clocks use penalized linear regression to predict chronological age from methylation levels using selected cytosine–guanine pairs (CpGs) along DNA. Although they predict chronological age within a few years and track mortality risk, there are several issues. Different clocks share a vanishingly small number of CpG sites, many of which show weak associations with age. Also, the clocks often do not transfer across methylation array platforms. This paper takes a network approach to better understand these issues. By using 12 public datasets from human blood, we build a co-methylation network of the sites that show the strongest age correlation. After pruning weak links, we find that it has a small number of large modules of covarying CpGs surrounded by many small modules and singleton sites. These modules are biologically interpretable, as they are associated with CpG island contexts and enriched for distinct Gene Ontology functions. We also map five established clocks onto this network (Horvath, Hannum, AltumAge, Skin & Blood, and Han) and find that they select some CpGs from the same module. This suggests that they are more similar than they appear. The network structure also suggests new ways to build clocks. A simple clock that retains one CpG per module matches the performance of established clocks. A second one, built from module-level principal components, outperforms all five established clocks in three validation cohorts and is transferable across array platforms (Illumina Infinium Methylation 450K or EPIC arrays). Overall, the network perspective shifts attention from individual CpG sites to modules of covarying sites. This perspective helps explain why DNA methylation clocks perform so well despite their differences and provides a more systematic approach for developing the next generation of aging biomarkers.

08.
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.

09.
arXiv (CS.CV) 2026-06-18

Multi-Class Brain Tumor Classification Using Advanced Deep Learning Models: A Comparative Study

Despite recent advancements in deep learning, accurately classifying brain tumors from MRI images continues to pose challenges. In this research, we present a comprehensive evaluation of five different convolutional neural networks (CNN) architectures, including a customized baseline model and four pre-trained models - for use in classifying multi-class brain tumors using a clinically-sourced dataset of approximately 10,000 MRI images. We have utilized five different architectures; VGG16, VGG19, DenseNet121, and EfficientNetB0, which were all tested and trained within an identical experimental framework. Performance was measured by both overall accuracy and tumor-wise recall as a means to measure the clinically-relevant performance of each architecture. We found that EfficientNetB0 had the best overall classification accuracy at 95%, when compared to the other architectures tested; specifically VGG16 (94.37%), VGG19 (92.29%), DenseNet121 (90.91%) and the customized CNN (78.00%). An especially important finding of our research was the considerable improvement in detecting meningiomas; specifically, while simple CNNs could detect meningiomas with a recall rate of approximately 20%, EfficientNetB0 was able to detect meningiomas with a recall rate of 89%. Meningiomas are often difficult to detect because they can appear very subtly on MRI images. Additionally, an interesting finding was that the deeper VGG19 performed worse than the shallower VGG16. This indicates that in many cases the architectural efficiency of a CNN model may be more important than its depth when working with medical images. Overall, EfficientNetB0 appears to provide the optimal trade-off between classification accuracy, number of parameters used in the model and clinically meaningful performance.

10.
arXiv (CS.CL) 2026-06-12

Helping Figures Tell their Story! Paper-Grounded Video Generation Explaining Complex Scientific Figures

Scientific figures compress complex pipelines into a single canvas, yet understanding them requires paper-grounded, step-by-step narration aligned with visual highlights a capability missing from current video generation systems and benchmarks. To address this, we introduce paper-grounded figure-to-video generation: generating narrated, region-grounded walkthrough videos from a figure and its paper. We propose MINARD (Multimodal Interpretation of Narrated Architecture via Region Decomposition), a pipeline that generates paper-grounded narrations and sequentially grounds them to figure regions. We also release FigTalk, a benchmark with new sequential and component-level grounding metrics derived. On FigTalk, MINARD generates humanlike, paper-faithful narrations and outperforms narration-conditioned figure spatial grounding compared to existing approaches in both automatic and human evaluation

