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01.
medRxiv (Medicine) 2026-06-17

Postoperative Cognitive Decline in Older Patients with Cardiovascular Disease and Preoperative Mild Cognitive Impairment

Objective. Older adults undergoing cardiac surgery may be vulnerable to postoperative cognitive decline. However, no studies have examined postoperative cognitive outcomes in older patients with cardiovascular disease (CVD) according to preoperative mild cognitive impairment (MCI). This study examined 12-month postoperative cognitive outcomes in older CVD patients according to preoperative MCI diagnosis and explored predictors of postoperative cognitive decline. Method. Twenty-two older CVD patients ([≥]65 years) and twenty-five controls were included. Neuropsychological assessment was conducted at baseline in both groups and repeated 12 months after surgery in the CVD group. MCI was diagnosed using current clinical criteria. Postoperative cognitive change was examined across preoperative MCI groups. Results. Fifty percent of patients met criteria for postoperative MCI, showing high diagnostic stability relative to preoperative frequency (45.5%). The preoperative CVD-MCI group showed a decline in working memory, executive functions, visual memory, and naming, whereas CVD-nMCI group declined only in verbal memory. Furthermore, CVD-MCI showed more heterogeneous postoperative cognitive trajectories of change than CVD-nMCI, who showed stability. Estimated IQ, APACHE-II score, and postoperative frailty were important variables in predicting the postoperative pattern. Conclusions. MCI frequency remained high and stable in older CVD patients across the preoperative and one-year postoperative period. However, this apparent diagnostic stability masks subclinical cognitive decline, particularly among patients with preoperative MCI, who showed greater susceptibility to further impairment. Estimated IQ, APACHE-II score, and postoperative frailty may be considered relevant predictors of outcome. These results highlight the value of preoperative neuropsychological assessment for characterizing postoperative cognitive risk in older CVD patients.

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

Patcher: Post-Hoc Patching of Backdoored Large Language Models

arXiv:2606.02995v2 Announce Type: replace-cross Abstract: Large language models remain vulnerable to jailbreak backdoor attacks, where adversaries poison safety alignment data to embed hidden triggers that bypass safety mechanisms. Existing defenses often require comprehensive attack information or multiple triggered examples, making them impractical when defenders only observe a single reported failure case without knowing whether it stems from a backdoor attack or a natural alignment bug. This paper presents Patcher, a post-hoc defense framework that repairs backdoored language models using only a single reported failure case and the model parameters. Patcher operates in two stages. First, it localizes backdoor triggers by computing response-conditioned gradient-based saliency scores and applying adaptive clustering to separate triggers from benign context. Second, it patches the model through a constrained fine-tuning objective that breaks the trigger-response association while preserving benign-task utility and robustness to non-triggered jailbreak attacks through KL-divergence constraints. We conduct extensive evaluations across multiple backdoor attack strategies and demonstrate that Patcher successfully localizes triggers and neutralizes backdoors while maintaining model utility. We further show robustness against adaptive attacks designed to evade our defense. This work represents a significant step toward practical defenses against training-time attacks in deployed language models.

03.
arXiv (CS.AI) 2026-06-16

Virtual Sensing to Enable Real-Time Monitoring of Inaccessible Locations & Unmeasurable Parameters

