Exploring structure diversity in atomic resolution microscopy with graph neural networks

The emergence of deep learning (DL) has provided great opportunities for the high-throughput analysis of atomic-resolution micrographs. However, the DL models trained by image patches in fixed size generally lack efficiency and flexibility when processing micrographs containing diversified atomic configurations. Herein, inspired by the similarity between the atomic structures and graphs, we describe a few-shot learning framework based on an equivariant graph neural network (EGNN) to analyze a library of atomic structures (e.g., vacancies, phases, grain boundaries, doping, etc.), showing significantly promoted robustness and three orders of magnitude reduced computing parameters compared to the image-driven DL models, which is especially evident for those aggregated vacancy lines with flexible lattice distortion. Besides, the intuitiveness of graphs enables quantitative and straightforward extraction of the atomic-scale structural features in batches, thus statistically unveiling the self-assembly dynamics of vacancy lines under electron beam irradiation. A versatile model toolkit is established by integrating EGNN sub-models for single structure recognition to process images involving varied configurations in the form of a task chain, leading to the discovery of novel doping configurations with superior electrocatalytic properties for hydrogen evolution reactions. This work provides a powerful tool to explore structure diversity in a fast, accurate, and intelligent manner.

Wound Segmentation with Dynamic Illumination Correction and Dual-view Semantic Fusion

Wound image segmentation is a critical component for the clinical diagnosis and in-time treatment of wounds. Recently, deep learning has become the mainstream methodology for wound image segmentation. However, the pre-processing of the wound image, such as the illumination correction, is required before the training phase as the performance can be greatly improved. The correction procedure and the training of deep models are independent of each other, which leads to sub-optimal segmentation performance as the fixed illumination correction may not be suitable for all images. To address aforementioned issues, an end-to-end dual-view segmentation approach was proposed in this paper, by incorporating a learn-able illumination correction module into the deep segmentation models. The parameters of the module can be learned and updated during the training stage automatically, while the dual-view fusion can fully employ the features from both the raw images and the enhanced ones. To demonstrate the effectiveness and robustness of the proposed framework, the extensive experiments are conducted on the benchmark datasets. The encouraging results suggest that our framework can significantly improve the segmentation performance, compared to the state-of-the-art methods.

Trusted Multi-Scale Classification Framework for Whole Slide Image

Despite remarkable efforts been made, the classification of gigapixels whole-slide image (WSI) is severely restrained from either the constrained computing resources for the whole slides, or limited utilizing of the knowledge from different scales. Moreover, most of the previous attempts lacked of the ability of uncertainty estimation. Generally, the pathologists often jointly analyze WSI from the different magnifications. If the pathologists are uncertain by using single magnification, then they will change the magnification repeatedly to discover various features of the tissues. Motivated by the diagnose process of the pathologists, in this paper, we propose a trusted multi-scale classification framework for the WSI. Leveraging the Vision Transformer as the backbone for multi branches, our framework can jointly classification modeling, estimating the uncertainty of each magnification of a microscope and integrate the evidence from different magnification. Moreover, to exploit discriminative patches from WSIs and reduce the requirement for computation resources, we propose a novel patch selection schema using attention rollout and non-maximum suppression. To empirically investigate the effectiveness of our approach, empirical experiments are conducted on our WSI classification tasks, using two benchmark databases. The obtained results suggest that the trusted framework can significantly improve the WSI classification performance compared with the state-of-the-art methods.

Underwater Acoustic Communication Channel Modeling using Reservoir Computing

Underwater acoustic (UWA) communications have been widely used but greatly impaired due to the complicated nature of the underwater environment. In order to improve UWA communications, modeling and understanding the UWA channel is indispensable. However, there exist many challenges due to the high uncertainties of the underwater environment and the lack of real-world measurement data. In this work, the capability of reservoir computing and deep learning has been explored for modeling the UWA communication channel accurately using real underwater data collected from a water tank with disturbance and from Lake Tahoe. We leverage the capability of reservoir computing for modeling dynamical systems and provided a data-driven approach to modeling the UWA channel using Echo State Network (ESN). In addition, the potential application of transfer learning to reservoir computing has been examined. Experimental results show that ESN is able to model chaotic UWA channels with better performance compared to popular deep learning models in terms of mean absolute percentage error (MAPE), specifically, ESN has outperformed deep neural network by 2% and as much as 40% in benign and chaotic UWA respectively.

3D Shuffle-Mixer: An Efficient Context-Aware Vision Learner of Transformer-MLP Paradigm for Dense Prediction in Medical Volume

Dense prediction in medical volume provides enriched guidance for clinical analysis. CNN backbones have met bottleneck due to lack of long-range dependencies and global context modeling power. Recent works proposed to combine vision transformer with CNN, due to its strong global capture ability and learning capability. However, most works are limited to simply applying pure transformer with several fatal flaws (i.e., lack of inductive bias, heavy computation and little consideration for 3D data). Therefore, designing an elegant and efficient vision transformer learner for dense prediction in medical volume is promising and challenging. In this paper, we propose a novel 3D Shuffle-Mixer network of a new Local Vision Transformer-MLP paradigm for medical dense prediction. In our network, a local vision transformer block is utilized to shuffle and learn spatial context from full-view slices of rearranged volume, a residual axial-MLP is designed to mix and capture remaining volume context in a slice-aware manner, and a MLP view aggregator is employed to project the learned full-view rich context to the volume feature in a view-aware manner. Moreover, an Adaptive Scaled Enhanced Shortcut is proposed for local vision transformer to enhance feature along spatial and channel dimensions adaptively, and a CrossMerge is proposed to skip-connects the multi-scale feature appropriately in the pyramid architecture. Extensive experiments demonstrate the proposed model outperforms other state-of-the-art medical dense prediction methods.

