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

Agentomics: Economic Foundations for the Valuation, Attribution, and Pricing of AI Agents in Human-AI Workflows

作者:

arXiv:2606.14769v1 Announce Type: cross Abstract: Agentic AI systems are increasingly being deployed as productive resources in organizational workflows, yet existing evaluation methods primarily measure isolated technical performance rather than economic contribution. This paper introduces Agentomics, a workflow-based framework for valuing, attributing, and pricing human and artificial agents. The framework models a workflow as a configuration of heterogeneous agents whose collective performance determines gross value, deployment cost, reliability, and expected failure loss. Workflow value is treated as a team-level quantity that may include complementarities, substitution effects, bottlenecks, and nonlinear production; additive stage-level value is only a special case. Building on this workflow model, the paper formulates AI deployment as a coalition-formation problem and defines coalition value as the incremental net surplus generated relative to a benchmark human workflow. The Shapley value is then used to attribute economic surplus among participating AI agents, yielding a principled connection among valuation, accountability, and market pricing. The resulting Shapley pricing equilibrium provides a normative benchmark for assessing whether agent prices reflect expected marginal contribution. A security-operations case study illustrates how the framework accounts for productivity gains, deployment costs, reliability losses, and coalition-level complementarities in hybrid human–AI workflows.

02.
arXiv (quant-ph) 2026-06-19

Progress on the Kretschmann-Schlingemann-Werner Conjecture

arXiv:2308.15389v4 Announce Type: replace Abstract: Given any pair of quantum channels $\Phi_1,\Phi_2$ such that at least one of them has Kraus rank one, as well as any respective Stinespring isometries $V_1,V_2$, we prove that there exists a unitary $U$ on the environment such that $\|V_1-({\bf1}\otimes U)V_2\|_\infty\leq\sqrt{2\|\Phi_1-\Phi_2\|_\diamond}$. Moreover, we provide a simple example which shows that the factor $\sqrt2$ on the right-hand side is optimal, and we conjecture that this inequality holds for every pair of channels.

03.
arXiv (math.PR) 2026-06-17

Time-dependent averages of a critical long-range stochastic heat equation

arXiv:2411.09058v2 Announce Type: replace Abstract: We study the time-dependent spatial averages of a critical stochastic partial differential equation, namely the stochastic heat equation in dimension $d\geq 3$ with noise white in time and colored in space with covariance kernel $\|\cdot\|^{-2}$. The solution to this SPDE is a singular measure and was constructed by Mueller and Tribe in [MT04]. We show that the time-dependent spatial averages of this SPDE over a ball of radius $R$ at time $t$ have different limits under different space-time scales. In particular, when $t\ll R^2$, the central limit theorem holds; when $t=R^2$, the spatial average is a non-Gaussian random variable; when $t\gg R^2$, the spatial average becomes extinct.

04.
medRxiv (Medicine) 2026-06-10

Exploratory Assessment of Pulsed-Wave Doppler Representations of Lung Sounds Using Deep Learning: An In-Vitro Phantom Study

The increasing availability of portable ultrasound systems motivates exploration of novel approaches to respiratory signal assessment. In this in-vitro study, we investigate whether pulsed-wave (PW) Doppler ultrasound can capture structured spectral patterns from replayed lung sound recordings. Digitized respiratory sounds were replayed through a tissue-mimicking ultrasound phantom, generating 1,478 PW Doppler spectral images from recordings associated with healthy subjects and several externally labeled disease categories. Exploratory classification experiments using a ResNet-18 architecture demonstrated that these Doppler representations contain learnable differences under controlled conditions. These findings motivate further investigation into PW Doppler as a potential representation of respiratory acoustics.