arXiv:2412.00107v2 Announce Type: replace-cross Abstract: Real-time monitoring of safety-critical interior states remains an open problem in energy systems where physical instrumentation is infeasible. Existing approaches rely on explicit governing equations, finite-dimensional state vectors, or per-instance retraining, which prevents mesh-independent, field-level inference at arbitrary interior coordinates under real-time constraints. We introduce operator-based virtual sensing for nuclear-grade thermal-fluid systems: we use the neural-operator framework to learn solution operators that map sparse boundary measurements to coupled internal fields in physically inaccessible regions, framing the problem class explicitly to distinguish it from classical state estimation and pointwise soft sensing. We instantiate this framework with MIMONet, a branch-trunk operator extended with three practical choices: multi-modal branch encoders for heterogeneous (scalar and function-valued) inputs; multiplicative branch fusion to preserve the bilinear PDE coupling structure; and shared-latent multi-field decoding with per-channel basis projections at the trunk's final layer. Evaluated across escalating complexity, from canonical lid-driven cavity flow to pressurized water reactor subchannels to fully coupled heat exchangers, MIMONet achieves below 5% relative errors and sub-millisecond inference on data-center accelerators (0.35 ms / 46 mJ per heat-exchanger inference on an NVIDIA H200, and sub-millisecond across the A40-H200-GH200 range), while remaining stable under 50% sensor noise. By staying accurate as geometric confinement and physics coupling intensify, MIMONet shows that operator-based virtual sensing can restore observability where physical instrumentation fails, establishing simulation-based feasibility within the evaluated operating envelopes as a step toward future experimental and cross-solver validation for safety-critical energy systems.

04.
arXiv (CS.CV) 2026-06-16

Towards Global AI-Driven Cervical Cancer Screening

The global elimination of cervical cancer is a key public health goal set by the World Health Organization (WHO), with screening programs reducing mortality by up to 80%. However, access to experts and biopsy services is limited in low- to middle-income countries (LMICs). Deep learning (DL)-based algorithms offer promising support for screening, but most existing approaches have been developed and validated on private datasets from single countries. We present the first DL-based approach to cervical cancer screening validated on data from multiple countries. Technically, we phrase the problem of detecting and classifying lesions in colposcopy images as a multi-task learning problem, in which we simultaneously perform image-level classification and lesion segmentation. Our model was trained on a private data set of acid stain colposcopy images with manually generated lesion segmentation masks and corresponding histopathological results, employing extensive data augmentation to address image variability. In an in-distribution validation with pathology results serving as ground truth, our algorithm outperformed medical experts (Balanced Accuracy: 0.68 vs 0.64) in CIN1- (Cervical intraepithelial neoplasia grade 1 or lower) versus CIN2+ (grade 2 or higher) classification. External validation on four colposcopy data sets from four countries featuring radical differences in prevalence and patient characteristics yielded superior performance of our method compared to baseline methods. Performance variability across countries was high with AUC values ranging from 0.54 - 0.80. Overall, algorithm performance varied with age, transformation zone (cervical area most prone to lesion development), presence of comorbidities and pathognomonic signs, with comorbidities having by far the largest negative effect. Future work should focus on improving model robustness and generalizability.

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

Ricci-Filtration: Boosting Retrieval-Augmented Generation Reranker to Query-Answer Tasks by Discrete Ricci Flow

arXiv:2606.15482v1 Announce Type: cross Abstract: Ricci flow is a curvature-guided diffusion process that deforms space by shrinking regions of high positive curvature and expanding those with negative curvature. Similarly, discrete Ricci flow on weighted graphs modifies edge weights by shrinking edges with positive Ricci curvature and stretching those with negative Ricci curvature, effectively increasing the separation between clusters. Inspired by these two cornerstone works, we propose a geometry-based RAG reranker enhancement procedure called Ricci-Filtration. By modeling the input query and initial retrieved chunks as a network, where the input query and chunks serve as nodes and embedding-based pairwise relations define an initial graph, Ricci-Filtration leverages discrete curvature and Ricci flow to evaluate the structural importance of each chunk with respect to the user query. The system first filters the initial chunks based on their geometric curvature relative to the query; then, a reranker processes the remaining chunks to enhance generative performance. We theoretically prove that normalized discrete Ricci flow can detect community structures by identifying distinct asymptotic behaviors in edge weights. This supports the removal of ``noisy'' document chunks characterized by large weights and negative Ricci curvature relative to the query node. Extensive experiments confirm that Ricci-Filtration outperforms several baseline reranking methods in accuracy, precision, recall, and F1 scores. Furthermore, ablation studies demonstrate that the Ricci-Filtration generally outperforms the baseline under various settings, highlighting the framework's robustness across different architectures.

