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01.
arXiv (CS.AI) 2026-06-16

Agent Economics: An Entropy-Controlled Pluralistic Alignment Framework for Preventing Artificial Hivemind in Autonomous Agents

Authors:

arXiv:2606.09039v2 Announce Type: replace Abstract: This study proposes the Behavioral Protocol Framework (BPF), an entropy-controlled pluralistic alignment framework designed to address two critical challenges in autonomous agent economies: the hivemind effect arising from excessive strategic convergence among agents and the lack of transparency in autonomous decision-making processes. The proposed BPF consists of three core modules: Mentalizing-based Social Intelligence (MbSI) grounded in Theory of Mind (ToM), Pluralistic Alignment (PA), and a Verifiable Execution Kernel (VEK). These modules are organically integrated within a closed-loop architecture that governs the entire lifecycle of agent behavior, from decision-making and execution to verification and feedback. To evaluate the proposed framework, a simulation environment implemented in Python and a Streamlit-based user interface will be developed. Through empirical experimentation, the study aims to examine whether the entropy-control mechanism of the PA module can effectively preserve strategic diversity among agents and mitigate collective convergence, while the VEK module provides a comprehensive and transparent audit trail of the decision-making process. The anticipated results are expected to demonstrate that the proposed framework can simultaneously enhance the stability, efficiency, and trustworthiness of autonomous agent economies. Consequently, this research offers a practical approach for developing robust, transparent, and accountable agent-native economic systems.

02.
arXiv (math.PR) 2026-06-17

How long does it take to train an Elephant Random Walk

Authors:

arXiv:2509.15049v2 Announce Type: replace Abstract: We study how conditioning on the first $k$ steps, which we think of as training, affects the long-term behavior of the Elephant Random Walk. When the elephant is conditioned to be at position $k$ at time $k$, the first return time to the origin scales as $k^{(4-4p)/(3-4p)}$ in the diffusive regime, and grows exponentially in the critical regime. We loosely interpret this as a measurement of the rate at which the elephant forgets its training.

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

Adaptive Kernel Density Estimation with Pre-training

arXiv:2605.13092v2 Announce Type: replace-cross Abstract: Density estimation in high-dimensional settings is an important and challenging statistical problem.Traditional methods based on kernel smoothing are inefficient in high dimensions due to the difficulties in specifying appropriate location-adaptive kernels. In this work, we introduce pre-training, a key idea behind many cutting-edge AI technologies, to the context of non-parametric density estimation. By establishing a pre-trained neural network that can recommend an appropriate location-adaptive kernel for each sample point, efficient density estimation with adaptive kernels is achieved in high dimensions. A wide range of numerical experiments show that this strategy is highly effective for improving density-estimation accuracy, when the target distribution is close to the distribution family for pre-training. When the target distribution is substantially different from the pre-training distribution family, the benefit from the proposed pre-training strategy may be diluted, but can be reactivated by an additional fine-tuning procedure.

05.
arXiv (quant-ph) 2026-06-15

No classical particle limit for massless quanta

arXiv:2606.14632v1 Announce Type: new Abstract: We investigate whether relativistic massless classical particles may emerge as the classical limit of massless quanta. To address this question independently of any specific dynamics, environment, or pointer basis, we develop an axiomatic and purely kinematical framework for the coarse-graining approach. In this formulation, a candidate classical phase space is taken as the outcome space of a POVM subject only to minimal classicality and covariance under the relevant spacetime symmetry group. Applying this framework to the Poincaré group, we prove a no-go theorem for massless particles: the covariance requirement is incompatible with the operational conditions for classicality. The theorem leaves open field-like limits of massless quanta, for example the emergence of electromagnetic or gravitational fields, while ruling out classical massless particles, such as classical photons or gravitons.