11.
arXiv (CS.AI) 2026-06-19

Flickering Multi-Armed Bandits

arXiv:2602.17315v3 Announce Type: replace-cross Abstract: We introduce Flickering Multi-Armed Bandits (FMAB) to model sequential decision-making in environments with changing action availability, where accessibility of the next action is restricted to a subset dependent on the agent's current choice. We formalize these constraints through stochastically evolving graphs where actions are limited to local neighborhoods. This mobility-constrained structure imposes a dual challenge: the statistical requirement of information acquisition and the physical overhead of navigation. We analyze FMAB under i.i.d. Erdős–R'enyi and Edge-Markovian process, proposing a two-phase lazy random walk algorithm for robust exploration. We establish high-probability sublinear regret bounds and prove near-optimality via a matching information-theoretic lower bound. Our results characterize the intrinsic cost of learning under local-move constraints, complemented by a robotic disaster-response simulation.

12.
arXiv (CS.AI) 2026-06-11

Autoregressive Direct Preference Optimization

arXiv:2602.09533v2 Announce Type: replace Abstract: Direct preference optimization (DPO) has emerged as a promising approach for aligning large language models (LLMs) with human preferences. However, the widespread reliance on the response-level Bradley-Terry (BT) model may limit its full potential, as the reference and learnable models are assumed to be autoregressive only after deriving the objective function. Motivated by this limitation, we revisit the theoretical foundations of DPO and propose a novel formulation that explicitly introduces the autoregressive assumption prior to applying the BT model. By reformulating and extending DPO, we derive a novel variant, termed Autoregressive DPO (ADPO), that explicitly integrates autoregressive modeling into the preference optimization framework. Without violating the theoretical foundations, the derived loss takes an elegant form: it shifts the summation operation in the DPO objective outside the log-sigmoid function. Furthermore, through theoretical analysis of ADPO, we show that there exist two length measures to be considered when designing DPO-based algorithms: the token length $\mu$ and the feedback length $\mu'$. To the best of our knowledge, we are the first to explicitly distinguish these two measures and analyze their implications for preference optimization in LLMs.

13.
arXiv (math.PR) 2026-06-12

Explosion and non-explosion in pure birth Crump–Mode–Jagers branching processes

arXiv:2601.06850v2 Announce Type: replace Abstract: In this short note, we provide an explicit sufficient condition for non-explosion of Crump–Mode–Jagers branching processes with pure birth reproduction. It shows that the standard sufficient condition for explosion, namely the convergence of the series of reciprocals of the birth rates, is – at least for rate sequences without excessive oscillations – remarkably close to being necessary. At the same time, it is not necessary in full generality: we construct a counterexample which also yields a general preferential attachment tree without fitness with an infinite path and no vertices of infinite degree, thereby answering an open question previously raised in the literature.

14.
arXiv (CS.AI) 2026-06-19

Improving Code-Switching ASR with Code-Mixing Guided Synthetic Speech

arXiv:2606.19381v1 Announce Type: cross Abstract: Code-switch (CS) Automatic Speech Recognition (ASR) remains challenging due to limited availability of high quality CS text-speech pairs for training. Although synthetic data augmentation via Text-to-speech (TTS) has been explored, existing CS TTS approaches primarily optimise reconstruction fidelity and do not explicitly enforce language-boundary consistency, thereby limiting their effectiveness for CS ASR augmentation. This paper proposes a code-mixing guided preference-learning framework that steers synthetic speech generation toward improved code-switching fidelity using the Code Mixing Index (CMI). Experiments on the SEAME Mandarin-English conversational corpus demonstrate that the proposed method enhances the utility of synthetic data for ASR fine-tuning. Specifically, when fine-tuning Whisper Large, the proposed approach reduces Mixed Error Rate (MER) from 12.1%/17.8% to 8.9%/14.2% on the DevMAN and DevSGE sets, respectively.

