scholarly journals Learning Class Prototypes via Structure Alignment for Zero-Shot Recognition

Author(s):  
Huajie Jiang ◽  
Ruiping Wang ◽  
Shiguang Shan ◽  
Xilin Chen
Keyword(s):  
2001 ◽  
Vol 43 (3) ◽  
pp. 235-245 ◽  
Author(s):  
Nathaniel Leibowitz ◽  
Zipora Y. Fligelman ◽  
Ruth Nussinov ◽  
Haim J. Wolfson

2004 ◽  
Vol 02 (01) ◽  
pp. 215-239 ◽  
Author(s):  
TOLGA CAN ◽  
YUAN-FANG WANG

We present a new method for conducting protein structure similarity searches, which improves on the efficiency of some existing techniques. Our method is grounded in the theory of differential geometry on 3D space curve matching. We generate shape signatures for proteins that are invariant, localized, robust, compact, and biologically meaningful. The invariancy of the shape signatures allows us to improve similarity searching efficiency by adopting a hierarchical coarse-to-fine strategy. We index the shape signatures using an efficient hashing-based technique. With the help of this technique we screen out unlikely candidates and perform detailed pairwise alignments only for a small number of candidates that survive the screening process. Contrary to other hashing based techniques, our technique employs domain specific information (not just geometric information) in constructing the hash key, and hence, is more tuned to the domain of biology. Furthermore, the invariancy, localization, and compactness of the shape signatures allow us to utilize a well-known local sequence alignment algorithm for aligning two protein structures. One measure of the efficacy of the proposed technique is that we were able to perform structure alignment queries 36 times faster (on the average) than a well-known method while keeping the quality of the query results at an approximately similar level.


2018 ◽  
Vol 99 (3) ◽  
pp. 219-231 ◽  
Author(s):  
Alex Stanczyk ◽  
Sarah Carnochan ◽  
Evelyn Hengeveld-Bidmon ◽  
Michael J. Austin

In 2014, California implemented the Family Stabilization (FS) program within its Temporary Assistance for Needy Families (TANF) program, California Work Opportunity and Responsibility to Kids (CalWORKs). FS fills two key service gaps in TANF that have been identified in the literature—namely, addressing participant barriers to work and supporting child well-being. Research on programs addressing these gaps in TANF remains limited. This qualitative policy implementation study describes FS program design and implementation in 11 California county human service agencies and explores links to agency and community context. We find that state-encouraged flexibility resulted in three distinct approaches to FS services, staffing, and structure. Alignment between agency context and program design emerged as central to implementation decisions. These findings yield implications for research, policy, and management practice among welfare-to-work administrators.


2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Che-Lun Hung ◽  
Yaw-Ling Lin

Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.


2013 ◽  
Vol 7 ◽  
pp. BBI.S10758 ◽  
Author(s):  
Bram Sebastian ◽  
Samuel E. Aggrey

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expressions by targeting the mRNAs especially in the 3′UTR regions. The identification of miRNAs has been done by biological experiment and computational prediction. The computational prediction approach has been done using two major methods: comparative and noncomparative. The comparative method is dependent on the conservation of the miRNA sequences and secondary structure. The noncomparative method, on the other hand, does not rely on conservation. We hypothesized that each miRNA class has its own unique set of features; therefore, grouping miRNA by classes before using them as training data will improve sensitivity and specificity. The average sensitivity was 88.62% for miR-Explore, which relies on within miRNA class alignment, and 70.82% for miR-abela, which relies on global alignment. Compared with global alignment, grouping miRNA by classes yields a better sensitivity with very high specificity for pre-miRNA prediction even when a simple positional based secondary and primary structure alignment are used.


2021 ◽  
Vol 14 ◽  
Author(s):  
Yiqin Cao ◽  
Zhenyu Zhu ◽  
Yi Rao ◽  
Chenchen Qin ◽  
Di Lin ◽  
...  

Deformable image registration is of essential important for clinical diagnosis, treatment planning, and surgical navigation. However, most existing registration solutions require separate rigid alignment before deformable registration, and may not well handle the large deformation circumstances. We propose a novel edge-aware pyramidal deformable network (referred as EPReg) for unsupervised volumetric registration. Specifically, we propose to fully exploit the useful complementary information from the multi-level feature pyramids to predict multi-scale displacement fields. Such coarse-to-fine estimation facilitates the progressive refinement of the predicted registration field, which enables our network to handle large deformations between volumetric data. In addition, we integrate edge information with the original images as dual-inputs, which enhances the texture structures of image content, to impel the proposed network pay extra attention to the edge-aware information for structure alignment. The efficacy of our EPReg was extensively evaluated on three public brain MRI datasets including Mindboggle101, LPBA40, and IXI30. Experiments demonstrate our EPReg consistently outperformed several cutting-edge methods with respect to the metrics of Dice index (DSC), Hausdorff distance (HD), and average symmetric surface distance (ASSD). The proposed EPReg is a general solution for the problem of deformable volumetric registration.


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