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

APEX: Adaptive Principle EXtraction A Three-Layer Self-Evolution Framework for Production AI Agents

arXiv:2606.15363v1 Announce Type: new Abstract: Self-improvement in AI agents has emerged as a key research frontier: systems that modify their own prompts, workflows, and decision rules based on accumulated operational experience. The state-of-the-art Self-Harness framework [1] achieves 14–21% improvement on Terminal-Bench-2.0 by mining failure clusters and patching the agent harness. However, Self-Harness optimises only one dimension – the prompt harness – leaving behavioural principles and workflow topology unchanged. We propose APEX (Adaptive Principle EXtraction), a three-layer co-evolution framework that simultaneously evolves: (L1) the harness via failure-mode patching, (L2) behavioural principles via success-trace distillation [2], and (L3) the agent workflow topology via structural fitness-based selection [6]. We implement APEX on Joe [13], a production-grade super AI Agent built on NVIDIA Nemotron and designed as an Edge AI Agent Factory for the NVIDIA Agent Challenge 2026, managing a 15-node compute fleet using 114 real task traces collected over 18 days. APEX achieves an APEX Health Score of 0.570 (+90% vs. baseline 0.300) in a single evolutionary run, distilling 6 novel reusable principles and selecting a research-first workflow topology scoring 0.900 (+20%). Our results demonstrate that multi-dimensional co-evolution substantially outperforms single-axis harness optimisation, at a cost of only 4 LLM calls (~270 s) on a local qwen2.5-coder:32b instance.

02.
arXiv (CS.LG) 2026-06-15

Structured Noise Adaptation for Sequential Bayesian Filtering with Embedded Latent Transfer Operators

arXiv:2606.14195v1 Announce Type: new Abstract: Kalman filters based on the Embedded Latent Transfer Operators (ELTO) emerge as novel statistical tools for sequential state estimation. However, a critical limitation stems from their use of simplified noise models, which fail to dynamically adapt to non-stationary processes. To address this limitation, we introduce an ELTO-based Bayesian filtering approach with a new structured parameterization for the filter's noise model. This parameterization enables structured noise adaptation, which couples the data-driven learning of an optimal time-invariant noise model with dynamic parameter adaptation that responds to changes in dynamics within non-stationary processes. Empirical results show that our structured noise adaptation improves the filter's dynamic state estimation performance in noisy, time-varying environments.

03.
bioRxiv (Bioinfo) 2026-06-14

Transposable elements as evolutionary substrates of proteindisorder in the human proteome

Intrinsically disordered regions (IDRs) are central contributors to protein function, evolution and human disease, yet the evolutionary routes that seed new disordered segments within pre-existing proteins are still poorly understood. Sequence insertions provide a powerful mechanism for disorder expansion, but the genomic donors of inserted IDR and its long-term conformational fate remain largely unknown. Transposable elements (TEs), abundant mobile genetic elements with distinctive compositional biases, represent compelling candidates for generating disorder within proteins. Here, we systematically mapped TE-derived segments across human proteins and isoforms, and we found that these insertions are strongly enriched in intrinsic disorder. The structural consequences of their insertion are shaped by TE class and family, reflecting the sequence biases of the elements from which they originate. Recent, Primate specific insertions preferentially generate disordered segments, whereas older insertions more frequently occupy ordered structural contexts, revealing an age-dependent transition in the conformational state of TE-derived sequences. TE-containing isoforms are expressed at lower levels than TE-free isoforms, particularly when insertions are young and disorder-rich, suggesting that intrinsic disorder may constrain the cellular tolerance of newly exonized sequences. These findings identify TEs as a major evolutionary mechanism linking genome mobility to the emergence of new disordered conformational ensembles in the human proteome.

