Single-cell RNA sequencing (scRNA-seq) provides high-throughput information about the genome-wide gene expression levels at the single-cell resolution, bringing a precise understanding on the transcriptome of individual cells. Unfortunately, the rapidly growing scRNA-seq data and the prevalence of dropout events pose substantial challenges for clustering and cell type annotation. Here, we propose a deep learning method, scHSC, that employs hard sample mining through contrastive learning for clustering scRNA-seq data. Focusing on hard samples, this approach simultaneously integrates gene expression and topological structure information between cells to improve clustering accuracy. By adjusting the weights of hard positive and hard negative samples during the iterative training process, scHSC employs an adaptive weighting strategy to integrate contrastive learning with a ZINB model for single-cell clustering tasks. Extensive experiments on 18 single-cell RNA-seq real datasets demonstrate that scHSC exhibits significant superiority in clustering performance compared to existing deep learning-based clustering methods. scHSC is implemented in Python based on the PyTorch framework. The source code and datasets are available via https://github.com/fangs25/scHSC.

Simulation speed is crucial for virtual reality simulators that simulate real-time cutting of deformable objects with haptic feedback, such as surgical simulators. This type of simulator combines visual feedback and haptic feedback, and therefore can be considered as a type of Multimedia Applications. To increase simulation speed, improvements are made in this paper to a previous deformable cutting method which divides a deformable object’s surface mesh into an interface mesh (including exterior surface mesh and interior surface mesh between different materials) constructed on a fine level linked voxel grid and a cut surface mesh constructed on a coarse level linked voxel grid. Our method changes the fine level linked voxel grid from a uniform grid to an octree. The algorithms for constructing and incrementally updating the object surface mesh and the collision proxy (an approximation of the object surface mesh used for collision processing) are changed accordingly. A new algorithm is proposed to resolve inconsistencies between partially cut and fully cut parts using visibility tests. Simulation tests show that our proposed method can moderately increase simulation speed during cutting and reduce CPU memory usage with almost imperceptible reductions in rendering qualities.

Single-channel EEG based sleep staging is of interest to researchers due to its broad application prospect in daily sleep monitoring recently. We proposed using contextual scalograms as input and developed a convolutional neural network with attention modules named Co-ScaleNet for sleep staging. The contextual scalograms were obtained by combining the same color channels of three original RGB scalograms from consecutive epochs, and a simple and efficient data augmentation was designed according to their various forms. The Co-ScaleNet consists of two main parts. Firstly, three parallel convolutional branches with attention modules correspondingly extract and fuse features from contextual scalograms at the top layers. The remaining part is a stack of lightweight blocks. We achieved an overall accuracy of 87.0% for healthy individuals, 84.7% for depressed patients. And we obtained comparable performance on the public Sleep-EDFx (82.8%), ISRUC (84.6%) and SHHS datasets (87.7%), including a high recall of N1. The contextual scalograms of R channel as input achieved the best performance, which conform to the features of interest in visual scoring. The attention modules improved the recall of N1 and N3. Overall, the contextual scalograms provided a novel scheme for both contextual information extraction and data augmentation. Our study successfully expanded its application to depression datasets, as well as patients with sleep apnea, demonstrating its wide applicability.

Developments of single-cell RNA sequencing (scRNA-seq) technologies have enabled biological discoveries at the single-cell resolution with high throughput. However, large scRNA-seq datasets always suffer from massive technical noises, including batch effects and dropouts, and the dropout is often shown to be batch-dependent. Most existing methods only address one of the problems, and we show that the popularly used methods failed in trading off batch effect correction and dropout imputation. Here, inspired by the idea of causal inference, we propose a novel propensity score matching method for scRNA-seq data (scPSM) by borrowing information and taking the weighted average from similar cells in the deep sequenced batch, which simultaneously removes the batch effect, imputes dropout and denoises data in the entire gene expression space. The proposed method is testified on two simulation datasets and a variety of real scRNA-seq datasets, and the results show that scPSM is superior to other state-of-the-art methods. First, scPSM improves clustering accuracy and mixes cells of the same type, suggesting its ability to keep cell type separation while correcting for batch. Besides, using the scPSM-integrated data as input yields results free of batch effects or dropouts in the differential expression analysis. Moreover, scPSM not only achieves ideal denoising but also preserves real biological structure for downstream gene-based analyses. Furthermore, scPSM is robust to hyperparameters and small datasets with a few cells but enormous genes. Comprehensive evaluations demonstrate that scPSM jointly provides desirable batch effect correction, imputation and denoising for recovering the biologically meaningful expression in scRNA-seq data.