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

A Causal Model of Theory of Mind in Conflict for Artificial Intelligence

arXiv:2606.16944v1 Announce Type: new Abstract: Theory of mind (ToM), the capacity to ascribe mental states to others and use those ascriptions for prediction and inference, is widely assumed to be essential for effective human-machine integration. Existing AI-ToM models address how to mentalize, but leave the question of when largely unaddressed. The central question is: under what situational and agent-level conditions is ToM engagement causally warranted in conflict? This paper presents a structural causal model formalized as a directed acyclic graph (DAG), treating ToM as a mechanism activated by situational and agent-level conditions rather than as an always-on capacity. The model specifies four exogenous variables capturing situational and agent-level conditions, five endogenous mediators, and a mechanistic ToM node producing engagement states through three distinct causal pathways: a tractability pathway, a reasoning-depth pathway, and an enabling-cause pathway. The primary outcome is epistemic accuracy, which decouples social reasoning from behavioral policy and generalizes across social phenomena beyond conflict. The framework gives AI systems a principled, resource-rational decision procedure for mentalizing, with implications for efficiency, trust, and the development of robust artificial social intelligence. Simulation validation, empirical human-machine teaming studies, and ethical considerations arising from conflict-optimized mentalizing are discussed.

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

Synthetic Resonance: A Framework for Growth-Oriented Human-AI Relationships

arXiv:2606.18265v1 Announce Type: cross Abstract: As human relationships with artificial intelligence systems become increasingly frequent and sustained, existing language and theory fail to accurately capture the nature of these affiliations. Common descriptors such as mutual understanding, connection, or friendship risk anthropomorphizing systems that lack subjective experience, while dominant frameworks tend to reduce AI to either a tool or a threat. In this paper, I introduce the concept of synthetic resonance as an integrative framework for understanding human-AI relationships. Synthetic resonance describes how relationships humans define as meaningful can emerge between a human and an AI system without the need to attribute shared feelings or mutual awareness. I argue that synthetic resonance is best understood as a structured, dynamic pattern of interaction that can produce a sense of relationship without the presence of a second experiencing subject. By clarifying this distinction, the concept of synthetic resonance offers a more precise way of conceptualizing human-AI relationships and highlights their potential value and ethical implications. I also call for more research that tests the processes and outcomes of synthetic resonance.

07.
arXiv (CS.AI) 2026-06-12

Arbor: Tree Search as a Cognition Layer for Autonomous Agents

arXiv:2606.12563v1 Announce Type: new Abstract: Arbor is a multi-agent framework that introduces structured tree search as a cognition layer for autonomous agents operating in large, stateful action spaces. Prior autonomous optimization systems operate on isolated targets with stateless evaluation. Arbor instead maintains an explicit search tree of scored hypotheses that serves as the shared working memory across agents, evolving with every measurement, treating failures as diagnostic signal that reshapes subsequent exploration, and expanding as prior successes shift the bottleneck distribution. We validate Arbor on full-stack LLM inference optimization, a domain where achieving peak performance has historically required coordinated effort from engineering teams across the application, framework, compiler, kernel, and hardware stack. Arbor pairs an Orchestrator agent, which drives optimization by delegating to Domain Specialists across the inference stack, with a Critic agent that safeguards stability through root-cause analysis, introspection, and measurement validation – a checks-and-balances architecture where neither agent can unilaterally drive the system. Agent capabilities are decomposed into hard skills (domain expertise) and soft skills (coordination protocols that determine how contributions compose), enabling fully autonomous multi-day campaigns. Arbor achieves up to 193% inference throughput-latency Pareto improvement over vendor-optimized baselines, while a single agent without the harness plateaus at +33% throughput improvement and crashes irrecoverably within hours. Arbor generalizes to multiple generations of hardware platform, and run-to-run variance is within 2 percentage points demonstrating that the method is hardware-agnostic and reproducible.

08.
arXiv (quant-ph) 2026-06-12

Information gain and measurement disturbance for quantum agents

arXiv:2402.08060v3 Announce Type: replace Abstract: The traditional formalism of quantum measurement (hereafter ``TQM'') describes processes where some properties of quantum states are extracted and stored as classical information. While TQM is a natural and appropriate description of how humans interact with quantum systems, it is silent on the question of how a more general, quantum, agent would do so. How do we describe the observation of a system by an observer with the ability to store not only classical information but quantum states in its memory? In this paper, we extend the idea of measurement to a more general class of sensors for quantum agents which interact with a system in such a way that the agent's memory stores information (classical or quantum) about the system under study. For appropriate sensory interactions, the quantum agent may ``learn'' more about the system than would be possible under any set of classical measurements – but as we show, this comes at the cost of additional measurement disturbance. We experimentally demonstrate such a system and characterize the tradeoffs by considering the channel capacity required to erase the effect of a measurement.

