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01.
arXiv (CS.CL) 2026-06-12

InnoEval: On Research Idea Evaluation as a Knowledge-Grounded, Multi-Perspective Reasoning Problem

The rapid evolution of Large Language Models has catalyzed a surge in scientific idea production, yet this leap has not been accompanied by a matching advance in idea evaluation. The fundamental nature of scientific evaluation needs knowledgeable grounding, collective deliberation, and multi-criteria decision-making. However, existing idea evaluation methods often suffer from narrow knowledge horizons, flattened evaluation dimensions, and the inherent bias in LLM-as-a-Judge. To address these, we regard idea evaluation as a knowledge-grounded, multi-perspective reasoning problem and introduce InnoEval, a deep innovation evaluation framework designed to emulate human-level idea assessment. We apply a heterogeneous deep knowledge search engine that retrieves and grounds dynamic evidence from diverse online sources. We further achieve review consensus with an innovation review board containing reviewers with distinct academic backgrounds, enabling a multi-dimensional decoupled evaluation across multiple metrics. We construct comprehensive datasets derived from authoritative peer-reviewed submissions to benchmark InnoEval. Experiments demonstrate that InnoEval can consistently outperform baselines in point-wise, pair-wise, and group-wise evaluation tasks, exhibiting judgment patterns and consensus highly aligned with human experts.

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

CRAX: Fast Safe Reinforcement Learning Benchmarking

arXiv:2606.20376v1 Announce Type: cross Abstract: Safety is a core concern for deploying reinforcement learning (RL) agents in real-world domains such as robotics and autonomous driving. While benchmarks have been central to progress in RL, existing safety benchmarks with high-fidelity 3D physics remain computationally slow, limiting large-scale experimentation and rapid prototyping. To address this gap, we propose CRAX (Constrained RL Accelerated with JAX). Built on top of the MuJoCo XLA (MJX) physics engine with realistic 3D dynamics, CRAX leverages vectorized operations and hardware acceleration, yielding up to ~100x speedups over comparable CPU-based safety benchmarks. The benchmark features six environment suites and three agent-specific tasks, each spanning three difficulty levels. Evaluating six popular safe RL methods shows that no single approach dominates across all tasks, and reveals the trade-offs between performance and safety. We find that curriculum learning across difficulty levels and safety transfer can improve performance over direct training in harder settings.

03.
arXiv (CS.CL) 2026-06-19

CzechDocs: A Multiway Parallel Dataset of Formatted Documents for Minority Languages in Czechia

We present CzechDocs, a multiway parallel dataset of formatted documents (HTML, DOCX, and PDF) covering Czech and minority languages used in Czechia-primarily Ukrainian and English, with smaller portions of Vietnamese, Russian and other languages. The dataset is designed to support the evaluation of machine translation systems that aim to preserve document formatting during translation. We provide a comparison of the most common approaches to format-preserving machine translation on a validation subset of the dataset. This validation split, together with the evaluation toolkit, is publicly released for further research. A held-out test split will be reserved for a future shared task focused on document-level translation with formatting preservation.

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

StarOR: Synergizing Tree Search and Test-Time Reinforcement Learning for Optimization Modeling

arXiv:2606.15197v1 Announce Type: cross Abstract: Optimization modeling is inherently hierarchical, requiring a precise sequence of symbolic commitments. Traditional learning-based automated optimization modeling methods improve modeling policies through large-scale annotated or curated training data, but are costly to adapt to new problem distributions. Meanwhile, one-shot generation remains brittle in hierarchical modeling, where early symbolic errors can propagate into invalid formulations. Test-time scaling offers a promising alternative by enabling structural exploration with additional instance-level computation; however, existing search-based methods typically rely on a fixed policy, causing repeated rollouts to inherit similar modeling biases and providing limited credit assignment for intermediate decisions. To address these limitations, we propose StarOR, a synergistic search-and-adaptation framework that couples MCTS with Test-Time Reinforcement Learning for optimization modeling. StarOR decomposes the modeling process into four stages and updates a transient LoRA adapter via GRPO at each non-terminal node. By using MCTS-generated siblings as local comparison sets, StarOR transforms search-time exploration into instance-specific policy refinement. Moreover, an unsupervised multi-faceted reward system provides fine-grained feedback for intermediate formulation decisions without ground-truth labels. Experiments across five optimization benchmarks show that StarOR achieves state-of-the-art performance even with a 4B backbone, outperforming existing methods and the frontier LLMs.

