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Sep 2

AQVolt26: High-Temperature r$^2$SCAN Halide Dataset for Universal ML Potentials and Solid-State Batteries

The demand for safe, high-energy-density batteries has spotlighted halide solid-state electrolytes, which offer the potential for enhanced ionic mobility, electrochemical stability, and interfacial deformability. Accelerating their discovery requires extensive molecular dynamics, which has been increasingly enabled by universal machine learning interatomic potentials trained on foundational datasets. However, the dynamic softness of halides poses a stringent test of whether general-purpose models can reliably replace first-principles calculations under the highly distorted, elevated-temperature regimes necessary to probe ion transport. Here, we present AQVolt26, a dataset of 322,656 r^2SCAN single-point calculations for lithium halides, generated via high-temperature configurational sampling across sim5K structures. We demonstrate that foundational datasets provide a strong baseline for stable halide chemistries and transfer local forces well, however absolute energy predictions degrade in distorted higher-temperature regimes. Co-training with AQVolt26 resolves this blind spot. Furthermore, incorporating Materials Project relaxation data improves near-equilibrium performance but degrades extreme-strain robustness without enhancing high-temperature force accuracy. These results demonstrate that domain-specific configurational sampling is essential for the reliable dynamic screening of halide electrolytes. Furthermore, our findings suggest that while foundational models provide a robust base, they are most effective for dynamically soft solid-state chemistries when augmented with targeted, high-temperature data. Finally, we show that near-equilibrium relaxation data serves as a task-specific complement rather than a universally beneficial addition.

  • 9 authors
·
Apr 1

EchoVLM: Dynamic Mixture-of-Experts Vision-Language Model for Universal Ultrasound Intelligence

Ultrasound imaging has become the preferred imaging modality for early cancer screening due to its advantages of non-ionizing radiation, low cost, and real-time imaging capabilities. However, conventional ultrasound diagnosis heavily relies on physician expertise, presenting challenges of high subjectivity and low diagnostic efficiency. Vision-language models (VLMs) offer promising solutions for this issue, but existing general-purpose models demonstrate limited knowledge in ultrasound medical tasks, with poor generalization in multi-organ lesion recognition and low efficiency across multi-task diagnostics. To address these limitations, we propose EchoVLM, a vision-language model specifically designed for ultrasound medical imaging. The model employs a Mixture of Experts (MoE) architecture trained on data spanning seven anatomical regions. This design enables the model to perform multiple tasks, including ultrasound report generation, diagnosis and visual question-answering (VQA). The experimental results demonstrated that EchoVLM achieved significant improvements of 10.15 and 4.77 points in BLEU-1 scores and ROUGE-1 scores respectively compared to Qwen2-VL on the ultrasound report generation task. These findings suggest that EchoVLM has substantial potential to enhance diagnostic accuracy in ultrasound imaging, thereby providing a viable technical solution for future clinical applications. Source code and model weights are available at https://github.com/Asunatan/EchoVLM.

  • 5 authors
·
Sep 18, 2025 2

HyClone: Bridging LLM Understanding and Dynamic Execution for Semantic Code Clone Detection

Code clone detection is a critical task in software engineering, aimed at identifying duplicated or similar code fragments within or across software systems. Traditional methods often fail to capture functional equivalence, particularly for semantic clones (Type 4), where code fragments implement identical functionality despite differing syntactic structures. Recent advances in large language models (LLMs) have shown promise in understanding code semantics. However, directly applying LLMs to code clone detection yields suboptimal results due to their sensitivity to syntactic differences. To address these challenges, we propose a novel two-stage framework that combines LLM-based screening with execution-based validation for detecting semantic clones in Python programs. In the first stage, an LLM evaluates code pairs to filter out obvious non-clones based on semantic analysis. For pairs not identified as clones, the second stage employs an execution-based validation approach, utilizing LLM-generated test inputs to assess functional equivalence through cross-execution validation. Our experimental evaluation demonstrates significant improvements in precision, recall, and F1-score compared to direct LLM-based detection, highlighting the framework's effectiveness in identifying semantic clones. Future work includes exploring cross-language clone detection and optimizing the framework for large-scale applications.

  • 5 authors
·
Aug 2, 2025

SimPLe: Similarity-Aware Propagation Learning for Weakly-Supervised Breast Cancer Segmentation in DCE-MRI

Breast dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) plays an important role in the screening and prognosis assessment of high-risk breast cancer. The segmentation of cancerous regions is essential useful for the subsequent analysis of breast MRI. To alleviate the annotation effort to train the segmentation networks, we propose a weakly-supervised strategy using extreme points as annotations for breast cancer segmentation. Without using any bells and whistles, our strategy focuses on fully exploiting the learning capability of the routine training procedure, i.e., the train - fine-tune - retrain process. The network first utilizes the pseudo-masks generated using the extreme points to train itself, by minimizing a contrastive loss, which encourages the network to learn more representative features for cancerous voxels. Then the trained network fine-tunes itself by using a similarity-aware propagation learning (SimPLe) strategy, which leverages feature similarity between unlabeled and positive voxels to propagate labels. Finally the network retrains itself by employing the pseudo-masks generated using previous fine-tuned network. The proposed method is evaluated on our collected DCE-MRI dataset containing 206 patients with biopsy-proven breast cancers. Experimental results demonstrate our method effectively fine-tunes the network by using the SimPLe strategy, and achieves a mean Dice value of 81%.

  • 2 authors
·
Jun 29, 2023

Symphony-Coord: Emergent Coordination in Decentralized Agent Systems

Multi-agent large language model systems can tackle complex multi-step tasks by decomposing work and coordinating specialized behaviors. However, current coordination mechanisms typically rely on statically assigned roles and centralized controllers. As agent pools and task distributions evolve, these design choices lead to inefficient routing, poor adaptability, and fragile fault recovery capabilities. We introduce Symphony-Coord, a decentralized multi-agent framework that transforms agent selection into an online multi-armed bandit problem, enabling roles to emerge organically through interaction. The framework employs a two-stage dynamic beacon protocol: (i) a lightweight candidate screening mechanism to limit communication and computational overhead; (ii) an adaptive LinUCB selector that routes subtasks based on context features derived from task requirements and agent states, continuously optimized through delayed end-to-end feedback. Under standard linear realizability assumptions, we provide sublinear regret bounds, indicating the system converges toward near-optimal allocation schemes. Validation through simulation experiments and real-world large language model benchmarks demonstrates that Symphony-Coord not only enhances task routing efficiency but also exhibits robust self-healing capabilities in scenarios involving distribution shifts and agent failures, achieving a scalable coordination mechanism without predefined roles.

  • 7 authors
·
Jan 31

Enabling Self-Improving Agents to Learn at Test Time With Human-In-The-Loop Guidance

Large language model (LLM) agents often struggle in environments where rules and required domain knowledge frequently change, such as regulatory compliance and user risk screening. Current approaches, like offline fine-tuning and standard prompting, are insufficient because they cannot effectively adapt to new knowledge during actual operation. To address this limitation, we propose the Adaptive Reflective Interactive Agent (ARIA), an LLM agent framework designed specifically to continuously learn updated domain knowledge at test time. ARIA assesses its own uncertainty through structured self-dialogue, proactively identifying knowledge gaps and requesting targeted explanations or corrections from human experts. It then systematically updates an internal, timestamped knowledge repository with provided human guidance, detecting and resolving conflicting or outdated knowledge through comparisons and clarification queries. We evaluate ARIA on the realistic customer due diligence name screening task on TikTok Pay, alongside publicly available dynamic knowledge tasks. Results demonstrate significant improvements in adaptability and accuracy compared to baselines using standard offline fine-tuning and existing self-improving agents. ARIA is deployed within TikTok Pay serving over 150 million monthly active users, confirming its practicality and effectiveness for operational use in rapidly evolving environments.

