scholarly journals Design of Generative Model for the Language of Traditional Suakin Using Parametric Shape Grammar

2016 ◽  
Vol 3 (2/3) ◽  
pp. 01-18
Author(s):  
Olakanbi Bolaji AbdulRaheem ◽  
Osama Abdulwahab Rayis
Keyword(s):  
Generative Model ◽  
Shape Grammar

AutoLinker: Automatic Fragment Linking with Deep Conditional Transformer Neural Networks

2020 ◽  
Author(s):  
Yuyao Yang ◽  
Shuangjia Zheng ◽  
Shimin Su ◽  
Jun Xu ◽  
Hongming Chen
Keyword(s):  
Neural Networks ◽  
Drug Discovery ◽  
Drug Design ◽  
State Of The Art ◽  
The State ◽  
Generative Model ◽  
Lead Optimization ◽  
Scaffold Hopping ◽  
Reference Models ◽  
Lead Generation

Fragment based drug design represents a promising drug discovery paradigm complimentary to the traditional HTS based lead generation strategy. How to link fragment structures to increase compound affinity is remaining a challenge task in this paradigm. Hereby a novel deep generative model (AutoLinker) for linking fragments is developed with the potential for applying in the fragment-based lead generation scenario. The state-of-the-art transformer architecture was employed to learn the linker grammar and generate novel linker. Our results show that, given starting fragments and user customized linker constraints, our AutoLinker model can design abundant drug-like molecules fulfilling these constraints and its performance was superior to other reference models. Moreover, several examples were showcased that AutoLinker can be useful tools for carrying out drug design tasks such as fragment linking, lead optimization and scaffold hopping.

Effective Image Auto-Annotation via Discriminative Hyperplane Tree Based Generative Model

2009 ◽  
Vol 20 (9) ◽  
pp. 2450-2461
Author(s):  
Mei WANG ◽  
Xiang-Dong ZHOU ◽  
Hong-Tao XU ◽  
Bai-Le SHI
Keyword(s):  
Generative Model

Clustering Count-based RNA Methylation Data Using a Nonparametric Generative Model

2018 ◽  
Vol 14 (1) ◽  
pp. 11-23 ◽  
Author(s):  
Lin Zhang ◽  
Yanling He ◽  
Huaizhi Wang ◽  
Hui Liu ◽  
Yufei Huang ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Methylation Level ◽  
Optimal Number ◽  
Generative Model ◽  
Methylation Data ◽  
Sequencing Data ◽  
Number Of Clusters ◽  
Rna Methylation ◽  
Clustering Effect ◽  
Optimal Number Of Clusters

Background: RNA methylome has been discovered as an important layer of gene regulation and can be profiled directly with count-based measurements from high-throughput sequencing data. Although the detailed regulatory circuit of the epitranscriptome remains uncharted, clustering effect in methylation status among different RNA methylation sites can be identified from transcriptome-wide RNA methylation profiles and may reflect the epitranscriptomic regulation. Count-based RNA methylation sequencing data has unique features, such as low reads coverage, which calls for novel clustering approaches. <P><P> Objective: Besides the low reads coverage, it is also necessary to keep the integer property to approach clustering analysis of count-based RNA methylation sequencing data. <P><P> Method: We proposed a nonparametric generative model together with its Gibbs sampling solution for clustering analysis. The proposed approach implements a beta-binomial mixture model to capture the clustering effect in methylation level with the original count-based measurements rather than an estimated continuous methylation level. Besides, it adopts a nonparametric Dirichlet process to automatically determine an optimal number of clusters so as to avoid the common model selection problem in clustering analysis. <P><P> Results: When tested on the simulated system, the method demonstrated improved clustering performance over hierarchical clustering, K-means, MClust, NMF and EMclust. It also revealed on real dataset two novel RNA N6-methyladenosine (m6A) co-methylation patterns that may be induced directly by METTL14 and WTAP, which are two known regulatory components of the RNA m6A methyltransferase complex. <P><P> Conclusion: Our proposed DPBBM method not only properly handles the count-based measurements of RNA methylation data from sites of very low reads coverage, but also learns an optimal number of clusters adaptively from the data analyzed. <P><P> Availability: The source code and documents of DPBBM R package are freely available through the Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/DPBBM/.

scholarly journals GREASE: A Generative Model for Relevance Search over Knowledge Graphs

2020 ◽  
Author(s):  
Tianshuo Zhou ◽  
Ziyang Li ◽  
Gong Cheng ◽  
Jun Wang ◽  
Yu'Ang Wei
Keyword(s):  
Generative Model ◽  
Knowledge Graphs

scholarly journals Deep Generative Model Using Unregularized Score for Anomaly Detection With Heterogeneous Complexity

2020 ◽  
pp. 1-13
Author(s):  
Takashi Matsubara ◽  
Kazuki Sato ◽  
Kenta Hama ◽  
Ryosuke Tachibana ◽  
Kuniaki Uehara
Keyword(s):  
Anomaly Detection ◽  
Generative Model
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