Workflows

CamelCases (1)

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this process splits up camelcases

Created: 2010-06-02

Creation of New Attribute Depending on Val... (1)

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The process shows the usage of the operator "Generate Attributes" in combination with an "if - then - else" condition and nominal values. The values "value0" and "value1" are mapped to "T1", other values are mapped to "T2" for the new attribute.

Created: 2010-06-01

Linear Regression of Italian bookshops se... (1)

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Someone could help me? Why the correlation between the actual value and the predictive value of the attribute "Quantita" is so low?

Created: 2010-05-28

Provenance Challenge 1 workflow -- mockup ... (1)

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simulates the image processing for the PC1 workflow using beanshell that simply track test strings an image is a pair (header, image) specified as a list of depth 1: [header,image] so each processor with image input takes an input list. Note that the processors are designed to operate on single images (except softmean that operates on a list of images), but because the initial input is a list of images, all are processed by implicit iteration.

Created: 2010-05-28

Credits: Paolo

Missing value count (1)

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This workflow enables users to filter examples by the number of missing values they contains; it inserts the numeric attribute 'Missings' - representing, for each example, the count of attributes with missing values.

Created: 2010-05-27 | Last updated: 2010-07-13

Plot round results of a backward elimination (1)

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This process will perform a backward elimination and logs all performance and deviation results of each round. This way, you can use the visualizations of rapidminer to asses the performance gain.

Created: 2010-05-26

Simple DPAS query (4)

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queries dpas for each time priode and instrument

Created: 2010-05-26 | Last updated: 2011-12-15

Credits: Anja Le Blanc

Retrieve Instruments for event dates (2)

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Queries the HELIO ICS web service and returns a list of instruments available for the time periodes in VOTable format

Created: 2010-05-26

Credits: Anja Le Blanc

A simple CQL query workflow in caGrid (1)

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1. CQL is a language to query data from caGrid/caBIG services. This workflow is tested with Taverna 2.1.2 and the caGrid Workflow Suite downloadable from http://www.mcs.anl.gov/~wtan/t2/. 2.More information regarding CQL can be found from http://wiki.cagrid.org/display/dataservices. 3. Sample input (95) is provided in the workflow. It is to query all the hybridization data within a microarray experiment whose id is 95.

Created: 2010-05-24 | Last updated: 2010-05-25

Credits: Wei Tan

Query caArray data service and retrieving ... (2)

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need to install Taverna 2 caGrid integration suite from http://www.mcs.anl.gov/~wtan/t2/ and get a cagrid Dorian account (see http://wiki.cagrid.org/display/caGrid13/Home)

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: Wei Tan

simple HEC query (2)

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HEC query for table 'goes_xray_flare'

Created: 2010-05-21 | Last updated: 2010-08-04

Credits: Anja Le Blanc

Warp2D - 2D Time Alignment Workflow (3)

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2D Time Alignment We describe a new time alignment method that takes advantage of both dimensions of LC-MS data to resolve ambiguities in peak matching while remaining computationally efficient. This approach, Warp2D, combines peak extraction with a two-dimensional correlation function to provide a reliable alignment scoring function that is insensitive to spurious peaks and background noise. One-dimensional alignment methods are often based on the total-ion-current eluti...

Created: 2010-05-20 | Last updated: 2010-11-22

Credits: Ishtiaq AHMAD

Exclude a Attribute/Variable (1)

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This simple process demonstrates how to exclude a attribute or set of attributes from an example set/data set. In particular the first "Select Attributes" filter excludes the Outlook attribute. The second filter excludes subset {Outlook, Humidity}.

Created: 2010-05-20

Filter Wrong Predicted/Classified Samples (1)

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This process demonstrates how to filter validation samples which are predicted incorrectly. Thee key operator is "Filter Examples" that is set up to "wrong_predictions"

Created: 2010-05-19 | Last updated: 2010-06-08

Apply Same Preprocessing to Learning and V... (1)

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This process demonstrates how to apply the same prepossessing work flow to learning data and test/validation data. Due to overview reasons the preprocessing is hidden in a Preprocessing subprocess. To perform the same preprocessing work flow on the learning and testing data, both are collected to a Collection of Data. Then the "Loop Collection" operator loops over each collection. The actual preprocessing is done inside the "Loop Collection" operator. In the example only a "Rename" is done...

Created: 2010-05-19

Write/Store Correlation Matrix to an Excel... (1)

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This process demonstrates how to write/store/export the correlation matrix of the "Correlation Matrix" operator to an Excel file. One need to generate a Report with the "Generate Report" operator and export the Report to an Excel file.

Created: 2010-05-19

OpenTox Handle Task (8)

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Waits for a task to be finished and returns resulting URI

Created: 2010-05-18

Discard Attribute with More than x% Missin... (1)

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This process loops over all attributes and calculates the fraction of missings for each attribute. If this fration is larger than the fraction defined in the first "Set Macro" operator (macro: max_unknown), the attribute will be removed from the example set.

