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Alignment-Based Trace Clustering [chapter]

Thomas Chatain, Josep Carmona, Boudewijn van Dongen
2017 Lecture Notes in Computer Science  
We believe alignment-based trace clustering provides results more useful for stakeholders.  ...  The core idea of the algorithm is to use model traces as centroids of the clusters detected, computed from a generalization of the notion of alignment.  ...  Acknowledgements We thank Bart Hompes for facilitating the clustering results of his tool for the example used in the experiments.  ... 
doi:10.1007/978-3-319-69904-2_24 fatcat:u6xko3hw3vg27izguhwztofvai

Clustering Traces Using Sequence Alignment [chapter]

Joerg Evermann, Tom Thaler, Peter Fettke
2016 Lecture Notes in Business Information Processing  
In this paper, we present a trace clustering method based on local alignment of sequences, subsequent multidimensional scaling, and k-means clustering.  ...  Trace clustering identifies homogeneous sets of traces within a heterogeneous log and allows for the discovery of multiple, simpler process models.  ...  Most existing trace clustering techniques are based on fairly generic methods for clustering in multivariate settings [1] .  ... 
doi:10.1007/978-3-319-42887-1_15 fatcat:gxiht7pw6rgqvacdpx7sakfvcu

Decomposed Process Mining: The ILP Case [chapter]

H. M. W. Verbeek, Wil M. P. van der Aalst
2015 Lecture Notes in Business Information Processing  
Some event logs are "big" because they contain many traces. Others are big in terms of different activities.  ...  ILP-based process mining techniques provide precise results and formal guarantees (e.g., perfect fitness), but are known to scale badly in the number of activities.  ...  A trace alignment for which only the first two requirements hold is called a weak trace alignment. A log alignment maps every trace of the log onto a trace alignment.  ... 
doi:10.1007/978-3-319-15895-2_23 fatcat:faidpgvvinejvjs2vigzyqckte

Accurate Detection of Very Sparse Sequence Motifs

Andreas Heger, Michael Lappe, Liisa Holm
2004 Journal of Computational Biology  
In a challenging benchmark based on the urease superfamily, MaxFlow yields better reliability and double coverage compared to available sequence alignment software.  ...  Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme  ...  INTRODUCTION P roteins can be clustered into families based on statistically significant sequence similarity.  ... 
doi:10.1089/cmb.2004.11.843 pmid:15700405 fatcat:rtb2xj7ecjagndgndc7h3lth3q

Accurate Detection of Very Sparse Sequence Motifs

Andreas Heger, Michael Lappe, Liisa Holm
2004 Journal of Computational Biology  
In a challenging benchmark based on the urease superfamily, MaxFlow yields better reliability and double coverage compared to available sequence alignment software.  ...  Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme  ...  INTRODUCTION P roteins can be clustered into families based on statistically significant sequence similarity.  ... 
doi:10.1089/1066527042432242 fatcat:qbv3zcj7izcmziunxkzlq377we

Accurate detection of very sparse sequence motifs

Andreas Heger, Michael Lappe, Liisa Holm
2003 Proceedings of the seventh annual international conference on Computational molecular biology - RECOMB '03  
In a challenging benchmark based on the urease superfamily, MaxFlow yields better reliability and double coverage compared to available sequence alignment software.  ...  Thus, MaxFlow is able to identify sparse and narrow active-site sequence signatures which are embedded in high-entropy sequence segments in the structure based multiple alignment of large diverse enzyme  ...  INTRODUCTION P roteins can be clustered into families based on statistically significant sequence similarity.  ... 
doi:10.1145/640075.640094 dblp:conf/recomb/HegerLH03 fatcat:xphk6pxeajetbhmce7z6phyv3a

Process diagnostics using trace alignment: Opportunities, issues, and challenges

R.P. Jagadeesh Chandra Bose, Wil M.P. van der Aalst
2012 Information Systems  
Therefore, we propose a new approach based on trace alignment. The goal is to align traces in such a way that event logs can be explored easily.  ...  Trace alignment can be used to explore the process in the early stages of analysis and to answer specific questions in later stages of analysis.  ...  First, we group similar traces in clusters [2] . Second, we visualize these clusters by aligning the traces.  ... 
doi:10.1016/j.is.2011.08.003 fatcat:dg3duja52renlgrjsd65krmsey

Trace Alignment in Process Mining: Opportunities for Process Diagnostics [chapter]

R. P. Jagadeesh Chandra Bose, Wil van der Aalst
2010 Lecture Notes in Computer Science  
Therefore, we propose a new approach based on trace alignment. The goal is to align traces in a way that event logs can be explored easily.  ...  Trace alignment can be used in a preprocessing phase where the event log is investigated or filtered and in later phases where detailed questions need to be answered.  ...  Based on the guide tree, the traces T 2 and T 3 would first be aligned using pairwise trace alignment. Next traces T 4 and T 5 would be aligned using pairwise trace alignment.  ... 
doi:10.1007/978-3-642-15618-2_17 fatcat:b4n6nizaz5eezbvfbbntia6oni