05.
arXiv (CS.AI) 2026-06-19

KG-SoftMAP: Soft Knowledge-Graph Priors for Bayesian Network Structure Learning from Sparse Discrete Data

arXiv:2606.10358v2 Announce Type: replace-cross Abstract: Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. However, imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. We propose KG-SoftMAP, which encodes such a KG as a finite-strength, confidence-weighted edge prior and maximizes a MAP objective combining the BDeu score with a logit-form prior; the KG may be expert-curated or LLM-extracted. On synthetic benchmarks with known DAGs, KG-SoftMAP reaches Directed-F1 (DF1) $0.19$–$0.32$ at observation rate $\rho=0.05$ and DF1 $0.44$–$0.97$ at $\rho\geq0.2$, while every data-only learner tested stays near zero under the same sparse masks. Recovery tracks KG quality: controlled corruption degrades it smoothly, a zero-signal KG yields DF1 $0.00$, and a blindly LLM-extracted KG with imperfect precision and recall still drives substantial recovery. On three real sparse educational datasets, the learned BN acts as a concept-level posterior model: on SAF it matches logistic regression (LR) within $0.03$ F1_FAIL while providing an inspectable concept graph, calibrated Fail probabilities, and tractable posterior queries from partial observations.

06.
medRxiv (Medicine) 2026-06-17

A non-invasive liquid biopsy resolves the diagnostic blind spot in chronic kidney disease

Chronic kidney disease is a major global health burden, and its early detection is critical for delaying progression to kidney failure using recently developed targeted therapies. However, current diagnostic screening relies heavily on blood markers that are confounded by muscle mass, and on urine tests that frequently miss structural damage occurring without protein leakage. This creates a critical diagnostic blind spot that hinders timely intervention. Here we show a non-invasive liquid biopsy platform that quantifies a specific protein marker, MUC1, on urinary extracellular vesicles to accurately assess renal parenchymal integrity. By bypassing the systemic metabolic noise of traditional blood tests, our assay provides a remarkably stable, person-specific functional signature. Following extensive validation across diverse cohorts, our longitudinal analysis demonstrated that the discrepancy between this novel urine-based readout and standard blood tests unmasks hidden renal vulnerability, successfully predicting rapid functional decline. By comprehensively evaluating both tubular and glomerular integrity from a single spot urine sample, these findings establish a completely non-invasive, highly scalable prescreening tool that resolves the diagnostic blind spot, enabling broader early detection strategies and ushering in a new era of proactive risk management.

07.
arXiv (CS.LG) 2026-06-16

ExpRL: Exploratory RL for LLM Mid-Training

arXiv:2606.17024v1 Announce Type: new Abstract: Sparse reward reinforcement learning (RL) has become a standard tool for improving LLM reasoning, but its success depends critically on the coverage present in the base model. In practice, models are often primed for RL through mid-training on curated reasoning traces that teach useful primitive skills such as decomposition, verification, or self-correction. Although effective, this strategy requires manually specifying what the model should learn, and it remains unclear whether such primitive coverage is enough for much harder problems, which require combining these skills into broader solution strategies. We study a more automated approach: RL-based mid-training using large corpora of human-written question-answer data. Rather than treating reference solutions as targets to imitate, our method, ExpRL, uses them as reward scaffolds: references are hidden from the policy and used only to construct problem-specific grading rubrics for judging on-policy reasoning traces. The policy samples from the original problem prompt, while an LLM judge compares the sampled reasoning trace against the reference solution and assigns outcome-level or process-level dense rewards. This lets ExpRL reinforce partial progress, useful intermediate reductions, and productive reasoning behaviors that sparse final-answer rewards often fail to upweight. On challenging math reasoning tasks, ExpRL yields stronger RL priming than SFT, sparse-reward GRPO, and self-distillation, and provides a better initialization for subsequent sparse-reward RL. Additional mixed-domain experiments further suggest that ExpRL can extend beyond the original math-only setting.

