We believe alignment-based trace clustering provides results more useful for stakeholders. Moreover, in case of log incompleteness, noisy logs or concept drift, they can be more robust for dealing with highly d
We compared with ProtTrans and five structure-based methods: cliques, GRAFENE, ORCA, CNN (influenced by DeepFRI) and GCN (influenced by the Kipf and Welling GAE). Adjusted mutual information was computed by comparing spectral clustering assignments with structural label assignments for each CATH ...
A larger amount of sequence data in private and public databases produced by next-generation sequencing put new challenges due to limitation associated with the alignment-based method for sequence comparison. So, there is a high need for faster sequence
SortMeRNA is a local sequence alignment tool for filtering, mapping and clustering.The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads...
Kececioglu [64, 63] introduced a graph-based formalization of multiple sequence alignment with sum-of-pairs cost function, the complete maximum-weight trace (CMWT) formalization. An ILP (integer linear programming) solution for this problem was presented in [84, 62]. In CMWT, the letters of...
The blue line shows the traceback of the optimal alignment. Right: score based banding with b=1. The reference is on top and the query on the left. The gray cells are inside the band and the blue line is the traceback. The red-circled cells are the minimum for each row, which are...
As a conse- quence, structural alignment based methods exceeded other methods due to its more efficient and more accu- rate performance. In 1996, Lichtarge et al. [17] developed the first struc- tural alignment based algorithm for protein-binding sites prediction, entitled evolutionary trace ...
Then, we precluster the messages based on the generated Bag-of-Words to improve the similarity of the message within a cluster. Finally, we propose an industrial control protocol message preclustering model for sequence alignment, namely, IMCSA. We evaluate it over five industrial control ...
the analysis than changing other preprocessing strategies. The clustering profiles were also highly similar between Chromap and CellRanger v2.0.0, no matter whether clustering was performed using the peak-based approach in MAESTRO or the bin-based approach in ArchR22(TableS4). On performance, ...
the computer system uses backpropagation to trace the loss back from the output layer through the intermediate layers of the neural network to the input layer. The values of the weights associated with the connections between the nodes in the neural network are thereby updated. The error is back...