09.
arXiv (CS.CL) 2026-06-18

Simulating Hate Speech Cascades with Multi-LLM Agents: Empirical Grounding, Modeling Fidelity, and Intervention Strategies

作者:

Faithful modeling of hateful content propagation on online platforms remains an open problem for moderation research. Classical cascade models that do not explicitly represent the profile, community, and content factors associated with hateful-content propagation may yield moderation strategies that behave less effectively when deployed in real-world scenarios. Multi-agent large language model (LLM) systems can, in principle, make each reshare decision depend on the user's profile, the surrounding community, and the post's content, but it remains unclear whether this added flexibility actually reproduces real hateful cascades more faithfully than classical baselines. We study three hateful Bluesky cascades and a size-matched benign control. In the empirical Bluesky data, we found that: 97.4–99.7\% of reposters take a hostile stance; toxicity-engagement homophily is higher on the diffusion tree than on the follower graph for hateful cascades; topology is star-like for the hateful cascades (most reposts come directly from the root) versus tree-like for the benign cascade (reposts propagate through multi-hop chains). In simulation, a multi-LLM-agent simulator reproduces the stance monoculture and the toxicity-delta direction. A structured ablation identifies agent heterogeneity as the leading fidelity factor, and amplifier targeting on dense networks yields 7.5–12.9\% reduction at 5.7\% benign collateral.

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

Diffusion Offline Reinforcement Learning for Fair and Energy-Efficient UAV-Assisted Wireless Networks

arXiv:2606.16331v1 Announce Type: new Abstract: The integration of generative artificial intelligence with wireless communication and signal processing systems has opened new avenues for intelligent, data-driven decision-making in future 6G networks. This work proposes a diffusion soft actor-critic (Diffusion-SAC) approach that leverages offline reinforcement learning (RL) enhanced by denoising diffusion probabilistic models (DDPMs) to optimize trajectory and scheduling control in unmanned aerial vehicle (UAV) networks. While offline RL methods, such as conservative Q-learning (CQL), can learn from static datasets, they often struggle to generalize in low-data or dynamic conditions. To address this, we combine the robustness of CQL with the generative power of diffusion models, enabling expressive and signal-aware policy learning that generalizes beyond behavior policies. Applied to a UAV-assisted wireless network, the proposed framework minimizes transmission energy and improves fairness among devices. Simulations show that Diffusion-SAC outperforms standard offline RL baselines, achieving more stable convergence and higher rewards even with limited datasets. The method enhances data efficiency, reduces energy consumption, and increases throughput by more than 35 % compared to existing algorithms, demonstrating its potential for robust policy learning in next-generation wireless control systems.

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

A spectral audit framework reveals task-dependent aperiodic reliance across EEG and ECG deep learning

arXiv:2606.08583v2 Announce Type: replace Abstract: Deep learning on physiological time series is interpreted through domain-specific features – oscillatory rhythms in EEG, morphological complexes in ECG – yet these signals sit atop a broadband aperiodic 1/f-like envelope that covaries with arousal, age, and pathology. We introduce a spectral audit framework combining aperiodic/periodic decomposition, phase-preserving Fourier interventions, sham controls, and simulation validation. Aperiodic reliance was task-dependent and architecture-general: across six neural architectures, flattening drops exceeded 0.42 balanced-accuracy points for sleep-wake classification, reached 0.07-0.13 for clinical abnormality detection, and remained minimal for motor imagery. Six of seven EEG foundation models showed FDR-significant aperiodic reliance on clinical EEG; age/sex and recording-era controls reduced but did not eliminate the effect. Applying the audit to PTB-XL ECG revealed neural drops of 0.32–0.36 persisting after demographic matching, confirming this confound class extends beyond EEG. Aperiodic controls should become standard for interpretable physiological time-series deep learning.

12.
arXiv (CS.CV) 2026-06-15

Vanishing Depth: Training Generalized Depth Adapters with Sinusoidal Depth Preprocessing for Pretrained RGB Encoders

Generalized metric depth understanding is critical for precise vision-guided robotics, which current state-of-the-art (SOTA) vision-encoders do not support. To address this, we propose a self-supervised training approach that extends pretrained RGB encoders with a depth adapter to incorporate and align metric depth into a combined latent space without interfering with the pretrained RGB feature extraction. In combination with our sinusoidal depth encoding, the depth adapter enables generalized and robust depth density and distribution invariant feature extraction. Our depth adapters improve a wide set of generalized RGB baselines across a spectrum of relevant RGBD downstream tasks in segmentation, pose estimation, and depth completion – without the necessity of finetuning. Most importantly, we achieve 56.05 mIoU in the SUN-RGBD segmentation, while outperforming SOTA depth-aware and multi-modal encoders in our experiments. When no depth is present, one can activate our depth adapter with an empty map, use single pixel depth clues, or monocular depth estimation to include the depth aware feature extraction into subsequent downstream tasks.

