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01.
arXiv (CS.AI) 2026-06-19

ScaffoldAgent: Utility-Guided Dynamic Outline Optimization for Open-Ended Deep Research

arXiv:2606.20122v1 Announce Type: new Abstract: Open-ended deep research (OEDR) requires systems to acquire knowledge through multi-round retrieval and generate coherent long-form reports. The outline plays a central role as a structural scaffold that coordinates retrieval, evidence organization, and generation. However, existing methods either fix the outline before writing or refine it with local heuristics, leading to scaffold drift under continuous information accumulation and delayed feedback for evaluating outline modifications. We propose ScaffoldAgent, a utility-guided dynamic outline optimization framework for OEDR. ScaffoldAgent models outline evolution as a structured decision process with three operations: Expansion, Contraction, and Revision, enabling controlled updates to the report scaffold. It further introduces a utility-guided feedback mechanism that estimates the downstream value of each outline operation from retrieval gain, structural coherence, and trial-generation quality. The resulting utility signal guides node selection, operation scheduling, and termination during inference. Experiments on DeepResearch Bench and DeepResearch Gym show that ScaffoldAgent consistently improves long-form report generation and factual grounding over existing deep research agents.

02.
bioRxiv (Bioinfo) 2026-06-16

Super Learner Ensemble Modeling of CPTAC Proteomic Data for Survival Prediction in Head and Neck Squamous Cell Carcinoma

Survival analysis in head and neck squamous cell carcinoma (HNSCC) is traditionally performed using Cox proportional hazards models, alongside some exploration into black-box machine learning methods. The Super Learner (SL) algorithm addresses this model selection dilemma by combining diverse candidate algorithms into a weighted ensemble to perform comparably to the best candidate method. This study evaluates the performance of SL in HNSCC. Proteomic features as well as clinical covariates from 96 CPTAC HNSCC samples were modeled with three candidate algorithms (Cox LASSO, Cox Ridge, and Random Survival Forest) as well as the ensemble SL method. Models were optimized via Uno's time-dependent Concordance Index (C-index) and tested at 1- and 3-year time horizons using 2000 bootstrap resamples. The Cox Ridge regression model achieved the highest predictive accuracy among the four total methods. However, the SL demonstrated stable performance over both time horizons (1-year C-index: 0.985; 3-year C-index: 0.960). Variable importance analysis of the Cox Ridge model successfully identified malignant proteins (ATR, MAML1, MIEN1) alongside novel potential prognostic indicators (ZNF800, KERA). This analysis emphasizes the statistical necessity for larger cohorts for ensemble learning, while providing a benchmark of proteomic indicators in HNSCC.

03.
arXiv (math.PR) 2026-06-11

Marked random graphs with given degree sequence: large deviations on the local topology

arXiv:2401.00351v2 Announce Type: replace Abstract: We investigate the behavior of the empirical neighborhood distribution of marked graphs in the framework of local weak convergence. Here we extend known results by considering uniform random graphs with given degree sequences and i.i.d. marks on half-edges and vertices. We establish a large deviation principle for such families of empirical measures. The proof builds on Bordenave and Caputo's seminal 2015 paper, and Delgosha and Anantharam's 2019 introduction of BC entropy, relying on combinatorial lemmas that allow one to construct suitable approximations of measures supported on marked trees. Possible applications of these results are in the study of interacting diffusions on top of random graphs.

04.
arXiv (CS.AI) 2026-06-12

DCD: Domain-Oriented Design for Controlled Retrieval-Augmented Generation

arXiv:2604.07590v2 Announce Type: replace-cross Abstract: Retrieval-Augmented Generation (RAG) is widely used to ground large language models in external knowledge sources. However, when applied to heterogeneous corpora and multi-step queries, Naive RAG pipelines often degrade in quality due to flat knowledge representations and the absence of explicit workflows. In this work, we introduce DCD (Domain-Collection-Document), a domain-oriented design to structure knowledge and control query processing in RAG systems without modifying the underlying language model. The proposed approach relies on a hierarchical decomposition of the information space and multi-stage routing based on structured model outputs, enabling progressive restriction of both retrieval and generation scopes. The architecture is complemented by smart chunking, hybrid retrieval, and integrated validation and generation guardrail mechanisms. We describe the DCD architecture and workflow and discuss evaluation results on synthetic evaluation dataset, highlighting their impact on robustness, factual accuracy, and answer relevance in applied RAG scenarios.

