FIB/SEM tomography represents an indispensable tool for the characterization of three-dimensional nanostructures in battery research and many other fields. However, contrast and 3D classification/reconstruction problems occur in many cases, which strongly limits the applicability of the technique especially on porous materials, like those used for electrode materials in batteries or fuel cells. Distinguishing the different components like active Li storage particles and carbon/binder materials is difficult and often prevents a reliable quantitative analysis of image data, or may even lead to wrong conclusions about structure-property relationships. In this contribution, we present a novel approach for data classification in three-dimensional image data obtained by FIB/SEM tomography and its applications to NMC battery electrode materials. We use two different image signals, namely the signal of the angled SE2 chamber detector and the Inlens detector signal, combine both signals and train a random forest, i.e. a particular machine learning algorithm. We demonstrate that this approach can overcome current limitations of existing techniques suitable for multi-phase measurements and that it allows for quantitative data reconstruction even where current state-of the art techniques fail, or demand for large training sets. This approach may yield as guideline for future research using FIB/SEM tomography.
PointNet++ is one of the most influential neural architectures for point cloud understanding. Although the accuracy of PointNet++ has been largely surpassed by recent networks such as PointMLP and Point Transformer, we find that a large portion of the performance gain is due to improved training strategies, i.e. data augmentation and optimization techniques, and increased model sizes rather than architectural innovations. Thus, the full potential of PointNet++ has yet to be explored. In this work, we revisit the classical PointNet++ through a systematic study of model training and scaling strategies, and offer two major contributions. First, we propose a set of improved training strategies that significantly improve PointNet++ performance. For example, we show that, without any change in architecture, the overall accuracy (OA) of PointNet++ on ScanObjectNN object classification can be raised from 77.9% to 86.1%, even outperforming state-of-the-art PointMLP. Second, we introduce an inverted residual bottleneck design and separable MLPs into PointNet++ to enable efficient and effective model scaling and propose PointNeXt, the next version of PointNets. PointNeXt can be flexibly scaled up and outperforms state-of-the-art methods on both 3D classification and segmentation tasks. For classification, PointNeXt reaches an overall accuracy of 87.7 on ScanObjectNN, surpassing PointMLP by 2.3%, while being 10x faster in inference. For semantic segmentation, PointNeXt establishes a new state-of-the-art performance with 74.9% mean IoU on S3DIS (6-fold cross-validation), being superior to the recent Point Transformer. The code and models are available at https://github.com/guochengqian/pointnext.
Aggregating neighbor features is essential for point cloud classification. In the existing work, each point in the cloud may inevitably be selected as the neighbors of multiple aggregation centers, as all centers will gather neighbor features from the whole point cloud independently. Thus each point has to participate in the calculation repeatedly and generates redundant duplicates in the memory, leading to intensive computation costs and memory consumption. Meanwhile, to pursue higher accuracy, previous methods often rely on a complex local aggregator to extract fine geometric representation, which further slows down the classification pipeline. To address these issues, we propose a new local aggregator of linear complexity for point cloud classification, coined as APP. Specifically, we introduce an auxiliary container as an anchor to exchange features between the source point and the aggregating center. Each source point pushes its feature to only one auxiliary container, and each center point pulls features from only one auxiliary container. This avoids the re-computation issue of each source point. To facilitate the learning of the local structure of cloud point, we use an online normal estimation module to provide the explainable geometric information to enhance our APP modeling capability. Our built network is more efficient than all the previous baselines with a clear margin while still consuming a lower memory. Experiments on both synthetic and real datasets demonstrate that APP-Net reaches comparable accuracies to other networks. It can process more than 10,000 samples per second with less than 10GB of memory on a single GPU. We will release the code in https://github.com/MCG-NJU/APP-Net.
We design deep neural networks (DNNs) and corresponding networks' splittings to distribute DNNs' workload to camera sensors and a centralized aggregator on head mounted devices to meet system performance targets in inference accuracy and latency under the given hardware resource constraints. To achieve an optimal balance among computation, communication, and performance, a split-aware neural architecture search framework, SplitNets, is introduced to conduct model designing, splitting, and communication reduction simultaneously. We further extend the framework to multi-view systems for learning to fuse inputs from multiple camera sensors with optimal performance and systemic efficiency. We validate SplitNets for single-view system on ImageNet as well as multi-view system on 3D classification, and show that the SplitNets framework achieves state-of-the-art (SOTA) performance and system latency compared with existing approaches.
