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01.
medRxiv (Medicine) 2026-06-17

Characterisation of disease progression in hantavirus haemorrhagic fever with renal syndrome

Hantaviruses can cause haemorrhagic fever with renal syndrome (HFRS). This is a clinically variable disease in which severe outcomes are hypothesized to arise from dysregulated host responses. To characterise this, longitudinal, label-free plasma proteomics was used to compare disease progression in a unique well-defined cohort of patients infected with either Dobrava virus (DOBV) or Puumala virus (PUUV) hantaviruses. Patients were stratified by clinical severity. The average viral load in the first available sample from hospitalized patients was higher in those who went on to have severe infection, and higher in patients infected with DOBV. There was marked separation of infected patients from controls across early, mid and late disease, including after viral RNA clearance, suggesting a sustained systemic host-response signature. Proteomic signatures were consistent with a strong acute-phase response in both mild and severe disease. There was evidence of activation of the adaptive humoral response at later stages. Hierarchical clustering identified severity-associated pathways linked to endothelial dysfunction, thrombocytopenia, vascular leakage and renal injury. These findings define a durable plasma proteomic signature of hantavirus disease and support a model in which severe HFRS is driven by persistent inflammatory, complement and platelet/coagulation pathway activation rather than viral burden alone.

02.
arXiv (CS.LG) 2026-06-12

Deep Learning-based Algebraic Reynolds Stress Closures for RANS Simulations of Turbulent Flows

arXiv:2605.26358v2 Announce Type: replace-cross Abstract: Turbulence is ubiquitous in engineering and science, yet direct simulation is prohibitively expensive. The Reynolds-averaged Navier-Stokes (RANS) equations provide savings exceeding ten orders of magnitude but introduce unclosed terms (the closure problem). Offline-trained machine-learning (ML) closures suffer distribution shift in predictive simulations, while ML methods that bypass the governing equations struggle to generalise from scarce high-fidelity data. We develop a physics-derived deep learning closure model for RANS, the Deep Algebraic Reynolds Stress Model (DARSM), which can be trained on small datasets and accurately generalise across Reynolds numbers, to unseen geometries, and to different flow regimes. A neural network maps flow invariants to empirical parameters in an implicit algebraic Reynolds stress equation, derived from the Reynolds stress transport equations under the weak-equilibrium assumption, imposing physics-based structure on the ML closure. End-to-end optimisation through the governing PDEs and the coupled implicit closure eliminates distribution shift, but both unrolled and implicit automatic differentiation fail on the stiff coupled solver. We derive adjoint equations that exploit the solver's implicit-explicit structure for efficient optimisation. On canonical square-duct and periodic-hill benchmarks, DARSM reduces average test velocity error over baseline RANS by $2$-$4\times$ across Reynolds number, geometries, and flow regimes, with peak case-level reductions of $12\times$. The model trained on attached, anisotropy-dominated flows (square duct) accurately generalises without retraining to separated flows (periodic hills), a regime change in the underlying physics. DARSM also outperforms five established ML methods: offline training, tensor-basis neural networks, field-inversion machine learning, DeepONets, and physics-informed neural networks.

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

Whole-Brain Connectomic Graph Model Enables Whole-Body Locomotion Control in Fruit Fly

arXiv:2602.17997v3 Announce Type: replace Abstract: Animals perform coordinated whole-body movements under the control of neural systems shaped by brain-wide connectivity. The mapping of the whole-brain neural connections, or the connectomes, provides a natural graph for modeling sensorimotor information flow, yet its potential as a neural controller for embodied agents remains largely unexplored. Here, we introduce the Fly-connectomic Graph Model, which directly instantiates the whole-brain connectome of an adult Drosophila as a graph-structured neural controller for movements of a simulated biomechanical fruit fly via deep reinforcement learning. We achieve stable performance across diverse locomotion tasks, as well as better sample efficiency compared to both graph and non-graph baselines. Our results demonstrate a biologically informed way towards effective control policy design by translating whole-brain wiring principles into actionable architectural priors, while also improving the interpretability through dynamic information flow. This work also highlights the potential to bridge neuromechanics with embodied intelligence by providing a computational platform for investigating the sensorimotor transformation underlying animal behavior and a paradigm to advance the development of more nature-aligned intelligent systems.

