arXiv subjects

Jiancheng Yang

Publications and source records attributed to Jiancheng Yang.

71 records · Page 4Linked to original sources

arXiv2021

MedMNIST Classification Decathlon: A Lightweight AutoML Benchmark for Medical Image Analysis

We present MedMNIST, a collection of 10 pre-processed medical open datasets. MedMNIST is standardized to perform classification tasks on lightweight 28x28 images, which requires no background knowledge. Covering the primary data modalities in medical image analysis, it is diverse on data scale (from 100 to 100,000) and tasks (binary/multi-class, ordinal regression and multi-label). MedMNIST could be used for educational purpose, rapid prototyping, multi-modal machine learning or AutoML in medical image analysis. Moreover, MedMNIST Classification Decathlon is designed to benchmark AutoML algorithms on all 10 datasets; We have compared several baseline methods, including open-source or commercial AutoML tools. The datasets, evaluation code and baseline methods for MedMNIST are publicly available at https://medmnist.github.io/.

cs.CV↗

arXiv2021

3D Human Action Representation Learning via Cross-View Consistency Pursuit

In this work, we propose a Cross-view Contrastive Learning framework for unsupervised 3D skeleton-based action Representation (CrosSCLR), by leveraging multi-view complementary supervision signal. CrosSCLR consists of both single-view contrastive learning (SkeletonCLR) and cross-view consistent knowledge mining (CVC-KM) modules, integrated in a collaborative learning manner. It is noted that CVC-KM works in such a way that high-confidence positive/negative samples and their distributions are exchanged among views according to their embedding similarity, ensuring cross-view consistency in terms of contrastive context, i.e., similar distributions. Extensive experiments show that CrosSCLR achieves remarkable action recognition results on NTU-60 and NTU-120 datasets under unsupervised settings, with observed higher-quality action representations. Our code is available at https://github.com/LinguoLi/CrosSCLR.

cs.CV↗

arXiv2021

Electron-Ion Collider in China

Lepton scattering is an established ideal tool for studying inner structure of small particles such as nucleons as well as nuclei. As a future high energy nuclear physics project, an Electron-ion collider in China (EicC) has been proposed. It will be constructed based on an upgraded heavy-ion accelerator, High Intensity heavy-ion Accelerator Facility (HIAF) which is currently under construction, together with a new electron ring. The proposed collider will provide highly polarized electrons (with a polarization of $\sim$80%) and protons (with a polarization of $\sim$70%) with variable center of mass energies from 15 to 20 GeV and the luminosity of (2-3) $\times$ 10$^{33}$ cm$^{-2}$ s$^{-1}$. Polarized deuterons and Helium-3, as well as unpolarized ion beams from Carbon to Uranium, will be also available at the EicC. The main foci of the EicC will be precision measurements of the structure of the nucleon in the sea quark region, including 3D tomography of nucleon; the partonic structure of nuclei and the parton interaction with the nuclear environment; the exotic states, especially those with heavy flavor quark contents. In addition, issues fundamental to understanding the origin of mass could be addressed by measurements of heavy quarkonia near-threshold production at the EicC. In order to achieve the above-mentioned physics goals, a hermetical detector system will be constructed with cutting-edge technologies. This document is the result of collective contributions and valuable inputs from experts across the globe. The EicC physics program complements the ongoing scientific programs at the Jefferson Laboratory and the future EIC project in the United States. The success of this project will also advance both nuclear and particle physics as well as accelerator and detector technology in China.

nucl-ex↗

arXiv2021

Reinventing 2D Convolutions for 3D Images

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.

eess.IV↗

arXiv2020

Learning Black-Box Attackers with Transferable Priors and Query Feedback

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.

cs.CR↗

arXiv2020

Learning Tumor Growth via Follow-Up Volume Prediction for Lung Nodules

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.

eess.IV↗

arXiv2020

MIA-Prognosis: A Deep Learning Framework to Predict Therapy Response

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 invasive, 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.

cs.LG↗

arXiv2020

Hierarchical Classification of Pulmonary Lesions: A Large-Scale Radio-Pathomics Study

Diagnosis of pulmonary lesions from computed tomography (CT) is important but challenging for clinical decision making in lung cancer related diseases. Deep learning has achieved great success in computer aided diagnosis (CADx) area for lung cancer, whereas it suffers from label ambiguity due to the difficulty in the radiological diagnosis. Considering that invasive pathological analysis serves as the clinical golden standard of lung cancer diagnosis, in this study, we solve the label ambiguity issue via a large-scale radio-pathomics dataset containing 5,134 radiological CT images with pathologically confirmed labels, including cancers (e.g., invasive/non-invasive adenocarcinoma, squamous carcinoma) and non-cancer diseases (e.g., tuberculosis, hamartoma). This retrospective dataset, named Pulmonary-RadPath, enables development and validation of accurate deep learning systems to predict invasive pathological labels with a non-invasive procedure, i.e., radiological CT scans. A three-level hierarchical classification system for pulmonary lesions is developed, which covers most diseases in cancer-related diagnosis. We explore several techniques for hierarchical classification on this dataset, and propose a Leaky Dense Hierarchy approach with proven effectiveness in experiments. Our study significantly outperforms prior arts in terms of data scales (6x larger), disease comprehensiveness and hierarchies. The promising results suggest the potentials to facilitate precision medicine.