In this paper, we investigate the dynamics-aware adversarial attack problem in deep neural networks. Most existing adversarial attack algorithms are designed under a basic assumption -- the network architecture is fixed throughout the attack process. However, this assumption does not hold for many recently proposed networks, e.g. 3D sparse convolution network, which contains input-dependent execution to improve computational efficiency. It results in a serious issue of lagged gradient, making the learned attack at the current step ineffective due to the architecture changes afterward. To address this issue, we propose a Leaded Gradient Method (LGM) and show the significant effects of the lagged gradient. More specifically, we re-formulate the gradients to be aware of the potential dynamic changes of network architectures, so that the learned attack better "leads" the next step than the dynamics-unaware methods when network architecture changes dynamically. Extensive experiments on various datasets show that our LGM achieves impressive performance on semantic segmentation and classification. Compared with the dynamic-unaware methods, LGM achieves about 20% lower mIoU averagely on the ScanNet and S3DIS datasets. LGM also outperforms the recent point cloud attacks.
Deep convolutional neural networks (CNNs) have become an essential tool in the medical imaging-based computer-aided diagnostic pipeline. However, training accurate and reliable CNNs requires large fine-grain annotated datasets. To alleviate this, weakly-supervised methods can be used to obtain local information from global labels. This work proposes the use of localized perturbations as a weakly-supervised solution to extract segmentation masks of brain tumours from a pretrained 3D classification model. Furthermore, we propose a novel optimal perturbation method that exploits 3D superpixels to find the most relevant area for a given classification using a U-net architecture. Our method achieved a Dice similarity coefficient (DSC) of 0.44 when compared with expert annotations. When compared against Grad-CAM, our method outperformed both in visualization and localization ability of the tumour region, with Grad-CAM only achieving 0.11 average DSC.
Multi-view projection methods have demonstrated promising performance on 3D understanding tasks like 3D classification and segmentation. However, it remains unclear how to combine such multi-view methods with the widely available 3D point clouds. Previous methods use unlearned heuristics to combine features at the point level. To this end, we introduce the concept of the multi-view point cloud (Voint cloud), representing each 3D point as a set of features extracted from several view-points. This novel 3D Voint cloud representation combines the compactness of 3D point cloud representation with the natural view-awareness of multi-view representation. Naturally, we can equip this new representation with convolutional and pooling operations. We deploy a Voint neural network (VointNet) to learn representations in the Voint space. Our novel representation achieves \sota performance on 3D classification, shape retrieval, and robust 3D part segmentation on standard benchmarks ( ScanObjectNN, ShapeNet Core55, and ShapeNet Parts).
A method of a Convolutional Neural Networks (CNN) for image classification with image preprocessing and hyperparameters tuning was proposed. The method aims at increasing the predictive performance for COVID-19 diagnosis while more complex model architecture. Firstly, the CNN model includes four similar convolutional layers followed by a flattening and two dense layers. This work proposes a less complex solution based on simply classifying 2D-slices of Computed Tomography scans. Despite the simplicity in architecture, the proposed CNN model showed improved quantitative results exceeding state-of-the-art when predicting slice cases. The results were achieved on the annotated CT slices of the COV-19-CT-DB dataset. Secondly, the original dataset was processed via anatomy-relevant masking of slice, removing none-representative slices from the CT volume, and hyperparameters tuning. For slice processing, a fixed-sized rectangular area was used for cropping an anatomy-relevant region-of-interest in the images, and a threshold based on the number of white pixels in binarized slices was employed to remove none-representative slices from the 3D-CT scans. The CNN model with a learning rate schedule and an exponential decay and slice flipping techniques was deployed on the processed slices. The proposed method was used to make predictions on the 2D slices and for final diagnosis at patient level, majority voting was applied on the slices of each CT scan to take the diagnosis. The macro F1 score of the proposed method well-exceeded the baseline approach and other alternatives on the validation set as well as on a test partition of previously unseen images from COV-19CT-DB dataset.
