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Ying Ding

Publications and source records attributed to Ying Ding.

At least 91 records · Page 5Linked to original sources

RoS-KD: A Robust Stochastic Knowledge Distillation Approach for Noisy Medical Imaging

AI-powered Medical Imaging has recently achieved enormous attention due to its ability to provide fast-paced healthcare diagnoses. However, it usually suffers from a lack of high-quality datasets due to high annotation cost, inter-observer variability, human annotator error, and errors in computer-generated labels. Deep learning models trained on noisy labelled datasets are sensitive to the noise type and lead to less generalization on the unseen samples. To address this challenge, we propose a Robust Stochastic Knowledge Distillation (RoS-KD) framework which mimics the notion of learning a topic from multiple sources to ensure deterrence in learning noisy information. More specifically, RoS-KD learns a smooth, well-informed, and robust student manifold by distilling knowledge from multiple teachers trained on overlapping subsets of training data. Our extensive experiments on popular medical imaging classification tasks (cardiopulmonary disease and lesion classification) using real-world datasets, show the performance benefit of RoS-KD, its ability to distill knowledge from many popular large networks (ResNet-50, DenseNet-121, MobileNet-V2) in a comparatively small network, and its robustness to adversarial attacks (PGD, FSGM). More specifically, RoS-KD achieves >2% and >4% improvement on F1-score for lesion classification and cardiopulmonary disease classification tasks, respectively, when the underlying student is ResNet-18 against recent competitive knowledge distillation baseline. Additionally, on cardiopulmonary disease classification task, RoS-KD outperforms most of the SOTA baselines by ~1% gain in AUC score.

cs.CV↗

Radiomics-Guided Global-Local Transformer for Weakly Supervised Pathology Localization in Chest X-Rays

Before the recent success of deep learning methods for automated medical image analysis, practitioners used handcrafted radiomic features to quantitatively describe local patches of medical images. However, extracting discriminative radiomic features relies on accurate pathology localization, which is difficult to acquire in real-world settings. Despite advances in disease classification and localization from chest X-rays, many approaches fail to incorporate clinically-informed domain knowledge. For these reasons, we propose a Radiomics-Guided Transformer (RGT) that fuses \textit{global} image information with \textit{local} knowledge-guided radiomics information to provide accurate cardiopulmonary pathology localization and classification \textit{without any bounding box annotations}. RGT consists of an image Transformer branch, a radiomics Transformer branch, and fusion layers that aggregate image and radiomic information. Using the learned self-attention of its image branch, RGT extracts a bounding box for which to compute radiomic features, which are further processed by the radiomics branch; learned image and radiomic features are then fused and mutually interact via cross-attention layers. Thus, RGT utilizes a novel end-to-end feedback loop that can bootstrap accurate pathology localization only using image-level disease labels. Experiments on the NIH ChestXRay dataset demonstrate that RGT outperforms prior works in weakly supervised disease localization (by an average margin of 3.6\% over various intersection-over-union thresholds) and classification (by 1.1\% in average area under the receiver operating characteristic curve). We publicly release our codes and pre-trained models at \url{https://github.com/VITA-Group/chext}.

cs.CV↗

Old can be Gold: Better Gradient Flow can Make Vanilla-GCNs Great Again

Despite the enormous success of Graph Convolutional Networks (GCNs) in modeling graph-structured data, most of the current GCNs are shallow due to the notoriously challenging problems of over-smoothening and information squashing along with conventional difficulty caused by vanishing gradients and over-fitting. Previous works have been primarily focused on the study of over-smoothening and over-squashing phenomena in training deep GCNs. Surprisingly, in comparison with CNNs/RNNs, very limited attention has been given to understanding how healthy gradient flow can benefit the trainability of deep GCNs. In this paper, firstly, we provide a new perspective of gradient flow to understand the substandard performance of deep GCNs and hypothesize that by facilitating healthy gradient flow, we can significantly improve their trainability, as well as achieve state-of-the-art (SOTA) level performance from vanilla-GCNs. Next, we argue that blindly adopting the Glorot initialization for GCNs is not optimal, and derive a topology-aware isometric initialization scheme for vanilla-GCNs based on the principles of isometry. Additionally, contrary to ad-hoc addition of skip-connections, we propose to use gradient-guided dynamic rewiring of vanilla-GCNs} with skip connections. Our dynamic rewiring method uses the gradient flow within each layer during training to introduce on-demand skip-connections adaptively. We provide extensive empirical evidence across multiple datasets that our methods improve gradient flow in deep vanilla-GCNs and significantly boost their performance to comfortably compete and outperform many fancy state-of-the-art methods. Codes are available at: https://github.com/VITA-Group/GradientGCN.