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

Normative Robustness as a Frontier for Non-Verifiable Reasoning in LLMs

arXiv:2606.12731v1 Announce Type: new Abstract: As LLMs increasingly serve in advisory and deliberative roles, users rely on them for non-verifiable reasoning in domains lacking objective ground truths. However, traditional evaluations of LLM reasoning focus almost exclusively on fact-based domains, such as mathematics and science, leaving uncertainty over whether and to what degree models can handle ambiguous, subjective, or value-laden problems over time. To address this concern, we propose moral reasoning as a paradigmatic subdomain of non-verifiable reasoning. We define moral robustness as a model's capacity to exhibit sound moral reasoning across time and contexts, and we introduce a scalable, adversarial, multi-turn evaluation framework to empirically measure this capability. We simulate 48,000 user-agent moral deliberations across four frontier LLMs, varying premise relevance, premise order, conversation duration, and the user's stated moral view. We find that models successfully ignore morally-irrelevant distractors, but shift their reasoning by up to 6.5%, on average, towards the user's stated preferred moral view, and varying their reasoning depending on factors such as order (altering moral judgments by order in 13-22% of the cases) and duration (altering moral judgments between single-turn and multi-turn in 10-24% of the cases). Our analysis indicates that models tailor not just their final verdicts but their underlying justifications to align with a user's moral viewpoint - a failure mode we characterize as moral deliberative sycophancy.

07.
arXiv (quant-ph) 2026-06-15

Efficient and simple Gibbs state preparation of the 2D toric code via duality to classical Ising chains

arXiv:2508.00126v2 Announce Type: replace Abstract: We introduce the notion of polynomial-depth duality transformations, which relates two sets of operator algebras through a conjugation by a poly-depth quantum circuit, and make use of this to construct efficient Gibbs samplers for a variety of interesting quantum Hamiltonians as they are poly-depth dual to classical Hamiltonians. This is for example the case for the 2D toric code, which is demonstrated to be poly-depth dual to two decoupled classical Ising spin chains for any system size, and we give evidence that such dualities hold for a wide class of stabilizer Hamiltonians. Additionally, we extend the above notion of duality to Lindbladians in order to show that mixing times and other quantities such as the spectral gap or the modified logarithmic Sobolev inequality are preserved under duality.

08.
arXiv (CS.CV) 2026-06-11

PT-WNO: Point Transformer with Wavelet Neural Operator for 3D Point Cloud Semantic Segmentation

Point cloud semantic segmentation requires architectures that capture both fine-grained local geometry and broad global scene structure. Transformer-based networks have demonstrated strong performance by focusing on detailed local feature aggregation; however, global context is conveyed primarily through skip connections across encoder-decoder stages, which we argue is insufficient for full scene understanding. We hypothesize that augmenting skip connections with a learnable global feature extraction module allows the network to acquire scene-level knowledge before descending into local detail, leading to richer and more contextually grounded representations. To this end, we propose Point Transformer with Wavelet Neural Operato (PT-WNO), which integrates a shared Wavelet Neural Operator (WNO) branch alongside the skip connections of a point cloud transformer backbone. At each encoder-decoder transition, point features are projected onto a dense 3D volumetric grid where the WNO captures multi-scale global spectral context through learnable wavelet decomposition and reconstruction. These global features are fused back into the network via lightweight adapters, complementing rather than replacing the existing skip connections. Experiments on four large-scale 3D point cloud benchmarks demonstrate the effectiveness of PT-WNO. On S3DIS (Area 5), PT-WNO achieves 71.59% mIoU, outperforming the Point Transformer v3 (PTv3) baseline by +1.03 points. On DALES it achieves 81.05% mIoU (+1.47 over the baseline). On ScanNet~v2, PT-WNO obtains 76.19% mIoU, remaining competitive with the baseline (76.36%).

09.
arXiv (CS.LG) 2026-06-12

Towards One-for-All Anomaly Detection for Tabular Data

arXiv:2603.14407v2 Announce Type: replace Abstract: Tabular anomaly detection (TAD) aims to identify samples that deviate from the majority in tabular data and is critical in many real-world applications. However, existing methods follow a ``one model for one dataset (OFO)'' paradigm, which relies on dataset-specific training and thus incurs high computational cost and yields limited generalization to unseen domains. To address these limitations, we propose OFA-TAD, a generalist one-for-all (OFA) TAD framework that only requires one-time training on multiple source datasets and can generalize to unseen datasets from diverse domains on-the-fly. To realize one-for-all tabular anomaly detection, OFA-TAD extracts neighbor-distance patterns as transferable cues, and introduces multi-view neighbor-distance representations from multiple transformation-induced metric spaces to mitigate the transformation sensitivity of distance profiles. To adaptively combine multi-view distance evidence, a Mixture-of-Experts (MoE) scoring network is employed for view-specific anomaly scoring and entropy-regularized gated fusion, with a multi-strategy anomaly synthesis mechanism to support training under the one-class constraint. Extensive experiments on 34 datasets from 14 domains demonstrate that OFA-TAD achieves superior anomaly detection performance and strong cross-domain generalizability under the strict OFA setting. The source code is available at https://github.com/Shiy-Li/OFA-TAD.