In recent years, semi-supervised learning has been widely explored and shows excellent data efficiency for 2D data. There is an emerging need to improve data efficiency for 3D tasks due to the scarcity of labeled 3D data. This paper explores how the coherence of different modelities of 3D data (e.g. point cloud, image, and mesh) can be used to improve data efficiency for both 3D classification and retrieval tasks. We propose a novel multimodal semi-supervised learning framework by introducing instance-level consistency constraint and a novel multimodal contrastive prototype (M2CP) loss. The instance-level consistency enforces the network to generate consistent representations for multimodal data of the same object regardless of its modality. The M2CP maintains a multimodal prototype for each class and learns features with small intra-class variations by minimizing the feature distance of each object to its prototype while maximizing the distance to the others. Our proposed framework significantly outperforms all the state-of-the-art counterparts for both classification and retrieval tasks by a large margin on the modelNet10 and ModelNet40 datasets.
The prevalence of relation networks in computer vision is in stark contrast to underexplored point-based methods. In this paper, we explore the possibilities of local relation operators and survey their feasibility. We propose a scalable and efficient module, called group relation aggregator. The module computes a feature of a group based on the aggregation of the features of the inner-group points weighted by geometric relations and semantic relations. We adopt this module to design our RPNet. We further verify the expandability of RPNet, in terms of both depth and width, on the tasks of classification and segmentation. Surprisingly, empirical results show that wider RPNet fits for classification, while deeper RPNet works better on segmentation. RPNet achieves state-of-the-art for classification and segmentation on challenging benchmarks. We also compare our local aggregator with PointNet++, with around 30% parameters and 50% computation saving. Finally, we conduct experiments to reveal the robustness of RPNet with regard to rigid transformation and noises.
Convolutional neural networks (CNNs) have made great breakthroughs in 2D computer vision. However, their irregular structure makes it hard to harness the potential of CNNs directly on meshes. A subdivision surface provides a hierarchical multi-resolution structure, in which each face in a closed 2-manifold triangle mesh is exactly adjacent to three faces. Motivated by these two observations, this paper presents SubdivNet, an innovative and versatile CNN framework for 3D triangle meshes with Loop subdivision sequence connectivity. Making an analogy between mesh faces and pixels in a 2D image allows us to present a mesh convolution operator to aggregate local features from nearby faces. By exploiting face neighborhoods, this convolution can support standard 2D convolutional network concepts, e.g. variable kernel size, stride, and dilation. Based on the multi-resolution hierarchy, we make use of pooling layers which uniformly merge four faces into one and an upsampling method which splits one face into four. Thereby, many popular 2D CNN architectures can be easily adapted to process 3D meshes. Meshes with arbitrary connectivity can be remeshed to have Loop subdivision sequence connectivity via self-parameterization, making SubdivNet a general approach. Extensive evaluation and various applications demonstrate SubdivNet's effectiveness and efficiency.
Owing to the development of research on local aggregation operators, dramatic breakthrough has been made in point cloud analysis models. However, existing local aggregation operators in the current literature fail to attach decent importance to the local information of the point cloud, which limits the power of the models. To fit this gap, we propose an efficient Vector Attention Convolution module (VAConv), which utilizes K-Nearest Neighbor (KNN) to extract the neighbor points of each input point, and then uses the elevation and azimuth relationship of the vectors between the center point and its neighbors to construct an attention weight matrix for edge features. Afterwards, the VAConv adopts a dual-channel structure to fuse weighted edge features and global features. To verify the efficiency of the VAConv, we connect the VAConvs with different receptive fields in parallel to obtain a Multi-scale graph convolutional network, VA-GCN. The proposed VA-GCN achieves state-of-the-art performance on standard benchmarks including ModelNet40, S3DIS and ShapeNet. Remarkably, on the ModelNet40 dataset for 3D classification, VA-GCN increased by 2.4% compared to the baseline.
