add gnn-node-aggregation.typ and its assets

add made.typ converted from made.tex

rename conv2d to 2d-convolution

assets/gnn-node-aggregation/gnn-node-aggregation.typ

@@ -0,0 +1,137 @@
+#import "@preview/cetz:0.3.1": canvas, draw
+
+#set page(width: auto, height: auto, margin: 8pt)
+
+#canvas({
+  import draw: line, content, circle, rect
+
+  // Styles
+  let arrow-style = (mark: (end: "stealth", fill: black, scale: 0.5, offset: 2pt), stroke: 0.5pt)
+  let edge-style = (stroke: 0.4pt)
+  let node-radius = 0.3
+  let graph-sep = 4.5 // separation between input graph and aggregation
+
+  // Node colors - ensure consistency
+  let colors = (
+    A: rgb("#ffd700"), // Gold
+    B: rgb("#ff4d4d"), // Red
+    C: rgb("#90ee90"), // Light green
+    D: rgb("#4d94ff"), // Blue
+    E: rgb("#9370db"), // Purple
+    F: rgb("#ff69b4"), // Pink
+  )
+
+  // Helper to draw a node with label
+  let draw-node(pos, label, name) = {
+    circle(
+      pos,
+      radius: node-radius,
+      fill: colors.at(label),
+      stroke: black + 0.5pt,
+      name: name,
+    )
+    content(pos, label, anchor: "center")
+  }
+
+  // Input Graph (left side)
+  // Define node positions
+  let target-pos = (-1.5, 1.2)
+  let b-pos = (0.5, 2)
+  let c-pos = (1, 1)
+  let d-pos = (-2.5, -.7)
+  let e-pos = (-0.25, -1.25)
+  let f-pos = (1.5, 0)
+
+  // Draw nodes
+  draw-node(target-pos, "A", "target")
+  draw-node(b-pos, "B", "b")
+  draw-node(c-pos, "C", "c")
+  draw-node(d-pos, "D", "d")
+  draw-node(e-pos, "E", "e")
+  draw-node(f-pos, "F", "f")
+
+  // Add target node label
+  content((rel: (0, 1.5), to: "target"), "Target Node", name: "target-label")
+  line("target-label.south", "target", ..arrow-style)
+
+  // Draw edges
+  for (start, end) in (
+    ("target", "b"),
+    ("target", "c"),
+    ("b", "c"),
+    ("target", "d"),
+    ("c", "e"),
+    ("c", "f"),
+    ("e", "f"),
+  ) {
+    line(start, end, ..edge-style)
+  }
+
+  // Add "Input Graph" label
+  content((0.25, -1.8), [Input Graph])
+
+  // Main aggregation box
+  let box-pos = (graph-sep, 0.5)
+  content(
+    box-pos,
+    [Aggregation\ for Node A],
+    name: "agg-box",
+    fill: rgb("ddd"),
+    frame: "rect",
+    stroke: 0.2pt,
+    padding: (3pt, 7pt),
+  )
+
+  // First layer nodes - renamed to show they're neighbors of A
+  let first-layer = (
+    (2, 2, "B", "a-to-b"),
+    (2, 0, "C", "a-to-c"),
+    (2, -2, "D", "a-to-d"),
+  )
+
+  // Draw first layer nodes and arrows
+  for (dx, dy, label, name) in first-layer {
+    draw-node((rel: (dx, dy), to: "agg-box.east"), label, name)
+    line(name, "agg-box.east", ..arrow-style)
+  }
+
+  content((rel: (0, .7), to: "a-to-b"), "Hop 1")
+
+  // Draw aggregation boxes for each first layer node
+  for node in ("a-to-b", "a-to-c", "a-to-d") {
+    let letter = node.split("-").at(-1)
+    content(
+      (rel: (2, 0), to: node),
+      [Aggr(#upper(letter))],
+      fill: rgb("ddd"),
+      frame: "rect",
+      stroke: 0.2pt,
+      padding: (2pt, 4pt),
+      name: "aggr-" + letter,
+    )
+    line("aggr-" + letter, node, ..arrow-style)
+  }
+
+
+  // Second layer nodes and connections - renamed to show full path
+  let second-layer = (
+    // From B-aggregation (B's neighbors)
+    ((2, 1), "A", "aggr-b", "b-to-a"),
+    ((2, 0), "C", "aggr-b", "b-to-c"),
+    // From C-aggregation (C's neighbors)
+    ((2, 1), "A", "aggr-c", "c-to-a"),
+    ((2, 0.25), "B", "aggr-c", "c-to-b"),
+    ((2, -0.5), "E", "aggr-c", "c-to-e"),
+    ((2, -1.25), "F", "aggr-c", "c-to-f"),
+    // From D-aggregation (D's neighbors)
+    ((2, 0), "A", "aggr-d", "d-to-a"),
+  )
+
+  // Draw second layer nodes and arrows
+  for ((dx, dy), label, parent, name) in second-layer {
+    draw-node((rel: (dx, dy), to: parent), label, name)
+    line(name, parent + ".east", ..arrow-style)
+  }
+
+  content((rel: (0, .7), to: "b-to-a"), "Hop 2")
+})

assets/gnn-node-aggregation/gnn-node-aggregation.yml

@@ -0,0 +1,37 @@
+title: GNN Node Aggregation Process
+description: >
+  Diagram illustrating the message-passing process in graph neural networks (GNNs).
+  Shows how information flows from neighboring nodes to a target node A through
+  multiple layers of aggregation. The first layer combines information from direct
+  neighbors (B, C, D) while the second layer incorporates information from nodes
+  two hops away (E, F), demonstrating how a node's receptive field grows with
+  network depth.
+
+authors:
+  - Janosh Riebesell
+  - William L. Hamilton
+
+references:
+  - hamilton_graph_2020:
+      title: Graph Representation Learning
+      authors: William L. Hamilton
+      year: 2020
+      page: 55
+      publisher: Morgan & Claypool Publishers
+      doi: 10.2200/S01045ED1V01Y202009AIM046
+
+tags:
+  - graph-neural-networks
+  - message-passing
+  - node-aggregation
+  - neural-networks
+  - deep-learning
+  - information-flow
+  - receptive-field
+
+components:
+  - input-graph
+  - target-node
+  - aggregation-layers
+  - message-passing
+  - node-states

assets/kohn-sham-cycle/kohn-sham-cycle.typ

@@ -15,6 +15,7 @@
     width: 22em,
     height: 12em,
     name: "enclosure",
+    radius: 5pt,
   )
 
   // Enclosure label
@@ -52,6 +53,7 @@
     width: 20em,
     name: "initial",
     padding: (3pt, 2em, 0),
+    radius: 1em,
   )
 
   // Potential box