  • 11 authors
·
Oct 9, 2025

Deep End-to-end Adaptive k-Space Sampling, Reconstruction, and Registration for Dynamic MRI

Dynamic MRI enables a range of clinical applications, including cardiac function assessment, organ motion tracking, and radiotherapy guidance. However, fully sampling the dynamic k-space data is often infeasible due to time constraints and physiological motion such as respiratory and cardiac motion. This necessitates undersampling, which degrades the quality of reconstructed images. Poor image quality not only hinders visualization but also impairs the estimation of deformation fields, crucial for registering dynamic (moving) images to a static reference image. This registration enables tasks such as motion correction, treatment planning, and quantitative analysis in applications like cardiac imaging and MR-guided radiotherapy. To overcome the challenges posed by undersampling and motion, we introduce an end-to-end deep learning (DL) framework that integrates adaptive dynamic k-space sampling, reconstruction, and registration. Our approach begins with a DL-based adaptive sampling strategy, optimizing dynamic k-space acquisition to capture the most relevant data for each specific case. This is followed by a DL-based reconstruction module that produces images optimized for accurate deformation field estimation from the undersampled moving data. Finally, a registration module estimates the deformation fields aligning the reconstructed dynamic images with a static reference. The proposed framework is independent of specific reconstruction and registration modules allowing for plug-and-play integration of these components. The entire framework is jointly trained using a combination of supervised and unsupervised loss functions, enabling end-to-end optimization for improved performance across all components. Through controlled experiments and ablation studies, we validate each component, demonstrating that each choice contributes to robust motion estimation from undersampled dynamic data.

  • 3 authors
·
Mar 20, 2025

DDoS-UNet: Incorporating temporal information using Dynamic Dual-channel UNet for enhancing super-resolution of dynamic MRI

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

  • 5 authors
·
Feb 10, 2022

Fine-tuning deep learning model parameters for improved super-resolution of dynamic MRI with prior-knowledge

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

  • 6 authors
·
Feb 4, 2021

AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

  • 12 authors
·
May 10

Fire Together Wire Together: A Dynamic Pruning Approach with Self-Supervised Mask Prediction

Dynamic model pruning is a recent direction that allows for the inference of a different sub-network for each input sample during deployment. However, current dynamic methods rely on learning a continuous channel gating through regularization by inducing sparsity loss. This formulation introduces complexity in balancing different losses (e.g task loss, regularization loss). In addition, regularization based methods lack transparent tradeoff hyperparameter selection to realize a computational budget. Our contribution is two-fold: 1) decoupled task and pruning losses. 2) Simple hyperparameter selection that enables FLOPs reduction estimation before training. Inspired by the Hebbian theory in Neuroscience: "neurons that fire together wire together", we propose to predict a mask to process k filters in a layer based on the activation of its previous layer. We pose the problem as a self-supervised binary classification problem. Each mask predictor module is trained to predict if the log-likelihood for each filter in the current layer belongs to the top-k activated filters. The value k is dynamically estimated for each input based on a novel criterion using the mass of heatmaps. We show experiments on several neural architectures, such as VGG, ResNet and MobileNet on CIFAR and ImageNet datasets. On CIFAR, we reach similar accuracy to SOTA methods with 15% and 24% higher FLOPs reduction. Similarly in ImageNet, we achieve lower drop in accuracy with up to 13% improvement in FLOPs reduction.

  • 4 authors
·
Oct 15, 2021

Contributions to Robust and Efficient Methods for Analysis of High Dimensional Data

A ubiquitous feature of data of our era is their extra-large sizes and dimensions. Analyzing such high-dimensional data poses significant challenges, since the feature dimension is often much larger than the sample size. This thesis introduces robust and computationally efficient methods to address several common challenges associated with high-dimensional data. In my first manuscript, I propose a coherent approach to variable screening that accommodates nonlinear associations. I develop a novel variable screening method that transcends traditional linear assumptions by leveraging mutual information, with an intended application in neuroimaging data. This approach allows for accurate identification of important variables by capturing nonlinear as well as linear relationships between the outcome and covariates. Building on this foundation, I develop new optimization methods for sparse estimation using nonconvex penalties in my second manuscript. These methods address notable challenges in current statistical computing practices, facilitating computationally efficient and robust analyses of complex datasets. The proposed method can be applied to a general class of optimization problems. In my third manuscript, I contribute to robust modeling of high-dimensional correlated observations by developing a mixed-effects model based on Tsallis power-law entropy maximization and discussed the theoretical properties of such distribution. This model surpasses the constraints of conventional Gaussian models by accommodating a broader class of distributions with enhanced robustness to outliers. Additionally, I develop a proximal nonlinear conjugate gradient algorithm that accelerates convergence while maintaining numerical stability, along with rigorous statistical properties for the proposed framework.

  • 1 authors
·
Sep 9, 2025

Glance and Focus Reinforcement for Pan-cancer Screening

Pan-cancer screening in large-scale CT scans remains challenging for existing AI methods, primarily due to the difficulty of localizing diverse types of tiny lesions in large CT volumes. The extreme foreground-background imbalance significantly hinders models from focusing on diseased regions, while redundant focus on healthy regions not only decreases the efficiency but also increases false positives. Inspired by radiologists' glance and focus diagnostic strategy, we introduce GF-Screen, a Glance and Focus reinforcement learning framework for pan-cancer screening. GF-Screen employs a Glance model to localize the diseased regions and a Focus model to precisely segment the lesions, where segmentation results of the Focus model are leveraged to reward the Glance model via Reinforcement Learning (RL). Specifically, the Glance model crops a group of sub-volumes from the entire CT volume and learns to select the sub-volumes with lesions for the Focus model to segment. Given that the selecting operation is non-differentiable for segmentation training, we propose to employ the segmentation results to reward the Glance model. To optimize the Glance model, we introduce a novel group relative learning paradigm, which employs group relative comparison to prioritize high-advantage predictions and discard low-advantage predictions within sub-volume groups, not only improving efficiency but also reducing false positives. In this way, for the first time, we effectively extend cutting-edge RL techniques to tackle the specific challenges in pan-cancer screening. Extensive experiments on 16 internal and 7 external datasets across 9 lesion types demonstrated the effectiveness of GF-Screen. Notably, GF-Screen leads the public validation leaderboard of MICCAI FLARE25 pan-cancer challenge, surpassing the FLARE24 champion solution by a large margin (+25.6% DSC and +28.2% NSD).

Baichuan-M2: Scaling Medical Capability with Large Verifier System

As large language models (LLMs) advance in conversational and reasoning capabilities, their practical application in healthcare has become a critical research focus. However, there is a notable gap between the performance of medical LLMs on static benchmarks such as USMLE and their utility in real-world clinical decision-making. This discrepancy arises because traditional exams fail to capture the dynamic, interactive nature of medical consultations. To address this challenge, we introduce a novel dynamic verification framework that moves beyond static answer verifier, establishing a large-scale, high-fidelity interactive reinforcement learning system. Our framework comprises two key components: a Patient Simulator that creates realistic clinical environments using de-identified medical records, and a Clinical Rubrics Generator that dynamically produces multi-dimensional evaluation metrics. Building on this foundation, we develop Baichuan-M2, a 32B-parameter medical augmented reasoning model trained through a multi-stage reinforcement learning strategy with an improved Group Relative Policy Optimization (GRPO) algorithm. Evaluated on HealthBench, Baichuan-M2 outperforms all other open-source models and most advanced closed-source counterparts, achieving a score above 32 on the challenging HealthBench Hard benchmark-previously exceeded only by GPT-5. Our work demonstrates that robust dynamic verifier system is essential for aligning LLM capabilities with practical clinical applications, establishing a new Pareto front in the performance-parameter trade-off for medical AI deployment.

