homology analysis
Recently Published Documents


TOTAL DOCUMENTS

69
(FIVE YEARS 19)

H-INDEX

13
(FIVE YEARS 2)

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Shen Wang ◽  
Xunzhi Jiang ◽  
Xiangzhan Yu ◽  
Xiaohui Su

Binary code homology analysis refers to detecting whether two pieces of binary code are compiled from the same piece of source code, which is a fundamental technique for many security applications, such as vulnerability search, plagiarism detection, and malware detection. With the increase in critical vulnerabilities in IoT devices, homology analysis is increasingly needed to perform cross-platform vulnerability searches. Existing methods for cross-platform binary code homology detection usually convert binary code to instruction sequences and do semantic embedding of the sequences as if they were natural language. However, the gap between natural language and binary code is large, and the spatial features of the binary code are easily lost by directly comparing the semantics. In this paper, we propose a GRU-based graph embedding method to compare the homology of binary functions. First, the attribute control flow graph (ACFG) is built for the assembly function, then the GRU-based graph embedding neural network is used to generate the embedding vector for the ACFG, and finally the homology of the binary code is determined by calculating the distance between the embedding vectors. The experimental results show that our method greatly improves the detection accuracy of negative samples compared with Gemini, the latest method based on graph embedding binary code similarity detection.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Anna Suzuki ◽  
Miyuki Miyazawa ◽  
James M. Minto ◽  
Takeshi Tsuji ◽  
Ippei Obayashi ◽  
...  

AbstractTopological data analysis is an emerging concept of data analysis for characterizing shapes. A state-of-the-art tool in topological data analysis is persistent homology, which is expected to summarize quantified topological and geometric features. Although persistent homology is useful for revealing the topological and geometric information, it is difficult to interpret the parameters of persistent homology themselves and difficult to directly relate the parameters to physical properties. In this study, we focus on connectivity and apertures of flow channels detected from persistent homology analysis. We propose a method to estimate permeability in fracture networks from parameters of persistent homology. Synthetic 3D fracture network patterns and their direct flow simulations are used for the validation. The results suggest that the persistent homology can estimate fluid flow in fracture network based on the image data. This method can easily derive the flow phenomena based on the information of the structure.


2021 ◽  
Author(s):  
Bingtao Gao ◽  
Lei Wang ◽  
Zhengang Zhai ◽  
Yuan Chen ◽  
Jiangang Wang

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chun-mei Chen ◽  
Min Wang ◽  
Xian-ping Li ◽  
Peng-ling Li ◽  
Jing-jing Tian ◽  
...  

An amendment to this paper has been published and can be accessed via the original article.


2021 ◽  
Vol 334 ◽  
pp. 127593
Author(s):  
Jie Zhang ◽  
Ning Zhao ◽  
Junnan Xu ◽  
Yiman Qi ◽  
Xinyuan Wei ◽  
...  

2020 ◽  
Author(s):  
Chun-mei Chen ◽  
Min Wang ◽  
Xian-ping Li ◽  
Peng-ling Li ◽  
Jing-jing Tian ◽  
...  

Abstract Background: Klebsiella pneumoniae is a leading cause of hospital-associated (HA) infections. It has been reported that gastrointestinal colonization (GI) is likely to be a common and significant reservoir for the transmission and infections of K. pneumoniae in both adults and neonates. However, the homologous relationship between clinically isolated extraintestinal and enteral K. pneumoniae in neonates hasn’t been characterized yet.Results: 43 isolates from 21 neonatal patients were collected in this study. The proportion of carbapenem resistance was 62.8%. There were 12 patients (12/21, 57.4%) whose antibiotic resistance phenotypes, genotypes, and ST types (STs) were concordant. Six sequence types were detected using MLST, with ST37 and ST54 being the dominant types. The results of MLST were consist with the results of PFGE.Conclusions: These data showed that there might be a close homologous relationship between extraintestinal K. pneumoniae (EXKP) and enteral K. pneumoniae (EKP) in neonates,indicating that the K. pneumoniae from the GI tract is possibly to be a significant reservoir for causing extraintestinal infections.


2020 ◽  
Author(s):  
Chun-mei Chen ◽  
Min Wang ◽  
Xian-ping Li ◽  
Peng-ling Li ◽  
Jing-jing Tian ◽  
...  

