SEASR Overview Loretta Auvil, Boris Capitanu National Center for Supercomputing Applications...

SEASR Overview Loretta Auvil, Boris Capitanu National Center for Supercomputing Applications University of Illinois at Urbana-Champaign [email protected], [email protected]

Overview of Course MondayTuesdayWednesdayThursdayFriday MORNINGMORNING SEASR Overview Overview of Course SEASR Overview and Motivation Example SEASR Analytics and Applications SEASR Architecture Introduction of Meandre SEASR Community Hub Meandre Workbench Overview of Workbench Overview of Repositories Designing and Constructing Flows SEASR Analytics for Zotero Demonstrations of SEASR Analytic Use of SEASR services with Zotero and VUE Creating Zotero Flows Configuration Mechanism Web Service Components Zotero-enabled Flows VUE-enabled Flows Mashups and Dashboards SEASR as a service Other services, like Tapor Text Application: JSTOR Text Application: Airport Data SEASR Apps and Future Work Audio Analytics: NEMA Text Analyitcs: Monk Workbench SEASR Central Future Meandre Features Future Meandre Workbench Features Attendee Plan Presentations AFTERNOONAFTERNOON Text Analytics Overview of Text Analytics Dunning Loglikelihood Comparison Text Clustering /Topic Modeling Frequent Patterns Analysis Entity Extraction SEASR Community Hub: Text Analytics Flows More Text Analytics Emotion Tracking Concept Tracking Entity Extraction Topic Modeling Work on Project Modify project plan Identify data set Identify analysis Installation, Tools and Deployment Installation Community Collaboration Tools Architecture Development Tools ZigZag Parallelization Example ZigZag flows with Zotero, VUE and Fedora

Outline Overview of Course SEASR Overview and Motivation Example SEASR Analytics and Applications Attendee Plan SEASR Architecture Introduction of Meandre SEASR Community Hub Hands-On

SEASR Overview

SEASR This project will focus on developing, integrating, deploying, and sustaining a set of reusable and expandable software components and a supporting framework, SEASR that will benefit a broad set of data mining applications for scholars in humanities The key goals established for this effort are a set of software centric directives: Support the development of a state-of-the-art software environment for unstructured data management and analysis of digital libraries, repositories and archives, as well as educational platforms that are expected to contribute to many of the humanities breakthroughs of the 21st century. Support the continued development, expansion, and maintenance of end-to-end software system user interfaces, workflow engines, data management, analysis and visualization tools, collaborative tools, and other software integrated into a complete environment SEASR to bring the full power of data analytics to the scholars. Support education and training for use of this software environment for analysis through workshops to promote its usage among scholars

The SEASR Picture

Workshop Objective The objective of the workshop is: To explain and demonstrate the utility of SEASR for digital humanities, and to bring you to a point where you could deploy, contribute and utilize the SEASR environment.

Workshop Goals The goals of the workshop are: LEARN: Provide a detailed understanding of the SEASR framework LEARN: Provide a foundation and examples for participant teams to use SEASR in a study or inquiry ADOPT: Share participant generated research plans to utilize SEASR INSTALL: Provide detailed instructions on how to install, build components, integrate existing applications, and maintain the SEASR environment SUPPORT: Develop plans for resolution of issues raised by the user community in utilization of SEASR SUSTAIN: Develop a plan for community driven future development and dissemination of SEASR

SEASR @ Work Tag Cloud Count tokens Filter options supported Stem words

SEASR @ Work Ngram Tag Cloud Count multiple words Filter options Stem

SEASR @ Work Dunning Loglikelihood Feature comparison of tokens Specify an analysis document/collection Specify a reference document/collection Perform statistics comparison using Dunning Loglikelihood Example showing over-represented Analysis Set: The Project Gutenberg EBook of A Tale of Two Cities, by Charles Dickens Reference Set: The Project Gutenberg EBook of Great Expectations, by Charles Dickens Example showing over-represented Analysis Set: The Project Gutenberg EBook of A Tale of Two Cities, by Charles Dickens Reference Set: The Project Gutenberg EBook of Great Expectations, by Charles Dickens

SEASR @ Work HITS Summarizer

SEASR @ Work Entity Mash-up Entity Extraction with OpenNLP or Stanford NER Locations viewed on Google Map Dates viewed on Simile Timeline

SEASR @ Work Entities To Network Identify entities Define relationships between entities within same sentence

SEASR @ Work: Topic Modeling Given: Set of documents Find: To reveal the semantic content in large collection of documents Usage: Mallet Topic Modeling tools Output: Shows the percentage of relevance for each document in each cluster Shows the key words and their counts for each topic

SEASR @ Work Text Clustering Clustering of Text by token counts Filtering options for stop words, Part of Speech Dendogram Visualization

NEMA: Executes a SEASR flow for each run Loads audio data Extracts features for every 10 sec moving window of audio Loads and applies the models Sends results back to the WebUI NESTER: Annotation of Audio via Spectral Analysis SEASR @ Work Audio Analysis