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

Curvature-Guided Geometric Representation for Protein-Ligand Binding Affinity Prediction

arXiv:2606.14159v1 Announce Type: new Abstract: Protein-ligand binding affinity (PLA) prediction is critical in drug discovery. Despite the notable advancements in machine learning-based approaches, existing methods struggle to jointly characterize local geometric organization and globally coordinated cross-molecular interactions, limiting their ability to model complex binding mechanisms. Here, we propose RicciBind, a geometric representation framework that integrates curvature-guided hierarchical structure learning with optimal transport (OT)-based cross-domain alignment to model molecular interactions. Specifically, RicciBind leverages Ricci curvature to capture local interaction tightness within molecular structures, enhancing structural awareness and organizing atomic interactions into curvature-aware hierarchical representations. An OT-based cluster matching mechanism then aligns protein and ligand clusters across heterogeneous domains under geometric constraints, enabling globally consistent correspondences and revealing higher-order interaction patterns beyond local neighborhoods. By coupling curvature-guided structure encoding with OT-driven cross-domain alignment, RicciBind effectively models complex interaction semantics and substantially improves both the accuracy and interpretability of binding affinity prediction. Extensive experiments demonstrate that RicciBind achieved superior predictive performance and generalization across PLA benchmarks and virtual screening tasks. Ablation studies further confirmed the essential role of Ricci curvature in enhancing molecular interaction representations.

09.
arXiv (CS.AI) 2026-06-17

LLM Consumer Behavior Theory: Foundations of a Novel Research Field

arXiv:2606.18005v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly deployed as autonomous agents that make consumption decisions on behalf of users. This shift raises fundamental questions for consumer theory, which has traditionally modeled humans as the primary decision-makers. In this paper, we introduce LLM Consumer Behavior Theory, a new field of study concerned with analyzing consumer behavior in agentic markets. Drawing on classical and behavioral economics alongside recent advances in Natural Language Processing, we formalize how human preferences are reflected and acted upon by LLM-based agents, and how agent-level decisions aggregate into market demand. We unify previously fragmented literature on LLM decision-making, human behavior simulation, and preference elicitation under a common economic lens, highlighting where assumptions, such as rationality and heterogeneity, may fail in agentic markets. Rather than providing empirical validation, this paper outlines the scope of LLM consumer behavior and identifies open research questions related to alignment, preference representation, and market dynamics.

10.
arXiv (CS.CV) 2026-06-11

MLT-Dedup: Efficient Large-Scale Online Video Deduplication via Multi-Level Representations and Spatial-Temporal Matching

The explosive growth of user-generated video content on online platforms is accompanied by the emergence of numerous near-duplicate videos–videos that are identical or highly similar but differ by partial edits. These duplicates degrade user experience and increase storage and bandwidth costs, making large-scale video deduplication a critical task. Existing video deduplication frameworks face a fundamental challenge in retrieving sufficient high-quality candidates under a limited index budget, as well as trade-offs between efficiency and precision. To address these issues, we propose MLT-Dedup, an efficient large-scale online video deduplication framework with Multi-Level representations and spatial-Temporal matching. Our approach employs a Multi-Level Video Encoder (ML-VE) to extract both fine-grained frame-level and sparse clip-level embeddings: sparse embeddings support efficient candidate retrieval, while fine-grained embeddings are loaded for precise pairwise matching. During matching, we introduce DiF-SiM, a Differential Feature-enhanced Similarity Module capable of locating duplicated temporal segments and providing reliable similarity evidence to support policy-driven deduplication decisions. Extensive experiments on a real-world large-scale platform demonstrate that MLT-Dedup reduces online repetition rates by 91% at 90% precision. Furthermore, our sparse retrieval design achieves a 5x increase in indexing capacity, enabling broader candidate coverage in real-world deployment.