We propose simple yet effective improvements in point representations and local neighborhood graph construction within the general framework of graph neural networks (GNNs) for 3D point cloud processing. As a first contribution, we propose to augment the vertex representations with important local geometric information of the points, followed by nonlinear projection using a MLP. As a second contribution, we propose to improve the graph construction for GNNs for 3D point clouds. The existing methods work with a k-nn based approach for constructing the local neighborhood graph. We argue that it might lead to reduction in coverage in case of dense sampling by sensors in some regions of the scene. The proposed methods aims to counter such problems and improve coverage in such cases. As the traditional GNNs were designed to work with general graphs, where vertices may have no geometric interpretations, we see both our proposals as augmenting the general graphs to incorporate the geometric nature of 3D point clouds. While being simple, we demonstrate with multiple challenging benchmarks, with relatively clean CAD models, as well as with real world noisy scans, that the proposed method achieves state of the art results on benchmarks for 3D classification (ModelNet40) , part segmentation (ShapeNet) and semantic segmentation (Stanford 3D Indoor Scenes Dataset). We also show that the proposed network achieves faster training convergence, i.e. ~40% less epochs for classification. The project details are available at https://siddharthsrivastava.github.io/publication/geomgcnn/
Learning 3D representations that generalize well to arbitrarily oriented inputs is a challenge of practical importance in applications varying from computer vision to physics and chemistry. We propose a novel multi-resolution convolutional architecture for learning over concentric spherical feature maps, of which the single sphere representation is a special case. Our hierarchical architecture is based on alternatively learning to incorporate both intra-sphere and inter-sphere information. We show the applicability of our method for two different types of 3D inputs, mesh objects, which can be regularly sampled, and point clouds, which are irregularly distributed. We also propose an efficient mapping of point clouds to concentric spherical images, thereby bridging spherical convolutions on grids with general point clouds. We demonstrate the effectiveness of our approach in improving state-of-the-art performance on 3D classification tasks with rotated data.
The 2.5-MDa 26S proteasome maintains proteostasis and regulates myriad cellular processes. How polyubiquitylated substrate interactions regulate proteasome activity is not understood. Here we introduce a deep manifold learning framework, named AlphaCryo4D, which enables atomic-level cryogenic electron microscopy (cryo-EM) reconstructions of nonequilibrium conformational continuum and reconstitutes hidden dynamics of proteasome autoregulation in the act of substrate degradation. AlphaCryo4D integrates 3D deep residual learning with manifold embedding of free-energy landscapes, which directs 3D clustering via an energy-based particle-voting algorithm. In blind assessments using simulated heterogeneous cryo-EM datasets, AlphaCryo4D achieved 3D classification accuracy three times that of conventional method and reconstructed continuous conformational changes of a 130-kDa protein at sub-3-angstrom resolution. By using AlphaCryo4D to analyze a single experimental cryo-EM dataset, we identified 64 conformers of the substrate-bound human 26S proteasome, revealing conformational entanglement of two regulatory particles in the doubly capped holoenzymes and their energetic differences with singly capped ones. Novel ubiquitin-binding sites are discovered on the RPN2, RPN10 and Alpha5 subunits to remodel polyubiquitin chains for deubiquitylation and recycle. Importantly, AlphaCryo4D choreographs single-nucleotide-exchange dynamics of proteasomal AAA-ATPase motor during translocation initiation, which upregulates proteolytic activity by allosterically promoting nucleophilic attack. Our systemic analysis illuminates a grand hierarchical allostery for proteasome autoregulation.
Multi-view projection methods have demonstrated their ability to reach state-of-the-art performance on 3D shape recognition. Those methods learn different ways to aggregate information from multiple views. However, the camera view-points for those views tend to be heuristically set and fixed for all shapes. To circumvent the lack of dynamism of current multi-view methods, we propose to learn those view-points. In particular, we introduce the Multi-View Transformation Network (MVTN) that regresses optimal view-points for 3D shape recognition, building upon advances in differentiable rendering. As a result, MVTN can be trained end-to-end along with any multi-view network for 3D shape classification. We integrate MVTN in a novel adaptive multi-view pipeline that can render either 3D meshes or point clouds. MVTN exhibits clear performance gains in the tasks of 3D shape classification and 3D shape retrieval without the need for extra training supervision. In these tasks, MVTN achieves state-of-the-art performance on ModelNet40, ShapeNet Core55, and the most recent and realistic ScanObjectNN dataset (up to 6% improvement). Interestingly, we also show that MVTN can provide network robustness against rotation and occlusion in the 3D domain. The code is available at https://github.com/ajhamdi/MVTN .
