Lesson index¶
The nine notebooks are arranged in three stages. Start at S01 for the full sequence, or open a later stage directly.
Start from the beginning → Set up locally
Run S01 online:
Stages¶
S01–S03
Represent, match, and align molecular graphs.
S04–S07
Map reactions, define graph edits, and extract reaction rules.
S08–S09
Apply rules and tune the trade-off between generality and specificity.
01 · Fundamentals¶
Represent, match, and align molecular graphs.
Representation
Convert chemical structures to labeled graph objects.
Matching
Work with isomorphism, symmetry, and subgraph matching.
Alignment
Use shared subgraphs for alignment, comparison, and reaction rebalancing.
02 · Rule construction¶
Map reactions, define graph edits, and extract reaction rules.
Atom mapping
Relate atom correspondences to ITS graphs and map-invariant representations.
DPO
Represent deleted, preserved, and created structure with double-pushout rules.
Canonicalization
Canonicalize mapped reactions for comparison, hashing, and deduplication.
Rule library
Extract a rule library from mapped reaction records.
03 · Prediction and evaluation¶
Apply rule libraries and control the trade-off between generality and specificity.
Prediction
Apply rules forward and backward to enumerate reaction candidates.
Context
Measure how context expansion changes rule specificity and prediction results.
Start at S01 if graph-based reaction modeling is new to you. Otherwise, use the stage links above.