Evaluation of Clusterings – Metrics and Visual Support
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Effect of Distance Measures on Partitional Clustering Algorithms
Sesham Anand et al, / (IJCSIT) International Journal of Computer Science and Information Technologies, Vol. 6 (6) , 2015, 5308-5312 Effect of Distance measures on Partitional Clustering Algorithms using Transportation Data Sesham Anand#1, P Padmanabham*2, A Govardhan#3 #1Dept of CSE,M.V.S.R Engg College, Hyderabad, India *2Director, Bharath Group of Institutions, BIET, Hyderabad, India #3Dept of CSE, SIT, JNTU Hyderabad, India Abstract— Similarity/dissimilarity measures in clustering research of algorithms, with an emphasis on unsupervised algorithms play an important role in grouping data and methods in cluster analysis and outlier detection[1]. High finding out how well the data differ with each other. The performance is achieved by using many data index importance of clustering algorithms in transportation data has structures such as the R*-trees.ELKI is designed to be easy been illustrated in previous research. This paper compares the to extend for researchers in data mining particularly in effect of different distance/similarity measures on a partitional clustering algorithm kmedoid(PAM) using transportation clustering domain. ELKI provides a large collection of dataset. A recently developed data mining open source highly parameterizable algorithms, in order to allow easy software ELKI has been used and results illustrated. and fair evaluation and benchmarking of algorithms[1]. Data mining research usually leads to many algorithms Keywords— clustering, transportation Data, partitional for similar kind of tasks. If a comparison is to be made algorithms, cluster validity, distance measures between these algorithms.In ELKI, data mining algorithms and data management tasks are separated and allow for an I. INTRODUCTION independent evaluation. -
Extraction of User's Stays and Transitions from Gps Logs: a Comparison of Three Spatio-Temporal Clustering Approaches
MASTERARBEIT EXTRACTION OF USER’S STAYS AND TRANSITIONS FROM GPS LOGS: A COMPARISON OF THREE SPATIO-TEMPORAL CLUSTERING APPROACHES Ausgeführt am Institut für Geoinformation und Kartographie der Technischen Universität Wien unter der Anleitung von Univ.Prof. Mag.rer.nat. Dr.rer.nat. Georg Gartner, TU Wien Univ.Lektor Dipl.-Ing. Dr.techn. Karl Rehrl, TU Wien Mag. DI(FH) Cornelia Schneider, Salzburg Research durch Francisco Daniel Porras Bernárdez Austrasse 3b 209, 5020 Salzburg Wien, 25 January 2016 _______________________________ Unterschrift (Student) MASTER’S THESIS EXTRACTION OF USER’S STAYS AND TRANSITIONS FROM GPS LOGS: A COMPARISON OF THREE SPATIO-TEMPORAL CLUSTERING APPROACHES Conducted at the Institute for Geoinformation und Kartographie der Technischen Universität Wien under the supervision of Univ.Prof. Mag.rer.nat. Dr.rer.nat. Georg Gartner, TU Wien Univ.Lektor Dipl.-Ing. Dr.techn. Karl Rehrl, TU Wien Mag. DI(FH) Cornelia Schneider, Salzburg Research by Francisco Daniel Porras Bernárdez Austrasse 3b 209, 5020 Salzburg Wien, 25 January 2016 _______________________________ Signature (Student) ACKNOWLEDGEMENTS First of all, I would like to express my deepest gratitude to Dr. Georg Gartner and Dr. Karl Rehrl for their supervision as well as Mag. DI(FH) Cornelia Schneider and all the time they have deserved to my person. I really appreciate their patience and continuous support. I am also very grateful for the amazing opportunity that Salzburg Research Forschungsgesellschaft m.b.H. has given to me allowing me to develop my thesis during an internship at the institute. I will be always grateful for the confidence Dr. Rehrl and Mag. DI(FH) Schneider placed in me. -
Performance Measures Outline 1 Introduction 2 Binary Labels