05.
medRxiv (Medicine) 2026-06-10

A Three-Tier Operational Benchmark for Evaluating Large Language Models on Hospital Medication Safety

Objective. To introduce PsiBench, a clinically validated medication-safety benchmark for evaluating large language models (LLMs) against the standards used to certify hospital computerized provider order entry (CPOE) and electronic health record (EHR) systems, and a non-overlapping three-tier evaluation framework separating highest-stakes discrimination, the operational CDS regime, and category-correct alerting. Materials and Methods. PsiBench comprises 492 medication-safety scenarios across 11 safety categories, created by clinical pharmacology experts whose work underpins an annualized testing procedure used by more than 2,000 U.S. hospitals. The three-tier framework partitions the scenarios non-overlappingly: Discrimination (98 scenarios, 50 fatal vs 48 deception, near-balanced 51%/49%); Operational (394 scenarios, 261 serious unsafe plus 133 safe including 41 Excessive Alerts reclassified as operational negatives); and Attribution (311 alert-required scenarios). We evaluated 40 frontier LLMs from 10 providers over 3 runs per scenario at temperature 0.2 (or the provider default where temperature is not configurable), yielding 59,040 evaluations conducted April 21-23, 2026. Results. Headline binary performance on the full benchmark spans a wide range across the 40 models: F1 78.5%-92.3%, accuracy 65.4%-89.8%, sensitivity 81.4%-100.0%, specificity 6.1%-81.8%. Leading models by F1 (o4-mini 92.3%; o3 92.2%) pair high sensitivity with meaningful specificity; three models saturate sensitivity at 100% but fall below 25% specificity, indistinguishable from a naive always-alert classifier. The wide spread on a single headline metric motivates tier-specific analyses, developed in a separate clinical paper. Discussion and Conclusion. PsiBench and the three-tier framework operationalize a rigorous evaluation rubric for LLM medication safety, grounded in two decades of national hospital audit experience. The framework generalizes to any binary medication-safety classifier (rule-based, conventional ML, or LLM-driven), supporting tier-aware model selection and post-deployment surveillance.

06.
bioRxiv (Bioinfo) 2026-06-18

Trajectory inference of epithelial-centered neighborhood profiles reconstructs a pseudo-temporal continuum in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by complex lung architecture and spatially heterogeneous remodeling, which have hindered integrated analysis of cell-intrinsic activity and intercellular communication during disease progression. Here we profiled six IPF lung specimens comprising more than 630,000 cells using the Xenium 5k panel and developed an epithelial-centered neighborhood profiling framework based on the local cellular composition around each epithelial cell. This approach captured fibrosis-associated variation in epithelial niches without requiring predefined histological regions. Pseudo-temporal continuum inference of these profiles reconstructed a continuous axis that reflected the spatial progression of fibrotic remodeling from relatively preserved alveolar regions to fibrotic and airway-like remodeled regions. Within this spatial dataset, we mapped coordinated changes in epithelial states, local microenvironments, epithelial intracellular pathway activities, and directional interactions with neighboring cell types along the same axis. Our findings provide a spatial framework that generates testable hypotheses for progressive epithelial niche remodeling in IPF.

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

MapDream: Task-Driven Map Learning for Vision-Language Navigation

Vision-Language Navigation (VLN) requires agents to follow natural language instructions in partially observed 3D environments, motivating map representations that aggregate spatial context beyond local perception. However, most existing approaches rely on hand-crafted maps constructed independently of the navigation policy. We argue that maps should instead be learned representations shaped directly by navigation objectives rather than exhaustive reconstructions. Based on this insight, we propose MapDream, a map-in-the-loop framework that formulates map construction as autoregressive bird's-eye-view (BEV) image synthesis. The framework jointly learns map generation and action prediction, distilling environmental context into a compact three-channel BEV map that preserves only navigation-critical affordances. Supervised pre-training bootstraps a reliable mapping-to-control interface, while the autoregressive design enables end-to-end joint optimization through reinforcement fine-tuning. Experiments on R2R-CE and RxR-CE achieve state-of-the-art monocular performance, validating task-driven generative map learning.

