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

Constrained Semantic Decompression in LLMs through Persian Proverb-Conditioned Story Generation

Transforming a dense, abstract proverb into an engaging and morally faithful narrative requires deep cultural understanding and robust semantic grounding. We frame this problem as a constrained semantic decompression task and study proverb-conditioned story generation as a testbed for abstraction-to-realization in large language models (LLMs). Focusing on Persian, we introduce the Proverb Aligned Narrative Dataset (PAND), pairing proverbs with human-written stories and explicit meanings. By a hybrid evaluation framework that combines human-calibrated LLM-as-a-Judge with structural metrics, we analyze model behavior across multiple prompting regimes. Our findings reveal a persistent decompression gap: current LLMs often achieve strong surface-level fluency while failing to faithfully instantiate the underlying moral and causal structure encoded in proverbs. We further show that explicit reasoning and iterative refinement can partially mitigate these failures, suggesting that many decompression errors arise from difficulties in translating abstract meaning into narrative form rather than a complete lack of relevant knowledge. Our proposed task naturally extends to other forms of compressed cultural knowledge.

02.
arXiv (CS.LG) 2026-06-16

Circuit Tracing in Autoregressive Protein Language Models

arXiv:2606.16044v1 Announce Type: new Abstract: Protein language models (pLMs) can generate novel protein sequences with properties beyond those observed in nature, yet the mechanisms underlying protein generation remain poorly understood. Existing mechanistic interpretability methods based on sparse autoencoders and transcoders primarily focus on protein representation learning models and do not capture the computation required for autoregressive generation. Here, we introduce ProGenMech, a mechanistic interpretability framework for generative protein language models that extends cross-layer transcoders (CLTs) to ProGen3, a sparse Mixture-of-Experts model trained for both causal generation and span infilling. Unlike per-layer approaches, CLTs reconstruct each layer using sparse latent variables from all preceding layers, enabling faithful recovery of inter-layer generative computation. We further develop a zero-shot circuit discovery framework to identify sparse latent circuits responsible for protein generation and fitness prediction. In causal generation and zero-shot fitness estimation tasks, ProGenMech outperforms local transcoder baselines in recovering ProGen3's probability distribution and functional scoring behavior, while matching the original model's generative distribution in span infilling tasks. Moreover, the recovered circuits reveal biologically meaningful motifs and functional regions associated with conserved sequence patterns and protein fitness landscapes, establishing a foundation for interpretable and steerable protein generation.

03.
arXiv (math.PR) 2026-06-12

On McDiarmid's Inequality under Dependence via Approximate Tensorization of Entropy

arXiv:2606.12720v1 Announce Type: new Abstract: We argue that dependent versions of McDiarmid's inequality are a useful but underutilized tool in mathematical statistics, learning theory and theoretical computer science. To make this point, we first highlight that approximate tensorization of entropy (ATE) implies McDiarmid's via the Entropy Method. Second, we derive McDiarmid's inequality for non-isotropic Gaussian random vectors $X \sim \mathcal N(\mu, \Sigma)$ through ATE with a constant of the order of the condition number of $\Sigma$. We both independently obtain this ATE through a simple application of stochastic localization and also discuss how a more general ATE for the Gibbs sampler due to Ascolani et al., 2026 generalizes McDiarmid's-like concentration to strongly log-concave and log-smooth probability measures. We then apply the resulting concentration inequalities to resolve a question on the concentration of $\operatorname{sign}(X)$ posed by Simone Bombari, investigate Erdős-Rényi graphs under dependence and prove a Dvoretzky-Kiefer-Wolfowitz-type inequality for observations from a joint measure fulfilling ATE and continuous marginal CDFs. For the class of strongly log-concave and log-smooth measures, this result improves upon a prior Dvoretzky-Kiefer-Wolfowitz-type inequality for non-i.i.d. observations due to Bobkov and Götze, 2010, by establishing the expected $1/\sqrt{n}$-rate of convergence under weak dependence instead of $n^{-1/3}$.

