model_graph.dot

digraph G {
    margin=0;
    newrank=true;

    graph [fontname = "Fira Sans", rankdir=LR, splines=ortho, ratio=auto];
    node [fontname = "Fira Sans", style="filled,solid", fillcolor=white, shape="box", margin=0.15];
    edge [fontname = "Fira Sans"];

    subgraph cluster_0 {
        rank="same";
        style=filled;
        margin=8;
        color="#f4dbd6";
        node [style=filled];
        edge[minlen=2];
        SMILES -> molgraph;
        label = "Parsing";
    }

    pre_graph[shape="point", width=0.001, height=0.001];
    
    subgraph cluster_1 {
        rank="same";
        style=filled;
        margin=8;
        color="#91d7e3";
        edge[minlen=2];
        G1 -> G2;
        G2 -> G3[style="dotted"];
        label = "Graph layers";
    }
    
    pre_pool[shape="point", width=0, height=0];
    
    subgraph cluster_2 {
        rank="same";
        style=filled;
        margin=25;
        color="#ee99a0";
        edge[minlen=2];
        D1 -> D2[style="dotted"];
        D1 -> D3[style="dotted"];
        D2 -> D3;
        label="Multi-layer\nperceptron";
    }
    
    subgraph cluster_3_margin {
        margin=15;
        style="invis";
        subgraph cluster_3 {
            style="dashed";
            label="Key";
            subgraph example_edges {
                rank="same";
                key[label="Layer name\n[Output\nDimensions]"];
                node[shape="point", width=0, height=0];
                subgraph full_edge {
                    eg3 -> eg4[dir=none];
                    eg4 -> eg5[xlabel="    Connection"];
                }
                subgraph dotted_edge {
                    edge[style="dotted"];
                    eg0 -> eg1[dir=none];
                    eg1 -> eg11[dir=none];
                    eg11 -> eg2[xlabel="    Connection\n    Choice"];
                }
            }
            dummy[style=invis, label="", width=0.3];
            key -> dummy[style=invis];
        }
    }
    
    molgraph -> pre_graph[dir=none];
    pre_graph -> G1;
    G3 -> pre_pool[dir=none];
    G2 -> pre_pool[style="dotted", dir=none];
    pre_pool -> pool;
    pool -> D1[style="dotted"];
    pool -> GP[style="dotted"];
    
    subgraph to_output{
        edge[dir=none];
        D3 -> pre_output;
        GP -> pre_output[constraint=false];
    }

    pre_output -> output;

    molgraph[label="Graph\n[N × ≥8]"];
    subgraph dimension_labels {
        G1[label=<G1<br/>[N × <i>H<sub>G1</sub></i>]>];
        G2[label=<G2<br/>[N × <i>H<sub>G2</sub></i>]>];
        G3[label=<G3<br/>[N × <i>H<sub>G3</sub></i>]>];

        pool[label=<Pool<br/>  [<i>H<sub>P</sub></i>]>, shape=box];
        
        D1[label=<D1<br/>[<i>H<sub>D1</sub></i>]>];
        D2[label=<D2<br/>[<i>H<sub>D2</sub></i>]>];
        D3[label=<D3<br/>[1]>];

        GP[ label="Gaussian Process\n[1]"];
    }
    
    
    pre_output[shape="point", width=0.001, height=0.001];
    output[label=<<b>Output</b>>, shape="ellipse"]
    
}