Ke Chen’s research while affiliated with Huazhong University of Science and Technology and other places

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Publications (137)


TransWild: Enhancing 3D interacting hands recovery in the wild with IoU-guided Transformer
  • Article

November 2024

Image and Vision Computing

Wanru Zhu

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Yichen Zhang

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Ke Chen

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Ultrasound-guided renal artery balloon catheter occluded hybrid partial nephrectomy (UBo-HPN) with branch renal artery occlusion: a single arm trial
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  • Full-text available

October 2024

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3 Reads

World Journal of Urology

Tianrun Ye

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Xu Shi

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Yang Yu

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[...]

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Heng Li

Background One key focus of partial nephrectomy is preserving renal function. Segmental renal artery occlusion with microdissection at the renal hilum confines ischemia, effectively reducing warm ischemic injury. Ultrasound-Guided Renal Artery Balloon Catheter Occluded Hybrid Partial Nephrectomy (UBo-HPN) can achieve branch occlusion without the need for dissecting the renal hilum. Objective To investigate the feasibility and safety of UBo-HPN of branch renal artery occlusion in the treatment of localized renal tumors. Subject and methods A prospective single-arm analysis involving 20 patients with renal localized tumors underwent robot assisted UBo-HPN with branch renal artery occlusion from August 2021 to July 2023, with an average follow-up of 12 months. Results All patient was successfully operated on without conversion to conventional arterial clamping or radical nephrectomy. One case (5%) of minor complication occurred in the whole cohort, which was bruising around the puncture site. The mean total operative time was 95.8 min, with a mean operative time of 21.25 min for vascular intervention. The mean warm ischemia time was 20.35 min, and the median estimated blood loss was 50 ml. The median eGFR preservation percentage at postoperative 48 h, 30 days, and the latest follow-up were 87.52%, 91.47%, and 92.2%, respectively. After a median follow-up of 10.2 (2.3–19.2) months, no patients had radiological tumor recurrence or died from tumor-related causes. Conclusions UBo-HPN with renal artery branch occlusion emerges as an efficient alternative to partial nephrectomy (PN), which achieved branch artery occlusion without dissecting the renal hilum. Long-term follow-up is expected for functional outcomes.

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Bridging Domain Gap of Point Cloud Representations via Self-Supervised Geometric Augmentation

September 2024

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5 Reads

Recent progress of semantic point clouds analysis is largely driven by synthetic data (e.g., the ModelNet and the ShapeNet), which are typically complete, well-aligned and noisy free. Therefore, representations of those ideal synthetic point clouds have limited variations in the geometric perspective and can gain good performance on a number of 3D vision tasks such as point cloud classification. In the context of unsupervised domain adaptation (UDA), representation learning designed for synthetic point clouds can hardly capture domain invariant geometric patterns from incomplete and noisy point clouds. To address such a problem, we introduce a novel scheme for induced geometric invariance of point cloud representations across domains, via regularizing representation learning with two self-supervised geometric augmentation tasks. On one hand, a novel pretext task of predicting translation distances of augmented samples is proposed to alleviate centroid shift of point clouds due to occlusion and noises. On the other hand, we pioneer an integration of the relational self-supervised learning on geometrically-augmented point clouds in a cascade manner, utilizing the intrinsic relationship of augmented variants and other samples as extra constraints of cross-domain geometric features. Experiments on the PointDA-10 dataset demonstrate the effectiveness of the proposed method, achieving the state-of-the-art performance.


Fig. 1: Paradigm for an integrated air-ground edge-cloud model evolution framework.
Fig. 2: System model for an integrated air-ground edge-cloud model evolution framework.
Fig. 3: Total bandwidth B versus mAP.
Fig. 4: Number of frames per second N versus mAP.
Fig. 5: Uplink and downlink spectrum efficiency versus mAP.