04.
arXiv (CS.LG) 2026-06-19

A fast direct solver based neural network for solving PDEs

arXiv:2606.19895v1 Announce Type: cross Abstract: The matrices arising from large scale $N$-body problems can be efficiently represented using hierarchical matrices, whose key idea is that the admissible off-diagonal sub-matrices can be well approximated by low-rank matrices across a hierarchy of matrix partitions. HODLR (Hierarchical Off-Diagonal Low-Rank) matrices are a subclass of hierarchical matrices in which all off-diagonal submatrices at every level of a recursive binary partition are low-rank. In this article, we present a neural network that learns the inverse operation of HODLR matrices based on the fast direct solver for HODLR matrices developed by Ambikasaran and Darve (2013). We further extend the architecture to learn nonlinear solution operators associated with PDEs by replacing some of the linear layers with deep sub-networks. We demonstrate the performance of the proposed architecture by performing a comprehensive set of experiments that include (i) solving a linear problem such as the Fredholm integral equation of the second kind, (ii) solving PDEs such as the nonlinear Schrödinger equation, Burgers' equation, and the steady-state Darcy's flow equation, (iii) generalization study across varying parameter values, (iv) comparing the inference time of the proposed network with the run time of a classical numerical solver, and (v) comparing the proposed network with some of the existing neural operator learning networks.

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

How to Score Experts for One-Shot MoE Expert Pruning: A Unified Formulation and Selection Principle

arXiv:2606.15716v1 Announce Type: new Abstract: Mixture-of-Experts (MoE) language models reduce per-token computation through sparse expert activation, yet deployment still requires storing the full expert pool, making one-shot expert pruning a practical approach for reducing memory usage. Although effective, existing criteria are largely heuristic, and no single criterion is universally optimal. Thus, establishing a principle for selecting pruning criteria suited to different deployment objectives remains an important yet largely underexplored problem in one-shot expert pruning. To this end, we introduce a unified formulation for one-shot MoE expert pruning organized around three factors: routing frequency, gate weighting, and activation strength. The formulation yields a criteria selection principle: task-agnostic pruning should favor routed-token-averaged, gate-free activation-based criteria, whereas task-specific pruning can benefit from retaining routing-frequency and gate-weight information. Beyond this principle, the formulation also provides a systematic view of existing heuristic criteria and gives rise to two new task-agnostic criteria, Mean Activation Norm (MAN) and Mean Squared Activation Norm (MSAN). Across four representative MoE models and 16 diverse benchmarks, MAN and MSAN are consistently strong in the task-agnostic setting, obtain the top-two average ranks, and improve average performance by up to 8.8 points over the strongest baseline.

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

Quantum Occam Learning: Sample-Supported Expressibility for Circuit-Based Quantum Learning

arXiv:2606.12211v1 Announce Type: cross Abstract: A central principle in quantum machine learning is that an ansatz should be expressive enough to represent the quantum data of interest. Yet, the expressibility is statistically meaningful only insofar as it can be learned from finitely many copies of an unknown quantum state. In this work, we develop an information-theoretic Occam theory for quantum data generated by finite-size quantum circuits. For the class $S_{n,G}$ of $n$-qubit pure states preparable with at most $G$ two-qubit gates, a metric-entropy argument gives the realizable sample law $\widetilde{\Theta}(G/\epsilon^2)$ in the circuit-limited regime. For an arbitrary source $\hat{\rho}$, we introduce the best $G$-gate approximation error $d_G(\hat{\rho})$ and the approximate circuit complexity $C_\eta(\hat{\rho})$. We prove an agnostic quantum Occam theorem: with $M$ copies, one can learn up to the best $G$-gate approximation error plus a statistical penalty $\widetilde{O}(\sqrt{G/M})$. We then remove the need to know $G$ in advance through an adaptive model-selection theorem whose oracle inequality selects the circuit complexity justified by the data. Matching lower bounds yield a sample-supported expressibility law: at trace-distance accuracy $\epsilon$, $M$ samples can support only $G_supported \simeq M\epsilon^2$ gates, up to logarithmic factors and tomography saturation at $2^n$. Thus, the circuit complexity becomes an adaptive statistical resource rather than a static promise. Our framework turns bounded circuit complexity into a model-selection principle for quantum machine learning.

