This paper addresses the challenging black-box adversarial attack problem, where only classification confidence of a victim model is available. Inspired by consistency of visual saliency between different vision models, a surrogate model is expected
to improve the attack performance via transferability. By combining transferability-based and query-based black-box attack, we propose a surprisingly simple baseline approach (named SimBA++) using the surrogate model, which significantly outperforms several state-of-the-art methods. Moreover, to efficiently utilize the query feedback, we update the surrogate model in a novel learning scheme, named High-Order Gradient Approximation (HOGA). By constructing a high-order gradient computation graph, we update the surrogate model to approximate the victim model in both forward and backward pass. The SimBA++ and HOGA result in Learnable Black-Box Attack (LeBA), which surpasses previous state of the art by considerable margins: the proposed LeBA significantly reduces queries, while keeping higher attack success rates close to 100% in extensive ImageNet experiments, including attacking vision benchmarks and defensive models. Code is open source at https://github.com/TrustworthyDL/LeBA.
Predicting clinical outcome is remarkably important but challenging. Research efforts have been paid on seeking significant biomarkers associated with the therapy response or/and patient survival. However, these biomarkers are generally costly and in
vasive, and possibly dissatifactory for novel therapy. On the other hand, multi-modal, heterogeneous, unaligned temporal data is continuously generated in clinical practice. This paper aims at a unified deep learning approach to predict patient prognosis and therapy response, with easily accessible data, e.g., radiographics, laboratory and clinical information. Prior arts focus on modeling single data modality, or ignore the temporal changes. Importantly, the clinical time series is asynchronous in practice, i.e., recorded with irregular intervals. In this study, we formalize the prognosis modeling as a multi-modal asynchronous time series classification task, and propose a MIA-Prognosis framework with Measurement, Intervention and Assessment (MIA) information to predict therapy response, where a Simple Temporal Attention (SimTA) module is developed to process the asynchronous time series. Experiments on synthetic dataset validate the superiory of SimTA over standard RNN-based approaches. Furthermore, we experiment the proposed method on an in-house, retrospective dataset of real-world non-small cell lung cancer patients under anti-PD-1 immunotherapy. The proposed method achieves promising performance on predicting the immunotherapy response. Notably, our predictive model could further stratify low-risk and high-risk patients in terms of long-term survival.
Follow-up serves an important role in the management of pulmonary nodules for lung cancer. Imaging diagnostic guidelines with expert consensus have been made to help radiologists make clinical decision for each patient. However, tumor growth is such
a complicated process that it is difficult to stratify high-risk nodules from low-risk ones based on morphologic characteristics. On the other hand, recent deep learning studies using convolutional neural networks (CNNs) to predict the malignancy score of nodules, only provides clinicians with black-box predictions. To this end, we propose a unified framework, named Nodule Follow-Up Prediction Network (NoFoNet), which predicts the growth of pulmonary nodules with high-quality visual appearances and accurate quantitative results, given any time interval from baseline observations. It is achieved by predicting future displacement field of each voxel with a WarpNet. A TextureNet is further developed to refine textural details of WarpNet outputs. We also introduce techniques including Temporal Encoding Module and Warp Segmentation Loss to encourage time-aware and shape-aware representation learning. We build an in-house follow-up dataset from two medical centers to validate the effectiveness of the proposed method. NoFoNet significantly outperforms direct prediction by a U-Net in terms of visual quality; more importantly, it demonstrates accurate differentiating performance between high- and low-risk nodules. Our promising results suggest the potentials in computer aided intervention for lung nodule management.
This paper addresses a fundamental challenge in 3D medical image processing: how to deal with imaging thickness. For anisotropic medical volumes, there is a significant performance gap between thin-slice (mostly 1mm) and thick-slice (mostly 5mm) volu
mes. Prior arts tend to use 3D approaches for the thin-slice and 2D approaches for the thick-slice, respectively. We aim at a unified approach for both thin- and thick-slice medical volumes. Inspired by recent advances in video analysis, we propose AlignShift, a novel parameter-free operator to convert theoretically any 2D pretrained network into thickness-aware 3D network. Remarkably, the converted networks behave like 3D for the thin-slice, nevertheless degenerate to 2D for the thick-slice adaptively. The unified thickness-aware representation learning is achieved by shifting and fusing aligned virtual slices as per the input imaging thickness. Extensive experiments on public large-scale DeepLesion benchmark, consisting of 32K lesions for universal lesion detection, validate the effectiveness of our method, which outperforms previous state of the art by considerable margins without whistles and bells. More importantly, to our knowledge, this is the first method that bridges the performance gap between thin- and thick-slice volumes by a unified framework. To improve research reproducibility, our code in PyTorch is open source at https://github.com/M3DV/AlignShift.