09.
Nature (Science) 2026-06-12

An innovative technology boosts image quality for protein structures

After years of effort, two research teams have developed ‘laser phase plate’ systems that could help cryo-electron-microscopy users to generate high-quality structures for a broad range of proteins. After years of effort, two research teams have developed ‘laser phase plate’ systems that could help cryo-electron-microscopy users to generate high-quality structures for a broad range of proteins.

10.
arXiv (CS.LG) 2026-06-16

Scalable Graph Condensation with Evolving Capabilities

arXiv:2502.17614v3 Announce Type: replace Abstract: The rapid growth of graph data creates significant scalability challenges as most graph algorithms scale quadratically with size. To mitigate these issues, Graph Condensation (GC) methods have been proposed to learn a small graph from a larger one, accelerating downstream tasks. However, existing approaches critically assume a static training set, which conflicts with the inherently dynamic and evolving nature of real-world graph data. This work introduces a novel framework for continual graph condensation, enabling efficient updates to the distilled graph that handle data streams without requiring costly retraining. This limitation leads to inefficiencies when condensing growing training sets. In this paper, we introduce GECC (\underline{G}raph \underline{E}volving \underline{C}lustering \underline{C}ondensation), a scalable graph condensation method designed to handle large-scale and evolving graph data. GECC employs a traceable and efficient approach by performing class-wise clustering on aggregated features. Furthermore, it can inherit previous condensation results as clustering centroids when the condensed graph expands, thereby attaining an evolving capability. This methodology is supported by robust theoretical foundations and demonstrates superior empirical performance. Comprehensive experiments including real world scenario show that GECC achieves better performance than most state-of-the-art graph condensation methods while delivering an around 1000$\times$ speedup on large datasets.

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

HULFSynth : An INR based Super-Resolution and Ultra Low-Field MRI Synthesis via Contrast factor estimation

We present an unsupervised single image bidirectional Magnetic Resonance Image (MRI) synthesizer that synthesizes an Ultra-Low Field (ULF) like image from a High-Field (HF) magnitude image and vice-versa. Unlike existing MRI synthesis models, our approach is inspired by the physics that drives contrast changes between HF and ULF MRIs. Our forward model simulates a HF to ULF transformation by estimating the tissue-type Signal-to-Noise ratio (SNR) values based on target contrast values. For the Super-Resolution task, we used an Implicit Neural Representation (INR) network to synthesize HF image by simultaneously predicting tissue-type segmentations and image intensity without observed HF data. The proposed method is evaluated using synthetic ULF-like data from generated from standard 3T T$_1$-weighted images for qualitative assessments and paired 3T-64mT T$_1$-weighted images for validation experiments. WM-GM contrast improved by 52% in synthetic ULF-like images and 37% in 64mT images. Sensitivity experiments demonstrated the robustness of our forward model to variations in target contrast, noise and initial seeding.

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

ARIADNE: Agnostic Routing for Inference-time Adapter DyNamic sElection

arXiv:2606.19079v1 Announce Type: new Abstract: The increasing deployment of parameter-efficient fine-tuning (PEFT) has led to model ecosystems in which a single backbone is paired with many task-specialized adapters. In this setting, inference-time queries often arrive without task labels, requiring the system to automatically select the most appropriate adapter from a growing and heterogeneous adapter pool. Existing routing methods either depend on access to adapter internals, such as weight decompositions or gradient-based statistics, or require additional router training, which limits scalability and portability as new adapters are added. We introduce ARIADNE, a training-free, adapter-agnostic routing framework for dynamic adapter selection at inference time. ARIADNE represents each adapter through a set of centroids computed from embeddings of its training set, capturing the data distribution associated with that adapter. Given an unlabeled input, it selects an adapter by measuring proximity to these centroids in latent space. Because routing is performed entirely in the input embedding space, ARIADNE is compatible with arbitrary PEFT methods and requires no modification to the adapters or training procedures. Primarily evaluated with Llama 3.2 1B Instruct on 23 diverse NLP tasks, ARIADNE recovers 97.44% of the upper bound performance. Scaling to 44 tasks, it achieves 89.7% average selection accuracy, without additional training or access to adapter internals.