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

CADO: From Imitation to Cost Minimization for Heatmap-based Solvers in Combinatorial Optimization

arXiv:2602.08210v2 Announce Type: replace Abstract: Heatmap-based solvers have emerged as a promising paradigm for Combinatorial Optimization (CO). However, we argue that the dominant Supervised Learning (SL) training paradigm suffers from a fundamental objective mismatch: minimizing imitation loss (e.g., cross-entropy) does not guarantee solution cost minimization. We dissect this mismatch into two deficiencies: Decoder-Blindness (being oblivious to the non-differentiable decoding process) and Cost-Blindness (prioritizing structural imitation over solution quality). We empirically demonstrate that these intrinsic flaws impose a hard performance ceiling. To overcome this limitation, we propose CADO (Cost-Aware Diffusion models for Optimization), a streamlined Reinforcement Learning fine-tuning framework that formulates the diffusion denoising process as an MDP to directly optimize the post-decoded solution cost. We introduce Label-Centered Reward, which repurposes ground-truth labels as unbiased baselines rather than imitation targets, and Hybrid Fine-Tuning for parameter-efficient adaptation. CADO achieves state-of-the-art performance across diverse benchmarks, validating that objective alignment is essential for unlocking the full potential of heatmap-based solvers.

08.
arXiv (CS.AI) 2026-06-12

Interaction-Centered Intelligence: Toward an Interaction-Based Theory of Human-AI Co-Creation

arXiv:2606.00807v2 Announce Type: replace Abstract: Traditional artificial intelligence has largely conceptualized intelligence as isolated computation occurring within bounded agents. Across classical AI, machine learning, and many generative systems, the dominant unit of analysis remains the individual model or autonomous system evaluated through outputs, benchmarks, prediction accuracy, or optimization performance. While these approaches have produced major advances, they often under-theorize the role of interaction in the emergence of intelligence, creativity, meaning, and adaptive behavior. This paper proposes interaction as the primary unit of analysis for co-creative AI and interaction-centered intelligence more broadly. Drawing from distributed cognition, embodied cognition, enaction, participatory sense-making, human-computer interaction, and computational creativity, the paper traces a historical progression toward increasingly relational accounts of intelligence. Building upon prior work in Creative Sense-Making, quantified co-creation, and co-creative systems such as the Drawing Apprentice and AI Drawing Partner, it argues that intelligence emerges through evolving interaction dynamics among agents, environments, and socio-technical systems rather than solely through internal computation. The paper introduces Interaction-Centered Intelligence as a framework for understanding human-AI co-creation, collaborative emergence, adaptive participation, and interactional dynamics. Rather than evaluating intelligence solely through generated outputs, the framework emphasizes interaction trajectories, coordination patterns, participatory engagement, adaptive regulation, and interactional drift unfolding through time. Implications for explainable co-creative AI, hybrid intelligence, enactive AI, and future human-AI systems are discussed.

09.
arXiv (math.PR) 2026-06-19

An alternative approach to well-posedness of McKean-Vlasov equations arising in Consensus-Based Optimization

arXiv:2512.19446v4 Announce Type: replace-cross Abstract: In this work we study the mean-field description of Consensus-Based Optimization (CBO), a derivative-free particle optimization method. Such a description is provided by a non-local SDE of McKean-Vlasov type, whose fields lack of global Lipschitz continuity. We propose a novel approach to prove the well-posedness of the mean-field CBO equation based on a truncation argument. The latter is performed through the introduction of a cut-off function, defined on the space of probability measures, acting on the fields. This procedure allows us to study the well-posedness problem in the classical framework of Sznitman. Through this argument, we recover the established result on the existence of strong solutions, and we extend the class of solutions for which pathwise uniqueness holds.

