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

QMaxCal: Path-Space Regularization for Open Quantum Control via Girsanov's Theorem

arXiv:2606.19947v1 Announce Type: cross Abstract: Reliable quantum control in the presence of decoherence requires policies that combat the effect of environmental noise on the controlled dynamics. Open quantum systems under continuous monitoring generate classical measurement records whose drift depends on the noise experienced by the system; the records of two evolutions sharing the same decoherence channels differ only in this drift, so Girsanov's theorem yields a closed-form, differentiable estimator of the KL divergence between their trajectory distributions. We instantiate this estimator with two physically motivated reference measures, yielding two regularizers that both drive the system toward states where the effects of decoherence are minimal: the Wiener KL (KL_W), which is empirically more effective under certain conditions on the noise model, and the drift-variance regularizer (R_DV), which works for all noise models. Both are qualitatively distinct from existing penalties on control fluence or smoothness: they penalize the observable consequences of control on the decoherence channels rather than the control amplitude itself. The regularizers outperform unregularized gradient-based and reinforcement-learning baselines across a range of open quantum systems – including single- and multi-qubit benchmarks and a multi-qubit chain calibrated to a published snapshot of the IBM Kingston processor – along several axes of evaluation: final-state fidelity, robustness to mismatch in the assumed noise model (gains grow from +17 pp at training noise to +27 pp under 2.5x noise mismatch), and occupation of forbidden states. The regularizers reduce infidelity by up to 50%, with ~16% gains on the calibrated IBM Kingston chain.

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

Beyond Static Endpoints: Tool Programs as an Interface for Flexible Agentic Web Services

arXiv:2606.19992v1 Announce Type: cross Abstract: In the agentic web era, LLM-based agents increasingly invoke web services as tools, yet most interfaces remain static endpoints that poorly express long-horizon workflows with loops, conditionals, joins, and retries. We present ToolPro, which represents an agent's tool intent as an executable tool program that compactly encodes multi-step service interactions with explicit effect types. ToolPro combines constraint-guided program construction, effect-aware replay for exactly-once state-modifying calls, and a profile-driven policy that decides when program execution outperforms stepwise calling. We instantiate ToolPro over MCP-style services with WebAssembly sandboxing and evaluate it on diverse workflows of real-world applications. ToolPro reduces end-to-end latency by up to 53.4\% and client-side traffic by up to 96.1\%, with larger gains under higher network latency and workflow complexity.

03.
arXiv (CS.AI) 2026-06-11

Using Explainability as a Training-Time Reliability Signal for Efficient ECG Classification

arXiv:2606.12252v1 Announce Type: cross Abstract: Training deep neural networks for clinical time-series analysis is computationally demanding, yet many healthcare settings lack the resources required for repeated model development and deployment. This challenge is particularly evident in electrocardiogram classification, where large datasets and long training schedules make efficiency practically important. Progressive Data Dropout reduces training cost by excluding samples from gradient updates once they are learned, but it relies on model confidence and may retain samples that are difficult due to noise or ambiguity rather than useful signal. In this work, we introduce ERTS, an explainability-based reliability training signal for efficient ECG classification. ERTS uses explanation quality during training to distinguish between informative and unreliable uncertainty. Building on progressive data selection, we compute Grad-CAM attention maps for candidate samples and derive a focus score that measures whether model predictions are supported by coherent and localised patterns. Samples with low focus are filtered out, while those with meaningful attention are prioritised for gradient updates. We evaluate ERTS across three ECG datasets and multiple backbone architectures, showing consistent improvements in macro-F1 alongside reduced effective training cost. These results suggest that explanation quality can serve as a practical signal for improving both efficiency and reliability in clinical time-series learning. Code will be released.

04.
arXiv (math.PR) 2026-06-16

A tree-free approach to 3D Yang-Mills Langevin dynamic. Analytic estimates and the existence of a model for a regularity structure

arXiv:2605.14616v2 Announce Type: replace Abstract: Using the multi-index approach to regularity structures due to F. Otto et al., we construct a regularity structure and a model for it associated to the stochastic Langevin equation for the 3D Euclidean Yang-Mills functional. For the model we also obtain global stochastic and global pointwise weighted Besov type estimates which hold almost surely. The model is defined as a limit of a sequence of smooth models introduced with the help of a mollified noise. When the mollification is removed the sequence converges in a certain topology defined with the help of the stochastic estimates. To obtain these results we develop the multi-index approach for systems of equations with vector-valued white noises. This project is motivated by the problem for constructing 3D Euclidean Yang-Mills measure and by the earlier results of the author on the related problem of canonical quantization of the Yang-Mills field on the Minkowski space.