eess.IV↗

arXiv2020

AlignShift: Bridging the Gap of Imaging Thickness in 3D Anisotropic Volumes

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) volumes. 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.

cs.CV↗

arXiv2020

Relational Learning between Multiple Pulmonary Nodules via Deep Set Attention Transformers

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.

eess.IV↗

arXiv2020

Decoupled Gradient Harmonized Detector for Partial Annotation: Application to Signet Ring Cell Detection

Early diagnosis of signet ring cell carcinoma dramatically improves the survival rate of patients. Due to lack of public dataset and expert-level annotations, automatic detection on signet ring cell (SRC) has not been thoroughly investigated. In MICCAI DigestPath2019 challenge, apart from foreground (SRC region)-background (normal tissue area) class imbalance, SRCs are partially annotated due to costly medical image annotation, which introduces extra label noise. To address the issues simultaneously, we propose Decoupled Gradient Harmonizing Mechanism (DGHM) and embed it into classification loss, denoted as DGHM-C loss. Specifically, besides positive (SRCs) and negative (normal tissues) examples, we further decouple noisy examples from clean examples and harmonize the corresponding gradient distributions in classification respectively. Without whistles and bells, we achieved the 2nd place in the challenge. Ablation studies and controlled label missing rate experiments demonstrate that DGHM-C loss can bring substantial improvement in partially annotated object detection.

cs.CV↗

arXiv2019

Probabilistic Radiomics: Ambiguous Diagnosis with Controllable Shape Analysis

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 (CNNs), 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.

eess.IV↗

arXiv2019

Evaluating and Boosting Uncertainty Quantification in Classification

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 are 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.

cs.LG↗

arXiv2019

Modeling Point Clouds with Self-Attention and Gumbel Subset Sampling

Geometric deep learning is increasingly important thanks to the popularity of 3D sensors. Inspired by the recent advances in NLP domain, the self-attention transformer is introduced to consume the point clouds. We develop Point Attention Transformers (PATs), using a parameter-efficient Group Shuffle Attention (GSA) to replace the costly Multi-Head Attention. We demonstrate its ability to process size-varying inputs, and prove its permutation equivariance. Besides, prior work uses heuristics dependence on the input data (e.g., Furthest Point Sampling) to hierarchically select subsets of input points. Thereby, we for the first time propose an end-to-end learnable and task-agnostic sampling operation, named Gumbel Subset Sampling (GSS), to select a representative subset of input points. Equipped with Gumbel-Softmax, it produces a "soft" continuous subset in training phase, and a "hard" discrete subset in test phase. By selecting representative subsets in a hierarchical fashion, the networks learn a stronger representation of the input sets with lower computation cost. Experiments on classification and segmentation benchmarks show the effectiveness and efficiency of our methods. Furthermore, we propose a novel application, to process event camera stream as point clouds, and achieve a state-of-the-art performance on DVS128 Gesture Dataset.

cs.CV↗

arXiv2015

Calculation of the coupled betatron motion introduced by cooler's solenoids of CSRm

Several solenoids are usually installed in electron cooler device to guide the motion of the electron beam in the cooler. However, the solenoids also have influence to the ion beam in the cooler storage ring. The transverse motion of the ion beam in storage ring will become coupled, if the solenoids installed in the electron cooler are not compensated perfectly. In this paper, the coupled transverse motion due to the uncompensated cooler's solenoids of CSRm (The main storage ring in the IMP, Lan Zhou, China) is studied, and the coupled beam envelopes are calculated by a new method.

physics.acc-ph↗

arXiv2015

Concept for a Future Super Proton-Proton Collider

Following the discovery of the Higgs boson at LHC, new large colliders are being studied by the international high-energy community to explore Higgs physics in detail and new physics beyond the Standard Model. In China, a two-stage circular collider project CEPC-SPPC is proposed, with the first stage CEPC (Circular Electron Positron Collier, a so-called Higgs factory) focused on Higgs physics, and the second stage SPPC (Super Proton-Proton Collider) focused on new physics beyond the Standard Model. This paper discusses this second stage.

physics.acc-ph↗

arXiv2014

The simulation of loss of U ions due to charge changing processes in the CSRm ring

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 aim 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.

physics.acc-ph↗