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

PCS-UQ: Uncertainty Quantification via the Predictability-Computability-Stability Framework

arXiv:2505.08784v2 Announce Type: replace-cross Abstract: As machine learning (ML) enters high-stakes domains, trustworthy uncertainty quantification (UQ) is essential for safety. In this paper we introduce PCS-UQ, a framework based on the Predictability, Computability, and Stability (PCS) principles for veridical data science. Starting with a candidate set of models or algorithms, PCS-UQ integrates a rigorous prediction-check to screen out unsuitable models in the set and utilizes bootstrap samples, in order to capture both inter-sample variability and algorithmic instability for the prediction-checked algorithms. We then introduce a novel multiplicative calibration scheme to enhance local adaptivity, which basically corresponds to a new score in conformal prediction. Moreover, we produce a compilation of 17 real-world regression datasets with manually-constructed subgroups. On this benchmark, PCS-UQ maintains the target coverage while outperforming or matching conformal methods equipped with oracle-selected algorithms in interval width. PCS-UQ achieves consistent subgroup coverage, outperforming these oracle-selected conformal methods. Notably, PCS-UQ stands out in achieving both competitive interval widths and consistent subgroup coverage.Across 6 classification datasets, PCS-UQ reduces prediction set sizes by 20\%. To scale the framework for deep learning, we propose computationally efficient variants that bypass expensive retraining. On three computer vision benchmarks, these variants reduce prediction set sizes by 20\% over conformal baselines. Finally, we provide theoretical proof that a modified PCS-UQ algorithm preserves valid coverage under exchangeability as a form of split conformal inference.

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

Priority-Aware Shapley Value

arXiv:2602.09326v2 Announce Type: replace Abstract: Shapley values are widely used for model-agnostic data valuation and feature attribution, yet they implicitly assume contributors are interchangeable. This can be problematic when contributors are dependent (e.g., reused/augmented data or causal feature orderings) or when contributions should be adjusted by factors such as trust or risk. We propose Priority-Aware Shapley Value (PASV), which incorporates both hard precedence constraints and soft, contributor-specific priority weights. PASV is applicable to general precedence structures, recovers precedence-only and weight-only Shapley variants as special cases, and is uniquely characterized by natural axioms. We develop an efficient adjacent-swap Metropolis-Hastings sampler for scalable Monte Carlo estimation and analyze limiting regimes induced by extreme priority weights. Experiments on data valuation (MNIST/CIFAR10) and feature attribution (Census Income) demonstrate more structure-faithful allocations and a practical sensitivity analysis via our proposed "priority sweeping".

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

The MAMA-MIA Challenge: Advancing Generalizability and Fairness in Breast MRI Tumor Segmentation and Treatment Response Prediction

arXiv:2603.01250v2 Announce Type: replace-cross Abstract: Breast cancer is the most frequently diagnosed malignancy among women worldwide and a leading cause of cancer-related mortality. Dynamic contrast-enhanced magnetic resonance imaging plays a central role in tumor characterization and treatment monitoring, particularly in patients receiving neoadjuvant chemotherapy. However, existing artificial intelligence models for breast magnetic resonance imaging are typically developed and evaluated using heterogeneous datasets, study populations, and assessment protocols, making direct comparison difficult and limiting understanding of model robustness across institutions and clinically relevant patient subgroups. The MAMA-MIA Challenge was designed to address these challenges by providing a standardized benchmark for the joint evaluation of primary tumor segmentation and prediction of pathologic complete response using pre-treatment magnetic resonance imaging only. The training cohort comprised 1,506 patients from multiple institutions in the United States, while evaluation was conducted on an external test set of 574 patients from three independent European centers to assess cross-continental and cross-institutional generalization. A unified scoring framework combined predictive performance with subgroup consistency across age, menopausal status, and breast density. Twenty-six international teams participated in the final evaluation phase. Results demonstrate substantial performance variability under a common external evaluation framework and reveal trade-offs between overall accuracy and subgroup fairness. The challenge provides standardized datasets, evaluation protocols, and public resources to promote the development of robust and equitable artificial intelligence systems for breast cancer imaging.

