Yunan Wu

Bingjie, Xu, Yunan Wu et al.

X-ray fluorescence spectroscopy (XRF) plays an important role for elemental analysis in a wide range of scientific fields, especially in cultural heritage. XRF imaging, which uses a raster scan to acquire spectra across artworks, provides the opportunity for spatial analysis of pigment distributions based on their elemental composition. However, conventional XRF-based pigment identification relies on time-consuming elemental mapping by expert interpretations of measured spectra. To reduce the reliance on manual work, recent studies have applied machine learning techniques to cluster similar XRF spectra in data analysis and to identify the most likely pigments. Nevertheless, it is still challenging for automatic pigment identification strategies to directly tackle the complex structure of real paintings, e.g. pigment mixtures and layered pigments. In addition, pixel-wise pigment identification based on XRF imaging remains an obstacle due to the high noise level compared with averaged spectra. Therefore, we developed a deep-learning-based end-to-end pigment identification framework to fully automate the pigment identification process. In particular, it offers high sensitivity to the underlying pigments and to the pigments with a low concentration, therefore enabling satisfying results in mapping the pigments based on single-pixel XRF spectrum. As case studies, we applied our framework to lab-prepared mock-up paintings and two 19th-century paintings: Paul Gauguin's Poèmes Barbares (1896) that contains layered pigments with an underlying painting, and Paul Cezanne's The Bathers (1899-1904). The pigment identification results demonstrated that our model achieved comparable results to the analysis by elemental mapping, suggesting the generalizability and stability of our model.

Jiaqi Guo, Santiago Lopez-Tapia, Wing Shun Li et al.

Computed tomography is a widely used imaging modality with applications ranging from medical imaging to material analysis. One major challenge arises from the lack of scanning information at certain angles, resulting in distortion or artifacts in the reconstructed images. This is referred to as the Limited Angle Computed Tomography (LACT) reconstruction problem. To address this problem, we propose the use of Residual Null-Space Diffusion Stochastic Differential Equations (RN-SDEs), which are a variant of diffusion models that characterize the diffusion process with mean-reverting (MR) stochastic differential equations. To demonstrate the generalizability of RN-SDEs, we conducted experiments with two different LACT datasets, ChromSTEM and C4KC-KiTS. Through extensive experiments, we demonstrate that by leveraging learned MR-SDEs as a prior and emphasizing data consistency using Range-Null Space Decomposition (RNSD) based rectification, we can recover high-quality images from severely degraded ones and achieve state-of-the-art performance in most LACT tasks. Additionally, we present a quantitative comparison of RN-SDE with other networks, in terms of computational complexity and runtime efficiency, highlighting the superior effectiveness of our proposed approach.

Yunan Wu, Francisco M. Castro-Macías, Pablo Morales-Álvarez et al.

Multiple Instance Learning (MIL) has been widely applied to medical imaging diagnosis, where bag labels are known and instance labels inside bags are unknown. Traditional MIL assumes that instances in each bag are independent samples from a given distribution. However, instances are often spatially or sequentially ordered, and one would expect similar diagnostic importance for neighboring instances. To address this, in this study, we propose a smooth attention deep MIL (SA-DMIL) model. Smoothness is achieved by the introduction of first and second order constraints on the latent function encoding the attention paid to each instance in a bag. The method is applied to the detection of intracranial hemorrhage (ICH) on head CT scans. The results show that this novel SA-DMIL: (a) achieves better performance than the non-smooth attention MIL at both scan (bag) and slice (instance) levels; (b) learns spatial dependencies between slices; and (c) outperforms current state-of-the-art MIL methods on the same ICH test set.

Yunan Wu, Amil Dravid, Ramsey Michael Wehbe et al.

Propose: To present DeepCOVID-Fuse, a deep learning fusion model to predict risk levels in patients with confirmed coronavirus disease 2019 (COVID-19) and to evaluate the performance of pre-trained fusion models on full or partial combination of chest x-ray (CXRs) or chest radiograph and clinical variables. Materials and Methods: The initial CXRs, clinical variables and outcomes (i.e., mortality, intubation, hospital length of stay, ICU admission) were collected from February 2020 to April 2020 with reverse-transcription polymerase chain reaction (RT-PCR) test results as the reference standard. The risk level was determined by the outcome. The fusion model was trained on 1657 patients (Age: 58.30 +/- 17.74; Female: 807) and validated on 428 patients (56.41 +/- 17.03; 190) from Northwestern Memorial HealthCare system and was tested on 439 patients (56.51 +/- 17.78; 205) from a single holdout hospital. Performance of pre-trained fusion models on full or partial modalities were compared on the test set using the DeLong test for the area under the receiver operating characteristic curve (AUC) and the McNemar test for accuracy, precision, recall and F1. Results: The accuracy of DeepCOVID-Fuse trained on CXRs and clinical variables is 0.658, with an AUC of 0.842, which significantly outperformed (p < 0.05) models trained only on CXRs with an accuracy of 0.621 and AUC of 0.807 and only on clinical variables with an accuracy of 0.440 and AUC of 0.502. The pre-trained fusion model with only CXRs as input increases accuracy to 0.632 and AUC to 0.813 and with only clinical variables as input increases accuracy to 0.539 and AUC to 0.733. Conclusion: The fusion model learns better feature representations across different modalities during training and achieves good outcome predictions even when only some of the modalities are used in testing.

