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  1. Article ; Online: Towards Adversarial Robustness in Unlabeled Target Domains.

    Zhang, Jiajin / Chao, Hanqing / Yan, Pingkun

    IEEE transactions on image processing : a publication of the IEEE Signal Processing Society

    2023  Volume PP

    Abstract: In the past several years, various adversarial training (AT) approaches have been invented to robustify deep learning model against adversarial attacks. However, mainstream AT methods assume the training and testing data are drawn from the same ... ...

    Abstract In the past several years, various adversarial training (AT) approaches have been invented to robustify deep learning model against adversarial attacks. However, mainstream AT methods assume the training and testing data are drawn from the same distribution and the training data are annotated. When the two assumptions are violated, existing AT methods fail because either they cannot pass knowledge learnt from a source domain to an unlabeled target domain or they are confused by the adversarial samples in that unlabeled space. In this paper, we first point out this new and challenging problem-adversarial training in unlabeled target domain. We then propose a novel framework named Unsupervised Cross-domain Adversarial Training (UCAT) to address this problem. UCAT effectively leverages the knowledge of the labeled source domain to prevent the adversarial samples from misleading the training process, under the guidance of automatically selected high quality pseudo labels of the unannotated target domain data together with the discriminative and robust anchor representations of the source domain data. The experiments on four public benchmarks show that models trained with UCAT can achieve both high accuracy and strong robustness. The effectiveness of the proposed components is demonstrated through a large set of ablation studies. The source code is publicly available at https://github.com/DIAL-RPI/UCAT.
    Language English
    Publishing date 2023-02-13
    Publishing country United States
    Document type Journal Article
    ISSN 1941-0042
    ISSN (online) 1941-0042
    DOI 10.1109/TIP.2023.3242141
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Revisiting the Trustworthiness of Saliency Methods in Radiology AI.

    Zhang, Jiajin / Chao, Hanqing / Dasegowda, Giridhar / Wang, Ge / Kalra, Mannudeep K / Yan, Pingkun

    Radiology. Artificial intelligence

    2024  Volume 6, Issue 1, Page(s) e220221

    Abstract: Purpose To determine whether saliency maps in radiology artificial intelligence (AI) are vulnerable to subtle perturbations of the input, which could lead to misleading interpretations, using prediction-saliency correlation (PSC) for evaluating the ... ...

    Abstract Purpose To determine whether saliency maps in radiology artificial intelligence (AI) are vulnerable to subtle perturbations of the input, which could lead to misleading interpretations, using prediction-saliency correlation (PSC) for evaluating the sensitivity and robustness of saliency methods. Materials and Methods In this retrospective study, locally trained deep learning models and a research prototype provided by a commercial vendor were systematically evaluated on 191 229 chest radiographs from the CheXpert dataset and 7022 MR images from a human brain tumor classification dataset. Two radiologists performed a reader study on 270 chest radiograph pairs. A model-agnostic approach for computing the PSC coefficient was used to evaluate the sensitivity and robustness of seven commonly used saliency methods. Results The saliency methods had low sensitivity (maximum PSC, 0.25; 95% CI: 0.12, 0.38) and weak robustness (maximum PSC, 0.12; 95% CI: 0.0, 0.25) on the CheXpert dataset, as demonstrated by leveraging locally trained model parameters. Further evaluation showed that the saliency maps generated from a commercial prototype could be irrelevant to the model output, without knowledge of the model specifics (area under the receiver operating characteristic curve decreased by 8.6% without affecting the saliency map). The human observer studies confirmed that it is difficult for experts to identify the perturbed images; the experts had less than 44.8% correctness. Conclusion Popular saliency methods scored low PSC values on the two datasets of perturbed chest radiographs, indicating weak sensitivity and robustness. The proposed PSC metric provides a valuable quantification tool for validating the trustworthiness of medical AI explainability.
    MeSH term(s) Humans ; Artificial Intelligence ; Retrospective Studies ; Radiology ; Radiography ; Radiologists
    Language English
    Publishing date 2024-01-02
    Publishing country United States
    Document type Journal Article
    ISSN 2638-6100
    ISSN (online) 2638-6100
    DOI 10.1148/ryai.220221
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Ultrasound Volume Reconstruction From Freehand Scans Without Tracking.