CIS 520: Machine Learning Spring 2018: Lecture 10 Performance Measures Lecturer: Shivani Agarwal Disclaimer: These notes are designed to be a supplement to the lecture. They may or may not cover all the material discussed in the lecture (and vice versa). Outline • Introduction • Binary labels • Multiclass labels 1 Introduction So far, in supervised learning problems with binary (or multiclass) labels, we have focused mostly on clas- sification with the 0-1 loss (where the error on an example is zero if a model predicts the correct label and one if it predicts a wrong label). In many problems, however, performance is measured differently from the 0-1 loss. In general, for any learning problem, the choice of a learning algorithm should factor in the type of training data available, the type of model that is desired to be learned, and the performance measure that will be used to evaluate the model; in essence, the performance measure defines the objective of learning.1 Here we discuss a variety of performance measures used in practice in settings with binary as well as multiclass labels. 2 Binary Labels Say we are given training examples S = ((x1; y1);:::; (xm; ym)) with instances xi 2 X and binary labels yi 2 {±1g. There are several types of models one might want to learn; for example, the goal could be to learn a classification model h : X →{±1g that predicts the binary label of a new instance, or to learn a class probability estimation (CPE) model ηb : X![0; 1] that predicts the probability of a new instance having label +1, or to learn a ranking or scoring model f : X!R that assigns higher scores to positive instances than to negative ones. -
The Difference Between Precision-Recall and ROC Curves for Evaluating the Performance of Credit Card Fraud Detection Models
Proc. of the 6th International Conference on Applied Innovations in IT, (ICAIIT), March 2018 The Difference Between Precision-recall and ROC Curves for Evaluating the Performance of Credit Card Fraud Detection Models Rustam Fayzrakhmanov, Alexandr Kulikov and Polina Repp Information Technologies and Computer-Based System Department, Perm National Research Polytechnic University, Komsomolsky Prospekt 29, 614990, Perm, Perm Krai, Russia [email protected], [email protected], [email protected] Keywords: Credit Card Fraud Detection, Weighted Logistic Regression, Random Undersampling, Precision- Recall curve, ROC Curve Abstract: The study is devoted to the actual problem of fraudulent transactions detecting with use of machine learning. Presently the receiver Operator Characteristic (ROC) curves are commonly used to present results for binary decision problems in machine learning. However, for a skewed dataset ROC curves don’t reflect the difference between classifiers and depend on the largest value of precision or recall metrics. So the financial companies are interested in high values of both precision and recall. For solving this problem the precision-recall curves are described as an approach. Weighted logistic regression is used as an algorithm- level technique and random undersampling is proposed as data-level technique to build credit card fraud classifier. To perform computations a logistic regression as a model for prediction of fraud and Python with sklearn, pandas and numpy libraries has been used. As a result of this research it is determined that precision-recall curves have more advantages than ROC curves in dealing with credit card fraud detection. The proposed method can be effectively used in the banking sector. -
Performance Measures Accuracy Confusion Matrix
Performance Measures • Accuracy Performance Measures • Weighted (Cost-Sensitive) Accuracy for Machine Learning • Lift • ROC – ROC Area • Precision/Recall – F – Break Even Point • Similarity of Various Performance Metrics via MDS (Multi-Dimensional Scaling) 1 2 Accuracy Confusion Matrix • Target: 0/1, -1/+1, True/False, … • Prediction = f(inputs) = f(x): 0/1 or Real Predicted 1 Predicted 0 correct • Threshold: f(x) > thresh => 1, else => 0 • If threshold(f(x)) and targets both 0/1: a b r True 1 1- targeti - threshold( f (x i )) ABS Â( ) accuracy = i=1KN N c d True 0 incorrect • #right / #total • p(“correct”): p(threshold(f(x)) = target) † threshold accuracy = (a+d) / (a+b+c+d) 3 4 1 Predicted 1 Predicted 0 Predicted 1 Predicted 0 true false TP FN Prediction Threshold True 1 positive negative True 1 Predicted 1 Predicted 0 false true FP TN 0 b • threshold > MAX(f(x)) True 1 True 0 positive negative True 0 • all cases predicted 0 • (b+d) = total 0 d • accuracy = %False = %0’s Predicted 1 Predicted 0 Predicted 1 Predicted 0 True 0 Predicted 1 Predicted 0 hits misses P(pr1|tr1) P(pr0|tr1) True 1 True 1 a 0 • threshold < MIN(f(x)) True 1 • all cases predicted 1 false correct • (a+c) = total P(pr1|tr0) P(pr0|tr0) c 0 • accuracy = %True = %1’s True 0 True 0 alarms rejections True 0 5 6 Problems with Accuracy • Assumes equal cost for both kinds of errors – cost(b-type-error) = cost (c-type-error) optimal threshold • is 99% accuracy good? – can be excellent, good, mediocre, poor, terrible – depends on problem 82% 0’s in data • is 10% accuracy bad? -