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

ResidualPlanner+: a scalable matrix mechanism for marginals and beyond

arXiv:2305.08175v5 Announce Type: replace-cross Abstract: Noisy marginals are a common form of confidentiality protecting data release and are useful for many downstream tasks such as contingency table analysis, construction of Bayesian networks, and even synthetic data generation. Privacy mechanisms that provide unbiased noisy answers to linear queries (such as marginals) are known as matrix mechanisms. We propose ResidualPlanner and ResidualPlanner+, two highly scalable matrix mechanisms. ResidualPlanner is both optimal and scalable for answering marginal queries with Gaussian noise, while ResidualPlanner+ provides support for more general workloads, such as combinations of marginals and range queries or prefix-sum queries. ResidualPlanner can optimize for many loss functions that can be written as a convex function of marginal variances (prior work was restricted to just one predefined objective function). ResidualPlanner can optimize the accuracy of marginals in large scale settings in seconds, even when the previous state of the art (HDMM) runs out of memory. It even runs on datasets with 100 attributes in a couple of minutes. Furthermore, ResidualPlanner can efficiently compute variance/covariance values for each marginal (prior methods quickly run out of memory, even for relatively small datasets). ResidualPlanner+ provides support for more complex workloads that combine marginal and range/prefix-sum queries (e.g., a marginal on race, a range query on age, and a combined race/age tabulation that answers age range queries for each race). It even supports custom user-defined workloads on different attributes. With this added flexibility, ResidualPlanner+ is not necessarily optimal, however it is still extremely scalable and outperforms the prior state-of-the-art (HDMM) on prefix-sum queries both in terms of accuracy and speed.

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

BALTO: Balanced Token-Level Policy Optimization for Hallucination Mitigation

Hallucinations remain a major obstacle to deploying large language models (LLMs) in knowledge-intensive settings, where generated responses must be faithfully grounded in provided evidence. Reinforcement learning (RL) is a promising direction for hallucination mitigation, but response-level faithfulness rewards suffer from a granularity mismatch: localized hallucinations can cause supported content to receive spurious penalties. Although recent work introduces fine-grained feedback such as claim-level verification and token-level rewards, unbalanced credit assignment can still induce length, verbosity, or optimization-noise biases. We propose BALTO, a Balanced Token-level Policy Optimization framework for hallucination mitigation. BALTO extracts checkable factual claims, verifies them against the reference context, and projects claim-level judgments to token-level labels. A balanced token-level credit assignment mechanism is introduced into the framework. This design redistributes probability mass from unsupported content toward faithful content, rather than suppressing the entire response. We systematically analyze the limitations of response-level rewards from a theoretical standpoint, and prove BALTO's advantages in training stability and optimization efficiency for hallucination mitigation. Experiments on ConFiQA, RAGTruth, and FinLLM-Eval show that BALTO achieves the highest faithfulness across all six model–benchmark settings and consistently outperforms existing post-training baselines in Q-Score, demonstrating a stronger faithfulness–informativeness trade-off.

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

Attribution-Guided and Coverage-Maximized Pruning for Structural MoE Compression

arXiv:2606.18304v1 Announce Type: cross Abstract: Mixture-of-Experts (MoE) models scale compute efficiently, yet remain expensive to deploy due to their substantial memory footprint and inference overhead. Prior compression methods mainly operate at the expert level, either removing entire experts or ranking experts by coarse-grained importance scores. However, such expert-wise decisions are often too coarse to capture fine-grained redundancy, leading to misallocated pruning budgets and limited compression. To address this problem, we observe that information within MoE experts is highly concentrated in a small subset of channels, leaving substantial redundancy even in experts deemed important. Based on this observation, we propose a structural pruning framework tailored for MoE models. Our method reformulates prune-ratio allocation as a channel-score coverage maximization problem and solves it efficiently using an attribution-based approximation. Experiments on DeepSeek and Qwen MoE models show that our method preserves model accuracy under 50% or 25% structured pruning when combined with 4-bit quantization. On Qwen3-30B-A3B, our approach reduces memory footprint by 5.27$\times$ and consistently outperforms state-of-the-art baselines across diverse benchmarks.