  • 34 authors
·
Sep 2, 2025 2

New combinational therapies for cancer using modern statistical mechanics

We investigate a new dynamical system that describes tumor-host interaction. The equation that describes the untreated tumor growth is based on non-extensive statistical mechanics. Recently, this model has been shown to fit successfully exponential, Gompertz, logistic, and power-law tumor growths. We have been able to include as many hallmarks of cancer as possible. We study also the dynamic response of cancer under therapy. Using our model, we can make predictions about the different outcomes when we change the parameters, and/or the initial conditions. We can determine the importance of different factors to influence tumor growth. We discover synergistic therapeutic effects of different treatments and drugs. Cancer is generally untreatable using conventional monotherapy. We consider conventional therapies, oncogene-targeted therapies, tumor-suppressors gene-targeted therapies, immunotherapies, anti-angiogenesis therapies, virotherapy, among others. We need therapies with the potential to target both tumor cells and the tumors' microenvironment. Drugs that target oncogenes and tumor-suppressor genes can be effective in the treatment of some cancers. However, most tumors do reoccur. We have found that the success of the new therapeutic agents can be seen when used in combination with other cancer-cell-killing therapies. Our results have allowed us to design a combinational therapy that can lead to the complete eradication of cancer.

  • 19 authors
·
Feb 2, 2019

CellCLIP -- Learning Perturbation Effects in Cell Painting via Text-Guided Contrastive Learning

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

  • 4 authors
·
May 16, 2025

An Embedding-Dynamic Approach to Self-supervised Learning

A number of recent self-supervised learning methods have shown impressive performance on image classification and other tasks. A somewhat bewildering variety of techniques have been used, not always with a clear understanding of the reasons for their benefits, especially when used in combination. Here we treat the embeddings of images as point particles and consider model optimization as a dynamic process on this system of particles. Our dynamic model combines an attractive force for similar images, a locally dispersive force to avoid local collapse, and a global dispersive force to achieve a globally-homogeneous distribution of particles. The dynamic perspective highlights the advantage of using a delayed-parameter image embedding (a la BYOL) together with multiple views of the same image. It also uses a purely-dynamic local dispersive force (Brownian motion) that shows improved performance over other methods and does not require knowledge of other particle coordinates. The method is called MSBReg which stands for (i) a Multiview centroid loss, which applies an attractive force to pull different image view embeddings toward their centroid, (ii) a Singular value loss, which pushes the particle system toward spatially homogeneous density, (iii) a Brownian diffusive loss. We evaluate downstream classification performance of MSBReg on ImageNet as well as transfer learning tasks including fine-grained classification, multi-class object classification, object detection, and instance segmentation. In addition, we also show that applying our regularization term to other methods further improves their performance and stabilize the training by preventing a mode collapse.

  • 5 authors
·
Jul 7, 2022

Weakly Supervised Realtime Dynamic Background Subtraction

Background subtraction is a fundamental task in computer vision with numerous real-world applications, ranging from object tracking to video surveillance. Dynamic backgrounds poses a significant challenge here. Supervised deep learning-based techniques are currently considered state-of-the-art for this task. However, these methods require pixel-wise ground-truth labels, which can be time-consuming and expensive. In this work, we propose a weakly supervised framework that can perform background subtraction without requiring per-pixel ground-truth labels. Our framework is trained on a moving object-free sequence of images and comprises two networks. The first network is an autoencoder that generates background images and prepares dynamic background images for training the second network. The dynamic background images are obtained by thresholding the background-subtracted images. The second network is a U-Net that uses the same object-free video for training and the dynamic background images as pixel-wise ground-truth labels. During the test phase, the input images are processed by the autoencoder and U-Net, which generate background and dynamic background images, respectively. The dynamic background image helps remove dynamic motion from the background-subtracted image, enabling us to obtain a foreground image that is free of dynamic artifacts. To demonstrate the effectiveness of our method, we conducted experiments on selected categories of the CDnet 2014 dataset and the I2R dataset. Our method outperformed all top-ranked unsupervised methods. We also achieved better results than one of the two existing weakly supervised methods, and our performance was similar to the other. Our proposed method is online, real-time, efficient, and requires minimal frame-level annotation, making it suitable for a wide range of real-world applications.

  • 2 authors
·
Mar 5, 2023

RED-PSM: Regularization by Denoising of Partially Separable Models for Dynamic Imaging

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

  • 3 authors
·
Apr 7, 2023

Auto-Formulating Dynamic Programming Problems with Large Language Models

Dynamic programming (DP) is a fundamental method in operations research, but formulating DP models has traditionally required expert knowledge of both the problem context and DP techniques. Large Language Models (LLMs) offer the potential to automate this process. However, DP problems pose unique challenges due to their inherently stochastic transitions and the limited availability of training data. These factors make it difficult to directly apply existing LLM-based models or frameworks developed for other optimization problems, such as linear or integer programming. We introduce DP-Bench, the first benchmark covering a wide range of textbook-level DP problems to enable systematic evaluation. We present Dynamic Programming Language Model (DPLM), a 7B-parameter specialized model that achieves performance comparable to state-of-the-art LLMs like OpenAI's o1 and DeepSeek-R1, and surpasses them on hard problems. Central to DPLM's effectiveness is DualReflect, our novel synthetic data generation pipeline, designed to scale up training data from a limited set of initial examples. DualReflect combines forward generation for diversity and backward generation for reliability. Our results reveal a key insight: backward generation is favored in low-data regimes for its strong correctness guarantees, while forward generation, though lacking such guarantees, becomes increasingly valuable at scale for introducing diverse formulations. This trade-off highlights the complementary strengths of both approaches and the importance of combining them.

  • 6 authors
·
Mar 31

Inverse Bayesian Inference for Extracting Lesion Dynamics from Longitudinal Spectral CT

Longitudinal medical imaging captures temporal evolution of lesions, yet extracting the underlying dynamical parameters governing this evolution remains challenging. We propose an inverse Bayesian framework for inferring lesion dynamics from longitudinal spectral CT. We decompose spectral feature (x) evolution into three components: equation* dx_i{dt} = A_i x_i + B \cdot n + C \cdot Δx_{sat} equation* where A_i captures intrinsic dynamics (lesion-autonomous evolution), B captures local environment tumour burden (organ tumour burden through satellite count coupling), and C captures environment/satellite state change (i.e., whether surrounding lesions move similarly or not). We demonstrate the framework on photon-counting NSCLC CT data from metastases, recovering distinct dynamical regimes: lung lesions exhibit significant satellite count coupling (B=-0.34, p<0.05) suggesting competitive dynamics, while liver lesions show synergistic satellite behaviour coupling (Capprox+1.0, p<0.05). Synthetic validation confirms parameter recovery, and cross-coupling analysis validates that our method detects non-zero coupling when present. This work establishes inverse dynamical inference as a principled methodology for extracting interpretable parameters from longitudinal imaging, moving beyond static feature extraction toward mechanistic characterisation of lesion behaviour. The code and data are available at: https://github.com/lukasf98/inverse-bayesian-inference

  • 9 authors
·
Jul 24

Development and evaluation of intraoperative ultrasound segmentation with negative image frames and multiple observer labels

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application.

  • 11 authors
·
Jul 28, 2021

Exploring Spatiotemporal Feature Propagation for Video-Level Compressive Spectral Reconstruction: Dataset, Model and Benchmark

Recently, Spectral Compressive Imaging (SCI) has achieved remarkable success, unlocking significant potential for dynamic spectral vision. However, existing reconstruction methods, primarily image-based, suffer from two limitations: (i) Encoding process masks spatial-spectral features, leading to uncertainty in reconstructing missing information from single compressed measurements, and (ii) The frame-by-frame reconstruction paradigm fails to ensure temporal consistency, which is crucial in the video perception. To address these challenges, this paper seeks to advance spectral reconstruction from the image level to the video level, leveraging the complementary features and temporal continuity across adjacent frames in dynamic scenes. Initially, we construct the first high-quality dynamic hyperspectral image dataset (DynaSpec), comprising 30 sequences obtained through frame-scanning acquisition. Subsequently, we propose the Propagation-Guided Spectral Video Reconstruction Transformer (PG-SVRT), which employs a spatial-then-temporal attention to effectively reconstruct spectral features from abundant video information, while using a bridged token to reduce computational complexity. Finally, we conduct simulation experiments to assess the performance of four SCI systems, and construct a DD-CASSI prototype for real-world data collection and benchmarking. Extensive experiments demonstrate that PG-SVRT achieves superior performance in reconstruction quality, spectral fidelity, and temporal consistency, while maintaining minimal FLOPs. Project page: https://github.com/nju-cite/DynaSpec