Abstract A software framework taking advantage of parallel processing capabilities of CPUs and GPUs is designed for the real‐time interactive cutting simulation of deformable objects. Deformable objects are modelled as voxels connected by links. The voxels are embedded in an octree mesh used for deformation. Cutting is performed by disconnecting links swept by the cutting tool and then adaptively refining octree elements near the cutting tool trajectory. A surface mesh used for visual display is reconstructed from disconnected links using the dual contour method. Spatial hashing of the octree mesh and topology‐aware interpolation of distance field are used for collision. Our framework uses a novel GPU implementation for inter‐object collision and object self collision, while tool‐object collision, cutting and deformation are assigned to CPU, using multiple threads whenever possible. A novel method that splits cutting operations into four independent tasks running in parallel is designed. Our framework also performs data transfers between CPU and GPU simultaneously with other tasks to reduce their impact on performances. Simulation tests show that when compared to three‐threaded CPU implementations, our GPU accelerated collision is 53–160% faster; and the overall simulation frame rate is 47–98% faster.

Rare category detection aims to find interesting and statistically significant anomalies and incorporates ideas from active learning and semisupervised learning. The challenge of rare category detection is to find the rare classes of the anomalies in a data set where the data distribution is skewed. Most existing rare category detection methods suppose that the user knows the specific number of all classes in advance, which cannot be satisfied in most real scenarios. In this paper, we propose a new rare category detection framework composed of active learning and semisupervised hierarchical density-based clustering. The advantage of our method is that it is prior free and can benefit the rare category detecting process with the labeled data. In addition, the proposed framework can handle tasks with nonlinear mappings, which increases the ability to find rare classes when the class boundary is sophisticated. Compared to existing methods, better results are achieved by our method on both real and synthetic data sets in the experiment.

3D dynamic surface tracking is an important research problem and plays a vital role in many computer vision and medical imaging applications. However, it is still challenging to efficiently register surface sequences which has large deformations and strong noise. In this paper, we propose a novel automatic method for non-rigid 3D dynamic surface tracking with surface Ricci flow and Teichmüller map methods. According to quasi-conformal Teichmüller theory, the Techmüller map minimizes the maximal dilation so that our method is able to automatically register surfaces with large deformations. Besides, the adoption of Delaunay triangulation and quadrilateral meshes makes our method applicable to low quality meshes. In our work, the 3D dynamic surfaces are acquired by a high speed 3D scanner. We first identified sparse surface features using machine learning methods in the texture space. Then we assign landmark features with different curvature settings and the Riemannian metric of the surface is computed by the dynamic Ricci flow method, such that all the curvatures are concentrated on the feature points and the surface is flat everywhere else. The registration among frames is computed by the Teichmüller mappings, which aligns the feature points with least angle distortions. We apply our new method to multiple sequences of 3D facial surfaces with large expression deformations and compare them with two other state-of-the-art tracking methods. The effectiveness of our method is demonstrated by the clearly improved accuracy and efficiency.

We study scalable routing for a sensor network deployed in complicated 3D settings such as underground tunnels in gas system or water system. The nodes are in general 3D space but they are very sparsely located and the network has complex topology. We propose a routing scheme by first embdding the network on a surface with possibly non-zero genus. Then we compute a canonical hyperbolic metric of the embedded surface, and use geodesics to decompose the network into canonical components called pairs of `pants' whose topology is simpler (with genus zero). The adjacency of the pants components is extracted as a high level routing map and stored at every node. With the hyperbolic metric one can use greedy routing to navigate within and across pants. Altogether this leads to a two-level routing scheme by first finding a sequence of pants and then realizing the route with greedy steps. We show by simulation that the number of pants is closely related to the true `genus' of the network and that the routing scheme is efficient and scalable.

In this paper we address the problem of scalable and load balanced routing for wireless sensor networks. Motivated by the analog of the continuous setting that geodesic routing on a sphere gives perfect load balancing, we embed sensor nodes on a convex polyhedron in 3D and use greedy routing to deliver messages between any pair of nodes with guaranteed success. This embedding is known to exist by the Koebe-Andreev-Thurston Theorem for any 3-connected planar graphs. In our paper we use discrete Ricci flow to develop a distributed algorithm to compute this embedding. Further, such an embedding is not unique and differs from one another by a Möbius transformation. We employ an optimization routine to look for the Möbius transformation such that the nodes are spread on the polyhedron as uniformly as possible. We evaluated the load balancing property of this greedy routing scheme and showed favorable comparison with previous schemes.