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01.
arXiv (CS.CV) 2026-06-17

Test-Time Training for Robust Text-Guided Open-Vocabulary Object Counting

Text-guided Open-vocabulary Object Counting (TOOC) enables counting arbitrary object categories specified by text prompts, offering substantially greater flexibility than conventional closed-set counting. However, existing TOOC methods are developed and evaluated primarily on ideal images, while real-world scenes often suffer from adverse conditions such as rain, fog, darkness, and sensor noise, which severely degrade visual quality and impair vision-language alignment. To bridge this gap, we introduce Robust-TOOC, the first benchmark for evaluating TOOC under diverse corruption conditions, which covers six representative degradation types: rain, fog, darkness, Gaussian noise, salt-and-pepper noise, and mixed corruption. To improve robustness while preserving the original counting architecture, we propose Dual-TTT, a dual-architecture test-time training framework for TOOC. Specifically, during test-time training, Dual-TTT updates only the Text-guided Lightweight Denoising module (TL-Denoiser), while keeping the original counting network frozen. Inspired by diffusion models, the TL-Denoiser is optimized to remove corruption-aware noise from image representations under degraded conditions. Since only the TL-Denoiser is trained at test time, Dual-TTT is annotation-free and can be seamlessly integrated into existing TOOC models without modifying their original architecture. Extensive experiments on multiple recent TOOC baselines demonstrate the effectiveness of our method.

02.
arXiv (CS.LG) 2026-06-25

From Uncertain to Safe: Conformal Adaptation of Diffusion Models for Safe PDE Control

arXiv:2502.02205v4 Announce Type: replace Abstract: The application of deep learning for partial differential equation (PDE)-constrained control is gaining increasing attention. However, existing methods rarely consider safety requirements crucial in real-world applications. To address this limitation, we propose Safe Diffusion Models for PDE Control (SafeDiffCon), which introduce the uncertainty quantile as model uncertainty quantification to achieve optimal control under safety constraints through both post-training and inference phases. Firstly, our approach post-trains a pre-trained diffusion model to generate control sequences that better satisfy safety constraints while achieving improved control objectives via a reweighted diffusion loss, which incorporates the uncertainty quantile estimated using conformal prediction. Secondly, during inference, the diffusion model dynamically adjusts both its generation process and parameters through iterative guidance and fine-tuning, conditioned on control targets while simultaneously integrating the estimated uncertainty quantile. We evaluate SafeDiffCon on three control tasks: 1D Burgers' equation, 2D incompressible fluid, and controlled nuclear fusion problem. Results demonstrate that SafeDiffCon is the only method that satisfies all safety constraints, whereas other classical and deep learning baselines fail. Furthermore, while adhering to safety constraints, SafeDiffCon achieves the best control performance. The code can be found at https://github.com/AI4Science-WestlakeU/safediffcon.

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

TUNI: Unifying Pre-training and Fine-tuning with Modality-Aware Mutual Learning and Rectification for RGB-T Semantic Segmentation

RGB-thermal (RGB-T) semantic segmentation improves the environmental perception of autonomous platforms in challenging conditions. Prevailing RGB-T segmentation frameworks suffer from suboptimal multi-modal feature extraction and fusion, unbalanced modality dependency, and inadequate utilization of thermal information. To address these challenges, we propose TUNI, a unified pre-training and fine-tuning framework for efficient and real-time RGB-T semantic segmentation. It pre-trains an RGB-T encoder that incorporates an RGB-T local module that selectively emphasizes salient consistent and distinct local features across modalities, thereby integrating cross-modal feature extraction and fusion in a unified manner. To alleviate the modality bias issue during RGB-T pre-training, modality-inverted contrastive mutual learning is introduced to enable knowledge exchange between two RGB-dominated and thermal-dominated encoders. In the fine-tuning phase, modality rectification learning fully exploits residual thermal information by focusing on correct yet divergent prediction regions between two modality-specific decoders. We further develop three TUNI variants, covering lightweight, balanced, and high-performance requirements. Extensive experiments on five RGB-T semantic segmentation datasets demonstrate that TUNI achieves superior accuracy, generalization, and compactness compared with 15 state-of-the-art models. The code is available at https://github.com/xiaodonguo/TUNI-v2.

