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module OpenTox
module Algorithm
class Regression
def self.local_weighted_average substance, neighbors
weighted_sum = 0.0
sim_sum = 0.0
neighbors.each do |neighbor|
sim = neighbor["similarity"]
activities = neighbor["toxicities"]
activities.each do |act|
weighted_sum += sim*act
sim_sum += sim
end if activities
end
sim_sum == 0 ? prediction = nil : prediction = weighted_sum/sim_sum
{:value => prediction}
end
def self.local_fingerprint_regression substance, neighbors, method='pls'#, method_params="sigma=0.05"
values = []
fingerprints = {}
weights = []
fingerprint_ids = neighbors.collect{|n| Compound.find(n["_id"]).fingerprint}.flatten.uniq.sort
neighbors.each do |n|
fingerprint = Substance.find(n["_id"]).fingerprint
activities = n["toxicities"]
activities.each do |act|
values << act
weights << n["similarity"]
fingerprint_ids.each do |id|
fingerprints[id] ||= []
fingerprints[id] << fingerprint.include?(id)
end
end if activities
end
variables = []
data_frame = [values]
fingerprints.each do |k,v|
unless v.uniq.size == 1
data_frame << v.collect{|m| m ? "T" : "F"}
variables << k
end
end
if variables.empty?
prediction = local_weighted_average substance, neighbors
prediction[:warning] = "No variables for regression model. Using weighted average of similar substances."
prediction
else
substance_features = variables.collect{|f| substance.fingerprint.include?(f) ? "T" : "F"}
prediction = r_model_prediction method, data_frame, variables, weights, substance_features
if prediction.nil? or prediction[:value].nil?
prediction = local_weighted_average substance, neighbors
prediction[:warning] = "Could not create local PLS model. Using weighted average of similar substances."
prediction
else
prediction[:prediction_interval] = [prediction[:value]-1.96*prediction[:rmse], prediction[:value]+1.96*prediction[:rmse]]
prediction[:value] = prediction[:value]
prediction[:rmse] = prediction[:rmse]
prediction
end
end
end
#def self.local_physchem_regression(substance:, neighbors:, feature_id:, dataset_id:, method: 'pls')#, method_params="ncomp = 4"
def self.local_physchem_regression substance, neighbors, method='pls' #, method_params="ncomp = 4"
activities = []
weights = []
pc_ids = neighbors.collect{|n| Substance.find(n["_id"]).physchem_descriptors.keys}.flatten.uniq
data_frame = []
data_frame[0] = []
neighbors.each_with_index do |n,i|
neighbor = Substance.find(n["_id"])
activities = neighbor["toxicities"]
activities.each do |act|
data_frame[0][i] = act
weights << n["similarity"]
neighbor.physchem_descriptors.each do |pid,values|
values = [values] unless values.is_a? Array
values.uniq!
warn "More than one value for '#{Feature.find(pid).name}': #{values.join(', ')}. Using the median." unless values.size == 1
j = pc_ids.index(pid)+1
data_frame[j] ||= []
data_frame[j][i] = values.for_R
end
end if activities
(0..pc_ids.size+1).each do |j| # for R: fill empty values with NA
data_frame[j] ||= []
data_frame[j][i] ||= "NA"
end
end
remove_idx = []
data_frame.each_with_index do |r,i|
remove_idx << i if r.uniq.size == 1 # remove properties with a single value
end
remove_idx.reverse.each do |i|
data_frame.delete_at i
pc_ids.delete_at i
end
if pc_ids.empty?
prediction = local_weighted_average substance, neighbors
prediction[:warning] = "No variables for regression model. Using weighted average of similar substances."
prediction
else
query_descriptors = pc_ids.collect do |i|
substance.physchem_descriptors[i] ? substance.physchem_descriptors[i].for_R : "NA"
end
remove_idx = []
query_descriptors.each_with_index do |v,i|
remove_idx << i if v == "NA"
end
remove_idx.reverse.each do |i|
data_frame.delete_at i
pc_ids.delete_at i
query_descriptors.delete_at i
end
prediction = r_model_prediction method, data_frame, pc_ids.collect{|i| "\"#{i}\""}, weights, query_descriptors
if prediction.nil?
prediction = local_weighted_average substance, neighbors
prediction[:warning] = "Could not create local PLS model. Using weighted average of similar substances."
prediction
else
prediction
end
end
end
def self.r_model_prediction method, training_data, training_features, training_weights, query_feature_values
R.assign "weights", training_weights
r_data_frame = "data.frame(#{training_data.collect{|r| "c(#{r.join(',')})"}.join(', ')})"
rlib = File.expand_path(File.join(File.dirname(__FILE__),"..","R"))
=begin
File.open("tmp.R","w+"){|f|
f.puts "suppressPackageStartupMessages({
library(iterators,lib=\"#{rlib}\")
library(foreach,lib=\"#{rlib}\")
library(ggplot2,lib=\"#{rlib}\")
library(grid,lib=\"#{rlib}\")
library(gridExtra,lib=\"#{rlib}\")
library(pls,lib=\"#{rlib}\")
library(caret,lib=\"#{rlib}\")
library(doMC,lib=\"#{rlib}\")
registerDoMC(#{NR_CORES})
})"
f.puts "data <- #{r_data_frame}\n"
f.puts "weights <- c(#{training_weights.join(', ')})"
f.puts "features <- c(#{training_features.join(', ')})"
f.puts "names(data) <- append(c('activities'),features)" #
f.puts "model <- train(activities ~ ., data = data, method = '#{method}')"
f.puts "fingerprint <- data.frame(rbind(c(#{query_feature_values.join ','})))"
f.puts "names(fingerprint) <- features"
f.puts "prediction <- predict(model,fingerprint)"
}
=end
R.eval "data <- #{r_data_frame}"
R.assign "features", training_features
begin
R.eval "names(data) <- append(c('activities'),features)" #
R.eval "model <- train(activities ~ ., data = data, method = '#{method}', na.action = na.pass)"
R.eval "fingerprint <- data.frame(rbind(c(#{query_feature_values.join ','})))"
R.eval "names(fingerprint) <- features"
R.eval "prediction <- predict(model,fingerprint)"
{
:value => R.eval("prediction").to_f,
:rmse => R.eval("getTrainPerf(model)$TrainRMSE").to_f,
:r_squared => R.eval("getTrainPerf(model)$TrainRsquared").to_f,
}
rescue
return nil
end
end
end
end
end
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