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

A Multi-Center Benchmark for Abdominal Disease Diagnosis and Report Generation from Non-Contrast CT

Multiphasic contrast-enhanced CT (CECT) is widely used for abdominal lesion characterization, yet it carries inherent risks of contrast-induced nephropathy, escalates acquisition burden, and heavily contributes to radiologist workload. To address these challenges, we introduce a novel multi-center benchmark for multi-organ abdominal disease diagnosis and automated radiology report generation, which learns to synthesize contrast-enhanced findings from single-phase non-contrast CT (NCCT). To support this, we curated a large-scale dataset of paired NCCT-CECT studies and their corresponding contrast-enhanced radiology reports from two centers, partitioned into internal sets and an external validation cohort. Under a unified evaluation protocol, we benchmarked five contemporary deep learning architectures encompassing chest-specific, abdomen-specific, and general-purpose multimodal domains. Extensive experiments demonstrate that NCCT retains diagnostic signals, achieving an average multi-organ AUC of 69.1% on the internal cohort and 63.1% on the external cohort, respectively. By releasing this dataset and standardized benchmark publicly, this study aims to catalyze future research into safer, resource-efficient, and globally accessible contrast-free abdominal imaging workflows. Code is available at: https://github.com/xmed-lab/TriALS-Report.

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

Instruct-Particulate: Scaling Feed-Forward 3D Object Articulation with Kinematic Control

Reconstructing articulated 3D objects is important for animation, gaming, and robotic simulations. Recent neural networks can estimate the articulated structure of 3D objects, but their generalization remains limited by the scarcity of annotated data for this task. To address this gap, we introduce Instruct-Particulate, a model that takes a 3D mesh together with a target kinematic specification, including part descriptions, connectivity, joint types, and optional point prompts, and predicts the corresponding kinematic part segmentation and joint motion parameters. The kinematic specification disambiguates the task and allows the model to target annotations of different granularity, thereby making it possible to use more abundant heterogeneous training data. At test time, the kinematic specification can be obtained automatically from large-scale vision-language models, so the model can be applied to any input mesh. To train our model at scale, we construct a heterogeneous dataset of more than 150,000 articulated 3D objects, extending existing publicly available collections with data obtained by partially labelling other 3D models (monolithic or already decomposed into parts) with kinematic labels by means of vision-language models. Experiments show that our model generalizes better across categories and to AI-generated meshes, enabling articulated asset reconstruction from real-world images via image-to-3D models.

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

Do We Really Need Diffusion? A Fast U-Net for Paired Medical Image Translation

Magnetic resonance imaging-signal fat fraction (MRI-SFF) quantifies tissue fat and serves as an established biomarker for metabolic and musculoskeletal disorders. The acquisition requires, however, specialized MRI sequences, which are not available routinely. We investigate whether SFF can be estimated from widely available T2-weighted (T2w) MRI via image-to-image translation (I2I). We further compare a lightweight 4-level U-Net to a state-of-the-art Denoising Diffusion Probabilistic Model (DDPM) using a dataset of 230 048 paired 2D images (183 517 train, 23 621 val, 22 910 test) from the German National Cohort (NAKO). Both models clearly outperform the identity baseline (Pearson correlation r = 0.769, mean absolute error MAE = 0.070 +/- 0.054), which confirms that the models learn a non-trivial cross-modal mapping. Interestingly, the lightweight U-Net outperforms the DDPM in both correlation (r = 0.975 vs. 0.962) and error (MAE = 0.014 +/- 0.015 vs. 0.019 +/- 0.019), while reducing inference time by a factor of 208 (25.2 ms vs. 5 227.2 ms per image using 50 Denoising Diffusion Implicit Model (DDIM) steps). The strong clinical performance at substantially reduced computational cost enables real-time clinical use.

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

Aligning Implied Statements for Implicit Hate Speech Generalizability with Context-Bounded Semi-hard Negative Mining

Classifying implicit hate speech remains a challenge, as intent is often masked through insinuation and context rather than explicit slurs. Prior supervised contrastive approaches improve in-domain detection but can overfit surface cues and struggle to transfer across datasets. We propose ImpSH, a triplet-based framework that aligns posts with implied statements when available and uses context-bounded semi-hard negatives to focus learning on near confusions. We also examine AugSH, which forms positives via data augmentation. In controlled evaluations on IHC, SBIC, and DynaHate with BERT and HateBERT, ImpSH is a viable alternative to standard supervised contrastive baselines and often improves cross-domain performance under matched preprocessing and tuning budgets. Representation analysis using alignment and uniformity indicates tighter positive pairs with balanced global spread, and qualitative nearest-neighbor case studies illustrate typical false negatives under domain shift. These results demonstrate that aligning posts with their implied statements via context-bounded mining provides a more stable, bijective-like mapping to related insinuations, overcoming the volatility inherent in traditional clustering-based representation learning.