cs.LG↗

Switching modulation of spin transport in ferromagnetic tetragonal silicene

We study the band structure and transport properties of ferromagnetic tetragonal silicene nanoribbons by using the non-equilibrium Green's function method. The band structure and spin-dependent conductance are discussed under the combined effect of the external electric field, potential energy, exchange field and the spin-orbit coupling. One can easily realize a phase transition from a semimetallic to a semiconducting state by changing the transverse width of the nanoribbon. Separation of spin-dependent conductances arises from the effect of exchange field and the spin-orbit coupling, while zero-conductance behaviors exhibit spin-dependent band gaps induced by the electric field. We propose a device configuration of four-terminal tetragonal silicene nanoribbon with two central channels. It is found that spin current can be controlled by utilizing two switches. The switch with a high potential barrier can block electrons flowing from the central scattering region into other terminals. Interestingly, applying only one switch can realize spin-dependent zero conductance and large spin polarization. Two switches can provide multiple operations for controlling spin-dependent transport properties. The two-channel ferromagnetic tetragonal silicene nanoribbon can realize an effective separation of spin current, which may be a potential candidate for spintronic devices.

cond-mat.mes-hall↗

Training Your Sparse Neural Network Better with Any Mask

Pruning large neural networks to create high-quality, independently trainable sparse masks, which can maintain similar performance to their dense counterparts, is very desirable due to the reduced space and time complexity. As research effort is focused on increasingly sophisticated pruning methods that leads to sparse subnetworks trainable from the scratch, we argue for an orthogonal, under-explored theme: improving training techniques for pruned sub-networks, i.e. sparse training. Apart from the popular belief that only the quality of sparse masks matters for sparse training, in this paper we demonstrate an alternative opportunity: one can carefully customize the sparse training techniques to deviate from the default dense network training protocols, consisting of introducing ``ghost" neurons and skip connections at the early stage of training, and strategically modifying the initialization as well as labels. Our new sparse training recipe is generally applicable to improving training from scratch with various sparse masks. By adopting our newly curated techniques, we demonstrate significant performance gains across various popular datasets (CIFAR-10, CIFAR-100, TinyImageNet), architectures (ResNet-18/32/104, Vgg16, MobileNet), and sparse mask options (lottery ticket, SNIP/GRASP, SynFlow, or even randomly pruning), compared to the default training protocols, especially at high sparsity levels. Code is at https://github.com/VITA-Group/ToST

cs.CV↗

Disorder-induced phase transitions in double Weyl semimetals

The double Weyl semimetal (DWSM) is a newly proposed topological material that hosts Weyl points with chiral charge n=2. The disorder effect in DWSM is investigated by adopting the tight-binding Hamiltonian. Using the transfer matrix method and the noncommutative Kubo formula, we numerically calculate the localization length and the Hall conductivity in the presence of the on-site nonmagnetic disorder or orbital (spin-flip) disorders, and give the corresponding global phase diagrams. For the on-site nonmagnetic disorder, the system undergoes the DWSM-3D quantum anomalous hall (3D QAH) and normal insulator (NI)-DWSM phase transitions, and evolves into the diffusive metal (DM) phase before being localized by strong disorders, which is consistent with the Weyl semimetal. For σ_x orbital disorder, we find that increasing disorder can generate a pair of Weyl nodes at the boundary of the Brillouin zone and induce a 3D QAH-DWSM phase transition. Then we investigate the combined effect of orbital disorders for both disordered 3D QAH phase and DWSM phase. The disorder-induced transitions can be well understood in terms of an effective medium theory based on self-consistent Born approximation.

