arXiv subjects

Bowen Jing

Publications and source records attributed to Bowen Jing.

At least 19 recordsLinked to original sources

arXiv2026

KnockGS:interaction-Grounded Calibrationof Physical Gaussian Representations

Physics-integrated 3D Gaussian representations now allow reconstructed deformable objects to be simulated and rendered under explicit material models. Existing pipelines, however, assume that material parameters are known or manually specified, limiting their applicability when these parameters must be inferred from observed object dynamics. We propose KnockGS, an interaction-response PhysicalGS framework that estimates the elasticity and density scales of a 3D Gaussian object from its dynamics under a known applied force. Rather than treating physical simulation only as a forward process, we turn the force-induced response into a calibration signal: temporal response features are xtracted from the observed dynamics, the two material scales are estimated from those features, and the estimate is then frozen and written back into the same simulator so that it can be tested on an interaction it was never fitted to.We evaluate the framework on both parameter recovery and response-level fidelity. The estimated scales are compared against hidden ground truth, and the re-simulated object is measured against the target using 3D particle trajectories, response-curve statistics, and rendered-frame quality. Across five held-out material targets, our method recovers the scales substantially more accurately than response retrieval, global regression, or a fixed default material, and the frozen estimate remains predictive under interactions that differ in direction and in magnitude. Interaction response therefore carries enough information to calibrate material scales in physically grounded 3D Gaussian representations.Our study is a first step toward interactive PhysicalGS systems that calibrate a Gaussian asset whose rendered appearance and simulated response are consistent.

cs.CV↗

arXiv2026

SoftVTBench: A Deformation-Aware Visuo-Tactile Dataset and Benchmark for Deformable-Object Manipulation

Physical interaction quality is central to deformable-object manipulation, yet most benchmarks evaluate task success alone. A policy may complete the task while allowing slip or causing excessive compression. A primary bottleneck is the absence of visuo-tactile datasets that pair policy-visible contact observations with independent physical ground truth over complete tasks. We introduce SoftVTBench, a visuo-tactile dataset for physical-interaction-aware deformable-object manipulation. It contains 4,000 expert demonstrations and more than 50 assets, including volumetric deformable objects and visually matched rigid twins. At 20 Hz, each episode synchronizes multi-view RGB, dual-finger tactile RGB and marker motion, proprioception, language, and binary and continuous gripper actions, alongside evaluator-only finite-element (FEM) states. Building upon this dataset, we establish a closed-loop benchmark that uses fixed object-specific calibration to define the Deformation-aware Success Rate (DSR), which counts a rollout as successful only when it completes the task and keeps peak normalized deformation within tolerance. Across Diffusion Policy, $\pi_{0.5}$, and FastWAM, all 12 in-distribution configurations contain successful rollouts that violate the deformation tolerance, accounting for 0.7--24% of each configuration's successes. Under distribution shift, visuo-tactile variants achieve higher task success in all six policy--suite comparisons and higher DSR in five, whereas their in-distribution benefits are mixed. These results show that making touch available does not by itself ensure effective multimodal fusion. SoftVTBench therefore provides a common visuo-tactile resource for studying not only whether a policy succeeds, but how it physically interacts with deformable objects and when touch improves that interaction.

cs.RO↗

arXiv2026

ST-WAM: Semantic-Temporal World Action Model for Robust Manipulation under Visual Distribution Shifts

World Action Models (WAMs) have emerged as a promising paradigm by jointly modeling robot actions and future visual dynamics. However, their reliance on pixel-generative future supervision can entangle action-relevant state transitions with task-irrelevant visual content, limiting robustness under visual distribution shifts. We identify Training-Distribution Hallucination, a recurring phenomenon in which futures conditioned on visually shifted observations hallucinate training-domain content rather than remain faithful to the current scene. A controlled frame-triplet diagnosis further shows that DINOv3 features remain more stable across visual shifts while better preserving task-state distinctions than Wan-VAE latents. Rather than correcting the predicted futures, we propose Semantic-Temporal WAM (ST-WAM) to improve action robustness by using DINOv3 as a shared semantic representation for future prediction and history retrieval while retaining fine-grained VAE dynamics. Its Dual-Space Future Experts (DSFE) jointly predict future VAE latents and DINO features, while Current-Anchored Intent Retrieval (CAIR) retrieves task-relevant evidence from recent DINO history under the current visual-language context. ST-WAM is trained end-to-end without additional embodied pretraining or task-specific annotations, and requires no explicit future generation at inference. It achieves 98.7% on LIBERO and 92.8% on RoboTwin 2.0; more importantly, compared with Fast-WAM, it improves zero-shot LIBERO-Plus performance by 21.3 percentage points and more than doubles real-world success under visual shifts from 25.8% to 61.5%. These results demonstrate that semantic-temporal modeling effectively complements pixel-generative dynamics for robust manipulation.

