diff options
Diffstat (limited to 'protein_corona.rb')
| -rw-r--r-- | protein_corona.rb | 57 |
1 files changed, 43 insertions, 14 deletions
diff --git a/protein_corona.rb b/protein_corona.rb index 35970dc..890b3ca 100644 --- a/protein_corona.rb +++ b/protein_corona.rb @@ -1,8 +1,35 @@ require 'json' require 'yaml' require 'csv' -#require_relative "../lazar/lib/lazar.rb" -#include OpenTox + +ENDPOINT = "Cell.association (Net cell association [mL/ug(Mg)])" + +def predict params + neighbors = [] + sim_sum = 0 + weighted_sum = 0 + match = nil + JSON.parse(File.read("./data.json")).each do |id,categories| + if params.values == categories["physchem"].values + match = {:id => categories} + else + sim = cosine_similarity(params.values,categories["physchem"].values) + neighbor = categories + neighbor["similarity"] = sim + neighbor["id"] = id + sim_sum += sim + weighted_sum += sim*Math.log(categories["tox"][ENDPOINT]) + neighbors << neighbor + end + end + neighbors.sort!{|a,b| b["similarity"] <=> a["similarity"]} + { + :query => params, + :match => match, + :prediction => {ENDPOINT => 10**(weighted_sum/sim_sum)}, + :neighbors => neighbors + } +end class Object def numeric? @@ -70,18 +97,20 @@ def csv2json data = {} csv.drop(12).each do |row| id = row.first - data[id] = {} - row.each_with_index do |col,i| - if i == 0 - data[id][:composition] = {} - elsif i < 5 - data[id][:composition][feature_names[i]] = col - elsif i < 7 - data[id][:tox] ||= {} - data[id][:tox][feature_names[i]] = col - else - data[id][:physchem] ||= {} - data[id][:physchem][feature_names[i]] = col + if id.match /^G/ # skip Ag, too many missing values + data[id] = {} + row.each_with_index do |col,i| + if i == 0 + data[id][:composition] = {} + elsif i < 5 + data[id][:composition][feature_names[i]] = col + elsif i == 5 + data[id][:tox] ||= {} + data[id][:tox][feature_names[i]] = col + elsif i > 6 + data[id][:physchem] ||= {} + data[id][:physchem][feature_names[i]] = col + end end end end |