Towards 3D object tracking in point clouds, a novel point-to-box network termed P2B is proposed in an endto-end learning manner. Our main idea is to first localize potential target centers in 3D search area embedded with target information. Then point-driven 3D target proposal and verification are executed jointly. In this way, the time-consuming 3D exhaustive search can be avoided. Specifically, we first sample seeds from the point clouds in template and search area respectively. Then, we execute permutation-invariant feature augmentation to embed target clues from template into search area seeds and represent them with target-specific features. Consequently, the augmented search area seeds regress the potential target centers via Hough voting. The centers are further strengthened with seed-wise targetness scores. Finally, each center clusters its neighbors to leverage the ensemble power for joint 3D target proposal and verification. We apply PointNet++ as our backbone and experiments on KITTI tracking dataset demonstrate P2B's superiority (∼10%'s improvement over state-of-the-art). Note that P2B can run with 40FPS on a single NVIDIA 1080Ti GPU. Our code and model are available at https://github.com/HaozheQi/P2B.
Motivation: Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related.Results: We present a novel context-specific alignment potential for protein threading, including alignment and template selection. Our alignment potential measures the log-odds ratio of one alignment being generated from two related proteins to being generated from two unrelated proteins, by integrating both local and global context-specific information. The local alignment potential quantifies how well one sequence residue can be aligned to one template residue based on context-specific information of the residues. The global alignment potential quantifies how well two sequence residues can be placed into two template positions at a given distance, again based on context-specific information. By accounting for correlation among a variety of protein features and making use of context-specific information, our alignment potential is much more sensitive than the widely used context-independent or profile-based scoring function. Experimental results confirm that our method generates significantly better alignments and threading results than the best profile-based methods on several large benchmarks. Our method works particularly well for distantly related proteins or proteins with sparse sequence profiles because of the effective integration of context-specific, structure and global information.Availability: http://raptorx.uchicago.edu/download/.Contact: jinboxu@gmail.com
Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA.
Abstract-Deregulated electricity markets use an auction mechanism to select offers and their power levels for energy and ancillary services. A settlement mechanism is then used to determine the payments resulting from the selected offers. Currently, most independent system operators (ISOs) in the United States use an auction mechanism that minimizes the total offer costs but determine payment costs using a settlement mechanism that pays uniform market clearing prices (MCPs) to all selected offers. Under this setup, the auction and settlement mechanisms are inconsistent since minimized costs are different from payment costs. Illustrative examples in the literature have shown that for a given set of offers, if an auction mechanism that directly minimizes the payment costs is used, then payment costs can be significantly reduced as compared to minimizing offer costs. This observation has led to discussions among stakeholders and policymakers in the electricity markets as to which of the two auction mechanisms is more appropriate for ISOs to use. While methods for minimizing offer costs abound, limited approaches for minimization of payment costs have been reported. This paper presents an effective method for directly minimizing payment costs. In view of the specific features of the problem including the nonseparability of its objective function, the discontinuity of offer curves, and the maximum term in defining MCPs, our key idea is to use augmented Lagrangian relaxation and to form and solve offer and MCP subproblems by using the surrogate optimization framework. Numerical testing results demonstrate that the method is effective, and the resulting payment costs are significantly lower than what are obtained by minimizing the offer costs for a given set of offers.Index Terms-Augmented Lagrangian relaxation, deregulated electricity markets, market clearing price (MCP), offer cost minimization, payment cost minimization, surrogate optimization.
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