cs.RO↗

arXiv2026

Comparing the Performance of Foundation Model Derived Embeddings with Traditional Approaches for Distant Metastasis Prediction in Head and Neck Cancer

Background: Early prediction of distant metastasis (DM) risk in head and neck cancer (HNC) can enable timely interventions that may improve treatment outcomes. Many current machine learning methods rely on prior knowledge of the region of interest such as tumor segmentations, which require expert knowledge, is time-consuming and introduces user-dependent variability. Medical image-based foundation models have recently been developed for specific imaging modalities to streamline down-stream prediction tasks by extracting modality-relevant features. Purpose: In this study, we evaluate the effectiveness of using a foundation model as the feature extractor to predict DM risk in HNC patients and compare its performance with traditional approaches that require prior knowledge on the regions of interest. Methods: Preoperative CT images of 2327 patients from the RADCURE dataset were used. Three features-sets were created including radiomics, deep-learning based features, and CT Foundation derived features. The feature-sets were used individually in a multi-layer perceptron (MLP) to predict DM risk. Results: The model using CT Foundation embeddings outperformed the radiomics and deep learning-based models, achieving a Receiver Operating Characteristic Area Under the Curve (AUC) of 0.791, compared to AUC values of 0.772 and 0.753 for the radiomics and deep learning-based models, respectively. The CT Foundation based model had similar performance to a model that combined the use of radiomics and deep learning-based features that achieved an AUC of 0.794. Conclusions: Features based on foundation models offer a promising alternative to traditional radiomics while reducing the need for domain expertise and extensively annotated datasets. Their minimal preprocessing requirements also make them a more accessible and scalable option.

cs.CV↗

arXiv2026

SoftVTBench: A Safety-Aware Visuo-Tactile Benchmark for Physically Constrained Robotic Manipulation of Deformable Objects (Early Version)

Deformable object manipulation poses challenges beyond task completion: successful execution must also maintain safe physical interaction, holding the object stably without slip or drop while avoiding excessive deformation. However, existing manipulation benchmarks are predominantly success-oriented and rarely evaluate whether a policy remains physically safe throughout execution. We present SoftVTBench, a safety-aware visuo-tactile benchmark for physically constrained deformable object manipulation. Built in Isaac Sim with finite-element-simulated deformable objects, SoftVTBench provides multi-view RGB observations, RGB tactile sensing with marker motion, proprioception, and language instructions, and defines four matched task suites over object type (deformable vs. rigid) and variation axis (object vs. spatial). It separately reports Goal Success and Safety Success; the latter additionally requires no drop and peak deformation below a calibrated object-specific threshold, measured from policy-hidden privileged Finite Element Method (FEM) states. We implement pi0.5-based baselines under this protocol. Experiments show that success-only evaluation substantially overstates policy performance, as a large fraction of goal-completing rollouts still violate physical safety. Furthermore, incorporating tactile sensing improves Safety Success (e.g., from 21.4% to 35.6% on object-centric deformable tasks) and reduces object deformation during execution, while maintaining comparable Goal Success. SoftVTBench provides a reproducible benchmark for studying visuo-tactile deformable manipulation under physical interaction constraints.

cs.RO↗

arXiv2026

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins

Multistate mechanisms underlie many of the complex functions observed in natural proteins. The ability to rationally design multistate proteins would have transformative implications for many areas of biotechnology, yet lies beyond the capabilities of existing deep learning frameworks for protein design. To address this gap, we introduce SwitchCraft, a versatile and programmatic framework for designing state-switching proteins based on backpropagation through compositional design constraints parameterized by structure prediction models. In silico evaluations demonstrate success on a wide range of state-switching functional primitives, from allosteric regulation of motifs to discrimination of bound ligand identities. Using these primitives, we demonstrate an in silico strategy for de novo design of fluorescent biosensors to arbitrary small molecule analytes. These results position SwitchCraft at the inception of a powerful paradigm for higher-order functional protein design. Code is available at https://github.com/bjing2016/switchcraft.

q-bio.BM↗

arXiv2026

AI-based experts' knowledge visualization of cultural heritage: A case study of Terracotta Warriors