cond-mat.mes-hall↗

Strain modulation of photocurrent in Weyl semimetal TaIrTe4

We study the effect of the strain on the energy bands of TaIrTe4 sheet and the photocurrent in the Cu-TaIrTe4-Cu heterojunction by using the quantum transport simulations. It is found that the Weyl points can be completely broken with increasing of the strain along z dirction. One can obtain a large photocurrent in the Cu-TaIrTe4-Cu heterojunction in the absence of the strain. While the photocurrent can be sharply enhanced by the strain and reach a large value. Accordingly, the maximum values of the photocurrent can be explained in terms of the transitions between peaks of density of states and band structures. The strain-induced energy bands and photocurrent exhibit anisotropic behaviors. Our results provide a novel route to effectively modulate the energy bands and the photocurrent by utilizing mechanical methods for TaIrTe4-based devices.

physics.optics↗

Team formation and team performance: The balance between team freshness and repeat collaboration

Incorporating fresh members in teams is considered a pathway to team creativity. However, whether freshness improves team performance or not remains unclear, as well as the optimal involvement of fresh members for team performance. This study uses a group of authors on the byline of a publication as a proxy for a scientific team. We extend an indicator, i.e., team freshness, to measure the extent to which a scientific team incorporates new members, by calculating the fraction of new collaboration relations established within the team. Based on more than 43 million scientific publications covering more than a half-century of research from Microsoft Academic Graph, this study provides a holistic picture of the current development of team freshness by outlining the temporal evolution of freshness, and its disciplinary distribution. Subsequently, using a multivariable regression approach, we examine the association between team freshness and papers'short-term and long-term citations.The major findings are as follows: (1)team freshness in scientific teams has been increasing in the past half-century; (2)there exists an inverted-U-shaped association between team freshness and papers' citations in all the disciplines and in different periods;(3)the inverted-U-shaped relationship between team freshness and papers' citations is only found in small teams, while, in large teams, team freshness is significantly positively related to papers' citations.

cs.DL↗

Pneumonia Detection on Chest X-ray using Radiomic Features and Contrastive Learning

Chest X-ray becomes one of the most common medical diagnoses due to its noninvasiveness. The number of chest X-ray images has skyrocketed, but reading chest X-rays still have been manually performed by radiologists, which creates huge burnouts and delays. Traditionally, radiomics, as a subfield of radiology that can extract a large number of quantitative features from medical images, demonstrates its potential to facilitate medical imaging diagnosis before the deep learning era. With the rise of deep learning, the explainability of deep neural networks on chest X-ray diagnosis remains opaque. In this study, we proposed a novel framework that leverages radiomics features and contrastive learning to detect pneumonia in chest X-ray. Experiments on the RSNA Pneumonia Detection Challenge dataset show that our model achieves superior results to several state-of-the-art models (> 10% in F1-score) and increases the model's interpretability.

cs.CV↗

Knowledge-Augmented Contrastive Learning for Abnormality Classification and Localization in Chest X-rays with Radiomics using a Feedback Loop

Building a highly accurate predictive model for classification and localization of abnormalities in chest X-rays usually requires a large number of manually annotated labels and pixel regions (bounding boxes) of abnormalities. However, it is expensive to acquire such annotations, especially the bounding boxes. Recently, contrastive learning has shown strong promise in leveraging unlabeled natural images to produce highly generalizable and discriminative features. However, extending its power to the medical image domain is under-explored and highly non-trivial, since medical images are much less amendable to data augmentations. In contrast, their prior knowledge, as well as radiomic features, is often crucial. To bridge this gap, we propose an end-to-end semi-supervised knowledge-augmented contrastive learning framework, that simultaneously performs disease classification and localization tasks. The key knob of our framework is a unique positive sampling approach tailored for the medical images, by seamlessly integrating radiomic features as a knowledge augmentation. Specifically, we first apply an image encoder to classify the chest X-rays and to generate the image features. We next leverage Grad-CAM to highlight the crucial (abnormal) regions for chest X-rays (even when unannotated), from which we extract radiomic features. The radiomic features are then passed through another dedicated encoder to act as the positive sample for the image features generated from the same chest X-ray. In this way, our framework constitutes a feedback loop for image and radiomic modality features to mutually reinforce each other. Their contrasting yields knowledge-augmented representations that are both robust and interpretable. Extensive experiments on the NIH Chest X-ray dataset demonstrate that our approach outperforms existing baselines in both classification and localization tasks.

cs.CV↗

Team Power Dynamics and Team Impact: New Perspectives on Scientific Collaboration using Career Age as a Proxy for Team Power