HIV-TRACE (TRAnsmission Cluster Engine): a Tool for Large Scale Molecular Epidemiology of HIV-1 and Other Rapidly Evolving Pathogens

Sergei L Kosakovsky Pond, Steven Weaver, Andrew J Leigh Brown, Joel O Wertheim, Beth Shapiro
2018 Molecular biology and evolution  
Importantly, several independent studies have shown that in many cases relevant to HIV-1 epidemiology, HIV-TRACE reports very similar sets of clusters to phylogeny-based methods (Poon, HIV-TRACE  ...  In HIV-TRACE, genetic linkage serves as a proxy for these direct or indirect epidemiological connections, and a cluster is constructed based on these connections.  ... 
doi:10.1093/molbev/msy016 pmid:29401317 fatcat:nik4dxqta5f4jfuyfbi4ukg75m

Computational SNP discovery in DNA sequence data

Gabor T Marth
2003 Msphere  
Process the sequence traces with the PHRED base-calling program.  ...  Buetow et al. (6) used UNIGENE (38), a collection of precomputed EST clusters as a starting point. ESTs within each cluster were multiply aligned with PHRAP (24).  ...  The program analyzes the multiple alignment and tags the sites of candidate SNPs, as identified by likely heterozygous peaks within sequence traces.  ... 
pmid:12491905 fatcat:6u7q6tarx5cyxm5ghifojik5rq

Event Log Preprocessing for Process Mining: A Review

Heidy M. Marin-Castro, Edgar Tello-Leal
2021 Applied Sciences  
Trace-clustering and trace/event level filtering resulted in being the most commonly used preprocessing techniques due to easy of implementation, and they adequately manage noise and incompleteness in  ...  The data cleaning requirements are dependent on the characteristics of the event logs (voluminous, a high variability in the set of traces size, changes in the duration of the activities.  ...  Year Authors Ref Model Approach Algorithms 2019 Boltenhagen et al. [50] Framework for Based on generalized alignment Trace clustering ATC, APOTC, trace clustering of or AMSTC process behavior 2019 Xu and  ... 
doi:10.3390/app112210556 fatcat:lls2qf6llnddxbdnego2okk2ya

SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

Frank Panitz, Henrik Stengaard, Henrik Hornshøj, Jan Gorodkin, Jakob Hedegaard, Susanna Cirera, Bo Thomsen, Lone B. Madsen, Anette Høj, Rikke K. Vingborg, Bujie Zahn, Xuegang Wang (+13 others)
2007 Computer applications in the biosciences : CABIOS  
Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces.  ...  MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions.  ...  As input sequencing trace files (ab1, abd, ab1 trace files), base quality information (phd files) and clustering and alignment information (ace files) are used.  ... 
doi:10.1093/bioinformatics/btm192 pmid:17646321 fatcat:mf4j7hb36vd5hb23cslhiw3via

The global trace graph, a novel paradigm for searching protein sequence databases

A. Heger, S. Mallick, C. Wilton, L. Holm
2007 Bioinformatics  
Results: Here, we report a novel graph clustering algorithm in which all known protein sequences simultaneously self-organize into hypothetical multiple sequence alignments.  ...  All edges of the alignment trace graph are given a weight based on their local consistency, defined as the relative overlap of neighbour sets.  ...  Database searching We call the clustered data structure the global trace graph (GTG).  ... 
doi:10.1093/bioinformatics/btm358 pmid:17823134 fatcat:6hhhi4hmubejxohotvm2vv65nm

An Evolutionary Trace method defines functionally important bases and sites common to RNA families

Ilya B. Novikov, Angela D. Wilkins, Olivier Lichtarge, Francois Major
2020 PLoS Computational Biology  
, (1) the top-ranked bases clustered in secondary and tertiary structures. (2) In turn, these clusters mapped functional regions for catalysis, binding proteins and drugs, post-transcriptional modification  ...  The approach follows the phylogenetic Evolutionary Trace (ET) paradigm, first developed and extensively validated on proteins.  ...  Each alignment was traced, and the trace was evaluated for clustering among ET bases as a function of ET coverage.  ... 
doi:10.1371/journal.pcbi.1007583 pmid:32208421 fatcat:c3vaent5zra4dlzn2ftbgtsd4q

The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution

J. Mohammed, A. S. Flynt, A. Siepel, E. C. Lai
2013 RNA: A publication of the RNA Society  
alignments currently available.  ...  More strikingly, we observe that mirtrons and clustered miRNAs both exhibit distinct evolutionary properties relative to solo, well-conserved miRNAs, even after controlling for sequence depth.  ...  Ambiguous bases were not altered in the alignments.  ... 
doi:10.1261/rna.039248.113 pmid:23882112 pmcid:PMC3753935 fatcat:oxvfszanxzctvm5hmh4wrodkpm
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