Browsing by Author "Chang, Yao-Lin"

Now showing 1 - 3 of 3

A Learning-Based Methodology for Routability Prediction in Placement
(2018-01-01)
Chen, Li-Chin
;
Huang, Chien-Chia
;
Chang, Yao-Lin
;
Chen, Hung-Ming
;
電子工程學系及電子研究所
The mutability of a circuit is a critical challenge due to the complexity of design rules. Global routing produces a congestion map on a coarse grid and feeds the results to the placer to optimize the design for reducing detailed-route DRC violations. However, there is a growing gap between global routing and the actual violations in detailed routing. This miscorrelation may end up unroutable for back-end detailed routing. In this work, a methodology as well as the framework How based on machine learning technique is proposed to effectively predict detailed routing violations. After extracting appropriate features from placement, fast global routing and detailed routing violations, we use support vector machine techniques to train the prediction model, different from regression framework. We then also develop a prediction model for DRC violation density which can be integrated into placers. Experimental results show that the proposed approach can effectively forecast routability during placement stage.
Evolutionary conservation and interacting preference for identifying Protein-DNA interactions
(2008)
Chang, Yao-Lin
;
Liu, I-Hsin
;
Kao, Cheng-Yan
;
Yang, Jinn-Moon
;
生物資訊及系統生物研究所
Protein-DNA interactions play a central role in many genetic processes of cells. With the growing crystal structures of protein-DNA complexes, the computational approaches are becoming more and more useful for modeling protein-DNA interactions. This paper proposes template-based alignment with a new scoring function which combined the evolutionary conservation and protein-DNA interacting scores of DNA-contact residues. We showed that the combined scoring function is better to model the protein-DNA interactions than applying only one. Our method achieved high accuracy in identifying DNA-binding domains of 69 representative families and with the correlation 0.6 in predicting the binding free energy of the alanine scanning data. By applying the method to the hormone receptor family, it showed that our method can identify the DNA-binding specificity in different subfamilies. The evolutionary conservation is able to reflect the evolution pressure of DNA-contact residues and the interaction preferences can indicate the binding affinity between the protein and DNA. Experimental results show that both the evolution conservation and the DNA-binding capability of the DNA-contact residues are essential for identifying DNA-binding domains and protein-DNA interactions.
Evolutionary conservation of DNA-contact residues in DNA-binding domains
(2008)
Chang, Yao-Lin
;
Tsai, Huai-Kuang
;
Kao, Cheng-Yan
;
Chen, Yung-Chian
;
Hu, Yuh-Jyh
Background: DNA-binding proteins are of utmost importance to gene regulation. The identification of DNA-binding domains is useful for understanding the regulation mechanisms of DNA-binding proteins. In this study, we proposed a method to determine whether a domain or a protein can has DNA binding capability by considering evolutionary conservation of DNA-binding residues. Results: Our method achieves high precision and recall for 66 families of DNA-binding domains, with a false positive rate less than 5% for 250 non-DNA-binding proteins. In addition, experimental results show that our method is able to identify the different DNA-binding behaviors of proteins in the same SCOP family based on the use of evolutionary conservation of DNA-contact residues. Conclusion: This study shows the conservation of DNA-contact residues in DNA-binding domains. We conclude that the members in the same subfamily bind DNA specifically and the members in different subfamilies often recognize different DNA targets. Additionally, we observe the co-evolution of DNA-contact residues and interacting DNA base-pairs.