Meta3D: Single-View 3D Object Reconstruction from Shape Priors in Memory

3D shape reconstruction from a single-view RGB image is an ill-posed problem due to the invisible parts of the object to be reconstructed. Most of the existing methods rely on large-scale data to obtain shape priors through tuning parameters of reconstruction models. These methods might not be able to deal with the cases with heavy object occlusions and noisy background since prior information can not be retained completely or applied efficiently. In this paper, we are the first to develop a memory-based meta-learning framework for single-view 3D reconstruction. A write controller is designed to extract shape-discriminative features from images and store image features and their corresponding volumes into external memory. A read controller is proposed to sequentially encode shape priors related to the input image and predict a shape-specific refiner. Experimental results demonstrate that our Meta3D outperforms state-of-the-art methods with a large margin through retaining shape priors explicitly, especially for the extremely difficult cases.

AITom: Open-source AI platform for cryo-electron Tomography data analysis

Cryo-electron tomography (cryo-ET) is an emerging technology for the 3D visualization of structural organizations and interactions of subcellular components at near-native state and sub-molecular resolution. Tomograms captured by cryo-ET contain heterogeneous structures representing the complex and dynamic subcellular environment. Since the structures are not purified or fluorescently labeled, the spatial organization and interaction between both the known and unknown structures can be studied in their native environment. The rapid advances of cryo-electron tomography (cryo-ET) have generated abundant 3D cellular imaging data. However, the systematic localization, identification, segmentation, and structural recovery of the subcellular components require efficient and accurate large-scale image analysis methods. We introduce AITom, an open-source artificial intelligence platform for cryo-ET researchers. AITom provides many public as well as in-house algorithms for performing cryo-ET data analysis through both the traditional template-based or template-free approach and the deep learning approach. Comprehensive tutorials for each analysis module are provided to guide the user through. We welcome researchers and developers to join this collaborative open-source software development project. Availability: https://github.com/xulabs/aitom

A Deep Learning System That Generates Quantitative CT Reports for Diagnosing Pulmonary Tuberculosis

We developed a deep learning model-based system to automatically generate a quantitative Computed Tomography (CT) diagnostic report for Pulmonary Tuberculosis (PTB) cases.501 CT imaging datasets from 223 patients with active PTB were collected, and another 501 cases from a healthy population served as negative samples.2884 lesions of PTB were carefully labeled and classified manually by professional radiologists.Three state-of-the-art 3D convolution neural network (CNN) models were trained and evaluated in the inspection of PTB CT images. Transfer learning method was also utilized during this process. The best model was selected to annotate the spatial location of lesions and classify them into miliary, infiltrative, caseous, tuberculoma and cavitary types simultaneously.Then the Noisy-Or Bayesian function was used to generate an overall infection probability.Finally, a quantitative diagnostic report was exported.The results showed that the recall and precision rates, from the perspective of a single lesion region of PTB, were 85.9% and 89.2% respectively. The overall recall and precision rates,from the perspective of one PTB case, were 98.7% and 93.7%, respectively. Moreover, the precision rate of the PTB lesion type classification was 90.9%.The new method might serve as an effective reference for decision making by clinical doctors.

Structured Modeling of Joint Deep Feature and Prediction Refinement for Salient Object Detection

Recent saliency models extensively explore to incorporate multi-scale contextual information from Convolutional Neural Networks (CNNs). Besides direct fusion strategies, many approaches introduce message-passing to enhance CNN features or predictions. However, the messages are mainly transmitted in two ways, by feature-to-feature passing, and by prediction-to-prediction passing. In this paper, we add message-passing between features and predictions and propose a deep unified CRF saliency model . We design a novel cascade CRFs architecture with CNN to jointly refine deep features and predictions at each scale and progressively compute a final refined saliency map. We formulate the CRF graphical model that involves message-passing of feature-feature, feature-prediction, and prediction-prediction, from the coarse scale to the finer scale, to update the features and the corresponding predictions. Also, we formulate the mean-field updates for joint end-to-end model training with CNN through back propagation. The proposed deep unified CRF saliency model is evaluated over six datasets and shows highly competitive performance among the state of the arts.

Practical and Robust Privacy Amplification with Multi-Party Differential Privacy

When collecting information, local differential privacy (LDP) alleviates privacy concerns of users, as users' private information is randomized before being sent to the central aggregator. However, LDP results in loss of utility due to the amount of noise that is added. To address this issue, recent work introduced an intermediate server and with the assumption that this intermediate server did not collude with the aggregator. Using this trust model, one can add less noise to achieve the same privacy guarantee; thus improving the utility. In this paper, we investigate this multiple-party setting of LDP. We first analyze the threat model and identify potential adversaries. We then make observations about existing approaches and propose new techniques that achieve a better privacy-utility tradeoff than existing ones. Finally, we perform experiments to compare different methods and demonstrate the benefits of using our proposed method.

Deep Learning-Based Strategy for Macromolecules Classification with Imbalanced Data from Cellular Electron Cryotomography

Deep learning model trained by imbalanced data may not work satisfactorily since it could be determined by major classes and thus may ignore the classes with small amount of data. In this paper, we apply deep learning based imbalanced data classification for the first time to cellular macromolecular complexes captured by Cryo-electron tomography (Cryo-ET). We adopt a range of strategies to cope with imbalanced data, including data sampling, bagging, boosting, Genetic Programming based method and. Particularly, inspired from Inception 3D network, we propose a multi-path CNN model combining focal loss and mixup on the Cryo-ET dataset to expand the dataset, where each path had its best performance corresponding to each type of data and let the network learn the combinations of the paths to improve the classification performance. In addition, extensive experiments have been conducted to show our proposed method is flexible enough to cope with different number of classes by adjusting the number of paths in our multi-path model. To our knowledge, this work is the first application of deep learning methods of dealing with imbalanced data to the internal tissue classification of cell macromolecular complexes, which opened up a new path for cell classification in the field of computational biology.

Learning Multi-level Deep Representations for Image Emotion Classification

In this paper, we propose a new deep network that learns multi-level deep representations for image emotion classification (MldrNet). Image emotion can be recognized through image semantics, image aesthetics and low-level visual features from both global and local views. Existing image emotion classification works using hand-crafted features or deep features mainly focus on either low-level visual features or semantic-level image representations without taking all factors into consideration. The proposed MldrNet combines deep representations of different levels, i.e. image semantics, image aesthetics, and low-level visual features to effectively classify the emotion types of different kinds of images, such as abstract paintings and web images. Extensive experiments on both Internet images and abstract paintings demonstrate the proposed method outperforms the state-of-the-art methods using deep features or hand-crafted features. The proposed approach also outperforms the state-of-the-art methods with at least 6% performance improvement in terms of overall classification accuracy.

Dual Pattern Learning Networks by Empirical Dual Prediction Risk Minimization

Motivated by the observation that humans can learn patterns from two given images at one time, we propose a dual pattern learning network architecture in this paper. Unlike conventional networks, the proposed architecture has two input branches and two loss functions. Instead of minimizing the empirical risk of a given dataset, dual pattern learning networks is trained by minimizing the empirical dual prediction loss. We show that this can improve the performance for single image classification. This architecture forces the network to learn discriminative class-specific features by analyzing and comparing two input images. In addition, the dual input structure allows the network to have a considerably large number of image pairs, which can help address the overfitting issue due to limited training data. Moreover, we propose to associate each input branch with a random interest value for learning corresponding image during training. This method can be seen as a stochastic regularization technique, and can further lead to generalization performance improvement. State-of-the-art deep networks can be adapted to dual pattern learning networks without increasing the same number of parameters. Extensive experiments on CIFAR-10, CIFAR- 100, FI-8, Google commands dataset, and MNIST demonstrate that our DPLNets exhibit better performance than original networks. The experimental results on subsets of CIFAR- 10, CIFAR-100, and MNIST demonstrate that dual pattern learning networks have good generalization performance on small datasets.

Respond-CAM: Analyzing Deep Models for 3D Imaging Data by Visualizations

The convolutional neural network (CNN) has become a powerful tool for various biomedical image analysis tasks, but there is a lack of visual explanation for the machinery of CNNs. In this paper, we present a novel algorithm, Respond-weighted Class Activation Mapping (Respond-CAM), for making CNN-based models interpretable by visualizing input regions that are important for predictions, especially for biomedical 3D imaging data inputs. Our method uses the gradients of any target concept (e.g. the score of target class) that flows into a convolutional layer. The weighted feature maps are combined to produce a heatmap that highlights the important regions in the image for predicting the target concept. We prove a preferable sum-to-score property of the Respond-CAM and verify its significant improvement on 3D images from the current state-of-the-art approach. Our tests on Cellular Electron Cryo-Tomography 3D images show that Respond-CAM achieves superior performance on visualizing the CNNs with 3D biomedical images inputs, and is able to get reasonably good results on visualizing the CNNs with natural image inputs. The Respond-CAM is an efficient and reliable approach for visualizing the CNN machinery, and is applicable to a wide variety of CNN model families and image analysis tasks.

Multi-task Learning for Macromolecule Classification, Segmentation and Coarse Structural Recovery in Cryo-Tomography

Cellular Electron Cryo-Tomography (CECT) is a powerful 3D imaging tool for studying the native structure and organization of macromolecules inside single cells. For systematic recognition and recovery of macromolecular structures captured by CECT, methods for several important tasks such as subtomogram classification and semantic segmentation have been developed. However, the recognition and recovery of macromolecular structures are still very difficult due to high molecular structural diversity, crowding molecular environment, and the imaging limitations of CECT. In this paper, we propose a novel multi-task 3D convolutional neural network model for simultaneous classification, segmentation, and coarse structural recovery of macromolecules of interest in subtomograms. In our model, the learned image features of one task are shared and thereby mutually reinforce the learning of other tasks. Evaluated on realistically simulated and experimental CECT data, our multi-task learning model outperformed all single-task learning methods for classification and segmentation. In addition, we demonstrate that our model can generalize to discover, segment and recover novel structures that do not exist in the training data.