04.
arXiv (math.PR) 2026-06-11

Capital Asset Pricing Model with Size Factor and Normalizing by Volatility Index

arXiv:2411.19444v5 Announce Type: replace-cross Abstract: The Capital Asset Pricing Model (CAPM) relates a well-diversified stock portfolio to a benchmark portfolio. We insert size effect in CAPM, capturing the observation that small stocks have higher risk and return than large stocks, on average. For some size-based stock portfolios, dividing their returns by the Volatility Index makes them closer to independent and normal. In this article, we combine these ideas to create a new discrete-time model, which includes volatility, relative size, and CAPM. We fit this model using real-world data, prove the long-term stability, and connect this research to Stochastic Portfolio Theory. We fill important gaps in our previous article on CAPM with the size factor.

05.
arXiv (CS.CV) 2026-06-11

MFEN:Multi-Frequency Expert Network for Visible-Infrared Person Re-ID

Visible-infrared person re-identification (VI-ReID) is challenging due to the large modality discrepancy between visible and infrared images. We contend that this discrepancy is largely related to differing lighting conditions, including differences in light wavelength and light source type. Recently, frequency-based VI-ReID approaches have achieved notable success because frequency information can better extract identity-relevant contours and details while excluding irrelevant lighting and color. However, existing methods either do not distinguish different frequency bands or focus on only one band, which is insufficient under diverse lighting conditions. To perform comprehensive frequency domain learning, we propose a Multi-Frequency Expert Network (MFEN) that enables multi-frequency modulation and adaptively combines different bands through a mixture-of-experts design. We further introduce Random Frequency Augmentation (RFA) and Frequency Auxiliary Optimization (FAO) to better train MFEN. The three modules are complementary and jointly capture critical frequency-domain details for robust representation learning. Extensive experiments on three VI-ReID datasets demonstrate the effectiveness of our approach.

06.
bioRxiv (Bioinfo) 2026-06-11

SPARK: A Systems-level Computational Framework for Reconstructing Transcriptomic State Organisation in Lung Adenocarcinoma

Lung adenocarcinoma (LUAD) exhibits substantial molecular heterogeneity, which complicates tumour stratification and limits the ability of mutation-centric models to capture tumour behaviour and predict patient outcomes. This study investigates whether coordinated transcriptomic programs can provide a systems-level representation of tumour states. Bulk RNA-sequencing data from the TCGA-LUAD cohort were analysed to reconstruct pathway-level transcriptomic organisation using a stability-optimised network framework (SPARK). This analysis identified eight transcriptomic modules representing coordinated biological processes active across tumours. Module activity scores were subsequently used to derive a composite Transcriptomic Risk Score through elastic-net Cox proportional hazards modelling. The resulting risk score showed a significant association with overall survival in the discovery cohort and improved prognostic discrimination beyond clinical variables. An independent evaluation in the CPTAC-LUAD cohort confirmed the prognostic signal and preserved risk stratification across patient groups. Unsupervised clustering of module activity further revealed three transcriptomic patient groups characterised by distinct biological programs, genomic alteration patterns, and survival outcomes. Single-cell analysis also demonstrated that the identified transcriptomic modules reflect coordinated organisation of the tumour-immune-stromal ecosystem across cellular compartments. Together, these findings suggest that LUAD heterogeneity can be organised into coordinated transcriptomic programs with measurable clinical relevance, providing a systems-level framework for representing tumour molecular states.

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

Remember, Don't Re-read: Stateful ReAct Agents for Token-Efficient Autonomous Experimentation

arXiv:2606.14945v1 Announce Type: new Abstract: The autoresearch pattern enables autonomous experimentation by having a large language model (LLM) iteratively modify code to optimize a target metric. Its stateless design, however, reconstructs experimental context from scratch at every iteration, incurring $O(n)$ token cost per iteration and $O(n^{2})$ total. This work reformulates the pattern as a stateful ReAct agent using LangGraph, where typed persistent state carries experimental history across iterations via a tool-calling interface. Two benchmarks are evaluated: hyperparameter tuning (15 iterations, small per-iteration observations) and code performance optimization (40 iterations, large per-iteration observations containing full source code and benchmark results). On hyperparameter tuning, the stateful agent consumes 90\% fewer tokens (2{,}492 vs.\ 24{,}465). On code optimization, the stateful agent consumes 52\% fewer tokens (627K vs.\ 1{,}275K) while achieving comparable optimization quality on both tasks. The token reduction is structural: the stateless agent re-reads the full history at $O(n)$ cost per iteration, while the stateful agent operates within a fixed-size conversation window at $O(1)$ cost. This paper describes the architecture in sufficient detail for practitioners to implement a stateful autoresearch agent for their own workflows.