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

Gaussian DP for Reporting Differential Privacy Guarantees in Machine Learning

arXiv:2503.10945v3 Announce Type: replace-cross Abstract: Current practices for reporting differential privacy (DP) guarantees for machine learning (ML) algorithms such as DP-SGD provide an incomplete and potentially misleading picture. For instance, if only a single $(\varepsilon, \delta)$ is known about a mechanism, standard analyses show that there could exist highly accurate inference attacks against training data records, when, upon a more careful analysis, such accurate attacks do not exist for most practical mechanisms. In this position paper, we argue that using _non-asymptotic_ Gaussian Differential Privacy (GDP) as the primary means of communicating DP guarantees in ML avoids these potential downsides. Using two recent developments in the DP literature: (i) open-source numerical accountants capable of computing the privacy profile and $f$-DP curves of DP-SGD to arbitrary accuracy, and (ii) a decision-theoretic metric over DP representations, we show how to provide non-asymptotic bounds on GDP using numerical accountants, and show that GDP can capture the entire privacy profile of DP-SGD and related algorithms with virtually no error, as quantified by the metric. To support our claims, we investigate the privacy profiles of state-of-the-art DP large-scale image classification, and the TopDown algorithm for the U.S. Decennial Census, observing that GDP fits their profiles remarkably well in all cases. We conclude with a discussion on the strengths and weaknesses of this approach, and discuss which other privacy mechanisms could benefit from GDP.

12.
arXiv (CS.AI) 2026-06-18

Correcting Sensor-Induced Distribution Drift with Wasserstein Adversarial Learning

arXiv:2606.18561v1 Announce Type: cross Abstract: The quality of recorded data depends on the stability of the sensor system that acquires it. Sensor motion and aging can degrade the performance and stability of downstream data-driven methods. We present a Wasserstein-GAN-inspired approach for unsupervised inference of physically interpretable transformation parameters that map a changed detector response distribution back to a nominal reference distribution. In contrast to standard generative modeling, the generator is used as a learnable calibration transformation whose trainable weights represent the sought parameters, while the critic provides a distributional distance signal via the Wasserstein objective. We validate the approach on a tracking-detector toy model with controlled layer shifts and demonstrate its application on high-granularity Geant4-simulated calorimeter data with cell-wise aging effects. The method recovers aging coefficients for individual cells with correlation to ground truth and improves agreement between calibrated and reference energy-sum distributions, while exhibiting the expected degradation at increasing channel-to-channel noise levels. These results indicate that adversarial distribution matching can serve as a data-driven component of calibration strategies in settings where direct labels for degradation parameters are unavailable.

13.
bioRxiv (Bioinfo) 2026-06-11

An AI-Powered Trisomy 21 Research Assistant

Down syndrome, caused by trisomy 21, increases the risk of diverse co-occurring conditions. With more than 34,000 related publications indexed in PubMed as of early 2026, keeping pace with this expanding literature is challenging. While general-purpose large language models are widely used for information retrieval, they often rely on broad training data rather than specific evidence. Retrieval-augmented generation (RAG) improves rigor and reliability of responses by linking model outputs to source texts. In research, source texts are peer-reviewed articles. Standard implementations treat all manuscript sections equally, allowing background text to rank as highly as experimental results. To focus model outputs on experimentally supported responses, we developed the T21 Research Assistant, a section-aware RAG system that prioritizes Results sections to ground responses in primary experimental evidence. The system draws exclusively from 1,789 open-access Down syndrome publications from PubMed Central, including 327 NIH INCLUDE-funded studies, and uses a multistage pipeline for query validation, retrieval, reranking, synthesis, and citation verification. Built on NVIDIA Nemotron models, it generates structured, cited responses. Evaluation using expert-curated questions demonstrated strong performance, achieving a BERTScore F1 of 0.712 and recall of 0.758, comparable to or exceeding leading proprietary and open-source models. T21 Research Assistant is available at: https://bioinformatics.cuanschutz.edu/t21-res-assi/