Diagnosis and treatment of multiple pulmonary nodules are clinically important but challenging. Prior studies on nodule characterization use solitary-nodule approaches on multiple nodular patients, which ignores the relations between nodules. In this
study, we propose a multiple instance learning (MIL) approach and empirically prove the benefit to learn the relations between multiple nodules. By treating the multiple nodules from a same patient as a whole, critical relational information between solitary-nodule voxels is extracted. To our knowledge, it is the first study to learn the relations between multiple pulmonary nodules. Inspired by recent advances in natural language processing (NLP) domain, we introduce a self-attention transformer equipped with 3D CNN, named {NoduleSAT}, to replace typical pooling-based aggregation in multiple instance learning. Extensive experiments on lung nodule false positive reduction on LUNA16 database, and malignancy classification on LIDC-IDRI database, validate the effectiveness of the proposed method.
There have been considerable debates over 2D and 3D representation learning on 3D medical images. 2D approaches could benefit from large-scale 2D pretraining, whereas they are generally weak in capturing large 3D contexts. 3D approaches are natively
strong in 3D contexts, however few publicly available 3D medical dataset is large and diverse enough for universal 3D pretraining. Even for hybrid (2D + 3D) approaches, the intrinsic disadvantages within the 2D / 3D parts still exist. In this study, we bridge the gap between 2D and 3D convolutions by reinventing the 2D convolutions. We propose ACS (axial-coronal-sagittal) convolutions to perform natively 3D representation learning, while utilizing the pretrained weights on 2D datasets. In ACS convolutions, 2D convolution kernels are split by channel into three parts, and convoluted separately on the three views (axial, coronal and sagittal) of 3D representations. Theoretically, ANY 2D CNN (ResNet, DenseNet, or DeepLab) is able to be converted into a 3D ACS CNN, with pretrained weight of a same parameter size. Extensive experiments on several medical benchmarks (including classification, segmentation and detection tasks) validate the consistent superiority of the pretrained ACS CNNs, over the 2D / 3D CNN counterparts with / without pretraining. Even without pretraining, the ACS convolution can be used as a plug-and-play replacement of standard 3D convolution, with smaller model size and less computation.
Radiomics analysis has achieved great success in recent years. However, conventional Radiomics analysis suffers from insufficiently expressive hand-crafted features. Recently, emerging deep learning techniques, e.g., convolutional neural networks (CN
Ns), dominate recent research in Computer-Aided Diagnosis (CADx). Unfortunately, as black-box predictors, we argue that CNNs are diagnosing voxels (or pixels), rather than lesions; in other words, visual saliency from a trained CNN is not necessarily concentrated on the lesions. On the other hand, classification in clinical applications suffers from inherent ambiguities: radiologists may produce diverse diagnosis on challenging cases. To this end, we propose a controllable and explainable {em Probabilistic Radiomics} framework, by combining the Radiomics analysis and probabilistic deep learning. In our framework, 3D CNN feature is extracted upon lesion region only, then encoded into lesion representation, by a controllable Non-local Shape Analysis Module (NSAM) based on self-attention. Inspired from variational auto-encoders (VAEs), an Ambiguity PriorNet is used to approximate the ambiguity distribution over human experts. The final diagnosis is obtained by combining the ambiguity prior sample and lesion representation, and the whole network named $DenseSharp^{+}$ is end-to-end trainable. We apply the proposed method on lung nodule diagnosis on LIDC-IDRI database to validate its effectiveness.
Emergence of artificial intelligence techniques in biomedical applications urges the researchers to pay more attention on the uncertainty quantification (UQ) in machine-assisted medical decision making. For classification tasks, prior studies on UQ a
re difficult to compare with each other, due to the lack of a unified quantitative evaluation metric. Considering that well-performing UQ models ought to know when the classification models act incorrectly, we design a new evaluation metric, area under Confidence-Classification Characteristic curves (AUCCC), to quantitatively evaluate the performance of the UQ models. AUCCC is threshold-free, robust to perturbation, and insensitive to the classification performance. We evaluate several UQ methods (e.g., max softmax output) with AUCCC to validate its effectiveness. Furthermore, a simple scheme, named Uncertainty Distillation (UDist), is developed to boost the UQ performance, where a confidence model is distilling the confidence estimated by deep ensembles. The proposed method is easy to implement; it consistently outperforms strong baselines on natural and medical image datasets in our experiments.
Significant beam loss caused by the charge exchange processes and ions impact induced outgassing play a crucial role in the limitation of the maximum number of accumulated heavy ions during the high intensity operation in the accelerators. With the a
im to control beam loss due to charge exchange processes and to confine the generated desorption gas, the tracking of the loss positions and installing the absorber blocks with low-desorption rate material at appropriate locations in the CSRm ring will be taken. The loss simulation of U ions having lost an electron will be presented in this report and the calculation of the collimation efficiency of the CSRm ring will be continued in the future.