04.
arXiv (CS.AI) 2026-06-11

Search Discipline for Long-Horizon Research Agents

arXiv:2606.11522v1 Announce Type: new Abstract: Autoresearch agents now propose, evaluate, and select scientific candidates against a metric, and that metric is usually an aggregate reduced over a heterogeneous space of regions, slices, or cohorts. We show that when scientific validity lives in that disaggregated structure, the aggregate can rank the wrong candidate first. The headline number improves while the structure underneath inverts, so a decision made on the number accepts a candidate that quietly breaks the model. The failure is not domain-specific. It appears wherever a candidate's validity is multi-dimensional but its verifier is a single reduction. We demonstrate the inversion on a fire-model task in the Ecosystem Demography model. The highest-scoring candidate and a slightly lower one are within noise of each other on global score, yet the top-scoring one collapses the protected boreal regions while the other preserves them. What separates them is the per-region behavior, not the headline number. This decision should not be left to the agent that produced the candidates. The agent optimizing the score is the last party likely to catch the score being wrong, and a prompt has no remaining turn once the agent has stopped. We move the decision to an external control loop that audits each candidate on its disaggregated behavior and acts after the agent has decided. It can demote a candidate the agent would have accepted, and it can reopen a run the agent had declared finished. Our contribution is the inversion finding itself, and a search-discipline protocol that decides on reviewable candidate-effect evidence instead of the score.

05.
arXiv (CS.CL) 2026-06-16

Depth-Attention: Cross-Layer Value Mixing for Language Models

Self-attention selects information freely across the sequence, but across depth, Transformers merely add each layer's output to the residual stream, so later layers cannot selectively reuse earlier-layer representations. Recent cross-layer methods improve this flow but operate on hidden states outside attention, adding state beyond the key-value cache at inference–a cost that becomes increasingly salient as modern LLMs compress the cache with grouped-query and multi-head latent attention. We introduce Depth-Attention, which performs this selection inside the attention module itself: before a layer attends over the sequence, its query attends over the keys of earlier layers at the same token position and mixes their values into the value that self-attention then reads. Because Depth-Attention reuses the standard attention queries, keys, and value-cache slots, storing depth-mixed values in place of the original values, it adds no parameters and introduces no persistent inference state beyond the standard key-value cache–the same cache size as a vanilla decoder and less than hidden-state-based cross-layer methods. On Qwen3-style decoders at 1.5B and 3B parameters, Depth-Attention attains the lowest perplexity and the highest average downstream accuracy, improving over the vanilla Transformer by up to 2.3 accuracy points and surpassing strong cross-layer baselines in perplexity and average accuracy, while adding under 0.01% extra arithmetic FLOPs and no additional persistent inference state. The gains hold from 360M to 3B parameters and extend to looped Transformers.

06.
Science (Express) 2026-04-16

Protein-templated synthesis of dinucleotide repeat DNA by an antiphage reverse transcriptase | Science

Authors: Unknown Author

Defense-associated reverse transcriptases (DRTs) are widespread bacterial anti-phage systems that use unconventional mechanisms of polynucleotide synthesis. We show that DRT3, which comprises two distinct RTs (Drt3a and Drt3b) and a noncoding RNA (ncRNA), synthesizes alternating poly(GT/AC) double-stranded DNA. Cryo–electron microscopy structures at 2.6 Å resolution reveal a D3-symmetric 6:6:6 complex of Drt3a, Drt3b, and ncRNA. Drt3a produces the poly(GT) strand using a conserved ACACAC template within the ncRNA. Notably, Drt3b synthesizes a complementary, protein-primed poly(AC) strand in the complete absence of a nucleic acid template, using conserved active site residues specific to Drt3b to enforce precise base alternation. These findings expand the functional landscape of nucleic acid polymerases, revealing a protein-templated mechanism for sequence-specific DNA synthesis.

07.
arXiv (math.PR) 2026-06-17

A note on the $\mathcal{W}_2$-convergence rate of the empirical measure of an ergodic $\mathbb{R}^d$-valued diffusion

arXiv:2502.07704v2 Announce Type: replace Abstract: In this note, we consider a Stochastic Differential Equation under a strong confluence and Lipschitz continuity assumption of the coefficients. For the unique stationary solution, we study the rate of convergence of its empirical measure toward the invariant probability measure. We provide rate for the Wasserstein distance in the mean quadratic and almost sure sense.