05.
arXiv (CS.CL) 2026-06-17

Environment-Grounded Automated Prompt Optimization for LLM Game Agents

LLM agents in interactive environments are highly sensitive to their prompts, yet prompt engineering remains a manual, task-specific process. We introduce an automated prompt optimization framework for LLM agents that decomposes the observation-to-action pipeline into a goal-conditioned descriptor agent and an action selection agent, and iteratively refines each module's prompt through an LLM-driven evolutionary loop guided by environment returns. We propose a behavior analyzer to attribute episode outcomes to specific prompt components, and a mutator to propose targeted revisions to the prompt, before validating them through environment rollouts. We evaluate on all five BabyAI tasks in the BALROG benchmark, comparing our pipeline against BALROG's RobustCoTAgent under both plain and guided prompt initializations. Optimization improves performance consistently across tasks and conditions, without requiring updates to the model weights. On PutNext, a multi-step coordination task where the RobustCoTAgent achieves 0% success, our framework reaches up to 72.5% success rate using the same underlying LLM with optimized prompts. These results suggest that a multi-agent framework, combined with automatic prompt optimization, enhances LLMs without the need for fine-tuning or extensive human supervision.

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

Resource-Efficient Variational Quantum Classifier

arXiv:2511.09204v3 Announce Type: replace-cross Abstract: We introduce the unambiguous quantum classifier based on Hamming distance measurements combined with classical post-processing. The proposed approach improves classification performance through a more effective use of ansatz expressivity, while requiring significantly fewer circuit evaluations. Moreover, the method demonstrates enhanced robustness to noise, which is crucial for near-term quantum devices. We evaluate the proposed method on a breast cancer classification dataset. The unambiguous classifier achieves an average accuracy of 90%, corresponding to an improvement of 6.9 percentage points over the baseline, while requiring eight times fewer circuit executions per prediction. In the presence of noise, the improvement is reduced to approximately 3.1 percentage points, with the same reduction in execution cost. We substantiate our experimental results with theoretical evidence supporting the practical performance of the approach.

07.
arXiv (CS.CL) 2026-06-15

Personal Care Utility: Health as Everyday Infrastructure

Healthcare is essential, expert, and episodic by design - built around the roughly one hour per year a person spends with a clinician. The 8,759 hours outside clinical settings, where eating, sleeping, movement, medication, and stress actually shape long-term health, have no comparable infrastructure. The bottleneck for personalized health is not raw data or reasoning capability; it is the absence of that infrastructure layer. This paper introduces the Personal Care Utility (PCU): a layered, event-driven architecture proposed as the missing utility for everyday health, in the way that payments, networks, and power are utilities for their domains. PCU organizes continuous personal signals into semantically meaningful life events through a Personicle, estimates dynamic health state against personal baselines, reasons about cause and context, and routes guidance through an orchestrator that separates clinical decision logic, behavioral strategy selection, and natural-language expression. This separation lets large language models support reasoning and communication while keeping safety-critical clinical decisions grounded in validated evidence. We instantiate PCU for Type 2 Diabetes - turning CGM, meal, activity, medication, sleep, stress, and clinical data into glycemic events, individualized state estimates, causal explanations, and knowledge-grounded interventions. A day-in-the-life scenario shows the same infrastructure producing real-time nudges, weekly summaries, medication check-ins, silence, or deterministic safety alerts depending on context and risk. We close with how PCU generalizes to other chronic conditions and the governance questions any always-on personal health utility must address. The result is a blueprint that treats personalization not as a final messaging layer, but as an architectural property of everyday health guidance.