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

Approximate Structured Diffusion for Sequence Labelling

Sequence labelling, a core task of Natural Language Processing (NLP), consists in assigning each token of an input sentence a label. From a Machine Learning point of view, sequence labelling is often cast as a Linear-Chain Conditional Random Field (CRF) parametrised by a neural network. While this approach gives good empirical results, CRFs assume a finite decision span (eg label bigrams) which can limit their expressivity and hurt performance when long-range dependencies are required. We show we can leverage diffusion to train a CRF conditioned on an entire label sequence, with the caveat that the condition is on a noisy version of labels. We show experimentally that this method, in conjunction with approximate CRF inference, improves label accuracy with a 16.5% error reduction for POS-tagging.

20.
arXiv (CS.CV) 2026-06-11

Real-Time Neural Hair Denoising

We propose a lightweight real-time method for reconstructing strand-based hair G-Buffers from severely undersampled rasterized inputs. Our pipeline first applies neural spatial reconstruction and temporal accumulation to recover hair coverage, i.e., fractional hair visibility within a pixel, and tangent. It then uses a tangent-guided reconstruction step to complete the position, which is subsequently used for physically based deferred hair shading. We evaluate our method across a diverse set of hairstyles, including straight, wavy, afro, and ponytail styles, under both static and dynamic scenarios. Our method achieves higher hair reconstruction quality than existing hair-specific denoising techniques and general industrial neural reconstruction solutions such as DLSS and FSR.

21.
arXiv (quant-ph) 2026-06-19

Electrical Noise Produced by Micron-Sized Particles above a Surface Paul Trap

arXiv:2606.19585v1 Announce Type: new Abstract: Electric field noise produced by the surface of ion trap electrodes reduces the fidelity of quantum computing operations. Despite decades of investigation its microscopic origins remain unclear. Here, we measure electric field noise at trapping locations along the symmetry axis of a linear surface Paul trap. We find that noise levels vary by three orders-of-magnitude in one 600$\,\mu$m section of the trap. Optical and scanning electron microscope images show micron-sized particles close to the trapping locations with the highest noise levels. We find that modeling the particles as a lossy dielectric with a effective loss tangent $\tan\theta=0.33(0.06)$ describes the magnitude of the noise, as well as its spatial and frequency dependence. Our observations may explain the large variation of reported noise levels in literature.

22.
medRxiv (Medicine) 2026-06-22

Repeat expansions in Parkinson's disease and parkinsonism across ancestries: insights from a global genetic cohort

Expanded short tandem repeats contribute to a broad spectrum of neurodegenerative diseases, yet their roles in Parkinson's disease (PD) and parkinsonism remain incompletely characterized, especially across diverse ancestries. We analyzed short-read whole-genome (WGS) and clinical exome sequencing (CES) data from 38,365 individuals (28,861 WGS; 9,504 CES), encompassing 23,242 patients with PD, 4,729 patients with atypical parkinsonism and 10,394 healthy controls from 11 genetic ancestries. To determine carrier frequencies and characterize repeat structures across diverse ancestries, we genotyped 12 established pathogenic loci where normal, intermediate, and pathogenic alleles can be reliably differentiated using short-read sequencing data. Additionally, we conducted threshold-based associations to determine the minimum threshold associated with increased PD risk in 15,995 individuals (8,591 PD, 7,404 controls) of European ancestry. Pathogenic repeat expansions were detected in 62 patients (56 PD and 6 atypical parkinsonism) and 5 controls across seven loci (AR, ATXN1, ATXN2, ATXN3, CACNA1A, HTT and THAP11), spanning seven ancestries. Among these, ATXN2 expansions were the most frequently observed in PD and were present in African, East Asian, European and Middle Eastern ancestries. Additionally, intermediate ATXN2 repeat expansions exhibited a strong, length-dependent association with PD risk in the European population, with individuals with [≥]32 repeats having a more than four-fold increased risk (odds ratio 4.25, 95% confidence interval 1.80-12.05). Overall, >92% of expanded alleles harbor CAA interruptions within the CAG tract. Pathogenic expansions at other loci, such as ATXN3 and THAP11, showed more ancestry-specific distributions. Clinically, individuals with pathogenic ATXN2 and ATXN3 expansions most often presented with typical PD features but frequently showed earlier disease onset and a strong family history of PD. This large-scale, multi-ancestry study comprehensively maps the genetic landscape of pathogenic and intermediate repeat expansions in PD. Our findings confirm a length- and structure-dependent risk association for ATXN2 with PD in the European population, and highlight the pleiotropic effects of repeat expansions across the parkinsonian spectrum.