04.
medRxiv (Medicine) 2026-06-18

Device assessed 24-hour movement behaviour and cardiovascular disease mortality amongst cancer survivors.

Background: Cancer survivors face elevated risks of mortality from cardiovascular disease (CVD). The potential importance of physical activity (PA) and other behaviours across the 24-hour day (e.g. sedentary behaviour (SB) and sleep) for CVD-mortality risk is not well understood in this at-risk population. Objectives: To assess the importance of 24-hour movement behaviour, using a compositional approach, for mitigating CVD-mortality amongst cancer survivors. Methods: Participants with a prior cancer diagnosis were drawn from the UK Biobank accelerometry sub-study (n=6,158). Accelerometer-derived movement (moderate-to-vigorous PA (MVPA), vigorous PA (VPA), moderate PA (MPA), light PA (LPA), SB, sleep) was examined in relation to CVD-mortality, identified from health record linkage data (using Fine-Gray Cox proportional-hazards models adjusted for demographic, health, lifestyle covariates). Results: Median follow-up was 8.0 years (Q1-Q3: 7.4-8.5), with n=500 (8.2%) deaths (CVD-deaths: n=118). Greater MVPA, in place of any other behaviour, was inversely associated with CVD-mortality with e.g. 10% lower hazard if MVPA theoretically replaced 7 minutes (mins)/day SB (Hazard ratio (HR): 0.91, (95% Confidence Interval: 0.86-0.95)), 9 mins/day LPA (HR: 0.90, 0.83-0.97), or 11 mins/day sleep (HR: 0.90, 0.83-0.97). The VPA component of MVPA proved critical, requiring only ~1-2 additional mins/day for equivalent hazard reduction. Sleep duration, was also inversely associated with CVD-mortality. A 10% lower hazard required replacing 29 mins/day of SB with sleep (HR: 0.90, 0.84-0.96); no other behavioural replacement amongst SB, sleep or LPA could provide an equivalent risk reduction. Conclusions: Among cancer survivors, the most potent reduction in CVD-mortality followed theoretically reallocating time to higher intensity movement.

05.
arXiv (CS.AI) 2026-06-24

VeriPilot: An LLM-Powered Verilog Debugging Framework

arXiv:2606.23759v1 Announce Type: cross Abstract: Verilog debugging remains one of the most time-consuming stages in digital circuit design. Recent advances in Large Language Models (LLMs) have enabled automated debugging; however, most existing approaches rely solely on test outputs and compiler feedback in an end-to-end manner, limiting their effectiveness on complex bugs. A key challenge is that the root cause of an error may be far removed from its observable outputs, making it difficult for LLMs to trace long dependency chains in code. This challenge is further exacerbated in large codebases, where long context lengths hinder efficient reasoning. To address these limitations, we propose VeriPilot, an LLM-powered debugging framework that leverages golden reference models to enable fine-grained bug localization and repair. VeriPilot goes beyond output-level comparison by aligning internal variable semantics between the Verilog design and its corresponding golden model through LLM-based analysis. It then performs step-by-step signal tracing using Control-Data-Flow Graphs (CDFGs) derived from static analysis, identifying a minimal set of suspicious code regions along with their correct counterparts from the golden model. These structured insights are subsequently provided to the LLM to guide reasoning and automated code repair. Experimental results on the Comprehensive Verilog Design Problems (CVDP) benchmark from NVIDIA demonstrate that VeriPilot improves the repair success rate of GPT-4o from 54.3\% to 85.71\%, significantly enhancing both bug localization accuracy and repair effectiveness for complex Verilog designs. The source code and benchmark are publicly available at Github https://github.com/YihanWn/VeriPilot.git.