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

Navigating Unreliable Parametric and Contextual Knowledge: Explicit Knowledge Conflict Resolution for LLM Inference

arXiv:2606.20245v1 Announce Type: new Abstract: Large language models (LLMs) have achieved strong performance across a wide range of language-based tasks by leveraging both extensive parametric knowledge and in-context learning ability, enabling them to incorporate external information provided in the input prompt. However, the integration of external knowledge can introduce conflicts, not only between the model's internal parametric knowledge and the external information, but also among multiple pieces of external contexts. Existing approaches typically assume that either the model or the provided context is reliable, overlooking the possibility that both sources may contain errors, and avoid conflicts by privileging one source over the other, rather than actively resolving inconsistencies. To address these limitations, we propose a novel framework MACR for LLM knowledge conflict resolution that moves beyond the conventional binary choice paradigm and incorporates an explicit conflict-resolution mechanism based on a multi-agent reasoning approach. Specifically, we first propose an adaptive knowledge assessment and retrieval approach that employs a modified semantic entropy measure to quantify an LLM's confidence in its answer to a given query. Based on this confidence estimation, MACR either externalizes the model's internal knowledge as textual representations or retrieves relevant external knowledge when internal knowledge is insufficient, generating basic contexts for subsequent reasoning. Then we introduce an inductive multi-agent reasoning framework with three specialized agents that, respectively, induce explicit rules, analyze potential conflicts, and resolve inconsistencies across all available contexts. Empirical results demonstrate that MACR significantly outperforms state-of-the-art baselines across benchmarks, while also providing interpretable resolutions of explicit conflicts.

15.
arXiv (quant-ph) 2026-06-19

Proposal of quantum arrival-time measurement with a Bose-Einstein condensate

arXiv:2606.20278v1 Announce Type: new Abstract: This work shows how a Bose-Einstein condensate of ultracold atoms could be used to address a long-standing question in quantum theory: how much time does it take for a particle to reach a detector? To this end, we propose a realistic experimental setup, whose key idea is not to measure arrival times directly, but the arrival flux on the detector as a function of its position. This novel approach not only solves practical issues with having a detector close to the system, but also results in signals that allow to unambiguously distinguish different theoretical predictions. This proposal raises prospects for resolving the decades-old debate on this fundamental issue.

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

SG2Loc: Sequential Visual Localization on 3D Scene Graphs

Visual localization in complex indoor environments remains a critical challenge for robotics and AR applications. Sequential localization, where pose estimates are refined over time, is important for autonomous agents. However, traditional methods often require storing extensive image databases or point clouds, leading to significant overhead. This paper introduces a novel, lightweight approach to sequential visual localization using 3D scene graphs. Our method represents the environment with a compact scene graph, where nodes represent objects (with coarse meshes) and edges encode spatial relationships. For each image in the localization phase, we extract per-patch semantic features, predicting object identities. Localization is performed within a particle filter framework. Each particle, representing a camera pose, projects the coarse object meshes from the scene graph into the image, assigning object identities to patches based on visibility. The similarity of the per-patch features, in the input image, and object features from the scene graph determines the weight of a particle. Subsequent images are incorporated sequentially, refining the pose estimate. By leveraging a compact scene graph and efficient semantic matching, our method significantly reduces storage while maintaining performance on real-world datasets. The code will be available at https://github.com/DmblnNicole/sg2loc.

