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  <info>Mining preferences for algorithms in the Clired/Siren redescription mining tools. A default preferences file can be obtained by calling the main mining routine <em>exec_clired.py --config</em> and a basic configuration template with <em>exec_clired.py --template</em>.</info>
  <section>
    <name>Mining</name>
    <section>
      <name>Method</name>
      <parameter>
        <name>mining_algo</name>
        <label>Mining algorithm</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>CORE Algorithm to use for mining, greedy ReReMi or based on classification trees (restrictions apply).</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>reremi</value>
          <value>layeredtrees</value>
          <value>splittrees</value>
          <value>cartwheel</value>
        </options>
      </parameter>
    </section>
    <section>
      <name>Queries</name>
      <parameter>
        <name>max_var_s0</name>
        <label>LHS max number of variables</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of variables in a left-hand side query, maximum tree depth in tree-based algorithms.</legend>
        <length>2</length>
        <default>
          <value>4</value>
        </default>
      </parameter>
      <parameter>
        <name>max_var_s1</name>
        <label>RHS max number of variables</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of variables in a right-hand side query, maximum tree depth in tree-based algorithms.</legend>
        <length>2</length>
        <default>
          <value>4</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Candidate filtering</name>
      <parameter>
        <name>batch_out</name>
        <label>Batch output</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of redescriptions returned from an expansion batch.</legend>
        <length>1</length>
        <default>
          <value>1</value>
        </default>
      </parameter>
      <parameter>
        <name>min_itm_c</name>
        <label>Min contribution</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum contribution, number of supporting entities impacted by the addition of a literal in ReReMi or minimum node size in tree-based algorithms. Values between 0 and 1 are interpreted as ratio of the total number of entities.</legend>
        <length>5</length>
        <default>
          <value>3</value>
        </default>
      </parameter>
      <parameter>
        <name>min_itm_in</name>
        <label>Min support</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>CORE Minimum number of supporting entities. Values between 0 and 1 are interpreted as ratio of the total number of entities.</legend>
        <length>5</length>
        <default>
          <value>0.05</value>
        </default>
      </parameter>
      <parameter>
        <name>min_itm_out</name>
        <label>Min uncovered</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>CORE Minimum number of uncovered entities. Values between 0 and 1 are interpreted as ratio of the total number of entities.</legend>
        <length>5</length>
        <default>
          <value>0.05</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Final filtering</name>
      <parameter>
        <name>min_fin_in</name>
        <label>Min support</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum number of supporting entities, applied for final filtering. Values between 0 and 1 are interpreted as ratio of the total number of entities.</legend>
        <length>5</length>
        <default>
          <value>-1</value>
        </default>
      </parameter>
      <parameter>
        <name>min_fin_out</name>
        <label>Min uncovered</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum number of uncovered entities, applied for final filtering. Values between 0 and 1 are interpreted as ratio of the total number of entities.</legend>
        <length>5</length>
        <default>
          <value>-1</value>
        </default>
      </parameter>
      <parameter>
        <name>min_fin_var</name>
        <label>Min total number of variables</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of variables per redescription, applied for final filtering.</legend>
        <length>2</length>
        <default>
          <value>2</value>
        </default>
      </parameter>
      <parameter>
        <name>min_fin_acc</name>
        <label>Min accuracy</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum accuracy, applied for final filtering.</legend>
        <length>5</length>
        <default>
          <value>0.01</value>
        </default>
      </parameter>
      <parameter>
        <name>max_fin_pval</name>
        <label>Max p-value</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Maximum p-value, applied for final filtering.</legend>
        <length>5</length>
        <default>
          <value>0.01</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Additional filtering</name>
      <parameter>
        <name>max_overlap_area</name>
        <label>Max Area Overlap</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Two redescriptions whose area overlap is beyond this ratio are considered redundant.</legend>
        <length>5</length>
        <default>
          <value>0.5</value>
        </default>
      </parameter>
      <parameter>
        <name>max_overlap_rows</name>
        <label>Max Rows Overlap</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Two redescriptions whose row overlap is beyond this ratio are considered redundant.</legend>
        <length>5</length>
        <default>
          <value>0.5</value>
        </default>
      </parameter>
    </section>
  </section>
  <section>
    <name>Mining adv.</name>
    <section>
      <name>Process</name>
      <parameter>
        <name>nb_processes</name>
        <label>Nb processes</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of mining processes to use in parallel.</legend>
        <default>
          <value>1</value>
        </default>
        <length>2</length>
      </parameter>
      <parameter>
        <name>verbosity</name>
        <label>Log verbosity</label>
        <parameter_type>range</parameter_type>
        <value_type>integer</value_type>
        <legend>Verbosity of the mining process output.</legend>
        <range_min>0</range_min>
        <range_max>10</range_max>
        <default>