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

Two-Layer Linear Auto-Regressive Models Estimate Latent States

arXiv:2606.12691v1 Announce Type: cross Abstract: Auto-regressive models have emerged as powerful tools for sequential data, from language to video. Understanding how and why these models learn latent representations remains an open theoretical question. In this work, we demonstrate that when trained by empirical risk minimization on data from partially observed linear dynamical systems, two-layer linear auto-regressive models naturally learn to approximate Kalman filtering. In particular, we show that the learned hidden representation coincides, up to a similarity transformation, with the state estimates produced by the optimal (Kalman) filter, even though the model has no explicit knowledge of the underlying dynamics or state. The result follows from three main insights. First, we establish that the Kalman filter is well approximated by an auto-regressive model with bounded truncation error. Second, we show that despite non-convexity, the two-layer optimization landscape is benign, i.e., all stationary points are either strict saddles or global minima. Finally, as our main contributions, we provide finite-sample guarantees on prediction error, parameter estimation error, and latent state recovery. Numerical simulations support the theoretical results and demonstrate that the latent representations of auto-regressive models recover state estimates.

07.
Nature (Science) 2026-06-24

AI tool spots antibiotics that fight drug-resistant gonorrhoea

Authors: Unknown Author

The bacterium Neisseria gonorrhoeae has evolved resistance to most antibiotics used to treat it, but a machine-learning screen reveals potential therapies. The bacterium Neisseria gonorrhoeae has evolved resistance to most antibiotics used to treat it, but a machine-learning screen reveals potential therapies.

08.
arXiv (CS.CL) 2026-06-16

CODA-BENCH: Can Code Agents Handle Data-Intensive Tasks?

Advanced agents are increasingly demonstrating the potential to operate as autonomous engineers, creating a growing demand for evaluation benchmarks that capture the complexity of real-world development. Such environments typically involve both complex code and large-scale data (i.e., file system). However, existing benchmarks usually evaluate code-centric or data-centric capabilities in isolation, leaving a clear gap with real development scenarios. In this paper, we bridge this gap by introducing CODA-BENCH, the first benchmark to jointly evaluate code and data intelligence in a data-intensive environment. We construct a data-intensive Linux sandbox based on the Kaggle ecosystem (containing hundreds of datasets), where agents must actively explore complex file hierarchies to identify relevant resources and generate code for data-driven analytical tasks. CODA-BENCH comprises 1,009 tasks spanning 31 communities, with each task environment containing an average of 980 files, simulating realistic data scale and noise. Evaluations of advanced agents reveal that even top-performing systems struggle to effectively integrate data discovery with code execution, achieving a success rate of only 61.1%. These results highlight a substantial gap in current agentic capabilities for data-intensive tasks and point to promising directions for future research.

09.
bioRxiv (Bioinfo) 2026-06-20

Seed variation impacts clustering stability in Single-Cell RNA-Seq and can be mitigated by StAbility-BasEd-Reassignment (SABER)

Single-cell RNA-seq clustering is commonly treated as reproducible once a random seed is fixed, yet the choice of seed itself may alter cell assignments and downstream interpretation. We systematically quantified seed-induced clustering variability by running Louvain and Leiden clustering across 100 seeds in Seurat and Scanpy on 28 single-cell RNA-seq datasets from the Human Cell Atlas and IMMUcan. Using Element-Centric Consistency, we found that seed choice affected a substantial fraction of cells, with Scanpy showing more unstable assignments than Seurat on average, 40.46% versus 26.78% unstable cells, respectively. This increased stability came at a marked computational cost: Seurat required approximately 19-fold higher median memory than Scanpy. Seed-dependent clustering variability also propagated to cell-type annotation, particularly among transcriptionally related populations including macrophage/monocyte, endothelial/epithelial and T/NK cell states. To mitigate this instability, we developed StAbility-BasEd Reassignment (SABER), a Scanpy-based framework that identifies seed-sensitive cells across repeated clusterings and reassigns them to stable cluster cores using cosine similarity. SABER improved clustering quality while preserving annotation concordance and reduced median memory usage 3.5-fold compared with Seurat-Louvain. Our results identify seed choice as an underappreciated source of variability in single-cell analysis and provide a scalable strategy to improve clustering robustness.