Power dynamics influence every aspect of scientific collaboration. Team power dynamics can be measured by team power level and team power hierarchy. Team power level is conceptualized as the average level of the possession of resources, expertise, or decision-making authorities of a team. Team power hierarchy represents the vertical differences of the possessions of resources in a team. In Science of Science, few studies have looked at scientific collaboration from the perspective of team power dynamics. This research examines how team power dynamics affect team impact to fill the research gap. In this research, all co-authors of one publication are treated as one team. Team power level and team power hierarchy of one team are measured by the mean and Gini index of career age of co-authors in this team. Team impact is quantified by citations of a paper authored by this team. By analyzing over 7.7 million teams from Science (e.g., Computer Science, Physics), Social Sciences (e.g., Sociology, Library & Information Science), and Arts & Humanities (e.g., Art), we find that flat team structure is associated with higher team impact, especially when teams have high team power level. These findings have been repeated in all five disciplines except Art, and are consistent in various types of teams from Computer Science including teams from industry or academia, teams with different gender groups, teams with geographical contrast, and teams with distinct size.

physics.soc-ph↗

Radiology Text Analysis System (RadText): Architecture and Evaluation

Analyzing radiology reports is a time-consuming and error-prone task, which raises the need for an efficient automated radiology report analysis system to alleviate the workloads of radiologists and encourage precise diagnosis. In this work, we present RadText, an open-source radiology text analysis system developed by Python. RadText offers an easy-to-use text analysis pipeline, including de-identification, section segmentation, sentence split and word tokenization, named entity recognition, parsing, and negation detection. RadText features a flexible modular design, provides a hybrid text processing schema, and supports raw text processing and local processing, which enables better usability and improved data privacy. RadText adopts BioC as the unified interface, and also standardizes the input / output into a structured representation compatible with Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM). This allows for a more systematic approach to observational research across multiple, disparate data sources. We evaluated RadText on the MIMIC-CXR dataset, with five new disease labels we annotated for this work. RadText demonstrates highly accurate classification performances, with an average precision of, a recall of 0.94, and an F-1 score of 0.92. We have made our code, documentation, examples, and the test set available at https://github.com/bionlplab/radtext .

cs.CL↗

The Gene of Scientific Success

This paper elaborates how to identify and evaluate causal factors to improve scientific impact. Currently, analyzing scientific impact can be beneficial to various academic activities including funding application, mentor recommendation, and discovering potential cooperators etc. It is universally acknowledged that high-impact scholars often have more opportunities to receive awards as an encouragement for their hard working. Therefore, scholars spend great efforts in making scientific achievements and improving scientific impact during their academic life. However, what are the determinate factors that control scholars' academic success? The answer to this question can help scholars conduct their research more efficiently. Under this consideration, our paper presents and analyzes the causal factors that are crucial for scholars' academic success. We first propose five major factors including article-centered factors, author-centered factors, venue-centered factors, institution-centered factors, and temporal factors. Then, we apply recent advanced machine learning algorithms and jackknife method to assess the importance of each causal factor. Our empirical results show that author-centered and article-centered factors have the highest relevancy to scholars' future success in the computer science area. Additionally, we discover an interesting phenomenon that the h-index of scholars within the same institution or university are actually very close to each other.

cs.DL↗

Prior Knowledge Enhances Radiology Report Generation

Radiology report generation aims to produce computer-aided diagnoses to alleviate the workload of radiologists and has drawn increasing attention recently. However, previous deep learning methods tend to neglect the mutual influences between medical findings, which can be the bottleneck that limits the quality of generated reports. In this work, we propose to mine and represent the associations among medical findings in an informative knowledge graph and incorporate this prior knowledge with radiology report generation to help improve the quality of generated reports. Experiment results demonstrate the superior performance of our proposed method on the IU X-ray dataset with a ROUGE-L of 0.384$\pm$0.007 and CIDEr of 0.340$\pm$0.011. Compared with previous works, our model achieves an average of 1.6% improvement (2.0% and 1.5% improvements in CIDEr and ROUGE-L, respectively). The experiments suggest that prior knowledge can bring performance gains to accurate radiology report generation. We will make the code publicly available at https://github.com/bionlplab/report_generation_amia2022.

