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Efficient Conformance Checking using Alignment Computation with Tandem Repeats [article]

Daniel Reißner, Abel Armas-Cervantes, Marcello La Rosa
2020 arXiv   pre-print
Alignments are an established technique to compute the distance between a trace in the event log and the closest execution trace of a corresponding process model.  ...  the alignment cost while guaranteeing that the cost result never under-approximates the optimal cost.  ...  This research is partly funded by the Australian Research Council (grant DP180102839).  ... 
arXiv:2004.01781v1 fatcat:4pang3mnbveafmytnt7uwfibre

Procrastination Leads to Efficient Filtration for Local Multiple Alignment [chapter]

Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna
2006 Lecture Notes in Computer Science  
The algorithm consumes O(wN ) memory and O(wN log wN ) time where N is the sequence length. We score the significance of multiple alignments using entropy-based motif scoring methods.  ...  We describe an efficient local multiple alignment filtration heuristic for identification of conserved regions in one or more DNA sequences.  ...  We score alignments generated by our method using the entropy equation and exact p-value method in [25] .  ... 
doi:10.1007/11851561_12 fatcat:ixasd5uir5bglac3ir7o5ndn4a

Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates

Chelsea J.-T. Ju, Zhuangtian Zhao, Wei Wang
2017 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we extend the work of PseudoLasso by grouping the homologous genomic regions into different communities using a community detection algorithm, followed by building a linear regression model  ...  The data analysis of an RNA-Seq experiment starts from aligning short reads to the reference genome/transcriptome or reconstructed transcriptome.  ...  Acknowledgments We thank Zhaojun Zhang for his comments and discussion, and Shunping Huang for his assistance in setting up the RNA simulator software, RNAseqSim.  ... 
doi:10.1109/tcbb.2016.2591533 pmid:27429446 pmcid:PMC5514313 fatcat:vgswsrxi6ngm5pa5gas4sac5fu

Efficient constrained local model fitting for non-rigid face alignment

Simon Lucey, Yang Wang, Mark Cox, Sridha Sridharan, Jeffery F. Cohn
2009 Image and Vision Computing  
The "project-out" algorithm for fitting an AAM achieves faster than real time performance (>200 fps) but suffers from poor generic alignment performance.  ...  From these N simple warp displacements, a single complex warp displacement is estimated using a weighted least-squares constraint.  ...  its computational efficiency.  ... 
doi:10.1016/j.imavis.2009.03.002 pmid:20046797 pmcid:PMC2799037 fatcat:ped6z77hgnffxk6ibx66mb4rcu


2005 Journal of Bioinformatics and Computational Biology  
This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms, 15 and with a worst-case guarantee on the quality of the  ...  The constrained multiple sequence alignment problem is to align a set of sequences of maximum length n subject to a given constrained sequence, which arises from some knowledge of the structure of the  ...  Acknowledgement We thank the reviewer for pointing out that the space of our pair-wise constrained alignment can be improved to O(αn).  ... 
doi:10.1142/s0219720005000977 pmid:15751109 fatcat:utsrodz2szgn7nh65334eb75ny

Accelerated off-target search algorithm for siRNA

T. Yamada, S. Morishita
2004 Bioinformatics  
The Basic Local Alignment Search Tool (BLAST) is the most powerful and popular sequence alignment tool used in biological research, which includes the siRNA or shRNA design.  ...  This two-phased arrangement of the algorithm significantly improves the efficiency of the original Smith-Waterman algorithm by concentrating the search on localized regions instead of the whole genome  ...  ACKNOWLEDGMENTS The authors would like to thank Dr. Joseph Manthey for his valuable discussion about the computational cost analysis and his critical reading of this manuscript.  ... 
doi:10.1093/bioinformatics/bti155 pmid:15564304 fatcat:natlgoxco5ahnnka7skwst6ipi

Aligning Modeled and Observed Behavior: A Compromise Between Computation Complexity and Quality [chapter]

Boudewijn van Dongen, Josep Carmona, Thomas Chatain, Farbod Taymouri
2017 Lecture Notes in Computer Science  
In spite of its importance, the current algorithmic support for computing alignments is limited: either techniques that explicitly explore the model behavior (which may be worst-case exponential with respect  ...  used and local decisions taken at each step.  ...  However, before discussing our algorithm, we first consider a method for computing optimal alignments of a given maximal length using the marking equation.  ... 
doi:10.1007/978-3-319-59536-8_7 fatcat:covkr4wdwnf2jfswty2j4htf6m

Two Extensions of Data Assimilation by Field Alignment [chapter]

Sai Ravela
2007 Lecture Notes in Computer Science  
First, the methodology is extended to multivariate fields commonly used in models, thus making this method readily applicable.  ...  The solution could be used with either ensemble or deterministic methods. In this paper, extension of this work in two directions is reported.  ...  The solution to the assimilation objective can be computed efficiently in two steps: diffeomorphic alignment followed by amplitude adjustment.  ... 
doi:10.1007/978-3-540-72584-8_150 fatcat:v4b4cnz3jvf5jpv3oohn4fspkq

