Module: ReplaceMissingValues

Included in:
FSelector::Base
Defined in:
lib/fselector/replace_missing_values.rb

Overview

replace missing feature values

Instance Method Summary (collapse)

Instance Method Details

- replace_by_fixed_value!(val)

Note:

data structure will be altered

replace missing feature value by a fixed value, applicable to both discrete and continuous feature



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# File 'lib/fselector/replace_missing_values.rb', line 11

def replace_by_fixed_value!(val)
  each_sample do |k, s|
    each_feature do |f|
      if not s.has_key? f
        s[f] = val
      end
    end
  end
  
  # clear variables
  clear_vars
end

- replace_by_knn_value!(k = 1)

Note:

data structure will be altered, and the nearest neighbors are determined by Euclidean distance

replace missing feature value by weighted k-nearest neighbors' value, applicable only to continuous feature

val = sigma_k (val_k * w_k)

where w_k = (sum_d - d_k) / ((K-1) * sum_d)
      sum_d = sigma_k (d_k)
      K: number of d_k
      sigma_k (w_k) = 1, normalized to 1

ref: Microarray missing data imputation based on a set theoretic framework and biological knowledge

Parameters:

  • k (Integer) (defaults to: 1)

    number of nearest neighbors



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# File 'lib/fselector/replace_missing_values.rb', line 134

def replace_by_knn_value!(k=1)
  each_sample do |ki, si|
    # potential features having missing value
    mv_fs = get_features - si.keys
    next if mv_fs.empty? # sample si has no missing value
    
    # record object value for each feature missing value
    f2val = {}
    mv_fs.each do |mv_f|
      knn_s, knn_d = [], []
      
      each_sample do |kj, sj|
        # sample sj also has missing value of mv_f
        next if not sj.has_key? mv_f
        
        d = euclidean_distance(si, sj)
        idx = knn_d.index { |di| d<di }
        
        if idx
          knn_s.insert(idx, sj)
          knn_d.insert(idx, d)
          
          if knn_s.size > k
            knn_s = knn_s[0...k]
            knn_d = knn_d[0...k]
          end
        else
          if knn_s.size < k
            knn_s << sj
            knn_d << d
          end
        end
      end
      
      # distance-weighted value from knn
      knn_d_sum = knn_d.sum
      sz = knn_d.size
      val = 0.0
      knn_s.each_with_index do |s, i|
        if sz > 1
          if not knn_d_sum.zero?
            val += s[mv_f] * (knn_d_sum-knn_d[i]) / ((sz-1)*knn_d_sum)
          else
            val += s[mv_f] * 1.0 / sz
          end
        else # only one nearest neighbor
          val = s[mv_f]
        end
      end
      
      f2val[mv_f] = val
     #pp [si, mv_f, knn_s, knn_d, val]
    end
    
    # set value
    f2val.each do |f, v|
      si[f] = v
    end
  end
  
  # clear variables
  clear_vars
end

- replace_by_mean_value!(mode = :by_column)

Note:

data structure will be altered

replace missing feature value by mean feature value, applicable only to continuous feature

Parameters:

  • mode (Symbol) (defaults to: :by_column)

    column or row mode
    - :by_column # use the mean value of the same feature among all instances
    - :by_row # use the mean value of different features in current instance



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# File 'lib/fselector/replace_missing_values.rb', line 35

def replace_by_mean_value!(mode = :by_column)
  each_sample do |k, s|
    mean = s.values.mean if mode == :by_row
    
    each_feature do |f|
      fv = get_feature_values(f)
      next if fv.size == get_sample_size # no missing values
      
      mean = fv.ave if mode == :by_column
      if not s.has_key? f
        s[f] = mean
      end
    end
  end
  
  # clear variables
  clear_vars
end

- replace_by_median_value!(mode = :by_column)

Note:

data structure will be altered

replace missing feature value by median feature value, applicable only to continuous feature

Parameters:

  • mode (Symbol) (defaults to: :by_column)

    column or row mode
    - :by_column # use the mean value of the same feature among all instances
    - :by_row # use the mean value of different features in current instance



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# File 'lib/fselector/replace_missing_values.rb', line 65

def replace_by_median_value!(mode = :by_column)
  each_sample do |k, s|
    median = s.values.median if mode == :by_row
    
    each_feature do |f|
      fv = get_feature_values(f)
      next if fv.size == get_sample_size # no missing values
      
      median = fv.median if mode == :by_column
      if not s.has_key? f
        s[f] = median
      end
    end
  end
  
  # clear variables
  clear_vars
end

- replace_by_most_seen_value!

Note:

data structure will be altered

replace missing feature value by most seen feature value, applicable only to discrete feature



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# File 'lib/fselector/replace_missing_values.rb', line 91

def replace_by_most_seen_value!
  each_sample do |k, s|
    each_feature do |f|
      fv = get_feature_values(f)
      next if fv.size == get_sample_size # no missing values
      
      seen_count, seen_value = 0, nil
      fv.uniq.each do |v|
        count = fv.count(v)
        if count > seen_count
          seen_count = count
          seen_value = v
        end
      end
      
      if not s.has_key? f
        s[f] = seen_value
      end
    end
  end
  
  # clear variables
  clear_vars
end