08.
arXiv (CS.LG) 2026-06-12

A Stationary (and Therefore Compatible) Representation is All You Need

arXiv:2606.12488v1 Announce Type: new Abstract: Learning compatible representations aims to learn feature representations that can be used interchangeably over time whenever a model undergoes updates. In this paper, we demonstrate that stationary representations learned by d-Simplex fixed classifiers imply compatibility as in its formal definition. This result establishes a foundation for future works and can be directly exploited in practical learning scenarios. We address the challenge of learning compatibility using $d$-Simplex fixed classifiers when the model is sequentially fine-tuned. Learning according to a d-Simplex fixed classifier with the cross-entropy loss aligns feature distributions at the first-order statistics. Consequently, it may not fully capture higher-order dependencies in the representation between model updates. To address this issue, we demonstrate that training the model using a $d$-Simplex fixed classifier through a convex combination of the cross-entropy loss and a contrastive loss not only captures higher-order dependencies, but is also equivalent to learning with the cross-entropy under the compatibility constraints. We confirm our findings with extensive experiments also considering a new scenario where a pre-trained model is sequentially fine-tuned and occasionally replaced with an improved model. We show that stationary representations enable uninterrupted retrieval services (without reprocessing gallery images) while improving performance during model updates and replacements, achieving state-of-the-art. Code at https://github.com/miccunifi/iamcl2r.

09.
arXiv (quant-ph) 2026-06-12

Invariant Measures and Weak-Magic-Injection Asymptotics in Random Monitored Quantum Circuits

arXiv:2606.13470v1 Announce Type: new Abstract: Monitored quantum circuits provide a natural setting in which scrambling, measurements, and measurement-conditioned updates compete within a stochastic many-body dynamics. From the viewpoint of nonstabilizer resource theory, this competition is especially relevant because Clifford-compatible operations preserve the stabilizer structure, while weak non-Clifford perturbations inject magic resource. Most of the existing understanding of monitored quantum circuits has been shaped by numerical simulations and phenomenological descriptions, while a rigorous dynamics theory remains less developed. In this paper, we address this gap by developing an analytical framework which lays a rigorous mathematical foundation for the study of random monitored quantum dynamics. Specifically, we study a class of monitored quantum circuits driven by random Clifford. We prove the existence and uniqueness of the stationary law, which gives an ergodic description of the long-time dynamics. We then resolve the leading asymptotics of steady magic in the weak-magic-injection limit. This tangent description makes the contrast between resource measures transparent: in odd-prime local dimension, the steady Gross–Wigner mana has a linear leading asymptotic, whereas in qubit systems the steady 2-stabilizer Rényi entropy has a quadratic leading asymptotic. These different powers reflect the distinct local geometries of the two resource measures near the stabilizer layer. In this way, this work develops an analytical framework that first establishes the stationary ergodic dynamics of random monitored quantum circuits.

10.
arXiv (quant-ph) 2026-06-16

Accelerating physics-informed neural networks for full waveform inversion using a hybrid quantum-classical finite-basis architecture

arXiv:2606.01110v2 Announce Type: replace-cross Abstract: Full waveform inversion (FWI) reconstructs heterogeneous material properties from receiver data but remains computationally demanding. Physics-informed neural networks (PINNs) and their domain-decomposed variants (FBPINNs) offer a mesh-free alternative but face convergence challenges when representing complex velocity fields. We present a hybrid quantum-classical FBPINN for acoustic FWI, bringing together quantum computing and classical machine learning, in which the decomposed wavefield network and the global velocity network are implemented as classical-to-quantum pipelines terminating in parameterized quantum circuits (PQCs). The PQCs are realized as differentiable JAX statevector simulators, enabling end-to-end automatic differentiation through the classical PINN, the quantum circuit, and the physics-informed loss. On a geophysical anomaly benchmark, the quantum hybrid reaches a lower L1 velocity error than the primary classical FBPINN baseline in approximately 8x fewer training iterations, despite using approximately 33% fewer trainable parameters, and it outperforms all 15 classical hyperparameter variants tested. A second benchmark (checkerboard) demonstrates the generality of the inversion pipeline, confirming that the quantum hybrid architecture can recover structured spatial variations beyond the localized anomaly benchmark. Our framework is broadly applicable to wave-based inverse problems beyond geophysics, including medical ultrasound tomography and non-destructive evaluation.