10.
arXiv (CS.AI) 2026-06-24

video-SALMONN-R$^3$: Learning to ReWatch, ReAsk, and ReAnswer for Efficient Video Understanding

arXiv:2606.24477v1 Announce Type: cross Abstract: Video large language models (LLMs) are often constrained by computation and memory budgets, leading them to use reduced frame rates and spatial resolutions, which may cause them to miss critical information for question answering (QA). A practical and efficient solution is a two-stage paradigm: first perform coarse video understanding to localize relevant segments, and then re-watch these segments at higher temporal or spatial fidelity. In this paper, we present video-SALMONN-R$^3$, the first end-to-end video-LLM that enables re-watch through reinforcement learning without relying on chain-of-thought (CoT) cold-start. This design removes the need for costly CoT data annotations and avoids CoT-based supervised fine-tuning (SFT), which can otherwise degrade the pretrained video understanding abilities. To address the mismatch between the reasoning-first behavior induced by re-watch and the answer-first tendency of pretrained video-LLMs, we propose a re-answer strategy, in which the model first produces a direct answer in the first watch and then refines it after re-watching. Finally, to improve question adherence during re-watching, we propose a re-ask mechanism that re-injects the query when revisiting localized segments. Experimental results show that video-SALMONN-R$^3$ consistently outperforms both the base model and the QA-SFT baseline, while surpassing prior re-watch-based approaches with significantly lower computational cost. Code, models, and data will be publicly released upon acceptance.

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

SuperThoughts: Reasoning Tokens in Superposition

Long Chain-of-Thought (CoT) reasoning improves LLM problem-solving but is computationally expensive due to sequential token generation. While recent works explore reasoning in continuous latent spaces to bypass discrete token generation, they often struggle with training stability and fail to scale to complex, long-horizon tasks due to lack of supervision signal. We propose SuperThoughts, which compresses pairs of consecutive CoT tokens into single latent representations and decodes two tokens per step via a lightweight Multi-Token Prediction (MTP) module. This preserves discrete token supervision at training time while doubling throughput at inference time. We finetune Qwen2.5-Math-1.5B-Instruct, Qwen2.5-Math-7B-Instruct, Qwen2.5-Math-14B-Instruct, and evaluate on MATH500, AMC, OlympiadBench, and GPQA-Diamond. With a confidence-based adaptive mechanism that falls back to standard decoding when uncertain, SuperThoughts achieves $\sim$20–30\% CoT length reduction while maintaining accuracy with minimal degradation (1-2 points accuracy drop on most tasks).

12.
arXiv (quant-ph) 2026-06-19

Robust Generation of Topological Biphoton Mode via Adiabatic Passage

arXiv:2606.19786v1 Announce Type: new Abstract: Topological waveguide arrays support robust mode propagation in the presence of fabrication imperfections, providing a significant advantage for on-chip quantum information processing. However, this robustness does not fully extend to nonlinear biphoton generation. Structural disorder can enhance the excitation of non-topological biphoton modes during nonlinear interactions, which degrades the quantum properties of the generated state. To overcome this limitation, we propose an adiabatic passage that connects an isolated site to a topological defect array. By initiating the nonlinear process in a strongly isolated regime, nonlinear coupling to unwanted modes is effectively suppressed, thereby preserving the Schmidt number of the generated state. The subsequent adiabatic connection facilitates the high fidelity transfer of the generated biphoton into the topological biphoton mode. Our numerical simulations demonstrate that, unlike conventional topological structures, the adiabatic scheme maintains both high biphoton fidelity and a unit Schmidt number in the presence of waveguide gap disorder. Furthermore, we show that this robustness extends to path entangled NOON states, achieving a near-unity quantum interference visibility. Our approach provides a practical design strategy for disorder-tolerant integrated quantum photonic devices.

13.
Nature Medicine 2026-06-17

General-purpose chatbots outperform clinical AI tools on physicians’ real-world questions

Authors: Unknown Author

Specialized clinical AI tools are entering medical practice with little independent testing. In a head-to-head evaluation across two public benchmarks and real questions from physicians, three general-purpose frontier large language models outperformed two leading clinical AI tools, which performed no better than Google search AI overview.