Created: 2010-05-15

Convert Nominal to Binominal to Numerical (1)

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This is a standard preprocessing subprocess taking nominal (categorical) attributes and introduces binominal dummy attributes before those are transformed to numerical which can be then used by learning schemes like SVM or Logistic Regression.

Created: 2010-05-15

Pivoting (1)

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This process shows the basics of Pivoting. A data set with three columns is loaded and partially generated. Afterwards, the data is rotated and missings are replaced by zero.

Created: 2010-05-15

Evaluating Multiple Models with Looped X-V... (1)

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This process shows how multiple different models can be evaluated with cross validation runs. This allows for the comparison of, for example, three prediction model types (e.g., ANN, SVM and DT) all at once under a x-fold cross validation. Having said that, the process actually performs the same cross validation several times using each time a different modeling scheme. It makes use of loops, collections, subprocess selection and macros and is therefore also an interesting showcase for more ...

Created: 2010-05-15

Setting an attribute value in a specific E... (1)

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This process will first generate an artificial dataset and tag it with ids. Then a Filter Examples Operator is used to get a dataset with exactly one example identified by it's id. Then a value is set in this example. Since the change in the data will be reflected in all views of the example set, a simply copy is passed by to the process' output. If you take a look at the attributes of the example with id 5, you will find the 12 there.

Created: 2010-05-14

Correct Attribute Type to Binominal (1)

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This process will first generate some artificial data to show a commonly known problem: Some attributes have only two values, but are not correctly stored as Binominal, instead RapidMiner recognizes them as nominal. In order to use them for some special operators, we have to change this to binominal. We can achieve this by using the Nominal to Binominal operator with the the parameter transform_binominals switched off. Please take a look at the data before and after the Nominal to Binominal o...

Created: 2010-05-14

EntrezGeneId_to_GOFunction (1)

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The workflow takes a list of Entrez gene ids and returns the corresponding GO function definitions. Example value: 1306 486 4712 108 9912 7639 23786

Created: 2010-05-13 | Last updated: 2010-05-13

Credits: Franck Tanoh

BLAST workflow (1)

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You can get three BLAST results against DDBJ, swiss-prot and PDB by using accession number of DDBJ.

Created: 2010-05-13 | Last updated: 2010-05-13

Credits: wabi

BLAST-ClustalW workflow (1)

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Execute blastn against DDBJ database with a given DNA sequence and compare the alignment regions of high similar sequences by using ClustalW.

Created: 2010-05-13 | Last updated: 2010-05-13

Credits: wabi

Virus genome extraction workflow (1)

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Retrieve genome entries which agree with the following conditions regarding the Definition item of entries from both VRL and PHG division in DDBJ. Includes "complete sequence" or includes "segment" and "complete sequence" Not include "TPA:" and "nearly complete"

Created: 2010-05-13 | Last updated: 2010-05-13

Credits: wabi

Homology workflow (1)

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There are many kinds of DNA data derived from many species in DDBJ. It makes possible to carry out the comparative study of genes of multiple species. The workflow provides a list of species and their genes that are similar to a human gene in response to a name of the human gene.

Created: 2010-05-12 | Last updated: 2010-05-12

Credits: wabi

Federated query using DCQL and credential ... (2)

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CDS_Activity issues an EPR of the delegated credential. FQP uses this EPR to fetch the actual delegated credential from CDS and uses it to invoke multiple data services (the query activity) on behalf of the invoker. CDS_Activity issues an EPR of the delegated credential. FQP uses this EPR to fetch the actual delegated credential from CDS and uses it to invoke multiple data services (the query activity) on behalf of the invoker. Need to install Taverna 2 caGrid integration suite from http://ww...

Created: 2010-05-11 | Last updated: 2010-11-05

Credits: Wei Tan

OpenTox Get Datasets (3)

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Gets a list of available data set URIs

Created: 2010-05-11

OpenTox Get Algorithms on TUM server (6)

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Get URIs of all available algorithms on TUM server

Created: 2010-05-11 | Last updated: 2011-05-11

OpenTox Apply Model On Dataset (3)

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Apply a model to predict a dataset

Created: 2010-05-11 | Last updated: 2010-05-11

OpenTox Apply Algorithm (7)

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Apply an OpenTox algorithm

Created: 2010-05-11 | Last updated: 2011-05-11

Defining positive class with Remap Binominal (1)

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This process shows how one can use the Remap Binominal operator to define which label value is treated as the positive class.

Created: 2010-05-11

iceLogo (1)

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This example workflow creates an iceLogo

Created: 2010-05-07 | Last updated: 2010-05-07

Credits: N. Colaert

Weighted Score Tables (1)

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This process calculates a weighted score as known from SAP BW. The first operator generates data similar to that used in the links you provided. The next operator (Discretize) defines the different age groups. The next three operators map each age group to the value used for scoring. The last operator finally calculates the score and adds it as a new column to your data set.