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

Beyond Defensive Reporting: Machine Learning for Active Anti-Money Laundering Control in Insurance

arXiv:2606.16663v1 Announce Type: new Abstract: Money laundering through insurance claims poses a threat to insurers both through fraudulent payouts and reputational and regulatory risk. Despite this, little research has examined how such laundering can be prevented. This paper examines whether machine learning can help insurers flag suspicious claims before payout, shifting the focus from passive reporting to active prevention. Using production data from a major Norwegian insurer, we train gradient-boosted decision tree models to detect claims later reported to authorities for suspected money laundering. Because fraud and laundering may share behavioural patterns, we also examine whether insurance fraud labels can serve as an auxiliary training signal. We compare different learning setups using the Budget-Weighted Capture Rate, a metric introduced in this paper to measure how many laundering cases are captured when only a small share of claims can be manually reviewed. The results show that incorporating fraud-related investigation labels substantially improves laundering detection. The best-performing model captures nearly two-thirds of laundering cases within the top-ranked 2 to 6 percent of claims selected for investigation. To our knowledge, this is the first empirical study of machine learning for money laundering detection in insurance claims.

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

BLUEmed: Retrieval-Augmented Multi-Agent Debate for Clinical Error Detection

Terminology substitution errors in clinical notes, where one medical term is replaced by a linguistically valid but clinically different term, pose a persistent challenge for automated error detection in healthcare. We introduce BLUEmed, a multi-agent debate framework augmented with hybrid Retrieval-Augmented Generation (RAG) that combines evidence-grounded reasoning with multi-perspective verification for clinical error detection. BLUEmed decomposes each clinical note into focused sub-queries, retrieves source-partitioned evidence through dense, sparse, and online retrieval, and assigns two domain expert agents distinct knowledge bases to produce independent analyses; when the experts disagree, a structured counter-argumentation round and cross-source adjudication resolve the conflict, followed by a cascading safety layer that filters common false-positive patterns. We evaluate BLUEmed on a clinical terminology substitution detection benchmark under both zero-shot and few-shot prompting with multiple backbone models spanning proprietary and open-source families. Experimental results show that BLUEmed achieves the best accuracy (69.13%), ROC-AUC (74.45%), and PR-AUC (72.44%) under few-shot prompting, outperforming both single-agent RAG and debate-only baselines. Further analyses across six backbone models and two prompting strategies confirm that retrieval augmentation and structured debate are complementary, and that the framework benefits most from models with sufficient instruction-following and clinical language understanding.

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

Time-multiplexed layer reuse for physical neural networks

arXiv:2511.00044v3 Announce Type: replace Abstract: Physical neural networks (PNNs) are promising candidates for next-generation computing, but existing demonstrations remain several orders of magnitude smaller than modern digital neural networks, whose recent advances have been driven by rapid growth in trainable parameters. This situation resembles the constraints of early digital neural networks, which led to ideas around parameter reuse. We investigate what similarly efficient hardware architectures may look like, focusing specifically on the common bottleneck of slow re-adjustment of the weights in PNNs. We propose the Time-Indexed Deep Alternating Layers Network (TIDAL-Net), which occupies an intermediate regime between recurrent and deep neural networks, specifically aimed at the scales and restrictions of common PNN prototypes. TIDAL-Net leverages the timescale separation found in many PNNs between fast forward dynamics and slowly trainable weights and biases, using layer-by-layer time multiplexing to increase effective depth while limiting implementation cost. Numerical experiments on image classification and natural language processing tasks show that TIDAL-Net improves performance with only minor modifications to conventional PNNs.

