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...Transitive functional annotation by shortest-path analysis of gene expression data
Xianghong Zhou*, Ming-Chih J. Kao*, and Wing Hung Wong*
*Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115; and Department of Statistics, ...
...University of Alaska Southeast
STAT 273-J01 & J02 Elementary Statistics Fall 2003
Location, Time and Days of Week: Section 1: EG 225; 10:20 a.m. 11:20 a.m.; Mon Wed Fri. Section 2: HB 204; 1:10 p.m. 2:10 p.m.; Mon Wed Fri. Instructor Informati...
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Tokenizing Stemming & Stemming Used in many IR applications For building equivalence classes Connect Connected Connecting Connection Connections Same class; suffixes irrelevant Porter Stemmer, simple and efficient Website: http://www.tartarus.org/~martin/PorterStemmer On patas: ~/dropbox/08-09/570/porter Stemming and Performance Does stemming help IR performance? Harman 91 indicated that it hurt as much as it helped Krovetz 93 shows that stemming does help Porter-like algorithms work well with smaller documents Krovetz proposes that stemming loses information Derivational morphemes tell us something that helps identify word senses (and helps in IR) Stemming them = information loss Evaluating Performance Measures of Stemming Performance rely on similar metrics used in IR: Precision: measure of the proportion of selected items the system got right precision = tp / (tp + fp) # of correct answers / # of answers given Recall: measure of the proportion of the target items the system selected recall = tp / (tp + fn) # of correct answers / # of possible correct answers Rule of thumb: as precision increases, recall drops, and vice versa What about for other NLP tasks, such as tagging? Metrics widely in adopted Stat NLP Precision and Recall Take a given stemming task Suppose there are 100 words that could be stemmed A stemmer gets 52 of these right (tp) But it inadvertently stems 10 others (fp) Precision = 52 / (52 + 10) = .84 Recall = 52 / (52 + 48) = .52 Note: easy to get precision of 1.0. Why? Baseline Tokenizer 1 Tokenizer 2 Tokenizer 3 After After After After coming coming coming coming close close close close to to to to a a a a partial partial partial partial settlement ettlement settlement settlement s a a a a year year year year ago ago ago ago , , , , shareholders shareholders shareholders shareholders who who who who filed filed filed filed civil civil civil civil suits suits suits suits against against against against Ivan Ivan Ivan Ivan F. F F. F. Boesky . Boesky Boesky & Boesky & & Co. & Co. Co L.P. Co L.P. . Drexel . Drexel's L.P. 's L.P plaintiffs Drexel plaintiffs . ' 's ' Drexel plaintiffs 's ' plaintiffs Tokenizer 4 After coming close to a partial settlement a year ago , shareholders who filed civil suits against Ivan F. Boesky & Co. L.P. Drexel 's plaintiffs ' Precision Recall F-Measure 0.8 0.888889 0.844444444 Tokenizer 1 Tokenizer 2 0.961538 0.925926 0.943732194 Tokenizer 3 0.928571 0.962963 0.945767196 1 1 1 Tokenizer 4 1
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Washington >> STAT >> 573 (Fall, 2008)
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Washington >> STAT >> 576 (Fall, 2008)
BIOSTAT/STAT 576 Statistical Methods for Survival Data MW 9:00am - 10:20am, Spring 2007; HST T530 Instructor: Ying Qing Chen Tel: 206.667.7051 Email: yqchen@u.washington.edu Oce hour: Th 2:30pm - 3:30pm; H657 Course Web Site: http:/www.scharp.org/u...
Washington >> STAT >> 576 (Fall, 2008)
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Washington >> STAT >> 579 (Fall, 2008)
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Washington >> STAT >> 579 (Fall, 2008)
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Washington >> STAT >> 579 (Fall, 2008)
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Washington >> STAT >> 581 (Fall, 2008)
STATISTICS 581: Advanced Theory of Statistical Inference Fall, 2008 Time: Place: Professor: Oce: Phone: e-mail: Oce Hours: Texts: 10:30 - 11:20 MWF (lecture) MEB 245 Jon A. Wellner B320 Padelford 206-543-6207 jaw@stat.washington.edu 1:30 - 3:30 MWF...