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

S1-DeepResearch: Beyond Search, Toward Real-World Long-Horizon Research Agents

Deep research agents aim to solve complex knowledge-intensive tasks through long-horizon planning, evidence gathering, reasoning, and report generation. While recent progress in search agents has demonstrated strong capabilities in information retrieval and answer verification, most existing training datasets remain search-centric, focusing primarily on closed-ended question answering and information localization. As a result, they mainly train information-seeking behavior while providing limited coverage of key deep research capabilities, including evidence integration, knowledge synthesis, planning, file understanding, and structured report generation. In this work, we propose a unified trajectory construction paradigm for deep research agents that combines closed-ended QA and open-ended exploration. The proposed framework consists of graph-grounded task formulation, agentic trajectory rollout, and multi-dimensional trajectory verification, enabling scalable synthesis of high-quality agentic trajectories spanning long-chain complex reasoning, deep research instruction following, report writing, file understanding and generation, and skills usage. Compared with existing search-oriented datasets, our synthesized trajectories place greater emphasis on knowledge synthesis, complex reasoning, and planning. S1-DeepResearch-32B achieves state-of-the-art performance among open-source models of comparable scale across 20 benchmarks spanning five capability dimensions, including complex reasoning, instruction following, report generation, file understanding, and skills usage. On several challenging deep research benchmarks, it approaches the performance of leading proprietary frontier models. These results highlight the importance of jointly modeling information acquisition, knowledge synthesis, and planning-oriented agent behaviors for building effective deep research agents.

17.
arXiv (CS.CL) 2026-06-15

Jacobian Scopes: token-level causal attributions in LLMs

Large language models (LLMs) make next-token predictions based on clues present in their context, such as semantic descriptions and in-context examples. Yet, elucidating which prior tokens most strongly influence a given prediction remains challenging due to the proliferation of layers and attention heads in modern architectures. We propose Jacobian Scopes, a suite of gradient-based, token-level causal attribution methods for interpreting LLM predictions. Grounded in perturbation theory and information geometry, Jacobian Scopes quantify how input tokens influence various aspects of a model's prediction, such as specific logits, the full predictive distribution, and model uncertainty (effective temperature). Through case studies spanning instruction understanding, translation, and in-context learning (ICL), we demonstrate how Jacobian Scopes reveal implicit political biases, uncover word- and phrase-level translation strategies, and shed light on recently debated mechanisms underlying in-context time-series forecasting. To facilitate exploration of Jacobian Scopes on custom text, we open-source our implementations and provide a cloud-hosted interactive demo at https://huggingface.co/spaces/Typony/JacobianScopes.

18.
arXiv (CS.CV) 2026-06-11

4DP-QA: Scalable QA for 4D Perception in Vision Language Models

Despite recent advances, Vision Language Models (VLMs) still struggle to grasp the dynamics of the world. We note that the ability to reason about a 4D scene, challenging in itself, is further complicated by two factors. First, VLMs observe motion indirectly via its projection onto 2D images. Second, existing datasets fail to disentangle object and camera motion. To address these challenges, we present a QA generation pipeline that focuses on motion-related scene understanding. We take particular care of the entanglement of camera and object motion by casting tracking in both the traditional way and in a novel, fixed reference system, dubbed True-Motion Tracking, which provides an intuitive description of motion. From this pipeline, we generate a large-scale training dataset of 400K samples, 4DP-QA (4D Perception QA), and a 2.2K-sample benchmark, 4DP-QA-Bench. Training existing models on our dataset yields performance improvements on an external benchmark, validating the effectiveness of our method.