08.
medRxiv (Medicine) 2026-06-18

Entrainment of cortical gamma oscillations predicts improved bradykinesia and dyskinesia in Parkinson's disease

Background: Deep brain stimulation (DBS) of the subthalamic nucleus (STN) is hypothesized to improve motor symptoms in Parkinson's disease (PD) by suppressing pathologically elevated beta activity and promoting "prokinetic" gamma activity in the cortico-basal ganglia-thalamo-cortical loop. Advances in bidirectional DBS devices have revealed that stimulation can modify gamma oscillations via subharmonic entrainment, though entrainment's therapeutic role remains unclear. Objectives: To identify stimulation parameters that entrain motor cortical and STN gamma oscillations in PD at rest and during movement, and examine their association with motor function. Methods: Sensorimotor cortex and STN field potentials were collected using a bidirectional DBS system in four subjects with PD over a range of stimulation amplitudes and frequencies. Entrainment amplitude at half the stimulation frequency was quantified at rest and during a finger-tapping task in the ON-medication state. The presence or absence of entrainment was studied as a physiomarker of motor symptom severity. Results: The amplitude of stimulation-entrained gamma oscillations was non-linearly related to stimulation intensity and frequency and varied by stimulation contact choice. Entrainment amplitude was highest in precentral gyrus and increased with movement. In the ON-medication state, precentral gyrus gamma entrainment was associated with reduced bradykinesia, dyskinesia, and dystonia. Subthalamic gamma entrainment predicted improved dystonia but was a less significant marker for motor benefit than cortical entrainment. Conclusions: Stimulation-entrained gamma oscillations in the motor network are a physiomarker for optimal DBS response in PD, and could have a role in physiology-guided DBS programming, complementing existing strategies based on suppression of basal ganglia beta activity.

09.
arXiv (CS.CV) 2026-06-16

SACE: Concept Erasure at the Semantic Singularity in Visual Autoregressive Models

The rapid progress of visual autoregressive (VAR) models has unlocked a transformative frontier for high-fidelity text-to-image synthesis, while heightening concerns over the safety alignment of generated content. Naive application of existing erasure techniques to VAR models causes catastrophic semantic collapse and visual artifacts, since they are predominantly designed for the homogeneous denoising steps of diffusion models. To address this foundational challenge, we first propose the Semantic Singularity Axiom, which posits that any target semantic concept embedded within a prompt is definitively locked at Scale-0. Then rigorously validate this axiom through our proposed Incremental Semantic Saliency Analysis (ISSA),which also enable the community to transparently inspect the coarse-to-fine semantic injection process. Guided by this insight, we introduce the first scale-aware concept erasure framework (SACE) for VAR models. By strictly confining interventions to the first scale, our approach couples an Entropy-Regularized Erasure Objective to prevent high-entropy sampling degeneration, alongside a restorative preservation loss to safely anchor the integrity of entangled benign priors. Extensive experiments demonstrate that our method achieves surgical concept erasure performance across various domains with minimal training overhead, timely and elegently resolute the critical safety vulnerabilities inherent in emerging VAR architectures. Code is available at: https://github.com/limerenceysy/SACE}{https://github.com/limerenceysy/SACE.

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

TMASC: Transmasculine Attitude and Speech Corpus

作者:

We introduce the Transmasculine Attitudes and Speech Corpus (TMASC), a multimodal corpus of 196 transmasculine individuals, including questionnaire responses and 66 audio recordings. The questionnaire includes items exploring the vocal health of transmasculine individuals. The audio recordings include cough and throat-clearing samples, a reading passage, and additional session-specific questions. This paper outlines the development of this corpus and the data collection procedures. To illustrate the utility of this corpus, we present three case studies demonstrating how this crowd-sourced multimodal corpus can be used to support transmasculine individuals. These include the integration of perceptual and acoustic data, the identification of group-level characteristics, and the calibration of acoustic measurements.

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

Boltzmann Attention: Learnable Ising Couplings for Cooperative Attention

arXiv:2606.12478v1 Announce Type: new Abstract: Attention mechanisms are central to modern sequence models, yet standard attention computes relevance primarily through individual query–key similarities. Although softmax normalization introduces competition among positions, a standard attention layer does not explicitly parameterize learnable interactions between attention decisions. This limits its ability to directly model cooperative or antagonistic co-attention structure within the attention mechanism itself. We propose Boltzmann attention, an energy-based generalization in which attention patterns are governed by an interacting Ising model. The method augments the usual data-dependent local fields with learnable pairwise couplings, allowing the model to represent inter-position correlations beyond those captured by softmax or sigmoid attention. Experiments on character-level language modeling and synthetic bracket matching show that Boltzmann attention consistently improves over standard softmax attention within a standard Transformer architecture, with the advantage becoming more pronounced as sequence length increases. A four-way ablation confirms that the improvement arises from the learnable pairwise couplings. These results suggest that explicit inter-position interactions provide a principled enhancement for attention-based sequence modeling. Moreover, the Ising formulation opens a natural path toward quantum-computing-based sampling strategies: we demonstrate that diabatic quantum annealing provides a practical training method while maintaining competitive performance with exact Boltzmann computation.