Washington >> STAT >> 581 (Fall, 2008)
References for Statistics 581, Fall 2008 Analysis: Bartle, R. G., The Elements of Integration. Rudin, W., Principles of Mathematical Analysis. Royden, H. L., Real Analysis. Luenberger, D., Optimization by Vector Space Methods. Probability: Will...
Washington >> STAT >> 581 (Fall, 2008)
Statistics 581, Chapter 2 Empirical Distribution Function and Empirical Process Figures Wellner; 10/24/2008 1 0.8 0.6 0.4 0.2 0.2 0.4 0.6 0.8 1 Figure 1: Uniform Empirical Distribution Function, n = 50. 1 0.75 0.5 0.25 0.2 -0.25 0.4 0.6...
Washington >> STAT >> 581 (Fall, 2008)
Statistics 581, Midterm Exam Wellner; 11/06/2006 This exam is to be taken without any books or notes. 1. (24 points) Dene any three of the following ve terms. (a) A uniformly integrable sequence of random variables. (b) Convergence in rth mean of a...
Washington >> STAT >> 582 (Fall, 2008)
Stat 582 W03 Midterm exam Please give as complete solutions as possible. More paper is available if needed. 1. Let (X,Y) be bivariate normal, mean zero, variance 1, correlation r. Find a minimal sufficient statistic for r. Is it complete? 2. Suppo...
Washington >> STAT >> 582 (Fall, 2008)
STAT 582 FINAL EXAM 1. Let T (F) = m 2 = ( xdF(x)2 . Find, using the asymptotic theory for statistical functionals, the limiting F distribution of T (F n ) when m F 0. 2. Let (X 1 , Y 1 ), . . . , (X n , Y n ) be independent random variables with ...
Washington >> STAT >> 582 (Fall, 2008)
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Washington >> STAT >> 583 (Fall, 2008)
STAT583 Sp04 Homework1solution 1. (a)(c) E X i - m = 2 xdF(x) = d 2 2 s (1+ 2e) and (1- e)s + 3es ) = p p 0 E(X - m) 2 = s 2 (1+ 8e) .Standardasymptotictheoryhasthat n ( s2 - s 2 (1+ 8e) N(0,t 2 ) where 2 = E(X - m) 4 - E 2 (X - m) 2 = s 4 (3...
Washington >> STAT >> 583 (Fall, 2008)
STAT 583 SPRING 2008 Lecture Notes 1 Statistical Functionals The Gteux derivative of a statistical functional T(F) is the limit T (F + (G F ) T(F) . d1T(F;G F) = lim If Q( ) = T (F + (G F ) has a McLaurin expansion, we get an expansion (the von...
Washington >> STAT >> 583 (Fall, 2008)
STAT 583 Sp08 Solutions, Homework 3 1. (a) T (F! ) = F + !(G \" F ) so IC(x) = x ! F . (b) By the same calculation as that for the median we get p ! 1(x < F !1 ( p) IC(x) = , x \" F !1 ( p) !1 f (F ( p) d 1 T (F + !(\" x # F) = (c) Using (b) d! 1 ...
Washington >> STAT >> 583 (Fall, 2008)
STAT 583 Sp08 Homework 2 Due April 16. 1. Let F be a cdf on [0,1], and define for ! > 1 T (F) = x\"[0,1] # ( F(x) ! F(x!) $ . (a) Compute the Gateux derivative of T at the uniform distribution U on [0,1]. (b) Show that nR1,n = n(T (Fn ) ! T (U ...
Washington >> STAT >> 592 (Fall, 2008)
Homework problems (more problems will be added as we go along) Stat 592, W09 1. For a stationary random field Z(s); s !D \" R 2 , observed at sites s1,.,sn, derive the unbiased linear estimator with the smallest variance. Hint: Use a Lagrange multipli...
Washington >> STAT >> 592 (Fall, 2008)
NRCSE SpatialStatisticalMethods peter@stat.washington.edu www.stat.washington.edu/peter/592 STAT592A(UW)526(UBCV) 8904(SFU) Coursecontent 1.Kriging 1.Gaussianregression 2.Simplekriging 3.Ordinaryanduniversalkriging 4.Effectofestimatedcovariance 5....