SEASR @ Work MONK Executes flows for each analysis requested Predictive modeling using Nave Bayes Predictive modeling using Support Vector Machines (SVM) Feature comparisons

SEASR @ Work DISCUS On-demand usage of analytics while surfing While navigating request analytics to be performed on page Text extraction and cleaning Summarization and key work extraction List the important terms on the page being analyzed Provide relevant short summaries Visual maps Provide a visual representation of the key concepts Show the graph of relations between concepts

SEASR @ Work Concept Mapping Goal is to have this type of Visualization to track emotions across a text document (Leveraging flare.prefuse.org)

SEASR @ Work Zotero Plugin to Firefox Zotero manages the collection Launch SEASR Analytics Citation Analysis uses the JUNG network importance algorithms to rank the authors in the citation network that is exported as RDF data from Zotero to SEASR Zotero Export to Fedora through SEASR Saves results from SEASR Analytics to a Collection Launch MONK Processing MONK DB Ingestion WorkflowMONK DB Ingestion Workflow

Repository Search & Browse Web Service Interactive Web Application Zotero Upload to Repository SEASR @ Work Fedora

Attendee Project Plan Explore tool usage during learning exercises Participate in discussion Design a project plan to use SEASR this week for some analysis Modify and develop the project plan over the week Present and discuss project plan and results on Friday

Attendee Project Plan (2) Study/Project Title Team Members and their Affiliation Procedural Outline of Study/Project Research Question/Purpose of Study Data Sources Analysis Tools Activity Timeline or Milestones Report or Project Outcome(s) Ideas on what your team needs from SEASR staff to help you achieve your goal.

SEASR Architecture

Components Virtualization Infrastructure Meandre Infrastructure Visualization Component Repository Component Discovery Meandre Data-Intensive Flows Apps Services Plugins Web Apps Analytics Data Developer Tools Repositories Data Analysis Components Flows Repositories Data Analysis Components Flows User Interfaces Cloud Computing Visualizations Meandre Workbench

Data Driven Models

SEASR: Reach + Relevance + Reuse + Repeatability SEASR emphasizes flexibility, scalability, modularity, provides community hub and access to heterogeneous data and computational systems Semantic driven environment for SOA interoperability Encourages sharing and participation for building communities Modular construction allows flows to be modified and configured to encourage reusability within and across domains Enables a mashup and integration of tools Data-intensive flows can be executed on a simple desktop or a large cluster(s) without modification Computation can be created for distributed execution on servers where the content lives User accessibility to control trust and compliance with required copyright license of content Relies on standardized Resource Description Framework (RDF) to define components and flow

Enables Humanist To ask key questions: What recurrent patterns would be of interest to literary scholars Which patterns are characteristic of the English language and which are characteristic of a particular author, work, topic, or time? Patterns based on words can be extracted from literary bodies; however, can patterns be extracted based on grammar or plot constructs? When are correlated patterns meaningful? Can they be organized based on such criteria? How can an authors intentionality be assessed given an extracted pattern?

SEASR Enables Scholarly Research Discovery What hypothesis or rules can be generated by the features of the corpus? What features or language of the corpus best describes the corpus? What are the similarities between elements, documents, or corpuses to each other.

Meandre: Infrastructure SEASR/Meandre Infrastructure: Dataflow execution paradigm Semantic-web driven Web Oriented Supports publishing services Modular components Encapsulation and execution mechanism Promotes reuse, sharing, and collaboration

Meandre: Semantic Web Concepts Relies on the usage of the resource description framework (RDF) which uses simple notation to express graph relations written usually as XML to provide a set of conventions and common means to exchange information Provides a common framework to share and reuse data across application, enterprise, and community boundaries Focuses on common formats for integration and combination of data drawn from diverse sources Pays special attention to the language used for recording how the data relates to real world objects Allows navigation to sets of data resources that are semantically connected.

Meandre: Metadata Ontologies Meandre's metadata relies on three ontologies: The RDF ontology serves as a base for defining Meandre descriptors The Dublin Core Elements ontology provides basic publishing and descriptive capabilities in the description of Meandre descriptors The Meandre ontology describes a set of relationships that model valid components, as understood by the Meandre execution engine architecture

@prefix meandre:. @prefix xsd:. @prefix dc:. @prefix rdfs:. @prefix rdf:. @prefix :. meandre:name "Limited iterations"^^xsd:string ; rdf:type meandre:executable_component ; dc:creator "Xavier Llora"^^xsd:string ; dc:date "2007-11-17T00:32:35"^^xsd:date ; dc:description "Allows only a limited number of iterations"^^xsd:string ; dc:format "java/class"^^xsd:string ; dc:rights "University of Illinois/NCSA Open Source License"^^xsd:string ; meandre:execution_context, ;... Existing Standards Meandre: Components in RDF

Meandre: Components Types Components are the basic building block of any computational task. There are two kinds of Meandre components: Executable components Perform computational tasks that require no human interactions during runtime Processes are initialized during flow startup and are fired when in accordance to the policies defined for it. Control components Used to pause dataflow during user interaction cycles WebUI may be a HTML Form, Applet, or Other user interface