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

AGDN: Learning to Solve Traveling Salesman Problem with Anisotropic Graph Diffusion Network

arXiv:2606.19185v1 Announce Type: new Abstract: The Traveling Salesman Problem (TSP) is a cornerstone of combinatorial optimization and arises in many practical scenarios. Although graph-based learning approaches have been explored for TSP, the question of how to exploit graph structure more effectively remains open. We present the Anisotropic Graph Diffusion Network (AGDN), a new Graph Neural Network framework designed to solve TSP. Our method tackles two central difficulties: (1) the lack of informative topological prior in fully connected TSP graphs, and (2) losing connected nodes in the optimal solution after the commonly used graph sparsification techniques. To overcome these issues, we construct a MixScore transition matrix that merges node similarity with pairwise distance, and we develop an anisotropic graph diffusion strategy that supports efficient information exchange across multiple hops. Comprehensive experiments spanning diverse instance sizes and node distributions show that AGDN consistently outperforms existing methods while keeping computation time competitive. Furthermore, AGDN generalizes well to problem sizes and distributions beyond those seen during training. The implementation is publicly available at: https://github.com/LabRAI/AGDN.

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

PT-WNO: Point Transformer with Wavelet Neural Operator for 3D Point Cloud Semantic Segmentation

Point cloud semantic segmentation requires architectures that capture both fine-grained local geometry and broad global scene structure. Transformer-based networks have demonstrated strong performance by focusing on detailed local feature aggregation; however, global context is conveyed primarily through skip connections across encoder-decoder stages, which we argue is insufficient for full scene understanding. We hypothesize that augmenting skip connections with a learnable global feature extraction module allows the network to acquire scene-level knowledge before descending into local detail, leading to richer and more contextually grounded representations. To this end, we propose Point Transformer with Wavelet Neural Operato (PT-WNO), which integrates a shared Wavelet Neural Operator (WNO) branch alongside the skip connections of a point cloud transformer backbone. At each encoder-decoder transition, point features are projected onto a dense 3D volumetric grid where the WNO captures multi-scale global spectral context through learnable wavelet decomposition and reconstruction. These global features are fused back into the network via lightweight adapters, complementing rather than replacing the existing skip connections. Experiments on four large-scale 3D point cloud benchmarks demonstrate the effectiveness of PT-WNO. On S3DIS (Area 5), PT-WNO achieves 71.59% mIoU, outperforming the Point Transformer v3 (PTv3) baseline by +1.03 points. On DALES it achieves 81.05% mIoU (+1.47 over the baseline). On ScanNet~v2, PT-WNO obtains 76.19% mIoU, remaining competitive with the baseline (76.36%).

08.
arXiv (CS.AI) 2026-06-16

AIChilles: Automatically Uncovering Hidden Weaknesses in AI-Evolved Systems

arXiv:2606.15834v1 Announce Type: new Abstract: The computer systems community has recently seen growing interest in AI-driven system evolution, where AI agents iteratively rewrite systems. Frameworks such as AdaEvolve and Engram report 12-60% score improvements over human-designed algorithms. While these results are promising, there are practical concerns if these AI-evolved programs can perform worse on unseen workloads and exhibit scalability regressions. Given the speed and scale of AI-generated code, we need automated mechanisms to uncover such identify hidden weaknesses in AI-evolved systems programs. To this end, we develop AIChilles that takes as input a baseline program $P$ and an AI-evolved program $P'$, AIChilles searches for valid workloads where $P'$ regresses relative to $P$ in correctness, runtime, memory usage, or output quality. To tackle the diversity in system applications, weakness types and potential bugs, AIChilles combines deterministic workload-parameter extraction, agent-based constraint inference, differential oracles, and code-frequency coverage to discover diverse failures. Across five system applications and 30 AI-evolved programs, AIChilles finds 49 distinct hidden weaknesses. We also show that explicitly including AIChilles in the AI-driven development lifecycle can mitigate several of these weaknesses.