Washington >> STAT >> 593 (Fall, 2008)
Course Syllabus: STAT 593 Modern Topics in Discrete Multivariate Analysis Spring Quarter 2008 Time and Location When: 10:30am-11:50am Tuesday and Thursday Where: TBA Instructor Adrian Dobra Oce: Padelford Hall B-303 E-mail: adobra@u.washington.edu ...
Washington >> HUM >> 202 (Fall, 2008)
Lecture 14: October 27, 2006 Questions Reading Lyrical Ballads (1798), published Anonymously; 3 poems by Coleridge; 20 poems by Wordsworth Preface added in 1800 2nd edition Lyrical Ballads: not just an experiment but a poeti...
Washington >> HUM >> 204 (Fall, 2008)
HUM 204 The Role of Perspective in History, Science, and Design Fall 2007 Lecture Meeting Times: Monday and Wednesday 12:30-1:50 Lecture Classroom: Kane 110 Instructors: Axel Roesler, Interaction Design Email: roesler@u.washington.edu Office Hours:...
Washington >> HUM >> 207 (Winter, 2008)
Molecular and Cellular Endocrinology 161 (2000) 117 120 www.elsevier.com/locate/mce Spermatogonial transplantation an update for the millennium Lonnie D. Russella *, Michael D. Griswoldb a Department of Physiology, School of Medicine, Southern Il...
Washington >> HUM >> 208 (Fall, 2008)
HUMANITIES 208: VIOLENCE, MYTH, AND MEMORY (SPRING 2008) Tuesday and Thursday 1:00-2:20, Johnson Hall 102 Francisco Benitez (Comp Lit) and Laurie Sears (History) TAs: Cheryll Alipio, Katrina Hagen, William Mitchell \"Violence, Myth, and Memory\" is bui...
Washington >> SWED >> 101 (Fall, 2008)
Lecture 36 Anthropogenic Effects on Climate It is well-documented that globally averaged land and sea-surface temperatures have increased 0.5 C in the last century. Is this the beginning of manmade global warming? Two major anthropogenic forcings on ...
Washington >> T C >> 402 (Winter, 2008)
Appendices to JFQA, Vol. 40, No. 2, June 2005, \"Horses and Rabbits? Trade-Off Theory and Optimal Capital Structure,\" by Nengjiu Ju, Robert Parrino, Allen M. Poteshman, and Michael S. Weisbach Horses and Rabbits? Trade-Off Theory and Optimal Capital ...
Washington >> T C >> 403 (Fall, 2008)
Kyle Kyros Starr TC 403 May 18, 2008 Do You Know the Way to San Jose? Exploring the Future During the course of this class, I have looked through a lens back at who I was in the past and evaluated that person against the person that I am now. In t...
Washington >> T C >> 493 (Fall, 2008)
Excerpts from Volume 1 of Capital (text from http:/www.marxists.org/archive/marx/works/1867-c1/index.htm) Introductory Note: Well discuss this in class, but just so you have it in front of you, Marx develops an analysis of capitalist production stres...
Washington >> T C >> 505 (Fall, 2008)
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Washington >> T C >> 505 (Fall, 2008)
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Washington >> T C >> 509 (Fall, 2008)
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Washington >> T C >> 509 (Fall, 2008)
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Washington >> T C >> 509 (Fall, 2008)
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Washington >> T C >> 516 (Fall, 2008)
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Washington >> T C >> 521 (Winter, 2008)
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Washington >> T C >> 521 (Winter, 2008)
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Washington >> T C >> 521 (Winter, 2008)
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Washington >> T C >> 598 (Fall, 2008)
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Washington >> T C >> 598 (Fall, 2008)
The Dav State Services \\WereSuspende d by Governor Dan Evans What if 24 hours? State services \\tere suspended for The federal government has been called local governments have been called omnipotent, and of American politics Ehe \"dark contine...
Washington >> THAI >> 302 (Fall, 2008)
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Washington >> IND E >> 101 (Fall, 2008)
Name: _Section/TA Name: _ Atmospheric Science 101, Spring 2003 Midterm 2 Thursday 22 May 2003 Version A Multiple Choice (2 points each) Choose the best answer and mark it on a Scantron sheet. 1. Choose the words which best complete the following sent...