  • 9 authors
·
Feb 28

Efficient Prediction of Pass@k Scaling in Large Language Models

Assessing the capabilities and risks of frontier AI systems is a critical area of research, and recent work has shown that repeated sampling from models can dramatically increase both. For instance, repeated sampling has been shown to increase their capabilities, such as solving difficult math and coding problems, but it has also been shown to increase their potential for harm, such as being jailbroken. Such results raise a crucial question for both capability and safety forecasting: how can one accurately predict a model's behavior when scaled to a massive number of attempts, given a vastly smaller sampling budget? This question is directly relevant to model providers, who serve hundreds of millions of users daily, and to governmental regulators, who seek to prevent harms. To answer this questions, we make three contributions. First, we find that standard methods for fitting these laws suffer from statistical shortcomings that hinder predictive accuracy, especially in data-limited scenarios. Second, we remedy these shortcomings by introducing a robust estimation framework, which uses a beta-binomial distribution to generate more accurate predictions from limited data. Third, we propose a dynamic sampling strategy that allocates a greater budget to harder problems. Combined, these innovations enable more reliable prediction of rare risks and capabilities at a fraction of the computational cost.

  • 7 authors
·
Oct 5, 2025

End-to-end Adaptive Dynamic Subsampling and Reconstruction for Cardiac MRI

Background: Accelerating dynamic MRI is vital for advancing clinical applications and improving patient comfort. Commonly, deep learning (DL) methods for accelerated dynamic MRI reconstruction typically rely on uniformly applying non-adaptive predetermined or random subsampling patterns across all temporal frames of the dynamic acquisition. This approach fails to exploit temporal correlations or optimize subsampling on a case-by-case basis. Purpose: To develop an end-to-end approach for adaptive dynamic MRI subsampling and reconstruction, capable of generating customized sampling patterns maximizing at the same time reconstruction quality. Methods: We introduce the End-to-end Adaptive Dynamic Sampling and Reconstruction (E2E-ADS-Recon) for MRI framework, which integrates an adaptive dynamic sampler (ADS) that adapts the acquisition trajectory to each case for a given acceleration factor with a state-of-the-art dynamic reconstruction network, vSHARP, for reconstructing the adaptively sampled data into a dynamic image. The ADS can produce either frame-specific patterns or unified patterns applied to all temporal frames. E2E-ADS-Recon is evaluated under both frame-specific and unified 1D or 2D sampling settings, using dynamic cine cardiac MRI data and compared with vSHARP models employing standard subsampling trajectories, as well as pipelines where ADS was replaced by parameterized samplers optimized for dataset-specific schemes. Results: E2E-ADS-Recon exhibited superior reconstruction quality, especially at high accelerations, in terms of standard quantitative metrics (SSIM, pSNR, NMSE). Conclusion: The proposed framework improves reconstruction quality, highlighting the importance of case-specific subsampling optimization in dynamic MRI applications.

  • 3 authors
·
Mar 20, 2025

Research on Optimizing Real-Time Data Processing in High-Frequency Trading Algorithms using Machine Learning

High-frequency trading (HFT) represents a pivotal and intensely competitive domain within the financial markets. The velocity and accuracy of data processing exert a direct influence on profitability, underscoring the significance of this field. The objective of this work is to optimise the real-time processing of data in high-frequency trading algorithms. The dynamic feature selection mechanism is responsible for monitoring and analysing market data in real time through clustering and feature weight analysis, with the objective of automatically selecting the most relevant features. This process employs an adaptive feature extraction method, which enables the system to respond and adjust its feature set in a timely manner when the data input changes, thus ensuring the efficient utilisation of data. The lightweight neural networks are designed in a modular fashion, comprising fast convolutional layers and pruning techniques that facilitate the expeditious completion of data processing and output prediction. In contrast to conventional deep learning models, the neural network architecture has been specifically designed to minimise the number of parameters and computational complexity, thereby markedly reducing the inference time. The experimental results demonstrate that the model is capable of maintaining consistent performance in the context of varying market conditions, thereby illustrating its advantages in terms of processing speed and revenue enhancement.

  • 6 authors
·
Dec 1, 2024

DynamicCity: Large-Scale LiDAR Generation from Dynamic Scenes

LiDAR scene generation has been developing rapidly recently. However, existing methods primarily focus on generating static and single-frame scenes, overlooking the inherently dynamic nature of real-world driving environments. In this work, we introduce DynamicCity, a novel 4D LiDAR generation framework capable of generating large-scale, high-quality LiDAR scenes that capture the temporal evolution of dynamic environments. DynamicCity mainly consists of two key models. 1) A VAE model for learning HexPlane as the compact 4D representation. Instead of using naive averaging operations, DynamicCity employs a novel Projection Module to effectively compress 4D LiDAR features into six 2D feature maps for HexPlane construction, which significantly enhances HexPlane fitting quality (up to 12.56 mIoU gain). Furthermore, we utilize an Expansion & Squeeze Strategy to reconstruct 3D feature volumes in parallel, which improves both network training efficiency and reconstruction accuracy than naively querying each 3D point (up to 7.05 mIoU gain, 2.06x training speedup, and 70.84% memory reduction). 2) A DiT-based diffusion model for HexPlane generation. To make HexPlane feasible for DiT generation, a Padded Rollout Operation is proposed to reorganize all six feature planes of the HexPlane as a squared 2D feature map. In particular, various conditions could be introduced in the diffusion or sampling process, supporting versatile 4D generation applications, such as trajectory- and command-driven generation, inpainting, and layout-conditioned generation. Extensive experiments on the CarlaSC and Waymo datasets demonstrate that DynamicCity significantly outperforms existing state-of-the-art 4D LiDAR generation methods across multiple metrics. The code will be released to facilitate future research.

  • 6 authors
·
Oct 23, 2024 2

Data Agent: Learning to Select Data via End-to-End Dynamic Optimization

Dynamic Data selection aims to accelerate training by prioritizing informative samples during online training. However, existing methods typically rely on task-specific handcrafted metrics or static/snapshot-based criteria to estimate sample importance, limiting scalability across learning paradigms and making it difficult to capture the evolving utility of data throughout training. To address this challenge, we propose Data Agent, an end-to-end dynamic data selection framework that formulates data selection as a training-aware sequential decision-making problem. The agent learns a sample-wise selection policy that co-evolves with model optimization, guided by a composite reward that integrates loss-based difficulty and confidence-based uncertainty signals. The reward signals capture complementary objectives of optimization impact and information gain, together with a tuning-free adaptive weighting mechanism that balances these signals over training. Extensive experiments across a wide range of datasets and architectures demonstrate that Data Agent consistently accelerates training while preserving or improving performance, e.g., reducing costs by over 50\% on ImageNet-1k and MMLU with lossless performance. Moreover, its dataset-agnostic formulation and modular reward make it plug-and-play across tasks and scenarios, e.g., robustness to noisy datasets, highlighting its potential in real-world scenarios. Code is available at https://github.com/Jackbrocp/Data-Agent.

  • 8 authors
·
May 12

ProARD: progressive adversarial robustness distillation: provide wide range of robust students

Adversarial Robustness Distillation (ARD) has emerged as an effective method to enhance the robustness of lightweight deep neural networks against adversarial attacks. Current ARD approaches have leveraged a large robust teacher network to train one robust lightweight student. However, due to the diverse range of edge devices and resource constraints, current approaches require training a new student network from scratch to meet specific constraints, leading to substantial computational costs and increased CO2 emissions. This paper proposes Progressive Adversarial Robustness Distillation (ProARD), enabling the efficient one-time training of a dynamic network that supports a diverse range of accurate and robust student networks without requiring retraining. We first make a dynamic deep neural network based on dynamic layers by encompassing variations in width, depth, and expansion in each design stage to support a wide range of architectures. Then, we consider the student network with the largest size as the dynamic teacher network. ProARD trains this dynamic network using a weight-sharing mechanism to jointly optimize the dynamic teacher network and its internal student networks. However, due to the high computational cost of calculating exact gradients for all the students within the dynamic network, a sampling mechanism is required to select a subset of students. We show that random student sampling in each iteration fails to produce accurate and robust students.