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

Beyond AHI: An Interpretable Causal-Discovery-Guided Framework for Sleep Recovery in Connected Health

arXiv:2606.18506v1 Announce Type: new Abstract: Objective sleep assessment relies on polysomnography (PSG), yet clinical impact is often better reflected in patient-reported outcomes (PROs) such as sleepiness and fatigue. Existing summary indices, including the Apnea-Hypopnea Index (AHI), provide limited insight into the multidomain physiology underlying functional recovery. We propose an interpretable, causal-discovery–guided framework for deriving a hierarchical Sleep Recovery Score (SRS) from multimodal PSG. Using two large population cohorts (MESA: n=1540; MrOS: n=825), we apply directed acyclic graph (DAG) learning to identify candidate physiological drivers spanning respiratory burden, hypoxic burden, sleep fragmentation, sleep architecture, and autonomic regulation. Although derived from clinical PSG, these domains map naturally to sensing streams increasingly available in connected health technologies, including wearable ECG, oximetry, and sleep-stage estimation devices. To preserve mechanistic plausibility, we introduce a two-stage screening process that combines physiology-based constraints with constrained LLM-assisted auditing to identify and remove structural confounders and construct-overlapping variables. Across cohorts, these five domains emerge as recurrent physiological domains associated with recovery, and the resulting SRS shows up to 2.5$\times$ stronger alignment with perceived recovery than AHI. By linking multimodal sleep physiology to patient-centered outcomes through an interpretable, bias-aware, and domain structured framework, this work provides a practical foundation for recovery modeling across both clinical sleep studies and emerging smart and connected health settings.

18.
arXiv (CS.CV) 2026-06-12

Bridging Modal Isolation in Interleaved Thinking: Supervising Modality Transitions via Stepwise Reinforcement

Interleaved thinking, where a unified multimodal model alternates between textual reasoning and visual generation, has shown promise on spatial and physical tasks. However, in complex long-chain scenarios, we identify a fundamental failure mode: generated images diverge from the textual context while subsequent text ignores the visual evidence, causing the two modalities to alternate without genuinely informing each other. We term this Modal Isolation and attribute it to compounding information loss at modality boundaries. We decompose each reasoning cycle into atomic operations and define modality transition loss, quantifying cross-modal hallucination (text-to-image) and visual utilization deficit (image-to-text) at each boundary. We propose MoTiF (Modality Tiransition Fidelity), a two-stage training framework that directly optimizes these transitions: Reflective SFT trains the model to detect and recover from erroneous visual outputs; Flow-GRPO improves image generation fidelity via reinforcement learning. All training signals in MoTiF derive from transition-level fidelity rather than end-task accuracy. Across four visual puzzle benchmarks, this transition-level supervision substantially improves both cross-modal coherence and final task accuracy. The results demonstrate that effective interleaved reasoning requires explicit structural supervision at modality boundaries, not merely scaling or end-task optimization.

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

Beyond Fully Random Masking: Attention-Guided Denoising and Optimization for Diffusion Language Models

Diffusion large language models (dLLMs) offer an efficient alternative to autoregressive models through parallel decoding, yet existing post-training methods largely rely on random masking strategies that overlook intrinsic token dependencies. In this work, we present an empirical analysis of attention in dLLMs and show that tokens attending more strongly to unmasked context exhibit greater generation stability and play a critical role in reasoning. Motivated by these findings, we propose AGDO, an attention-guided denoising and optimization framework that aligns both training and optimization with attention-derived dependencies. AGDO determines the denoising order based on attention structure and emphasizes attention-critical tokens during supervised fine-tuning and reinforcement learning. Experiments on mathematical and coding benchmarks demonstrate that AGDO consistently improves reasoning performance, outperforming state-of-the-art post-training methods for dLLMs.

20.
arXiv (CS.CL) 2026-06-16

Not What, But How: A Framework for Auditing LLM Responses across Positioning, Generalization, Anthropomorphism, and Maxims

Large language models (LLMs) are being increasingly used to answer subjective, information-seeking questions, where users are sensitive to how responses are communicated, not just whether the answers are correct. Existing LLM evaluations for subjective cultural queries largely focus on factual correctness, ignoring how the response is framed. To this end, we introduce FRANZ, an automated FRAmework for respoNse characteriZation to conduct communicative audit of LLM responses along four dimensions: cultural positioning, use of generalizing language, anthropomorphic cues, and adherence to conversational maxims. To enable this evaluation, we contribute SQUARE - a corpus of 376k subjective questions sourced from 57 subreddits, and mapped to 7 countries and 19 question categories. We demonstrate FRANZ's applicability by scoring responses from three open-weight LLMs. We observe that LLMs show statistically significant differences in the frequency with which they employ each response characteristic. Unlike single-dimensional audits, FRANZ reveals that insider positioning and anthropomorphism are positively coupled, with the degree of coupling varying by country, providing a diagnostic lens for identifying framing divergences.

