Neural implicit representations have emerged as a promising solution for providing dense geometry in Simultaneous Localization and Mapping (SLAM). However, existing methods in this direction fall short in terms of global consistency and low latency. This paper presents NGEL-SLAM to tackle the above challenges. To ensure global consistency, our system leverages a traditional feature-based tracking module that incorporates loop closure. Additionally, we maintain a global consistent map by representing the scene using multiple neural implicit fields, enabling quick adjustment to the loop closure. Moreover, our system allows for fast convergence through the use of octree-based implicit representations. The combination of rapid response to loop closure and fast convergence makes our system a truly low-latency system that achieves global consistency. Our system enables rendering high-fidelity RGB-D images, along with extracting dense and complete surfaces. Experiments on both synthetic and real-world datasets suggest that our system achieves state-of-the-art tracking and mapping accuracy while maintaining low latency.

Ensuring robust tracking of controllers’ movement is critical for human-robot interaction in virtual reality (VR) scenarios. This paper proposes a robust tracking algorithm based on a novel wearable ring-shaped controller equipped with an inertial measurement unit (IMU) and a light-emitting diode (LED). This novel controller design allows users to free up their hands for more immersive experiences. To track the controller’s motion accurately and robustly, we resort to various forms of visual measurements, including 6 DoF and 5 DoF pose measurements from hand gesture detection, as well as 3 DoF position measurement and 2 DoF image measurement derived from the LED. We theoretically analyze the performances of these observation models and propose an optimal observation model combination scheme. Moreover, the necessity and rationale of online estimating system gravity are illustrated. The effectiveness of our tracking method is validated through extensive experiments.

Visual inertial odometry (VIO) is widely used in various kinds of mobile platforms to provide the ego-pose of the platforms. With the help of pre-built map information, the drift of the VIO can be constrained. However, constructing a globally consistent map is a tough job, especially for large scenes. In this paper, we propose a filter-based framework aiming to leverage multiple isolated maps to improve the performance of VIO such that building a globally consistent map can be avoided. In this framework, the relative transformations between the local VIO reference frame and the multiple map reference frames are regarded as 6 degrees of freedom (DoF) pose features to be online estimated. We call these relative transformations asaugmented variables. With theseaugmented variables, the map-based information can be tightly coupled into the VIO system to ease the drift of VIO. To fuse these maps consistently, we first theoretically analyze the observability properties of our proposed framework. Based on the analysis, the Schmidt extended Kalman filter (EKF) and the first-estimate Jacobian (FEJ) are employed to maintain the consistency of the system. Simulation and real-world experiments are conducted to demonstrate the effectiveness and consistency of our framework.Note to Practitioners—Visual inertial odometry (VIO) is widely applied to positioning mobile platforms including autonomous vehicles, robots, and virtual/augmented reality (VR/AR) devices. However, VIO inevitably suffers from drift, which will reduce positioning accuracy. This problem can be solved by fusing prior maps into VIO. Existing works mainly support online fusing one map into VIO. This requires users to offline merge multiple maps into one beforehand, which is complicated and troublesome and sometimes even unrealizable (e.g., the multiple maps have no overlap). According to theoretical analyses, this paper introduces a new system that can online fuse multiple maps into VIO. Our system has the following benefits: 1) It is a light-weighted filter-based system suitable for onboard deployments; 2) It can online fuse multiple maps such that pre-work of merging multiple maps into one can be bypassed; 3) Our system can consistently fuse the multi-map information while keeps the computation at a low level. Experiments show that with our system, the VIO’s drift can be significantly alleviated to benefit downstream tasks like planning, navigation, and control. However, our system needs to fix some linearization points to maintain the correct observability of the system, which will sacrifice some precision. Future works will include investigating more elegant techniques to maintain the observability of the system.

Liquid-liquid phase separation (LLPS) of proteins and nucleic acids underlies the formation of biomolecular condensates in cell. Dysregulation of protein LLPS is closely implicated in a range of intractable diseases. A variety of tools for predicting phase-separating proteins (PSPs) have been developed with the increasing experimental data accumulated and several related databases released. Comparing their performance directly can be challenging due to they were built on different algorithms and datasets. In this study, we evaluate eleven available PSPs predictors using negative testing datasets, including folded proteins, the human proteome, and non-PSPs under near physiological conditions, based on our recently updated LLPSDB v2.0 database. Our results show that the new generation predictors FuzDrop, DeePhase and PSPredictor perform better on folded proteins as a negative test set, while LLPhyScore outperforms other tools on the human proteome. However, none of the predictors could accurately identify experimentally verified non-PSPs. Furthermore, the correlation between predicted scores and experimentally measured saturation concentrations of protein A1-LCD and its mutants suggests that, these predictors could not consistently predict the protein LLPS propensity rationally. Further investigation with more diverse sequences for training, as well as considering features such as refined sequence pattern characterization that comprehensively reflects molecular physiochemical interactions, may improve the performance of PSPs prediction.

This article focuses on designing a consistent and efficient filter for visual-inertial localization given a prebuilt map. First, we propose a new Lie group with its algebra based on which a novel invariant extended Kalman filter (invariant EKF) is designed. We theoretically prove that, when we do not consider the uncertainty of map information, the proposed invariant EKF is able to naturally preserve the correct observability properties of the system. To consider the uncertainty of map information, we introduce a Schmidt filter. With the Schmidt filter, the uncertainty of map information can be taken into consideration to avoid overconfident estimation while the computation cost only increases linearly with the size of the map keyframes. In addition, we introduce an easily implemented observability-constrained technique because directly combining the invariant EKF with the Schmidt filter cannot maintain the correct observability properties of the system that considers the uncertainty of map information. Finally, we validate our proposed system's high consistency, accuracy, and efficiency via extensive simulations and real-world experiments.

In recent years, Visual-Inertial Odometry (VIO) has achieved many significant progresses. However, VIO meth-ods suffer from localization drift over long trajectories. In this paper, we propose a First-Estimates Jacobian Visual-Inertial-Ranging Odometry (FEJ-VIRO) to reduce the localization drifts of VIO by incorporating ultra-wideband (UWB) ranging measurements into the VIO framework consistently. Consid-ering that the initial positions of UWB anchors are usually unavailable, we propose a long-short window structure to initialize the UWB anchors' positions as well as the covariance for state augmentation. After initialization, the FEJ - VIRO estimates the UWB anchors' positions simultaneously along with the robot poses. We further analyze the observability of the visual-inertial-ranging estimators and proved that there are four unobservable directions in the ideal case, while one of them vanishes in the actual case due to the gain of spurious information. Based on these analyses, we leverage the FEJ technique to enforce the unobservable directions, hence reducing inconsistency of the estimator. Finally, we validate our analysis and evaluate the proposed FEJ-VIRO with both simulation and real-world experiments.

SUMMARY: Emerging evidences have suggested that liquid-liquid phase separation (LLPS) of proteins plays a vital role both in a wide range of biological processes and in related diseases. Whether a protein undergoes phase separation not only is determined by the chemical and physical properties of biomolecule themselves, but also is regulated by environmental conditions such as temperature, ionic strength, pH, as well as volume excluded by other macromolecules. A web accessible database LLPSDB was developed recently by our group, in which all the proteins involved in LLPS in vitro as well as corresponding experimental conditions were curated comprehensively from published literatures. With the rapid increase of investigations in biomolecular LLPS and growing popularity of LLPSDB, we updated the database, and developed a new version LLPSDB v2.0. In comparison of the previously released version, more than double contents of data are curated, and a new class 'Ambiguous system' is added. In addition, the web interface is improved, such as that users can search the database by selecting option 'phase separation status' alone or combined with other options. We anticipate that this updated database will serve as a more comprehensive and helpful resource for users. AVAILABILITY AND IMPLEMENTATION: LLPSDB v2.0 is freely available at: http://bio-comp.org.cn/llpsdbv2. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

BACKGROUND: The liquid-liquid phase separation (LLPS) of biomolecules in cell underpins the formation of membraneless organelles, which are the condensates of protein, nucleic acid, or both, and play critical roles in cellular function. Dysregulation of LLPS is implicated in a number of diseases. Although the LLPS of biomolecules has been investigated intensively in recent years, the knowledge of the prevalence and distribution of phase separation proteins (PSPs) is still lag behind. Development of computational methods to predict PSPs is therefore of great importance for comprehensive understanding of the biological function of LLPS. RESULTS: Based on the PSPs collected in LLPSDB, we developed a sequence-based prediction tool for LLPS proteins (PSPredictor), which is an attempt at general purpose of PSP prediction that does not depend on specific protein types. Our method combines the componential and sequential information during the protein embedding stage, and, adopts the machine learning algorithm for final predicting. The proposed method achieves a tenfold cross-validation accuracy of 94.71%, and outperforms previously reported PSPs prediction tools. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which is accessible for prediction of potential PSPs. CONCLUSIONS: PSPredictor could identifie novel scaffold proteins for stress granules and predict PSPs candidates in the human genome for further study. For further applications, we built a user-friendly PSPredictor web server ( http://www.pkumdl.cn/PSPredictor ), which provides valuable information for potential PSPs recognition.

We have presented a no-reference quality prediction method for asymmetrically distorted stereoscopic images, which aims to transfer the information from source feature domain to its target quality domain using a label consistent K-singular value decomposition classification framework. To this end, we construct a category-deviation database for dictionary learning that assigns a label for each stereoscopic image to indicate if it is noticeable or unnoticeable by human eyes. Then, by incorporating a category consistent term into the objective function, we learn view-specific feature and quality dictionaries to establish a semantic framework between the source feature domain and the target quality domain. The quality pooling is comparatively simple and only needs to estimate the quality score based on the classification probability. The experimental results demonstrate the effectiveness of our blind metric.

MOTIVATION: Experimental evidence suggests that certain short protein segments have stronger amyloidogenic propensities than others. Identification of the fibril-forming segments of proteins is crucial for understanding diseases associated with protein misfolding and for finding favorable targets for therapeutic strategies. RESULT: In this study, we used the microcrystal structure of the NNQQNY peptide from yeast prion protein and residue-based statistical potentials to establish an algorithm to identify the amyloid fibril-forming segment of proteins. Using the same sets of sequences, a comparable prediction performance was obtained from this study to that from 3D profile method based on the physical atomic-level potential ROSETTADESIGN. The predicted results are consistent with experiments for several representative proteins associated with amyloidosis, and also agree with the idea that peptides that can form fibrils may have strong sequence signatures. Application of the residue-based statistical potentials is computationally more efficient than using atomic-level potentials and can be applied in whole proteome analysis to investigate the evolutionary pressure effect or forecast other latent diseases related to amyloid deposits. AVAILABILITY: The fibril prediction program is available at ftp://mdl.ipc.pku.edu.cn/pub/software/pre-amyl/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.