A Practioner's Guide to Evaluating Entity Resolution Results
A Practioner’s Guide to Evaluating Entity Resolution Results Matt Barnes [email protected] School of Computer Science Carnegie Mellon University October, 2014 1. Introduction Entity resolution (ER) is the task of identifying records belonging to the same entity (e.g. individual, group) across one or multiple databases. Ironically, it has multiple names: deduplication and record linkage, among others. In this paper we survey metrics used to evaluate ER results in order to iteratively improve performance and guarantee sufficient quality prior to deployment. Some of these metrics are borrowed from multi-class clas- sification and clustering domains, though some key differences exist differentiating entity resolution from general clustering. Menestrina et al. empirically showed rankings from these metrics often conflict with each other, thus our primary motivation for studying them [1]. This paper provides practitioners the basic knowledge to begin evaluating their entity resolution results. 2. Problem Statement Our notation follows that of [1]. Consider an input set of records I = a, b, c, d, e where a, b, c, d, and e are unique records. Let R = a, b, d , c, e denote an{ entity resolution} clustering output, where ... denotes a cluster.{h Let Si hbe thei} true clustering, referred to as the “gold standard.” Theh i goal of any entity resolution metric is to measure error (or arXiv:1509.04238v1 [cs.DB] 14 Sep 2015 similarity) of R compared to the gold standard S. 3. Pairwise Metrics Pairwise metrics consider every pair of records as samples for evaluating performance. Let P airs(R) denote all the intra-cluster pairs in the clustering R. -
BETULA: Numerically Stable CF-Trees for BIRCH Clustering?
BETULA: Numerically Stable CF-Trees for BIRCH Clustering? Andreas Lang[0000−0003−3212−5548] and Erich Schubert[0000−0001−9143−4880] TU Dortmund University, Dortmund, Germany fandreas.lang,[email protected] Abstract. BIRCH clustering is a widely known approach for clustering, that has influenced much subsequent research and commercial products. The key contribution of BIRCH is the Clustering Feature tree (CF-Tree), which is a compressed representation of the input data. As new data arrives, the tree is eventually rebuilt to increase the compression. After- ward, the leaves of the tree are used for clustering. Because of the data compression, this method is very scalable. The idea has been adopted for example for k-means, data stream, and density-based clustering. Clustering features used by BIRCH are simple summary statistics that can easily be updated with new data: the number of points, the linear sums, and the sum of squared values. Unfortunately, how the sum of squares is then used in BIRCH is prone to catastrophic cancellation. We introduce a replacement cluster feature that does not have this nu- meric problem, that is not much more expensive to maintain, and which makes many computations simpler and hence more efficient. These clus- ter features can also easily be used in other work derived from BIRCH, such as algorithms for streaming data. In the experiments, we demon- strate the numerical problem and compare the performance of the orig- inal algorithm compared to the improved cluster features. 1 Introduction The BIRCH algorithm [23,24,22] is a widely known cluster analysis approach, that won the 2006 SIGMOD Test of Time Award. -
Benchmarking Differential Expression Analysis Tools for RNA-Seq: Normalization-Based Vs. Log-Ratio Transformation-Based Methods Thomas P