12.
arXiv (quant-ph) 2026-06-11

Quantum ergodicity and semiclassical measures: mathematical results

arXiv:2606.12098v1 Announce Type: new Abstract: In this chapter we review some results describing the high-frequency eigenmodes of the Laplacian on compact manifolds, or Euclidean domains, for which the geodesic flow is chaotic. We focus on the macroscopic distribution of these eigenmodes, which is described by the concept of semiclassical measure. The main result on the question is the Quantum Ergodicity theorem, originally due to Schnirelman. We provide the detailed proof of this theorem, including the adjustments necessary to treat the case of manifolds with boundary. We also discuss the Quantum Unique Ergodicity conjecture, and some progress towards this conjecture for strongly chaotic (Anosov) systems. In particular, we describe the constraints on admissible semiclassical measures, in terms of their Kolmogorov-Sinai entropy, as well as more recent delocalization results.

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

Trust Region On-Policy Distillation

On-Policy Distillation (OPD) is a fundamental technique for efficient post-training of large language models (LLMs), with broad applications in agent learning, multi-task enhancement, and model compression. However, OPD training becomes unstable when the teacher and student distributions differ substantially, as teacher supervision on student-generated tokens may yield unreliable policy gradients and even cause optimization failure. This work addresses reliable on-policy token-level supervision through credit assignment strategies, and proposes Trust Region On-Policy Distillation, TrOPD. It features the following characteristics: 1) Trust-Region On-Policy Learning: TrOPD performs OPD only in regions where the teacher provides reliable supervision, mitigating the optimization difficulty of the K1 reverse-KL estimator under distribution mismatch. 2) Outlier Estimation: For outlier regions, we explore gradient clipping, masking, and forward-KL estimation to reduce the adverse effects of unreliable supervision. 3) Off-Policy Guidance: The student continues generation from teacher prefixes and uses forward KL to imitate off-policy guidance, encouraging on-policy exploration toward reliable regions. Experiments show that TrOPD consistently outperforms SoTA OPD baselines, including OPD, EOPD, and REOPOLD, across mathematical reasoning, code generation, and general-domain benchmarks.

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

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

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

LLMs+Graphs: Toward Graph-Native, Synergistic AI Systems

arXiv:2606.11560v1 Announce Type: cross Abstract: Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.

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

STaR-DRO: Stateful Tsallis Reweighting for Group-Robust Structured Prediction

arXiv:2604.09737v2 Announce Type: replace-cross Abstract: Structured prediction with large language models requires outputs that are label-accurate, ontology-constrained, structurally valid, and evidence-grounded under label imbalance and heterogeneous group difficulty. We present a unified framework for ontology-constrained generation. First, we introduce a modular prompt-engineering architecture combining XML-style structure, expert disambiguation rules, chain-of-thought reasoning, metadata-aware decision logic, schema contracts, and a self-validation gate. It targets recurrent in-context failures, including format drift, label ambiguity, evidence hallucination, and metadata-conditioned confusion. Second, we propose STaR-DRO, combining Tsallis mirror ascent, sparse entmax-style primal mapback, EMA-smoothed group-loss tracking, rescaled ascent signals, and bounded excess-only multipliers. Unlike conventional DRO, which relies on dense Shannon-entropy exponentiated-gradient updates, can introduce high-variance stochastic reweighting, assigns positive adversarial mass to groups that are not persistently hard, and incurs costs through simplex competition, STaR-DRO upweights only persistently hard groups without suppressing easier ones. We evaluate the framework on EPPC Miner, a clinically grounded high-stakes structured-prediction task requiring hierarchical label prediction and evidence-span extraction from patient-provider secure messages. Across 1B-70B Llama models, prompt engineering improves zero-shot extraction, yielding an average label F1 gain of +14.46 and a Span F1 gain of +17.40. Building on supervised fine-tuning, STaR-DRO further improves accuracy and robustness, increasing average label F1 by +1.08 and +2.20 while reducing mean groupwise validation cross-entropy by 21.3% and 14.8% relative to SFT and standard DRO, respectively. These results advance reliable automated communication mining for patient-centered clinical care analysis.