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

Intelligent Automation for Embodied Benchmark Construction: Pipelines, Embodiments, Simulators, and Trends

arXiv:2606.12207v1 Announce Type: cross Abstract: Embodied intelligence now spans navigation, household assistance, manipulation, autonomous driving, aerial agents, and multimodal large-model control. This expansion has made benchmark construction a central bottleneck for reliable evaluation. Unlike static datasets, embodied benchmarks combine task specifications, environments, robot data, demonstrations, annotations, metrics, evaluation scripts, and release policies into a single evaluation system. This survey reviews the literature through a five-stage construction pipeline: requirement and task construction, data acquisition, data cleaning and annotation, benchmark suite generation and metric definition, and evaluation execution with diagnostic feedback. For each stage, the survey analyzes the transition from manual curation to traditional automation, foundation-model assistance, and agentic closed-loop workflows. It also compares qualitative construction costs across human labor, data and asset acquisition, compute and simulation, validation and debugging, governance and maintenance, and rework risk. The main conclusion is that automation does not simply reduce benchmark cost. Instead, it often shifts cost toward validation, auditability, version control, and long-term governance. Progress in embodied evaluation will therefore depend not only on larger benchmark suites, but also on construction pipelines that are diagnosable, auditable, and responsibly refreshable.

12.
Nature Medicine 2026-06-10

Brain Health for Economic Resilience: a data-driven framework for the brain-positive economic transition

Announced in this Comment and in collaboration with Nature Medicine is the convening of the Brain Health for Economic Resilience Commission, a global, transdisciplinary effort to define, measure and operationalize brain health and cognitive capacity as foundational drivers of economic resilience.

13.
arXiv (CS.CV) 2026-06-12

Radar-Guided Polynomial Fitting for Metric Depth Estimation

We propose POLAR, a novel radar-guided depth estimation method that introduces polynomial fitting to efficiently transform scaleless depth predictions from pretrained monocular depth estimation (MDE) models into metric depth maps. Unlike existing approaches that rely on complex architectures or expensive sensors, our method is grounded in a fundamental insight: although MDE models often infer reasonable local depth structure within each object or local region, they may misalign these regions relative to one another, making a linear scale and shift (affine) transformation insufficient given three or more of these regions. To address this limitation, we use polynomial coefficients predicted from cheap, ubiquitous radar data to adaptively adjust predictions non-uniformly across depth ranges. In this way, POLAR generalizes beyond affine transformations and is able to correct such misalignments by introducing inflection points. Importantly, our polynomial fitting framework preserves structural consistency through a novel training objective that enforces local monotonicity via first-derivative regularization. POLAR achieves state-of-the-art performance across three datasets, outperforming existing methods by an average of 24.9% in MAE and 33.2% in RMSE, while also achieving state-of-the-art efficiency in terms of latency and computational cost.

14.
arXiv (CS.LG) 2026-06-15

A Low-Rank Subspace Analysis of LLM Interventions

arXiv:2606.14388v1 Announce Type: new Abstract: Interventions designed to modify a particular behavior in LLMs, such as refusal or sycophancy, often produce unintended changes in other behaviors. This lack of targeted control makes it difficult to design and implement reliable safety controls. To understand these side-effects, we introduce a diagnostic framework for analyzing interacting behaviors in LLMs. We model behaviors as low-rank subspaces in activation space, and study how interventions influence across behaviors. Across multiple instruction-tuned models (7B-70B) and across refusal, jailbreak, and sycophancy settings, we find that different behaviors share internal representations, and intervening on one behavior alters others in asymmetric ways. Some behaviors act as upstream control points whose interventions propagate broadly across other behaviors, while others remain more isolated. We relate these effects to two geometric quantities: (i) the overlap between behavior subspaces, measured as the average squared cosine of principal angles, and (ii) the angle between each behavior subspace and the decision subspace (capturing the model's final decision e.g., refuse vs. comply). Empirically, intervention effects on other behaviors tend to be larger for behavior pairs with higher subspace overlap, and for source behaviors whose subspaces lie closer (smaller angle) to the decision subspace. These findings highlight a challenge for targeted behavior control: behaviors are difficult to modify independently, as interventions can propagate through shared representations and asymmetric interactions.