  • 3 authors
·
Jun 9, 2025

Ultrafast Sampling-based Kinodynamic Planning via Differential Flatness

Motion planning under dynamics constraints, i.e., kinodynamic planning, enables safe robot operation by generating dynamically feasible trajectories that the robot can accurately track. For high-\dof robots such as manipulators, sampling-based motion planners are commonly used, especially for complex tasks in cluttered environments. However, enforcing constraints on robot dynamics in such planners requires solving either challenging two-point boundary value problems (BVPs) or propagating robot dynamics over time, both of which are computational bottlenecks that drastically increase planning times. Meanwhile, recent efforts have shown that sampling-based motion planners can generate plans in microseconds using parallelization, but are limited to geometric paths. This paper develops AkinoPDF, a fast parallelized sampling-based kinodynamic motion planning technique for a broad class of differentially flat robot systems, including manipulators, ground and aerial vehicles, and more. Differential flatness allows us to transform the motion planning problem from the original state space to a flat output space, where an analytical time-parameterized solution of the BVP and dynamics integration can be obtained. A trajectory in the flat output space is then converted back to a closed-form dynamically feasible trajectory in the original state space, enabling fast validation via ``single instruction, multiple data" parallelism. Our method is fast, exact, and compatible with any sampling-based motion planner. We extensively verify the effectiveness of our approach in both simulated benchmarks and real experiments with cluttered and dynamic environments, requiring mere microseconds to milliseconds of planning time.

  • 5 authors
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Mar 16

Mamba-FSCIL: Dynamic Adaptation with Selective State Space Model for Few-Shot Class-Incremental Learning

Few-shot class-incremental learning (FSCIL) confronts the challenge of integrating new classes into a model with minimal training samples while preserving the knowledge of previously learned classes. Traditional methods widely adopt static adaptation relying on a fixed parameter space to learn from data that arrive sequentially, prone to overfitting to the current session. Existing dynamic strategies require the expansion of the parameter space continually, leading to increased complexity. To address these challenges, we integrate the recently proposed selective state space model (SSM) into FSCIL. Concretely, we propose a dual selective SSM projector that dynamically adjusts the projection parameters based on the intermediate features for dynamic adaptation. The dual design enables the model to maintain the robust features of base classes, while adaptively learning distinctive feature shifts for novel classes. Additionally, we develop a class-sensitive selective scan mechanism to guide dynamic adaptation. It minimizes the disruption to base-class representations caused by training on novel data, and meanwhile, forces the selective scan to perform in distinct patterns between base and novel classes. Experiments on miniImageNet, CUB-200, and CIFAR-100 demonstrate that our framework outperforms the existing state-of-the-art methods. The code is available at https://github.com/xiaojieli0903/Mamba-FSCIL.

  • 6 authors
·
Jul 8, 2024

D^2-Monitor: Dynamic Safety Monitoring for Diffusion LLMs via Hesitation-Aware Routing

Despite the emergence of diffusion large language models (D-LLMs) as an alternative to autoregressive large language models (AR-LLMs), safety monitoring for D-LLMs remains largely unexplored. Unlike AR-LLMs, D-LLMs generate text through a multi-step denoising process, exposing intermediate hidden representations that may contain safety-relevant information unavailable in standard single-step monitoring setups. Motivated by the suitability of lightweight probes for always-on monitoring, we analyze which trajectory-level signals best indicate when such probes are likely to struggle. We find that the most informative signal is safety hesitation: intermediate hidden states repeatedly falling within a small margin of the probe's decision boundary. The number of such hesitation steps in D-LLM's trajectory predicts probe failure effectively, providing a proxy of sample difficulty. Building on this analysis, we propose D^2-Monitor, a bi-level safety monitor for D-LLMs. D^2-Monitor adopts a lightweight probe as an always-on monitor to jointly estimate hesitation and perform base classification. When the hesitation level exceeds a threshold, a more expressive but computationally heavier probe is activated. This dynamic routing mechanism allocates monitoring resources efficiently at test time. Evaluated on 3 datasets (WildguardMix, ToxicChat, OpenAI-Moderation) across 4 D-LLMs, D^2-Monitor achieves state-of-the-art performance with a compact parameter footprint (leq 0.85M parameters), and exhibits the best trade-off between effectiveness and efficiency relative to 8 baselines.

Aortic Valve Disease Detection from PPG via Physiology-Informed Self-Supervised Learning

Traditional diagnosis of aortic valve disease relies on echocardiography, but its cost and required expertise limit its use in large-scale early screening. Photoplethysmography (PPG) has emerged as a promising screening modality due to its widespread availability in wearable devices and its ability to reflect underlying hemodynamic dynamics. However, the extreme scarcity of gold-standard labeled PPG data severely constrains the effectiveness of data-driven approaches. To address this challenge, we propose and validate a new paradigm, Physiology-Guided Self-Supervised Learning (PG-SSL), aimed at unlocking the value of large-scale unlabeled PPG data for efficient screening of Aortic Stenosis (AS) and Aortic Regurgitation (AR). Using over 170,000 unlabeled PPG samples from the UK Biobank, we formalize clinical knowledge into a set of PPG morphological phenotypes and construct a pulse pattern recognition proxy task for self-supervised pre-training. A dual-branch, gated-fusion architecture is then employed for efficient fine-tuning on a small labeled subset. The proposed PG-SSL framework achieves AUCs of 0.765 and 0.776 for AS and AR screening, respectively, significantly outperforming supervised baselines trained on limited labeled data. Multivariable analysis further validates the model output as an independent digital biomarker with sustained prognostic value after adjustment for standard clinical risk factors. This study demonstrates that PG-SSL provides an effective, domain knowledge-driven solution to label scarcity in medical artificial intelligence and shows strong potential for enabling low-cost, large-scale early screening of aortic valve disease.

  • 7 authors
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Feb 3

Depthwise-Dilated Convolutional Adapters for Medical Object Tracking and Segmentation Using the Segment Anything Model 2

Recent advances in medical image segmentation have been driven by deep learning; however, most existing methods remain limited by modality-specific designs and exhibit poor adaptability to dynamic medical imaging scenarios. The Segment Anything Model 2 (SAM2) and its related variants, which introduce a streaming memory mechanism for real-time video segmentation, present new opportunities for prompt-based, generalizable solutions. Nevertheless, adapting these models to medical video scenarios typically requires large-scale datasets for retraining or transfer learning, leading to high computational costs and the risk of catastrophic forgetting. To address these challenges, we propose DD-SAM2, an efficient adaptation framework for SAM2 that incorporates a Depthwise-Dilated Adapter (DD-Adapter) to enhance multi-scale feature extraction with minimal parameter overhead. This design enables effective fine-tuning of SAM2 on medical videos with limited training data. Unlike existing adapter-based methods focused solely on static images, DD-SAM2 fully exploits SAM2's streaming memory for medical video object tracking and segmentation. Comprehensive evaluations on TrackRad2025 (tumor segmentation) and EchoNet-Dynamic (left ventricle tracking) datasets demonstrate superior performance, achieving Dice scores of 0.93 and 0.97, respectively. To the best of our knowledge, this work provides an initial attempt at systematically exploring adapter-based SAM2 fine-tuning for medical video segmentation and tracking. Code, datasets, and models will be publicly available at https://github.com/apple1986/DD-SAM2.