08.
arXiv (CS.AI) 2026-06-17

Embedded Machine Learning for Microcontroller-Class Edge Devices: Data, Feature, Evaluation, and Deployment Pipelines

arXiv:2606.18122v1 Announce Type: cross Abstract: Embedded machine learning moves inference from cloud services to resource-constrained devices that must acquire data, preprocess signals, run a model, and act within tight limits on memory, energy, and latency. This paper presents a systems-oriented synthesis of an embedded machine-learning workflow for microcontroller-class platforms. The emphasis is placed on engineering decisions that are often hidden in generic machine-learning introductions: sampling and buffering, feature extraction as dimensionality reduction, validation under class imbalance, model/runtime co-design, and streaming deployment. Two representative signal families are used throughout the paper. The first is inertial motion recognition, where a two-second, three-axis accelerometer window is transformed from raw samples into root-mean-square and spectral features before classification. The second is keyword spotting, where audio is sampled, anti-aliased, transformed into mel-frequency cepstral coefficients, and processed by a compact one-dimensional convolutional network. The paper concludes with practical design rules for robust on-device inference, including data curation, quantization, thresholding, scheduling, and field monitoring.

09.
arXiv (CS.LG) 2026-06-17

Meta-classification of one-class classification models using ranking correlation and nearest neighbor

arXiv:2606.17858v1 Announce Type: new Abstract: Machine Learning (ML) techniques have been applied to various problems. However, applying ML to ML models is an unexplored direction. For this purpose, this paper considers a meta-classification of one-class classification (OCC) models, because all ML models could be approximated as OCC models. The proposal represents OCC models as normality rankings and classifies them using nearest-neighbor and ranking-correlation metrics. The experiment classifies OCC models, where classes correspond to training datasets, algorithms, and hyperparameters. The proposal achieves high accuracy when class labels are datasets. Moreover, it can classify algorithms when the training datasets contain the same class. In addition, the discussion highlights that the classification of OCC models is essentially the classification of datasets that treats multiple samples as a single input. The experiment demonstrates the classification of datasets using sleeping records. The proposed method can provide a unified solution for classifying OCC models, datasets, and rankings. Source code is uploaded to the public repository https://github.com/ToshiHayashi/ClassOCC.

10.
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.

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

Q-Fold: Query-Aware Focus-Context Spatio-Temporal Folding for Long Video Understanding

Long-video understanding remains challenging for multimodal large language models, because temporally extended videos often contain thousands of frames and are therefore expensive to process exhaustively. Existing methods usually construct compact visual inputs from long videos under a limited visual budget. However, most of them still follow a frame-centric paradigm and apply similar representations to retained content regardless of its importance. This makes it difficult to preserve both high-fidelity visual evidence and broad temporal coverage. To address this issue, we propose Q-Fold, a training-free input construction framework for long-video understanding. Instead of treating isolated frames as the basic modeling unit, Q-Fold operates on contiguous temporal segments and constructs a heterogeneous Focus–Context representation under query guidance. Query-relevant segments are preserved as high-fidelity Focus Frames, while less relevant segments are folded into chronology-preserving contextual layouts. In this way, Q-Fold preserves critical visual evidence and broad temporal coverage, while better maintaining local temporal continuity within short segments. Experiments on four long-video benchmarks with multiple Video-MLLMs show that Q-Fold consistently improves performance without increasing the input budget. Notably, it achieves gains of up to 9.1 percentage points on an ultra-long video benchmark. Code will be made publicly available.

12.
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.