13.
medRxiv (Medicine) 2026-06-15

A controlled human infection model for symptomatic pertussis in North America using the pertactin-producing clinical isolate D420

Background Despite widespread vaccination, pertussis remains a poorly controlled disease globally and results in substantial annual morbidity and mortality, particularly in young children. Controlled human infection models (CHIMs) using the causative agent Bordetella pertussis are promising systems to enable the study of pertussis disease pathogenesis and immunology and to rapidly assess vaccines and therapeutics. While a pertussis CHIM that produces asymptomatic infection has been established in Europe, the development of a CHIM that leads to symptomatic illness would be advantageous for evaluating vaccine efficacy against both infection and disease. Methods Healthy participants 18-40 years of age were inoculated intranasally with one of eight doses (ranging from 104 to 108 colony forming units (CFU)) of the pertactin-producing B. pertussis isolate D420 at the challenge facility within the Canadian Center for Vaccinology (Nova Scotia, Canada). The study occurred in two stages. In stage one, the B. pertussis dose was escalated in cohort groups of five to six participants until reaching an endpoint where 70-90% of participants exhibited mild (non-severe, Grade 1 or 2) symptomatic infection, defined as the Human Infectious Dose 70-90 (HID70-90). In stage two, additional challenges were conducted for doses below, at, and above the identified HID70-90 to characterize the emerging pertussis model. For all challenge doses, participants were closely monitored during an inpatient stay of up to 24 days and post-discharge for laboratory-confirmed infection, pertussis symptoms, safety, and IgG antibody responses to four B. pertussis antigens including pertussis toxin, filamentous hemagglutinin, fimbriae, and pertactin. All participants received a five-day course of azithromycin, where timing of initiation depended on B. pertussis testing and symptoms. The study was conducted between July 4, 2022 and March 19, 2025. Findings Seventy-five participants were inoculated with one of the eight B. pertussis D420 challenge doses and completed the inpatient stay. From the stage-one dose escalation, we found that 107 CFU of B. pertussis D420 was the lowest dose that achieved the HID70-90, where 9 of 12 participants (75.0%) exhibited mild symptomatic infection. Following stage-two challenges, 16 of 22 total participants at 107 CFU (72.7%) developed mild symptomatic infection, thus verifying the HID70-90. The symptomatic infection rate below the HID70-90 at 5x106 CFU of D420 was 20.0% and above the HID70-90 at 5x107 and 108 CFU were 58.3% and 55.6%, respectively. Symptoms with elevated frequency for symptomatic infection (relative to background symptoms in non-infected) included nasal congestion, runny nose, fatigue, malaise, and cough. At the HID70-90, 50% of symptomatic infections included cough. Serological analyses of the four highest (stage-two) challenge doses (5x106, 107, 5x107, 108 CFU) revealed that antibody titres increased over time post-challenge. Seroconversion for at least one of the four studied antibodies was nearly twice as common for symptomatic (70.0%) than asymptomatic (35.7%) infection and was absent (0%) for non-infected. All infections were cleared following azithromycin treatment (100%) and there were no study-related serious adverse events. Interpretation A safe and reproducible symptomatic pertussis CHIM was achieved, providing a model for research on pertussis disease pathogenesis and immunology and for assessing vaccines and therapeutics. (Clinicaltrials.gov, NCT05136599).

14.
arXiv (CS.CL) 2026-06-16

Multimodal Evaluator Preference Collapse: Cross-Modal Contagion in Self-Evolving Agents

Authors:

When AI agents use language models to evaluate their own outputs in a feedback loop, systematic biases emerge. We show that Evaluator Preference Collapse (EPC) is dramatically amplified in multimodal settings. Using GPT-4o to evaluate DeepSeek-chat across text and visual tasks, we find that a single strategy (step_by_step) absorbs 48.4% of all weight – 3.2x the collapse observed in text-only self-evaluation – while three visual-domain strategies receive only 9.1% combined weight. We then demonstrate a novel phenomenon we term cross-modal contagion: evaluator preferences acquired on one modality transfer to and corrupt strategy selection on another. Through a four-phase isolation training paradigm, we measure contagion coefficients and document strategy inversion – the optimal strategy for a modality reverses after cross-modal exposure. A Phase 3 statistical validation across four evaluator configurations (N=53 total independent repetitions, 15,592 API calls) reveals a clear hierarchy: cross-model evaluation (GPT-4o, N=8) produces strong but symmetric bidirectional contagion (mean gamma_{T->V}=1.176, gamma_{V->T}=1.089, Delta=-0.088, p=0.575, Cohen's d=0.29); high round counts (DashScope, 50 rounds) cause collapse to single-strategy dominance (70% zero contagion); and self-evaluation provides near-complete immunity – 97% of runs (N=30, DeepSeek-chat) yield exactly zero contagion (mean gamma=0.033, 95% CI [-0.031, 0.010], p=0.642, d=0.07). No evaluator condition shows statistically significant directional asymmetry. We introduce the contagion matrix indexed by evaluator identity, release the MM-EPC experimental framework, and identify cross-model evaluator architecture as the primary risk factor for preference contagion.

