Created
March 24, 2016 14:18
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| { | |
| "name": "t_SNE", | |
| "doc": "t-Distributed Stochastic Neighbor Embedding,\na technique for dimensionality reduction.\n", | |
| "metadata": { | |
| "docker_image": "hbpmip/r-tsne:latest" | |
| }, | |
| "input": { | |
| "type": "null" | |
| }, | |
| "output": { | |
| "doc": "New representation for the data", | |
| "type": "array", | |
| "items": { | |
| "type": "record", | |
| "name": "ReducedData", | |
| "fields": [ | |
| { | |
| "name": "1", | |
| "type": "double", | |
| "doc": "Reduced dimension 1" | |
| }, | |
| { | |
| "name": "2", | |
| "type": "double", | |
| "doc": "Reduced dimension 2" | |
| }, | |
| { | |
| "name": "prov", | |
| "type": { | |
| "type": "enum", | |
| "name": "Enumprov", | |
| "symbols": [ | |
| "AD1", | |
| "AD2" | |
| ] | |
| }, | |
| "doc": "Variable prov" | |
| }, | |
| { | |
| "name": "age", | |
| "type": "double", | |
| "doc": "Variable age" | |
| } | |
| ] | |
| } | |
| }, | |
| "cells": { | |
| "query": { | |
| "type": { | |
| "doc": "Definition of the query that has produced this model", | |
| "name": "Query", | |
| "type": "record", | |
| "fields": [ | |
| { | |
| "name": "variables", | |
| "doc": "List of dependent variables", | |
| "type": { | |
| "type": "array", | |
| "items": { | |
| "type": "string" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "covariables", | |
| "doc": "List of explanatory variables", | |
| "type": { | |
| "type": "array", | |
| "items": { | |
| "type": "string" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "grouping", | |
| "doc": "List of groupings", | |
| "type": { | |
| "type": "array", | |
| "items": { | |
| "type": "string" | |
| } | |
| } | |
| }, | |
| { | |
| "name": "parameters", | |
| "doc": "Additional parameters for tSNE function", | |
| "type": { | |
| "type": "record", | |
| "name": "AdditionalParameters", | |
| "fields": [ | |
| { | |
| "name": "dims", | |
| "type": "int", | |
| "doc": "Output dimensionality" | |
| }, | |
| { | |
| "name": "initial_dims", | |
| "type": "int", | |
| "doc": "the number of dimensions that should be retained in the initial PCA step" | |
| }, | |
| { | |
| "name": "perplexity", | |
| "type": "double", | |
| "doc": "Perplexity parameter" | |
| }, | |
| { | |
| "name": "theta", | |
| "type": "double", | |
| "doc": "Speed/accuracy trade-off" | |
| }, | |
| { | |
| "name": "pca", | |
| "type": "boolean", | |
| "doc": "Whether an initial PCA step should be performed" | |
| }, | |
| { | |
| "name": "max_iter", | |
| "type": "int", | |
| "doc": "Maximum number of iterations" | |
| } | |
| ] | |
| } | |
| }, | |
| { | |
| "name": "sql", | |
| "type": "string", | |
| "doc": "SQL query" | |
| }, | |
| { | |
| "name": "count", | |
| "type": "int", | |
| "doc": "Number of records selected by the query" | |
| } | |
| ] | |
| }, | |
| "init": { | |
| "variables": [ | |
| "age" | |
| ], | |
| "covariables": [ | |
| "left_amygdala", | |
| "left_splsupparlob", | |
| "right_poparoper", | |
| "right_pogpostcgyr" | |
| ], | |
| "grouping": [ | |
| "prov" | |
| ], | |
| "parameters": { | |
| "dims": 2, | |
| "initial_dims": 50, | |
| "perplexity": 1, | |
| "theta": 0.5, | |
| "pca": true, | |
| "max_iter": 1000 | |
| }, | |
| "sql": "select * from brain", | |
| "count": 9 | |
| } | |
| }, | |
| "reduced_data": { | |
| "type": { | |
| "doc": "New representation for the data, with the covariables projected to N dimensions, where N is the dims parameter\nand groupings added for visualisation and further processing\n", | |
| "type": "array", | |
| "items": { | |
| "type": "record", | |
| "name": "ReducedData", | |
| "fields": [ | |
| { | |
| "name": "1", | |
| "type": "double", | |
| "doc": "Reduced dimension 1" | |
| }, | |
| { | |
| "name": "2", | |
| "type": "double", | |
| "doc": "Reduced dimension 2" | |
| }, | |
| { | |
| "name": "prov", | |
| "type": { | |
| "type": "enum", | |
| "name": "Enumprov", | |
| "symbols": [ | |
| "AD1", | |
| "AD2" | |
| ] | |
| }, | |
| "doc": "Variable prov" | |
| }, | |
| { | |
| "name": "age", | |
| "type": "double", | |
| "doc": "Variable age" | |
| } | |
| ] | |
| } | |
| }, | |
| "init": [ | |
| { | |
| "1": -17.11878893, | |
| "2": -102.96461404, | |
| "prov": "AD1", | |
| "age": 81.2 | |
| }, | |
| { | |
| "1": 288.97005935, | |
| "2": 198.74859944, | |
| "prov": "AD1", | |
| "age": 81.2 | |
| }, | |
| { | |
| "1": -24.82965194, | |
| "2": -84.44473342, | |
| "prov": "AD1", | |
| "age": 81.2 | |
| }, | |
| { | |
| "1": -36.26630739, | |
| "2": -56.97799786, | |
| "prov": "AD1", | |
| "age": 73.6 | |
| }, | |
| { | |
| "1": 306.68069692, | |
| "2": 243.7006467, | |
| "prov": "AD1", | |
| "age": 73.6 | |
| }, | |
| { | |
| "1": 299.5901311, | |
| "2": 225.99492791, | |
| "prov": "AD1", | |
| "age": 73.6 | |
| }, | |
| { | |
| "1": -5.52277366, | |
| "2": -130.82548993, | |
| "prov": "AD1", | |
| "age": 73.6 | |
| }, | |
| { | |
| "1": -405.99128461, | |
| "2": -137.37420226, | |
| "prov": "AD2", | |
| "age": 70.1 | |
| }, | |
| { | |
| "1": -405.51208084, | |
| "2": -155.85713656, | |
| "prov": "AD2", | |
| "age": 70.1 | |
| } | |
| ] | |
| } | |
| }, | |
| "action": [ | |
| { | |
| "cell": "reduced_data" | |
| } | |
| ] | |
| } |
"items": "ReducedData" ... that looks too simple! Many thanks for spotting this one.
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Here's a corrected version: