User engagement is greatly enhanced by fully immersive multi-modal experiences that combine visual and auditory stimuli. Consequently, the next frontier in VR/AR technologies lies in immersive volumetric videos with complete scene capture, large 6-DoF interaction space, multimodal feedback, and high resolution & frame-rate contents. To stimulate the reconstruction of immersive volumetric videos, we introduce ImViD, a multi-view, multi-modal dataset featuring complete space-oriented data capture and various indoor/outdoor scenarios. Our capture rig supports multi-view video-audio capture while on the move, a capability absent in existing datasets, significantly enhancing the completeness, flexibility, and efficiency of data capture.The captured multi-view videos (with synchronized audios) are in 5K resolution at 60FPS, lasting from 1-5 minutes, and include rich foreground-background elements, and complex dynamics. We benchmark existing methods using our dataset and establish a base pipeline for constructing immersive volumetric videos from multi-view audiovisual inputs for 6-DoF multi-modal immersive VR experiences. The benchmark and the reconstruction and interaction results demonstrate the effectiveness of our dataset and baseline method, which we believe will stimulate future research on immersive volumetric video production. Project Page: https://yzxqh.github.io/ImViD/

Lane detection is a critical and challenging task in autonomous driving, particularly in real-world scenarios where traffic lanes can be slender, lengthy, and often obscured by other vehicles, complicating detection efforts. Existing anchor-based methods typically rely on prior lane anchors to extract features and subsequently refine the location and shape of lanes. While these methods achieve high performance, manually setting prior anchors is cumbersome, and ensuring sufficient coverage across diverse datasets often requires a large amount of dense anchors. Furthermore, the use ofNon-Maximum Suppression(NMS) to eliminate redundant predictions complicates real-world deployment and may under-perform in complex scenarios. In this paper, we proposePolar R-CNN, an end-to-end anchor-based method for lane detection. By incorporating both local and global polar coordinate systems, Polar R-CNN facilitates flexible anchor proposals and significantly reduces the number of anchors required without compromising performance. Additionally, we introduce a triplet head with heuristic structure that supports NMS-free paradigm, enhancing deployment efficiency and performance in scenarios with dense lanes. Our method achieves competitive results on five popular lane detection benchmarks—Tusimple,CULane,LLAMAS,CurveLanes, andDL-Rail—while maintaining a lightweight design and straightforward structure. Our source code is available athttps://github.com/ShqWW/PolarRCNN

Protein-to-protein interaction (PPI) prediction aims to predict whether two given proteins interact or not. Compared with traditional experimental methods of high cost and low efficiency, the current deep learning based approach makes it possible to discover massive potential PPIs from large-scale databases. However, deep PPI prediction models perform poorly on unseen species, as their proteins are not in the training set. Targetting on this issue, the paper first proposes PPITrans, a Transformer based PPI prediction model that exploits a language model pre-trained on proteins to conduct binary PPI prediction. To validate the effectiveness on unseen species, PPITrans is trained with Human PPIs and tested on PPIs of other species. Experimental results show that PPITrans significantly outperforms the previous state-of-the-art on various metrics, especially on PPIs of unseen species. For example, the AUPR improves 0.339 absolutely on Fly PPIs. Aiming to explore the knowledge learned by PPITrans from PPI data, this paper also designs a series of probes belonging to three categories. Their results reveal several interesting findings, like that although PPITrans cannot capture the spatial structure of proteins, it can obtain knowledge of PPI type and binding affinity, learning more than binary PPI.

Motion forecasting plays a crucial role in autonomous driving, with the aim of predicting the future reasonable motions of traffic agents. Most existing methods mainly model the historical interactions between agents and the environment, and predict multi-modal trajectories in a feedforward process, ignoring potential trajectory changes caused by future interactions between agents. In this paper, we propose a novel Future Feedback Interaction Network (FFINet) to aggregate the current, observations and potential future interaction features for trajectory prediction. Firstly, we employ different spatial-temporal encoders to embed the decomposed position vectors and the current position of each scene, providing rich features for the subsequent cross-temporal aggregation. Secondly, the relative interaction and cross-temporal aggregation strategies are sequentially adopted to integrate features in the current fusion module, observation interaction module, future feedback module and global fusion module, in which the future feedback module can enable the understanding of pre-action by feeding the influence of preview information to feedforward prediction. Thirdly, the comprehensive interaction features are further fed into final predictor to generate the joint predicted trajectories of multiple agents. Extensive experimental results show that our FFINet achieves the state-of-the-art performance on Argoverse 1 and Argoverse 2 motion forecasting benchmarks.

Lane detection is usually regarded as a semantic segmentation task, however, segmentation-based methods require expensive computational costs, and it is difficult to segment the lanes with heavy noises. Therefore, this paper proposes a lane detection method based on multi-scale key point regression, which directly uses the position of the key points of the lane instead of predicting the pixel-wise outputs. First, we design a lightweight backbone to extract a series of feature maps with a forward view image as input, and then apply a multi-scale fusion network on these feature maps to obtain the location and confidence information of the key points of the lane. Finally, a clustering and curve fitting mechanism with quadratic inverse proportion are used to obtain the final lane detection. Our proposed model can recognize dashed lane markings and handle many extreme scenarios where lanes are completely occluded or heavily noised. In addition, our model uses a relatively explicit framework, which contributes to ensuring real-time performance at 30Hz. In order to prove our method's performance, we conduct experiments on the TuSimple benchmark and RVD dataset, and results demonstrate that our method achieves competitive results compared with other methods.

Edge cloud computing is a new paradigm in which the computation and storage services of remote cloud data centers are moved to Edge Cloud Nodes (ECNs) in network edges. Compared to traditional cloud data centers, ECNs are geographically close to mobile users so the communication latency is significantly reduced. In this paper, we study the problem of allocating Virtual Machine (VM) resources in geo-distributed ECNs to mobile users by using the auction theory. First, we treat mobile users and ECNs as the buyers and sellers of the VM resource auction, respectively. Then, we model the VM resource allocation problem as an$n$-to-one weighted bipartite graph matching problem with 0-1 knapsack constraints. Since this problem is NP-hard, we design a greedy approximation algorithm to determine the winners of the auction, based on which we propose a truthful Auction-based VM resource Allocation (AVA) mechanism to solve the problem. Moreover, we prove that the AVA mechanism not only achieves an approximately optimal solution for winner selection, but also has the properties of truthfulness, individual rationality, and computational efficiency. Finally, we conduct extensive simulations on real traces to verify the significant performances of the proposed AVA mechanism.

MOTIVATION: Numerous public microarray datasets are valuable resources for the scientific communities. Several online tools have made great steps to use these data by querying related datasets with users' own gene signatures or expression profiles. However, dataset annotation and result exhibition still need to be improved. RESULTS: ExpTreeDB is a database that allows for queries on human and mouse microarray experiments from Gene Expression Omnibus with gene signatures or profiles. Compared with similar applications, ExpTreeDB pays more attention to dataset annotations and result visualization. We introduced a multiple-level annotation system to depict and organize original experiments. For example, a tamoxifen-treated cell line experiment is hierarchically annotated as 'agent→drug→estrogen receptor antagonist→tamoxifen'. Consequently, retrieved results are exhibited by an interactive tree-structured graphics, which provide an overview for related experiments and might enlighten users on key items of interest. AVAILABILITY AND IMPLEMENTATION: The database is freely available at http://biotech.bmi.ac.cn/ExpTreeDB. Web site is implemented in Perl, PHP, R, MySQL and Apache.

MOTIVATION: Human miRNAs have recently been found to have important roles in viral replication. Understanding the patterns and details of human miRNA interactions during virus-host interactions may help uncover novel antiviral therapies. Based on the abundance of knowledge available regarding protein-protein interactions (PPI), virus-host protein interactions, experimentally validated human miRNA-target pairs and transcriptional regulation of human miRNAs, it is possible to explore the complex regulatory network that exists between viral proteins and human miRNAs at the system level. RESULTS: By integrating current data regarding the virus-human interactome and human miRNA-target pairs, the overlap between targets of viral proteins and human miRNAs was identified and found to represent topologically important proteins (e.g. hubs or bottlenecks) at the global center of the human PPI network. Viral proteins and human miRNAs were also found to significantly target human PPI pairs. Furthermore, an overlap analysis of virus targets and transcription factors (TFs) of human miRNAs revealed that viral proteins preferentially target human miRNA TFs, representing a new pattern of virus-host interactions. Potential feedback loops formed by viruses, human miRNAs and miRNA TFs were also identified, and these may be exploited by viruses resulting in greater virulence and more effective replication strategies.

UNLABELLED: The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets. AVAILABILITY: PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. Four information content (IC)- and a graph-based methods are implemented in the GOSemSim package, multiple species including human, rat, mouse, fly and yeast are also supported. The functions provided by the GOSemSim offer flexibility for applications, and can be easily integrated into high-throughput analysis pipelines. AVAILABILITY: GOSemSim is released under the GNU General Public License within Bioconductor project, and freely available at http://bioconductor.org/packages/2.6/bioc/html/GOSemSim.html.

BACKGROUND: Robustness, maintaining a constant phenotype despite perturbations, is a fundamental property of biological systems that is incorporated at various levels of biological complexity. Although robustness has been frequently observed in nature, its evolutionary origin remains unknown. Current hypotheses suggest that robustness originated as a direct consequence of natural selection, as an intrinsic property of adaptations, or as a congruent correlate of environment robustness. To elucidate the evolutionary origins of robustness, a convenient computational package is strongly needed. RESULTS: In this study, we developed the open-source integrated system EvoRSR (Evolution of RNA Structural Robustness) to explore the evolution of robustness based on biologically important landscapes induced by RNA folding. EvoRSR is object-oriented, modular, and freely available at http://biotech.bmi.ac.cn/EvoRSR under the GNU/GPL license. We present an overview of EvoRSR package and illustrate its features with the miRNA gene cel-mir-357. CONCLUSION: EvoRSR is a novel and flexible package for exploring the evolution of robustness. Accordingly, EvoRSR can be used for future studies to investigate the evolution and origin of robustness and to address other common questions about robustness. While the current EvoRSR environment is a versatile analysis framework, future versions can include features to enhance evolutionary studies of robustness.

BACKGROUND: Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent years, as such indices can be used to compare, identify and classify RNAs. Although the topological indices presented before characterize the main topological features of RNA secondary structures, information on RNA structural details is ignored to some degree. Therefore, it is necessity to identify topological features with low degeneracy based on complete and fine-grained RNA graphical representations. RESULTS: In this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertex-weighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded completely in the ECGs. The relationship among the three typical topological index families defined by their ECGs and RNA secondary structures was investigated from a dataset of 6,305 ncRNAs. The applicability of topological indices is illustrated by three application case studies. Based on the applied small dataset, we find that the topological indices can distinguish true pre-miRNAs from pseudo pre-miRNAs with about 96% accuracy, and can cluster known types of ncRNAs with about 98% accuracy, respectively. CONCLUSION: The results indicate that the topological indices can characterize the details of RNA structures and may have a potential role in identifying and classifying ncRNAs. Moreover, these indices may lead to a new approach for discovering novel ncRNAs. However, further research is needed to fully resolve the challenging problem of predicting and classifying noncoding RNAs.

BACKGROUND: Local structures of target mRNAs play a significant role in determining the efficacies of antisense oligonucleotides (ODNs), but some structure-based target site selection methods are limited by uncertainties in RNA secondary structure prediction. If all the predicted structures of a given mRNA within a certain energy limit could be used simultaneously, target site selection would obviously be improved in both reliability and efficiency. In this study, some key problems in ODN target selection on the basis of multiple predicted target mRNA structures are systematically discussed. RESULTS: Two methods were considered for merging topologically different RNA structures into integrated representations. Several parameters were derived to characterize local target site structures. Statistical analysis on a dataset with 448 ODNs against 28 different mRNAs revealed 9 features quantitatively associated with efficacy. Features of structural consistency seemed to be more highly correlated with efficacy than indices of the proportion of bases in single-stranded or double-stranded regions. The local structures of the target site 5' and 3' termini were also shown to be important in target selection. Neural network efficacy predictors using these features, defined on integrated structures as inputs, performed well in "minus-one-gene" cross-validation experiments. CONCLUSION: Topologically different target mRNA structures can be merged into integrated representations and then used in computer-aided ODN design. The results of this paper imply that some features characterizing multiple predicted target site structures can be used to predict ODN efficacy.

BACKGROUND: The diverse functions of ncRNAs critically depend on their structures. Mutations in ncRNAs disrupting the structures of functional sites are expected to be deleterious. RNA deleterious mutations have attracted wide attentions because some of them in cells result in serious disease, and some others in microbes influence their fitness. RESULTS: The RDMAS web server we describe here is an online tool for evaluating structural deleteriousness of single nucleotide mutation in RNA genes. Several structure comparison methods have been integrated; sub-optimal structures predicted can be optionally involved to mitigate the uncertainty of secondary structure prediction. With a user-friendly interface, the web application is easy to use. Intuitive illustrations are provided along with the original computational results to facilitate quick analysis. CONCLUSION: RDMAS can be used to explore the structure alterations which cause mutations pathogenic, and to predict deleterious mutations which may help to determine the functionally critical regions. RDMAS is freely accessed via http://biosrv1.bmi.ac.cn/rdmas.

UNLABELLED: TargetFinder is a PC/Windows program for interactive effective antisense oligonucleotide (AO) selection based on mRNA accessible site tagging (MAST) and secondary structures of target mRNA. To make MAST result intuitive, both the alignment result and tag frequency profile is illustrated. As theoretical reference, secondary structure and single strand probability profile of target mRNA is also represented. All of these sequences and profiles are displayed in aligned mode, which facilitates identification of the accessible sites in target mRNA. Graphical, user-friendly interface makes TargetFinder a useful tool in AO target site selection. AVAILABILITY: The software is freely available at http://www.bioit.org.cn/ao/targetfinder.htm CONTACT: [email protected].