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

SafeSpec: Fast and Safe LLM via Dynamic Reflective Sampling

arXiv:2606.19755v1 Announce Type: cross Abstract: Speculative inference accelerates large language model (LLM) decoding but provides no inherent safety guarantees. Existing safety defenses are largely incompatible with speculative inference: they either introduce additional computation or disrupt the draft-verify mechanism, negating acceleration benefits. This reveals a fundamental incompatibility between current safety methods and speculative decoding. We propose SafeSpec, a safety-aware speculative inference framework that integrates risk estimation directly into the verification process. SafeSpec attaches a lightweight latent safety head to the target model to jointly evaluate semantic validity and safety in a single forward pass. When unsafe generations are detected, SafeSpec applies rollback and safety-guided reflective multi-sampling to recover safe continuations rather than terminating generation. We model jailbreak attacks as distributional shifts over generative trajectories, where adversarial prompts increase the probability of harmful continuations without eliminating safe ones. Under this model, SafeSpec performs risk-aware trajectory recovery within the speculative decoding process. Across multiple models and adversarial benchmarks, SafeSpec achieves a substantially improved safety-efficiency trade-off. On Qwen3-32B, SafeSpec reduces attack success rates by 15% while preserving a 2.06x inference speedup on benign workloads, demonstrating that speculative acceleration and inference-time safety can be jointly optimized.

15.
arXiv (quant-ph) 2026-06-24

Syndrome aware mitigation of logical errors

arXiv:2512.23810v2 Announce Type: replace Abstract: Broad applications of quantum computers will require error correction (EC). However, hardware roadmaps indicate that physical qubit numbers will remain limited in the foreseeable future, leading to residual logical errors that constrain the size and accuracy of achievable computations. Recent work suggested logical error mitigation (LEM), which applies known error mitigation (EM) methods to logical errors, eliminating their effect at the cost of a runtime overhead. We introduce syndrome-aware logical error mitigation (SALEM), which mitigates logical errors conditioned on the error syndromes measured during error correction. The runtime overhead of SALEM is exponentially lower than that of LEM schemes which do not make use of syndrome data, enabling substantially larger circuit volumes that can be executed accurately. Compared to the routinely used combination of error correction and syndrome rejection (post-selection), SALEM increases the size of reliably executable computations by orders of magnitude. In the practical setting where space and time overheads are fixed and error reduction methods are compared by their resulting estimation errors, we observe a surprising phenomenon: SALEM, which tightly combines EC with EM, can outperform physical EM even above the standard fault-tolerance (pseudo) threshold. Thus, SALEM can make use of EC in regimes of physical error rates where EC is commonly deemed useless.

16.
arXiv (CS.CL) 2026-06-11

Layer-Isolated Evaluation: Gating the Deterministic Scaffold of a Production LLM Agent with a No-LLM, Regression-Locked Test Harness

End-to-end task-success is the dominant way to evaluate LLM agents, but one aggregate number tells you that an agent regressed, not where. We present layer-isolated evaluation: a deployed ordering agent is decomposed into a fixed taxonomy of layers (ontology, intent, routing, decomposition, escalation, safety, memory, and cross-cutting envelope/defense), each exercised by its own assertion slice in a deterministic, no-LLM "pure" mode. The pure suite (238 cases across 23 slices; 225 run in 2.39 s, ~10 ms/case) runs in CI on every change against a locked per-slice baseline. We validate by controlled regression injection, degrading one layer at a time across seven non-safety layers. The effect we did not design in is masking: the aggregate pass-rate barely moves (-1.7 to -5.9 pp for six local regressions), while the matching slice craters (-25 to -91 pp). A layer's slice reacting to its own fault is partly by construction; the measured results are (i) the aggregate masking and (ii) that damage stays off the other slices: the injected layer's slice is the single worst-hit in 5 of 7 cases and top-3 in 7 of 7 (mean rank 1.29 of 19). Localization replicates on a second, structurally different tenant (Starbucks SG): all seven matching slices crater, so it is not a single-catalog artifact. We position it as a concrete, deterministic instantiation of the component-level evaluation EDDOps prescribes but leaves unimplemented, with CheckList as ancestor and as the deterministic mirror image of whole-workflow stochastic mutation testing. Our contributions: (a) a fully decomposed, sub-second, no-LLM per-layer harness for a production agent, (b) a coverage-honesty test-adequacy criterion that refuses to score an unexercised layer, and (c) the regression-injection demonstration that per-slice baseline-locked gates localize regressions an aggregate metric masks.