Quinn et al. BMC Bioinformatics (2018) 19:274 https://doi.org/10.1186/s12859-018-2261-8 RESEARCH ARTICLE Open Access Benchmarking differential expression analysis tools for RNA-Seq: normalization-based vs. log-ratio transformation-based methods Thomas P. Quinn1,2* , Tamsyn M. Crowley1,2,3 and Mark F. Richardson2,4 Abstract Background: Count data generated by next-generation sequencing assays do not measure absolute transcript abundances. Instead, the data are constrained to an arbitrary “library size” by the sequencing depth of the assay, and typically must be normalized prior to statistical analysis. The constrained nature of these data means one could alternatively use a log-ratio transformation in lieu of normalization, as often done when testing for differential abundance (DA) of operational taxonomic units (OTUs) in 16S rRNA data. Therefore, we benchmark how well the ALDEx2 package, a transformation-based DA tool, detects differential expression in high-throughput RNA-sequencing data (RNA-Seq), compared to conventional RNA-Seq methods such as edgeR and DESeq2. Results: To evaluate the performance of log-ratio transformation-based tools, we apply the ALDEx2 package to two simulated, and two real, RNA-Seq data sets. One of the latter was previously used to benchmark dozens of conventional RNA-Seq differential expression methods, enabling us to directly compare transformation-based approaches. We show that ALDEx2, widely used in meta-genomics research, identifies differentially expressed genes (and transcripts) from RNA-Seq data with high precision and, given sufficient sample sizes, high recall too (regardless of the alignment and quantification procedure used). Although we show that the choice in log-ratio transformation can affect performance, ALDEx2 has high precision (i.e., few false positives) across all transformations. -
Anomaly Detection in Application Log Data
UTRECHT UNIVERSITY MASTER THESIS Anomaly Detection in Application Log Data Author: First supervisor: Patrick KOSTJENS Dr. A.J. FEELDERS Second supervisor: Prof. Dr. A.P.J.M. SIEBES A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Computing Science in the Algorithmic Data Analysis Group Department of Information and Computing Sciences August 2016 ICA-3733327 iii UTRECHT UNIVERSITY Abstract Faculty of Science Department of Information and Computing Sciences Master of Science in Computing Science Anomaly Detection in Application Log Data by Patrick KOSTJENS Many applications within the Flexyz network generate a lot of log data. This data used to be difficult to reach and search. It was therefore not used unless a problem was reported by a user. One goal of this project was to make this data available in a single location so that it becomes easy to search and visualize it. Additionally, automatic analysis can be performed on the log data so that problems can be detected before users notice them. This analysis is the core of this project and is the topic of a case study in the domain of application log data analysis. We compare four algorithms that take different approaches to this prob- lem. We perform experiments with both artificial and real world data. It turns out that the relatively simple KNN algorithm gives the best perfor- mance, although it still produces a lot of false positives. However, there are several ways to improve these results in future research. Keywords: Anomaly detection, data streams, log analysis v Acknowledgements First and foremost, I would like to express my gratitude to Dr. -
Research Techniques in Network and Information Technologies, February
Tools to support research M. Antonia Huertas Sánchez PID_00185350 CC-BY-SA • PID_00185350 Tools to support research The texts and images contained in this publication are subject -except where indicated to the contrary- to an Attribution- ShareAlike license (BY-SA) v.3.0 Spain by Creative Commons. This work can be modified, reproduced, distributed and publicly disseminated as long as the author and the source are quoted (FUOC. Fundació per a la Universitat Oberta de Catalunya), and as long as the derived work is subject to the same license as the original material. The full terms of the license can be viewed at http:// creativecommons.org/licenses/by-sa/3.0/es/legalcode.ca CC-BY-SA • PID_00185350 Tools to support research Index Introduction............................................................................................... 5 Objectives..................................................................................................... 6 1. Management........................................................................................ 7 1.1. Databases search engine ............................................................. 7 1.2. Reference and bibliography management tools ......................... 18 1.3. Tools for the management of research projects .......................... 26 2. Data Analysis....................................................................................... 31 2.1. Tools for quantitative analysis and statistics software packages ...................................................................................... -
Software Benchmark—Classification Tree Algorithms for Cell Atlases
Article Software Benchmark—Classification Tree Algorithms for Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data Omar Alaqeeli 1 , Li Xing 2 and Xuekui Zhang 1,* 1 Department of Mathematics and Statistics, University of Victoria, Victoria, BC V8P 5C2, Canada; [email protected] 2 Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, SK S7N 5A2, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-250-721-7455 Abstract: Classification tree is a widely used machine learning method. It has multiple implementa- tions as R packages; rpart, ctree, evtree, tree and C5.0. The details of these implementations are not the same, and hence their performances differ from one application to another. We are interested in their performance in the classification of cells using the single-cell RNA-Sequencing data. In this paper, we conducted a benchmark study using 22 Single-Cell RNA-sequencing data sets. Using cross-validation, we compare packages’ prediction performances based on their Precision, Recall, F1-score, Area Under the Curve (AUC). We also compared the Complexity and Run-time of these R packages. Our study shows that rpart and evtree have the best Precision; evtree is the best in Recall, F1-score and AUC; C5.0 prefers more complex trees; tree is consistently much faster than others, although its complexity is often higher than others. Citation: Alaqeeli, O.; Xing, L.; Zhang, X. Software Benchmark— Keywords: classification tree; single-cell RNA-Sequencing; benchmark; precision; recall; F1-score; Classification Tree Algorithms for complexity; Area Under the Curve; run-time Cell Atlases Annotation Using Single-Cell RNA-Sequencing Data. -
Evaluation Criteria (For Binary Classification)
San José State University Math 251: Statistical and Machine Learning Classification Evaluation Criteria (for binary classification) Dr. Guangliang Chen Outline of the presentation: • Evaluation criteria – Precision, recall/sensitivity, specificity, F1 score – ROC curves, AUC • References – Stanford lecture1 – Wikipedia page2 1http://cs229.stanford.edu/section/evaluation_metrics_spring2020.pdf 2https://en.wikipedia.org/wiki/Receiver_operating_characteristic Evaluation criteria Motivation The two main criteria we have been using for evaluating classifiers are • Accuracy (overall) • Running time The overall accuracy does not reflect the classwise accuracy scores, and can be dominated by the largest class(es). For example, with two imbalanced classes (80 : 20), the constant prediction with the dominant label will achieve 80% accuracy overall. Dr. Guangliang Chen | Mathematics & Statistics, San José State University3/20 Evaluation criteria The binary classification setting More performance metrics can be introduced for binary classification, where the data points only have two different labels: • Logistic regression: y = 1 (positive), y = 0 (negative), • SVM: y = 1 (positive), y = −1 (negative) Dr. Guangliang Chen | Mathematics & Statistics, San José State University4/20 Evaluation criteria Additionally, we suppose that the classifier outputs a continuous score instead of a discrete label directly, e.g., 1 • Logistic regression: p(x; θ) = 1+e−θ·x • SVM: w · x + b A threshold will need to be specified in order to make predictions (i.e., to convert scores to labels). Dr. Guangliang Chen | Mathematics & Statistics, San José State University5/20 Evaluation criteria Interpretation of the confusion matrix The confusion table summarizes the 4 different combinations of true conditions and predicted labels: Predicted Actual (H0: Test point is negative) Positive Negative (H1: Test point is positive) Positive TPFP FP: Type-I error Negative FNTN FN: Type-II error The overall accuracy of the classifier is TP + TN Accuracy = TP + FP + FN + TN Dr.