Point Cloud Quality Assessment using 3D Saliency Maps

Point cloud quality assessment (PCQA) has become an appealing research field in recent days. Considering the importance of saliency detection in quality assessment, we propose an effective full-reference PCQA metric which makes the first attempt to utilize the saliency information to facilitate quality prediction, called point cloud quality assessment using 3D saliency maps (PQSM). Specifically, we first propose a projection-based point cloud saliency map generation method, in which depth information is introduced to better reflect the geometric characteristics of point clouds. Then, we construct point cloud local neighborhoods to derive three structural descriptors to indicate the geometry, color and saliency discrepancies. Finally, a saliency-based pooling strategy is proposed to generate the final quality score. Extensive experiments are performed on four independent PCQA databases. The results demonstrate that the proposed PQSM shows competitive performances compared to multiple state-of-the-art PCQA metrics

Clustering System and Clustering Support Vector Machine for Local Protein Structure Prediction

Protein tertiary structure plays a very important role in determining its possible functional sites and chemical interactions with other related proteins. Experimental methods to determine protein structure are time consuming and expensive. As a result, the gap between protein sequence and its structure has widened substantially due to the high throughput sequencing techniques. Problems of experimental methods motivate us to develop the computational algorithms for protein structure prediction. In this work, the clustering system is used to predict local protein structure. At first, recurring sequence clusters are explored with an improved K-means clustering algorithm. Carefully constructed sequence clusters are used to predict local protein structure. After obtaining the sequence clusters and motifs, we study how sequence variation for sequence clusters may influence its structural similarity. Analysis of the relationship between sequence variation and structural similarity for sequence clusters shows that sequence clusters with tight sequence variation have high structural similarity and sequence clusters with wide sequence variation have poor structural similarity. Based on above knowledge, the established clustering system is used to predict the tertiary structure for local sequence segments. Test results indicate that highest quality clusters can give highly reliable prediction results and high quality clusters can give reliable prediction results. In order to improve the performance of the clustering system for local protein structure prediction, a novel computational model called Clustering Support Vector Machines (CSVMs) is proposed. In our previous work, the sequence-to-structure relationship with the K-means algorithm has been explored by the conventional K-means algorithm. The K-means clustering algorithm may not capture nonlinear sequence-to-structure relationship effectively. As a result, we consider using Support Vector Machine (SVM) to capture the nonlinear sequence-to-structure relationship. However, SVM is not favorable for huge datasets including millions of samples. Therefore, we propose a novel computational model called CSVMs. Taking advantage of both the theory of granular computing and advanced statistical learning methodology, CSVMs are built specifically for each information granule partitioned intelligently by the clustering algorithm. Compared with the clustering system introduced previously, our experimental results show that accuracy for local structure prediction has been improved noticeably when CSVMs are applied

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. Multicomponent persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for chemical and biological problems. Extensive numerical experiments involving more than 4,000 protein-ligand complexes from the PDBBind database and near 100,000 ligands and decoys in the DUD database are performed to test respectively the scoring power and the virtual screening power of the proposed topological approaches. It is demonstrated that the present approaches outperform the modern machine learning based methods in protein-ligand binding affinity predictions and ligand-decoy discrimination

A Survey on Ear Biometrics

Recognizing people by their ear has recently received significant attention in the literature. Several reasons account for this trend: first, ear recognition does not suffer from some problems associated with other non contact biometrics, such as face recognition; second, it is the most promising candidate for combination with the face in the context of multi-pose face recognition; and third, the ear can be used for human recognition in surveillance videos where the face may be occluded completely or in part. Further, the ear appears to degrade little with age. Even though, current ear detection and recognition systems have reached a certain level of maturity, their success is limited to controlled indoor conditions. In addition to variation in illumination, other open research problems include hair occlusion; earprint forensics; ear symmetry; ear classification; and ear individuality. This paper provides a detailed survey of research conducted in ear detection and recognition. It provides an up-to-date review of the existing literature revealing the current state-of-art for not only those who are working in this area but also for those who might exploit this new approach. Furthermore, it offers insights into some unsolved ear recognition problems as well as ear databases available for researchers

3D-Spatiotemporal Forecasting the Expansion of Supernova Shells Using Deep Learning toward High-Resolution Galaxy Simulations

Supernova (SN) plays an important role in galaxy formation and evolution. In high-resolution galaxy simulations using massively parallel computing, short integration timesteps for SNe are serious bottlenecks. This is an urgent issue that needs to be resolved for future higher-resolution galaxy simulations. One possible solution would be to use the Hamiltonian splitting method, in which regions requiring short timesteps are integrated separately from the entire system. To apply this method to the particles affected by SNe in a smoothed-particle hydrodynamics simulation, we need to detect the shape of the shell on and within which such SN-affected particles reside during the subsequent global step in advance. In this paper, we develop a deep learning model, 3D-MIM, to predict a shell expansion after a SN explosion. Trained on turbulent cloud simulations with particle mass $m_{\rm gas}=1$M$_\odot$, the model accurately reproduces the anisotropic shell shape, where densities decrease by over 10 per cent by the explosion. We also demonstrate that the model properly predicts the shell radius in the uniform medium beyond the training dataset of inhomogeneous turbulent clouds. We conclude that our model enables the forecast of the shell and its interior where SN-affected particles will be present.Comment: 14 pages, 14 figures, 3 tables, accepted for MNRA

Swin transformer for fast MRI

Magnetic resonance imaging (MRI) is an important non-invasive clinical tool that can produce high-resolution and reproducible images. However, a long scanning time is required for high-quality MR images, which leads to exhaustion and discomfort of patients, inducing more artefacts due to voluntary movements of the patients and involuntary physiological movements. To accelerate the scanning process, methods by k-space undersampling and deep learning based reconstruction have been popularised. This work introduced SwinMR, a novel Swin transformer based method for fast MRI reconstruction. The whole network consisted of an input module (IM), a feature extraction module (FEM) and an output module (OM). The IM and OM were 2D convolutional layers and the FEM was composed of a cascaded of residual Swin transformer blocks (RSTBs) and 2D convolutional layers. The RSTB consisted of a series of Swin transformer layers (STLs). The shifted windows multi-head self-attention (W-MSA/SW-MSA) of STL was performed in shifted windows rather than the multi-head self-attention (MSA) of the original transformer in the whole image space. A novel multi-channel loss was proposed by using the sensitivity maps, which was proved to reserve more textures and details. We performed a series of comparative studies and ablation studies in the Calgary-Campinas public brain MR dataset and conducted a downstream segmentation experiment in the Multi-modal Brain Tumour Segmentation Challenge 2017 dataset. The results demonstrate our SwinMR achieved high-quality reconstruction compared with other benchmark methods, and it shows great robustness with different undersampling masks, under noise interruption and on different datasets. The code is publicly available at https://github.com/ayanglab/SwinMR.This work was supported in part by the UK Research and Inno- vation Future Leaders Fellowship [MR/V023799/1], in part by the Medical Research Council [MC/PC/21013], in part by the European Research Council Innovative Medicines Initiative [DRAGON, H2020-JTI-IMI2 101005122], in part by the AI for Health Imaging Award [CHAIMELEON, H2020-SC1-FA-DTS-2019-1 952172], in part by the British Heart Foundation [Project Number: TG/18/5/34111, PG/16/78/32402], in part by the NVIDIA Academic Hardware Grant Program, in part by the Project of Shenzhen International Cooper- ation Foundation [GJHZ20180926165402083], in part by the Bas- que Government through the ELKARTEK funding program [KK- 2020/00049], and in part by the consolidated research group MATHMODE [IT1294-19