Boxiang Wang, Yunan Wu, Chenglong Ye

Transfer learning is an essential tool for improving the performance of primary tasks by leveraging information from auxiliary data resources. In this work, we propose Adaptive Robust Transfer Learning (ART), a flexible pipeline of performing transfer learning with generic machine learning algorithms. We establish the non-asymptotic learning theory of ART, providing a provable theoretical guarantee for achieving adaptive transfer while preventing negative transfer. Additionally, we introduce an ART-integrated-aggregating machine that produces a single final model when multiple candidate algorithms are considered. We demonstrate the promising performance of ART through extensive empirical studies on regression, classification, and sparse learning. We further present a real-data analysis for a mortality study.

Yi Li, Yunan Wu, Aggelos K. Katsaggelos

The advancement of The Laser Interferometer Gravitational-Wave Observatory (LIGO) has significantly enhanced the feasibility and reliability of gravitational wave detection. However, LIGO's high sensitivity makes it susceptible to transient noises known as glitches, which necessitate effective differentiation from real gravitational wave signals. Traditional approaches predominantly employ fully supervised or semi-supervised algorithms for the task of glitch classification and clustering. In the future task of identifying and classifying glitches across main and auxiliary channels, it is impractical to build a dataset with manually labeled ground-truth. In addition, the patterns of glitches can vary with time, generating new glitches without manual labels. In response to this challenge, we introduce the Cross-Temporal Spectrogram Autoencoder (CTSAE), a pioneering unsupervised method for the dimensionality reduction and clustering of gravitational wave glitches. CTSAE integrates a novel four-branch autoencoder with a hybrid of Convolutional Neural Networks (CNN) and Vision Transformers (ViT). To further extract features across multi-branches, we introduce a novel multi-branch fusion method using the CLS (Class) token. Our model, trained and evaluated on the GravitySpy O3 dataset on the main channel, demonstrates superior performance in clustering tasks when compared to state-of-the-art semi-supervised learning methods. To the best of our knowledge, CTSAE represents the first unsupervised approach tailored specifically for clustering LIGO data, marking a significant step forward in the field of gravitational wave research. The code of this paper is available at https://github.com/Zod-L/CTSAE

Jiaqi Guo, Yunan Wu, Evangelos Kaimakamis et al.

With the advent of the COVID-19 pandemic, ultrasound imaging has emerged as a promising technique for COVID-19 detection, due to its non-invasive nature, affordability, and portability. In response, researchers have focused on developing AI-based scoring systems to provide real-time diagnostic support. However, the limited size and lack of proper annotation in publicly available ultrasound datasets pose significant challenges for training a robust AI model. This paper proposes MeDiVLAD, a novel pipeline to address the above issue for multi-level lung-ultrasound (LUS) severity scoring. In particular, we leverage self-knowledge distillation to pretrain a vision transformer (ViT) without label and aggregate frame-level features via dual-level VLAD aggregation. We show that with minimal finetuning, MeDiVLAD outperforms conventional fully-supervised methods in both frame- and video-level scoring, while offering classification reasoning with exceptional quality. This superior performance enables key applications such as the automatic identification of critical lung pathology areas and provides a robust solution for broader medical video classification tasks.

Francisco M. Castro-Macías, Pablo Morales-Álvarez, Yunan Wu et al.

The Multiple Instance Learning (MIL) paradigm is attracting plenty of attention in medical imaging classification, where labeled data is scarce. MIL methods cast medical images as bags of instances (e.g. patches in whole slide images, or slices in CT scans), and only bag labels are required for training. Deep MIL approaches have obtained promising results by aggregating instance-level representations via an attention mechanism to compute the bag-level prediction. These methods typically capture both local interactions among adjacent instances and global, long-range dependencies through various mechanisms. However, they treat attention values deterministically, potentially overlooking uncertainty in the contribution of individual instances. In this work we propose a novel probabilistic framework that estimates a probability distribution over the attention values, and accounts for both global and local interactions. In a comprehensive evaluation involving {\color{review} eleven} state-of-the-art baselines and three medical datasets, we show that our approach achieves top predictive performance in different metrics. Moreover, the probabilistic treatment of the attention provides uncertainty maps that are interpretable in terms of illness localization.

