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Diverse Scenario Exploration in Model Finders Using Graph Kernels and Clustering [chapter]

Robert Clarisó, Jordi Cabot
2020 Lecture Notes in Computer Science  
With this metric, it is possible to cluster scenarios effectively, improving the usability of model finders and making testing and validation more efficient.  ...  To solve this problem, we propose the use of graph kernels, a family of methods for computing the (dis)similarity among pairs of graphs.  ...  This paper proposes a method for distilling diverse instances in the model finder output based on the use of clustering.  ... 
doi:10.1007/978-3-030-48077-6_3 fatcat:l4t2rlf6rfeoval4lcffvtn4me

An Empirical-cum-Statistical Approach to Power-Performance Characterization of Concurrent GPU Kernels [article]

Nilanjan Goswami, Amer Qouneh, Chao Li, Tao Li
2020 arXiv   pre-print
Diversity analysis of proposed multi-kernels confirms characteristic variation and power-profile diversity within the suite.  ...  Realization of exascale computing using accelerators requires further improvements in power efficiency.  ...  Hence, we use PCA/clustering based analysis to observe the intra-suite diversity.  ... 
arXiv:2011.02368v2 fatcat:xgce6gvcjjcilfwem452yd3hsi

GraphClust2: Annotation and discovery of structured RNAs with scalable and accessible integrative clustering

Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, Rolf Backofen
2019 GigaScience  
GraphClust2 bridges the gap between high-throughput sequencing and structural RNA analysis and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner  ...  Background RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function.  ...  We thank Sean Eddy for the helpful comments and discussions. We also thank Sita J. Saunders and Mehmet Tekman for providing feedback about this manuscript.  ... 
doi:10.1093/gigascience/giz150 pmid:31808801 pmcid:PMC6897289 fatcat:d2lexbowt5glhgycldteocgo74

Scanflow: A multi-graph framework for Machine Learning workflow management, supervision, and debugging [article]

Gusseppe Bravo-Rocca, Peini Liu, Jordi Guitart, Ajay Dholakia, David Ellison, Jeffrey Falkanger, Miroslav Hodak
2021 arXiv   pre-print
The framework allows defining and deploying ML workflows in containers, tracking their metadata, checking their behavior in production, and improving the models by using both learned and human-provided  ...  In this paper, we propose a novel containerized directed graph framework to support and accelerate end-to-end ML workflow management, supervision, and debugging.  ...  Five scenarios were tested to proof the usefulness of using learning and symbolic special nodes in the Scanflow graph structure.  ... 
arXiv:2111.03003v1 fatcat:lpllikyryff4zmyridyuuc4vtu

Computationally Inexpensive Appearance Based Terrain Learning in Unknown Environments

Prabhakar Mishra, Anirudh Viswanathan
2013 Journal of Artificial Intelligence and Soft Computing Research  
Color based clustering using dominant terrain texture is then performed in perception sub-space.  ...  The scheme allows for on-line, and in-motion update of the terrain model.  ...  Aknowledgements The authors gratefully acknowledge Professor Koshy George, Director at the PES Centre for Intelligent Systems, for his feedback and suggestions.  ... 
doi:10.2478/jaiscr-2014-0014 fatcat:g32rwiosv5daxe5yuu225bwogq

Clustering static analysis defect reports to reduce maintenance costs

Zachary P. Fry, Westley
2013 2013 20th Working Conference on Reverse Engineering (WCRE)  
We evaluate our technique using 8,948 defect reports produced by the Coverity Static Analysis and FindBugs tools in both C and Java programs totaling over 14 million lines of code.  ...  We propose to automatically cluster machine-generated defect reports so that similar bugs can be triaged and potentially fixed in aggregate.  ...  ACKNOWLEDGMENTS The authors are sincerely indebted to Andy Chou of Coverity for initial ideas, guidance, and technical support.  ... 
doi:10.1109/wcre.2013.6671303 dblp:conf/wcre/FryW13 fatcat:rzccesx5kbcexmrk7eiqsnyiyy

Statelets: high dimensional predominant shapes in dynamic functional network connectivity [article]

Md Abdur Rahaman, Eswar Damaraju, Debbrata Kumar Saha, Sergey M. Plis, Vince Calhoun
2020 bioRxiv   pre-print
We handle scale differences using the earth mover distance as our similarity metric and utilizing kernel density estimation to build a probability density profile for each shapelet.  ...  Unlike clustering the time series, we approximate short, variable-length connectivity patterns using the probability density profile of the shapelets from lower dimensions.  ...  For a smoother density model, the common practice uses the Gaussian kernel, simplifying the following kernel density model. p(x)= 1 n ∑ 1 (2πh 2 ) D 2 n i = 1 e - | x -x i | 2 2h 2 (9) here ℎ is the standard  ... 
doi:10.1101/2020.08.16.252999 fatcat:3quvhptuobgljdf3tca5jiu2ze

An Introduction to Text Mining [chapter]

Charu C. Aggarwal, ChengXiang Zhai
2012 Mining Text Data  
It is an important task in text mining and has been extensively studied in various research communities including natural language processing, information retrieval and Web mining.  ...  It has a wide range of applications in domains such as biomedical literature mining and business intelligence.  ...  In some cases, however, our goal is to find all the potentially useful facts from a large and diverse corpus such as the Web.  ... 
doi:10.1007/978-1-4614-3223-4_1 fatcat:qg4qqp2ulzd6znc5okogc3civy