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

Human-in-the-Loop Atlas-Based 3D Asset Segmentation for Interactive Content Workflows

Segmenting 3D assets into meaningful regions remains challenging, especially when segmentation criteria are application-dependent and require user control. We present a human-in-the-loop pipeline for generating a segmented 2D parameterized atlas from a 3D model for interactive media, game, and XR content workflows. Our method first selects a compact set of rendered views using a greedy set cover strategy over sampled surface points, and then supports interactive segmentation of these views with SAM~2 and Label Studio. The resulting masks are back-projected onto the model's UV parameterization to produce a unified segmented atlas that supports downstream production tasks such as segment-wise material assignment, style transfer, and semantic labeling. We assess the pipeline through a demonstration-based technical evaluation on eight cultural heritage objects. The results show that the approach can generate usable segmented atlases across diverse geometries while revealing recurring sources of manual correction, particularly fine structures, cavities, and weak appearance boundaries.

10.
arXiv (CS.AI) 2026-06-12

PRISMR: Overcoming Parse Collapse in Multimodal Listwise Ranking via Parameterized Representation Internalization

arXiv:2606.12942v1 Announce Type: new Abstract: Generative listwise ranking with Large Multimodal Models (LMMs) aims to capture global list context in a single forward pass, but its effectiveness degrades in long-context multimodal scenarios. We identify a recurring failure mode, parse collapse, where the autoregressive decoder produces fluent yet incomplete rankings by silently omitting candidates and terminating early. This failure stems from limited context utilization rather than simple formatting mistakes, making prompt engineering and constrained decoding insufficient. We propose PRISMR (Parameterized Representation Internalization for Semantic Multimodal Ranking), a framework that replaces transient in-context list processing with parametric structural conditioning. PRISMR uses a lightweight hypernetwork to encode multimodal candidates in parallel and generate item-specific LoRA weights, which are synthesized into an instance-specific adapter for a LMM. This paradigm enables more robust internalization of list structure while preserving the base model. We further introduce a large-scale multimodal review-ranking benchmark for evaluation. Experiments demonstrate that PRISMR substantially reduces parse collapse, improves listwise ranking performance, and transfers effectively across domains and instruction-tuned backbones.

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

DreamReg: Belief-Driven World Model for 2D-3D Ultrasound Registration

Ultrasound (US) is widely used for surgical navigation, yet real-time registration between intraoperative 2D slices and preoperative 3D volumes remains challenging due to partial observability, speckle noise, and the action-dependent US acquisition. Existing methods are one-shot or short-horizon, making it hard for them to gather evidence over time or capture how surgeons adjust probe motion based on on-screen feedback. We propose DreamReg, a belief-driven world-model framework that formulates 2D-3D registration as belief updating over rigid transformations. DreamReg maintains a latent belief state that summarizes past observations and poses information, and continuously refines the transformation through learned dynamics as new slices arrive. During training, DreamReg is exposed to probe-motion trajectories that mimic clinical scanning behavior and learns to update its belief by conditioning pose refinement on the current US observation. During inference, DreamReg refines registration via internal imagination: it rolls out the learned world model to simulate candidate probe motions and their predicted observations, and integrates these imagined outcomes to converge to an accurate rigid transformation. Experiments on CAMUS and u-RegPro datasets demonstrate improved robustness and competitive registration accuracy for real-time guidance compared with state-of-the-art methods.

12.
arXiv (quant-ph) 2026-06-15

Path superposition activating perfect quantum teleportation ability for separable states