Washington >> IND E >> 101 (Fall, 2008)
ABET Course Description IND E 101 Introduction to Industrial Engineering Elective Course Catalog course description: Examines the basic concepts and methods of industrial engineering through team-based hands-on activities. Explores the profession of ...
Washington >> IND E >> 250 (Fall, 2008)
ABET Course Description IND E 250 Fundamentals of Engineering Economy Required Course Catalog course description: Basics of industrial cost analysis and accounting. Application of engineering economics to decision making. Analysis of engineering alte...
Washington >> IND E >> 316 (Fall, 2008)
ABET Course Description IND E 316 Design of Experiments and Regression Analysis Required Course Catalog course description: Introduction to the analysis of data from planned experiments. Analysis of variance for multiple factors and applications of o...
Washington >> IND E >> 351 (Spring, 2008)
ABET Course Description IND E 351 Human Factors in Design Elective Course Catalog Course Description: Engineering considerations of the abilities and limitations of the human aspect in the design of operational systems and components. Functional, psy...
Washington >> IND E >> 410 (Fall, 2008)
UNIVERSITY OF OREGON Department of History Spring, 2006 Professor Quintard Taylor Office: 364 McKenzie Hall Email: qtaylor@uoregon.edu Phone: 346-6160 Web: http:/faculty.washington.edu/qtaylor/ Office Hours: 2:00-3:30 Tuesday History 410/510 Urban Ar...
Washington >> IND E >> 412 (Fall, 2008)
ABET Course Description IND E 412 Integer and Dynamic Programming Elective Course Catalog course description: Modeling and optimization of problems and dynamic programming approach to optimization. Topics include: integer programming formulation tech...
Washington >> IND E >> 424 (Winter, 2008)
ABET Course Description IND E 424 Simulation Elective Course Catalog course description: In this course, students will learn the processes, tools, and techniques for performing effective simulation analyses, specifically: i) (the basic underlying pri...
Washington >> IND E >> 426 (Spring, 2008)
ABET Course Description IND E 426 Reliability Engineering and System Safety Elective Course Catalog Course Description: Reliability and system safety measures. Life distributions and their applications in reliability. System reliability models. Desig...
Washington >> IND E >> 439 (Fall, 2008)
ABET Course Description IND E 439 Plant Layout and Material Handling Elective Course Catalog course description: In this course, students will learn how to apply the concept of material flow in: 1) facilities design (designing high-performance interi...
Washington >> IND E >> 455 (Fall, 2008)
ABET Course Description IND E 455 User Interface Design Elective Course Catalog Course Description: Design oriented to cover fundamentals of user interface design; models on human computer interaction, software psychology, input devices, usability, c...
Washington >> IND E >> 494 (Winter, 2008)
ABET Course Description IND E 494 Design in the Manufacturing Firm Required Course Catalog course description: Engineering design in manufacturing firms is presented. Topics include design methodology, concurrent engineering, and project management. ...
Washington >> IND E >> 537 (Fall, 2008)
Date 09/27 10/02 10/04 10/09 10/11 10/16 10/18 10/23 10/25 10/30 11/01 11/06 11/08 11/13 11/15 11/20 11/22 11/27 11/29 12/04 12/06 12/10 IND E 337A/537A INTRODUCTION TO MANUFACTURING SYSTEMS AUTUMN 2007 Topic Assignment _ Introduction _ Manu. Issues...
Washington >> INDN >> 401 (Fall, 2008)
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Washington >> INDON >> 111 (Fall, 2008)
ATM S 111 Global Warming: Understanding the Debate Fall 2008 Syllabus Course overview Human-induced climate change - popularly known as \"global warming\" - is emerging as one of the great challenges facing society in the 21st century. If we ignore ...
Washington >> INDON >> 111 (Fall, 2008)
Land Clearing and the Biofuel Carbon Debt Joseph Fargione, et al. Science 319, 1235 (2008); DOI: 10.1126/science.1152747 The following resources related to this article are available online at www.sciencemag.org (this information is current as of Ap...