    Guo, Hengtao / Chao, Hanqing / Xu, Sheng / Wood, Bradford J / Wang, Jing / Yan, Pingkun

    IEEE transactions on bio-medical engineering

    2023  Volume 70, Issue 3, Page(s) 970–979

    Abstract: Transrectal ultrasound is commonly used for guiding prostate cancer biopsy, where 3D ultrasound volume reconstruction is often desired. Current methods for 3D reconstruction from freehand ultrasound scans require external tracking devices to provide ... ...

    Abstract Transrectal ultrasound is commonly used for guiding prostate cancer biopsy, where 3D ultrasound volume reconstruction is often desired. Current methods for 3D reconstruction from freehand ultrasound scans require external tracking devices to provide spatial information of an ultrasound transducer. This paper presents a novel deep learning approach for sensorless ultrasound volume reconstruction, which efficiently exploits content correspondence between ultrasound frames to reconstruct 3D volumes without external tracking. The underlying deep learning model, deep contextual-contrastive network (DC
    MeSH term(s) Male ; Humans ; Imaging, Three-Dimensional/methods ; Ultrasonography/methods ; Neural Networks, Computer ; Prostate/diagnostic imaging ; Movement
    Language English
    Publishing date 2023-02-17
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 160429-6
    ISSN 1558-2531 ; 0018-9294
    ISSN (online) 1558-2531
    ISSN 0018-9294
    DOI 10.1109/TBME.2022.3206596
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Volatilomics-Based Discovery of Key Volatiles Affecting Flavor Quality in Tomato.

    Zhang, Zhonghui / Ye, Weizhen / Li, Chun / Zhou, Haihong / Wang, Chao / Liu, Penghui / Zhou, Binxin / Zhao, Hanqing / Wang, Shouchuang / Yang, Jun

    Foods (Basel, Switzerland)

    2024  Volume 13, Issue 6

    Abstract: Volatile accumulation during tomato ripening greatly affects the fruit flavor. In this study, four accessions from each of the three tomato subgroups (BIG, ...

    Abstract Volatile accumulation during tomato ripening greatly affects the fruit flavor. In this study, four accessions from each of the three tomato subgroups (BIG,
    Language English
    Publishing date 2024-03-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods13060879
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Identifying Progression-Specific Alzheimer's Subtypes Using Multimodal Transformer.

    Machado Reyes, Diego / Chao, Hanqing / Hahn, Juergen / Shen, Li / Yan, Pingkun / For The Alzheimer's Disease Neuroimaging Initiative

    Journal of personalized medicine

    2024  Volume 14, Issue 4

    Abstract: Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet its current treatments are limited to stopping disease progression. Moreover, the effectiveness of these treatments remains uncertain due to the heterogeneity of the disease. ... ...

    Abstract Alzheimer's disease (AD) is the most prevalent neurodegenerative disease, yet its current treatments are limited to stopping disease progression. Moreover, the effectiveness of these treatments remains uncertain due to the heterogeneity of the disease. Therefore, it is essential to identify disease subtypes at a very early stage. Current data-driven approaches can be used to classify subtypes during later stages of AD or related disorders, but making predictions in the asymptomatic or prodromal stage is challenging. Furthermore, the classifications of most existing models lack explainability, and these models rely solely on a single modality for assessment, limiting the scope of their analysis. Thus, we propose a multimodal framework that utilizes early-stage indicators, including imaging, genetics, and clinical assessments, to classify AD patients into progression-specific subtypes at an early stage. In our framework, we introduce a tri-modal co-attention mechanism (Tri-COAT) to explicitly capture cross-modal feature associations. Data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) (slow progressing = 177, intermediate = 302, and fast = 15) were used to train and evaluate Tri-COAT using a 10-fold stratified cross-testing approach. Our proposed model outperforms baseline models and sheds light on essential associations across multimodal features supported by known biological mechanisms. The multimodal design behind Tri-COAT allows it to achieve the highest classification area under the receiver operating characteristic curve while simultaneously providing interpretability to the model predictions through the co-attention mechanism.
    Language English
    Publishing date 2024-04-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662248-8
    ISSN 2075-4426
    ISSN 2075-4426
    DOI 10.3390/jpm14040421
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Age-related noncanonical TRMT6-TRMT61A signaling impairs hematopoietic stem cells.