arXiv:2505.11398v2 Announce Type: replace Abstract: Quantum teleportation is a quintessential quantum communication protocol that enables the transmission of an arbitrary quantum state between two distant parties without physically transmitting the state with the help of shared entanglement and limited classical communication. We show that it is possible to relax the entanglement requirement in quantum teleportation if we have access to a certain strain of superposition of quantum processes. Two types of superposition of quantum processes are generally considered in the literature: superposition of paths identified with quantum maps and superposition of indefinite causal orders of the maps. We find that when superposition of paths is incorporated in the protocol, quantum teleportation with unit fidelity becomes possible with nonzero probability of 1/4 even when the two parties share certain classes of separable states, including pure product states. In contrast, the assistance of superposition of indefinite causal order of quantum maps in teleportation protocol does not enable any quantum advantage for shared pure product states. Furthermore, we show that separable Werner states can also yield quantum advantage in quantum teleportation assisted by the superposition of paths. Finally, we establish that the presence of quantum coherence in the control qubit is both necessary and sufficient to achieve quantum advantage in quantum teleportation assisted with superposition of paths. The results potentially uncover yet another role of quantum superposition, in general, in teleportation versus entanglement.

13.
arXiv (CS.LG) 2026-06-17

Finite-Time Queue Peak Laws in Stochastic Networks: Logarithmic Scaling After Geometric Thresholds

arXiv:2606.18218v1 Announce Type: cross Abstract: We study finite-horizon queue peaks in generalized switches, a standard stochastic-network model in which many queues share constrained service resources. Arrivals may be dependent, time-varying, and adapted to the past; the standing load condition is uniform interior slack, meaning the conditional mean arrival vector stays in a fixed contraction of the capacity region. We show that this slack reshapes the finite-time peak law for drift-minimizing scheduling policies such as MaxWeight. The square-root envelope that is sharp without slack persists only up to a geometry-dependent threshold; beyond that threshold, the running maximum grows only logarithmically with the horizon, both with high probability and in expectation. The mechanism is self-normalization: in the current queue direction, the projected fluctuation scale is normalized by the stabilizing drift scale. This removes capacity geometry from the logarithmic coefficient, while geometry remains in the threshold. Matching lower bounds show that both the logarithmic term and a geometric threshold are unavoidable. When finite-time state-space collapse is available, the threshold can be sharpened using local bottleneck geometry. For generalized input-queued switches, we obtain finite-time peak bounds with tight logarithmic coefficients. Simulations illustrate the two-phase envelope, local geometric refinements, and variance-sensitive improvements predicted by the theory.

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

Short-Term-to-Long-Term Memory Transfer for Knowledge Graphs under Partial Observability

arXiv:2605.22142v2 Announce Type: replace-cross Abstract: Reinforcement learning under partial observability requires deciding what information to retain, yet most memory-based approaches do not explicitly model short-term-to-long-term transfer of symbolic observations. We study this transfer process in a temporal knowledge-graph memory setting and cast it as a neuro-symbolic value-based decision problem: for each observed triple, the agent chooses whether to keep or drop it before long-term insertion. To handle variable-sized short-term buffers, we use a per-item Q-learning design with shared parameters and a practical temporal-difference update over matched items across consecutive steps. On the RoomKG benchmark at long-term memory capacity 128, learned transfer decisions outperform symbolic and neural baselines, including symbolic baselines with temporal annotations and history-based LSTM/Transformer baselines. Across transfer-policy ablations, a lightweight local short-term-only variant performs best, and step-level behavior shows that the policy keeps navigation- and query-relevant facts while discarding lower-value candidate facts, supporting explicit and interpretable memory decisions under memory constraints.

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

Landmark-free Assessment of Lower-limb Alignment with Implicit Neural Shape Functions from Knee Radiographs

Radiographic assessment of lower-limb alignment (LLA) is important for predicting joint health and surgical outcomes in total knee arthroplasty. Traditional measurement methods are manual and time-consuming, while recent machine learning approaches typically rely on locating a fixed set of anatomical landmarks. This dependence limits flexibility and may require re-annotation when clinical definitions change. To address this, we propose an automated workflow using Implicit Neural Shape Functions (INSF). Rather than relying on explicit landmark coordinates, we encode the anatomy into a compact latent space and regress clinical alignment measurements directly from these latent codes. This architecture allows for rapid extendability to new tasks without altering the backbone representation. We trained our method on an internal dataset of 566 knee radiographs, each annotated with the outline of the femur and tibia. We evaluated it on both an internal test dataset of 50 patients and a separate external set of 402 preoperative cases from the MRKR dataset. Manual clinical measurements are available for these data, and the MRKR measurements will be made publicly accessible. Performance was comparable to state-of-the-art landmark-based methods and manual agreement, while offering a flexible shape representation that can be extended to additional measurement tasks.