15.
arXiv (CS.LG) 2026-06-11

A theory of learning data statistics in diffusion models, from easy to hard

arXiv:2603.12901v2 Announce Type: replace-cross Abstract: While diffusion models have emerged as a powerful class of generative models, their learning dynamics remain poorly understood. We address this issue first by empirically showing that standard diffusion models trained on natural images exhibit a distributional simplicity bias, learning simple, pair-wise input statistics before specializing to higher-order correlations. We reproduce this behaviour in simple denoisers trained on a minimal data model, the mixed cumulant model, where we precisely control both pair-wise and higher-order correlations of the inputs. We identify a scalar invariant of the model that governs the sample complexity of learning pair-wise and higher-order correlations that we call the diffusion information exponent, in analogy to related invariants in different learning paradigms. Using this invariant, we prove that the denoiser learns simple, pair-wise statistics of the inputs at linear sample complexity, while more complex higher-order statistics, such as the fourth cumulant, require at least cubic sample complexity. We also prove that the sample complexity of learning the fourth cumulant is linear if pair-wise and higher-order statistics share a correlated latent structure. Our work describes a key mechanism for how diffusion models can learn distributions of increasing complexity.

16.
arXiv (quant-ph) 2026-06-17

Coupled-Mode Equations with Arbitrary Mode Combinations for Kinetic-Inductance Superconducting Traveling-Wave Parametric Devices: Theory and Experimental Validation

arXiv:2606.17264v1 Announce Type: cross Abstract: The coupled-mode equations (CMEs) have proven very successful in describing parametric processes in nonlinear optics. More recently, the same formulation has been used to model microwave superconducting parametric amplifiers and frequency multipliers. However, when applied to the microwave regime, not all assumptions remain valid and losses play a more dramatic role. Here, we revisit the CMEs applied to traveling-wave superconducting amplifiers to include losses and provide a formulation that enables their systematic derivation for any combination of traveling waves. As examples, we discuss the impact of unwanted harmonics and intermodulation products on parametric amplification, as well as harmonic generation. We verify that, if not properly accounted for, device performance can deviate considerably from the ideal case. Furthermore, using a superconducting CPW-based artificial transmission line and combining an independent experimental determination of its nonlinear parameter $I'_*$ with simulations of its linear properties, we obtain a parameter-free validation of this formulation. The nonlinear parameter was determined to be $I'_* \approx 27$ mA which, surprisingly, scales with the theoretical depairing current and not with the much smaller critical current of the device. For the validation, we measured multiple-harmonic generation and found excellent agreement between theory and experiment. The fact that $I'_* \gg I_C$ has direct implications for device design.

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

DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

arXiv:2606.15931v1 Announce Type: cross Abstract: Historical medical archives and traditional medicines hold immense potential for drug discovery and remain a primary source for current drug development. However, pre-ontological prose and idiosyncratic taxonomies prevent the standardization and medical modernization of the data for use in current biomedical pipelines. Furthermore, no existing LLM agent system, whether tool-calling, retrieval-augmented, or agentic deep-research, can convert such text into verifiable drug-discovery leads at scale. We close this gap with DeepRoot, a multi-agent LLM system that jointly builds and utilizes a verified knowledge graph, showing that grounding and reasoning – often conflated – are separable axes the system can compose for therapeutic reasoning. Applied to the Shen Nong Ben Cao Jing, DeepRoot recovers $10$ of $21$ held-out compound-disease treatment pairs at R@$20$ ($47.6\%$ vs $4.8\%$ for a raw corpus LLM and $\sim\!2.4\%$ random) and dominates an LLM-as-judge audit for reasoning quality over baseline LLMs and LLMs with direct tool-call access to the same APIs DeepRoot itself queries. Tool-using LLMs hallucinate evidence on $87\%$ of claims, versus 7-10% for DeepRoot. Graph-only inference hallucinates $0\%$ but ranks lowest on reasoning coherence; DeepRoot KG+LLM is the only condition to win on both axes, pointing toward a route for systematic mining and repurposing of historical medical knowledge.