21.
PLOS Computational Biology 2026-06-11

A zero-parameter first-principles gate framework for full-length TP53 missense variant interpretation

by Masamichi Iizumi Missense variant interpretation often achieves useful predictive performance but remains mechanistically opaque, particularly in proteins that combine structured domains with intrinsically disordered regions (IDRs). We developed Gate & Channel, a zero-parameter, first-principles framework for full-length TP53 missense variant analysis in which each prediction is generated by explicit IF-THEN gates derived from physicochemistry, geometry, structural constraints, and polymer physics rather than fitted weights. Variants are evaluated across independent channels representing distinct physical failure modes; a variant is predicted disruptive if any gate closes. A second hierarchical layer (“Geta”) encodes physically grounded post-closure exceptions, allowing sensitivity and specificity to be improved on disjoint variant populations. The v18 framework consists of 12 channels and 2 Getas spanning structured domains and IDRs, capturing DNA-contact disruption, Zn coordination, burial-dependent packing, secondary-structure compatibility, post-translational modification chemistry, short linear motif disruption (including a multi-partner coupled-folding face), proline-directed kinase recognition, and IDR-specific proline and glycine backbone constraints. Across 1,369 TP53 missense variants, the framework achieved 84.5% sensitivity and 89.1% positive predictive value, with 90.9% sensitivity preserved in the DNA-binding core and all 9/9 hotspot mutations captured. A post hoc audit of discordant IDR calls indicated that many apparent false positives had plausible molecular rationales, consistent with a distinction between molecular mechanism disruption and clinical penetrance. Applied to KRAS, TDP-43, and BRCA1, the same channels capture the dominant pathogenic mechanisms in each protein as a proof of principle, while residual missed variants name specific gates yet to be written. The framework is distributed as the open-source Python package pathogenicity-gates (v0.5.1, MIT). These results show that a substantial fraction of full-length TP53 missense variation can be resolved through explicit, auditable physical gates that carry meaning beyond TP53, with each remaining failure naming the next rule to be written.

22.
medRxiv (Medicine) 2026-06-18

Avidity of anti-pertussis toxin antibodies is associated with symptomatic Bordetella pertussis infection in a novel controlled human infection model

Background The association between functional antibody responses following Bordetella pertussis infection and symptomatic disease remains unclear. We characterized the maturation of anti-pertussis toxin (PT) IgG avidity after human challenge with B. pertussis and determined its association with symptomatic infection. Methods Healthy adults were intranasally inoculated with live B. pertussis organisms in a controlled human infection model and monitored for development of pertussis symptoms (NCT05136599). Serum samples were collected one day before inoculation and at 14, 28, 56, 180, and 365 days post challenge. Anti PT IgG avidity was tested using a titration of ammonium isothiocyanate (the bond breaking agent) to quantify a wide range of antibody avidities from low to very-high. Associations between covariates and avidity were examined using linear regression models, and high dimensional analyses were used to integrate all data. Findings Anti PT IgG avidity increased in both symptomatic (n=20) and asymptomatic (n=10) participants after the challenge, reached maximum levels at day 56, and then declined through day 365. Symptomatic participants developed significantly higher levels of high- and very high-avidity anti-PT antibodies at 28, 56, 180, and 365 days post-challenge compared with those who remained asymptomatic. In multivariate analyses, symptomatic infection was associated with higher levels of high and very high avidity anti-PT IgG at day180 and365 after challenge. Distinct avidity profiles in symptomatic vs asymptomatic participants emerged at day28 onwards, with the former group having higher levels of antibodies with higher avidities. However, levels of medium-high, high and very high avidity antibodies in symptomatic participants were lower at day 365 after challenge compared to their peak levels. Interpretation Anti-PT IgG avidity was associated with symptomatic B. pertussis infection and thus may serve as a surrogate of clinical disease outcome. These results highlight that antibody avidity provides an additional functional assay besides antibody quantitation to dissect immune responses to pertussis. Further investigation of anti PT IgG avidity should be pursued in natural pertussis outbreaks to determine whether it might be used to differentiate symptomatic from asymptomatic infections for epidemiologic purposes.

