Network analysis of Heraclitus fragments
Analýza Hérakleitových zlomků pomocí teorie sití

Table of Contents

2.1 Fragments Visualization

2.1.1 Ordering fragments by fragment degree

2.1.2 Hierarchical layout (direction of flow)

2.1.3 Hierarchical mapping (yfiles)

2.2 Keywords visualization & clustering

2.2.1 Edge weighted spring embedded layout

2.2.2 MCODE clustering

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: 0_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: 1_mnt_atrey_www_kolymbetes_results_he_frags_circle_nests.svg

Nests grouping by contracting nests & edge bundling

image: 2_mnt_atrey_www_kolymbetes_results_he_frags_circle_nests-eb.svg

Sorted by nests

image: 3_mnt_atrey_www_kolymbetes_results_he_frags_circle_nests_sorted.svg

Sorted by nests & edge bundling

image: 4_mnt_atrey_www_kolymbetes_results_he_frags_circle_nests_sorted-eb.svg

1.1.2 Hierarchical layout (“direction of flow”)

image: 5_mnt_atrey_www_kolymbetes_results_he_frags_plain_hierarchy.svg

1.1.3 Hierarchical mapping (yfiles)

image: 6_mnt_atrey_www_kolymbetes_results_he_frags_hierarchy.svg

image: 7_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: 8_mnt_atrey_www_kolymbetes_results_he_frags-nests_group_attr-edge_bundle.png

Nests grouping by contracting nests

image: 9_mnt_atrey_www_kolymbetes_results_he_frags_contract-nests_group_attr.png

Nests grouping by contracting nests & edge bundle

image: 10_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: 11_mnt_atrey_www_kolymbetes_results_he_spring.png

1.2 Iterative decomposition of fragments

image: 12_mnt_atrey_www_kolymbetes_results_iterative_he_histo.png

It's clear that two nodes 1 (degree 72) & 30 (degree 50) could be cut, where to make the threshold is way less clear. Head:

Count Nest Frag

72 1 1

50 8 30

41 5 45

39 15 129

Colors legens used below:

image: 13_mnt_atrey_www_kolymbetes_results_iterative_keys_fragments_network_INT_txt--glay-legend.png

1.2.1 Glay

image: 14_mnt_atrey_www_kolymbetes_results_iterative_frags_fragments_network_INT_txt_1--glay.svg

1.2.2 MCL

image: 15_mnt_atrey_www_kolymbetes_results_iterative_frags_fragments_network_INT_txt_1--mcl.svg

1.2.3 MCODE

image: 16_mnt_atrey_www_kolymbetes_results_iterative_frags_fragments_network_INT_txt_1--mcode.svg

1.3 Keywords visualization & clustering

1.3.1 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: 17_mnt_atrey_www_kolymbetes_results_he_keys_network.svg

1.3.2 Clustering via MCODE

image: 18_mnt_atrey_www_kolymbetes_results_cluster_keys_combined.png

1.3.3 Community cluster (GLay)

image: 19_mnt_atrey_www_kolymbetes_results_cluster_keys_glay_cluster.svg

1.4 Iterative decomposition of keywords

image: 20_mnt_atrey_www_kolymbetes_results_iterative_keys_he_keys_histo.png

Key Count

panta 192

logos 134

anthropoi 122

We cluster the network after removing three most connected keywords from the network.

1.4.1 Community Glay

image: 21_mnt_atrey_www_kolymbetes_results_iterative_k___twork_panta_logos_anthropoi--clustered-glay.svg

1.4.2 MCode

image: 22_mnt_atrey_www_kolymbetes_results_iterative_k___work_panta_logos_anthropoi--clustered-mcode.svg

1.4.3 MCL

image: 23_mnt_atrey_www_kolymbetes_results_iterative_k___etwork_panta_logos_anthropoi--clustered-MCL.svg

1.5 Fragments Clustering

1.5.1 No keyword unification

Simple clustering

image: 24_mnt_atrey_www_kolymbetes_anal_visualization_before_unification_clusters.svg

Affinity propagation

image: 25_mnt_atrey_www_kolymbetes_anal_visualization_before_unification_clusters_affinity_propagation.svg

MCode

image: 26_mnt_atrey_www_kolymbetes_anal_visualization_before_unification_clusters_mcode.svg

Network organic

image: 27_mnt_atrey_www_kolymbetes_anal_visualization_before_unification_fragments_network_organic.svg

Autosome

image: 28_mnt_atrey_www_kolymbetes_anal_visualization_before_unification_clusters_autosome.svg

1.5.2 (Sub)keywords unification

MCode

image: 29_mnt_atrey_www_kolymbetes_anal_visualization____n_dis_fragment_full_validity_clusters_mcode.svg

Autosome - threshold 0.01

image: 30_mnt_atrey_www_kolymbetes_anal_visualization____l_validity_clusters_autosome-threshold-0_01.svg

Community glay

image: 31_mnt_atrey_www_kolymbetes_anal_visualization____gment_full_validity_clusters_community_glay.svg

Organic

image: 32_mnt_atrey_www_kolymbetes_anal_visualization_____dis_fragment_full_validity_network_organic.svg

Affinity propagation - threshold 1.51

image: 33_mnt_atrey_www_kolymbetes_anal_visualization____lusters_affinity_propagation-threshold-1_51.svg

Average shortest path length

image: 33_mnt_atrey_www_kolymbetes_anal_visualization____lusters_affinity_propagation-threshold-1_51.svg

Manual separation

Manual group attributes (file)

image: 34_mnt_atrey_www_kolymbetes_anal_visualization____ll_validity_network_group_attributes-manual.svg

MCode group attributes - manual reorder (file)

image: 35_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: 36_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_circle_plain.png

2.1.2 Hierarchical layout (“direction of flow”)

image: 37_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_hierarchy_plain.png

2.1.3 Hierarchical mapping (yfiles)

image: 38_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_hierarchy.png

image: 39_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_hierarchy_circuit.png

Edge weighted spring embedded layout

image: 40_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_spring.png

2.2 Keywords visualization & clustering

2.2.1 Edge weighted spring embedded layout

image: 41_mnt_atrey_www_kolymbetes_results_anaxagoras_ana_keys_network.svg

2.2.2 MCODE clustering

image: 42_mnt_atrey_www_kolymbetes_results_anaxagoras_cluster_keys_combined.png