  • 3 authors
·
Jul 19, 2025 2

Comparing Conditional Diffusion Models for Synthesizing Contrast-Enhanced Breast MRI from Pre-Contrast Images

Dynamic contrast-enhanced (DCE) MRI is essential for breast cancer diagnosis and treatment. However, its reliance on contrast agents introduces safety concerns, contraindications, increased cost, and workflow complexity. To this end, we present pre-contrast conditioned denoising diffusion probabilistic models to synthesize DCE-MRI, introducing, evaluating, and comparing a total of 22 generative model variants in both single-breast and full breast settings. Towards enhancing lesion fidelity, we introduce both tumor-aware loss functions and explicit tumor segmentation mask conditioning. Using a public multicenter dataset and comparing to respective pre-contrast baselines, we observe that subtraction image-based models consistently outperform post-contrast-based models across five complementary evaluation metrics. Apart from assessing the entire image, we also separately evaluate the region of interest, where both tumor-aware losses and segmentation mask inputs improve evaluation metrics. The latter notably enhance qualitative results capturing contrast uptake, albeit assuming access to tumor localization inputs that are not guaranteed to be available in screening settings. A reader study involving 2 radiologists and 4 MRI technologists confirms the high realism of the synthetic images, indicating an emerging clinical potential of generative contrast-enhancement. We share our codebase at https://github.com/sebastibar/conditional-diffusion-breast-MRI.

  • 10 authors
·
Aug 19, 2025

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

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

  • 46 authors
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Jun 18

Dynamic Novel View Synthesis in High Dynamic Range

High Dynamic Range Novel View Synthesis (HDR NVS) seeks to learn an HDR 3D model from Low Dynamic Range (LDR) training images captured under conventional imaging conditions. Current methods primarily focus on static scenes, implicitly assuming all scene elements remain stationary and non-living. However, real-world scenarios frequently feature dynamic elements, such as moving objects, varying lighting conditions, and other temporal events, thereby presenting a significantly more challenging scenario. To address this gap, we propose a more realistic problem named HDR Dynamic Novel View Synthesis (HDR DNVS), where the additional dimension ``Dynamic'' emphasizes the necessity of jointly modeling temporal radiance variations alongside sophisticated 3D translation between LDR and HDR. To tackle this complex, intertwined challenge, we introduce HDR-4DGS, a Gaussian Splatting-based architecture featured with an innovative dynamic tone-mapping module that explicitly connects HDR and LDR domains, maintaining temporal radiance coherence by dynamically adapting tone-mapping functions according to the evolving radiance distributions across the temporal dimension. As a result, HDR-4DGS achieves both temporal radiance consistency and spatially accurate color translation, enabling photorealistic HDR renderings from arbitrary viewpoints and time instances. Extensive experiments demonstrate that HDR-4DGS surpasses existing state-of-the-art methods in both quantitative performance and visual fidelity. Source code will be released.

  • 6 authors
·
Sep 26, 2025

Control of Medical Digital Twins with Artificial Neural Networks

The objective of personalized medicine is to tailor interventions to an individual patient's unique characteristics. A key technology for this purpose involves medical digital twins, computational models of human biology that can be personalized and dynamically updated to incorporate patient-specific data collected over time. Certain aspects of human biology, such as the immune system, are not easily captured with physics-based models, such as differential equations. Instead, they are often multi-scale, stochastic, and hybrid. This poses a challenge to existing model-based control and optimization approaches that cannot be readily applied to such models. Recent advances in automatic differentiation and neural-network control methods hold promise in addressing complex control problems. However, the application of these approaches to biomedical systems is still in its early stages. This work introduces dynamics-informed neural-network controllers as an alternative approach to control of medical digital twins. As a first use case for this method, the focus is on agent-based models, a versatile and increasingly common modeling platform in biomedicine. The effectiveness of the proposed neural-network control method is illustrated and benchmarked against other methods with two widely-used agent-based model types. The relevance of the method introduced here extends beyond medical digital twins to other complex dynamical systems.

  • 3 authors
·
Mar 18, 2024

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

  • 6 authors
·
Aug 27, 2024

DyEdgeGAT: Dynamic Edge via Graph Attention for Early Fault Detection in IIoT Systems

In the Industrial Internet of Things (IIoT), condition monitoring sensor signals from complex systems often exhibit nonlinear and stochastic spatial-temporal dynamics under varying conditions. These complex dynamics make fault detection particularly challenging. While previous methods effectively model these dynamics, they often neglect the evolution of relationships between sensor signals. Undetected shifts in these relationships can lead to significant system failures. Furthermore, these methods frequently misidentify novel operating conditions as faults. Addressing these limitations, we propose DyEdgeGAT (Dynamic Edge via Graph Attention), a novel approach for early-stage fault detection in IIoT systems. DyEdgeGAT's primary innovation lies in a novel graph inference scheme for multivariate time series that tracks the evolution of relationships between time series, enabled by dynamic edge construction. Another key innovation of DyEdgeGAT is its ability to incorporate operating condition contexts into node dynamics modeling, enhancing its accuracy and robustness. We rigorously evaluated DyEdgeGAT using both a synthetic dataset, simulating varying levels of fault severity, and a real-world industrial-scale multiphase flow facility benchmark with diverse fault types under varying operating conditions and detection complexities. The results show that DyEdgeGAT significantly outperforms other baseline methods in fault detection, particularly in the early stages with low severity, and exhibits robust performance under novel operating conditions.

  • 2 authors
·
Jan 24, 2024

DVPT: Dynamic Visual Prompt Tuning of Large Pre-trained Models for Medical Image Analysis

Limited labeled data makes it hard to train models from scratch in medical domain, and an important paradigm is pre-training and then fine-tuning. Large pre-trained models contain rich representations, which can be adapted to downstream medical tasks. However, existing methods either tune all the parameters or the task-specific layers of the pre-trained models, ignoring the input variations of medical images, and thus they are not efficient or effective. In this work, we aim to study parameter-efficient fine-tuning (PEFT) for medical image analysis, and propose a dynamic visual prompt tuning method, named DVPT. It can extract knowledge beneficial to downstream tasks from large models with a few trainable parameters. Firstly, the frozen features are transformed by an lightweight bottleneck layer to learn the domain-specific distribution of downstream medical tasks, and then a few learnable visual prompts are used as dynamic queries and then conduct cross-attention with the transformed features, attempting to acquire sample-specific knowledge that are suitable for each sample. Finally, the features are projected to original feature dimension and aggregated with the frozen features. This DVPT module can be shared between different Transformer layers, further reducing the trainable parameters. To validate DVPT, we conduct extensive experiments with different pre-trained models on medical classification and segmentation tasks. We find such PEFT method can not only efficiently adapt the pre-trained models to the medical domain, but also brings data efficiency with partial labeled data. For example, with 0.5\% extra trainable parameters, our method not only outperforms state-of-the-art PEFT methods, even surpasses the full fine-tuning by more than 2.20\% Kappa score on medical classification task. It can saves up to 60\% labeled data and 99\% storage cost of ViT-B/16.

  • 5 authors
·
Jul 19, 2023

Catheter Detection and Segmentation in X-ray Images via Multi-task Learning

Automated detection and segmentation of surgical devices, such as catheters or wires, in X-ray fluoroscopic images have the potential to enhance image guidance in minimally invasive heart surgeries. In this paper, we present a convolutional neural network model that integrates a resnet architecture with multiple prediction heads to achieve real-time, accurate localization of electrodes on catheters and catheter segmentation in an end-to-end deep learning framework. We also propose a multi-task learning strategy in which our model is trained to perform both accurate electrode detection and catheter segmentation simultaneously. A key challenge with this approach is achieving optimal performance for both tasks. To address this, we introduce a novel multi-level dynamic resource prioritization method. This method dynamically adjusts sample and task weights during training to effectively prioritize more challenging tasks, where task difficulty is inversely proportional to performance and evolves throughout the training process. Experiments on both public and private datasets have demonstrated that the accuracy of our method surpasses the existing state-of-the-art methods in both single segmentation task and in the detection and segmentation multi-task. Our approach achieves a good trade-off between accuracy and efficiency, making it well-suited for real-time surgical guidance applications.

