A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes

Constructing of molecular structural models from Cryo-Electron Microscopy (Cryo-EM) density volumes is the critical last step of structure determination by Cryo-EM technologies. Methods have evolved from manual construction by structural biologists to perform 6D translation-rotation searching, which is extremely compute-intensive. In this paper, we propose a learning-based method and formulate this problem as a vision-inspired 3D detection and pose estimation task. We develop a deep learning framework for amino acid determination in a 3D Cryo-EM density volume. We also design a sequence-guided Monte Carlo Tree Search (MCTS) to thread over the candidate amino acids to form the molecular structure. This framework achieves 91% coverage on our newly proposed dataset and takes only a few minutes for a typical structure with a thousand amino acids. Our method is hundreds of times faster and several times more accurate than existing automated solutions without any human intervention.Comment: 8 pages, 5 figures, 4 table

Development of a Computer Vision-Based Three-Dimensional Reconstruction Method for Volume-Change Measurement of Unsaturated Soils during Triaxial Testing

Problems associated with unsaturated soils are ubiquitous in the U.S., where expansive and collapsible soils are some of the most widely distributed and costly geologic hazards. Solving these widespread geohazards requires a fundamental understanding of the constitutive behavior of unsaturated soils. In the past six decades, the suction-controlled triaxial test has been established as a standard approach to characterizing constitutive behavior for unsaturated soils. However, this type of test requires costly test equipment and time-consuming testing processes. To overcome these limitations, a photogrammetry-based method has been developed recently to measure the global and localized volume-changes of unsaturated soils during triaxial test. However, this method relies on software to detect coded targets, which often requires tedious manual correction of incorrectly coded target detection information. To address the limitation of the photogrammetry-based method, this study developed a photogrammetric computer vision-based approach for automatic target recognition and 3D reconstruction for volume-changes measurement of unsaturated soils in triaxial tests. Deep learning method was used to improve the accuracy and efficiency of coded target recognition. A photogrammetric computer vision method and ray tracing technique were then developed and validated to reconstruct the three-dimensional models of soil specimen

Learning single-image 3D reconstruction by generative modelling of shape, pose and shading

We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, most existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to existing approaches, while also supporting weaker supervision. Importantly, it can be trained purely from 2D images, without pose annotations, and with only a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to reason over lighting parameters and exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach in various settings, showing that: (i) it learns to disentangle shape from pose and lighting; (ii) using shading in the loss improves performance compared to just silhouettes; (iii) when using a standard single white light, our model outperforms state-of-the-art 2D-supervised methods, both with and without pose supervision, thanks to exploiting shading cues; (iv) performance improves further when using multiple coloured lights, even approaching that of state-of-the-art 3D-supervised methods; (v) shapes produced by our model capture smooth surfaces and fine details better than voxel-based approaches; and (vi) our approach supports concave classes such as bathtubs and sofas, which methods based on silhouettes cannot learn.Comment: Extension of arXiv:1807.09259, accepted to IJCV. Differentiable renderer available at https://github.com/pmh47/dir