Recent breakthroughs in high resolution imaging of biomolecules in solution with cryo-electron microscopy (cryo-EM) have unlocked new doors for the reconstruction of molecular volumes, thereby promising further advances in biology, chemistry, and pharmacological research amongst others. Despite significant headway, the immense challenges in cryo-EM data analysis remain legion and intricately inter-disciplinary in nature, requiring insights from physicists, structural biologists, computer scientists, statisticians, and applied mathematicians. Meanwhile, recent next-generation volume reconstruction algorithms that combine generative modeling with end-to-end unsupervised deep learning techniques have shown promising results on simulated data, but still face considerable hurdles when applied to experimental cryo-EM images. In light of the proliferation of such methods and given the interdisciplinary nature of the task, we propose here a critical review of recent advances in the field of deep generative modeling for high resolution cryo-EM volume reconstruction. The present review aims to (i) compare and contrast these new methods, while (ii) presenting them from a perspective and using terminology familiar to scientists in each of the five aforementioned fields with no specific background in cryo-EM. The review begins with an introduction to the mathematical and computational challenges of deep generative models for cryo-EM volume reconstruction, along with an overview of the baseline methodology shared across this class of algorithms. Having established the common thread weaving through these different models, we provide a practical comparison of these state-of-the-art algorithms, highlighting their relative strengths and weaknesses, along with the assumptions that they rely on. This allows us to identify bottlenecks in current methods and avenues for future research.
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Objective: When patients develop acute respiratory failure, accurately identifying the underlying etiology is essential for determining the best treatment. However, differentiating between common medical diagnoses can be challenging in clinical practice. Machine learning models could improve medical diagnosis by aiding in the diagnostic evaluation of these patients. Materials and Methods: Machine learning models were trained to predict the common causes of acute respiratory failure (pneumonia, heart failure, and/or COPD). Models were trained using chest radiographs and clinical data from the electronic health record (EHR) and applied to an internal and external cohort. Results: The internal cohort of 1,618 patients included 508 (31%) with pneumonia, 363 (22%) with heart failure, and 137 (8%) with COPD based on physician chart review. A model combining chest radiographs and EHR data outperformed models based on each modality alone. Models had similar or better performance compared to a randomly selected physician reviewer. For pneumonia, the combined model area under the receiver operating characteristic curve (AUROC) was 0.79 (0.77-0.79), image model AUROC was 0.74 (0.72-0.75), and EHR model AUROC was 0.74 (0.70-0.76). For heart failure, combined: 0.83 (0.77-0.84), image: 0.80 (0.71-0.81), and EHR: 0.79 (0.75-0.82). For COPD, combined: AUROC = 0.88 (0.83-0.91), image: 0.83 (0.77-0.89), and EHR: 0.80 (0.76-0.84). In the external cohort, performance was consistent for heart failure and increased for COPD, but declined slightly for pneumonia. Conclusions: Machine learning models combining chest radiographs and EHR data can accurately differentiate between common causes of acute respiratory failure. Further work is needed to determine how these models could act as a diagnostic aid to clinicians in clinical settings.
Anomalies represent rare observations (e.g., data records or events) that deviate significantly from others. Over several decades, research on anomaly mining has received increasing interests due to the implications of these occurrences in a wide range of disciplines. Anomaly detection, which aims to identify rare observations, is among the most vital tasks in the world, and has shown its power in preventing detrimental events, such as financial fraud, network intrusion, and social spam. The detection task is typically solved by identifying outlying data points in the feature space and inherently overlooks the relational information in real-world data. Graphs have been prevalently used to represent the structural information, which raises the graph anomaly detection problem - identifying anomalous graph objects (i.e., nodes, edges and sub-graphs) in a single graph, or anomalous graphs in a database/set of graphs. However, conventional anomaly detection techniques cannot tackle this problem well because of the complexity of graph data. For the advent of deep learning, graph anomaly detection with deep learning has received a growing attention recently. In this survey, we aim to provide a systematic and comprehensive review of the contemporary deep learning techniques for graph anomaly detection. We compile open-sourced implementations, public datasets, and commonly-used evaluation metrics to provide affluent resources for future studies. More importantly, we highlight twelve extensive future research directions according to our survey results covering unsolved and emerging research problems and real-world applications. With this survey, our goal is to create a "one-stop-shop" that provides a unified understanding of the problem categories and existing approaches, publicly available hands-on resources, and high-impact open challenges for graph anomaly detection using deep learning.
We present PHORHUM, a novel, end-to-end trainable, deep neural network methodology for photorealistic 3D human reconstruction given just a monocular RGB image. Our pixel-aligned method estimates detailed 3D geometry and, for the first time, the unshaded surface color together with the scene illumination. Observing that 3D supervision alone is not sufficient for high fidelity color reconstruction, we introduce patch-based rendering losses that enable reliable color reconstruction on visible parts of the human, and detailed and plausible color estimation for the non-visible parts. Moreover, our method specifically addresses methodological and practical limitations of prior work in terms of representing geometry, albedo, and illumination effects, in an end-to-end model where factors can be effectively disentangled. In extensive experiments, we demonstrate the versatility and robustness of our approach. Our state-of-the-art results validate the method qualitatively and for different metrics, for both geometric and color reconstruction.
Rumor detection has become an emerging and active research field in recent years. At the core is to model the rumor characteristics inherent in rich information, such as propagation patterns in social network and semantic patterns in post content, and differentiate them from the truth. However, existing works on rumor detection fall short in modeling heterogeneous information, either using one single information source only (e.g. social network, or post content) or ignoring the relations among multiple sources (e.g. fusing social and content features via simple concatenation). Therefore, they possibly have drawbacks in comprehensively understanding the rumors, and detecting them accurately. In this work, we explore contrastive self-supervised learning on heterogeneous information sources, so as to reveal their relations and characterize rumors better. Technically, we supplement the main supervised task of detection with an auxiliary self-supervised task, which enriches post representations via post self-discrimination. Specifically, given two heterogeneous views of a post (i.e. representations encoding social patterns and semantic patterns), the discrimination is done by maximizing the mutual information between different views of the same post compared to that of other posts. We devise cluster-wise and instance-wise approaches to generate the views and conduct the discrimination, considering different relations of information sources. We term this framework as Self-supervised Rumor Detection (SRD). Extensive experiments on three real-world datasets validate the effectiveness of SRD for automatic rumor detection on social media.
Numerous sand dust image enhancement algorithms have been proposed in recent years. To our best acknowledge, however, most methods evaluated their performance with no-reference way using few selected real-world images from internet. It is unclear how to quantitatively analysis the performance of the algorithms in a supervised way and how we could gauge the progress in the field. Moreover, due to the absence of large-scale benchmark datasets, there are no well-known reports of data-driven based method for sand dust image enhancement up till now. To advance the development of deep learning-based algorithms for sand dust image reconstruction, while enabling supervised objective evaluation of algorithm performance. In this paper, we presented a comprehensive perceptual study and analysis of real-world sand dust images, then constructed a Sand-dust Image Reconstruction Benchmark (SIRB) for training Convolutional Neural Networks (CNNs) and evaluating algorithms performance. In addition, we adopted the existing image transformation neural network trained on SIRB as baseline to illustrate the generalization of SIRB for training CNNs. Finally, we conducted the qualitative and quantitative evaluation to demonstrate the performance and limitations of the state-of-the-arts (SOTA), which shed light on future research in sand dust image reconstruction.
Cross-slide image analysis provides additional information by analysing the expression of different biomarkers as compared to a single slide analysis. These biomarker stained slides are analysed side by side, revealing unknown relations between them. During the slide preparation, a tissue section may be placed at an arbitrary orientation as compared to other sections of the same tissue block. The problem is compounded by the fact that tissue contents are likely to change from one section to the next and there may be unique artefacts on some of the slides. This makes registration of each section to a reference section of the same tissue block an important pre-requisite task before any cross-slide analysis. We propose a deep feature based registration (DFBR) method which utilises data-driven features to estimate the rigid transformation. We adopted a multi-stage strategy for improving the quality of registration. We also developed a visualisation tool to view registered pairs of WSIs at different magnifications. With the help of this tool, one can apply a transformation on the fly without the need to generate transformed source WSI in a pyramidal form. We compared the performance of data-driven features with that of hand-crafted features on the COMET dataset. Our approach can align the images with low registration errors. Generally, the success of non-rigid registration is dependent on the quality of rigid registration. To evaluate the efficacy of the DFBR method, the first two steps of the ANHIR winner's framework are replaced with our DFBR to register challenge provided image pairs. The modified framework produces comparable results to that of challenge winning team.
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream structural biology techniques because of its ability to determine high-resolution structures of dynamic bio-molecules. However, cryo-EM data acquisition remains expensive and labor-intensive, requiring substantial expertise. Structural biologists need a more efficient and objective method to collect the best data in a limited time frame. We formulate the cryo-EM data collection task as an optimization problem in this work. The goal is to maximize the total number of good images taken within a specified period. We show that reinforcement learning offers an effective way to plan cryo-EM data collection, successfully navigating heterogenous cryo-EM grids. The approach we developed, cryoRL, demonstrates better performance than average users for data collection under similar settings.
Transformers have dominated the field of natural language processing, and recently impacted the computer vision area. In the field of medical image analysis, Transformers have also been successfully applied to full-stack clinical applications, including image synthesis/reconstruction, registration, segmentation, detection, and diagnosis. Our paper presents both a position paper and a primer, promoting awareness and application of Transformers in the field of medical image analysis. Specifically, we first overview the core concepts of the attention mechanism built into Transformers and other basic components. Second, we give a new taxonomy of various Transformer architectures tailored for medical image applications and discuss their limitations. Within this review, we investigate key challenges revolving around the use of Transformers in different learning paradigms, improving the model efficiency, and their coupling with other techniques. We hope this review can give a comprehensive picture of Transformers to the readers in the field of medical image analysis.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
Recent advance in fluorescence microscopy enables acquisition of 3D image volumes with better quality and deeper penetration into tissue. Segmentation is a required step to characterize and analyze biological structures in the images. 3D segmentation using deep learning has achieved promising results in microscopy images. One issue is that deep learning techniques require a large set of groundtruth data which is impractical to annotate manually for microscopy volumes. This paper describes a 3D nuclei segmentation method using 3D convolutional neural networks. A set of synthetic volumes and the corresponding groundtruth volumes are generated automatically using a generative adversarial network. Segmentation results demonstrate that our proposed method is capable of segmenting nuclei successfully in 3D for various data sets.
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