cs.CL↗

Fluid structure interaction: Insights into biomechanical implications of endograft after thoracic endovascular aortic repair

Thoracic endovascular aortic repair (TEVAR) has developed to be the most effective treatment for aortic diseases. This study aims to evaluate the biomechanical implications of the implanted endograft after TEVAR. We present a novel image-based, patient-specific, fluid-structure computational framework. The geometries of blood, endograft, and aortic wall were reconstructed based on clinical images. Patient-specific measurement data was collected to determine the parameters of the three-element Windkessel. We designed three postoperative scenarios with rigid wall assumption, blood-wall interaction, blood-endograft-wall interplay, respectively, where a two-way fluid-structure interaction (FSI) method was applied to predict the deformation of the composite stent-wall. Computational results were validated with Doppler ultrasound data. Results show that the rigid wall assumption fails to predict the waveforms of blood outflow and energy loss (EL). The complete storage and release process of blood flow energy, which consists of four phases is captured by the FSI method. The endograft implantation would weaken the buffer function of the aorta and reduce mean EL by 19.1%. The closed curve area of wall pressure and aortic volume could indicate the EL caused by the interaction between blood flow and wall deformation, which accounts for 68.8% of the total EL. Both the FSI and endograft have a slight effect on wall shear stress-related-indices. The deformability of the composite stent-wall region is remarkably limited by the endograft. Our results highlight the importance of considering the interaction between blood flow, the implanted endograft, and the aortic wall to acquire physiologically accurate hemodynamics in post-TEVAR computational studies and the deformation of the aortic wall is responsible for the major EL of the blood flow.

physics.med-ph↗

Giant anisotropic photocurrent modulated by strain in type-II Weyl semimetal Td-MoTe2

We build a Cu-MoTe2-Cu device model and use first-principles density functional theory to study the transport properties of single-layer Td-MoTe2. We obtained the effect of strain on the energy band structure, transport properties, and photocurrent. The strain-induced photocurrent shows an anisotropy that reflects the modulation of the energy bands, including the Weyl point, by strain. The photocurrent can be suppressed to almost zero when the strain is applied along the vacuum direction. In contrast, the photocurrent can be significantly increased when the strain is applied along the transport direction. The transport properties and magnitude of the photocurrent in the MoTe2-based device can be effectively modulated by adjusting the strength and direction of the strain.

cond-mat.mtrl-sci↗

RadBERT-CL: Factually-Aware Contrastive Learning For Radiology Report Classification

Radiology reports are unstructured and contain the imaging findings and corresponding diagnoses transcribed by radiologists which include clinical facts and negated and/or uncertain statements. Extracting pathologic findings and diagnoses from radiology reports is important for quality control, population health, and monitoring of disease progress. Existing works, primarily rely either on rule-based systems or transformer-based pre-trained model fine-tuning, but could not take the factual and uncertain information into consideration, and therefore generate false-positive outputs. In this work, we introduce three sedulous augmentation techniques which retain factual and critical information while generating augmentations for contrastive learning. We introduce RadBERT-CL, which fuses these information into BlueBert via a self-supervised contrastive loss. Our experiments on MIMIC-CXR show superior performance of RadBERT-CL on fine-tuning for multi-class, multi-label report classification. We illustrate that when few labeled data are available, RadBERT-CL outperforms conventional SOTA transformers (BERT/BlueBert) by significantly larger margins (6-11%). We also show that the representations learned by RadBERT-CL can capture critical medical information in the latent space.

cs.LG↗

Pandemics are catalysts of scientific novelty: Evidence from COVID-19

Scientific novelty drives the efforts to invent new vaccines and solutions during the pandemic. First-time collaboration and international collaboration are two pivotal channels to expand teams' search activities for a broader scope of resources required to address the global challenge, which might facilitate the generation of novel ideas. Our analysis of 98,981 coronavirus papers suggests that scientific novelty measured by the BioBERT model that is pre-trained on 29 million PubMed articles, and first-time collaboration increased after the outbreak of COVID-19, and international collaboration witnessed a sudden decrease. During COVID-19, papers with more first-time collaboration were found to be more novel and international collaboration did not hamper novelty as it had done in the normal periods. The findings suggest the necessity of reaching out for distant resources and the importance of maintaining a collaborative scientific community beyond nationalism during a pandemic.

cs.DL↗