13.
arXiv (CS.AI) 2026-06-18

Why SWAVE May Not Be All You Need:A Concept-Evolution Retrospective on Complex-Valued Recurrent Language Models

arXiv:2606.18324v1 Announce Type: cross Abstract: SWave is a complex-valued recurrent language model (169.26M parameters, D=384, L=16, T=2048) trained on FineWeb-Edu using 2xH100 NVL. It was designed around three founding premises: that representing language as complex waves rather than real-valued numbers enables richer information encoding; that a Cayley-parameterised unitary transition provides a mathematical guarantee against state decay or explosion; and that a hidden state which rotates rather than shrinks preserves signal integrity over arbitrarily long contexts. The core of SWave evolved substantially across three development phases. The Resonance Head was found to structurally admit imaginary-channel collapse as a global loss minimum (a failure mode we term cos-domination collapse) and was superseded by an untied head with independent real and imaginary embedding tables from the Phase-Associative Memory (PAM) architecture. This resolved the degenerate minimum and enabled stable 200,000-step training (best-step PPL 22.0 at step 89,861). ComplexNorm and the Wave Propagation Scan proved load-bearing throughout all three phases and were retained to the final architecture. ProtectGatedScan was reframed as a structural prior rather than a learned behaviour. The four multi-scale retention concepts showed no measurable improvement under controlled evaluation and were found non-load-bearing. The ComplexGatedUnit was superseded by a real-valued squared-ReLU channel mixer with fewer parameters. The auxiliary training objectives showed no benefit once structural constraints were resolved. The investigation yields a formal characterisation of cos-domination collapse, a parallel scan with a log-space backward pass for numerical stability, six transferable engineering principles for complex-valued recurrent training, and a plan-to-code traceability methodology for catching structural divergences that conventional test suites miss.

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

Mapping Geopolitical Bias in 11 Large Language Models: A Bilingual, Dual-Framing Analysis of U.S.-China Tensions

Large language models are how hundreds of millions of people now encounter contested political questions, raising a subtle measurement problem: a model that simply agrees with whatever it is told can masquerade as biased, contaminating any claim that models hold political opinions. We address this by importing balanced keying from survey psychometrics, posing each proposition and its swapped reverse and signing the response so acquiescence cancels and genuine conviction accumulates. The result is a reproducible, quantitative instrument that maps geopolitical stance across 11 models and 2 languages (19,712 responses). Developer origin, query language and issue domain emerge as three near-equal, additive factors; every model, including those built in the United States, leans more Pro-China in Mandarin; and two models with identical agreement bias are told apart, one neutral, one biased. We release it as an open, interactive tool that extends to any contested-opinion domain.

16.
arXiv (CS.CV) 2026-06-12

Fully Distributed Multi-View 3D Tracking in Real-Time

Multi-camera tracking with overlapping fields of view typically relies on centralized fusion, which creates computational bottlenecks that prevent deployment at scale. We present MV3DT, a fully distributed framework for real-time multi-view 3D tracking that achieves accurate identity propagation and occlusion recovery through peer-to-peer coordination, eliminating the need for central aggregation. Each camera node executes a lightweight modular pipeline comprising monocular 3D perception, distributed multi-view association, and collaborative fusion via lightweight messaging. MV3DT achieves 94.3% IDF1 and 93.3% MOTA on WILDTRACK, competitive with state-of-the-art centralized methods, while demonstrating superior scalability by sustaining 30 FPS on 100 cameras with less than 10 ms inter-camera latency and only 2.2% communication overhead. MV3DT operates in a zero-shot regime given camera calibrations, requiring no scene-specific learning and making it directly deployable in new environments. These results establish MV3DT as a practical solution for real-time multi-view tracking in large-scale overlapping camera networks.