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

Flux-Guard: Facial Identity Protection using diffusion models

The widespread deployment of face recognition (FR) systems exposes personal images shared on social media and public platforms to identity linkage and privacy risks. Existing adversarial privacy protection methods can degrade unauthorized FR performance but are not compatible with generative face editing. Artificial intelligence-driven face editing tools are gaining popularity, which has significantly increased user demand for personalized portrait generation and social sharing. However, current editing methods often preserve identity features, making the edited images still susceptible to tracking by malicious FR systems. Thus, this paper proposes Flux-Guard, a privacy-preserving face editing framework based on adversarial attacks, which integrates face editing and privacy protection within a unified generative process. Specifically, we design a flow trajectory control method to align semantic manipulations with the generative process and introduce latent-space adversarial optimization with an adaptive perceptual-loss-driven weighting strategy, dynamically adjusting adversarial strength to maximize attack effectiveness while preserving visual quality. Extensive experiments demonstrate that Flux-Guard supports face editing while significantly improving attack success rates against cross-domain face recognition models on the CelebA-HQ and LADN datasets. Furthermore, evaluation results for commercial APIs have confirmed its effectiveness in real-world applications. The code is released at https://github.com/JLMWang/Flux-Guard.

18.
arXiv (quant-ph) 2026-06-24

On the localization transition from MAA to AA models

arXiv:2606.24720v1 Announce Type: cross Abstract: Despite their potential similarity between the mosaic Aubry-André (MAA) and AA models, the MAA model allows mobility edges (MEs), whereas the AA model does not. Here we develop a new double quasiperiodic MAA (DMAA) model consisting of one primitive MAA with nonzero even-site potentials and the other modified one with both nonzero odd-site potentials and a tunable amplitude factor, to reveal how localization transitions evolve from MAA to AA models. Interplays and competitions among the extended, critical and localized states arising from superpositions of double quasi-periodic MAA potentials enable new twice and multiple localization-delocalization transitions besides the original single localization transition. Our numerical calculations on inverse participation ratio, normalized participation ratio, fractal dimension and real-space wavefunction distribution confirm such localization features. The continuum model simulations on the experimental polariton modes also yield consistent results and hence validate their experimental feasibility. The constructed DMAA model provides a new framework for studying the localization transition processes between two analogous quasiperiodic models and broadens the understanding of Anderson localization.

19.
arXiv (CS.AI) 2026-06-24

MGI: Member vs Generated Inference

arXiv:2606.23872v1 Announce Type: cross Abstract: As generative models increasingly produce samples that are indistinguishable from human-created content, it becomes difficult to determine whether a given data point was part of a model's natural training set or was generated by the model itself, especially when models memorize and reproduce training data. We formalize this challenge as Member vs Generated Inference (MGI): given a sample and a target generative model, infer whether the sample is a true training member or a generated output of that model. Focusing on image generation, we show that existing membership inference methods systematically misclassify generated samples as training members, while attribution-based methods often misclassify true members as generated. This failure arises because both approaches rely on likelihood-related signals that are similarly elevated for training examples and for the model's own outputs. To address MGI, we propose Data Circuit Breaker (DCB), a three-stage method that combines complementary signals from a generative model's autoencoder and latent generator to distinguish training members from generated samples. Across multiple generative models, including image autoregressive and diffusion models, DCB consistently addresses the shortcomings of membership inference and attribution methods, remains effective even when models reproduce near-duplicates of training samples, and generalizes to challenging model derivative settings in which new models are trained on generated data.