Created: 2010-05-05

Generating Example Weights depending on label (1)

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This process uses a Generate Attribute operator for assigning new weights to examples. It uses the if condition of this operator to distinguish between labels. This can be especially useful if you have a strong bias in your class frequency, which can harm learning. Please note that you must use a learning algorithm that supports weighted examples.

Created: 2010-05-03

Uniprot Protein Visualization (1)

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Jmol 3D visualization of a protein structure.

Created: 2010-05-01 | Last updated: 2010-05-01

Genes encoded by KEGG pathway (1)

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Takes a KEGG pathway (e.g. hsa00232), finds the proteins that those genes code for and returns the sequences of those proteins.

Created: 2010-04-30 | Last updated: 2010-05-01

Get KEGG gene descriptions and pathways (1)

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This workflow takes a list of KEGG gene identifiers and supplies descriptions associated to said genes + pathways including all genes and the descriptions associated to said pathways. The list_to_string local beanshell scripts merely transform a given list into a string of unique not-null elements separated by new lines (for batch btit use). Note that the input is a real taverna list : multiple values must be declared as multiple values instead of a single string value with distinct identif...

Created: 2010-04-30 | Last updated: 2010-04-30

Credits: Nadia Cerezo Paul Fisher

Attributions: Get Kegg Gene information

Transaction Analysis Demo from RM 5 Intro Day (1)

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This is the demo process presented at the RapidMiner 5 Intro Day. It combines customer segmentation with direct mailing. It loads some transaction data, aggregates and pivotes the data so it can be used by a clustering to perform a customer segmentation. Then, additional data is joined with the clustered data. First, response/no-response data is joined, and them some additional information about the users is added. Finally, customers are classified into response/no-response classes. The dat...

Created: 2010-04-30 | Last updated: 2010-05-05

Stacking (1)

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RapidMiner supports Meta Learning by embedding one or several basic learners as children into a parent meta learning operator. Here, we use a three base learners inside the stacking operator: decision tree induction, linear regression, and a nearest neighbours classifier. Finally, a Naive Bayes learner is used as a stacking learner which uses the predictions of the preceeding three learners to make a combined prediction.

Created: 2010-04-29

Crossvalidation with SVM (1)

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Performs a crossvalidation on a given data set with nominal label, using a Support Vector Machine as a learning algorithm. Inside the cross validation, the first subprocess generates an SVM model, and the second subprocess evaluates it. applying it on a so-far unused subset of the data and counting the misclassifications.

Created: 2010-04-29

Looping over Examples for doing de-aggrega... (1)

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This process is based on (artificially generated) data that looks like it has been aggregated before. The integer attribute Qty specifies the quantity of the given item that is represented by the rest of the example. The process now loops over every example and performs on each example another loop, that will append the current example to a new example set. This example set has been created as empty copy of the original example set, so that the attributes are equally. To get access to and rem...

Created: 2010-04-29

ChEBI mashup from searched string (1)

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A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint.A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint. First a full text search query is done, then we do a reverse link query to get all the related topic. Finally with a describe queries we obtain the complete graph of each topic. The ntriples result is a mashup of what is known about this searched topic form ChEBI. This graph can then be loaded in a triplestore for further exploration.

Created: 2010-04-29

Credits: Francois Belleau

Get survey data from SurveyMapper (2)

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Extracting public data (such as public surveys and their questions) from SurveyMapper. SurveyMapper (http://www.surveymapper.com/) a free real-time geographic survey and polling tool from the nice people at the Centre for Advanced Spatial Analysis, University College London.

Created: 2010-04-21 | Last updated: 2010-06-18

Credits: Alex Nenadic

Census data service (1)

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Census data services, invoked with a fixed SQL query

Created: 2010-04-21 | Last updated: 2010-04-21

Credits: Alex Nenadic

Census data and PRM services integration (1)

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This workflow combines services that provide census data with PRM (Population Reconstruction Model) services.

Created: 2010-04-21 | Last updated: 2010-04-21

Credits: Alex Nenadic

retrieve data for all instruments for even... (1)

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This workflow uses the HEC to retrieve events for a time spane given by the user from a HEC table given by the user as well. It uses all instruments available in the DPAS to retrieve data for the events Output: XML as returned by the DPASThis workflow uses the HEC to retrieve events for a time spane given by the user from a HEC table given by the user as well. It uses all instruments available in the DPAS to retrieve data for the events; empty results are filtered out, the data is combind wi...

Created: 2010-04-21

Credits: Anja Le Blanc

Attributions: DPAS general query HEC standard query Retrieve all data for all instruments for a given periode of time

DPAS general query with sorted field (1)

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same as DPAS general query. Calling the DPAS sortedQuery web service. additional input: partialSorting input boolean true or false false all result entries are sorted by start measurementTime true each request is sorted by measurement time; no overall time order, but queries stay in the order they there asked.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc