Recent advancements in point cloud compression have primarily emphasized geometry compression while comparatively fewer efforts have been dedicated to attribute compression. This study introduces an end-to-end learned dynamic lossy attribute coding approach, utilizing an efficient high-dimensional convolution to capture extensive inter-point dependencies. This enables the efficient projection of attribute features into latent variables. Subsequently, we employ a context model that leverage previous latent space in conjunction with an auto-regressive context model for encoding the latent tensor into a bitstream. Evaluation of our method on widely utilized point cloud datasets from the MPEG and Microsoft demonstrates its superior performance compared to the core attribute compression module Region-Adaptive Hierarchical Transform method from MPEG Geometry Point Cloud Compression with $38.1 \%$ Bjontegaard Delta-rate saving in average while ensuring a low-complexity encoding/decoding.

In this paper, we provide an in-depth assessment on the Bjøntegaard Delta. We construct a large data set of video compression performance comparisons using a diverse set of metrics including PSNR, VMAF, bitrate, and processing energies. These metrics are evaluated for visual data types such as classic perspective video, 360° video, point clouds, and screen content. As compression technology, we consider multiple hybrid video codecs as well as state-of-the-art neural network based compression methods. Using additional supporting points in-between standard points defined by parameters such as the quantization parameter, we assess the interpolation error of the Bjøntegaard-Delta (BD) calculus and its impact on the final BD value. From the analysis, we find that the BD calculus is most accurate in the standard application of rate-distortion comparisons with mean errors below 0.5 percentage points. For other applications and special cases, e.g., VMAF quality, energy considerations, or inter-codec comparisons, the errors are higher (up to 5 percentage points), but can be halved by using a higher number of supporting points. We finally come up with recommendations on how to use the BD calculus such that the validity of the resulting BD-values is maximized. Main recommendations are as follows: First, relative curve differences should be plotted and analyzed. Second, the logarithmic domain should be used for saturating metrics such as SSIM and VMAF. Third, BD values below a certain threshold indicated by the subset error should not be used to draw recommendations. Fourth, using two supporting points is sufficient to obtain rough performance estimates.

In recent years, several point cloud geometry compression methods that utilize advanced deep learning techniques have been proposed, but there are limited works on attribute compression, especially lossless compression. In this work, we build an end-to-end multiscale point cloud attribute coding method (MNeT) that progressively projects the attributes onto multiscale latent spaces. The multiscale architecture provides an accurate context for the attribute probability modeling and thus minimizes the coding bitrate with a single network prediction. Besides, our method allows scalable coding that lower quality versions can be easily extracted from the losslessly compressed bitstream. We validate our method on a set of point clouds from MVUB and MPEG and show that our method outperforms recently proposed methods and on par with the latest G-PCC version 14. Besides, our coding time is substantially faster than G-PCC.

MOTIVATION: Molecular quantitative trait locus (QTL) mapping has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by genome-wide association studies. Recently, this success has been extended to circular RNA (circRNA), a potential group of RNAs that can serve as markers for the diagnosis, prognosis, or therapeutic targets of various human diseases. However, a well-developed computational pipeline for circRNA QTL (circQTL) discovery is still lacking. RESULTS: We introduce an integrative method for circQTL mapping and implement it as an automated pipeline based on Nextflow, named cscQTL. The proposed method has two main advantages. Firstly, cscQTL improves the specificity by systematically combining outputs of multiple circRNA calling algorithms to obtain highly confident circRNA annotations. Secondly, cscQTL improves the sensitivity by accurately quantifying circRNA expression with the help of pseudo references. Compared to the single method approach, cscQTL effectively identifies circQTLs with an increase of 20%-100% circQTLs detected and recovered all circQTLs that are highly supported by the single method approach. We apply cscQTL to a dataset of human T cells and discover genetic variants that control the expression of 55 circRNAs. By colocalization tests, we further identify circBACH2 and circYY1AP1 as potential candidates for immune disease regulation. AVAILABILITY AND IMPLEMENTATION: cscQTL is freely available at: https://github.com/datngu/cscQTL and https://doi.org/10.5281/zenodo.7851982.

In recent years, we have witnessed the presence of point cloud data in many aspects of our life, from immersive media, autonomous driving to healthcare, although at the cost of a tremendous amount of data. In this paper, we present an efficient lossless point cloud compression method that uses sparse tensor-based deep neural networks to learn point cloud geometry and color probability distributions. Our method represents a point cloud with both occupancy feature and three attribute features at different bit depths in a unified sparse representation. This allows us to efficiently exploit feature-wise and point-wise dependencies within point clouds using a sparse tensor-based neural network and thus build an accurate auto-regressive context model for an arithmetic coder. To the best of our knowledge, this is the first learning-based lossless point cloud geometry and attribute compression approach. Compared with the-state-of-the-art lossless point cloud compression method from Moving Picture Experts Group (MPEG), our method achieves 22.6% reduction in total bitrate on a diverse set of test point clouds while having 49.0% and 18.3% rate reduction on geometry and color attribute component, respectively.

Most point cloud compression methods operate in the voxel or octree domain which is not the original representation of point clouds. Those representations either remove the geometric information or require high computational power for processing. In this paper, we propose a context-based lossless point cloud geometry compression that directly processes the point representation. Operating on a point representation allows us to preserve geometry correlation between points and thus to obtain an accurate context model while significantly reduce the computational cost. Specifically, our method uses a sparse convolution neural network to estimate the voxel occupancy sequentially from the x, y, z input data. Experimental results show that our method outperforms the state-of-the-art geometry compression standard from MPEG with average rate savings of 52% on a diverse set of point clouds from four different datasets.

Despite the rapid development of sequencing technology, single-nucleotide polymorphism (SNP) arrays are still the most cost-effective genotyping solutions for large-scale genomic research and applications. Recent years have witnessed the rapid development of numerous genotyping platforms of different sizes and designs, but population-specific platforms are still lacking, especially for those in developing countries. SNP arrays designed for these countries should be cost-effective (small size), yet incorporate key information needed to associate genotypes with traits. A key design principle for most current platforms is to improve genome-wide imputation so that more SNPs not included in the array (imputed SNPs) can be predicted. However, current tag SNP selection methods mostly focus on imputation accuracy and coverage, but not the functional content of the array. It is those functional SNPs that are most likely associated with traits. Here, we propose LmTag, a novel method for tag SNP selection that not only improves imputation performance but also prioritizes highly functional SNP markers. We apply LmTag on a wide range of populations using both public and in-house whole-genome sequencing databases. Our results show that LmTag improved both functional marker prioritization and genome-wide imputation accuracy compared to existing methods. This novel approach could contribute to the next generation genotyping arrays that provide excellent imputation capability as well as facilitate array-based functional genetic studies. Such arrays are particularly suitable for under-represented populations in developing countries or non-model species, where little genomics data are available while investment in genome sequencing or high-density SNP arrays is limited. $\textrm{LmTag}$ is available at: https://github.com/datngu/LmTag.

This paper presents a learning-based, lossless compression method for static point cloud geometry, based on context-adaptive arithmetic coding. Unlike most existing methods working in the octree domain, our encoder operates in a hybrid mode, mixing octree and voxel-based coding. We adaptively partition the point cloud into multi-resolution voxel blocks according to the point cloud structure, and use octree to signal the partitioning. On the one hand, octree representation can eliminate the sparsity in the point cloud. On the other hand, in the voxel domain, convolutions can be naturally expressed, and geometric information (i.e., planes, surfaces, etc.) is explicitly processed by a neural network. Our context model benefits from these properties and learns a probability distribution of the voxels using a deep convolutional neural network with masked filters, called VoxelDNN. Experiments show that our method outperforms the state-of-the-art MPEG G-PCC standard with average rate savings of 28% on a diverse set of point clouds from the Microsoft Voxelized Upper Bodies (MVUB) and MPEG. The implementation is available at https://github.com/Weafre/VoxelDNN.

BACKGROUND: Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and autoimmune diseases. Current methods for detection of circRNA from RNA sequencing (RNA-seq) focus mostly on improving mapping quality of reads supporting the back-splicing junction (BSJ) of a circRNA to eliminate false positives (FPs). We show that mapping information alone often cannot predict if a BSJ-supporting read is derived from a true circRNA or not, thus increasing the rate of FP circRNAs. RESULTS: We have developed Circall, a novel circRNA detection method from RNA-seq. Circall controls the FPs using a robust multidimensional local false discovery rate method based on the length and expression of circRNAs. It is computationally highly efficient by using a quasi-mapping algorithm for fast and accurate RNA read alignments. We applied Circall on two simulated datasets and three experimental datasets of human cell-lines. The results show that Circall achieves high sensitivity and precision in the simulated data. In the experimental datasets it performs well against current leading methods. Circall is also substantially faster than the other methods, particularly for large datasets. CONCLUSIONS: With those better performances in the detection of circRNAs and in computational time, Circall facilitates the analyses of circRNAs in large numbers of samples. Circall is implemented in C++ and R, and available for use at https://www.meb.ki.se/sites/biostatwiki/circall and https://github.com/datngu/Circall.

This paper proposes a lossless point cloud (PC) geometry compression method that uses neural networks to estimate the probability distribution of voxel occupancy. First, to take into account the PC sparsity, our method adaptively partitions a point cloud into multiple voxel block sizes. This partitioning is signalled via an octree. Second, we employ a deep auto-regressive generative model to estimate the occupancy probability of each voxel given the previously encoded ones. We then employ the estimated probabilities to code efficiently a block using a context-based arithmetic coder. Our context has variable size and can expand beyond the current block to learn more accurate probabilities. We also consider using data augmentation techniques to increase the generalization capability of the learned probability models, in particular in the presence of noise and lower-density point clouds. Experimental evaluation, performed on a variety of point clouds from four different datasets and with diverse characteristics, demonstrates that our method reduces significantly (by up to 37%) the rate for lossless coding compared to the state-of-the-art MPEG codec.