13.
arXiv (math.PR) 2026-06-19

Maximal rigidity of random measure and uniqueness pairs: stealthy processes, quasicrystals and periodicity

arXiv:2512.10686v2 Announce Type: replace Abstract: This article investigates the phenomenon of maximal rigidity in spatial processes, where perfect interpolation of the process is possible from partial information, specifically, from its restriction to a strict subdomain, often resulting in a trivial tail $\sigma$algebra. A classical example known since the 1930's is that a time series is fully determined by its values on the negative integers if its spectrum has a gap, or at least a sufficiently deep zero. We extend such results to higher dimensions and continuous settings by establishing a connection with the concept of uniqueness pairs, rooted in the uncertainty principle of harmonic analysis. We present several other manifestations of this principle, unify and strengthen seemingly unrelated results across different models: quasicrystals and stealthy processes are shown to be maximally rigid on cones, and discrete integer-valued processes are necessarily periodic when they have a simply connected spectrum. Finally, we identify a surprising class of continuous fields with seemingly standard behavior, such as linear variance and finite dependency range, that undergo a phase transition: they are perfectly interpolable on B(0, $\rho$) for $\rho$ ___ 2 $\pi$ but exhibit no rigidity for $\rho$ > 2.

14.
arXiv (CS.AI) 2026-06-18

DeFAb: A Verifiable Benchmark for Defeasible Abduction in Foundation Models

arXiv:2606.18557v1 Announce Type: new Abstract: A rule-based logic solver resolves every instance in our benchmark in under 50 microseconds with 100% accuracy; the best frontier language model reaches 65% at best and drops to 23.5% under rendering-robust evaluation (worst case over four surface renderings). We introduce DeFAb (Defeasible Abduction Benchmark), a dataset and generation pipeline that converts four decades of publicly funded knowledge bases into formally grounded instances for defeasible abduction: constructing hypotheses that explain anomalies by overriding defaults while preserving unrelated expectations. Because every hypothesis must pass polynomial-time checks for valid derivation, conservativity, and minimality, DeFAb makes logical rigor the instrument for measuring creativity and theoretical reasoning, scoring the disciplined construction of theory revisions rather than fluent but theory-destroying prose. The pipeline pairs taxonomic hierarchies (OpenCyc, YAGO, Wikidata) with behavioral property graphs (ConceptNet, UMLS) to produce 372,648+ instances across 33.75M materialized rules from 18 sources, in three levels with polynomial-time verifiable gold standards. Four frontier models do not reliably internalize defeasible reasoning: rendering-robust Level 2 accuracy is 7.8-23.5%; chain-of-thought variance (~36 pp) exceeds any inter-model gap; and a matched contamination control isolates a +19.4 pp Level 3 gap. We further release DeFAb-Hard (a 235-instance Level 3 difficulty variant; best model 53.3% vs 100% symbolic) and CONJURE (a kernel-verified transformative-creativity variant of 560 Lean 4/Mathlib instances whose gold answers are definitions the proof kernel did not previously contain, judge-free verifier; a pilot finds zero novel concepts). The same verifier doubles as an exact reward for preference optimization (DPO, RLVR/GRPO). Released under MIT at https://huggingface.co/datasets/PatrickAllenCooper/DeFAb.

15.
bioRxiv (Bioinfo) 2026-06-16

RetroMol: Parsing a shared encoding from natural products and their biosynthetic gene clusters

Natural products such as polyketides and nonribosomal peptides (NRPs) are important sources of bioactive compounds, including many antibiotics. Many of them are assembled by modular enzyme complexes and further modified and diversified by tailoring reactions encoded by biosynthetic gene clusters (BGCs). Although natural products and their coding BGCs describe different data modalities of the same biochemical process, a unified language to jointly describe their biochemistry is lacking. Here we introduce a sequence-based representation of the core biosynthesis of modular natural products, which we call primary sequences, that bridges chemical structures and BGCs. We also present RetroMol, an algorithm that parses either natural product structures or their encoding BGCs into their primary sequences of natural product building blocks. RetroMol allows for similarity scoring between natural products and BGCs, enabling the retrieval of compounds, BGCs, and a combination of the two, based on their biosynthetic similarity. This can, for instance, be used to retrieve biosynthetically similar but structurally dissimilar compounds, or link natural products to candidate coding BGCs in large experimental datasets. We demonstrate the latter by rediscovering the nocardichelin B BGC as a proof of principle. We also exemplify the utility of biosynthetic similarity by showing various pairs of biosynthetically similar compounds with low structural similarity. Together, these results establish primary sequences as a shared biosynthetic encoding for natural product comparison and BGC prioritization.