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

Rethinking the Pointer Loss in Table Structure Recognition: Geometry-Aware Pointer Loss for Spatial Locality

Table Structure Recognition (TSR) using a pointer network achieves impressive results by predicting HTML sequences while aligning tags to detected text (or cell) regions. However, our analysis reveals that when pointer networks fail, 79.6% of errors occur between spatially adjacent cells (Manhattan distance

19.
medRxiv (Medicine) 2026-06-16

Exercise Training Improves Skeletal Muscle Insulin Sensitivity and Reprograms the Adipose Transcriptome in Heavier Monozygotic Twins

Exercise training improves skeletal muscle insulin sensitivity, yet its effects on white adipose tissue remain incompletely understood. We investigated how adiposity and exercise training influence insulin-stimulated glucose uptake in skeletal muscle and abdominal subcutaneous adipose tissue (ASAT), alongside adaptations in gene expression and DNA-methylation. Ten monozygotic twin pairs discordant for BMI underwent [18F]FDG-PET/CT imaging of skeletal muscle (vastus lateralis, VL) and ASAT during a euglycemic-hyperinsulinaemic clamp before and after six months of exercise training. VL and ASAT biopsies were analyzed using mRNA-sequencing and reduced representation bisulfite sequencing. Exercise training improved whole-body and VL insulin sensitivity in leaner and heavier co-twins (p

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

FLAT: Feedforward Latent Triangle Splatting for Geometrically Accurate Scene Generation

Generating explorable 3D scenes from a single image requires strong generative priors and accurate geometric representations suitable for downstream use. Current video diffusion models offer high-quality generation and implicitly encode multi-view geometric structure in latent space. However, existing feedforward latent scene decoders typically output volumetric 3D Gaussians that lack a well-defined surface, limiting their use in simulation or standard graphics pipelines. This motivates decoding surface-aligned primitives that are not only renderable but also closer to explicit geometric assets. We ask whether compressed video diffusion latents can be mapped directly to explicit surface primitives in a single pass. To this end, we introduce FLAT and, for the first time, show that triangle splats can be decoded directly from video diffusion latents. Compared with decoding 3D Gaussians, predicting flat primitives is notoriously more challenging due to high sensitivity to primitive orientations, oftentimes leading to poor gradient flow. FLAT solves with two key ingredients: a ray-centered rotation parameterization for triangle regression and a novel product window function that improves gradient flow during differentiable triangle rendering. On standard benchmarks, FLAT achieves significantly better geometric accuracy while maintaining competitive visual quality compared to state-of-the-art feedforward baselines. We further show that a lightweight test-time refinement step converts the predicted triangle soup into a fully opaque, game-engine-ready representation that supports real-time rendering. By evaluating 3DGS, 2DGS, and triangle splatting variants under an identical training setup, we provide the first systematic analysis of representation tradeoffs in feedforward scene generation. The project page is available at https://flat-splat.github.io

21.
medRxiv (Medicine) 2026-06-24

A Custom Global Screening Array for Integrated Familial Hypercholesterolemia Detection and Polygenic Risk Assessment in a Multi-Ethnic New Zealand Population

Background: Cardiovascular disease (CVD) is the leading cause of mortality in New Zealand, with significant inequities affecting M[a]ori and Pacific peoples. Familial hypercholesterolaemia (FH) affects approximately 1 in 313 individuals globally, yet over 90% remain undiagnosed. Standard polygenic risk scores (PRS) derived from European cohorts may not be portable to diverse ancestries. We developed the HoloQ Omniscan Waka Te Ira, a custom Illumina Global Screening Array (GSA) v3 enriched with FH mutations, coronary artery disease (CAD) PRS markers, and network medicine-derived content. Methods: We customised the GSA v3 by adding 43,437 single nucleotide polymorphisms (SNPs) targeting FH and CAD. Content included 6,717 unique variants in primary FH genes; 14,005 pathogenic or likely pathogenic cardiovascular and pharmacogene variants; and 5,845 copy number variant probes. We further incorporated 5,232 network medicine derived CAD SNPs, 14,806 rare variants for a multiancestry PRS, and 407 globally diverse and population-specific variants. The final design comprised 47,027 target SNPs. Validation utilised large-scale genotype and whole-genome sequencing (WGS) datasets with PRS benchmarking. Results: In a large European-ancestry dataset, we observed high recovery for common PRS loci but low recovery for population-specific founder variants. The array captured 938 (84%) of all pathogenic or likely pathogenic FH variants catalogued in ClinVar, representing a 26.4% expansion beyond the standard backbone array. WGS validation identified additional carriers of rare high impact variants present only in the custom content. The selected CAD PRS model achieved an adjusted area under the receiver operating characteristic curve of 0.786. Conclusion: The HoloQ Omniscan Waka Te Ira enhances detection of clinically relevant FH variants and provides robust PRS coverage. The low recovery of population-specific alleles underscores the necessity of this custom array for equitable genomic medicine in New Zealand's multi-ethnic population.