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Large Models for Aerial Edges: An Edge-Cloud Model Evolution and Communication Paradigm

August 2024

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16 Reads

The future sixth-generation (6G) of wireless networks is expected to surpass its predecessors by offering ubiquitous coverage through integrated air-ground facility deployments in both communication and computing domains. In this network, aerial facilities, such as unmanned aerial vehicles (UAVs), conduct artificial intelligence (AI) computations based on multi-modal data to support diverse applications including surveillance and environment construction. However, these multi-domain inference and content generation tasks require large AI models, demanding powerful computing capabilities, thus posing significant challenges for UAVs. To tackle this problem, we propose an integrated edge-cloud model evolution framework, where UAVs serve as edge nodes for data collection and edge model computation. Through wireless channels, UAVs collaborate with ground cloud servers, providing cloud model computation and model updating for edge UAVs. With limited wireless communication bandwidth, the proposed framework faces the challenge of information exchange scheduling between the edge UAVs and the cloud server. To tackle this, we present joint task allocation, transmission resource allocation, transmission data quantization design, and edge model update design to enhance the inference accuracy of the integrated air-ground edge-cloud model evolution framework by mean average precision (mAP) maximization. A closed-form lower bound on the mAP of the proposed framework is derived, and the solution to the mAP maximization problem is optimized accordingly. Simulations, based on results from vision-based classification experiments, consistently demonstrate that the mAP of the proposed framework outperforms both a centralized cloud model framework and a distributed edge model framework across various communication bandwidths and data sizes.


Generative AI on SpectrumNet: An Open Benchmark of Multiband 3D Radio Maps

August 2024

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42 Reads

Radio map is an efficient demonstration for visually displaying the wireless signal coverage within a certain region. It has been considered to be increasingly helpful for the future sixth generation (6G) of wireless networks, as wireless nodes are becoming more crowded and complicated. However, the construction of high resolution radio map is very challenging due to the sparse sampling in practical systems. Generative artificial intelligence (AI), which is capable to create synthetic data to fill in gaps in real-world measurements, is an effective technique to construct high precision radio maps. Currently, generative models for radio map construction are trained with two-dimension (2D) single band radio maps in urban scenario, which has poor generalization in diverse terrain scenarios, spectrum bands, and heights. To tackle this problem, we provide a multiband three-dimension (3D) radio map dataset with consideration of terrain and climate information, named SpectrumNet. It is the largest radio map dataset in terms of dimensions and scale, which contains the radio map of 3 spacial dimensions, 5 frequency bands, 11 terrain scenarios, and 3 climate scenarios. We introduce the parameters and settings for the SpectrumNet dataset generation, and evaluate three baseline methods for radio map construction based on the SpectrumNet dataset. Experiments show the necessity of the SpectrumNet dataset for training models with strong generalization in spacial, frequency, and scenario domains. Future works on the SpectrumNet dataset are also discussed, including the dataset expansion and calibration, as well as the extended studies on generative models for radio map construction based on the SpectrumNet dataset.


Label-Efficient Point Cloud Semantic Segmentation: A Holistic Active Learning Approach

August 2024

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2 Reads

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16 Citations

World Scientific Annual Review of Artificial Intelligence

Deep learning models are the state of the art for semantic segmentation of point clouds, the success of which relies on the availability of large-scale annotated datasets. However, it can be prohibitively costly to prepare such datasets. In this work, we propose a holistic active learning (AL) approach to maximize model performance given limited annotation budgets. We investigate the appropriate sample granularity for active selection under the realistic “click” measurement of annotation cost, and demonstrate that superpoint-based selection allows for most efficient usage of the limited budget, when compared with point-level, polygon-level and instance/shape-level selection. We further propose new objective for AL acquisition function and exploit local consistency constraints to boost the performance of our superpoint-based approach. We evaluate our methods on three benchmark datasets, ShapeNet and PartNet and S3DIS. The results demonstrate that AL is an effective strategy to address the high annotation costs in semantic point cloud segmentation.



Boosting Cross-Domain Point Classification via Distilling Relational Priors from 2D Transformers