16.
arXiv (quant-ph) 2026-06-17

Optimal Probe State for Phase Estimation Under Covariant Measurement

arXiv:2606.18169v1 Announce Type: new Abstract: We study the optimization of input states for phase estimation under covariant measurements. Building on Holevo's framework, which provides the optimal covariant measurement for a fixed input state, we further optimize over the input state itself. For a general even $2\pi$-periodic cost function with non-negative Fourier coefficients, we derive a necessary and sufficient condition for the optimal input state: Its Fock coefficients are determined, up to arbitrary phases, by the eigenvector corresponding to the largest eigenvalue of a Toeplitz matrix defined by the cost function. This characterization yields an explicit expression for the attainable lower bound of the average cost under optimal covariant measurements and shows that this bound asymptotically approaches zero in the infinite-energy limit. For the specific cost function $W(\theta,\tilde{\theta})=4\sin^2[(\theta-\tilde{\theta})/2]$, we obtain the optimal input state and the corresponding minimum average cost in closed form, demonstrating Heisenberg scaling with respect to the mean photon number.

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

DIFF-ERO: A Conformance-Aware Loss for Deep Learning in Process Mining

arXiv:2606.14283v1 Announce Type: cross Abstract: Deep learning has driven many recent advances in process analytics, especially for predictive and prescriptive monitoring. However, standard objectives such as cross-entropy optimize local next-step likelihoods and only implicitly capture control-flow structure. As a result, models can achieve high token-level accuracy while permitting imprecise global behaviour. We introduce DIFF-ERO, a conformance-aware loss function for deep learning models on process data. DIFF-ERO is a differentiable formulation of entropy-based stochastic conformance that incorporates control-flow information during training. Our approach constructs batch-level stochastic transition matrices with soft edge memberships, allowing structural precision and recall signals to directly inform backpropagation. The loss is model-agnostic and can be applied whenever the final representation parametrizes stochastic transitions. We instantiate DIFF-ERO in transformer encoder-decoder pipelines for next-activity prediction and use it jointly with cross-entropy to analyse its theoretical components with respect to convergence. Across benchmarks comparing other loss functions and targets, DIFF-ERO shows improved predictive performance where structure matters most while maintaining parity elsewhere. At the same time, the learned stochastic automaton converges towards the structural ground truth, indicating that the network internalizes process model structure.

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

CareTransition-Audit: A Benchmark to Audit Discharge Summaries for Efficient Care Transitions

arXiv:2604.05435v2 Announce Type: replace Abstract: Incomplete or inconsistent discharge documentation drives care fragmentation and avoidable readmissions. Despite its critical role in patient safety, auditing discharge summaries relies on manual review and does not scale. We propose an automated framework for auditing discharge summaries using large language models (LLMs). Our approach operationalizes the DISCHARGED framework into a checklist of 46 questions. Using 50 summaries from the MIMIC-IV database, with clinician ground-truth labels, we benchmark 11 LLMs. Model-assessed mean documentation completeness ranges from 54.9% to 74.2%, and the best-performing models achieve a Cohen's kappa values around 0.5 against clinician labels, indicating moderate agreement. All models struggle to identify ambiguous documentation (Unclear), highlighting a key gap in current automated auditing. This work provides a clinician-validated benchmark and zero-shot baselines for systematic quality improvement in clinical documentation.