23.
arXiv (CS.CV) 2026-06-16

Akasha 2: Hamiltonian State Space Duality and Visual-Language Joint Embedding Predictive Architectur

Authors:

We present Akasha 2, a state-of-the-art multimodal architecture that integrates Hamiltonian State Space Duality (H-SSD) with Visual-Language Joint Embedding Predictive Architecture (VL-JEPA). The system leverages the Mamba-3 Selective State Space Model (SSM) augmented by a Sparse Mixture of Hamiltonian Experts (SMoE-HE) that enforces latent physical conservation laws through symplectic integration. For visual synthesis, we introduce Hamiltonian Flow Matching (HFM) and persistent 3D Gaussian Splatting (3DGS), enabling ultra-low latency (

24.
bioRxiv (Bioinfo) 2026-06-10

GEOAgent: An AI-driven Autonomous Framework for Intelligent GEO Data Retrieval and Standardized Preprocessing

Datasets in the Gene Expression Omnibus (GEO) remain difficult to reuse at scale because sample annotations are heterogeneous and raw sequencing data require assay-specific preprocessing. We present GEOAgent, an AI-driven autonomous framework designed for intelligent dataset retrieval and standardized preprocessing by coupling autonomous semantic governance with an automated Nextflow pipeline named bioStream. Metadata from 181,760 sequencing series and 84,756 associated PubMed records were organized in a relational database and semantic index to support natural-language dataset retrieval. The framework automatically determines assay modalities, resolves experimental design pairings, and standardizes sample naming to minimize manual curation overhead. Based on these parsed attributes, the framework generates deployment-ready manifests to automatically execute containerized workflows across bulk and single-cell omics modalities. In expert-curated benchmarks, the workflow achieved 96% retrieval precision alongside 100% accuracy in assay classification and sample relationship resolution. The web platform is publicly accessible, while the source code and associated databases are openly available via GitHub and Zenodo.

25.
arXiv (CS.CL) 2026-06-11

Can AI Reason Like an Urban Planner? Benchmarking Large Language Models Against Professional Judgment

Problem, Research Strategy, and Findings: The rise of large language models (LLMs) raises a key question for urban planning: which forms of professional planning knowledge can AI replicate, and which still require human judgment? Although AI tools are increasingly used in planning practice, there is still no systematic framework for testing whether they can reason with the contextual sensitivity, value awareness, and institutional literacy central to planning expertise. This paper introduces Urban Planning Bench (UPBench), a domain-specific evaluation framework that assesses LLM reasoning through a 4x5 matrix of four knowledge pillars and five cognitive levels adapted from Bloom's revised taxonomy. Evaluating 25 LLMs with automated scoring and expert review, we find a non-monotonic cognitive curve: models perform better on higher-order analytical tasks than on factual recall and integrative judgment. This suggests that planning knowledge often treated as lower-order is deeply shaped by institutional, jurisdictional, and temporal context, making it hard for LLMs to generalize. We summarize these limits as four epistemic diagnostics: regulatory hallucination, conceptual conflation, wickedness paralysis, and phronetic deficit. Takeaway for Practice: The findings support differential delegation in planning. LLMs can assist with cross-disciplinary synthesis, literature review, scenario generation, and preliminary policy analysis. However, they remain unreliable for jurisdiction-specific regulation, normative conflict resolution, and context-sensitive procedure. Agencies should require verification for AI-assisted regulatory analysis, while planning education should emphasize institutional literacy, normative judgment, and contextual sensitivity.