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

From Digital to Physical: Digital Agents as Autonomous Coaches for Physical Intelligence

arXiv:2601.21570v2 Announce Type: replace Abstract: The field of Embodied AI is witnessing a rapid evolution toward general-purpose robotic systems, fueled by high-fidelity simulation and large-scale data collection. However, this scaling capability remains severely bottlenecked by a reliance on labor-intensive manual oversight from intricate reward shaping to hyperparameter tuning across heterogeneous backends. Inspired by LLMs' success in software automation and science discovery, we introduce \textsc{EmboCoach-Bench}, a benchmark evaluating the capacity of LLM agents to autonomously engineer embodied policies. Spanning 32 expert-curated RL and IL tasks, our framework posits executable code as the universal interface. We move beyond static generation to assess a dynamic closed-loop workflow, where agents leverage environment feedback to iteratively draft, debug, and optimize solutions, spanning improvements from physics-informed reward design to policy architectures such as diffusion policies. Extensive evaluations yield three critical insights: (1) autonomous agents can qualitatively surpass human-engineered baselines by 26.5\% in average success rate; (2) agentic workflow with environment feedback effectively strengthens policy development and substantially narrows the performance gap between open-source and proprietary models; and (3) agents exhibit self-correction capabilities for pathological engineering cases, successfully resurrecting task performance from near-total failures through iterative simulation-in-the-loop debugging. Ultimately, this work establishes a foundation for self-evolving embodied intelligence, accelerating the paradigm shift from labor-intensive manual tuning to scalable, autonomous engineering in embodied AI field.

17.
arXiv (CS.AI) 2026-06-18

SwitchBraidNet: Quantisation-Aware Lightweight Architecture for Hybrid Brain-Computer Interface

arXiv:2606.18816v1 Announce Type: cross Abstract: Hybrid brain-computer interfaces (BCIs) that integrate motor imagery (MI) and steady-state visual evoked potentials (SSVEP) provide high-dimensional neural decoding but typically exceed the computational limits of embedded hardware. To address this, we propose SwitchBraidNet, a compact EEG classification architecture designed for low-power deployment. The model employs a dual-path temporal braid to extract multiscale oscillatory features, an adaptive squeeze-and-excitation spatial switch for electrode gating, and a log-variance readout layer for direct band-power encoding. Furthermore, through systematic quantisation-aware training on the OpenBMI dataset, we compared SwitchBraidNet against four established baselines across FP32, FP16, and INT8 precisions. Experimental results demonstrate superior efficiency and performance, achieving MI accuracy of 69.49% (FP16), SSVEP accuracy of 93.48% (FP32), and a hybrid information transfer rate of 64.82 bits/min (FP16). With an INT8 footprint of only 3.03 KB, SwitchBraidNet maintains high accuracy across varying numerical precisions, demonstrating its suitability for low-power embedded BCI deployment.

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

UP-NRPA: User Portrait based Nested Rollout Policy Adaptation for Planning with Large Language Models in Goal-oriented Dialogue Systems

To address the challenge that current dialogue policy planning methods struggle to dynamically adapt to diverse user characteristics, this paper proposes a User Portrait based Nested Rollout Policy Adaptation (UP-NRPA) online framework with Large Language Models. In contrast to conventional approaches dependent on model training and require offline reinforcement learning policy models for user groups, UP-NRPA enables dynamic customization of dialogue strategies through an adaptive mechanism. This is achieved by leveraging real-time user feedback alongside personality, preferences, and objectives mapped from the current user portrait, thereby adapting to user characteristics without offline reinforcement learning. In collaborative and non-collaborative dialogue benchmarks, UP-NRPA demonstrated considerable benefits, achieving an impressive 100% success rate in multiple dialogue tasks. Particularly in negotiation tasks, the sale-to-list ratio (SL) increased by 56.41%. This demonstrates that UP-NRPA can adapt to diverse user needs without requiring a training mechanism, enabling the dialogue system to adapt to user characteristics.