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

Adjoint Method versus Physics-Informed Neural Networks in PDE-Constrained Inverse Problems

arXiv:2606.12337v1 Announce Type: cross Abstract: Inverse problems governed by partial differential equations (PDEs) are central to computational mechanics and are commonly solved by adjoint-based optimization, while physics-informed neural networks (PINNs) have emerged as a flexible alternative. Their relative performance remains difficult to assess because the two approaches are often compared under different formulations, parameterizations, optimizers, and regularization choices. We present a fair comparison of adjoint optimization and PINNs for PDE-constrained inverse problems. From a common abstract formulation, we instantiate both methods on identical domains, governing equations, observation models, and regularization terms, while matching the optimizer, unknown parameterization, and arithmetic precision wherever applicable. The benchmarks include unsteady Burgers, noisy Darcy permeability inversion, three-dimensional Allen–Cahn reaction identification, and unsteady Navier–Stokes viscosity identification. The results show that the representation of the unknown largely determines the preferred method: grid-based fields favor the discrete adjoint, whereas neural representations are native to PINNs and relevant for closure and constitutive modeling. For time-dependent problems, adjoint inversion can be dominated by trajectory storage and differentiation, while PINNs provide satisfactory reconstructions at lower cost. A PINN-warm-started adjoint strategy then recovers adjoint-level accuracy at substantially reduced cost.

18.
arXiv (CS.LG) 2026-06-16

Enhancing Physics-Informed Neural Networks Through Feature Engineering

arXiv:2502.07209v4 Announce Type: replace Abstract: Physics-Informed Neural Networks (PINNs) seek to solve partial differential equations (PDEs) with deep learning. Mainstream approaches that deploy fully-connected multi-layer deep learning architectures require prolonged training to achieve even moderate accuracy, while recent work on feature engineering allows higher accuracy and faster convergence. This paper introduces SAFE-NET, a Single-layered Adaptive Feature Engineering NETwork that achieves orders-of-magnitude lower errors with far fewer parameters than baseline feature engineering methods. SAFE-NET returns to basic ideas in machine learning, using Fourier features, a simplified single hidden layer network architecture, and an effective optimizer that improves the conditioning of the PINN optimization problem. Numerical results show that SAFE-NET converges faster and typically outperforms deeper networks and more complex architectures. It consistently uses fewer parameters – on average, 65% fewer than the competing feature engineering methods – while achieving comparable accuracy in less than 30% of the training epochs. Moreover, each SAFE-NET epoch is 95% faster than those of competing feature engineering approaches. These findings challenge the prevailing belief that modern PINNs effectively learn features in these scientific applications and highlight the efficiency gains possible through feature engineering.

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

Geometric Algebra Quantum Gate Decomposition

arXiv:2606.12480v1 Announce Type: new Abstract: Quantum gates are usually described through matrix and tensor-product formalisms that often obscure their geometric structure. In this work, we formulate the Pauli and Clifford groups within the complex Geometric Algebra (GA) framework. We show that the Pauli group is naturally identified with the group of blades up to a global phase, thereby providing a geometric interpretation of Pauli operators and their commutation relations in terms of oriented subspaces. We further prove that Clifford operators are generated by products of {\pi}/4-Pauli rotors and introduce a greedy Pauli rotor decomposition algorithm whose empirical behavior suggests unexpectedly compact decompositions for Clifford operators. Finally, we show that Clifford+T universality admits a natural geometric interpretation through {\pi}/8-rotors within this framework.

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

From Awareness to Adherence: Bridging the Context Gap in Spoken Dialogue Systems via Context-Aware Decoding

Despite the success of end-to-end (E2E) spoken dialogue systems, maintaining strict context adherence in multi-round conversations remains a challenge. While prior works attribute these failures to models forgetting dialogue history, we highlight an equally critical but overlooked bottleneck: a gap between latent context awareness and active adherence. Although models internally recognize relevant past utterances, strong parametric priors often overshadow these signals during decoding. To bridge this gap, we propose an audio-adapted Context-Aware Decoding (CAD) approach. By leveraging internal attention mechanisms to isolate key historical rounds, our approach contrasts output distributions with and without this key context during inference, directly amplifying multimodal contextual signals. Evaluations on the Audio MultiChallenge benchmark demonstrate significant improvements in Semantic Memory and Self Coherence subtasks, successfully enforcing strict, context-faithful adherence.