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

Rethinking RAG in Long Videos: What to Retrieve and How to Use It?

arXiv:2606.13141v1 Announce Type: new Abstract: Retrieval-augmented generation is moving beyond text into long, egocentric video, where systems must select query-relevant chunks across multiple modalities and temporal granularities. Yet progress in VideoRAG is limited by two gaps: existing benchmarks allow queries to be answered without the video, obscuring retrieval errors, and prior methods apply a single modality-granularity configuration per query, ignoring chunk-level variability. We address both by introducing V-RAGBench, a benchmark of $\langle$query, evidence chunk, answer$\rangle$ triplets that enables faithful, decoupled evaluation of retrieval and generation, and CARVE, a simple method that runs parallel retrievers across configurations and employs chunk-adaptive reranking to identify the winning configuration for each chunk. Each chunk then enters the generator under its winning configuration selected during retrieval, yielding an interleaved evidence form where the chunk-level decision propagates across both stages. CARVE outperforms eight recent VideoRAG baselines, with the chunks supplied to the generator interleaving multiple configurations rather than sharing a single one, a behavior unattainable by query-level methods.

21.
arXiv (CS.CL) 2026-06-12

Trait, Not State: The Durability of Reading Identity in Social Highlighting

Prior work on a social web highlighter located individuality in selection – which documents a person chooses to highlight – but measured it cross-sectionally. We ask the temporal question: is a reader's selection signature a trait or a state? We freeze each reader's first six months of highlighting as a profile and track its own-vs-other advantage on their later selections at growing gaps (to 24+ months), with negatives drawn from the same calendar era – so supply drift cannot masquerade as personal drift – at a coarse global level and at a fine level whose negatives and controls come from the reader's own interest neighborhood; the anchor cell reproduces the prior cross-sectional level (+0.188 vs +0.169), validating the harness. Four results. Within the same users, the fine-layer advantage shows no statistically detectable paired decline at any horizon (6-12 month retention R = 1.00 [0.85, 1.18], n = 212; the farthest bin is compatible with a modest decline; the only contrast whose interval excludes zero is the coarse layer at 12-24 months, about 13%). The signal is not reducible to repeated domains (~90% survives excluding all profile sources). Within-person drift is slow (a recent-half profile beats the old half by +0.042). Prospectively, personal profiles – even one built from a reader's earliest documents, median 20 months before evaluation – rank their next reads at roughly 3x the AP of every simple non-personal prior tested. We use "trait" operationally (a stable signature under continued engagement); the scope is heavy, long-tenured readers of one platform, and exposure is not separable from choice.

22.
arXiv (CS.CL) 2026-06-17

Evaluating Second-Order Bias of LLMs Through Epistemic Entitlement

Evaluations of social bias in LLMs largely focus on whether models generate or imply biased content. However, as LLMs are increasingly used as judges of bias, they may exhibit social biases in subtler ways in how they evaluate biased content, which current methods do not systematically capture. We call this second-order bias: social bias in an LLM's judgment about social bias, which we evaluate through a novel, philosophically grounded reasoning task. Drawing on entitlement epistemology, we conceptualize bias as misplaced foundational knowledge that shapes an agent's rational inquiry, and derive a logical reasoning task for LLMs to judge to whom a biased text is acceptable or non-acceptable. We develop two simple metrics to measure how biased LLM judges are in inferring demographics for acceptability without sufficient support, and how these inferences vary across groups targeted by biased texts. Evaluating open and closed models, we find that our task evades safety guardrails by surfacing bias in model judgment. It varies systematically across target groups, reflects implicit social maps, and shows how models are still triggered by demographic labels. Our work points to the need for LLM bias evaluation in judgment tasks and broadly, for more theoretically grounded approaches to bias evaluation in NLP. We release our code and model responses at https://github.com/uofthcdslab/second-order-bias.