Meandre: Dataflow Example Dataflow Addition Example Logical Operation + Requires two inputs Produces one output When two inputs are available Logical operation can be preformed Sum is output When output is produced Reset internal values Wait for two new input values to become available Value1 Value2 Sum

Meandre: Create, Publish, & Share Components and Flows have RDF descriptors Easily shared, fosters sharing, & reuse Allow machines to read and interpret Independent of the implementations Combine different implementation & platforms Components: Java, Python, Lisp, Web Services Execution: On a Laptop or a High Performance Cluster A Location is RDF descriptor of one to many components, one to many flows, and their implementations

Meandre: Repository & Locations Each location represents a set components/flows Users can Combine different locations together Create components Assemble flows Share components and flows Repositories Help Administrate complex environments Organize components and flows

Meandre: Metadata Properties Components and Flows share properties such as component name, creator, creation date, description, tags, and rights. Components specific metadata to describe the components' behavior, its location, type of implementation, firing policy, runnable, format, resource location, and execution context Flow specific metadata describes the directed graph of components, components instances, connectors, connector instance data port source, connector, instance data port target, connector instance source, connector instance target, instance name

Meandre: Programming Paradigm The programming paradigm creates complex tasks by linking together a bunch of specialized components. Meandre's publishing mechanism allows components developed by third parties to be assembled in a new flow. There are two ways to develop flows : Meandres Workbench visual programming tool Meandres ZigZag scripting language

Locations Components Flows Meandre: Workbench Existing Flow Web-based UI Components and flows are retrieved from server Additional locations of components and flows can be added to server Create flow using a graphical drag and drop interface Change property values Execute the flow

Meandre: ZigZag Script Language ZigZag is a simple language for describing data- intensive ows Modeled on Python for simplicity. ZigZag is declarative language for expressing the directed graphs that describe ows. Command-line tools allow ZigZag files to compile and execute. A compiler is provided to transform a ZigZag program (.zz) into Meandre archive unit (.mau). Mau(s) can then be executed by a Meandre engine.

Community Hub Explore existing flows to find others of interest Keyword Cloud Connections Find related flows Execute flow Comments

Community Hub: Keyword Cloud Design

Community Hub

Keyword Cloud Implementation Keyword Cloud functionality is currently implemented as a wordpress plugin

Detail View of Application Detail View with Related Flows

Community Hub: Connections Design

Demonstration Community Hub Keyword Cloud Functionality Tag Cloud Viewer Ngram Tag Cloud Viewer HITS Summarizer Date Entity to Simile Timeline Location Entity to Google Map Google Search to Tag Cloud Viewer Entity to Protovis Network Graph Readability NEMA's Son of Blinkie

Learning Exercises: Community Hub 1.Explore Community Hub's Keyword Cloud Functionality A.Open browser and go to http://seasr.org B.Click on "View Projects C.Click on "Keyword Cloud D.Click on "visualization" to see all the existing applications that have a tag of "visualization" E.Click on "cluster" to see all the existing applications that have a tag of "visualization" and "cluster F.Click on the delete button to remove "cluster" from the selection G.Click on the "Tag Cloud Viewer" for more detail information about this application

Learning Exercises: Tag Cloud Viewer 2.Perform analysis using "Tag Cloud Viewer" on a hard coded web page A.Open browser and go to http://seasr.org/documentation/example-flows/tag-cloud-viewer/ http://seasr.org/documentation/example-flows/tag-cloud-viewer/ B.Click on the "Execute" button to launch the creation of a tag cloud view for "Emma" by Jane Austen retrieved from Project Gutenberg 3.Perform analysis using Tag Cloud Viewer" on a webpage of your choice A.Open browser and go to http://seasr.org/documentation/example-flows/tag-cloud-viewer/ http://seasr.org/documentation/example-flows/tag-cloud-viewer/ B.Find a web url that you are interested in analyzing C.Click on the "Custom Execute" button to launch the application where you can copy and paste a web url that you are interested in analyzing

Learning Exercises: Google Search 4.Perform analysis using "Google Search to Tag Cloud Viewer" on a topic of your choice A.Use Community Hub to open the "Google Search to Tag Cloud Viewer" page or open browser and go to http://seasr.org/documentation/example- flows/google-search-to-tag-cloud-viewer/ http://seasr.org/documentation/example- flows/google-search-to-tag-cloud-viewer/ B.Click on the "Custom Execute" button to launch the application where you can type your Google query for analysis

Attendee Project Plan Study/Project Title Team Members and their Affiliation Procedural Outline of Study/Project Research Question/Purpose of Study Data Sources Analysis Tools Activity Timeline or Milestones Report or Project Outcome(s) Ideas on what your team needs from SEASR staff to help you achieve your goal. Identify Research Question Identify Research Question

Discussion Questions What are data repositories that you utilize in your scholarly research? What tools or applications are being utilized against these repositories?

SEASR Overview Loretta Auvil, Boris Capitanu National Center for Supercomputing Applications...

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