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| author | Andreas Maunz <andreas@maunz.de> | 2011-12-09 13:32:36 +0100 |
|---|---|---|
| committer | Andreas Maunz <andreas@maunz.de> | 2011-12-09 13:32:36 +0100 |
| commit | 427aff8780e2039ebe3149a8bb282315c5f0de13 (patch) | |
| tree | 98d4bbe29be7d4a6bebe71b9bf94aed9da91273c | |
| parent | 86db0cb63b83fdba2151776e44f77f03def290bd (diff) | |
fixed max_perc_neighbors ON + weighting
| -rw-r--r-- | lib/algorithm.rb | 12 | ||||
| -rw-r--r-- | lib/model.rb | 2 |
2 files changed, 9 insertions, 5 deletions
diff --git a/lib/algorithm.rb b/lib/algorithm.rb index 49c1a5d..2229e75 100644 --- a/lib/algorithm.rb +++ b/lib/algorithm.rb @@ -372,6 +372,7 @@ module OpenTox n_prop = params[:n_prop].collect q_prop = params[:q_prop].collect acts = params[:acts].collect + sims = params[:sims].collect maxcols = params[:maxcols] nr_cases, nr_features = get_sizes n_prop @@ -410,7 +411,7 @@ module OpenTox @r.eval "suppressPackageStartupMessages(library(\"robustbase\"))" @r.eval "outlier_threshold = 0.999" - # outlier removal -- changes cases; adjust acts accordingly (stop if query is outlier) + # outlier removal -- changes cases; adjust acts and sims accordingly (stop if query is outlier) outliers = [] begin LOGGER.debug "Outliers..." @@ -431,17 +432,20 @@ module OpenTox if (outliers.include?(-1)) raise "Query is an outlier." end - temp_dm = []; temp_acts = [] + temp_dm = []; temp_acts = []; temp_sims = [] data_matrix.to_a.each_with_index { |elem, idx| temp_dm << elem unless outliers.include? idx } nr_cases, nr_features = get_sizes temp_dm data_matrix = GSL::Matrix.alloc(temp_dm.flatten, nr_cases, nr_features) acts.each_with_index { |elem, idx| temp_acts << elem unless outliers.include? idx } acts = temp_acts # same nr_features + sims.each_with_index { |elem, idx| temp_sims << elem unless outliers.include? idx } + sims = temp_sims # same nr_features @r.eval 'fstr <- "y ~ ."' @r.x = data_matrix.to_a.flatten @r.y = acts.to_a.flatten + @r.w = sims.to_a.flatten @r.q = query_matrix.to_a.flatten @r.eval "x <- matrix(x, #{nr_cases}, #{nr_features}, byrow=T)" @@ -449,7 +453,7 @@ module OpenTox @r.eval 'idx = rep(T,dim(x)[2])' - # optimize selection of training instances -- changes features; adjust query accordingly + # optimize selection features; adjust query accordingly begin LOGGER.debug "Best subset..." @r.eval 'suppressPackageStartupMessages(library("leaps"))' @@ -475,7 +479,7 @@ module OpenTox @r.eval 'suppressPackageStartupMessages(library("MASS"))' @r.eval 'df <- df[,idx]' - @r.eval 'fit <- rlm( as.formula(fstr), data=df, psi = psi.bisquare, method="MM")' + @r.eval 'fit <- rlm( as.formula(fstr), data=df, psi = psi.bisquare, method="MM", weights=w, wt.method="case")' @r.eval 'q <- q[idx[2:length(idx)]]' @r.eval 'q <- data.frame( matrix( q, 1, length(q) ) )' diff --git a/lib/model.rb b/lib/model.rb index 3c25007..01b2335 100644 --- a/lib/model.rb +++ b/lib/model.rb @@ -394,7 +394,7 @@ module OpenTox params[:training_compound_features_hits] = training_compound_features_hits sim = eval("#{@similarity_algorithm}(training_features, @compound_features, @p_values, params)") - if sim > @min_sim + if sim > @min_sim || @max_perc_neighbors @activities[training_compound].each do |act| @neighbors << { :compound => training_compound, |