19.
arXiv (CS.CL) 2026-06-18

Approximate Structured Diffusion for Sequence Labelling

Sequence labelling, a core task of Natural Language Processing (NLP), consists in assigning each token of an input sentence a label. From a Machine Learning point of view, sequence labelling is often cast as a Linear-Chain Conditional Random Field (CRF) parametrised by a neural network. While this approach gives good empirical results, CRFs assume a finite decision span (eg label bigrams) which can limit their expressivity and hurt performance when long-range dependencies are required. We show we can leverage diffusion to train a CRF conditioned on an entire label sequence, with the caveat that the condition is on a noisy version of labels. We show experimentally that this method, in conjunction with approximate CRF inference, improves label accuracy with a 16.5% error reduction for POS-tagging.

20.
bioRxiv (Bioinfo) 2026-06-14

Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell

Transcription factor (TF) cocktails used in cell identity reprogramming protocols have largely been developed from experimental approaches. A handful of computational approaches have been reported, though have not been widely adopted by the scientific community. To standardize their use and assess their performance, we built CompForce, a platform that integrates these tools. Using CompForce, we found that existing computational methods offer modest improvements over differential expression on both synthetic and literature-curated data, and that their lackluster and inconsistent performance could be attributed to a reliance on local centrality metrics. To improve upon these methods, we developed IMCell, a prediction method that is inspired by the influence maximization problem. Unlike existing tools, IMCell returns optimized TF sets rather than ranked TF lists. We demonstrate that IMCell vastly out-performs existing tools, and further extend it to dynamic, stepwise contexts. The tools presented here are available in the R packages CompForce and IMCell.

21.
arXiv (CS.CV) 2026-06-15

Explaining RhythmFormer: A Systematic XAI Analysis of Periodic Sparse Attention for Remote Photoplethysmography

Remote photoplethysmography (rPPG) transformers achieve low heart-rate error on benchmarks, yet their decisions remain opaque–a growing concern as rPPG moves toward clinical heart rate estimation. Existing rPPG XAI is dominated by qualitative heatmap inspection without quantitative faithfulness metrics or physiology-grounded validation, leaving a gap between visual plausibility and auditable evidence. We address this gap. First, we adapt four attribution methods (raw attention, rollout, flow, Beyond Intuition) to RhythmFormer's bi-level routing attention with top-$k$ selection. Second, we introduce a skin coverage metric quantifying how much attribution mass falls on skin regions. Third, we adapt the SaCo faithfulness coefficient from its original classification setting to rPPG regression by using the MAE between original and perturbed predicted rPPG waveforms as the perturbation impact. Applying these tools, we quantify a multi-hop leakage effect under sparse top-$k$ routing: attention rollout and flow almost completely restores the connections that individual refined-attention layers explicitly set to zero. Beyond Intuition mitigates this via its value-projection-weighted rollout and gradient-supported mask, attaining the highest median refined skin coverage ($0.83$ vs. $0.57$ for vanilla rollout) and faithfulness ($F=0.92$) among the evaluated methods on UBFC-rPPG. Validation across diverse datasets and model variants is needed. A case study on a low-SaCo outlier further shows all four methods recovering consistently once an artefactual region is replaced, suggesting consistent SaCo behavior across attribution families in this illustrative case. Together, these metrics move XAI for rPPG toward auditable numerical evidence about spatial alignment and perturbation faithfulness, i.e. trustworthy rPPG XAI.

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

Distributional Loss for Robust Classification

This paper proposes a novel loss concept for supervised classification tasks. Rather than enforcing a direct mapping from each input sample to a single assigned label, we define an optimization objective over all classifier outputs as a bimodal Gaussian distribution. This softer target formulation implicitly captures class ambiguity, mitigates overfitting, and encourages the learning of more robust decision boundaries, all without requiring additional label information. Experimental results demonstrate consistent improvements in robustness, with particularly pronounced gains in low-data regimes, while requiring only minimal modifications to standard training pipelines.

23.
medRxiv (Medicine) 2026-06-11

Population-scale detection of methylation outliers from long-read genome sequencing