    He, Hanqing / Wang, Yuqian / Zhang, Xiaoting / Li, Xiaoyu / Liu, Chao / Yan, Dingfei / Deng, Haiteng / Sun, Wanling / Yi, Chengqi / Wang, Jianwei

    Nature aging

    2024  Volume 4, Issue 2, Page(s) 213–230

    Abstract: Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation bias toward myeloid lineages. However, the molecular mechanism behind HSC aging remains largely unknown. In this study, we observed that RNA ... ...

    Abstract Aged hematopoietic stem cells (HSCs) exhibit compromised reconstitution capacity and differentiation bias toward myeloid lineages. However, the molecular mechanism behind HSC aging remains largely unknown. In this study, we observed that RNA N
    MeSH term(s) Mice ; Animals ; Hematopoietic Stem Cells ; Cell Differentiation/genetics ; Signal Transduction ; Aging/genetics
    Language English
    Publishing date 2024-01-17
    Publishing country United States
    Document type Journal Article
    ISSN 2662-8465
    ISSN (online) 2662-8465
    DOI 10.1038/s43587-023-00556-1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Hollow Carbon and MXene Dual-Reinforced MoS

    Pan, Hanqing / Huang, Yan / Cen, Xinnuo / Zhang, Ming / Hou, Jianhua / Wu, Chao / Dou, Yuhai / Sun, Bing / Wang, Ying / Zhang, Binwei / Zhang, Lei

    Advanced science (Weinheim, Baden-Wurttemberg, Germany)

    2024  , Page(s) e2400364

    Abstract: Sodium-ion batteries (SIBs) and sodium-ion capacitors (SICs) are promising candidates for cost-effective and large-scale energy storage devices. However, sluggish kinetics and low capacity of traditional anode materials inhibit their practical ... ...

    Abstract Sodium-ion batteries (SIBs) and sodium-ion capacitors (SICs) are promising candidates for cost-effective and large-scale energy storage devices. However, sluggish kinetics and low capacity of traditional anode materials inhibit their practical applications. Herein, a novel design featuring a layer-expanded MoS
    Language English
    Publishing date 2024-01-22
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 2808093-2
    ISSN 2198-3844 ; 2198-3844
    ISSN (online) 2198-3844
    ISSN 2198-3844
    DOI 10.1002/advs.202400364
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A film-lever actuated switch technology for multifunctional, on-demand, and robust manipulation of liquids.

    Liang, Chao / Yang, Zihang / Jiang, Hanqing

    Nature communications

    2022  Volume 13, Issue 1, Page(s) 4902

    Abstract: A lab-on-a-chip system with Point-of-Care testing capability offers rapid and accurate diagnostic potential and is useful in resource-limited settings where biomedical equipment and skilled professionals are not readily available. However, a Point-of- ... ...

    Abstract A lab-on-a-chip system with Point-of-Care testing capability offers rapid and accurate diagnostic potential and is useful in resource-limited settings where biomedical equipment and skilled professionals are not readily available. However, a Point-of-Care testing system that simultaneously possesses all required features of multifunctional dispensing, on-demand release, robust operations, and capability for long-term reagent storage is still a major challenge. Here, we describe a film-lever actuated switch technology that can manipulate liquids in any direction, provide accurate and proportional release response to the applied pneumatic pressure, as well as sustain robustness during abrupt movements and vibrations. Based on the technology, we also describe development of a polymerase chain reaction system that integrates reagent introduction, mixing and reaction functions all in one process, which accomplishes "sample-in-answer-out" performance for all clinical nasal samples from 18 patients with Influenza and 18 individual controls, in good concordance of fluorescence intensity with standard polymerase chain reaction (Pearson coefficients > 0.9). The proposed platform promises robust automation of biomedical analysis, and thus can accelerate the commercialization of a range of Point-of-Care testing devices.
    MeSH term(s) Automation ; Humans ; Lab-On-A-Chip Devices ; Microfluidic Analytical Techniques ; Point-of-Care Systems ; Point-of-Care Testing ; Polymerase Chain Reaction
    Language English
    Publishing date 2022-08-20
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-022-32676-4
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: GaitSet: Cross-View Gait Recognition Through Utilizing Gait As a Deep Set.

