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

Decoupled Motion Representation Learning for Moving Infrared Small Target Detection

Infrared small target detection in dynamic scenes remains challenging due to the highly coupled motions among targets, imaging platforms, and dynamic backgrounds. Existing multi-frame methods usually perform implicit temporal modeling, where coherent background dynamics dominate motion correspondence learning, leading to an inherent trade-off between detection and false alarms. In this work, we observe that background motions exhibit strong global coherence, whereas small targets mainly correspond to sparse local motion anomalies. Moreover, many false-alarm responses maintain high consistency with globally coherent motion patterns, indicating that they mainly originate from coherent background dynamics rather than genuine target motions. Based on these observations, we propose a decoupled motion representation learning framework for moving infrared small target detection. Specifically, an explicit motion branch is introduced to model globally coherent motion dynamics using pretrained optical flow priors, together with a structure-preserving self-supervised adaptation strategy for infrared motion correspondence learning. Meanwhile, an implicit motion branch based on deformable feature alignment is designed to capture target-sensitive local motion anomalies under coherent motion guidance. Furthermore, a coherent-motion-guided local anomaly reasoning module is proposed to identify and suppress coherent-motion-induced false responses during localized motion modeling. Extensive experiments on two challenging infrared small target detection benchmarks demonstrate that the proposed method consistently outperforms existing state-of-the-art approaches, particularly in dynamic scenes with complex motions, while maintaining favorable inference efficiency.

02.
arXiv (math.PR) 2026-06-11

Second-order PACF asymptotics and discrimination between fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$

Authors:

arXiv:2605.31416v2 Announce Type: replace-cross Abstract: Fractional Gaussian noise and $\operatorname{FARIMA}(0,d,0)$ have the same long-memory pole $|\theta|^{-2d}$ and hence the same leading PACF law $\alpha(n)\sim d/n$. We show that this agreement breaks at the first non-universal order. For $0

03.
arXiv (CS.AI) 2026-06-19

Structuring and Tokenizing Distributed User Interest Context for Generative Recommendation

arXiv:2606.20554v1 Announce Type: cross Abstract: Generative recommendation is an emerging paradigm that has shown promise in industrial recommendation systems, aiming to predict users' next interactions from their historical behaviors. At the core of generative recommendation lies item tokenization, which bridges item semantics and recommendation models. However, existing methods often struggle to effectively organize and inject complex user-behavioral and item-semantic contexts into recommendation models simultaneously. On the one hand, existing graph-based integration methods, such as graph serialization and graph neural networks, either suffer from scalability issues or exploit only local graph information. On the other hand, existing semantic tokenization methods typically rely on heuristics and lack explicit supervision signals, which may lead to inaccurate or suboptimal semantic representations. To address these limitations in user interest context modeling, we propose G2Rec, a scalable framework that unifies holistic graph-based user co-engagement modeling with semantic tokenization for industrial-scale generative recommendation. Overall, G2Rec enables recommendation models to capture holistic and semantically grounded user interest prototypes without requiring ground-truth user interests, thereby providing more comprehensive and accurate modeling of user behavior contexts in industrial sequential recommendation. Online deployment across product surfaces and extensive experiments on public datasets demonstrate the superiority of G2Rec over existing methods.

04.
Nature Biotechnology 2026-06-23

Mapping and engineering the human cell–cell interactome

Authors:

Efforts to systematically understand how cell interactions tune tissue-level function have motivated transformative advances in single-cell transcriptomics and spatial profiling. Although these technologies can measure molecular states in individual cells and their spatial mapping within tissues, they also reveal that there exists a fundamental knowledge gap of how cells influence each other in context. In this Perspective, we propose an initiative to map and engineer the human cell–cell interactome: a functional atlas of how all major human cell types communicate. We highlight how recent innovations can make this vision achievable. As a first moonshot, we propose the ‘Billion Cell×Cell Project’, which systematically characterizes the outcomes of defined cell–cell dyads across diverse cell types and conditions. We envision this multistage initiative will produce progressively deeper insights and unlock additional avenues for therapeutic discovery. We call on the scientific community to join us in building the tools, datasets and models that will decode and rewrite the language of life between cells. Di Carlo and colleagues discuss technologies required to map and engineer the human cell–cell interactome and the therapeutic avenues such an atlas could unlock.