Amil Dravid, Florian Schiffers, Yunan Wu et al.

Generative Adversarial Networks (GANs) have shown promise in augmenting datasets and boosting convolutional neural networks' (CNN) performance on image classification tasks. But they introduce more hyperparameters to tune as well as the need for additional time and computational power to train supplementary to the CNN. In this work, we examine the potential for Auxiliary-Classifier GANs (AC-GANs) as a 'one-stop-shop' architecture for image classification, particularly in low data regimes. Additionally, we explore modifications to the typical AC-GAN framework, changing the generator's latent space sampling scheme and employing a Wasserstein loss with gradient penalty to stabilize the simultaneous training of image synthesis and classification. Through experiments on images of varying resolutions and complexity, we demonstrate that AC-GANs show promise in image classification, achieving competitive performance with standard CNNs. These methods can be employed as an 'all-in-one' framework with particular utility in the absence of large amounts of training data.

Emanuel A. Azcona, Pierre Besson, Yunan Wu et al.

We propose a mesh-based technique to aid in the classification of Alzheimer's disease dementia (ADD) using mesh representations of the cortex and subcortical structures. Deep learning methods for classification tasks that utilize structural neuroimaging often require extensive learning parameters to optimize. Frequently, these approaches for automated medical diagnosis also lack visual interpretability for areas in the brain involved in making a diagnosis. This work: (a) analyzes brain shape using surface information of the cortex and subcortical structures, (b) proposes a residual learning framework for state-of-the-art graph convolutional networks which offer a significant reduction in learnable parameters, and (c) offers visual interpretability of the network via class-specific gradient information that localizes important regions of interest in our inputs. With our proposed method leveraging the use of cortical and subcortical surface information, we outperform other machine learning methods with a 96.35% testing accuracy for the ADD vs. healthy control problem. We confirm the validity of our model by observing its performance in a 25-trial Monte Carlo cross-validation. The generated visualization maps in our study show correspondences with current knowledge regarding the structural localization of pathological changes in the brain associated to dementia of the Alzheimer's type.

Yunan Wu, Lan Wang

We propose a new procedure for inference on optimal treatment regimes in the model-free setting, which does not require to specify an outcome regression model. Existing model-free estimators for optimal treatment regimes are usually not suitable for the purpose of inference, because they either have nonstandard asymptotic distributions or do not necessarily guarantee consistent estimation of the parameter indexing the Bayes rule due to the use of surrogate loss. We first study a smoothed robust estimator that directly targets the parameter corresponding to the Bayes decision rule for optimal treatment regimes estimation. This estimator is shown to have an asymptotic normal distribution. Furthermore, we verify that a resampling procedure provides asymptotically accurate inference for both the parameter indexing the optimal treatment regime and the optimal value function. A new algorithm is developed to calculate the proposed estimator with substantially improved speed and stability. Numerical results demonstrate the satisfactory performance of the new methods.

Yunan Wu, Lan Wang

Penalized (or regularized) regression, as represented by Lasso and its variants, has become a standard technique for analyzing high-dimensional data when the number of variables substantially exceeds the sample size. The performance of penalized regression relies crucially on the choice of the tuning parameter, which determines the amount of regularization and hence the sparsity level of the fitted model. The optimal choice of tuning parameter depends on both the structure of the design matrix and the unknown random error distribution (variance, tail behavior, etc). This article reviews the current literature of tuning parameter selection for high-dimensional regression from both theoretical and practical perspectives. We discuss various strategies that choose the tuning parameter to achieve prediction accuracy or support recovery. We also review several recently proposed methods for tuning-free high-dimensional regression.

Yunan Wu, Feng Yang, Ying Liu et al.

Effective detection of arrhythmia is an important task in the remote monitoring of electrocardiogram (ECG). The traditional ECG recognition depends on the judgment of the clinicians' experience, but the results suffer from the probability of human error due to the fatigue. To solve this problem, an ECG signal classification method based on the images is presented to classify ECG signals into normal and abnormal beats by using two-dimensional convolutional neural networks (2D-CNNs). First, we compare the accuracy and robustness between one-dimensional ECG signal input method and two-dimensional image input method in AlexNet network. Then, in order to alleviate the overfitting problem in two-dimensional network, we initialize AlexNet-like network with weights trained on ImageNet, to fit the training ECG images and fine-tune the model, and to further improve the accuracy and robustness of ECG classification. The performance evaluated on the MIT-BIH arrhythmia database demonstrates that the proposed method can achieve the accuracy of 98% and maintain high accuracy within SNR range from 20 dB to 35 dB. The experiment shows that the 2D-CNNs initialized with AlexNet weights performs better than one-dimensional signal method without a large-scale dataset.