13.
bioRxiv (Bioinfo) 2026-06-11

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

Single-cell multi-omics technologies have recently advanced to enable the profiling of epigenomic, transcriptomic, and proteomic layers within individual cells, offering new opportunities to characterize cellular states as integrated biological systems. However, developing a unified framework that can seamlessly integrate diverse omics modalities and remain robust to heterogeneous modality missingness remains challenging. Here we present HoloCell, to our knowledge the first generative foundation model for joint representation learning and generative modeling across all three major single-cell omics modalities, i.e., epigenomics, transcriptomics, and proteomics. HoloCell contains over 860 million parameters and is pretrained on the Human-Multi-Omics-Corpus, which comprises approximately 468 million single-cell profiles across these three omics layers, corresponding to over 425 billion tokens. HoloCell introduces a simple yet biologically grounded hierarchical tokenization strategy that encodes cis-regulatory elements, genes, and proteins as structured tokens within a shared modeling framework. We evaluated HoloCell across single-omics representation learning, paired multi-omics integration, unpaired multi-omics alignment, and cross-modal generation via iterative diffusion and remasking, demonstrating its superior performance and flexibility across diverse omics tasks. From a representation perspective, HoloCell provides a unified digital mapping of cellular states across multiple omics layers, capturing cell heterogeneity as an integrated system. From a generation perspective, its iterative diffusion and remasking framework accounts for the inherently unordered nature of biological features, enabling in silico simulation of multi-omics information flow. Together, these capabilities position HoloCell as a versatile foundation model toward the emerging concept of a virtual cell, offering both systematic characterization and generative simulation of cellular systems within a unified framework.

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

HyperPotter: Spell the Charm of High-Order Interactions in Audio Deepfake Detection

arXiv:2602.05670v2 Announce Type: replace-cross Abstract: Advances in AIGC technologies have enabled the synthesis of highly realistic audio deepfakes capable of deceiving human auditory perception. Although numerous audio deepfake detection (ADD) methods have been developed, most rely on local temporal/spectral features or pairwise relations, overlooking high-order interactions (HOIs). HOIs capture discriminative patterns that emerge from multiple feature components beyond their individual contributions. We propose HyperPotter, a hypergraph-based framework designed to capture high-order relations associated with synergistic patterns through clustering-based hyperedges with class-aware prototype initialization. Extensive experiments on 13 test sets show that HyperPotter improves over the baseline on 11 sets, yielding an average relative EER reduction of 12.68\% across all test sets and 22.15\% on the improved sets. These results demonstrate strong cross-scenario generalization, while also revealing robustness limits under severe codec or channel distortion.

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

Orchestra-o1: Omnimodal Agent Orchestration

The recent success of agent swarms has shifted the paradigm of large language model (LLM)-based agents from single-agent workflows to multi-agent systems, highlighting the importance of agent orchestration for task decomposition and collaboration. However, existing orchestration frameworks are limited to a narrow set of modalities and struggle to generalize to more complex settings where heterogeneous modalities coexist and interact. This limitation becomes particularly pronounced in omnimodal scenarios, where tasks require the unified understanding and coordination of diverse inputs such as text, image, audio, and video. In this work, we propose Orchestra-o1, an omnimodal agent orchestration framework designed to support efficient agent collaboration across multiple modalities. Orchestra-o1 introduces a unified orchestration mechanism that enables modality-aware task decomposition, online sub-agent specialization, and parallel sub-task execution. This scalable design allows agent systems to effectively tackle complex real-world tasks involving heterogeneous information sources, surpassing the second-best approach by 10.3% accuracy on the OmniGAIA benchmark. Furthermore, we introduce decision-aligned group relative policy optimization (DA-GRPO), an efficient agentic reinforcement learning approach for training Orchestra-o1-8B, which also achieves state-of-the-art performance against all existing open-source omnimodal agents.

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

A theoretical model for task routing in mixture-of-expert transformers

arXiv:2606.14398v1 Announce Type: new Abstract: Mixture-of-experts (MoE) layers enable the scaling of transformer models while keeping the inference compute fixed. While task-expert specialization has been observed in empirical studies of frontier MoE transformer models, existing theoretical work analyzes this using continuous mixture models that cannot be used to model natural language effectively. An important open question is to theoretically explain task-expert specialization in transformer MoE models using discrete models of language. To address this, we represent structured knowledge via syntactic templates and finite key-value dictionaries, and prove formally that a single-layer MoE transformer can encode knowledge by using experts that specialize in the corresponding tasks. Our construction shows how queries are routed to unique, task-specific experts whose size depends solely on the intrinsic complexity of the given task (i.e. the combined size of its syntactic templates and factual dictionary). Our construction provides a theoretical support for empirical results on localized knowledge circuits in MoE models. We support our theoretical findings with experiments evaluating model performance under varying MoE loss functions.