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

From Observation to Intervention: A Causal Audit of Expert Importance in Mixture-of-Experts Models

Interpretability methods routinely use population-level summary statistics over observed model behaviour to license claims about the effects of targeted interventions on specific computations; in Pearl's terms, they treat rung-1 associational evidence as if it supported rung-2 interventional conclusions, a move whose validity is rarely tested. We examine one concrete instance: the use of routing statistics in Mixture-of-Experts (MoE) pruning, where utilization rates, activation norms, and routing weight distributions are treated as predictors of which experts can be removed without functional cost. A token-level interventional audit across three high-redundancy MoE architectures (OLMoE-1B-7B-0924, Qwen1.5-MoE-A2.7B, DeepSeek-V2-Lite) finds no observational metric predicts causal expert importance in any model: across all 60 metric-layer combinations effect sizes stay below Cohen's $d = 0.23$, and no metric is reliably positive under our corrected, dual-test criterion. A per-token routing weight control, run with identical $n$, rules out insufficient power, recovering a signal whose CI excludes zero at OLMoE's final MoE layer ($d = +0.231$, 95\% CI $[+0.09, +0.37]$, $p = 0.0013$). Existing pruning methods succeed in this regime not by identifying dispensable experts but because early-layer redundancy renders most selection criteria interchangeable. Our results provide an explicit counterexample to the common inferential step from population-level observational summaries to token-level interventional claims about expert importance, and illustrate how interventional audits can calibrate the evidential standards for interpretability claims.

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

GUMP-Net: An interpretable model-data-driven intelligent algorithm for multi-class pelvic segmentation

Pelvic segmentation is one of the most important and fundamental research problems in precise and intelligent diagnosis and treatment, as well as surgical planning and navigation for pelvic fractures. By combining an improved geodesic active contour model with deep neural networks, we propose GUMP-Net, an interpretable model-data-driven intelligent algorithm for multi-class pelvic segmentation, in which three network modules are designed to constitute the overall segmentation framework together: the object detection module for automatic level set initialization, the edge detector module for learning an anatomy-aware edge detector function and the iteration module for deep level set evolution. Leveraging the advantages of level set representation and deep learning, GUMP-Net shows more accurate, robust and consistent segmentation performance, especially in small training data situation, compared to the state-of-the-art methods. Extensive experiments on pelvic datasets demonstrate the rationality and effectiveness of the proposed algorithm. Further experiments extended to ankle dataset indicate broader applications to other anatomies. The proposed algorithm not only provides an efficient segmentation method for complex fracture reduction, but also gives an interpretable geometric perspective for understanding deep learning segmentation.

07.
arXiv (CS.CL) 2026-06-11

SOMA-SQL: Resolving Multi-Source Ambiguity in NL-to-SQL via Synthetic Log and Execution Probing

Natural language interfaces to databases aim to translate user questions into executable SQL, yet remain brittle in real-world settings where questions are underspecified and schemas are large and ambiguous. Ambiguity across user questions, database schemas, and model interpretations are central failure modes in NL2SQL, leading to misaligned intent, incorrect schema grounding, and erroneous SQL generation. Existing approaches rely on human clarification or treat ambiguity as a schema representation problem, but these do not scale nor resolve ambiguity autonomously. We propose SOMA-SQL to automatically resolve ambiguity via targeted synthetic query log and ambiguity-driven probing. SOMA-SQL constructs synthetic query log to ground schema interpretation and guide candidate SQL generation; it then executes targeted probing queries, driven by a structured ambiguity taxonomy and candidate disagreements, to produce disambiguation evidence for final SQL selection and repair. This active approach to ambiguity discovery and resolution generalizes across unseen schemas and query distributions without human-in-the-loop. Experiments on six public benchmarks demonstrate that SOMA-SQL improves execution accuracy by 13.0% on average over state-of-the-art baselines, with gains of up to 16.7% on ambiguous questions.

08.
medRxiv (Medicine) 2026-06-12

Conversational Artificial Intelligence-Enabled Precision Oncology Reveals Context-Specific TGFβ and JAK/STAT Alterations in Pancreatic Cancer

Background: Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive molecular complexity, profound stromal remodeling, and limited responsiveness to systemic therapies. Although gemcitabine-based regimens remain widely utilized, the molecular pathways that influence treatment-associated biological variation are incompletely understood. The TGF{beta} and JAK/STAT signaling networks are recognized regulators of tumor progression, immune modulation, and therapeutic resistance; however, their genomic architecture in clinically stratified PDAC populations remains poorly defined. Methods: We employed a conversational artificial intelligence-driven analytical framework to investigate TGF{beta} and JAK/STAT pathway alterations in a cohort of 184 PDAC patients. Clinical and molecular data were integrated to generate age- and treatment-stratified cohorts, enabling pathway-level and gene-level analyses according to gemcitabine exposure. Findings generated through AI-assisted interrogation were subsequently evaluated using conventional statistical approaches. Results: TGF{beta} pathway alterations were identified in approximately one-quarter to one-third of tumors across clinical subgroups and demonstrated relatively stable frequencies regardless of age at diagnosis or gemcitabine treatment status. Gene-level analyses revealed that pathway disruption was predominantly driven by recurrent alterations in SMAD4, with additional low-frequency events involving TGFBR1 and TGFBR2. Notably, TGFBR2 mutations were significantly more frequent among late-onset PDAC patients receiving gemcitabine compared with untreated late-onset patients (8.8% vs. 1.4%; p = 0.04), suggesting a potential treatment-associated enrichment. In contrast, JAK/STAT pathway alterations were rare throughout the cohort, with only isolated mutations observed in pathway components including JAK1, JAK2, JAK3, STAT1, STAT3, and related regulatory genes. No significant differences in JAK/STAT alteration frequencies were identified according to age or treatment exposure. Conclusions: TGF{beta} and JAK/STAT pathways exhibit distinct genomic architectures in PDAC. TGF{beta} pathway disruption represents a recurrent feature of disease biology, largely driven by SMAD4 alterations, while TGFBR2 enrichment in gemcitabine-treated late-onset tumors suggests a potential context-specific association worthy of further investigation. Conversely, genomic alterations within the JAK/STAT pathway are uncommon, indicating that pathway activity may be regulated predominantly through non-genomic mechanisms. These findings demonstrate the utility of conversational artificial intelligence agents for rapid, scalable, and clinically contextualized pathway interrogation and support future studies integrating multi-omic data to refine precision medicine strategies in PDAC.

09.
medRxiv (Medicine) 2026-06-18

Development and Initial Validation of the Quality of life Evaluation in NF2-related Schwannomatosis Trials (QUEST) Assessment

Individuals with NF2-related schwannomatosis (NF2-SWN) experience a complex constellation of physical, emotional, and social symptoms that substantially impact quality of life (QoL). Although disease-specific patient-reported outcome measures are increasingly important for evaluating treatment benefit in clinical trials, existing NF2-SWN QoL measures have limitations in content coverage and sensitivity to change. This study describes the development and initial validation a new disease-specific QoL assessment – the Quality of Life Evaluation in NF2-related Schwannomatosis Trials (QUEST). Using a three-phase, mixed-methods approach, items were generated through concept elicitation interviews with individuals with NF2-SWN and clinicians, prioritized via patient survey data, and refined through iterative cognitive debriefing procedures. The resulting 21-item QUEST assesses the extent to which NF2-SWN has negatively impacted a persons daily life over the past seven days. Initial psychometric evaluation was conducted in an international sample of 174 individuals with NF2-SWN aged 15 years and older (117 women (67%), 158 White individuals (89%)). Exploratory factor analysis supported a four-factor structure, and the total score demonstrated excellent internal consistency and strong test-retest reliability. Evidence of construct validity was demonstrated through hypothesized associations with disease-specific, generic, and domain-specific QoL measures, as well as known-groups validity based on self-reported disease severity and number of prior surgeries. Incremental validity analyses indicated that QUEST explained unique variance beyond existing measures. Together, findings support the QUEST as a reliable and valid disease-specific QoL measure with strong content validity and feasibility for use as a clinical trial endpoint in NF2-SWN.