Advancements in 3D modeling,digital display technologies,and the growing availability of digital cultural heritage data have significantly improved the accuracy of heritage depictions and expanded opportunities for analysis.However,while many studies focus on presenting specific cultural heritage figurines,an often overlooked aspect is the visualization of the Terracotta Warriors as a unified entity.This involves concisely representing the distribution of features and their relationships,providing a clear and insightful presentation that engages practitioners, academics,and wider audiences.To tackle the challenges mentioned above,this research seeks to explore the application of AI methods in processing cultural heritage data.It aims to optimize and augment the dataset,analyze the distribution and relationships of various attributes, and interpret the analysis results through visualization techniques.The Terracotta Warriors,among China's most significant cultural heritages and renowned for their abundance,exquisite workmanship,and magnitude,are chosen as a case study.The contribution of this paper is primarily twofold.Firstly,we constructed a dataset of Terracotta Warriors from Pit No.1,detailing the attributes significant for identifying different Terracotta Warriors.Secondly,we employ various AI methods,such as generative adversarial network and random forest,to process and analyze these attributes,followed by visualizing the analysis results for an intuitive presentation.This study introduces a novel scheme for presenting information on a collection of cultural relics,offering a practical case for analyzing and visualizing the Terracotta Warriors'attributes as a whole entity,rather than showcasing individual relics'information in isolation.

cs.HC↗

arXiv2026

CounterScene: Counterfactual Causal Reasoning in Generative World Models for Safety-Critical Closed-Loop Evaluation

Generating safety-critical driving scenarios requires understanding why dangerous interactions arise, rather than merely forcing collisions. However, existing methods rely on heuristic adversarial agent selection and unstructured perturbations, lacking explicit modeling of interaction dependencies and thus exhibiting a realism--adversarial trade-off. We present CounterScene, a framework that endows closed-loop generative BEV world models with structured counterfactual reasoning for safety-critical scenario generation. Given a safe scene, CounterScene asks: what if the causally critical agent had behaved differently? To answer this, we introduce causal adversarial agent identification to identify the critical agent and classify conflict types, and develop a conflict-aware interactive world model in which a causal interaction graph is used to explicitly model dynamic inter-agent dependencies. Building on this structure, stage-adaptive counterfactual guidance performs minimal interventions on the identified agent, removing its spatial and temporal safety margins while allowing risk to emerge through natural interaction propagation. Extensive experiments on nuScenes demonstrate that CounterScene achieves the strongest adversarial effectiveness while maintaining superior trajectory realism across all horizons, improving long-horizon collision rate from 12.3% to 22.7% over the strongest baseline with better realism (ADE 1.88 vs.2.09). Notably, this advantage further widens over longer rollouts, and CounterScene generalizes zero-shot to nuPlan with state-of-the-art realism.

cs.RO↗

arXiv2026

ReconDrive: Fast Feed-Forward 4D Gaussian Splatting for Autonomous Driving Scene Reconstruction

High-fidelity visual reconstruction and novel-view synthesis are essential for realistic closed-loop evaluation in autonomous driving. While 4D Gaussian Splatting (4DGS) offers a promising balance of accuracy and efficiency, existing per-scene optimization methods require costly iterative refinement, rendering them unscalable for extensive urban environments. Conversely, current feed-forward approaches often suffer from degraded photometric quality. To address these limitations, we propose ReconDrive, a feed-forward framework that leverages and extends the 3D foundation model VGGT for rapid, high-fidelity 4DGS generation. Our architecture introduces two core adaptations to tailor the foundation model to dynamic driving scenes: (1) Hybrid Gaussian Prediction Heads, which decouple the regression of spatial coordinates and appearance attributes to overcome the photometric deficiencies inherent in generalized foundation features; and (2) a Static-Dynamic 4D Composition strategy that explicitly captures temporal motion via velocity modeling to represent complex dynamic environments. Benchmarked on nuScenes, ReconDrive significantly outperforms existing feed-forward baselines in reconstruction, novel-view synthesis, and 3D perception. It achieves performance competitive with per-scene optimization while being orders of magnitude faster, providing a scalable and practical solution for realistic driving simulation.

cs.CV↗

arXiv2025

AI-based Methods for Simulating, Sampling, and Predicting Protein Ensembles

Advances in deep learning have opened an era of abundant and accurate predicted protein structures; however, similar progress in protein ensembles has remained elusive. This review highlights several recent research directions towards AI-based predictions of protein ensembles, including coarse-grained force fields, generative models, multiple sequence alignment perturbation methods, and modeling of ensemble descriptors. An emphasis is placed on realistic assessments of the technological maturity of current methods, the strengths and weaknesses of broad families of techniques, and promising machine learning frameworks at an early stage of development. We advocate for "closing the loop" between model training, simulation, and inference to overcome challenges in training data availability and to enable the next generation of models.