19.
arXiv (CS.CV) 2026-06-17

Advances in 4D Representation: Geometry, Motion, and Interaction

We present a survey on 4D generation and reconstruction, a fast-evolving subfield of computer graphics whose developments have been propelled by recent advances in neural fields, geometric and motion deep learning, as well as 3D generative artificial intelligence (GenAI). While our survey is not the first of its kind, we build our coverage of the domain from a unique and distinctive perspective of 4D representations, to model 3D geometry evolving over time while exhibiting motion and interaction. Specifically, instead of offering an exhaustive enumeration of many works, we take a more selective approach by focusing on representative works to highlight both the desirable properties and ensuing challenges of each representation under different computation, application, and data scenarios. The main take-away message we aim to convey to the readers is on how to select and then customize the appropriate 4D representations for their tasks. Organizationally, we separate the 4D representations based on three key pillars: geometry, motion, and interaction. Our discourse will not only encompass the most popular representations of today, such as neural radiance fields (NeRFs) and 3D Gaussian Splatting (3DGS), but also bring attention to relatively under-explored representations in the 4D context, such as structured models and long-range motions. Throughout our survey, we will reprise the role of large language models (LLMs) and video foundational models (VFMs) in a variety of 4D applications, while steering our discussion towards their current limitations and how they can be addressed. We also provide a dedicated coverage on what 4D datasets are currently available, as well as what is lacking, in driving the subfield forward. Project page:https://mingrui-zhao.github.io/4DRep-GMI/

20.
bioRxiv (Bioinfo) 2026-06-14

Somatic variant detection in normal tissues from single-cell sequencing data

A crucial advantage of single-cell sequencing (SCS) is its ability to identify somatic variants in individual cells, enabling phylogenetic analysis of cellular populations within bulk tissues. While identifying somatic variants in tumor tissues via SCS has become a common practice, doing so in normal tissues remains challenging due to the rarity of somatic variants in normal cells. To evaluate the feasibility of somatic variant calling from widely available single-nucleus RNA-seq (snRNA-seq) and single-nucleus ATAC-seq (snATAC-seq) data, we profiled a Cell-line mix of six HapMap samples prepared by the SMaHT consortium using 10x Genomics 5' snRNA-seq (12k cells with 36k mean reads per cell) and snATAC-seq (11k cells with 14k median high-quality fragments per cell) for variant calling. PacBio long-read whole genome sequencing (WGS) data (109x) generated from individual cell lines were used as ground truth. Two computational tools, Monopogen and SComatic, were used for somatic variant calling from the SCS data. Monopogen achieved single nucleotide variant (SNV) detection accuracies of 93.30% in the snRNA-seq and 99.64% in the snATAC-seq data, both of which outperformed SComatic (74.35% and 94.29%, respectively). Monopogen also consistently detected somatic SNVs at cellular fractions as low as 0.5% (2.54% in snRNA and 0.81% in snATAC) in individual samples. Notably, snATAC-seq exhibited higher genomic coverage breadth and larger number of variants detected than snRNA-seq. While the SCS data have lower overall genome coverage than that of the bulk WGS, the single-cell level variant resolution allows Monopogen to assign variants to their cells of origin with over 80% accuracy in both RNA and ATAC modalities, thereby facilitating studies of clonal evolution and cell-type-specific mutagenesis. Other benchmarking methods were also evaluated (DeepVariant, Cellsnp-lite and Mutect2) for comparison. In conclusion, our study demonstrated the feasibility of performing reliable single-cell somatic mutation calling in a cell-line mixture and discussed the strengths and limitations of current computational methods when applied to normal tissues.