A survey of methods for time series change point detection

Samaneh Aminikhanghahi, Diane J. Cook
2016 Knowledge and Information Systems  
Detection of change points is useful in modelling and prediction of time series and is found in application areas such as medical condition monitoring, climate change detection, speech and image analysis  ...  Definition 5: In a time series, using sliding window X t as a sample instead of x t , an interval χ t with Hankel matrix {X t , X t+1 , ... , X t+n-1 } as shown in Figure 2 will be a set of n retrospective  ...  In this survey we will explain the problem of change point detection and explore how different supervised and unsupervised methodologies can be used for detecting change points in time series data.  ... 
doi:10.1007/s10115-016-0987-z pmid:28603327 pmcid:PMC5464762 fatcat:qtjvqsgdkjgwtivwlmjn27xyde

Task-parallel Analysis of Molecular Dynamics Trajectories [article]

Ioannis Paraskevakos and Andre Luckow and Mahzad Khoshlessan and George Chantzialexiou and Thomas E. Cheatham and Oliver Beckstein and Geoffrey C. Fox and Shantenu Jha
2018 arXiv   pre-print
In this paper, we investigate three task-parallel frameworks: Spark, Dask and RADICAL-Pilot with respect to their ability to support data analytics on HPC resources and compare them with MPI.  ...  We propose and evaluate different approaches for parallelization of a representative set of MD trajectory analysis algorithms, in particular the computation of path similarity and leaflet identification  ...  Acknowledgements We thank Andre Merzky for useful discussions. This work is funded by NSF 1443054 and 1440677.  ... 
arXiv:1801.07630v3 fatcat:m7tb4qef2vagdod4xfwswdyr4a

Semantic Mapping Using Mobile Robots

D.F. Wolf, G.S. Sukhatme
2008 IEEE Transactions on robotics  
Both approaches have been tested and experimentally validated in two problem domains: terrain mapping and activity-based mapping.  ...  We present two methods, the first based on hidden Markov models and the second on support vector machines.  ...  ACKNOWLEDGMENTS The authors thank Dieter Fox and Wolfram Burgard for the initial ideas and discussions on terrain mapping using HMM.  ... 
doi:10.1109/tro.2008.917001 fatcat:5xqvlcgh4rgmrnyronxfju5yfu

Mapping for the Support of First Responders in Critical Domains

Alexander Kleiner, Christian Dornhege
2011 Journal of Intelligent and Robotic Systems  
The algorithm processes data from laser range finder and gyroscope only, thereby it is independent from the robot platform.  ...  In critical domains such as urban search and rescue (USAR), and bomb disposal, the deployment of teleoperated robots is essential to reduce the risk of first responder personnel.  ...  Large clusters are visible for both the RBPF and DCMapping. We identified the relations in those clusters and marked the corresponding relations in the resulting maps.  ... 
doi:10.1007/s10846-010-9520-x fatcat:jivvvdahpze6teorj4akc7zefm

Collective Mind, Part II: Towards Performance- and Cost-Aware Software Engineering as a Natural Science [article]

Grigori Fursin and Abdul Memon and Christophe Guillon and Anton Lokhmotov
2015 arXiv   pre-print
hardware to be able to predict best optimizations and improve compilers and hardware depending on usage scenarios and requirements.  ...  The community can then collaboratively classify solutions, prune redundant ones, and correlate them with various features of software, its inputs (data sets) and used hardware either manually or using  ...  set either manually as we did in [37] , or using Codelet Finder from CAPS Entreprise as we did om the MILEPOST project [39] , or using semi-manual extraction of OpenCL/CUDA kernels combined with OpenME  ... 
arXiv:1506.06256v1 fatcat:l3xrlisen5gglk5jtiusfx67dy

SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data

Ivan Dotu, Scott I. Adamson, Benjamin Coleman, Cyril Fournier, Emma Ricart-Altimiras, Eduardo Eyras, Jeffrey H. Chuang, Claus O. Wilke
2018 PLoS Computational Biology  
SARNAclust computes similarity between sequence/structure objects using a graph kernel, providing the ability to isolate the impact of specific features through the bulge graph formalism.  ...  SARNAclust can deconvolve multiple motifs simultaneously and determine the importance of specific features through a graph kernel and bulge graph formalism.  ...  Acknowledgments The authors thank Gene Yeo for assistance with the ENCODE CLIP-seq data, Chris Burge and Daniel Dominguez for sharing constructs and experimental advice, and Brent Graveley and Olga Anczukow-Camarda  ... 
doi:10.1371/journal.pcbi.1006078 pmid:29596423 pmcid:PMC5892938 fatcat:q5erpcq32vh5pctdyughtjmfpq

Reducing Efficiency of Connectivity-Splitting Attack on Newscast via Limited Gossip [chapter]

Jakub Muszyński, Sébastien Varrette, Pascal Bouvry
2016 Lecture Notes in Computer Science  
useful in a number of relevant application scenarios.  ...  For many problems however, this is not the case and it would be more appropriate to model such problems using dynamic graphs.  ... 
doi:10.1007/978-3-319-31204-0_20 fatcat:27rnwllk75cv5kncys2u7utreq
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