23.
arXiv (CS.AI) 2026-06-24

MultiMem: Measuring and Mitigating Memorization in Multi-Modal Contrastive Learning

arXiv:2606.22220v2 Announce Type: replace-cross Abstract: Memorization in machine learning models enables high performance on rare in-distribution samples by capturing their atypical patterns. However, it also causes harmful retention of noise and outliers, degrading generalization. While memorization has been extensively studied in both supervised and self-supervised learning in the vision domain, it remains unexplored in multi-modal contrastive learning. We address this gap by introducing MultiMem, the first metric designed to quantify memorization in multi-modal contrastive learning. Through our systematic analysis, we demonstrate that cross-modal semantic misalignment has the strongest influence on memorization, with text being the dominant modality driving memorization, followed by video, image, and audio. We show that targeted augmentations applied across all modalities effectively reduce memorization as measured by our MultiMem metric and improve model performance. Overall, this work establishes the first framework for measuring and mitigating memorization in multi-modal contrastive learning, preventing harmful data retention and contributing to higher-performing models.

24.
bioRxiv (Bioinfo) 2026-06-18

segSHAPE: RNA secondary structure prediction from nanopore direct RNA sequencing

RNAs adopt complex structures that regulate key biological processes, making accurate structure prediction essential. Chemical probing coupled with Nanopore direct RNA sequencing (DRS) offers a route to single-molecule structural inference, but current tools are limited by inaccurate signal-to-sequence alignment, which degrades modification-rate estimation and downstream structure prediction. Here we introduce segSHAPE for RNA secondary structure prediction from Nanopore DRS data (both RNA002 and RNA004 chemistries), a probe-agnostic framework that improves signal alignment using prior information of basecalling and per-read signal baseline shift correction, learns position-specific k-mer raw signal parameters, and estimates per-nucleotide modification rates with an unsupervised anomaly detector. On three public RNA002 DRS datasets spanning different chemical probes (AcIm, NAI-N3) and RNAs from 421 to 1552 nt, segSHAPE achieves the highest F1 score and Matthews correlation coefficient (MCC) on all RNAs, exceeding the strongest baseline by 3.4 to 5.8 percentage points in MCC. It additionally captures the ligand-induced conformational change of the thiamine pyrophosphate (TPP) riboswitch RNA directly from RNA002 DRS data using the DEPC probe. On a public RNA004 DRS dataset, segSHAPE improves over the sm-PORE-cupine baseline by 17 ROC-AUC points in modification rate estimation and by 6.7 MCC points in structure prediction. These results establish segSHAPE as a unified, probe-agnostic pipeline for RNA structure prediction from Nanopore DRS data.

25.
medRxiv (Medicine) 2026-06-18

Urinary Creatine Riboside Complements PSA to Improve Disease Detection in the Diagnostic Gray Zone of Prostate Cancer

Circulating prostate-specific antigen (PSA) discriminates poorly in the diagnostic gray zone (3.0-9.99 ng/mL), where ~75% of biopsies yield no clinically significant prostate cancer (PCa). We evaluated whether urinary creatine riboside (CR), a tumor-derived metabolite excreted through the prostatic urethra, complements PSA for gray-zone detection and independently predicts prostate-cancer-specific mortality (PCSM). In the NCI-Maryland PCa Case-Control Study (951 cases, 962 controls; 47.6% African American men; median follow-up 11.5 years), urinary CR was quantified by UPLC-MS/MS. Within the PSA gray zone (n = 668), urinary CR was complementary to PSA, with markedly higher single-marker discrimination than PSA (AUC 0.93, 95% CI 0.88-0.98 vs 0.77, 0.66-0.89) and additive when combined ({Delta}AUC +0.17, p < 0.001; 91.4% sensitivity at 80% specificity). After adjustment for 11 clinical and sociodemographic covariates, urinary CR independently predicted PCSM complementary to PSA (Fine-Gray SHR 1.72, 1.35-2.19 for CR; 1.35, 1.08-1.68 for PSA; Harrell's C 0.85 for CR + PSA vs 0.77 for PSA alone), with strongest signal in African American men (SHR 2.43, 1.57-3.75 for CR). We conclude that urinary CR is a candidate non-invasive biomarker complementary to PSA - improving gray-zone triage and predicting PCSM; prospective validation in biopsy-referred cohorts is warranted.