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

UniTemp: Unlocking Video Generation in Any Temporal Order via Bidirectional Distillation

Autoregressive video diffusion models have emerged as a promising approach for long video generation, achieving strong performance in streaming settings. However, existing methods are restricted to forward temporal generation, whereas practical video creation often requires flexible generation order, e.g., conditioning on future context to extend backward, or on both past and future context for inbetween generation. We bridge this gap by training an autoregressive model that supports generation in arbitrary temporal directions. A key technical challenge arises from the Causal 3D VAE widely used in video diffusion models, which encodes latents strictly conditioned on past context. While suited for forward generation, this causal structure causes inter-block discontinuities when generation proceeds backward. To address this, we introduce blockwise anchor latents, a set of auxiliary latents that restore the missing past context at block boundaries during backward generation. Built on this design, we propose UniTemp, a bidirectional distillation framework that trains a single autoregressive student model for any-direction video generation. At inference time, UniTemp conditions on arbitrary past and/or future frames, improving controllability for both bidirectional and inbetween generation. Experiments show that UniTemp maintains competitive performance on short and long video generation compared to forward-only methods, while enabling diverse workflows such as bidirectional video extension, inbetween generation, looping video generation, scene transition, and visual story generation. Project website: https://lzhangbj.github.io/projects/unitemp/

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

Fi-Gaussian: Frequency-Aware Implicit Gaussian Splatting for Single Image Dehazing

Single image dehazing continues to be hindered by the loss of high-frequency details and the difficulty of accurate physical scattering modeling. To address these issues, we propose Fi-Gaussian, a frequency-aware implicit Gaussian splatting network for single image dehazing. Unlike explicit rendering methods that rely on 3D point clouds, our method employs implicit Gaussian splatting to adaptively model the underlying distribution of clear images as a continuous representation in 2D feature space. The core of the network is a frequency-aware implicit Gaussian splatting module, which decouples low-frequency structural information and high-frequency texture information in the frequency domain and then performs adaptive Gaussian aggregation with complex-valued weights to recover fine details. In addition, a physics-driven scattering renormalization mechanism is introduced to estimate the transmission map and atmospheric light under the guidance of implicit Gaussian priors. Extensive experiments on multiple benchmark datasets demonstrate that Fi-Gaussian achieves state-of-the-art quantitative performance and produces visually superior dehazed results, validating the effectiveness of implicit Gaussian splatting for low-level vision tasks.

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

DriveReward: A Comprehensive Dataset and Generative Vision-Language Reward Model for Autonomous Driving

Reward models play a pivotal role in reinforcement learning (RL) and multi-modal trajectory selection for autonomous driving. However, acquiring such rewards typically relies on hand-crafted rule-based objectives or perception ground truth, which hinders generalization for data-scaling. While Vision-Language Models (VLMs) have demonstrated feasibility as reward models in other domains, their effectiveness in driving tasks remains underexplored. In this work, we bridge this gap by (1) introducing DriveReward, a reasoning trajectory evaluation dataset rigorously labeled via temporally-grounded visual guidance, and augmented with counterfactual driving behaviors., (2) alongside a specialized Vision-Language Reward Model. To address the scarcity of failure cases in conventional datasets, we propose a counterfactual data annotation scheme to construct cases encompassing diverse driving styles and erroneous behaviors. Evaluations on our proposed benchmark reveal that even leading open-source and proprietary VLMs fail to excel across all tasks, highlighting significant room for improvement in existing models. Building on these findings, we subsequently tailor a specialized 1B reward model that outperforms larger VLMs on task-specific reward alignment. Finally, we validate our reward model's effectiveness by integrating it into RL finetuning and multi-modal trajectory scoring across multiple baselines, achieving performance comparable to rule-based reward calculations in both open-loop and closed-loop evaluation.

