Added min_frequency search.

2 files changed, 148 insertions, 24 deletions

diff --git a/bbrc-sample/bbrc_sample_dv.rb b/bbrc-sample/bbrc_sample_dv.rb
index 6a7c167..923469e 100644
--- a/bbrc-sample/bbrc_sample_dv.rb
+++ b/bbrc-sample/bbrc_sample_dv.rb
@@ -57,6 +57,83 @@ for i in 1..50
   puts "[#{Time.now.iso8601(4).to_s}] Split result: #{datasets.to_yaml}"
   puts
 
+  # Find "good" min_frequency
+  
+  min_params = {}
+  min_params["dataset_uri"] = datasets[:training_ds]
+
+  ds = OpenTox::Dataset.find(datasets[:training_ds])
+#  ds_nr_de = ds.data_entries.size
+  ds_nr_com = ds.compounds.size
+
+  min_params["backbone"] = backbone
+  durations = []
+  x = ds_nr_com
+  ds_result_nr_f = 0
+  y = x
+  y_old = 0
+#  puts
+#  puts "----- Initialization: -----"
+  while ds_result_nr_f < (ds_nr_com/4).to_i do
+    y_old = y
+    y = x
+    x = (x/2).to_i
+    min_params["min_frequency"] = x
+#    puts "[#{Time.now.iso8601(4).to_s}] min_freq #{x}"
+    t = Time.now
+    result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params )
+    durations << Time.now - t
+    ds_result = OpenTox::Dataset.find(result_uri)
+    ds_result_nr_f = ds_result.features.size
+#    puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}"
+#    puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}"
+#    puts "-------------"
+#    puts
+  end  
+
+#  puts "----- Main phase: -----"
+#  puts
+  max_duration = durations[0] +(ds_nr_com.to_f * 0.003)
+#  puts "max duration: #{max_duration}"
+#  puts
+  min_params["min_frequency"] = y
+  y = y_old
+  found = false
+  cnt = 0
+  min_f = min_params["min_frequency"]
+  while found == false || cnt == 4 do
+    if min_f == min_params["min_frequency"]
+      cnt = cnt + 1
+    end
+    min_f = min_params["min_frequency"]
+#    puts "[#{Time.now.iso8601(4).to_s}] min_freq #{min_params["min_frequency"]}"
+    t = Time.now
+    result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params )
+    durations << Time.now - t
+    ds_result = OpenTox::Dataset.find(result_uri)
+    ds_result_nr_f = ds_result.features.size
+#    ds_result_nr_de = ds_result.data_entries.size
+#    ds_result_nr_com = ds_result.compounds.size
+#    puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}"
+#    puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}"
+#    puts "-------------"
+#    puts
+#    puts "smaller than #{(ds_nr_com*0.45).to_i} and larger than #{(ds_nr_com/10).to_i}"
+#    puts "x  #{x}, y #{y}, min_freq #{min_params["min_frequency"]}"
+    if ds_result_nr_f.to_i < (ds_nr_com/2).to_i && ds_result_nr_f.to_i > (ds_nr_com/10).to_i
+      if durations.last < max_duration
+        found = true
+        min_freq = min_params["min_frequency"]
+      else
+        x = min_params["min_frequency"]
+        min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i
+      end
+    else
+      y = min_params["min_frequency"]
+      min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i
+    end
+  end
+
   # BBRC sample
   puts "                ----- bbrc feature calulation -----"
   algo_params = {}
diff --git a/bbrc-sample/find_pm.rb b/bbrc-sample/find_pm.rb
index a541793..761e538 100644
--- a/bbrc-sample/find_pm.rb
+++ b/bbrc-sample/find_pm.rb
@@ -27,42 +27,89 @@ ds_name = ARGV[1] # e.g. MOU
 ds = YAML::load_file("#{path}")
 ds_uri = ds[ds_name]["dataset"]
 
-algo_params = {}
-algo_params["dataset_uri"] = ds_uri
+min_params = {}
+min_params["dataset_uri"] = ds_uri
 
 
 ds = OpenTox::Dataset.find(ds_uri)
 ds_nr_de = ds.data_entries.size
 ds_nr_com = ds.compounds.size
 