          <value>4</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Other common parameters</name>
      <parameter>
        <name>in_weight</name>
        <label>Weight Inside</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Weight for entities inside selected area (only applies when such an area is specified).</legend>
        <default>
          <value>10</value>
        </default>
      </parameter>
      <parameter>
        <name>out_weight</name>
        <label>Weight Outside</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Weight for entities outside selected area (only applies when such an area is specified).</legend>
        <default>
          <value>1</value>
        </default>
      </parameter>
      <parameter>
        <name>var_compat</name>
        <label>Var group compatibility</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>Fixes whether group ids should differ or match for variables to be considered compatible (gid=-1 is universally compatible).</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>differ</value>
          <value>match</value>
        </options>
      </parameter>
      <parameter>
        <name>method_pval</name>
        <label>p-value formula</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>Formula used for computing the p-value.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>marg</value>
          <value>supp</value>
          <value>over</value>
        </options>
      </parameter>
      <parameter>
        <name>parts_type</name>
        <label>Missing values belief</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>How to consider missing values when computing support statistics.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>rejective</value>
          <value>optimistic</value>
          <value>pessimistic</value>
          <value>basic</value>
          <value>exclu</value>
        </options>
      </parameter>
    </section>
    <section>
      <name>Tree-based algorithms</name>
      <parameter>
        <name>max_rounds</name>
        <label>Max rounds in CartWheel</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of alternations in CartWheel algorithm.</legend>
        <length>3</length>
        <default>
          <value>10</value>
        </default>
      </parameter>
      <parameter>
        <name>split_criterion</name>
        <label>Split criterion</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>Score used to evaluate splits during decision tree induction.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>gini</value>
          <value>entropy</value>
        </options>
      </parameter>
    </section>
  </section>
  <section>
    <name>ReReMi</name>
    <section>
      <name>Queries</name>
      <parameter>
        <name>neg_query_s0_1</name>
        <label>LHS Literals Bool</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the left-hand side queries for Boolean literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>neg_query_s0_2</name>
        <label>LHS Literals Cat</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the left-hand side queries for categorical literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>neg_query_s0_3</name>
        <label>LHS Literals Num</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the left-hand side queries for numerical literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>ops_query_s0</name>
        <label>LHS Operators</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Type of operators allowed in the left-hand side queries.</legend>
        <default>
          <value>0</value>
          <value>1</value>
        </default>
        <options>
          <value>Conjunction</value>
          <value>Disjunction</value>
        </options>
      </parameter>
      <parameter>
        <name>neg_query_s1_1</name>
        <label>RHS Literals Bool</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the right-hand side queries for Boolean literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>neg_query_s1_2</name>
        <label>RHS Literals Cat</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the right-hand side queries for categorical literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>neg_query_s1_3</name>
        <label>RHS Literals Num</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Types of literals allowed in the right-hand side queries for numerical literals.</legend>
        <default>
          <value>0</value>
        </default>
        <options>
          <value>Positive</value>
          <value>Negative</value>
        </options>
      </parameter>
      <parameter>
        <name>ops_query_s1</name>
        <label>RHS Operators</label>
        <parameter_type>multiple_options</parameter_type>
        <value_type>text</value_type>
        <legend>Type of operators allowed in the right-hand side queries.</legend>
        <default>
          <value>0</value>
          <value>1</value>
        </default>
        <options>
          <value>Conjunction</value>
          <value>Disjunction</value>
        </options>
      </parameter>
      <parameter>
        <name>single_side_or</name>
        <label>Single side OR</label>
        <parameter_type>boolean</parameter_type>
        <legend>Restrict use of disjunction to only one side.</legend>
        <default>
          <value>1</value>
        </default>
      </parameter>
      <parameter>
        <name>multi_cats</name>
        <label>Multi categories</label>
        <parameter_type>boolean</parameter_type>
        <legend>Allow combining multiple categories of a categorical variable.</legend>
        <default>
          <value>0</value>
        </default>
      </parameter>
      <parameter>
        <name>add_condition</name>
        <label>Conditional</label>
        <parameter_type>boolean</parameter_type>
        <legend>Allow making conditional redescriptions, if suitable data is provided.</legend>
        <default>
          <value>0</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Initial pairs</name>
      <parameter>
        <name>max_pairs</name>
        <label>Max number of pairs</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of initial pairs extended, -1 leads to expand all.</legend>
        <length>4</length>
        <default>
          <value>100</value>
        </default>
      </parameter>
      <parameter>
        <name>pair_sel</name>
