Network analysis of Heraclitus fragments
Analýza Hérakleitových zlomků pomocí teorie sití

Table of Contents

Work in gradual slow progress, eventually we might wrap it as an paper. / Práce na síťové analýze probíhá šnečím tempem, jakkoli – jednoho dne doufáme sesbíraný materiál publikovat v méně divoké podobě.

1 Heraclitus

1.1 Fragments Visualization

1.1.1 Ordering fragments by fragment degree

Link between nodes indicates existence of common keyword.
image: 39_mnt_atrey_WWW_kolymbetes_results_he_frags_basic_circle.svg

Color labeling by nests
Each nest defined manually by 2006 Book, links as in previous section. Session file with colors in he_frags.cys.
image: 40_mnt_atrey_WWW_kolymbetes_results_he_frags_circle_nests.svg
Nests grouping by contracting nests & edge bundling
image: 41_mnt_atrey_WWW_kolymbetes_results_he_frags_circle_nests-eb.svg
Sorted by nests
image: 42_mnt_atrey_WWW_kolymbetes_results_he_frags_circle_nests_sorted.svg
Sorted by nests & edge bundling
image: 43_mnt_atrey_WWW_kolymbetes_results_he_frags_circle_nests_sorted-eb.svg

1.1.2 Hierarchical layout (“direction of flow”)

image: 44_mnt_atrey_WWW_kolymbetes_results_he_frags_plain_hierarchy.svg

1.1.3 Hierarchical mapping (yfiles)

image: 45_mnt_atrey_WWW_kolymbetes_results_he_frags_hierarchy.svg      image: 46_mnt_atrey_WWW_kolymbetes_results_he_frags_hierarchy_circuit.svg
The Hierarchic layout algorithm portraits the precedence relation of directed graphs. Use this algorithm to highlight the main direction or flow within a directed graph.

1.1.4 Nests grouping

Group attributes layout & bundle edges
image: 11_mnt_atrey_WWW_kolymbetes_results_he_frags-nests_group_attr-edge_bundle.png
Nests grouping by contracting nests
image: 12_mnt_atrey_WWW_kolymbetes_results_he_frags_contract-nests_group_attr.png
Nests grouping by contracting nests & edge bundle
image: 13_mnt_atrey_WWW_kolymbetes_results_he_frags_contract-nests_group_attr-edge_bundle.png
Edge weighted spring embedded layout
Small local changes to improve readability of labels and extreme points were done, all points stays in global picture as they are.
image: 14_mnt_atrey_WWW_kolymbetes_results_he_spring.png

1.2 Keywords visualization & clustering

1.2.1 Edge weighted spring embedded layout

Manual local (only) changes were done to improve labels readability (and moving extreme points) it won't change the global position wrt other labels.
image: 37_mnt_atrey_WWW_kolymbetes_results_he_keys_network.svg

1.2.2 Clustering via MCODE

image: 16_mnt_atrey_WWW_kolymbetes_results_cluster_keys_combined.png

1.2.3 Community cluster (GLay)

image: 38_mnt_atrey_WWW_kolymbetes_results_cluster_keys_glay_cluster.svg

1.3 Fragments Clustering

1.3.1 No keyword unification

Simple clustering
image: 18_mnt_atrey_WWW_kolymbetes_anal_visualization_before_unification_clusters.svg
Affinity propagation
image: 19_mnt_atrey_WWW_kolymbetes_anal_visualization_before_unification_clusters_affinity_propagation.svg
MCode
image: 20_mnt_atrey_WWW_kolymbetes_anal_visualization_before_unification_clusters_mcode.svg
Network organic
image: 21_mnt_atrey_WWW_kolymbetes_anal_visualization_before_unification_fragments_network_organic.svg
Autosome
image: 22_mnt_atrey_WWW_kolymbetes_anal_visualization_before_unification_clusters_autosome.svg

1.3.2 (Sub)keywords unification

MCode
image: 23_mnt_atrey_WWW_kolymbetes_anal_visualization____n_dis_fragment_full_validity_clusters_mcode.svg clusters_mcode.svg
Autosome - threshold 0.01
image: 24_mnt_atrey_WWW_kolymbetes_anal_visualization____l_validity_clusters_autosome-threshold-0_01.svg
Community glay
image: 25_mnt_atrey_WWW_kolymbetes_anal_visualization____gment_full_validity_clusters_community_glay.svg
Organic
image: 26_mnt_atrey_WWW_kolymbetes_anal_visualization_____dis_fragment_full_validity_network_organic.svg
Affinity propagation - threshold 1.51
image: 27_mnt_atrey_WWW_kolymbetes_anal_visualization____lusters_affinity_propagation-threshold-1_51.svg
Average shortest path length
image: 27_mnt_atrey_WWW_kolymbetes_anal_visualization____lusters_affinity_propagation-threshold-1_51.svg
Manual separation
image: 28_mnt_atrey_WWW_kolymbetes_anal_visualization____ll_validity_network_group_attributes-manual.svg
image: 29_mnt_atrey_WWW_kolymbetes_anal_visualization____dity_clusters_mcode-group_attributes_manual.svg

2 Anaxagoras

2.1 Fragments Visualization

2.1.1 Ordering fragments by fragment degree

Link between nodes indicates existence of common keyword.
image: 30_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_circle_plain.png

2.1.2 Hierarchical layout (“direction of flow”)

image: 31_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_hierarchy_plain.png

2.1.3 Hierarchical mapping (yfiles)

image: 32_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_hierarchy.png      image: 33_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_hierarchy_circuit.png
Edge weighted spring embedded layout
image: 34_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_spring.png

2.2 Keywords visualization & clustering

2.2.1 Edge weighted spring embedded layout

image: 47_mnt_atrey_WWW_kolymbetes_results_anaxagoras_ana_keys_network.svg

2.2.2 MCODE clustering

image: 36_mnt_atrey_WWW_kolymbetes_results_anaxagoras_cluster_keys_combined.png