q-bio.BM↗

arXiv2025

Transformer Enhanced Relation Classification: A Comparative Analysis of Contextuality, Data Efficiency and Sequence Complexity

In the era of large language model, relation extraction (RE) plays an important role in information extraction through the transformation of unstructured raw text into structured data (Wadhwa et al., 2023). In this paper, we systematically compare the performance of deep supervised learning approaches without transformers and those with transformers. We used a series of non-transformer architectures such as PA-LSTM(Zhang et al., 2017), C-GCN(Zhang et al., 2018), and AGGCN(attention guide GCN)(Guo et al., 2019), and a series of transformer architectures such as BERT, RoBERTa, and R-BERT(Wu and He, 2019). Our comparison included traditional metrics like micro F1, as well as evaluations in different scenarios, varying sentence lengths, and different percentages of the dataset for training. Our experiments were conducted on TACRED, TACREV, and RE-TACRED. The results show that transformer-based models outperform non-transformer models, achieving micro F1 scores of 80-90% compared to 64-67% for non-transformer models. Additionally, we briefly review the research journey in supervised relation classification and discuss the role and current status of large language models (LLMs) in relation extraction.

cs.CL↗

arXiv2025

Learning residue level protein dynamics with multiscale Gaussians

Many methods have been developed to predict static protein structures, however understanding the dynamics of protein structure is essential for elucidating biological function. While molecular dynamics (MD) simulations remain the in silico gold standard, its high computational cost limits scalability. We present DynaProt, a lightweight, SE(3)-invariant framework that predicts rich descriptors of protein dynamics directly from static structures. By casting the problem through the lens of multivariate Gaussians, DynaProt estimates dynamics at two complementary scales: (1) per-residue marginal anisotropy as $3 \times 3$ covariance matrices capturing local flexibility, and (2) joint scalar covariances encoding pairwise dynamic coupling across residues. From these dynamics outputs, DynaProt achieves high accuracy in predicting residue-level flexibility (RMSF) and, remarkably, enables reasonable reconstruction of the full covariance matrix for fast ensemble generation. Notably, it does so using orders of magnitude fewer parameters than prior methods. Our results highlight the potential of direct protein dynamics prediction as a scalable alternative to existing methods.

q-bio.BM↗

arXiv2025

Continuously Tempered Diffusion Samplers

Annealing-based neural samplers seek to amortize sampling from unnormalized distributions by training neural networks to transport a family of densities interpolating from source to target. A crucial design choice in the training phase of such samplers is the proposal distribution by which locations are generated at which to evaluate the loss. Previous work has obtained such a proposal distribution by combining a partially learned transport with annealed Langevin dynamics. However, isolated modes and other pathological properties of the annealing path imply that such proposals achieve insufficient exploration and thereby lower performance post training. To remedy this, we propose continuously tempered diffusion samplers, which leverage exploration techniques developed in the context of molecular dynamics to improve proposal distributions. Specifically, a family of distributions across different temperatures is introduced to lower energy barriers at higher temperatures and drive exploration at the lower temperature of interest. We empirically validate improved sampler performance driven by extended exploration. Code is available at https://github.com/eje24/ctds.

cs.LG↗

arXiv2025

StyleDrive: Towards Driving-Style Aware Benchmarking of End-To-End Autonomous Driving

Personalization, while extensively studied in conventional autonomous driving pipelines, has been largely overlooked in the context of end-to-end autonomous driving (E2EAD), despite its critical role in fostering user trust, safety perception, and real-world adoption. A primary bottleneck is the absence of large-scale real-world datasets that systematically capture driving preferences, severely limiting the development and evaluation of personalized E2EAD models. In this work, we introduce the first large-scale real-world dataset explicitly curated for personalized E2EAD, integrating comprehensive scene topology with rich dynamic context derived from agent dynamics and semantics inferred via a fine-tuned vision-language model (VLM). We propose a hybrid annotation pipeline that combines behavioral analysis, rule-and-distribution-based heuristics, and subjective semantic modeling guided by VLM reasoning, with final refinement through human-in-the-loop verification. Building upon this dataset, we introduce the first standardized benchmark for systematically evaluating personalized E2EAD models. Empirical evaluations on state-of-the-art architectures demonstrate that incorporating personalized driving preferences significantly improves behavioral alignment with human demonstrations.