Manifold Learning in Quotient Spaces

Eloi Mehr, Andre Lieutier, Fernando Sanchez Bermudez, Vincent Guitteny, Nicolas Thome, Matthieu Cord
2018 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition  
Finally, we extend our quotient autoencoder to quotient by non-rigid transformations.  ...  Moreover, our model learns a rotation-invariant representation, leading to interesting results in shapes co-alignment.  ...  In this context, the main challenge is to be able to compute the gradient ∇ w,w ′ E qae (w, w ′ ) in Equation (3) .  ... 
doi:10.1109/cvpr.2018.00955 dblp:conf/cvpr/MehrLBGTC18 fatcat:5ib5i2txtfdfxkljuvjmrlnv64

Correspondence-Less Non-rigid Registration of Triangular Surface Meshes

Zsolt Santa, Zoltan Kato
2013 2013 IEEE Conference on Computer Vision and Pattern Recognition  
Each equation is generated by integrating a nonlinear function over the object's domains. We derive recursive formulas for the efficient computation of these integrals.  ...  The proposed method works without landmark extraction and feature correspondences. The aligning transformation is found simply by solving a system of nonlinear equations.  ...  Acknowledgment This research was partially supported by the grant  ... 
doi:10.1109/cvpr.2013.295 dblp:conf/cvpr/SantaK13 fatcat:go5gu64bhbb77ozl2y3rtmv7py

A Spatio-Temporal Modeling Method for Shape Representation

Heng Huang, Li Shen, Rong Zhang, Fillia Makedon, Justin Pearlman
2006 Third International Symposium on 3D Data Processing, Visualization, and Transmission (3DPVT'06)  
Because SPHARM based 3D models can derive functional information analysis and classify different pathological symptoms, it has been used in many applications in biomedical image computing.  ...  Furthermore, an evaluation criterion for spatio-temporal shape modeling efficiency is proposed and the comparison results showed the good performance of our method.  ...  First, we only use a part of shapes from the initial data and keep the shape at timing phase e as test data, marking its volume as V real .  ... 
doi:10.1109/3dpvt.2006.20 dblp:conf/3dpvt/HuangSZMP06 fatcat:ieajy2ncinhk3jwimmtcs3b54m

Non-rigid face tracking with local appearance consistency constraint

Yang Wang, Simon Lucey, Jeffrey F. Cohn, Jason Saragih
2008 2008 8th IEEE International Conference on Automatic Face & Gesture Recognition  
More importantly, we show that the global warp update can be optimized jointly in an efficient manner using convex quadratic fitting.  ...  In this paper, we extend the CLM method into the spatio-temporal domain by enforcing the appearance consistency constraint of each local patch between neighboring frames.  ...  The authors would like to thank Mark Cox for the helpful discussions. This work was partially supported by the NIH Grant R01 MH051435.  ... 
doi:10.1109/afgr.2008.4813409 fatcat:b7thg3bttnfanlqfn2nqzjzkgm

A Resistive CAM Processing-in-Storage Architecture for DNA Sequence Alignment

Roman Kaplan, Leonid Yavits, Ran Ginosar, Uri Weiser
2017 IEEE Micro  
A novel processing-in-storage (PRinS) architecture based on Resistive CAM (ReCAM) is described and proposed for Smith-Waterman (S-W) sequence alignment.  ...  The ReCAM massively-parallel compare operation finds matching base-pairs in a fixed number of cycles, regardless of sequence length.  ...  Any computational expression can be efficiently implemented in ReCAM storage using line-by-line execution of the truth table of the expression [8] .  ... 
doi:10.1109/mm.2017.3211121 fatcat:b5shco7zqjb7db2rfegicrmxza

Non-rigid face tracking with enforced convexity and local appearance consistency constraint

Simon Lucey, Yang Wang, Jason Saragih, Jeffery F. Cohn
2010 Image and Vision Computing  
More importantly, we show, as in the original CQF formulation, that the global warp update can be optimized jointly in an efficient manner.  ...  More importantly, we show, as in the original CQF formulation, that the global warp update can be optimized jointly in an efficient manner.  ...  curve fitting parameters A k , b k and c k from Equation 13 for each patch. (4) Compute the weights λ (t)k using Equation 16.  ... 
doi:10.1016/j.imavis.2009.09.009 pmid:25242852 pmcid:PMC4167730 fatcat:ribmcq32sngnpjdvemefqybznm

CalcGen Sequence Assembler Using a Spatio-temporally Efficient DNA Sequence Search Algorithm

Kyong Oh Yoon, Sung-Bae Cho
2013 Procedia Computer Science  
Also, the current advances in the bio-industry bring forward the era of personalized medicine using individual genome information.  ...  Furthermore, based on the proposed algorithm, we have developed a sequence analysis program called CalcGen assembler, and show the usefulness of the program with several experiments.  ...  The equation for evaluation is as follows. (1) In the above equation, E save is storage efficiency, S len is the length of nucleotide sequence, I len is bit number of integer type, and k is the length  ... 
doi:10.1016/j.procs.2013.10.016 fatcat:pe5xbvg7unfebm2eiiqtiaiv7y
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