  • 6 authors
·
Mar 4, 2025

Integrating Biological Knowledge for Robust Microscopy Image Profiling on De Novo Cell Lines

High-throughput screening techniques, such as microscopy imaging of cellular responses to genetic and chemical perturbations, play a crucial role in drug discovery and biomedical research. However, robust perturbation screening for de novo cell lines remains challenging due to the significant morphological and biological heterogeneity across cell lines. To address this, we propose a novel framework that integrates external biological knowledge into existing pretraining strategies to enhance microscopy image profiling models. Our approach explicitly disentangles perturbation-specific and cell line-specific representations using external biological information. Specifically, we construct a knowledge graph leveraging protein interaction data from STRING and Hetionet databases to guide models toward perturbation-specific features during pretraining. Additionally, we incorporate transcriptomic features from single-cell foundation models to capture cell line-specific representations. By learning these disentangled features, our method improves the generalization of imaging models to de novo cell lines. We evaluate our framework on the RxRx database through one-shot fine-tuning on an RxRx1 cell line and few-shot fine-tuning on cell lines from the RxRx19a dataset. Experimental results demonstrate that our method enhances microscopy image profiling for de novo cell lines, highlighting its effectiveness in real-world phenotype-based drug discovery applications.

  • 4 authors
·
Jul 14, 2025

Splatography: Sparse multi-view dynamic Gaussian Splatting for filmmaking challenges

Deformable Gaussian Splatting (GS) accomplishes photorealistic dynamic 3-D reconstruction from dense multi-view video (MVV) by learning to deform a canonical GS representation. However, in filmmaking, tight budgets can result in sparse camera configurations, which limits state-of-the-art (SotA) methods when capturing complex dynamic features. To address this issue, we introduce an approach that splits the canonical Gaussians and deformation field into foreground and background components using a sparse set of masks for frames at t=0. Each representation is separately trained on different loss functions during canonical pre-training. Then, during dynamic training, different parameters are modeled for each deformation field following common filmmaking practices. The foreground stage contains diverse dynamic features so changes in color, position and rotation are learned. While, the background containing film-crew and equipment, is typically dimmer and less dynamic so only changes in point position are learned. Experiments on 3-D and 2.5-D entertainment datasets show that our method produces SotA qualitative and quantitative results; up to 3 PSNR higher with half the model size on 3-D scenes. Unlike the SotA and without the need for dense mask supervision, our method also produces segmented dynamic reconstructions including transparent and dynamic textures. Code and video comparisons are available online: https://interims-git.github.io/

  • 3 authors
·
Nov 7, 2025

Attention-based Dynamic Subspace Learners for Medical Image Analysis

Learning similarity is a key aspect in medical image analysis, particularly in recommendation systems or in uncovering the interpretation of anatomical data in images. Most existing methods learn such similarities in the embedding space over image sets using a single metric learner. Images, however, have a variety of object attributes such as color, shape, or artifacts. Encoding such attributes using a single metric learner is inadequate and may fail to generalize. Instead, multiple learners could focus on separate aspects of these attributes in subspaces of an overarching embedding. This, however, implies the number of learners to be found empirically for each new dataset. This work, Dynamic Subspace Learners, proposes to dynamically exploit multiple learners by removing the need of knowing apriori the number of learners and aggregating new subspace learners during training. Furthermore, the visual interpretability of such subspace learning is enforced by integrating an attention module into our method. This integrated attention mechanism provides a visual insight of discriminative image features that contribute to the clustering of image sets and a visual explanation of the embedding features. The benefits of our attention-based dynamic subspace learners are evaluated in the application of image clustering, image retrieval, and weakly supervised segmentation. Our method achieves competitive results with the performances of multiple learners baselines and significantly outperforms the classification network in terms of clustering and retrieval scores on three different public benchmark datasets. Moreover, our attention maps offer a proxy-labels, which improves the segmentation accuracy up to 15% in Dice scores when compared to state-of-the-art interpretation techniques.

  • 3 authors
·
Jun 17, 2022

Scaling Structure Aware Virtual Screening to Billions of Molecules with SPRINT

Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too slow to allow for broad proteome-scale screens, limiting their application in screening for off-target effects or new molecular mechanisms. Recently, vector-based methods using protein language models (PLMs) have emerged as a complementary approach that bypasses explicit 3D structure modeling. Here, we develop SPRINT, a vector-based approach for screening entire chemical libraries against whole proteomes for DTIs and novel mechanisms of action. SPRINT improves on prior work by using a self-attention based architecture and structure-aware PLMs to learn drug-target co-embeddings for binder prediction, search, and retrieval. SPRINT achieves SOTA enrichment factors in virtual screening on LIT-PCBA, DTI classification benchmarks, and binding affinity prediction benchmarks, while providing interpretability in the form of residue-level attention maps. In addition to being both accurate and interpretable, SPRINT is ultra-fast: querying the whole human proteome against the ENAMINE Real Database (6.7B drugs) for the 100 most likely binders per protein takes 16 minutes. SPRINT promises to enable virtual screening at an unprecedented scale, opening up new opportunities for in silico drug repurposing and development. SPRINT is available on the web as ColabScreen: https://bit.ly/colab-screen

  • 7 authors
·
Jan 19, 2025

HyperTopo-Adapters: Geometry- and Topology-Aware Segmentation of Leaf Lesions on Frozen Encoders

Leaf-lesion segmentation is topology-sensitive: small merges, splits, or false holes can be biologically meaningful descriptors of biochemical pathways, yet they are weakly penalized by standard pixel-wise losses in Euclidean latents. I explore HyperTopo-Adapters, a lightweight, parameter-efficient head trained on top of a frozen vision encoder, which embeds features on a product manifold -- hyperbolic + Euclidean + spherical (H + E + S) -- to encourage hierarchical separation (H), local linear detail (E), and global closure (S). A topology prior complements Dice/BCE in two forms: (i) persistent-homology (PH) distance for evaluation and selection, and (ii) a differentiable surrogate that combines a soft Euler-characteristic match with total variation regularization for stable training. I introduce warm-ups for both the hyperbolic contrastive term and the topology prior, per-sample evaluation of structure-aware metrics (Boundary-F1, Betti errors, PD distance), and a min-PD within top-K Dice rule for checkpoint selection. On a Kaggle leaf-lesion dataset (N=2,940), early results show consistent gains in boundary and topology metrics (reducing Delta beta_1 hole error by 9%) while Dice/IoU remain competitive. The study is diagnostic by design: I report controlled ablations (curvature learning, latent dimensions, contrastive temperature, surrogate settings), and ongoing tests varying encoder strength (ResNet-50, DeepLabV3, DINOv2/v3), input resolution, PH weight, and partial unfreezing of late blocks. The contribution is an open, reproducible train/eval suite (available at https://github.com/ChimdiWalter/HyperTopo-Adapters) that isolates geometric/topological priors and surfaces failure modes to guide stronger, topology-preserving architectures.

  • 2 authors
·
Dec 28, 2025

ViTally Consistent: Scaling Biological Representation Learning for Cell Microscopy

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

  • 13 authors
·
Nov 4, 2024

DynamicScaler: Seamless and Scalable Video Generation for Panoramic Scenes

The increasing demand for immersive AR/VR applications and spatial intelligence has heightened the need to generate high-quality scene-level and 360{\deg} panoramic video. However, most video diffusion models are constrained by limited resolution and aspect ratio, which restricts their applicability to scene-level dynamic content synthesis. In this work, we propose the DynamicScaler, addressing these challenges by enabling spatially scalable and panoramic dynamic scene synthesis that preserves coherence across panoramic scenes of arbitrary size. Specifically, we introduce a Offset Shifting Denoiser, facilitating efficient, synchronous, and coherent denoising panoramic dynamic scenes via a diffusion model with fixed resolution through a seamless rotating Window, which ensures seamless boundary transitions and consistency across the entire panoramic space, accommodating varying resolutions and aspect ratios. Additionally, we employ a Global Motion Guidance mechanism to ensure both local detail fidelity and global motion continuity. Extensive experiments demonstrate our method achieves superior content and motion quality in panoramic scene-level video generation, offering a training-free, efficient, and scalable solution for immersive dynamic scene creation with constant VRAM consumption regardless of the output video resolution. Our project page is available at https://dynamic-scaler.pages.dev/.