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

Contour Field based Elliptical Shape Prior for the Segment Anything Model

The elliptical shape prior information plays a vital role in improving the accuracy of image segmentation for specific tasks in medical and natural images. Existing deep learning-based segmentation methods, including the Segment Anything Model (SAM), often struggle to produce segmentation results with elliptical shapes efficiently. This paper proposes a new approach to integrate the prior of elliptical shapes into the deep learning-based SAM image segmentation techniques using variational methods. The proposed method establishes a parameterized elliptical contour field, which constrains the segmentation results to align with predefined elliptical contours. Utilizing the dual algorithm, the model seamlessly integrates image features with elliptical priors and spatial regularization priors, thereby greatly enhancing segmentation accuracy. By decomposing SAM into four mathematical sub-problems, we integrate the variational ellipse prior to design a new SAM network structure, ensuring that the segmentation output of SAM consists of elliptical regions. Experimental results on some specific image datasets demonstrate an improvement over the original SAM.

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

Towards Deep Learning Surrogate for the Forward Problem in Electrocardiology: A Scalable Alternative to Physics-Based Models

arXiv:2512.13765v2 Announce Type: replace-cross Abstract: The forward problem in electrocardiology, computing body surface potentials from cardiac electrical activity, is traditionally solved using physics-based models such as the bidomain or monodomain equations. While accurate, these approaches are computationally expensive, limiting their use in real-time and large-scale clinical applications. We propose a proof-of-concept deep learning (DL) framework as an efficient surrogate for forward solvers. The model adopts a time-dependent, attention-based sequence-to-sequence architecture to predict electrocardiogram (ECG) signals from cardiac voltage propagation maps. A hybrid loss combining Huber loss with a spectral entropy term was introduced to preserve both temporal and frequency-domain fidelity. Using 2D tissue simulations incorporating healthy, fibrotic, and gap junction-remodelled conditions, the model achieved high accuracy (mean $R^2 = 0.99 \pm 0.01$). Ablation studies confirmed the contributions of convolutional encoders, time-aware attention, and spectral entropy loss. These findings highlight DL as a scalable, cost-effective alternative to physics-based solvers, with potential for clinical and digital twin applications.

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

MedLatentDx: Latent Multi-Agent Communication for Cross-Hospital Rare-Disease Diagnosis

Rare diseases affect over $300$ million patients across more than $7{,}000$ conditions, yet no single hospital encounters enough cases of any one condition for reliable diagnosis. Cross-hospital collaboration could help by allowing a diagnosing institution to use distributed, case-specific diagnostic evidence, but privacy regulations restrict the transmission of identifiable clinical text across institutional boundaries. This setting raises two challenges: existing medical agent systems often rely on textual evidence exchange, while raw latent states such as hidden states and KV caches may still reveal prompt-derived clinical content. We introduce MedLatentDx, a latent multi-agent communication framework in which hospital agents keep private clinical records and retrieved cases local, and send compact latent KV blocks to a host agent for rare-disease diagnosis. MedLatentDx supports two deployment settings: same-backbone hospital agents use latent KV distillation, while hospitals with different LLM backbones use cross-family latent alignment. On CrossRare-Bench, a self-built large-scale rare-disease benchmark with hospital-level partitions, MedLatentDx improves cross-hospital diagnostic performance while reducing reconstructable clinical content relative to raw-latent communication baselines.

20.
medRxiv (Medicine) 2026-06-15

Two Blood-based Endotypes Reveal Divergent Clinical Outcomes of Fibrotic Hypersensitivity Pneumonitis

Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an antigen-driven, life-threatening interstitial lung disease characterized by heterogeneous radiologic features, clinical outcomes, and treatment responses. Objectives: To identify blood-based fHP endotypes that inform mechanism, prognosis and therapeutic response. Methods: We performed integrative analyses of multi-compartment transcriptomic data derived from whole blood, peripheral blood mononuclear cells, bronchoalveolar lavage, and surgical lung biopsies, alongside circulating plasma proteomics. Multiple clustering algorithms were cross-compared to ensure robustness and reproducibility of endotypes identification. Immune cell composition was inferred using bulk RNA-seq deconvolution and annotated with BAL single-cell RNA-seq. Pathway activities were characterized using Gene Set Enrichment Analysis. Transplant-free survival (TFS) was evaluated for endotype and corticosteroid exposure by Kaplan-Meier methods, with hazard ratios analyzed using multivariable Cox proportional hazards models. Results: Two molecular endotypes, lymphocytic-associated (L-fHP) and non-lymphocytic-associated (N-fHP), were identified and validated. L-fHP showed enrichment of adaptive immune signaling and lymphocyte predominance, whereas N-fHP demonstrated myeloid-cell activation with neutrophil and macrophage predominance. Corticosteroid exposure was associated with worse TFS in L-fHP but not in N-fHP after adjusting for age, sex, and baseline pulmonary function. Compared to L-fHP, N-fHP had poorer baseline pulmonary function, faster 12-month FVC decline, and shorter TFS. N-fHP also exhibited elevated neutrophil-associated markers, including matrix metalloproteinase-9, across paired transcriptomic and proteomic datasets, supporting a neutrophil-driven, cross-compartment disease process. Conclusion: Multi-omic, multi-compartment analysis identifies two reproducible fHP endotypes with distinct clinical outcomes and corticosteroid responses, supporting a precision medicine approach beyond current clinical and radiologic classification.

21.
arXiv (CS.AI) 2026-06-19

Computational Identifiability

arXiv:2606.19361v1 Announce Type: cross Abstract: Identification conditions describe the computability of a target query or parameter of interest as a function of the type and amount of information available. In causal identification, this information is often expressed in the form of a causal graph, and data are observed or collected for some subset of variables in the graph. Target queries may be for a single effect alone or for a class of effects in a given model. The derivation of an identification algorithm then defines mathematically the process by which the desired causal effect(s) can be uniquely determined, theoretically, in expectation. Identifiability in expectation, or 'theoretical identifiability,' generally assumes asymptotic properties, infinite data, or other mathematically idealized conditions. In this paper, we explore a fundamental distinction between this theoretical, idealized notion of identifiability and a proposed alternative that is computation-bound. The framework we propose - 'computational identifiability' - is to instead define a finite computational search procedure for an empirical estimator. If this process finds an estimator empirically, within a desired error tolerance, then identifiability is satisfied, conditional on the specified assumptions of the search (i.e., a prior distribution over the parameters) and conditional on the search procedure itself. Through several experiments, we demonstrate how this framework allows us to answer fine-grained, practical identification questions, such as identification with small finite samples, with ambiguous graphical criteria, with mixed observational-interventional data, and across counterfactual data and estimands. Code is available at https://github.com/lbynum/metadentify.

22.
arXiv (CS.AI) 2026-06-16

SDFLoRA: Selective Decoupled Federated LoRA for Privacy-preserving Fine-tuning with Heterogeneous Clients

arXiv:2601.11219v3 Announce Type: replace-cross Abstract: Federated learning (FL) for large language models (LLMs) has attracted increasing attention as a privacy-preserving approach for adapting models over distributed data, where parameter-efficient methods such as Low-Rank Adaptation (LoRA) are widely adopted to reduce communication and memory costs. However, practical deployments often exhibit rank and data heterogeneity: clients operate under different low-rank budgets and data distributions, making direct aggregation of LoRA updates biased and unstable. Existing approaches either enforce a unified rank or align heterogeneous updates into a single shared subspace, which tends to mix transferable and client-specific directions and consequently undermines personalization. Moreover, under differential privacy (DP), perturbing such structurally mixed updates injects noise into directions that should remain purely local, leading to unnecessary utility degradation. To address these issues, we propose Selective Decoupled Federated LoRA (SDFLoRA), a structure-aware LoRA framework that decouples each client update into a shared component for aggregation and a private component that preserves client-specific semantics. Only the shared component participates in subspace alignment, while the private component remains local and uncommunicated, making the training DP-compatible and stabilizing aggregation under rank heterogeneity. By injecting noise only into the aggregated shareable update, this approach avoids perturbations to local directions and improves the utility-privacy trade-off. Experiments on multiple benchmarks demonstrate that SDFLoRA outperforms federated LoRA baselines and achieves a strong utility-privacy trade-off.