21.
bioRxiv (Bioinfo) 2026-06-22

Multivariate Random Forests for Cross-Modal Multi-Omics Integration

Multi-omics studies are widely used across many areas of biomedical research. In many diseases, some signals are shared across data types, while others are strongest in a single omics layer. Current multi-omics clustering methods often either merge all data types into a single representation, which can blur biology that is strong in one layer, or rely on linear structure that may miss more complex relationships across data types. We introduce multiRF, a random-forest-based method that handles complex data types and separates shared and modality-specific structure for multi-omics data. multiRF learns sample similarities across omics layers from multivariate random forests, combines them across data types, and uses the resulting weights to estimate the part of each omics layer that is predictable from the others. The remaining residual is treated as modality-specific signal, allowing shared and modality-specific similarities to be clustered separately. In simulations, multiRF recovered shared clusters as well as or better than established integrative methods while more reliably separating modality-specific signal under nonlinear data structures. In TCGA head and neck squamous cell carcinoma, the shared component aligned with the main subtype structure across established reference classifications, while gene- and miRNA-specific components revealed additional immune and developmental biology. In the ADNI cohort with matched blood DNA methylation and structural MRI, the shared cross-modal aging signal was associated with future conversion to mild cognitive impairment or Alzheimer's disease, and a DNAm-specific residual signal showed exploratory additional information. These results show that multiRF can recover a common disease axis while retaining biologically meaningful signals specific to one data type. multiRF is available as an open-source R package at https://github.com/novawz/multiRF.

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

Evaluating Open-Source LLMs for Multi-Label ATT&CK Technique Classification on CTI Reports

arXiv:2606.18166v1 Announce Type: cross Abstract: Classifying Cyber Threat Intelligence (CTI) using MITRE Adversarial Tactics, Techniques, and Common Knowledge (ATT&CK) is essential for proactive defense, but historically required extensive human effort. Pre-Large Language Model (LLM) automation sped up this process, but could not resolve the complex language and multi-step attack patterns found in unstructured CTI reports. LLMs addressed previous limitations by using contextual reasoning to understand unstructured text. However, current evaluations rely on simplified, single-technique sentences that ignore the complexity of real-world CTI reports, which often leads to inflated performance results. Consequently, the baseline performance of open-source LLMs on complex unstructured CTI reports remains unevaluated. To address this gap, we constructed a ground-truth dataset of 2,076 human-annotated sentences (1,281 technique-positive, 795 negative) from 83 complex unstructured CTI reports. These sentences were mapped to 114 unique ATT&CK techniques using a six-phase annotation process, achieving \k{appa} = 0.68 inter-annotator agreement. Using this dataset, we evaluated seven open-source LLMs ranging from 8B to 236B parameters across prompt strategy and temperature configurations. The highest-performing LLM achieved a micro-averaged F1 score of 0.22, establishing the empirical baseline for multi-label ATT&CK classification on complex unstructured CTI. Parameter size showed a statistically significant positive correlation with F1 score. Prompt strategy and temperature produced no statistically significant gains across model configurations. These results indicate that current open-source LLMs are insufficient for production-grade ATT&CK classification. The dataset, benchmark, and findings provide a reproducible foundation for future CTI research.