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

MVOFormer: Flow-Semantic Transformer for Robust Monocular Visual Odometry

Monocular visual odometry (MVO) is foundational to autonomous navigation and robotic localization. However, existing learning-based MVO approaches often struggle with either a lack of interpretable, complementary features or overly complex multi-stage architectures. These limitations inherently restrict their robustness and cross-domain generalization. In this work, we propose MVOFormer, a novel transformer framework for robust monocular visual odometry. Our architecture features a Flow-Semantic Dual Branch Encoder that synergizes dense geometric motion cues with object-centric semantic priors, explicitly distinguishing static structures from dynamic distractors. These representations are then fused by an Iterative Multimodal Decoder, enabling coarse-to-fine pose refinement while dynamically suppressing attention on unreliable regions. Extensive evaluations demonstrate that, without any target-domain fine-tuning, MVOFormer achieves superior zero-shot generalization and robustness, significantly outperforming prior learning-based frame-to-frame methods across diverse benchmarks including TartanAir, KITTI, TUM-RGBD, and ETH3D-SLAM.

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

PACE-RAG: Patient-Aware Contextual and Evidence-Constrained RAG for Clinical Drug Recommendation

Drug recommendation requires a deep understanding of individual patient context, especially for complex conditions like Parkinson's disease. While LLMs possess broad medical knowledge, they fail to capture the subtle nuances of actual prescribing patterns. Existing RAG methods also struggle with these complexities because guideline-based retrieval remains too generic and similar-patient retrieval often replicates majority patterns without accounting for the unique clinical nuances of individual patients. To bridge this gap, we propose PACE-RAG (Patient-Aware Contextual and Evidence-Constrained RAG). Rather than directly copying frequent medications from retrieved patients, PACE-RAG personalizes recommendations by first extracting patient-specific clinical features, retrieving cases around these features, and then refining the final prescription using the patient's current symptoms, active medication history, and focus-specific prescribing tendencies. By analyzing treatment patterns tailored to specific clinical features, PACE-RAG generates patient-specific medication recommendations along with an explainable clinical summary. Evaluated on a Parkinson's cohort and the MIMIC-IV benchmark using Llama-3.1-8B and Qwen3-8B, PACE-RAG achieved state-of-the-art performance, reaching F1 scores of 80.84% and 47.22%, respectively. These results suggest that PACE-RAG is a robust and clinically grounded framework for personalized decision support. Our code is available at: https://github.com/ChaeYoungHuh/PACE-RAG.

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

DAM-VLA: Decoupled Asynchronous Multimodal Vision Language Action model

Vision-language-action (VLA) models inherit a shared synchronous clock from vision-language pretraining, processing every input at one rate. This is misaligned with physical interaction, where a high-frequency modality changes at hundreds of hertz, vision evolves more slowly, and language stays constant across an episode. A synchronous VLA oversamples slow modalities, undersamples fast ones, and caps action generation at the lowest effective frequency. We hypothesize that decoupling temporal processing per modality, letting each update and retain information at its own sensor rate, yields stronger representations and more robust control. We present DAM-VLA, which maintains per-modality latent buffers refreshed at sensor rates and read continuously by the action head, integrating new high-frequency modalities through gated cross-attention that leaves the pretrained backbone intact. Across seven contact-rich real-world manipulation tasks, DAM-VLA more than doubles the average success rate of the strongest synchronous baseline (95.2\% vs.\ 40.95\%) while sustaining smooth, reactive 100\,Hz control. Project website: \href{https://intuitive-robots.github.io/DAM-VLA/}{intuitive-robots.github.io/DAM-VLA/}