Abstract Background: Klebsiella pneumoniae is a leading cause of hospital-associated (HA) infections . It has been reported that gastrointestinal colonization (GI) is likely to be a common and significant reservoir for the transmission and infections of K. pneumoniae in both adults and neonates. However, the homologous relationship between clinically isolated extraintestinal and enteral K. pneumoniae in neonates hasn’t been characterized yet. Results: 43 isolates from 21 neonatal patients were collected in this study. The proportion of carbapenem resistance was 62.8%. There were 12 patients (12/21, 57.4%) whose antibiotic resistance phenotypes, genotypes, and ST types (STs) were concordant. Six sequence types were detected using MLST, with ST37 and ST54 being the dominant types. The results of MLST were consist with the results of PFGE. Conclusions: These data showed that there might be a close homologous relationship between EXKP and EKP in neonates,indicating that the K. pneumoniae from the GI tract is possibly to be a significant reservoir for causing extraintestinal infections.


2020 ◽  
Vol 15 ◽  
Author(s):  
Sheng-hao Li ◽  
Shu-de Li ◽  
Kun-li Wu ◽  
Jun-Yi Li ◽  
Hong-juan Li ◽  
...  

Objective: To identify the possible virulence factors (VFs) of P. proliferus Methods: By Illumina HiSeq 4000 RNA-Seq platform, transcriptomes of adult P. proliferus worms were sequenced to predict VFs via screening the homologues of traditional VFs of parasites based on the annotations in the functional databases. Homology analysis was also performed to screen homologous genes between P. proliferus and other four Paragonimus species (i.e., P. kellicotti, P. skrjabini, P. miyazakii and P. westermani) whose transcriptomes were downloaded from the National Center for Biotechnology Information (NCBI) database, and then the differential-expressed homologous genes (DEHGs) were screened via comparisons of P. proliferus and P. kellicotti, P. skrjabini, P. miyazakii and P. westermani, respectively. Finally, an overlap of the predicted VFs and DEHGs were performed to identify possible key VFs those do not only belong to the predicted VFs but also DEHGs Results: A total of 1,509 genes of P. proliferus homologous to traditional VFs, including surface antigens (SAGs), secreted proteins (SPs), ATP-Binding Cassette (ABC) Transporters, actin-related proteins (ARPs), aminopeptidases (APases), glycoproteins (GPs), cysteine proteases (CPs), and heat shock proteins (HSPs), were identified. Meanwhile, homology analysis identified 6279 DEHGs among the five species, of which there were 48 DEHGs being mutually differentialexpressed among the four pairs of comparisons, such as MRP, Tuba 3, PI3K, WASF2, ADK, Nop56, DNAH1, PFK- 2/FBPase2, Ppp1r7, SSP7. Furthermore, the overlap between the predicted VFs and DEHGs shew 97 genes of the predicted VFs simultaneously belonged to DEHGs. Strikingly, of these 97 genes, only 26, including Chymotrypsin, Leucine APases, Cathepsin L, HSP 70, and so on, were higher expressed in P. proliferus while all the remaining were lower expressed than in the four other species Conclusions: This work provides a fundamental context for further studies of the pathogenicity of P. proliferus. Most of the predicted VFs which simultaneously belonged to DEHGs were lower expressed in P. proliferus


2020 ◽  
Author(s):  
Chun-mei Chen ◽  
Min Wang ◽  
Xian-ping Li ◽  
Peng-ling Li ◽  
Jing-jing Tian ◽  
...  

Abstract Background: Klebsiella pneumoniae is a leading cause of hospital-associated (HA) infections. It has been reported in many studies that gastrointestinal colonization (GI) is likely to be a common and significant reservoir for the transmission and infections of K. pneumoniae in both adults and neonates. But the homologous relationship between clinically isolated extraintestinal and enteral K. pneumoniae in neonates hasn’t been characterized yet.Results: 43 isolates from 21 neonatal patients were collected in this study. The proportion of carbapenem resistance was 62.8%. There were 12 patients (12/21, 57.4%) whose antibiotic resistance phenotypes, genotypes and ST types (STs) were concordant. Six sequence types were detected using MLST, with ST37 and ST54 being the dominant types. Conclusions: These data showed that there might be a close homologous relationship between EXKP and EKP in neonates,indicating that the K. pneumoniae from the GI tract is possibly to be a significant reservoir for causing extraintestinal infections.


2020 ◽  
Vol 20 (5&6) ◽  
pp. 375-399
Author(s):  
Ricardo Mengoni ◽  
Alessandra Di Pierro ◽  
Leleh Memarzadeh ◽  
Stefano Mancini

We introduce a homology-based technique for the classification of multiqubit state vectors with genuine entanglement. In our approach, we associate state vectors to data sets by introducing a metric-like measure in terms of bipartite entanglement, and investigate the persistence of homologies at different scales. This leads to a novel classification of multiqubit entanglement. The relative occurrence frequency of various classes of entangled states is also shown.


Sign in / Sign up

Export Citation Format

Share Document