A Deep Learning Model for Forecasting Global Monthly Mean Sea Surface Temperature Anomalies

Sea surface temperature (SST) variability plays a key role in the global weather and climate system, with phenomena such as El Ni\~{n}o-Southern Oscillation regarded as a major source of interannual climate variability at the global scale. The ability to be able to make long-range forecasts of sea surface temperature anomalies, especially those associated with extreme marine heatwave events, has potentially significant economic and societal benefits. We have developed a deep learning time series prediction model (Unet-LSTM) based on more than 70 years (1950-2021) of ECMWF ERA5 monthly mean sea surface temperature and 2-metre air temperature data. The Unet-LSTM model is able to learn the underlying physics driving the temporal evolution of the 2-dimensional global sea surface temperatures. The model accurately predicts sea surface temperatures over a 24 month period with a root mean square error remaining below 0.75$^\circ$C for all predicted months. We have also investigated the ability of the model to predict sea surface temperature anomalies in the Ni\~{n}o3.4 region, as well as a number of marine heatwave hot spots over the past decade. Model predictions of the Ni\~{n}o3.4 index allow us to capture the strong 2010-11 La Ni\~{n}a, 2009-10 El Nino and the 2015-16 extreme El Ni\~{n}o up to 24 months in advance. It also shows long lead prediction skills for the northeast Pacific marine heatwave, the Blob. However, the prediction of the marine heatwaves in the southeast Indian Ocean, the Ningaloo Ni\~{n}o, shows limited skill. These results indicate the significant potential of data driven methods to yield long-range predictions of sea surface temperature anomalies.

Fusion of medical imaging and electronic health records with attention and multi-head machanisms

Doctors often make diagonostic decisions based on patient's image scans, such as magnetic resonance imaging (MRI), and patient's electronic health records (EHR) such as age, gender, blood pressure and so on. Despite a lot of automatic methods have been proposed for either image or text analysis in computer vision or natural language research areas, much fewer studies have been developed for the fusion of medical image and EHR data for medical problems. Among existing early or intermediate fusion methods, concatenation of features from both modalities is still a mainstream. For a better exploiting of image and EHR data, we propose a multi-modal attention module which use EHR data to help the selection of important regions during image feature extraction process conducted by traditional CNN. Moreover, we propose to incorporate multi-head machnism to gated multimodal unit (GMU) to make it able to parallelly fuse image and EHR features in different subspaces. With the help of the two modules, existing CNN architecture can be enhanced using both modalities. Experiments on predicting Glasgow outcome scale (GOS) of intracerebral hemorrhage patients and classifying Alzheimer's Disease showed the proposed method can automatically focus on task-related areas and achieve better results by making better use of image and EHR features.

HEROHE Challenge: assessing HER2 status in breast cancer without immunohistochemistry or in situ hybridization

Breast cancer is the most common malignancy in women, being responsible for more than half a million deaths every year. As such, early and accurate diagnosis is of paramount importance. Human expertise is required to diagnose and correctly classify breast cancer and define appropriate therapy, which depends on the evaluation of the expression of different biomarkers such as the transmembrane protein receptor HER2. This evaluation requires several steps, including special techniques such as immunohistochemistry or in situ hybridization to assess HER2 status. With the goal of reducing the number of steps and human bias in diagnosis, the HEROHE Challenge was organized, as a parallel event of the 16th European Congress on Digital Pathology, aiming to automate the assessment of the HER2 status based only on hematoxylin and eosin stained tissue sample of invasive breast cancer. Methods to assess HER2 status were presented by 21 teams worldwide and the results achieved by some of the proposed methods open potential perspectives to advance the state-of-the-art.

Large-Scale Unsupervised Person Re-Identification with Contrastive Learning

Existing public person Re-Identification~(ReID) datasets are small in modern terms because of labeling difficulty. Although unlabeled surveillance video is abundant and relatively easy to obtain, it is unclear how to leverage these footage to learn meaningful ReID representations. In particular, most existing unsupervised and domain adaptation ReID methods utilize only the public datasets in their experiments, with labels removed. In addition, due to small data sizes, these methods usually rely on fine tuning by the unlabeled training data in the testing domain to achieve good performance. Inspired by the recent progress of large-scale self-supervised image classification using contrastive learning, we propose to learn ReID representation from large-scale unlabeled surveillance video alone. Assisted by off-the-shelf pedestrian detection tools, we apply the contrastive loss at both the image and the tracklet levels. Together with a principal component analysis step using camera labels freely available, our evaluation using a large-scale unlabeled dataset shows far superior performance among unsupervised methods that do not use any training data in the testing domain. Furthermore, the accuracy improves with the data size and therefore our method has great potential with even larger and more diversified datasets.

Convolutional Neural Network-Based Age Estimation Using B-Mode Ultrasound Tongue Image

Ultrasound tongue imaging is widely used for speech production research, and it has attracted increasing attention as its potential applications seem to be evident in many different fields, such as the visual biofeedback tool for second language acquisition and silent speech interface. Unlike previous studies, here we explore the feasibility of age estimation using the ultrasound tongue image of the speakers. Motivated by the success of deep learning, this paper leverages deep learning on this task. We train a deep convolutional neural network model on the UltraSuite dataset. The deep model achieves mean absolute error (MAE) of 2.03 for the data from typically developing children, while MAE is 4.87 for the data from the children with speech sound disorders, which suggest that age estimation using ultrasound is more challenging for the children with speech sound disorder. The developed method can be used a tool to evaluate the performance of speech therapy sessions. It is also worthwhile to notice that, although we leverage the ultrasound tongue imaging for our study, the proposed methods may also be extended to other imaging modalities (e.g. MRI) to assist the studies on speech production.