cs.CV↗

arXiv2025

Advanced Deep Learning Methods for Protein Structure Prediction and Design

After AlphaFold won the Nobel Prize, protein prediction with deep learning once again became a hot topic. We comprehensively explore advanced deep learning methods applied to protein structure prediction and design. It begins by examining recent innovations in prediction architectures, with detailed discussions on improvements such as diffusion based frameworks and novel pairwise attention modules. The text analyses key components including structure generation, evaluation metrics, multiple sequence alignment processing, and network architecture, thereby illustrating the current state of the art in computational protein modelling. Subsequent chapters focus on practical applications, presenting case studies that range from individual protein predictions to complex biomolecular interactions. Strategies for enhancing prediction accuracy and integrating deep learning techniques with experimental validation are thoroughly explored. The later sections review the industry landscape of protein design, highlighting the transformative role of artificial intelligence in biotechnology and discussing emerging market trends and future challenges. Supplementary appendices provide essential resources such as databases and open source tools, making this volume a valuable reference for researchers and students.

q-bio.BM↗

arXiv2025

ProtComposer: Compositional Protein Structure Generation with 3D Ellipsoids

We develop ProtComposer to generate protein structures conditioned on spatial protein layouts that are specified via a set of 3D ellipsoids capturing substructure shapes and semantics. At inference time, we condition on ellipsoids that are hand-constructed, extracted from existing proteins, or from a statistical model, with each option unlocking new capabilities. Hand-specifying ellipsoids enables users to control the location, size, orientation, secondary structure, and approximate shape of protein substructures. Conditioning on ellipsoids of existing proteins enables redesigning their substructure's connectivity or editing substructure properties. By conditioning on novel and diverse ellipsoid layouts from a simple statistical model, we improve protein generation with expanded Pareto frontiers between designability, novelty, and diversity. Further, this enables sampling designable proteins with a helix-fraction that matches PDB proteins, unlike existing generative models that commonly oversample conceptually simple helix bundles. Code is available at https://github.com/NVlabs/protcomposer.

q-bio.BM↗

arXiv2025

Generative Adversarial Networks Bridging Art and Machine Intelligence

Generative Adversarial Networks (GAN) have greatly influenced the development of computer vision and artificial intelligence in the past decade and also connected art and machine intelligence together. This book begins with a detailed introduction to the fundamental principles and historical development of GANs, contrasting them with traditional generative models and elucidating the core adversarial mechanisms through illustrative Python examples. The text systematically addresses the mathematical and theoretical underpinnings including probability theory, statistics, and game theory providing a solid framework for understanding the objectives, loss functions, and optimisation challenges inherent to GAN training. Subsequent chapters review classic variants such as Conditional GANs, DCGANs, InfoGAN, and LAPGAN before progressing to advanced training methodologies like Wasserstein GANs, GANs with gradient penalty, least squares GANs, and spectral normalisation techniques. The book further examines architectural enhancements and task-specific adaptations in generators and discriminators, showcasing practical implementations in high resolution image generation, artistic style transfer, video synthesis, text to image generation and other multimedia applications. The concluding sections offer insights into emerging research trends, including self-attention mechanisms, transformer-based generative models, and a comparative analysis with diffusion models, thus charting promising directions for future developments in both academic and applied settings.

cs.LG↗

arXiv2025

A two-stage dual-task learning strategy for early prediction of pathological complete response to neoadjuvant chemotherapy for breast cancer using dynamic contrast-enhanced magnetic resonance images

Rationale and Objectives: Early prediction of pathological complete response (pCR) can facilitate personalized treatment for breast cancer patients. To improve prediction accuracy at the early time point of neoadjuvant chemotherapy, we proposed a two-stage dual-task learning strategy to train a deep neural network for early prediction of pCR using early-treatment magnetic resonance images. Methods: We developed and validated the two-stage dual-task learning strategy using the dataset from the national-wide, multi-institutional I-SPY2 clinical trial, which included dynamic contrast-enhanced magnetic resonance images acquired at three time points: pretreatment (T0), after 3 weeks (T1), and after 12 weeks of treatment (T2). First, we trained a convolutional long short-term memory network to predict pCR and extract the latent space image features at T2. At the second stage, we trained a dual-task network to simultaneously predict pCR and the image features at T2 using images from T0 and T1. This allowed us to predict pCR earlier without using images from T2. Results: The conventional single-stage single-task strategy gave an area under the receiver operating characteristic curve (AUROC) of 0.799 for pCR prediction using all the data at time points T0 and T1. By using the proposed two-stage dual-task learning strategy, the AUROC was improved to 0.820. Conclusions: The proposed two-stage dual-task learning strategy can improve model performance significantly (p=0.0025) for predicting pCR at the early stage (3rd week) of neoadjuvant chemotherapy. The early prediction model can potentially help physicians to intervene early and develop personalized plans at the early stage of chemotherapy.

cs.CV↗