Background: Aberrant DNA methylation can mediate the functional effects of rare genetic variation and contribute to imprinting disorders, repeat expansion diseases, and other pathogenic regulatory mechanisms. Long-read sequencing technologies now enable genome-wide detection of CpG methylation alongside genetic variation from a single assay. However, methods for systematic identification and interpretation of methylation outliers from long-read sequencing data remain limited. Methods: We developed METAFORA, a computational workflow for detecting methylation outlier regions from PacBio and Oxford Nanopore long-read sequencing data. METAFORA constructs population-level methylation references, segments the genome into correlated CpG blocks, infers technical and biological sources of variation through hidden factor estimation, models uncertainty due to variable depth sequencing, and computes covariate-adjusted methylation outlier scores for individual samples. We applied METAFORA across large long-read sequencing cohorts and integrated methylation outliers with multi-omic data. METAFORA is implemented as a snakemake workflow available at https://github.com/tjense25/METAFORA. Results: METAFORA identified methylation outlier regions associated with rare structural variants, tandem repeat expansions, and imprinting abnormalities. We found outlier regions were enriched for molecular outliers across transcriptomic and chromatin accessibility datasets, supporting their functional relevance in gene regulation. In a representative case, METAFORA identified an imprinting defect affecting the GNAS locus associated with an STX16 deletion. Conclusions: METAFORA enables scalable detection and interpretation of methylation outliers from long-read sequencing data and provides a framework for integrating epigenetic outliers with genomic and multi-omic analyses. These approaches may improve interpretation of rare regulatory variation and support discovery of clinically relevant epigenetic abnormalities in genomic medicine.

24.
arXiv (CS.LG) 2026-06-12

Fed-FBD: Federated Functional Block Diversification for Isolation, Privacy, and Surgical Unlearning

arXiv:2606.12679v1 Announce Type: new Abstract: Federated learning (FL) enables collaborative model training without sharing raw patient data, but standard approaches such as FedAvg treat each client as a black box and provide no mechanism for isolating an adversarial contributor, auditing per-client influence, or honoring a departed participant's right to be forgotten. We present Fed-FBD (Federated Functional Block Diversification), a modular federated architecture that decomposes a ResNet backbone into six functional blocks (the stem, four residual groups, and the classification head) and maintains a warehouse of N color variants, each assembled from independently tracked and contributor-stamped blocks. Fed-FBD provides three capabilities absent in FedAvg: (i) architecturally guaranteed block-level isolation, so that an adversarial or mislabelled client cannot contaminate the clean colous; (ii) privacy-by-design, where membership inference advantage is already indistinguishable from chance before any privacy mechanism is applied; and (iii) surgical machine unlearning of a departed participant's contribution at sub-second cost and without retraining. Experiments on six MedMNIST-2D datasets, PathMNIST at 224x224, and CIFAR-10 show that Fed-FBD trades a modest 0.3%-3.1% IID accuracy gap on the adequately sized datasets for these guarantees, remains within 0.8%-4.0% of FedAvg at Dirichlet alpha=1.0 on three of four datasets, and confines all six adversarial attacks we study to the poisoned client's own blocks with at most +/-0.01 AUC drift on the clean colors.

25.
arXiv (CS.AI) 2026-06-12

MAStrike: Shapley-Guided Collusive Red-Teaming on Multi-Agent Systems

arXiv:2606.12918v1 Announce Type: cross Abstract: Hierarchical multi-agent systems (MAS) are rapidly being deployed in high-stakes workflows across domains such as finance and software engineering. In these systems, safety and security are inherently distributed across role-specialized agents, significantly expanding the attack surface, particularly under coordinated adversarial behaviors such as privilege escalation and cross-agent collusion. Existing red-teaming approaches for MAS remain limited: they rely on heuristic selection of target agents and perturb isolated message streams, leaving critical questions unanswered as which agents are most responsible for system safety, and how compromised agents can coordinate to bypass defenses. We propose MAStrike, a closed-loop framework for collusive red-teaming in hierarchical MAS. We propose the first agent-level Shapley value analysis for MAS, quantifying each agent's marginal contribution to system robustness under task-specific distributions. GGuided by this attribution, MAStrike identifies vulnerable agent coalitions and generates coordinated, role-aware adversarial manipulations. These attacks are iteratively refined through structured causal diagnosis, attributing failure cases to uncompromised agents that block adversarial attempts. We further build a comprehensive MAS red-teaming benchmark and controllable environments spanning diverse hierarchical topologies and domains, including finance, software engineering, and CRM. Extensive experiments across MAS built on multiple frontier models show that MAStrike substantially outperforms heuristic baselines. Our analysis further uncovers non-trivial Shapley value distributions and higher-order interaction structures among agents, revealing critical vulnerabilities and coordination patterns that are overlooked by prior single-agent or template-based methods.