13.
arXiv (quant-ph) 2026-06-12

Resourcefulness of non-classical continuous-variable quantum gates

arXiv:2410.09226v4 Announce Type: replace Abstract: In continuous-variable quantum computation, identifying key elements that enable a quantum computational advantage is a long-standing issue. Starting from the standard results on the necessity of Wigner negativity, we develop a comprehensive and versatile approach in which the techniques of $(s)$-ordered quasiprobabilities are exploited to provide rigorous statements on the simulability of photonic quantum circuits consisting of previously characterized gates and thereby identifying the contribution of each quantum gate to the potential achievement of quantum computational advantage. This is achieved by means of an analysis of the so-called transfer function, allowing us to highlight the resourcefulness of a gate set. As such this technique can be straightforwardly applied to current continuous-variables quantum circuits, while also constraining the tolerable amount of losses above which any potential quantum advantage can be ruled out. We use $(s)$-ordered quasiprobability distributions on phase-space to capture the non-classical features in the protocol, and focus our technique entirely on the ordering parameter $s$. This allows us to highlight the resourcefulness and robustness to loss of a universal set of unitary gates comprising three distinct Gaussian gates and any non-Gaussian unitary gate, providing important insight on the role of non-Gaussianity.

14.
arXiv (CS.CL) 2026-06-19

Towards Truly Multilingual ASR: Generalizing Code-Switching ASR to Unseen Language Pairs

Automatic Speech Recognition (ASR) has become a key technology for human–AI interaction. However, code-switching ASR (CS-ASR) remains particularly challenging due to the severe scarcity of multilingual CS speech resources across diverse language pairs. Existing approaches primarily improve CS-ASR performance through synthetic CS speech generation or pair-specific fine-tuning on limited bilingual datasets. Nevertheless, these approaches face an inherent scalability limitation, as support for CS must be developed separately for language pairs whose number grows combinatorially with the number of supported languages. In this work, we investigate whether CS capabilities learned from a limited set of seen language pairs can generalize to unseen language pairs through model merging and domain generalization methods. Our experiments show that merged bilingual CS-ASR models modestly generalize to unseen language pairs, suggesting limited transfer of bilingual CS capabilities across language pairs.

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

Attention Expansion: Enhancing Keyphrase Extraction from Long Documents with Attention-Augmented Contextualized Embeddings

Pre-trained language models (PLMs) have achieved strong performance in keyphrase extraction (KPE), largely due to their ability to generate rich contextualized representations. However, long-document KPE remains challenging because salient keyphrase evidence may be scattered across distant document sections that cannot be jointly captured within the limited context window of most PLMs. Although long-context large language models (LLMs) can process broader textual contexts, their computational cost limits their practicality for efficient and high-throughput KPE. To overcome this limitation, we propose an attention expansion mechanism that augments PLM token representations with information from surrounding out-of-context chunks using pre-trained word embeddings. The proposed mechanism expands the effective contextual scope of PLM-based KPE models without requiring full-document attention or expensive LLM-based inference. We evaluate our approach across five PLM backbones, including general-purpose, scientific, task-specific, and long-context encoders, using two training regimes and five benchmark corpora from scientific and news domains. Experimental results demonstrate that attention expansion consistently enhances KPE performance across all evaluation settings, outperforming state-of-the-art models and yielding notable improvements in F1 score. The improvements extend to domain-specific, task-specialized, and native long-context models, showing that the proposed mechanism provides complementary information rather than merely compensating for limited input length. These results establish attention expansion as an efficient and effective strategy for long-document KPE.

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

Robust Spoofed Speech Detection via Temporal Pyramid Modeling

Spoofed speech detection is increasingly challenged by realistic synthesis, voice conversion, and replay attacks, with cross-dataset generalization remaining a major limitation. This work we propose a Temporal Pyramid Adapter that utilize parallel temporal convolutions with varying receptive fields to capture multi-scale spoofing cues, ranging from local artifacts to global prosodic irregularities. We also integrated self-supervised XLS-R representations combined with front-end adapters, including Mel, Sinc, and a Temporal Pyramid design for multi-scale temporal modeling. The proposed model is evaluated cross multiple benchmark including ASVspoof 2017, ASVspoof 2021 (DF/LA), PartialSpoof, DiffSSD, and multilingual HQ-MPSD datasets. Experimental results demonstrate that Temporal Pyramid model obtained AUC of 99.24% and a EER of 3.87% on the PartialSpoof database, which is significantly outperforming the base model and several SOTA baseline such as LCNN-BLSTM (9.87% EER) and TRACE (8.08% EER). Additionally, multilingual evaluations confirm that while spoofing artifact are independent from language. While self-supervised representations improve robustness, performance degrades under domain and language shifts, highlighting the need for better adaptation and calibration strategies.