19.
arXiv (CS.CL) 2026-06-11

MemToolAgent: Leveraging Memory for Tool Using Agents Based on Environment and User Feedback

Modern large language model (LLM) agents can use external tools to help users solve complex tasks. However, for problems that require learning from long-term historical events or from previous agent-environment interactions, LLM agents are required to use memory mechanisms to store and retrieve experiences. While sophisticated memory systems exist for dialogue agents, few studies have empirically examined how to improve agents' tool-using capabilities through past user-agent conversations. We propose MemToolAgent, a framework that improves tool use through memory management. Our approach contains a memory extraction module that processes past experiences into structured memory entries, and a retrieval module that dynamically selects a subset of the stored memory entries. This enables more personalized and accurate responses aligned with user preferences and feedback without requiring LLM fine-tuning. In summary, this work has three main contributions: (1) a unified memory entry format that improves both general-purpose and personalized tool use without LLM fine-tuning, (2) a reflection-based memory extraction that uses environment and user feedback to distill wrong executions into critiques to store, and (3) a retrieval module that chooses how many past experiences to use based on the memory similarity distribution. MemToolAgent achieves 29%, 80%, and 17% relative improvements compared to strong baselines on the WorkBench, NESTFUL, and PEToolBench benchmarks, respectively.

21.
arXiv (quant-ph) 2026-06-19

Maximum entropy principle for quantum processes

arXiv:2506.24079v3 Announce Type: replace Abstract: The maximum entropy principle, as applied to quantum systems, is a fundamental prescript positing that for a quantum system for which we only have partial knowledge, the maximum entropy state consistent with the partial knowledge is a valuable choice as the system's state. An intriguing result is that in case the only prior knowledge is of a fixed energy, the maximum entropy state turns out to be the thermal state, a ubiquitous state in several arenas, especially in statistical mechanics. We extend the consequences of this principle from static quantum states to dynamic quantum processes. We establish that a quantum channel attains maximal output entropy under a fixed energy constraint if and only if it is an absolutely thermalizing channel, where the fixed output is the thermal state corresponding to that energy. Our results have potential implications for understanding the informational and thermodynamic utility of quantum channels under physical constraints. As an application, we examine the consequences for private randomness distillation from fixed energy constrained quantum processes.

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

CAP: Towards PPG Universal Representation Learning with Patient-level Supervision

arXiv:2606.15284v1 Announce Type: cross Abstract: Photoplethysmography (PPG) plays a central role in wearable health monitoring and clinical decision support. Yet existing approaches to universal PPG representation learning largely focus on signal-level objectives and often overlook patient-level health context, which limits generalization to complex clinical tasks and heterogeneous cohorts. To address this gap, we construct a large-scale paired PPG-EHR multimodal dataset by distilling fragmented medical histories and clinical records into cohesive, patient-level electronic health records (EHR). Building on this resource, we propose Clinical Anchored Pretraining for PPG (CAP). During pretraining, CAP performs cross-modal contrastive alignment that anchors PPG representations to patient-level clinical semantics, guiding the encoder beyond waveform fitting toward modeling consistency in a patient's overall physiological state. During downstream adaptation, the pretrained PPG encoder provides clinically grounded representations that strengthen inductive bias and improve robustness and transferability. Experiments demonstrate that CAP consistently outperforms strong baselines on four diverse downstream tasks. CAP achieves a particularly large gain on respiratory rate prediction (up to +87.6% relative improvement over the state-of-the-art baseline) and delivers an average relative +26.7% across all tasks. We further enhance the interpretability of our approach through comprehensive analyses, including ablations and multiple complementary visualizations of the learned representations. The code for our experiments is available at: https://github.com/gody123gody/CAP .

23.
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.

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

ASTEROID: A Spatiotemporal Information Transformer for Forecasting Multi-Step Time Series of Molecular Dynamics

arXiv:2606.17668v1 Announce Type: cross Abstract: Molecular dynamics (MD) simulation is computationally demanding, particularly for large-scale systems requiring long-term analysis. Accurate forecast of the outcomes of a MD simulation is not only an attractive scientific challenge but also has substantial practical value. In this work, we developed a data-driven framework, termed ASTEROID (Advanced Spatiotemporal TransformER fOr Inferring Dynamics), that can directly predict multi-step atomic coordinates, avoiding conventional iterative integration. For this purpose, our ASTEROID reformulates MD trajectories as high-dimensional spatiotemporal sequences and integrates the Spatiotemporal Information (STI) Transformation equation into a Transformer architecture. The core innovation of ASTEROID lies in its ability to model multiscale spatiotemporal dependencies. In particular, for spatial dependencies, a local-global self-attention mechanism captures both short- and long-range interactions. For temporal dependencies, an encoder-decoder structure integrates global context with autoregressive forecasting. ASTEROID was evaluated on several quantum-mechanics derived molecular datasets. Our results indicate that ASTEROID achieved not only a higher level of accuracy in multi-step prediction than existing methods on various benchmarks, but also significantly reduced computational cost of conventional MD simulation. Moreover, the model supports iterative multi-step forecasting over an extended time scale. This work establishes a robust and generalizable data-driven paradigm for accelerating MD simulations.

25.
medRxiv (Medicine) 2026-06-16

Adverse Childhood Experiences and Growth Outcomes in Childhood: A Longitudinal EHR-Based Study

Question Are adverse childhood experiences (ACEs) associated with altered growth trajectories in childhood? Findings In this cohort study of 412,549 children and adolescents, ACEs were associated with lower height throughout childhood, earlier pubertal timing, and shorter final stature. Height differences emerged approximately 2 years before ACE documentation and were greatest among those with earlier documentation. Meaning These findings suggest that early adversity affects physical growth in children and may serve as a measurable indicator of the biological consequences of early-life stress, especially in those with documentation of ACEs prior to the onset of typical pubertal growth. Importance Adverse childhood experiences (ACEs) are among the strongest risk factors for long-term mental and physical health complications, yet their impact on physical growth in childhood remains incompletely understood. Objective To determine the association of ACEs on childhood growth trajectories and growth dynamics. Design, Setting and Participants Retrospective cohort study using longitudinal electronic health record data. Data was collected from participants between February 1999 and August 2025. A large academic medical center biobank linked to deidentified electronic health records in the southeastern United States. A total of 412,549 individuals with at least 2 recorded height measurements between the ages of 2 and 20 were included in the primary analysis. Growth curve analyses were performed in a subset of 199,844 individuals with at least 3 height measurements spanning at least 2 years. Genetic analyses were performed in a subset of 10,114 individuals of primarily European ancestry. Exposure(s) Documented exposure to adverse childhood experiences before age 18 years identified through a natural language processing algorithm. Main Outcome(s) and Measure(s) Height-for-age z-scores across childhood, final attained height, and growth curve parameters estimated using SuperImposition by Translation and Rotation (SITAR) modeling. Results Among 412,549 participants, 18,502 (4.5%) had clinically documented ACEs during childhood. ACE documentation was associated with lower height-for-age z-scores throughout childhood and adolescence. Final attained height was significantly lower among ACE-documented individuals, with mean differences of -3.0 cm among males (174.0 cm vs 177.0 cm, p < 0.001) and -1.3 cm among females (161.8 cm vs 163.1 cm, p < 0.001). Height differences emerged approximately 2 years before clinical ACE documentation. Earlier age at first ACE documentation was associated with progressively shorter final attained height, with each year decrease in age at ACE documentation associated with a decrease in final height of -0.20 cm in females and -0.35 cm in males. Those with first ACE documented prior to pubertal age also showed the most pronounced growth dynamic differences, with males demonstrating a mean reduction in size of 5.25 cm (95% CI, -6.79 cm to -3.70 cm) and 1.26-year earlier pubertal timing (95% CI, -1.50 to -1.03 years), and females demonstrating a reduction in growth curve size of 3.62 cm (95% CI, -4.83 to -2.41 cm) and 1.14-year earlier pubertal timing (95% CI, -1.29 to -0.99 years). Conclusions and Relevance In this large clinical cohort, clinically documented ACEs were associated with time-dependent reductions in stature, earlier pubertal timing, and short final attained height. These findings suggest that early childhood adversity may have lasting effects on physical development and highlight growth trajectories as a potential marker of the biological consequences of early-life stress.