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

DICE: Diffusion Large Language Models Excel at Generating CUDA Kernels

Diffusion large language models (dLLMs) have emerged as a compelling alternative to autoregressive (AR) LLMs, owing to their capacity for parallel token generation. This paradigm is particularly well-suited for code generation, where holistic structural planning and non-sequential refinement are critical. Despite this potential, tailoring dLLMs for CUDA kernel generation remains challenging, obstructed not only by the high specialization but also by the severe lack of high-quality training data. To address these challenges, we construct CuKe, an augmented supervised fine-tuning dataset optimized for high-performance CUDA kernels. On top of it, we propose a bi-phase curated reinforcement learning (BiC-RL) framework consisting of a CUDA kernel infilling stage and an end-to-end CUDA kernel generation stage. Leveraging this training framework, we introduce DICE, a series of diffusion large language models designed for CUDA kernel generation, spanning three parameter scales, 1.7B, 4B, and 8B. Extensive experiments on KernelBench demonstrate that DICE significantly outperforms both autoregressive and diffusion LLMs of comparable scale, establishing a new state-of-the-art for CUDA kernel generation.

19.
arXiv (CS.AI) 2026-06-15

Capability Minimization as a Safety Primitive: Risk-Aware Causal Gating for Least-Privilege LLM Agents

arXiv:2606.13884v1 Announce Type: new Abstract: Modern decision systems increasingly rely on learned components whose outputs may be confident yet wrong, exposing downstream actions to costly errors. We introduce Risk-Aware Causal Gating (RACG), a framework that decides whether to act on, defer, or abstain from a model's prediction by combining causal effect estimation with calibrated risk control. RACG models the causal pathway from candidate actions to outcomes and gates each decision according to an estimated counterfactual risk rather than raw predictive confidence. To make gating reliable, we derive distribution-free bounds on the probability of acting under high-risk conditions and show how these bounds translate into operating thresholds that satisfy user-specified safety constraints. We further propose an adaptive gating policy that adjusts to distribution shift by monitoring discrepancies between predicted and realized outcomes, tightening the gate when causal assumptions appear violated. Across simulated interventions and real-world decision benchmarks, RACG reduces high-cost errors substantially while preserving most of the utility of an ungated policy, and it outperforms confidence-based and selective-prediction baselines at matched abstention rates. Our results indicate that explicitly separating causal risk from predictive uncertainty yields decision systems that are both safer and more transparent, offering a principled mechanism for trustworthy automation in high-stakes settings.

20.
arXiv (CS.CV) 2026-06-18

Revealing Hidden Vulnerabilities in Autoencoders through Gradient Signal Restoration

Adversarial robustness of deep autoencoders (AEs) has received less attention than that of discriminative models, although their compressed latent representations induce ill-conditioned mappings that can amplify small input perturbations and destabilize reconstructions. Existing white-box attacks for AEs, which optimize norm-bounded adversarial perturbations to maximize reconstruction damage, often converge to suboptimal perturbations, thereby potentially overstating AE robustness. We show that this limitation is linked to vanishing adversarial loss gradients during backpropagation through ill-conditioned layers, associated with near-zero singular values in their intermediate weight matrices. To address this, we propose GRILL (Gradient Signal Restoration in Ill-Conditioned Layers), a framework designed to mitigate gradient degradation and improve the reliability of adversarial robustness evaluation in encoder-decoder architectures. GRILL is designed to mitigate adversarial gradient degradation during optimization, enabling attacks to better approximate high-distortion perturbations under fixed norm constraints. Through extensive experiments across multiple AE architectures, under both sample-specific and universal attacks, as well as standard and adaptive attack settings, we show that GRILL significantly increases attack effectiveness, thereby exposing vulnerabilities hidden by existing attack limitations. Beyond AEs, we provide preliminary evidence that modern multimodal encoder-decoder architectures exhibit similar vulnerabilities.

21.
arXiv (math.PR) 2026-06-17

Large deviation principle for friendship-biases in Galton–Watson trees

arXiv:2606.17381v1 Announce Type: new Abstract: In this paper we consider the friendship-bias of the vertices in an infinite rooted Galton–Watson tree. The friendship-bias of a vertex is the difference between the average degree of the neighbours of the vertex and the degree of the vertex itself. A vertex is said to be of type $\chi \in S$, with $S = \{-,0,+\}$, when its friendship-bias is, respectively, strictly negative, zero or strictly positive. We consider the fractions $f_l^\chi$ of vertices of type $\chi \in S$ along a random downward path up to branching depth $l \in \mathbb{N}$ and derive a large deviation principle (LDP) for the triple $(f_l^\chi)_{\chi \in S}$ as $l\to\infty$. The branching depth of a vertex counts the number of branchings that occur along the path that connects the vertex to the root of the tree. The rate in the LDP is $l$, while the rate function in the LDP is identified in terms of a variational formula minimising a relative entropy under a linear constraint. We focus on the case of binary branching, for which the rate function is already quite involved. We identify the qualitative properties of the rate function and show how it can be computed numerically. We briefly indicate how to proceed for more general branching and for vertex types along a tree consisting of a finite number of random downward paths. Our paper is the first to consider large deviations of vertex types.

