Determining sequencing depth in a single-cell RNA-seq experiment

An underlying question for virtually all single-cell RNA sequencing experiments is how to allocate the limited sequencing budget: deep sequencing of a few cells or shallow sequencing of many cells? Here we present a mathematical framework which reveals that, for estimating many important gene properties, the optimal allocation is to sequence at a depth of around one read per cell per gene. Interestingly, the corresponding optimal estimator is not the widely-used plug-in estimator, but one developed via empirical Bayes

Multi-hierarchical Convolutional Network for Efficient Remote Photoplethysmograph Signal and Heart Rate Estimation from Face Video Clips

Heart beat rhythm and heart rate (HR) are important physiological parameters of the human body. This study presents an efficient multi-hierarchical spatio-temporal convolutional network that can quickly estimate remote physiological (rPPG) signal and HR from face video clips. First, the facial color distribution characteristics are extracted using a low-level face feature Generation (LFFG) module. Then, the three-dimensional (3D) spatio-temporal stack convolution module (STSC) and multi-hierarchical feature fusion module (MHFF) are used to strengthen the spatio-temporal correlation of multi-channel features. In the MHFF, sparse optical flow is used to capture the tiny motion information of faces between frames and generate a self-adaptive region of interest (ROI) skin mask. Finally, the signal prediction module (SP) is used to extract the estimated rPPG signal. The experimental results on the three datasets show that the proposed network outperforms the state-of-the-art methods.Comment: 33 pages,9 figure

Source-free Active Domain Adaptation for Diabetic Retinopathy Grading Based on Ultra-wide-field Fundus Image

Domain adaptation (DA) has been widely applied in the diabetic retinopathy (DR) grading of unannotated ultra-wide-field (UWF) fundus images, which can transfer annotated knowledge from labeled color fundus images. However, suffering from huge domain gaps and complex real-world scenarios, the DR grading performance of most mainstream DA is far from that of clinical diagnosis. To tackle this, we propose a novel source-free active domain adaptation (SFADA) in this paper. Specifically, we focus on DR grading problem itself and propose to generate features of color fundus images with continuously evolving relationships of DRs, actively select a few valuable UWF fundus images for labeling with local representation matching, and adapt model on UWF fundus images with DR lesion prototypes. Notably, the SFADA also takes data privacy and computational efficiency into consideration. Extensive experimental results demonstrate that our proposed SFADA achieves state-of-the-art DR grading performance, increasing accuracy by 20.9% and quadratic weighted kappa by 18.63% compared with baseline and reaching 85.36% and 92.38% respectively. These investigations show that the potential of our approach for real clinical practice is promising

Spiking Neural Network for Ultra-low-latency and High-accurate Object Detection

Spiking Neural Networks (SNNs) have garnered widespread interest for their energy efficiency and brain-inspired event-driven properties. While recent methods like Spiking-YOLO have expanded the SNNs to more challenging object detection tasks, they often suffer from high latency and low detection accuracy, making them difficult to deploy on latency sensitive mobile platforms. Furthermore, the conversion method from Artificial Neural Networks (ANNs) to SNNs is hard to maintain the complete structure of the ANNs, resulting in poor feature representation and high conversion errors. To address these challenges, we propose two methods: timesteps compression and spike-time-dependent integrated (STDI) coding. The former reduces the timesteps required in ANN-SNN conversion by compressing information, while the latter sets a time-varying threshold to expand the information holding capacity. We also present a SNN-based ultra-low latency and high accurate object detection model (SUHD) that achieves state-of-the-art performance on nontrivial datasets like PASCAL VOC and MS COCO, with about remarkable 750x fewer timesteps and 30% mean average precision (mAP) improvement, compared to the Spiking-YOLO on MS COCO datasets. To the best of our knowledge, SUHD is the deepest spike-based object detection model to date that achieves ultra low timesteps to complete the lossless conversion.Comment: 14 pages, 10 figure

BanditPAM++: Faster kk-medoids Clustering

Clustering is a fundamental task in data science with wide-ranging applications. In $k$-medoids clustering, cluster centers must be actual datapoints and arbitrary distance metrics may be used; these features allow for greater interpretability of the cluster centers and the clustering of exotic objects in $k$-medoids clustering, respectively. $k$-medoids clustering has recently grown in popularity due to the discovery of more efficient $k$-medoids algorithms. In particular, recent research has proposed BanditPAM, a randomized $k$-medoids algorithm with state-of-the-art complexity and clustering accuracy. In this paper, we present BanditPAM++, which accelerates BanditPAM via two algorithmic improvements, and is $O(k)$ faster than BanditPAM in complexity and substantially faster than BanditPAM in wall-clock runtime. First, we demonstrate that BanditPAM has a special structure that allows the reuse of clustering information $\textit{within}$ each iteration. Second, we demonstrate that BanditPAM has additional structure that permits the reuse of information $\textit{across}$ different iterations. These observations inspire our proposed algorithm, BanditPAM++, which returns the same clustering solutions as BanditPAM but often several times faster. For example, on the CIFAR10 dataset, BanditPAM++ returns the same results as BanditPAM but runs over 10$\times$ faster. Finally, we provide a high-performance C++ implementation of BanditPAM++, callable from Python and R, that may be of interest to practitioners at https://github.com/motiwari/BanditPAM. Auxiliary code to reproduce all of our experiments via a one-line script is available at https://github.com/ThrunGroup/BanditPAM_plusplus_experiments.Comment: NeurIPS 202

Polymicrobial periodontal disease triggers a wide radius of effect and unique virome.

Periodontal disease is a microbially-mediated inflammatory disease of tooth-supporting tissues that leads to bone and tissue loss around teeth. Although bacterially-mediated mechanisms of alveolar bone destruction have been widely studied, the effects of a polymicrobial infection on the periodontal ligament and microbiome/virome have not been well explored. Therefore, the current investigation introduced a new mouse model of periodontal disease to examine the effects of a polymicrobial infection on periodontal ligament (PDL) properties, changes in bone loss, the host immune response, and the microbiome/virome using shotgun sequencing. Periodontal pathogens, namely Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Fusobacterium nucleatum were used as the polymicrobial oral inoculum in BALB/cByJ mice. The polymicrobial infection triggered significant alveolar bone loss, a heightened antibody response, an elevated cytokine immune response, a significant shift in viral diversity and virome composition, and a widening of the PDL space; the latter two findings have not been previously reported in periodontal disease models. Changes in the PDL space were present at sites far away from the site of insult, indicating that the polymicrobial radius of effect extends beyond the bone loss areas and site of initial infection and wider than previously appreciated. Associations were found between bone loss, specific viral and bacterial species, immune genes, and PDL space changes. These findings may have significant implications for the pathogenesis of periodontal disease and biomechanical properties of the periodontium. This new polymicrobial mouse model of periodontal disease in a common mouse strain is useful for evaluating the features of periodontal disease