21.
arXiv (CS.CV) 2026-06-17

Phys4D: Fine-Grained Physics-Consistent 4D Modeling from Video Diffusion

Recent video diffusion models have achieved impressive capabilities as large-scale generative world models. However, these models often struggle with fine-grained physical consistency, exhibiting physically implausible dynamics over time. In this work, we present Phys4D, a pipeline for learning physics-consistent 4D world representations from video diffusion models. Phys4D adopts a three-stage training paradigm that progressively lifts appearance-driven video diffusion models into physics-consistent 4D world representations. We first bootstrap robust geometry and motion representations through large-scale pseudo-supervised pretraining, establishing a foundation for 4D scene modeling. We then perform physics-grounded supervised fine-tuning using simulation-generated data, enforcing temporally consistent 4D dynamics. Finally, we apply simulation-grounded reinforcement learning to correct residual physical violations that are difficult to capture through explicit supervision. To evaluate fine-grained physical consistency beyond appearance-based metrics, we introduce a set of 4D world consistency evaluation that probe geometric coherence, motion stability, and long-horizon physical plausibility. Experimental results demonstrate that Phys4D substantially improves fine-grained spatiotemporal and physical consistency compared to appearance-driven baselines, while maintaining strong generative performance. Our project page is available at https://sensational-brioche-7657e7.netlify.app/

22.
arXiv (CS.CL) 2026-06-18

MemRerank: Preference Memory for Personalized Product Reranking

LLM-based shopping agents increasingly rely on long purchase histories and multi-turn interactions for personalization, yet naively appending raw history to prompts is often ineffective due to noise, length, and relevance mismatch. We propose MemRerank, a preference memory framework that distills user purchase history into concise, query-independent signals for personalized product reranking. To study this problem, we build an end-to-end benchmark and evaluation framework centered on an LLM-based 1-in-5 selection task, which measures both memory quality and downstream reranking utility. We further train the memory extractor with reinforcement learning (RL), using downstream reranking performance as supervision. Experiments with two LLM-based rerankers show that MemRerank consistently outperforms no-memory, raw-history, and off-the-shelf memory baselines, yielding up to +10.61 absolute points in 1-in-5 accuracy. These results suggest that explicit preference memory is a practical and effective building block for personalization in agentic e-commerce systems.

23.
arXiv (CS.LG) 2026-06-19

Comparing Linear Probes with Mahalanobis Cosine Similarity

arXiv:2606.19603v1 Announce Type: new Abstract: Linear probes are widely used in interpretability research and often compared by cosine similarity. The Mahalanobis cosine similarity (MCS) between two directions, which reweights the inner product by test data covariance, is a natural task-aware refinement. Ying et al. (2026) report that a probe's MCS to a reference probe trained on the out-of-distribution (OOD) data near-perfectly linearly predicts the probe's OOD AUROC (R^2 = 0.98). Here, we extend this empirical finding across models, layers, and concept domains, and prove this general phenomenon in closed form: For balanced classes whose projections are Gaussian, OOD AUROC and MCS to the reference probe are linear because both are sigmoid-shaped functions of the probe's signal-to-noise ratio (SNR) on the test data. The theory also predicts when this linearity fails, which we verify empirically. MCS offers a theoretically grounded and empirically effective alternative to Euclidean cosine similarity for comparing linear probes.

24.
arXiv (math.PR) 2026-06-15

Scaling limits of multitype Bienaymé trees

arXiv:2507.23241v2 Announce Type: replace Abstract: We consider critical multitype Bienaymé trees that are either irreducible or possess a critical irreducible component with attached subcritical components. These trees are studied under two distinct conditioning frameworks: first, conditioning on the value of a linear combination of the numbers of vertices of given types; and second, conditioning on the precise number of vertices belonging to a selected subset of types. We prove that, under a finite exponential moment condition, the scaling limit as the tree size tends to infinity is given by the Brownian Continuum Random Tree. Additionally, we establish strong nonasymptotic tail bounds for the height of such trees. Our main tools include a flattening operation applied to multitype trees and sharp estimates regarding the structure of monotype trees with a given sequence of degrees.

25.
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.