23.
bioRxiv (Bioinfo) 2026-06-15

Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifacts

The existence and functional relevance of mitochondrial DNA methylation remain controversial. Here, we systematically profiled cytosine methylation and hydroxymethylation across human brain and blood tissues spanning healthy and malignant states using orthogonal sequencing approaches that avoid chemical conversion during library preparation. While nuclear DNA exhibited canonical methylation patterns, mitochondrial DNA consistently showed negligible signal, indistinguishable from background technical noise. By mapping cytosine-guanine sites between mitochondrial DNA and nuclear-embedded mitochondrial sequences, we demonstrate the potential of these nuclear counterparts to confound not only cytosine methylation but also hydroxymethylation measurements, corroborating and extending prior findings implicating nuclear contamination as a potential source of apparent mitochondrial epigenetic signals. Additional technical factors that inflate apparent mtDNA methylation signals were identified, including sequence context biases, flow cell chemistries, and coverage-dependent discrepancies between the heavy and light strands. Collectively, these results provide convergent evidence against the presence of biologically meaningful cytosine methylation or hydroxymethylation in mitochondrial DNA. These findings caution against interpreting apparent mtDNA methylation signals in human adult tissues as meaningful without rigorous orthogonal validation and comprehensive consideration of technical and analytical confounding factors.

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

Learning Fair Pareto-Optimal Policies in Multi-Objective Reinforcement Learning

arXiv:2606.18111v1 Announce Type: cross Abstract: Fairness is an important aspect of decision-making in multi-objective reinforcement learning (MORL), where policies must ensure both optimality and equity across multiple, potentially conflicting objectives. While single-policy MORL methods can learn fair policies for fixed user preferences using welfare functions such as the generalized Gini welfare function (GGF), they fail to provide the diverse set of policies necessary for dynamic or unknown user preferences. To address this limitation, we formalize the fair optimization problem in multi-policy MORL, where the goal is to learn a set of Pareto-optimal policies that ensure fairness across all possible user preferences. Our key technical contributions are threefold: (1) We show that for concave, piecewise-linear welfare functions (e.g., GGF), fair policies remain in the convex coverage set (CCS), which is an approximated Pareto front for linear scalarization. (2) We demonstrate that non-stationary policies, augmented with accrued reward histories, and stochastic policies improve fairness by dynamically adapting to historical inequities. (3) We propose three novel algorithms, which include integrating GGF with multi-policy multi-objective Q-Learning (MOQL), state-augmented multi-policy MOQL for learning non-statoinary policies, and its novel extension for learning stochastic policies. We evaluate our algorithms across various domains and compare our methods against the state-of-the-art MORL baselines. The empirical results show that our methods learn a set of fair policies that accommodate different user preferences.

25.
arXiv (CS.LG) 2026-06-11

Higher-Order Token Interactions via Quantum Attention

arXiv:2606.11673v1 Announce Type: cross Abstract: Standard dot-product self-attention computes, in a single layer, only pairwise (order-2) interactions between tokens; representing a generic order-$k$ interaction is known to require either super-quadratic resources in one layer or composition across depth. We introduce Quantum Higher-Order Attention (QHA), a shallow, hardware-realizable quantum attention head that, via data re-uploading and an all-to-all non-Clifford entangler, synthesizes order-$k$ token interactions inside the circuit and exposes them through a local single-qubit read-out. We prove (i) an expressivity separation: any single standard self-attention layer with embedding dimension $m$, $H$ heads and $p$-bit precision satisfying $mHp=o(N/\log\log N)$ cannot represent the order-$k$ correlation family that one QHA head represents with circuit depth $O(\log k)$ ($O(k)$ two-qubit gates); and (ii) a trainability guarantee for its local-design instantiation: with a local read-out and $O(\log n)$ depth the gradient variance is $\Omega(1/\mathrm{poly}(n))$ (no barren plateau), which we confirm empirically – while being explicit that the more expressive all-to-all instantiation we benchmark is trained empirically and shows exponentially decaying gradients. Empirically, at a $6.5\times$ smaller parameter budget, QHA generalizes hidden-subset parity of every order $k\le6$ from disjoint inputs, whereas the larger classical attention head collapses past order~2; consistent with theory, the size of the advantage tracks the target's Fourier degree - largest for parity and shrinking when low-order structure is present. As an application, QHA serves as a compact high-order interaction detector across three domains - genetic epistasis, learning-parity-with-noise, and graph triangle detection - reaching the noise ceiling at the smallest parameter budget where field-standard linear methods fail.