Args description refined, papers references added

README.md

@@ -2,7 +2,7 @@
 Extremely fast evaluation of the extrinsic clustering measures: *various F1 measures (including F1-Score) for overlapping multi-resolution clusterings with unequal node base (and optional node base synchronization)* and standard NMI for non-overlapping clustering on a single resolution.  
 `xmeasures` evaluates F1 and NMI for collections of hundreds thousands clusters withing a dozen seconds on an ordinary laptop using a single CPU core. The computational time is O(N) unlike O(N*C) of the existing state of the art implementations, where N is the number of nodes in the network and C is the number of clusters.
 `xmeasures` is one of the utilities designed for the [PyCaBeM](https://github.com/eXascaleInfolab/PyCABeM) clustering benchmark to evaluate clustering of large networks.  
-A paper about the implemented F1 measures (F1p is much more discriminative than the standard F1-Score, NMI measures and their applicability is being written now and the reference will be specified before Summer, 2017.
+A paper about the implemented F1 measures (F1p is much more discriminative than the standard [Average F1-Score](https://cs.stanford.edu/people/jure/pubs/bigclam-wsdm13.pdf)), [NMI measures](www.jmlr.org/papers/volume11/vinh10a/vinh10a.pdf) and their applicability is being written now and the reference will be specified before Summer, 2017.
 > Standard NMI is implemented considering overlapping and multi-resolution clustering only to demonstrate non-applicability of the standard NMI for such cases, it yield unfair results. See [GenConvNMI](https://github.com/eXascaleInfolab/GenConvNMI) for the fair generalized NMI evaluation.
 
 Author (c)  Artem Lutov <[email protected]>

args.ggo

@@ -1,7 +1,7 @@
 # Configuration file for the automatic generation of the input options parsing
 
 package "xmeasures"
-version "3.0.1"
+version "3.0.2"
 
 purpose "Extrinsic measures evaluation: F1 (prob, harm and score) for overlapping\
  multi-resolution clusterings with possible unequal node base and standard NMI for\
@@ -10,10 +10,10 @@ purpose "Extrinsic measures evaluation: F1 (prob, harm and score) for overlappin
 description "Extrinsic measures are evaluated, i.e. clustering (collection of\
  clusters) is compared to another collection, which is typically the ground-truth.
 Evaluating measures are:
-  - F1  - various F1 measures of the Greatest (Max) Match including the standard\
+  - F1  - various F1 measures of the Greatest (Max) Match including the Average\
  F1-Score with optional weighting;
-  - NMI  - Normalized Mutual Information, normalized by either max or also avg\
- and min information content denominators.
+  - NMI  - Normalized Mutual Information, normalized by either max or also sqrt,\
+ avg and min information content denominators.
 ATTENTION: this is standard NMI, which should be used ONLY for the HARD\
  partitioning evaluation (non-overlapping clustering on a single resolution).\
   it penalizes overlapping and multi-resolution structures.
@@ -70,7 +70,7 @@ args "--default-optional --unamed-opts=clusterings"   # Set opional opions, allo
 
 
 # = Changelog =
-# v3.0.+ - NMI_sqrt added
+# v3.0.2 - NMI_sqrt added
 # v3.0 - Command line interface changed for F1
 #	- Standard F1-Score added
 #	- Option for the detailed results output added

autogen/cmdline.c

@@ -31,7 +31,7 @@ const char *gengetopt_args_info_usage = "Usage: xmeasures [OPTIONS] clustering1
 
 const char *gengetopt_args_info_versiontext = "";
 
-const char *gengetopt_args_info_description = "Extrinsic measures are evaluated, i.e. clustering (collection of clusters) is\ncompared to another collection, which is typically the ground-truth.\nEvaluating measures are:\n  - F1  - various F1 measures of the Greatest (Max) Match including the\nstandard F1-Score with optional weighting;\n  - NMI  - Normalized Mutual Information, normalized by either max or also avg\nand min information content denominators.\nATTENTION: this is standard NMI, which should be used ONLY for the HARD\npartitioning evaluation (non-overlapping clustering on a single resolution).\nit penalizes overlapping and multi-resolution structures.\nNOTE: unequal node base in the clusterings is allowed, it penalizes the match.\nUse [GenConvNMI](https://github.com/eXascaleInfolab/GenConvNMI) for arbitrary\ncollections evaluation.\n";
+const char *gengetopt_args_info_description = "Extrinsic measures are evaluated, i.e. clustering (collection of clusters) is\ncompared to another collection, which is typically the ground-truth.\nEvaluating measures are:\n  - F1  - various F1 measures of the Greatest (Max) Match including the Average\nF1-Score with optional weighting;\n  - NMI  - Normalized Mutual Information, normalized by either max or also\nsqrt, avg and min information content denominators.\nATTENTION: this is standard NMI, which should be used ONLY for the HARD\npartitioning evaluation (non-overlapping clustering on a single resolution).\nit penalizes overlapping and multi-resolution structures.\nNOTE: unequal node base in the clusterings is allowed, it penalizes the match.\nUse [GenConvNMI](https://github.com/eXascaleInfolab/GenConvNMI) for arbitrary\ncollections evaluation.\n";
 
 const char *gengetopt_args_info_help[] = {
   "  -h, --help              Print help and exit",

autogen/cmdline.h

@@ -31,7 +31,7 @@ extern "C" {
 
 #ifndef CMDLINE_PARSER_VERSION
 /** @brief the program version */
-#define CMDLINE_PARSER_VERSION "3.0.1"
+#define CMDLINE_PARSER_VERSION "3.0.2"
 #endif
 
 enum enum_f1 { f1__NULL = -1, f1_arg_partprob = 0, f1_arg_harmonic, f1_arg_standard };