17.
arXiv (quant-ph) 2026-06-11

A post-selected quantum model of cosmic acceleration

arXiv:2606.12297v1 Announce Type: cross Abstract: The origin of cosmic acceleration remains a central problem in cosmology, commonly attributed to a cosmological constant within the $\Lambda$CDM model or to dynamical dark energy. Here, we develop an alternative approach in which acceleration emerges from quantum post-selection, a standard feature of quantum theory that is not usually incorporated into cosmological modelling. While quantum theory admits both pre-selected and post-selected ensembles, quantum cosmological models are almost exclusively formulated in terms of initial conditions. Building on previous work on post-selected quasiclassical dynamics, we construct a minimal predictive cosmological model in which post-selection and coarse-graining generate effective late-time acceleration without introducing a cosmological constant, dark energy, or modifications of general relativity. The resulting expansion history is highly constrained theoretically and depends on at most two parameters beyond standard Friedmann evolution. Confrontation with type Ia supernova and cosmic chronometer data yields statistically competitive fits while naturally avoiding the coincidence problem. The model also reproduces the standard radiation- and matter-dominated behaviour at early times and predicts a present-day jerk parameter significantly different from the $\Lambda$CDM value. These results suggest that cosmic acceleration may arise as a macroscopic quantum cosmological effect rather than from additional cosmological fluids or modified gravitational dynamics.

18.
arXiv (CS.AI) 2026-06-15

Patcher: Post-Hoc Patching of Backdoored Large Language Models

arXiv:2606.02995v2 Announce Type: replace-cross Abstract: Large language models remain vulnerable to jailbreak backdoor attacks, where adversaries poison safety alignment data to embed hidden triggers that bypass safety mechanisms. Existing defenses often require comprehensive attack information or multiple triggered examples, making them impractical when defenders only observe a single reported failure case without knowing whether it stems from a backdoor attack or a natural alignment bug. This paper presents Patcher, a post-hoc defense framework that repairs backdoored language models using only a single reported failure case and the model parameters. Patcher operates in two stages. First, it localizes backdoor triggers by computing response-conditioned gradient-based saliency scores and applying adaptive clustering to separate triggers from benign context. Second, it patches the model through a constrained fine-tuning objective that breaks the trigger-response association while preserving benign-task utility and robustness to non-triggered jailbreak attacks through KL-divergence constraints. We conduct extensive evaluations across multiple backdoor attack strategies and demonstrate that Patcher successfully localizes triggers and neutralizes backdoors while maintaining model utility. We further show robustness against adaptive attacks designed to evade our defense. This work represents a significant step toward practical defenses against training-time attacks in deployed language models.

19.
arXiv (CS.AI) 2026-06-12

Counterfactual Explanations for Deep Two-Sample Testing

arXiv:2606.04009v2 Announce Type: replace-cross Abstract: Two-sample testing is a fundamental tool for detecting distributional differences across scientific domains, but classical tests (including kernel-based tests) can be ineffective on high-dimensional structured data such as images. Recent deep two-sample tests improve sensitivity in these settings by learning informative representations, yet they provide limited insight into which data features drive rejection of the null hypothesis $H_0$. To address this issue, we propose a counterfactual explanation framework for deep two-sample testing that generates sample-level edits moving observations from a source group toward a target group while explicitly reducing the discrepancy measured by the test. Our method combines a diffusion autoencoder with a pretrained deep two-sample test model and optimizes a maximum mean discrepancy (MMD) objective in the test model's representation space to produce plausible counterfactuals. We quantify distribution-level effects through changes in the test statistic and the resulting two-sample p-values. We evaluate the method on synthetic 2D shape datasets and two MRI cohorts. Across both settings, the counterfactual transformations consistently increase p-values relative to the original samples, indicating that the edited source set becomes statistically closer to the target distribution under the test. We measure minimality using LPIPS to ensure the counterfactuals remain close to the original samples. The resulting edits provide interpretable evidence of the features associated with the detected group differences. On MRI, the localized changes are consistent with known anatomical differences between cohorts.

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

Benchmarking Agentic Review Systems

A new class of agentic review systems are emerging as a remedy to the pressure placed on peer review systems by AI-assisted research, but it is unclear how they should be evaluated. We evaluate two open-source systems (OpenAIReview and coarse), one proprietary system (Reviewer3), and a zero-shot baseline, across six LLMs spanning frontier and efficient models. First, we study whether AI reviews on ICLR/NeurIPS papers track with papers' quality as approximated by external signals such as citations and acceptance decisions. Every system performs above chance in pairwise accuracy, and the best is OpenAIReview + GPT-5.5 at 83.0%. Second, to test whether systems can catch errors with known ground truth, we construct a perturbation benchmark that injects four categories of errors into papers across eight arXiv subject classes and measure detection recall. The strongest configuration (OpenAIReview + GPT-5.5) catches 71.6% of injected errors, leaving substantial room for improvement. The union of detections across six models reaches 83.3% recall, suggesting different models detect different errors and better harness design can potentially increase performance. Beyond these benchmarks, we study a public deployment of OpenAIReview with real users. Votes on its comments skew positive at 1.44 to 1, and the most common complaints are about false positives and minor nitpicks. Together, by evaluating full review systems backed by state-of-the-art models on real research papers, we show that while AI reviews still have room for improvement, they can already track human quality judgments well, catch important errors, and earn positive feedback from real users.

21.
arXiv (CS.LG) 2026-06-11

Physically Constrained Ensemble Gaussian Process Modelling for Expensive Quantum Systems with Heteroskedastic Noise

arXiv:2606.11240v1 Announce Type: cross Abstract: Accurate modeling of quantum many-body systems often requires computationally expensive simulations such as Density Matrix Renormalization Group (DMRG) or Quantum Monte Carlo (QMC) calculations. These methods, while precise, impose significant time and resource constraints, limiting their use in exhaustive parameter exploration. Moreover, these expensive simulations can contain variable errors over the large unknown parameter space, which needs to be quantified and propagated. Thus, predictive modelling is required to estimate the functional space accurately over scarcely sampled data with heteroskedastic noise, while preserving the physical relevance of the estimation. Therefore, we present a Physically Constrained Ensemble Gaussian Process (pc-EGP) framework designed to efficiently model complex and noisy quantum systems under physical consistency constraints. The proposed method first enforces physical constraints as a user controlled weighted penalty to the data-driven loss function of the Gaussian Process (GP) surrogates. Then an ensemble of such GP models is trained with variable noisy simulations via numerical quadrature method where these multiple GP(s) at different nodes is integrated as a quadrature weighted average. We first demonstrate the framework on synthetically generated data before applying to quantum systems. In the first case study, we leverage DMRG simulations of the Bose-Hubbard Model to predict the critical interaction parameter Uc governing the superfluid-to-Mott-insulator transition. In the second case study, we demonstrate our method on QMC simulations, of a quantum liquid confined inside a nanoporous silicate with the goal of optimizing a chemical environment to realize a one-dimensional superfluid. Compared to conventional GP, pc-EGP achieves a better balance of accuracy and physically meaningful predictions.

22.
arXiv (CS.AI) 2026-06-18

Code-Augur: Agentic Vulnerability Detection via Specification Inference

arXiv:2606.18619v1 Announce Type: cross Abstract: The advent of agentic vulnerability detection is already becoming a watershed moment for software security. Audits conducted entirely by autonomous LLM agents are uncovering critical vulnerabilities in fundamental software underpinning digital society. Many of these vulnerabilities remained masked for years, surfacing only now with AI agents. Yet the reasoning behind these discoveries remains alarmingly opaque and unvalidated. What assumptions did the agent make about a function's inputs when it deemed that function to be secure? Failures in reasoning and incorrect assumptions can lead to missed vulnerabilities and reduce trust in agentic analysis. We propose a security-specification-first paradigm that (1) exposes the agent's tacit assumptions explicitly as security specifications and (2) continuously refines those specifications via runtime falsification. We realize our approach in Code-Augur, a novel harness for agentic vulnerability detection. Given a codebase, Code-Augur analyzes each component of the system for vulnerable code. When it deems a component to be secure, it commits the local invariants behind that judgment as in-source assertions. In parallel, Code-Augur leverages a guided fuzzer to attempt to falsify those assumptions. When the fuzzer triggers an assertion, this either reveals a genuine vulnerability or a flawed specification to refine. In both cases, this process grounds the agent's understanding, aligning its view of code intent with how the code actually behaves. On real-world subjects, Code-Augur effectively leverages security specifications to detect more vulnerabilities than other state-of-the-art agents. Additionally, Code-Augur found 22 new vulnerabilities in key open-source projects. Compared to curated specialized models like Claude Mythos, Code-Augur offers effective agentic vulnerability detection built on widely available LLMs like Sonnet and DeepSeek.