23.
arXiv (CS.AI) 2026-06-17

Beyond Parallel Sampling: Diverse Query Initialization for Agentic Search

arXiv:2606.17209v1 Announce Type: new Abstract: Test-time scaling for agentic search typically increases depth (i.e., more turns and tokens per trajectory) or breadth (i.e., more parallel rollouts). Here we focus on breadth scaling, showing that standard parallel sampling yields diminishing returns, tracing this to query redundancy at the first turn. When models issue similar first queries across rollouts, the threads retrieve overlapping evidence, and subsequent turns are conditioned on this shared retrieval. We address this limitation with DivInit, a training-free intervention at the first turn. Rather than sampling k independent first queries, DivInit draws n candidates from a single call, picks k < n diverse seeds, and runs them as parallel trajectories. Across five open-weight models and eight benchmarks, DivInit consistently improves over standard parallel sampling, with average gains of five to seven points on multi-hop QA at matched compute. Code available at https://github.com/cxcscmu/diverse-query-initialization

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

MARS: Efficient, Adaptive Co-Scheduling for Heterogeneous Agentic Systems

arXiv:2604.26963v2 Announce Type: replace-cross Abstract: Large language models (LLMs) are increasingly deployed as the execution core of autonomous agents rather than as standalone text generators. Agentic workloads induce a temporal shift from single-turn inference to multi-turn LLM-tool loops, and a spatial shift from chat-scale, GPU-only execution to repository-scale, GPU-CPU co-located execution. Consequently, coordinating heterogeneous resource demands of agentic execution has emerged as a critical system challenge. We design and implement MARS, an efficient and adaptive co-scheduling system that globally coordinates heterogeneous agentic workloads under coupled GPU-CPU resource pressure. By establishing holistic visibility across GPU inference and CPU tool execution via a unified information stream, an external control plane in MARS decouples admission from execution to prevent heterogeneous resource oversubscription. An internal agent-centric scheduler further minimizes the end-to-end critical path by prioritizing latency-sensitive continuations and adaptively retaining KV cache state only when warm resumption yields a latency benefit. Our evaluations show that MARS reduces end-to-end latency by up to 5.94x while maintaining nearly maximal system throughput. We further integrate MARS as the serving backend for the OpenHands coding agent framework, demonstrating its real-world effectiveness by accelerating end-to-end task completion time by up to 1.87x. Our source code is publicly available at https://github.com/Afterglow231/MARS_preview .

25.
arXiv (quant-ph) 2026-06-11

Additivity and chain rules for quantum entropies via multi-index Schatten norms

arXiv:2502.01611v3 Announce Type: replace Abstract: The primary entropic measures for quantum states are additive under the tensor product. In the analysis of quantum information processing tasks, the minimum entropy of a set of states, e.g., the minimum output entropy of a channel, often plays a crucial role. A fundamental question in quantum information and cryptography is whether the minimum output entropy remains additive under the tensor product of channels. Here, we establish a general additivity statement for the optimized sandwiched Rényi entropy of quantum channels. For that, we generalize the results of [Devetak, Junge, King, Ruskai, CMP 2006] to multi-index Schatten norms. As an application, we strengthen the additivity statement of [Van Himbeeck and Brown, 2025] thus allowing the analysis of time-adaptive quantum cryptographic protocols. In addition, we establish chain rules for Rényi conditional entropies that are similar to the ones used for the generalized entropy accumulation theorem of [Metger, Fawzi, Sutter, Renner, CMP 2024].