23.
arXiv (CS.LG) 2026-06-15

Lifted Schrödinger Bridges for Gaussian Mixture Endpoints: Projection Gaps and Path-Space Obstructions

arXiv:2605.24795v2 Announce Type: replace-cross Abstract: We study stochastic density control between Gaussian-mixture endpoint distributions under Brownian prior dynamics. Since the direct Schrödinger bridge between Gaussian mixtures is generally not available in closed form, we introduce a lifted path-space construction in which each trajectory is augmented with a source–target component label. Consequently, the problem decomposes into Gaussian component-to-component Schrödinger bridges with explicit marginal, drift, and cost formulas, while the mixture-level assignment reduces to a finite-dimensional entropic coupling problem with a Sinkhorn scaling form. We then analyze the projection obtained by discarding or forgetting the label. By construction, the projected law satisfies the original Gaussian-mixture endpoint constraints, but its relative entropy generally differs from the lifted relative entropy by a nonnegative conditional label-information gap. This gap reveals a path-space obstruction: the lifted optimizer cannot, in general, be identified with the direct unlabeled Schrödinger bridge after projection. We also derive the posterior-averaged Markov drift associated with the projected marginal flow, prove a kinetic-energy upper bound, and identify a common path-potential condition under which the projection gap vanishes. Several numerical illustrations showing density and shape control are recorded for a self-contained exposition.

24.
bioRxiv (Bioinfo) 2026-06-10

HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues

Cellular heterogeneity is a major confounder in bulk DNA methylation data for epigenome-wide association studies. Existing reference-based DNAm deconvolution methods often ignore hierarchies among related cell types and may generalize poorly across datasets due to limited variability in reference profiles. We developed HOMED (Hierarchically Optimized Methylation Deconvolution), a framework that integrates cell-lineage hierarchies, single-cell RNA sequencing-guided deconvolution, and paired bulk RNA-seq/DNAm data for CpG signature optimization. Across simulated and real peripheral blood mononuclear cell, lung, and placental datasets, HOMED consistently yielded the highest PCCs and lowest RMSEs, outperforming existing scRNA-seq-guided DNAm deconvolution methods, improving accuracy, resolution, and cross-tissue generalizability.

25.
bioRxiv (Bioinfo) 2026-06-18

Accounting for allelic diversity and multicopy gene detection improves the accuracy of antibiotic resistance genotypic determination

Background Genomic prediction of antimicrobial resistance (AMR) relies on the accurate detection of resistance genes or allelic variants of core genes from raw or assembled genomes sequences. For several bacterial species and antibiotics, AMR genotype-phenotype discrepancies are common, indicating that important sources of error remain unresolved. For Enterococcus faecium, we focused on identifying the sources of discrepancies for tetracycline resistance, for which genotypic detection had shown particularly low accuracy. We investigated the effect of structural variation in antibiotic resistance genes (ARGs), including gene duplications, truncations, interruptions, and mixed configurations of complete and partial gene copies, as a source of genotype-phenotype discrepancies from short-read data. We conduct further extended investigations to other antibiotic families and into another bacterial species: Escherichia coli. Methods We analyzed collections of E. faecium and E. coli genomes, integrating high-quality complete assemblies, simulated Illumina short reads, and matched AMR phenotypic data. The integrity, copy number, and allelic diversity of ARGs were examined for multiple antibiotic classes, and their impact on ARG detection and accuracy of AMR determination was assessed using several commonly used bioinformatic tools (SRST2, ARIBA and AMRFinderPlus). Results For E. faecium, after ruling out the effect of specific tet allelic variants on tetracycline susceptibility, we found that the integrity and copy number of tet(M) had a major effect on detection accuracy. Duplicated and incomplete ARGs are also common in E. faecium genomes, particularly for macrolides (erm(B)) and aminoglycosides (ant(6)-Ia and aph(3')-IIIa). In E. coli, similar patterns were observed for tet(A), erm(B) and aminoglycoside-associated genes (aph(3')-IIIa and ant(6)-Ia). Across ARGs in both species, short-read mapping methods wrongly reported interrupted genes as complete in some instances, while assembly-based methods often failed to resolve complete copies of duplicated genes. Detection accuracy improved when tools were adapted to account for gene integrity and when extended AMR databases incorporating species-specific alleles were included. Conclusions Our findings reveal that bioinformatic limitations in dealing with ARG copy number and completeness, and in accounting for allelic variation, underly a substantial source of genotype-phenotype errors, highlighting the need for improved AMR databases and bioinformatic tools that consider these factors to achieve reliable genomic prediction of AMR.