July 2024

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2 Reads

Semantic pattern of an object point cloud is determined by its topological configuration of local geometries. Learning discriminative representations can be challenging due to large shape variations of point sets in local regions and incomplete surface in a global perspective, which can be made even more severe in the context of unsupervised domain adaptation (UDA). In specific, traditional 3D networks mainly focus on local geometric details and ignore the topological structure between local geometries, which greatly limits their cross-domain generalization. Recently, the transformer-based models have achieved impressive performance gain in a range of image-based tasks, benefiting from its strong generalization capability and scalability stemming from capturing long range correlation across local patches. Inspired by such successes of visual transformers, we propose a novel Relational Priors Distillation (RPD) method to extract relational priors from the well-trained transformers on massive images, which can significantly empower cross-domain representations with consistent topological priors of objects. To this end, we establish a parameter-frozen pre-trained transformer module shared between 2D teacher and 3D student models, complemented by an online knowledge distillation strategy for semantically regularizing the 3D student model. Furthermore, we introduce a novel self-supervised task centered on reconstructing masked point cloud patches using corresponding masked multi-view image features, thereby empowering the model with incorporating 3D geometric information. Experiments on the PointDA-10 and the Sim-to-Real datasets verify that the proposed method consistently achieves the state-of-the-art performance of UDA for point cloud classification. The source code of this work is available at https://github.com/zou-longkun/RPD.git.


An Evaluation of the Tumor Microenvironment through CALR, IL1R1, IFNB1, and IFNG to Assess Prognosis and Immunotherapy Response in Bladder Cancer Patients

May 2024

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4 Reads

Immunogenic cell death (ICD) is a type of cell death sparking adaptive immune responses, can reshape the tumor microenvironment (TME). Exploring key ICD-related genes in bladder cancer (BLCA) could enhance personalized treatment. TCGA BLCA patients were divided into two ICD subtypes: ICD-high and ICD-low. High ICD expression linked to increased immune cell infiltration and longer survival, but with potentially suppressed immune function. The high ICD group responded better to PD1-targeted therapy. A risk-scoring model with four ICD-related genes (CALR, IL1R1, IFNB1, IFNG) was validated across TCGA, GEO datasets, and tissue samples, showing higher risk-score correlated with weaker anti-tumor immune function, more tumor-promoting elements, lower immunotherapy response rates, and shorter patient survival.This study connects ICD-related genes to BLCA prognosis and immune infiltration, offering a vital tool for personalized treatment guidance.


Adversarial Geometric Transformations of Point Clouds for Physical Attack

March 2024

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15 Reads

Lecture Notes in Computer Science

Towards adversarial physical attack in real world, we argue that the main challenge lies in discounting adversarial effects by changes of point density along object surface. Most of existing point-wise perturbation based attackers concern on suppressing geometric irregularities, but it remains challenging to produce adversarial shape with geometric smoothness. Adversarial attack via the isometry transformation can alleviate irregular geometries but suffer from its rotation-sensitive nature, so its impractical assumption of category-level pre-alignment on benign object point clouds cannot be relaxed. In light of this, we explore non-rigid geometric transformations for geometry-aware adversaries with a flexible density-aware transformation on the whole point sets, which can thus impose constraints of global and local surface properties when adversarially deforming points. Experiment results on publicly benchmarking ModelNet40 and ScanObjectNN datasets verify the effectiveness of our transformation-based generation algorithms for adversarial shape and physical attack against both rotation sensitive and agnostic point classifiers, significantly outperforming existing adversarial point attackers under diverse recent defenses and the state-of-the-art physical attack methods.


Citations (56)


... Deng et al. [27] proposed an iterative algorithm to generate superpoints by combining geometry-based and color-based region growing methods. Similarly, geometry-based superpoints have been proven to leverage large-scale point clouds and act as priors in weakly supervised learning [28][29][30][31]. We will review these deep learning networks in detail in the following sections. ...

Reference:

A review of point cloud segmentation for understanding 3D indoor scenes
Label-Efficient Point Cloud Semantic Segmentation: A Holistic Active Learning Approach
  • Citing Article
  • August 2024

World Scientific Annual Review of Artificial Intelligence

... These results showcase that AIDO.RNA can benefit RNA sequence design. [60] contains similar data sources. We analyze the data and find that approximately 85% of the sequences within MARS are whole-genome shotgun sequences, 9 . ...

MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search

Genomics Proteomics & Bioinformatics

... In recent years, several RNA FMs have been proposed [11,12,13,9,14,15,16,17,7,10,8,18], most of which are encoder-only transformers pre-trained using the Masked Language Modeling (MLM) objective [19,20] (See Appendix E). These models have shown impressive results in RNA secondary structure prediction and function prediction [9, 10], demonstrating the potential of large language models (LLMs) in the RNA domain. ...