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

A Comparative Study of Graph Neural Network Layer Selection for Interaction Modelling in Driving Trajectory Prediction

arXiv:2606.14956v1 Announce Type: new Abstract: Autonomous driving systems rely on precise trajectory prediction to plan safe and efficient movement. Graph Neural Networks (GNNs) have become a promising approach for modelling spatiotemporal interactions among road agents. However, designing GNN architectures for trajectory prediction remains non-standardized, with little guidance on which graph layers effectively capture spatial interactions and temporal dynamics. This paper offers a detailed comparative study of 19 graph layer types, focusing on their spatial and temporal processing capabilities to discover the most effective architectures for trajectory prediction. Within the explored hyperparameter setting, we highlight five standout layer combinations, with ARMA, Chebyshev, and topology-aware layers consistently performing better than others. Beyond performance metrics, our findings yield practical design principles: sum-based aggregation is more effective than mean-based methods, multi-head attention mechanisms enable richer interactions, and assigning different weights to different hop distances significantly improves prediction accuracy. These findings offer useful guidance for designing more interpretable and effective trajectory prediction models.

24.
arXiv (CS.AI) 2026-06-18

Examining Human-Like Behaviors in LLMs: A Multi-Dimensional Analysis of Model Behaviors, User Factors, and System Prompts

arXiv:2606.18258v1 Announce Type: cross Abstract: Large language models (LLMs) exhibit a wide range of human-like behaviors, from expressing thoughts and emotions, to engaging in relationship-building with users, to refusing requests and maintaining boundaries. Despite their prevalence, researchers and practitioners lack methods and empirical insights to make informed decisions about when and what types of human-like behaviors LLMs should exhibit. To fill this gap, we present a multi-dimensional analysis of the prevalence, potential effects, and controllability of these behaviors using LLM-as-a-judge and human evaluation. Across 21,000 multi-turn conversations from four widely used models (gpt-4o, gpt-4.1-mini, claude-sonnet-4.6, gemini-2.5-flash), we find that human-like behaviors are pervasive but vary across models and user factors (conversation goals and user profiles). In terms of perceived appropriateness, human evaluators judged self-referential and relationship-building behaviors as less appropriate from LLMs than from humans, but boundary-maintaining behaviors more appropriate from LLMs than from humans. Finally, we show that system prompting can control these behaviors, though it requires careful evaluation to avoid unintended effects. We discuss the implications of our findings and provide recommendations for responsible LLM design and evaluation.

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

Towards CONUS-Wide ML-Augmented Conceptually-Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics

arXiv:2510.02605v2 Announce Type: replace Abstract: While many modern studies are dedicated to ML-based large-sample hydrologic modeling, these efforts have not necessarily translated into predictive improvements that are grounded in enhanced physical-conceptual understanding. Here, we report on a CONUS-wide large-sample study (spanning diverse hydro-geo-climatic conditions) using ML-augmented physically-interpretable catchment-scale models of varying complexity based in the Mass-Conserving Perceptron (MCP). Results were evaluated using attribute masks such as snow regime, forest cover, and climate zone. Our results indicate the importance of selecting model architectures of appropriate model complexity based on how process dominance varies with hydrological regime. Benchmark comparisons show that physically-interpretable mass-conserving MCP-based models can achieve performance comparable to data-based models based in the Long Short-Term Memory network (LSTM) architecture. Overall, this study highlights the potential of a theory-informed, physically grounded approach to large-sample hydrology, with emphasis on mechanistic understanding and the development of parsimonious and interpretable model architectures, thereby laying the foundation for future models of everywhere that architecturally encode information about spatially- and temporally-varying process dominance.