  • 4 authors
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Dec 15, 2024 3

A Retrospective Systematic Study on Hierarchical Sparse Query Transformer-assisted Ultrasound Screening for Early Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC), ranking as the third leading cause of cancer-related mortality worldwide, demands urgent improvements in early detection to enhance patient survival. While ultrasound remains the preferred screening modality due to its cost-effectiveness and real-time capabilities, its sensitivity (59%-78%) heavily relies on radiologists' expertise, leading to inconsistent diagnostic outcomes and operational inefficiencies. Recent advancements in AI technology offer promising solutions to bridge this gap. This study introduces the Hierarchical Sparse Query Transformer (HSQformer), a novel hybrid architecture that synergizes CNNs' local feature extraction with Vision Transformers' global contextual awareness through latent space representation and sparse learning. By dynamically activating task-specific experts via a Mixture-of-Experts (MoE) framework, HSQformer achieves hierarchical feature integration without structural redundancy. Evaluated across three clinical scenarios: single-center, multi-center, and high-risk patient cohorts, HSQformer outperforms state-of-the-art models (e.g., 95.38% AUC in multi-center testing) and matches senior radiologists' diagnostic accuracy while significantly surpassing junior counterparts. These results highlight the potential of AI-assisted tools to standardize HCC screening, reduce dependency on human expertise, and improve early diagnosis rates. The full code is available at https://github.com/Asunatan/HSQformer.

  • 11 authors
·
Feb 5, 2025

DynaVid: Learning to Generate Highly Dynamic Videos using Synthetic Motion Data

Despite recent progress, video diffusion models still struggle to synthesize realistic videos involving highly dynamic motions or requiring fine-grained motion controllability. A central limitation lies in the scarcity of such examples in commonly used training datasets. To address this, we introduce DynaVid, a video synthesis framework that leverages synthetic motion data in training, which is represented as optical flow and rendered using computer graphics pipelines. This approach offers two key advantages. First, synthetic motion offers diverse motion patterns and precise control signals that are difficult to obtain from real data. Second, unlike rendered videos with artificial appearances, rendered optical flow encodes only motion and is decoupled from appearance, thereby preventing models from reproducing the unnatural look of synthetic videos. Building on this idea, DynaVid adopts a two-stage generation framework: a motion generator first synthesizes motion, and then a motion-guided video generator produces video frames conditioned on that motion. This decoupled formulation enables the model to learn dynamic motion patterns from synthetic data while preserving visual realism from real-world videos. We validate our framework on two challenging scenarios, vigorous human motion generation and extreme camera motion control, where existing datasets are particularly limited. Extensive experiments demonstrate that DynaVid improves the realism and controllability in dynamic motion generation and camera motion control.

Self Expanding Convolutional Neural Networks

In this paper, we present a novel method for dynamically expanding Convolutional Neural Networks (CNNs) during training, aimed at meeting the increasing demand for efficient and sustainable deep learning models. Our approach, drawing from the seminal work on Self-Expanding Neural Networks (SENN), employs a natural expansion score as an expansion criteria to address the common issue of over-parameterization in deep convolutional neural networks, thereby ensuring that the model's complexity is finely tuned to the task's specific needs. A significant benefit of this method is its eco-friendly nature, as it obviates the necessity of training multiple models of different sizes. We employ a strategy where a single model is dynamically expanded, facilitating the extraction of checkpoints at various complexity levels, effectively reducing computational resource use and energy consumption while also expediting the development cycle by offering diverse model complexities from a single training session. We evaluate our method on the CIFAR-10 dataset and our experimental results validate this approach, demonstrating that dynamically adding layers not only maintains but also improves CNN performance, underscoring the effectiveness of our expansion criteria. This approach marks a considerable advancement in developing adaptive, scalable, and environmentally considerate neural network architectures, addressing key challenges in the field of deep learning.

  • 5 authors
·
Jan 11, 2024

QR-SPPS: Quantum-Native Retail Supply Chain Risk Simulation via VQE, ADAPT-VQE Counterfactual Policy Ranking, and DOS-QPE Boltzmann Tail Risk Quantification

Classical supply chain risk models treat node failures as statistically independent events, systematically underestimating cascade probabilities when supplier dependencies are strongly correlated. At n=40 nodes, the full correlated failure distribution requires O(2^n) classical samples, a regime where exact simulation demands 17.6 TB of memory and over 369,000 hours of computation on a standard workstation. We present QR-SPPS (Quantum-Native Retail Shock Propagation and Policy Stress Simulator), a three-algorithm quantum pipeline implemented using the Qiskit framework with the Aer statevector_simulator backend. First, a 40-node, 4-tier retail supply network is encoded as a 40-qubit Ising Hamiltonian using OpenFermion QubitOperator, where ZZ coupling terms encode correlated cascade probabilities structurally absent from classical Monte Carlo. Second, a hardware-efficient VQE circuit finds the ground-state stress distribution with zero error, detecting entangled cascade failures in 14/40 nodes with max|ΔP|=0.637 versus classical Monte Carlo. Third, we introduce the first application of ADAPT-VQE gradient screening to counterfactual macroeconomic policy evaluation: six crisis interventions are ranked in O(1) Qiskit operator evaluations per policy, a 287x speedup over sequential VQE re-optimisation. Fourth, Density-of-States QPE (DOS-QPE) reconstructs the full eigenspectrum via 32-step Trotter evolution and introduces a novel mapping of the Boltzmann catastrophe probability P_cat(T) to VIX-equivalent market volatility temperature, enabling direct integration into regulatory Value-at-Risk frameworks. Qiskit Aer scaling benchmarks confirm exponential classical intractability at 40 qubits.

  • 1 authors
·
Mar 20

Iteratively-Refined Interactive 3D Medical Image Segmentation with Multi-Agent Reinforcement Learning

Existing automatic 3D image segmentation methods usually fail to meet the clinic use. Many studies have explored an interactive strategy to improve the image segmentation performance by iteratively incorporating user hints. However, the dynamic process for successive interactions is largely ignored. We here propose to model the dynamic process of iterative interactive image segmentation as a Markov decision process (MDP) and solve it with reinforcement learning (RL). Unfortunately, it is intractable to use single-agent RL for voxel-wise prediction due to the large exploration space. To reduce the exploration space to a tractable size, we treat each voxel as an agent with a shared voxel-level behavior strategy so that it can be solved with multi-agent reinforcement learning. An additional advantage of this multi-agent model is to capture the dependency among voxels for segmentation task. Meanwhile, to enrich the information of previous segmentations, we reserve the prediction uncertainty in the state space of MDP and derive an adjustment action space leading to a more precise and finer segmentation. In addition, to improve the efficiency of exploration, we design a relative cross-entropy gain-based reward to update the policy in a constrained direction. Experimental results on various medical datasets have shown that our method significantly outperforms existing state-of-the-art methods, with the advantage of fewer interactions and a faster convergence.

  • 8 authors
·
Nov 22, 2019

Experimental Design for Multi-Channel Imaging via Task-Driven Feature Selection

This paper presents a data-driven, task-specific paradigm for experimental design, to shorten acquisition time, reduce costs, and accelerate the deployment of imaging devices. Current approaches in experimental design focus on model-parameter estimation and require specification of a particular model, whereas in imaging, other tasks may drive the design. Furthermore, such approaches often lead to intractable optimization problems in real-world imaging applications. Here we present a new paradigm for experimental design that simultaneously optimizes the design (set of image channels) and trains a machine-learning model to execute a user-specified image-analysis task. The approach obtains data densely-sampled over the measurement space (many image channels) for a small number of acquisitions, then identifies a subset of channels of prespecified size that best supports the task. We propose a method: TADRED for TAsk-DRiven Experimental Design in imaging, to identify the most informative channel-subset whilst simultaneously training a network to execute the task given the subset. Experiments demonstrate the potential of TADRED in diverse imaging applications: several clinically-relevant tasks in magnetic resonance imaging; and remote sensing and physiological applications of hyperspectral imaging. Results show substantial improvement over classical experimental design, two recent application-specific methods within the new paradigm, and state-of-the-art approaches in supervised feature selection. We anticipate further applications of our approach. Code is available: https://github.com/sbb-gh/experimental-design-multichannel

  • 3 authors
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Oct 13, 2022