Washington >> INDON >> 111 (Fall, 2008)
Climate Change 2007 Mitigation Edited by Bert Metz Co-chair Working Group III Netherlands Environmental Assessment Agency Ogunlade Davidson Co-chair Working Group III University of Sierra Leone Peter Bosch Rutu Dave Technical Support Unit IPCC ...
Washington >> INDON >> 111 (Fall, 2008)
Climate Change 2007: Impacts, Adaptation and Vulnerability The Intergovernmental Panel on Climate Change (IPCC) was set up jointly by the World Meteorological Organization and the United Nations Environment Programme to provide an authoritative inter...
Washington >> INDON >> 211 (Fall, 2008)
Atmospheric Sciences 211: Climate and Climate Change Homework Set 3. Due February 14, 2000 February 7, 2000 1 Background: The purpose of this problem set is to use some of the concepts we have studied on atmospheric circulations and the hydrological...
Washington >> INDON >> 211 (Fall, 2008)
Atmospheric Sciences 211:Final Review Session: March 7, 2000 1 Early Climate 1. Brie y describe the global mean surface temperature behavior over the past 2 billion years 4 million years twenty thousand years thousand years hundred years 2. What kin...
Washington >> INDON >> 211 (Fall, 2008)
ATMOS SCI 211 HOMEWORK 4 Due: MONDAY, MAY 3 Part A About 11,000 years ago, when Europe and North America were recovering from the last ice age, the climate of Europe suddenly became colder again for several hundred years, before warming resumed. Wall...
Washington >> INDON >> 211 (Fall, 2008)
ATMS 211: Climate and Climate Change SQ2008 Assignment #5 Due Wed 28 May, 2008, in class or online via collect it. Name SOLNS Quiz Section: A (10:30) | B (11:30) Work with others, but write up answers independently. Points in bold after each questi...
Washington >> UCONJ >> 450 (Winter, 2008)
UCONJ 450: Healthcare in Underserved Communities Offered Winter Quarter Elective course 1 credit with credit/no-credit grading Course description: Healthcare in the Underserved Community is a course organized by the Students in the Community (SITC) ...
Washington >> UCONJ >> 540 (Winter, 2008)
Mercury (Hg) in the Dental Setting Mercury Toxicity Elemental Mercury Little or no toxic effect when ingested Mercury vapors Readily absorb in tissue Significant toxicity if inhaled Targets: lungs, CNS, kidneys Mercury is a Common, Everyday ...
Washington >> INFO >> 198 (Fall, 2008)
# # ChangeLog for /ethnomed.contenttypes/trunk/docs/HISTORY.txt # # Generated by Trac 0.10.5 # 01/18/09 07:24:25 # 10/20/08 15:41:10 dunlapm [198] * ethnomed.contenttypes/trunk/docs/HISTORY.txt (modified) forgot to make notes in History 09/10/08 16:1...
Washington >> INFO >> 200 (Fall, 2008)
Econ 200 D Summer 2008 Game Theory Game theory is the study of multiperson decision problems; the goal is to make predictions of the decisions, or strategic interactions. This arises a lot in economics Industrial Organization: Models of oligopoly ...
Washington >> INFO >> 221 (Summer, 2008)
General Suggestions based on the Yellow Hill Report (11/5/02) Paul R. Cereghino - raphael@u.washington.edu Your papers are practice for writing professional reports. Write as a scientist reporting an experiment to a group of peers. Use language, form...
Washington >> INFO >> 300 (Fall, 2008)
INFO 300 Intellectual Foundations of Informatics Assignment 1 Information Is Everywhere Autumn 2007 Informationtechnology, systems, policies, uses, issuespervade all aspects of human endeavor. In this assignment, you are to investigate the nature, s...
Washington >> INFO >> 300 (Fall, 2008)
INFO 300 Intellectual Foundations of Informatics MajorAssignmentIssuesPaper (16%ofCourseGrade) DueDate:March24 Purpose:Toconductacriticalexaminationofoneormoreofthearguments/topics/ issuespresentedintheassignedreadings. Parameters: Thisisanindivid...
Washington >> INFO >> 300 (Fall, 2008)
INFO 300 Intellectual Foundations of Informatics Major Assignment 2 - Theory Applied A Value-Added Evaluation of an Information System Purpose: To analyze information systems using Taylors Value-Added Model. Overview: How well do information systems ...
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