+
 [true,false].each do |bb|
-  min_freq = 110
-  duration = 0.0
-  while duration < 60.0 && min_freq > 10 do
-    min_freq = min_freq - 10
-    algo_params["min_frequency"] = min_freq.to_s + "pm"
-    algo_params["backbone"] = bb
-    #algo_params["nr_hits"] = false
-    #algo_params["feature_type"] = true
-    
-    
-    puts "[#{Time.now.iso8601(4).to_s}] #{algo_params.to_yaml}"
+  min_params["backbone"] = bb
+  #min_freq = 110
+  durations = []
+  x = ds_nr_com
+  ds_result_nr_f = 0
+  y = x
+  y_old = 0 
+  puts
+  puts "----- Initialization: -----" 
+  while ds_result_nr_f < (ds_nr_com/4).to_i do 
+    y_old = y
+    y = x
+    x = (x/2).to_i
+    min_params["min_frequency"] = x
+    puts "[#{Time.now.iso8601(4).to_s}] min_freq #{x}"
     t = Time.now
-    result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), algo_params )
-    duration = Time.now - t
+    result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params )
+    durations << Time.now - t
     ds_result = OpenTox::Dataset.find(result_uri)
-    ds_result_nr_de = ds_result.data_entries.size
-    ds_result_nr_com = ds_result.compounds.size
     ds_result_nr_f = ds_result.features.size
-    
+    puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}"
+    puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}"
+    puts "-------------"
     puts
-    puts "[#{Time.now.iso8601(4).to_s}] Bbrc result: #{result_uri}"
-    puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_de} , (of #{ds_nr_de} ), #{(ds_result_nr_de/(ds_nr_de/100)).to_f.round}%"
-    puts "[#{Time.now.iso8601(4).to_s}] nr compounds: #{ds_result_nr_com} , (of #{ds_nr_com} ), #{(ds_result_nr_com/(ds_nr_com/100)).to_f.round}%"
-    puts "[#{Time.now.iso8601(4).to_s}] nr features: #{ds_result_nr_f}, , #{(ds_result_nr_f/(ds_nr_de/100)).to_f.round}%"
-    puts "[#{Time.now.iso8601(4).to_s}] Duration: #{duration}"
-    puts "------------------------"
+  end
+  puts "----- Main phase: -----" 
+  puts 
+  max_duration = durations[0] +(ds_nr_com.to_f * 0.003)
+  puts "max duration: #{max_duration}"
+  puts
+  min_params["min_frequency"] = y
+  y = y_old
+  found = false
+  cnt = 0
+  min_f = min_params["min_frequency"]
+  while found == false || cnt == 4 do
+    if min_f == min_params["min_frequency"]
+      cnt = cnt + 1
+    end 
+    min_f = min_params["min_frequency"]
+    puts "[#{Time.now.iso8601(4).to_s}] min_freq #{min_params["min_frequency"]}"
+    t = Time.now
+    result_uri = OpenTox::RestClientWrapper.post( File.join(CONFIG[:services]["opentox-algorithm"],"fminer/bbrc/"), min_params )
+    durations << Time.now - t
+    ds_result = OpenTox::Dataset.find(result_uri)
+    ds_result_nr_f = ds_result.features.size
+    ds_result_nr_de = ds_result.data_entries.size
+    ds_result_nr_com = ds_result.compounds.size
+    puts "[#{Time.now.iso8601(4).to_s}] nr features #{ds_result_nr_f}"
+    puts "[#{Time.now.iso8601(4).to_s}] duration #{durations.last}"
+    puts "-------------"
     puts
+    puts "smaller than #{(ds_nr_com*0.45).to_i} and larger than #{(ds_nr_com/10).to_i}" 
+    puts "x  #{x}, y #{y}, min_freq #{min_params["min_frequency"]}" 
+    if ds_result_nr_f.to_i < (ds_nr_com/2).to_i && ds_result_nr_f.to_i > (ds_nr_com/10).to_i
+      if durations.last < max_duration
+        found = true 
+      else
+        x = min_params["min_frequency"]
+        min_params["min_frequency"] = ((min_params["min_frequency"]+y)/2).to_i
+      end
+    else
+      y = min_params["min_frequency"]
+      min_params["min_frequency"] = ((x+min_params["min_frequency"])/2).to_i
+    end
   end
+  
+  puts
+  puts "[#{Time.now.iso8601(4).to_s}] Bbrc result: #{result_uri}"
+  puts "[#{Time.now.iso8601(4).to_s}] nr dataentries: #{ds_result_nr_de} , (of #{ds_nr_de} ), #{(ds_result_nr_de/(ds_nr_de/100)).to_f.round}%"
+  puts "[#{Time.now.iso8601(4).to_s}] nr compounds: #{ds_result_nr_com} , (of #{ds_nr_com} ), #{(ds_result_nr_com/(ds_nr_com/100)).to_f.round}%"
+  puts "[#{Time.now.iso8601(4).to_s}] nr features: #{ds_result_nr_f}, , #{(ds_result_nr_f/(ds_nr_de/100)).to_f.round}%"
+  puts "[#{Time.now.iso8601(4).to_s}] Duration: #{durations.last}"
+  puts "------------------------"
   puts
 end