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

TextHOI-3D: Text-to-3D Hand-Object Interaction via Discrete Multi-View Generation and Joint Mesh Optimization

Text-conditioned 3D generation has progressed rapidly for images and isolated objects, but producing a hand-object mesh remains challenging: the output must preserve language semantics, cross-view consistency, object geometry, articulated hand shape, and physically plausible contact. We present TextHOI-3D, a staged framework that uses generated multi-view observations as an explicit interface between text-conditioned visual generation and geometry-aware hand-object recovery. TextHOI-3D learns a compact VQ token space for fixed-camera hand-object observations, predicts multi-view visual tokens from text with a CLIP-conditioned visual autoregressive model, and recovers a unified hand-object mesh through prior initialization, multi-view joint optimization, and anti-penetration refinement. The design separates semantic generation from geometric recovery while keeping both stages connected by a discrete multi-view representation. On HO3D-derived evaluations, the multi-view setting reduces object CD from 17.26 mm to 4.92 mm and penetration volume from 5.3721 cm^3 to 0.2193 cm^3 compared with a single-view counterpart, while improving hand errors and surface F-scores. These results support multi-view visual tokens as an effective intermediate representation for text-driven 3D hand-object mesh creation.

18.
Nature (Science) 2026-06-10

A prognostic human brain network for diffuse midline glioma

Authors:

Diffuse midline gliomas (DMGs) are near-universally lethal tumours of the childhood central nervous system1,2. In animal models, DMGs form brain-wide integrated networks through neuron-to-glioma synapses3–6 and glioma-to-glioma gap junctional coupling3. This extensive connectivity robustly promotes the growth and invasion of DMG3–9 and other glial malignancies10–12 through paracrine mechanisms and direct neuron-to-glioma synapses. However, the organization and clinical implications of these connections in the living human brain remain to be elucidated. Here, we develop tumour network mapping to compute the brain-wide connectivity profile of DMG, defining a conserved brain network across pontine and thalamic DMG associated with patient short-term survival (DMG network). Tumour functional connectivity with the DMG network was independently predictive of patient overall survival across two external validation cohorts. Tumour growth mapped to DMG network-specific trajectories and peak in-network neurometabolic changes across development spatiotemporally aligned with the peak age incidence of DMG. Analyses of single-nucleus RNA sequencing data confirmed diverse synaptic gene enrichment in high-connectivity DMG. Strikingly, incidental surgical resection of high-connectivity thalamic DMG tissue conferred a significant survival advantage. Collectively, these data define a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMGs exploit otherwise healthy brain circuits to promote tumour growth. Tumour network mapping of diffuse midline glioma (DMG) defines a conserved and prognostically important brain network in children with DMG, consistent with the hypothesis that DMGs exploit otherwise healthy brain circuits to promote tumour growth.

19.
PLOS Computational Biology 2026-06-22

CoDaLoMic: An R package for modeling microbiome compositional and longitudinal data

by Irene Creus-Martí, Andrés Moya, Francisco J. Santonja In this paper we present CoDaLoMic, an R package for analyzing longitudinal and compositional microbiome datasets. The CoDaLoMic package implements three models specifically designed for the analysis of microbiome data that are both compositional and longitudinal. Unlike many existing methods that focus solely on pairwise interactions, CoDaLoMic also captures interactions among groups of bacteria, providing a more robust methodological framework for studying microbial relationships at the community level. In addition, the package facilitates the analysis of microbiome variability in relation to host health status and allows for the identification of groups of taxa that exhibit similar temporal dynamics. Working with time series data makes it possible to understand not only the current state of a microbial community but also its dynamics over time, which is essential for identifying patterns of ecological succession, detecting events of dysbiosis or recovery, and inferring potential causal relationships between taxa. On the other hand, focusing on interactions among groups of bacteria, rather than analyzing only pairwise relationships, enables a more integrated and functionally meaningful view of the microbiome. Many key ecological functions are the result of the collective behavior of functionally related groups of taxa. Two datasets have been considered in CoDaLoMic, one real and one simulated. The real dataset contains the information of the genera present in the microbiome of the Blatella germanica cockroach at 105 time points. The simulated dataset is defined taking Lotka-Volterra structure into account. CoDaLoMic is available at CRAN.

20.
arXiv (CS.CL) 2026-06-15

Large Language Model Agents Are Not Always Faithful Self-Evolvers

Self-evolving large language model (LLM) agents continually improve by accumulating and reusing past experience, yet it remains unclear whether they faithfully rely on that experience to guide their behavior. We present the first systematic investigation of experience faithfulness, the causal dependence of an agent's decisions on the experience it is given, in self-evolving LLM agents. Using controlled causal interventions on both raw and condensed forms of experience, we comprehensively evaluate four representative frameworks across 13 LLM backbones and 9 environments. Our analysis uncovers a striking asymmetry: while agents consistently depend on raw experience, they often disregard or misinterpret condensed experience, even when it is the only experience provided. This gap persists across single- and multi-agent configurations and across backbone scales. We trace its underlying causes to three factors: the semantic limitations of condensed content, internal processing biases that suppress experience, and task regimes where pretrained priors already suffice. These findings challenge prevailing assumptions about self-evolving methods and underscore the need for more faithful and reliable approaches to experience integration.

21.
PLOS Computational Biology 2026-06-23

A novel biclustering algorithm for mining m<sup>6</sup>A co-methylation patterns based on beta-binomial distribution and data screening strategy

Authors:

by Zhaoyang Liu, Yuteng Xiao, Dao Xiang, Hao Shi, Kaijian Xia Studies have shown that m6A plays a key role in different life processes such as RNA metabolism, physiology and pathology. However, due to the complexity of life processes, its specific regulatory details are still not revealed. The computational approach based on co-methylation pattern mining of m6A sequencing data can assist in revealing its mechanism and save time and economic cost, however, the current algorithms suffer from the problems of insufficient robustness to low signal-to-noise data and unreliable performance. Based on this, this paper proposes an enhanced beta-binomial distribution biclustering algorithm (EBBM) based on data screening strategy. This algorithm is based on the framework of Bayesian, adopts Gibbs sampling method for parameter inference, and introduces the data screening strategy in the process of parameter inference, which effectively removes the problem that the low signal-to-noise data in the original sequencing data of m6A affects the reliability of the clustering results. The simulation experiment results show that this algorithm can effectively deal with the interference of low signal-to-noise data and accurately mine the co-methylation patterns pre-planted in the data, which is significantly better than the current mainstream biclustering algorithm. In real human m6A sequencing data with 32 samples, this algorithm mined two effective co-methylation patterns, which were enriched to different biological processes, such as negative regulation of phosphorylation and peptidyl lysine methylation, etc. The scoring results of GEO_Score indicate that the results of this algorithm are more biologically meaningful than the clustering results of current mainstream m6A co-methylation pattern mining algorithms.

22.
arXiv (math.PR) 2026-06-11

On the spatio-temporal increments of nonlinear parabolic SPDEs and the open KPZ equation

arXiv:2508.05032v3 Announce Type: replace Abstract: We study spatio-temporal increments of the solutions to nonlinear parabolic SPDEs on a bounded interval with Dirichlet, Neumann, or Robin boundary conditions. We identify the exact local and uniform spatio-temporal moduli of continuity for the sample functions of the solutions. These moduli of continuity results imply the existence of random points in space-time at which spatio-temporal oscillations are exceptionally large. We also establish small-ball probability estimates and Chung-type laws of the iterated logarithm for spatio-temporal increments. Our method yields extension of some of these results to the open KPZ equation on the unit interval with inhomogeneous Neumann boundary conditions. Our key ingredients include new strong local non-determinism results for linear stochastic heat equation under various types of boundary conditions, and detailed estimates for the errors in linearization of spatio-temporal increments of the solution to the nonlinear equation.

23.
arXiv (CS.CL) 2026-06-18

Beyond Reward Engineering: A Data Recipe for Long-Context Reinforcement Learning

Long-context reasoning is an essential capability for large language models, particularly when they are deployed as autonomous agents that must reason over lengthy trajectories. Reinforcement learning (RL) has recently emerged as a dominant paradigm for improving this ability, yet existing work largely focuses on reward engineering while diverse training data remains scarce. We revisit this problem from a data-centric perspective and show that a simple yet effective data recipe alone, paired with a minimal outcome-based GRPO setup, suffices to substantially improve long-context reasoning. Our recipe targets three complementary task families – retrieval, multi-evidence synthesis, and reasoning – for which we construct and curate eight datasets totaling ~14K examples. Experiments on three models (Qwen3-4B/8B/30B-A3B) yield average gains of +7.2/+3.2/+6.4 points across seven long-context benchmarks, surpassing prior RL training sets. We further demonstrate that these gains transfer to agentic tasks, where continuing RL training on an agent-tuned model with our data recipe improves GAIA by +4.8 and BrowseComp by +7.0 points. We will release our datasets to facilitate future research.

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

AIPatient Arena: EHR-grounded evaluation of large language models in end-to-end clinical consultation workflows

Large language models (LLMs) are increasingly considered for use in clinical consultation tasks, yet most medical evaluations remain static, single-turn, or narrowly outcome-based, limiting their ability to reflect the sequential, uncertain, and interactive nature of real-world care. Here, we propose AIPatient Arena, an EHRs-grounded evaluation framework for assessing the clinical utility of LLMs across eight dimensions of clinical competence. The framework integrates EHR data into patient-specific knowledge graphs, enabling multi-turn physician-patient interactions. We applied AIPatient Arena on a primary cohort of 437 patients and two out-of-distribution validation cohorts of 119 and 67 patients. We observe that LLMs performed well in medical interview questioning skills (QS; mean scores, 4.43-4.99/5), ethical and professional conduct (ET; 4.38-4.93/5), and clarity and transparency of clinical explanations (EX; 3.80-4.72/5). Performance was moderate in information integration (II; 3.19-4.21/5) and medication safety and justification (MS; 3.13-3.78/5), but persistent weaknesses were observed in handling of ambiguous patient responses (HR; 2.57-3.32/5), information coverage (IC; 2.08-3.02/5), and diagnostic accuracy and reasoning (Dx; 2.63-3.55/5). Process-based evaluation revealed recurrent interaction failures, including repetitive questioning, omission of past medical history, and inadequate handling of uncertainty. Richer conversational context improved diagnostic reasoning but yielded limited gains in treatment planning. These findings indicate that final-answer accuracy alone is insufficient for evaluating clinical readiness and highlight the importance of assessing how models gather, interpret, and communicate information throughout a consultation. AIPatient Arena provides an EHR-grounded framework for workflow-oriented pre-deployment evaluation of medical LLMs.

25.
arXiv (CS.CL) 2026-06-18

Compact Geometric Representations of Hierarchies

Computing geometric representations of data is a cornerstone of modern machine learning, typically achieved by training dual encoders which map queries and documents into a shared embedding space. Recent work of You et al. [NeurIPS '25] has extended this approach to hierarchical retrieval, where relevance is determined by the ancestor-descendant relationships in a Directed Acyclic Graph (DAG). While previous work has shown that valid embeddings exist when the number of descendants is small, these bounds degrade significantly for deep hierarchies, requiring dimensions as large as the total number of nodes. In this paper, we investigate compact reachability embeddings for more general graph classes and provide theoretical guarantees for representing hierarchies using embeddings whose dimension depends on structural graph parameters. We prove that for any directed tree, there exists a reachability embedding in constant dimension 3, independent of the tree's size or depth. We generalize this result to graphs characterized by treewidth $t$, constructing embeddings of dimension $O(t \log n)$, where $n$ is the number of nodes. Complementing these upper bounds, we provide matching or near-matching lower bounds, showing that dimension $\Omega(n)$ is necessary for general DAGs and $\Omega(t/\log(n/t))$ is required for graphs of treewidth $t$. We also obtain upper and lower bounds parameterized by the number of cross-edges in the DAG. We additionally show that our embeddings can be constructed on real world datasets, and that they give much smaller dimensions in high recall regimes compared to prior embeddings with theoretical guarantees.