    Chao, Hanqing / Wang, Kun / He, Yiwei / Zhang, Junping / Feng, Jianfeng

    IEEE transactions on pattern analysis and machine intelligence

    2022  Volume 44, Issue 7, Page(s) 3467–3478

    Abstract: Gait is a unique biometric feature that can be recognized at a distance; thus, it has broad applications in crime prevention, forensic identification, and social security. To portray a gait, existing gait recognition methods utilize either a gait ... ...

    Abstract Gait is a unique biometric feature that can be recognized at a distance; thus, it has broad applications in crime prevention, forensic identification, and social security. To portray a gait, existing gait recognition methods utilize either a gait template which makes it difficult to preserve temporal information, or a gait sequence that maintains unnecessary sequential constraints and thus loses the flexibility of gait recognition. In this paper, we present a novel perspective that utilizes gait as a deep set, which means that a set of gait frames are integrated by a global-local fused deep network inspired by the way our left- and right-hemisphere processes information to learn information that can be used in identification. Based on this deep set perspective, our method is immune to frame permutations, and can naturally integrate frames from different videos that have been acquired under different scenarios, such as diverse viewing angles, different clothes, or different item-carrying conditions. Experiments show that under normal walking conditions, our single-model method achieves an average rank-1 accuracy of 96.1 percent on the CASIA-B gait dataset and an accuracy of 87.9 percent on the OU-MVLP gait dataset. Under various complex scenarios, our model also exhibits a high level of robustness. It achieves accuracies of 90.8 and 70.3 percent on CASIA-B under bag-carrying and coat-wearing walking conditions respectively, significantly outperforming the best existing methods. Moreover, the proposed method maintains a satisfactory accuracy even when only small numbers of frames are available in the test samples; for example, it achieves 85.0 percent on CASIA-B even when using only 7 frames. The source code has been released at https://github.com/AbnerHqC/GaitSet.
    MeSH term(s) Algorithms ; Deep Learning ; Gait ; Software ; Walking
    Language English
    Publishing date 2022-06-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1939-3539
    ISSN (online) 1939-3539
    DOI 10.1109/TPAMI.2021.3057879
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Multimodal Neurodegenerative Disease Subtyping Explained by ChatGPT

    Reyes, Diego Machado / Chao, Hanqing / Hahn, Juergen / Shen, Li / Yan, Pingkun

    2024  

    Abstract: Alzheimer's disease (AD) is the most prevalent neurodegenerative disease; yet its currently available treatments are limited to stopping disease progression. Moreover, effectiveness of these treatments is not guaranteed due to the heterogenetiy of the ... ...

    Abstract Alzheimer's disease (AD) is the most prevalent neurodegenerative disease; yet its currently available treatments are limited to stopping disease progression. Moreover, effectiveness of these treatments is not guaranteed due to the heterogenetiy of the disease. Therefore, it is essential to be able to identify the disease subtypes at a very early stage. Current data driven approaches are able to classify the subtypes at later stages of AD or related disorders, but struggle when predicting at the asymptomatic or prodromal stage. Moreover, most existing models either lack explainability behind the classification or only use a single modality for the assessment, limiting scope of its analysis. Thus, we propose a multimodal framework that uses early-stage indicators such as imaging, genetics and clinical assessments to classify AD patients into subtypes at early stages. Similarly, we build prompts and use large language models, such as ChatGPT, to interpret the findings of our model. In our framework, we propose a tri-modal co-attention mechanism (Tri-COAT) to explicitly learn the cross-modal feature associations. Our proposed model outperforms baseline models and provides insight into key cross-modal feature associations supported by known biological mechanisms.
    Keywords Computer Science - Machine Learning ; Computer Science - Computer Vision and Pattern Recognition
    Subject code 006
    Publishing date 2024-01-31
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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