22.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning

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

AGE-MIL: Anchor-Guided Evidence Learning for Patient-Level Prediction

Existing computational pathology methods predominantly operate within whole-slide image (WSI)-level multiple instance learning (MIL) paradigms, while patient-level modeling remains underexplored. In routine pathological practice, however, pathologists derive diagnostic and prognostic conclusions by integrating evidence across multiple WSIs rather than relying on any single slide. This discrepancy creates a fundamental misalignment when patient-level supervision is directly imposed on conventional MIL frameworks, often leading to unstable optimization and degraded predictive reliability. To address this issue, we propose Anchor-Guided Evidence MIL (AGE-MIL), a weakly supervised framework for patient-level prediction. AGE-MIL constructs a patient-level anchor from slide representations to capture global pathological context and guide the retrieval and integration of diagnostically relevant local patches, enabling robust patient-level modeling. Patient-level risk is further modeled as an evidence accumulation process, promoting stable optimization under weak supervision. AGE-MIL is evaluated on six clinically relevant patient-level prediction tasks from two independent cohorts. Experimental results show that the proposed framework consistently outperforms eight state-of-the-art MIL methods. Code is available at https://github.com/wodeniua/AGE-MIL.

24.
arXiv (CS.LG) 2026-06-17

A Bayesian Boolean Matrix Factorization with Application to Copy Number Analysis in Cancer

arXiv:2606.17491v1 Announce Type: cross Abstract: Binary data factorization is common, but real-valued methods ignore discreteness and yield hard-to-interpret factors. Boolean Matrix Factorization (BooMF) instead decomposes a binary matrix into two lower-rank binary matrices via logical AND and OR, expressing the data as a Boolean disjunction of interpretable patterns. In cancer genomics, BooMF can reveal coordinated feature changes that may drive tumor evolution, unlike rotational or additive decompositions. Most existing BooMF methods are heuristic, greedy, sensitive to initialization, prone to local optima, and do not support principled model selection or uncertainty quantification. We introduce Bayesian Boolean Matrix Factorization (BBMF), a fully conjugate generative model with sparsity-inducing priors. It enforces Boolean constraints, yields interpretable latent factors with coherent uncertainty quantification, and admits Gibbs sampling with closed-form full conditionals. Because cancer evolution often involves widespread, near-simultaneous chromosome-number changes (e.g., whole-genome duplication followed by instability and selection), Boolean factorizations capture these patterns more naturally than additive models. Applied to arm-level copy-number alteration data in multiple myeloma, where entries indicate presence/absence of chromosomal-arm amplifications, BBMF finds a small set of interpretable bicliques linking patient subsets to recurrently co-altered chromosomal arms, providing a compact, biologically meaningful summary of tumor heterogeneity and demonstrating BBMF's utility for uncovering discrete latent structure in complex binary data.

25.
arXiv (CS.LG) 2026-06-19

AgentArmor: A Framework, Evaluation, \& Mitigation of Coding Agent Failures

arXiv:2606.19380v1 Announce Type: cross Abstract: Software engineering and deployment are increasingly being delegated to AI coding agents. The scale of their adoption is surfacing rare, but highly destructive, failure modes. In this paper, we study these failure modes as stemming from three distinct mechanisms: underspecification, where default model behavior is unsafe; capability errors, where the safe action is available but the model does not adhere to it due to bias or capability limitations; and agent harness errors, where the model fails to execute the safe action through the harness. We evaluate these across 8 different evaluations, each inspired by real-life deployment failures, totaling 20 coding environments and 59 synthetic transcript templates. Based on this evaluation, we propose AgentArmor, an agent harness modification, to mitigate these errors. By adding an extended system prompt, a separate command classifier, a ``3 strikes'' policy, deterministic guardrails, and tools for the agent to edit its own context, we show that AgentArmor is safer across a statistically significant number of samples. Thus, we suggest concrete mitigations for current coding agents and a design philosophy for future agent harness features.