Multiple sequence alignment-based RNA language model and its application to structural inference

Nucleic Acids Research

... Deep neural networks have shown potential in recent years across diverse fields, including biophysics in structure prediction [38][39][40]. Well-established methods are available for modeling the 3D structures of proteins [41][42][43][44][45][46], RNAs [47][48][49][50][51][52][53][54], and protein-protein complexes [55][56][57]. Recent studies have shown that machine learning is now excelling in evaluating RNA-protein complex structures. ...

RNA tertiary structure modeling with BRiQ potential in CASP15
  • Citing Article
  • August 2023

Proteins Structure Function and Bioinformatics

... In the context of unsupervised domain adaptation (UDA) of point cloud classification [8], the goal of representation learning is to extract domain-invariant geometric patterns from one labeled source domain and another unlabeled target domain, which is supervised by target codes of semantic classes. Evidently, the aim of the semantic task cannot ensure inducing geometric invariance across domains into point cloud representations [9], which encourages a number of explorations to incorporate geometric information through adversarial training [10], [11], [12], [13], self-training [14], [15], [16] and self-supervised learning such as rotation prediction [17], scaling factors [18], distorted part localization [19] and generation of masked parts [20]. Existing pretext tasks concern on either achieving representations' generalization on rotation and scale changes of objects or incorporating cross-arXiv:2409.06956v1 ...

Manifold-Aware Self-Training for Unsupervised Domain Adaptation on Regressing 6D Object Pose
  • Citing Conference Paper
  • August 2023

... However, GAN-based methods struggle to capture the latent associations between attribute sets and class labels in relational data. To address this issue, Zhang, C. et al. [59] proposed an end-to-end self-training scheme called quality-aware self-training (QAST) for synthesizing rare relational data. QAST generates labeled synthetic data using GAN-based synthesis and pseudo-labeling. ...

Quality-Aware Self-Training on Differentiable Synthesis of Rare Relational Data
  • Citing Article
  • June 2023

Proceedings of the AAAI Conference on Artificial Intelligence

... At the front end, this involves building large biomolecular complexes that provide physically realistic starting models. Recently proposed Large Language Models (LLMs) will accelerate the process of generating alternative protein and RNA structures 48,49 and predicting functional protein sequences 50 in protein design. In addition, AI/ML methods can be used in a computational design process for the simulations in order to minimize uncertainties in the simulation results (above). ...

Multiple sequence-alignment-based RNA language model and its application to structural inference
  • Citing Preprint
  • March 2023

... We downloaded 4069 RNA families ( version 14.7 ) from https://rfam.xfam.org on 09 / 04 / 2022. The fully automatic RNAcmap3 for homolog search and sequence alignment ( 33 ) was employed for these 4069 RNA families by using their covariance models (CMs) for each family. Although the language model is unsupervised learning, we excluded the Rfam families which contain RNA sequences with experimentally determined structures in order to minimize potential overfitting for structural inference. ...

The Master Database of All Possible RNA Sequences and Its Integration with RNAcmap for RNA Homology Search

... Nizi et al, 10 reported two phenylquinoline derivatives as potential inhibitors of SARS-CoV-2 replication, using a colorimetric formazan-based MTS assay. Amongst the studied compounds, Compound 27 bearing two methoxy groups at the C-4 position of the 2-phenylquinoline core, showed significant inhibitory activity against SARS-CoV-2 helicase (nsp13) with an IC 50 74 investigated chloroxine and hybrids of tanshinone IIA sulfonate sodium (TSS) as potential inhibitors of SARS-CoV-2 PL pro using a fluorescence polarization assay (FPA) and cell-based assay. Amongst them, chloroxine 31 inhibited the binding of SARS-CoV-2 PL pro to ISG15 (which plays an important role in viral replication) with an IC 50 value of 6.0μM. ...

Investigating Derivatives of Tanshinone IIA Sulfonate Sodium and Chloroxine for Their Inhibition Activities against the SARS-CoV-2 Papain-like Protease

ACS Omega

... The drawback is that the parameters of our method for different ship targets are different. We comment that this problem can be solved by constructing a parameter database for typical ship types and applying existing classification methods [31][32][33] to acquire the type of target ship. ...

Classification of single-view object point clouds
  • Citing Article
  • March 2023

Pattern Recognition