        <label>Expansion order</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>Order in which the initial pairs are processed, either overall next best score or alternating between side considering next best variables in turn.</legend>
        <default>
          <value>1</value>
        </default>
        <options>
          <value>overall</value>
          <value>alternate</value>
        </options>
      </parameter>
      <parameter>
        <name>min_pairscore</name>
        <label>Min score</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum score for an initial pair to be considered.</legend>
        <length>3</length>
        <default>
          <value>0.01</value>
        </default>
      </parameter>
      <parameter>
        <name>pairs_productivity</name>
        <label>Pairs productivity</label>
        <parameter_type>single_options</parameter_type>
        <value_type>text</value_type>
        <legend>Productivity when creating an initial pair of literals from non-Boolean variables.</legend>
        <default>
          <value>1</value>
        </default>
        <options>
          <value>low</value>
          <value>medium</value>
          <value>high</value>
        </options>
      </parameter>
      <parameter>
        <name>pe_balance</name>
        <label>Pairs-expand balance</label>
        <parameter_type>range</parameter_type>
        <value_type>integer</value_type>
        <legend>Balance between generating initial pairs and expanding them (0 means generating all pairs first).</legend>
        <range_min>0</range_min>
        <range_max>10</range_max>
        <default>
          <value>4</value>
        </default>
      </parameter>
    </section>
  </section>
  <section>
    <name>ReReMi exp.</name>
    <section>
      <name>Candidate expansion</name>
      <parameter>
        <name>min_impr</name>
        <label>Min improvement</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Minimum improvement score for an acceptable extension.</legend>
        <length>4</length>
        <default>
          <value>0</value>
        </default>
      </parameter>
      <parameter>
        <name>score.impacc</name>
        <label>Accuracy improvement coefficient</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Coefficient of the accuracy improvement for scoring extension candidates.</legend>
        <length>4</length>
        <default>
          <value>1</value>
        </default>
      </parameter>
      <parameter>
        <name>score.rel_impacc</name>
        <label>Relative Accurracy improvement coefficient</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Coefficient of the relative accuracy improvement for scoring extension candidates.</legend>
        <length>4</length>
        <default>
          <value>0</value>
        </default>
      </parameter>
      <parameter>
        <name>score.pval_red</name>
        <label>Redescription p-value coefficient</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Coefficient of the redescription p-value for scoring extension candidates. Negative values are interpreted as a threshold weighted by p-value factor.</legend>
        <length>4</length>
        <default>
          <value>0.01</value>
        </default>
      </parameter>
      <parameter>
        <name>score.pval_query</name>
        <label>Query p-value coefficient</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Coefficient of the query p-value for scoring extension candidates. Negative values are interpreted as a threshold weighted by p-value factor.</legend>
        <length>4</length>
        <default>
          <value>0.01</value>
        </default>
      </parameter>
      <parameter>
        <name>score.pval_fact</name>
        <label>p-value factor</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Weight for p-value in case of using thresholds for scoring extension candidates.</legend>
        <length>4</length>
        <default>
          <value>1</value>
        </default>
      </parameter>
      <parameter>
        <name>batch_cap</name>
        <label>Batch capacity</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of candidates expanded at each step of the search.</legend>
        <length>1</length>
        <default>
          <value>4</value>
        </default>
      </parameter>
      <parameter>
        <name>amnesic</name>
        <label>Amnesic</label>
        <parameter_type>boolean</parameter_type>
        <legend>Not amnesic means the algorithm remembers previously generated redescriptions and avoid generating them again.</legend>
        <default>
          <value>0</value>
        </default>
      </parameter>
    </section>
    <section>
      <name>Numerical attributes discretization</name>
      <parameter>
        <name>max_seg</name>
        <label>Max number segments</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of segments, i.e. distinct values for a numerical variable.</legend>
        <length>3</length>
        <default>
          <value>20</value>
        </default>
      </parameter>
      <parameter>
        <name>lower_tail_agg</name>
        <label>Lower tail aggregate</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Threshold for the lower tail, when aggregating keeping only extreme values.</legend>
        <length>3</length>
        <default>
          <value>0</value>
        </default>
      </parameter>
      <parameter>
        <name>upper_tail_agg</name>
        <label>Upper tail aggregate</label>
        <parameter_type>open</parameter_type>
        <value_type>float</value_type>
        <legend>Threshold for the upper tail, when aggregating keeping only extreme values.</legend>
        <length>3</length>
        <default>
          <value>0</value>
        </default>
      </parameter>
      <parameter>
        <name>max_agg</name>
        <label>Max aggregation</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum number of buckets aggregated together.</legend>
        <length>3</length>
        <default>
          <value>15</value>
        </default>
      </parameter>
      <parameter>
        <name>max_prodbuckets</name>
        <label>Max product buckets</label>
        <parameter_type>open</parameter_type>
        <value_type>integer</value_type>
        <legend>Maximum product of the number of buckets on either side.</legend>
        <length>6</length>
        <default>
          <value>5000</value>
        </default>
      </parameter>
    </section>
  </section>
</root>