Weakly supervised disease classification of CT imaging suffers from poor localization owing to case-level annotations, where even a positive scan can hold hundreds to thousands of negative slices along multiple planes. Furthermore, although deep learning segmentation and classification models extract distinctly unique combinations of anatomical features from the same target class(es), they are typically seen as two independent processes in a computer-aided diagnosis (CAD) pipeline, with little to no feature reuse. In this research, we propose a medical classifier that leverages the semantic structural concepts learned via multi-resolution segmentation feature maps, to guide weakly supervised 3D classification of chest CT volumes. Additionally, a comparative analysis is drawn across two different types of feature aggregation to explore the vast possibilities surrounding feature fusion. Using a dataset of 1593 scans labeled on a case-level basis via rule-based model, we train a dual-stage convolutional neural network (CNN) to perform organ segmentation and binary classification of four representative diseases (emphysema, pneumonia/atelectasis, mass and nodules) in lungs. The baseline model, with separate stages for segmentation and classification, results in AUC of 0.791. Using identical hyperparameters, the connected architecture using static and dynamic feature aggregation improves performance to AUC of 0.832 and 0.851, respectively. This study advances the field in two key ways. First, case-level report data is used to weakly supervise a 3D CT classifier of multiple, simultaneous diseases for an organ. Second, segmentation and classification models are connected with two different feature aggregation strategies to enhance the classification performance.
In this paper, we focus on exploring the fusion of images and point clouds for 3D object detection in view of the complementary nature of the two modalities, i.e., images possess more semantic information while point clouds specialize in distance sensing. To this end, we present a novel two-stage multi-modal fusion network for 3D object detection, taking both binocular images and raw point clouds as input. The whole architecture facilitates two-stage fusion. The first stage aims at producing 3D proposals through sparse point-wise feature fusion. Within the first stage, we further exploit a joint anchor mechanism that enables the network to utilize 2D-3D classification and regression simultaneously for better proposal generation. The second stage works on the 2D and 3D proposal regions and fuses their dense features. In addition, we propose to use pseudo LiDAR points from stereo matching as a data augmentation method to densify the LiDAR points, as we observe that objects missed by the detection network mostly have too few points especially for far-away objects. Our experiments on the KITTI dataset show that the proposed multi-stage fusion helps the network to learn better representations.
Most attempts to represent 3D shapes for deep learning have focused on volumetric grids, multi-view images and point clouds. In this paper we look at the most popular representation of 3D shapes in computer graphics - a triangular mesh - and ask how it can be utilized within deep learning. The few attempts to answer this question propose to adapt convolutions & pooling to suit Convolutional Neural Networks (CNNs). This paper proposes a very different approach, termed MeshWalker, to learn the shape directly from a given mesh. The key idea is to represent the mesh by random walks along the surface, which "explore" the mesh's geometry and topology. Each walk is organized as a list of vertices, which in some manner imposes regularity on the mesh. The walk is fed into a Recurrent Neural Network (RNN) that "remembers" the history of the walk. We show that our approach achieves state-of-the-art results for two fundamental shape analysis tasks: shape classification and semantic segmentation. Furthermore, even a very small number of examples suffices for learning. This is highly important, since large datasets of meshes are difficult to acquire.
3D ultrasound (US) can facilitate detailed prenatal examinations for fetal growth monitoring. To analyze a 3D US volume, it is fundamental to identify anatomical landmarks of the evaluated organs accurately. Typical deep learning methods usually regress the coordinates directly or involve heatmap-matching. However, these methods struggle to deal with volumes with large sizes and the highly-varying positions and orientations of fetuses. In this work, we exploit an object detection framework to detect landmarks in 3D fetal facial US volumes. By regressing multiple parameters of the landmark-centered bounding box (B-box) with a strict criteria, the proposed model is able to pinpoint the exact location of the targeted landmarks. Specifically, the model uses a 3D region proposal network (RPN) to generate 3D candidate regions, followed by several 3D classification branches to select the best candidate. It also adopts an IoU-balance loss to improve communications between branches that benefits the learning process. Furthermore, it leverages a distance-based graph prior to regularize the training and helps to reduce false positive predictions. The performance of the proposed framework is evaluated on a 3D US dataset to detect five key fetal facial landmarks. Results showed the proposed method outperforms some of the state-of-the-art methods in efficacy and efficiency.