22.
arXiv (CS.CV) 2026-06-12

LaME: Learning to Think in Latent Space for Multimodal Embedding via Information Bottleneck

Reasoning-driven universal multimodal embedding has advanced rapidly by introducing Chain-of-Thought (CoT) reasoning into the embedding pipeline. Despite the strong performance across both general and complex tasks, this paradigm suffers from two core limitations: (i) autoregressive CoT reasoning incurs high computational cost, making it impractical for low-latency retrieval; and (ii) embedding performance is heavily coupled with CoT annotation quality, making large-scale training unreliable. These raise fundamental questions: Is textual CoT the optimal form of reasoning for embedding, and can effective embedding reasoning be accomplished in latent space? To this end, we propose LaME (Latent Reasoning Multimodal Embedding), which formulates embedding-oriented latent reasoning as a weakly supervised information bottleneck. LaME employs K learnable reason tokens as a fixed-capacity bottleneck, completing all reasoning within a single forward pass. The two weak supervision signals structurally decouple contrastive from autoregressive objectives and eliminate dependence on CoT annotations, while a two-stage training pipeline ensures stable convergence. Experiments on MMEB-v2 and MRMR show that LaME achieves competitive performance, surpassing some explicit CoT-based models, while delivering 60x faster inference than explicit CoT methods and 2x faster than latent baselines with throughput comparable to discriminative embedding models. Code will be released.

23.
arXiv (CS.AI) 2026-06-11

Mind the Perspective: Let's Reason Recursively for Theory of Mind

arXiv:2606.11724v1 Announce Type: new Abstract: Theory of Mind (ToM) reasoning requires inferring agents' beliefs from partial and asymmetric observations, which remains an open challenge for LLMs. Existing prompting-based approaches improve ToM reasoning through observable-event filtering or temporal belief chains, without explicitly modeling nested beliefs. We introduce RecToM, an inference-time framework for ToM reasoning that models nested beliefs via recursive perspective construction. RecToM constructs each character perspective from the preceding character perspective along the character chain specified by the question, reducing higher-order belief questions to actual-world questions within the final constructed perspective. We further provide a KD45 analysis showing that RecToM's perspective construction induces a well-formed belief modality beyond simple event filtering. Experiments on ToM benchmarks, including Hi-ToM, Big-ToM, and FanToM, across multiple LLM backbones show that RecToM consistently outperforms recent advanced approaches, achieving state-of-the-art performance. Notably, RecToM reaches 100\% accuracy on Hi-ToM with GPT-5.4 and Qwen3.5, a benchmark requiring higher-order ToM reasoning.

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

A Training-Free Mixture-of-Agents Framework for Multi-Document Summarization using LLMs and Knowledge Graphs

Multi-Document Summarization (MDS) plays a critical role in distilling essential information from collections of textual data. Existing approaches often struggle to capture complex inter-document relationships, rely heavily on large amounts of labeled data for supervised training, or exhibit limited generalization across domains and languages. To address these limitations, we present a training-free mixture-of-agents framework for MDS that leverages the complementary strengths of large language models (LLMs) and knowledge graphs. Our approach decomposes summarization into specialized agent tasks: extractive selection, knowledge-aware abstraction, and iterative refinement, each operating without task-specific fine-tuning. We unify their outputs using a multi-perspective consistency mechanism guided by LLMs. Experiments across four datasets in English and Vietnamese demonstrate state-of-the-art or competitive performance, validating the effectiveness and adaptability of our modular design.

25.
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.