├── .gitignore ├── BPS ├── RACKET.md ├── README.TXT ├── README.md ├── RUN.TXT ├── RUN.md ├── atms │ ├── Expected-Disablement-for-Bronchitis.png │ ├── Richens2020.ipynb │ ├── adata.lisp │ ├── ainter.lisp │ ├── aplanr.lisp │ ├── aqueens.lisp │ ├── arules.lisp │ ├── atest.lisp │ ├── atms.lisp │ ├── atre.lisp │ ├── atret.lisp │ ├── bcode.lisp │ ├── blocks.lisp │ ├── causality-ex.lisp │ ├── causality.lisp │ ├── csp.lisp │ ├── funify.lisp │ ├── id.lisp │ ├── interactive-ex.lisp │ ├── my.lisp │ ├── plan-a.lisp │ ├── plan-e.lisp │ ├── prob.lisp │ ├── sudoku.lisp │ └── unify.lisp ├── cps │ ├── algebra.lisp │ ├── boston.lisp │ ├── cps.lisp │ ├── match.lisp │ ├── search.lisp │ ├── simplify.lisp │ ├── subways.lisp │ └── variants.lisp ├── ftre │ ├── fdata.lisp │ ├── finter.lisp │ ├── fnd-ex.lisp │ ├── fnd.lisp │ ├── fqrule.lisp │ ├── fqueens.lisp │ ├── frules.lisp │ ├── ftre.lisp │ ├── funify.lisp │ ├── my-fnd-ex.lisp │ ├── my-fnd.lisp │ └── unify.lisp ├── gde │ ├── 2bit.txt │ ├── atcon.lisp │ ├── condef.lisp │ ├── diagrams.lisp │ ├── gde.lisp │ ├── my.lisp │ ├── polyex.txt │ └── sudoku.lisp ├── jtms │ ├── bms-ex.rkt │ ├── bms.rkt │ ├── carnival-load.lisp │ ├── carnival.lisp │ ├── dds.lisp │ ├── funify.lisp │ ├── funify.rkt │ ├── ijtms-arguing.rkt │ ├── ijtms-ex.rkt │ ├── ijtms.rkt │ ├── jbms-ex.rkt │ ├── jdata.lisp │ ├── jinter.lisp │ ├── jqrule.lisp │ ├── jqueens.lisp │ ├── jqueens.rkt │ ├── jrules.lisp │ ├── jsaint-rules.rkt │ ├── jsaint.lisp │ ├── jsaint.rkt │ ├── jsops.lisp │ ├── jsrules.lisp │ ├── jtest.lisp │ ├── jtest.rkt │ ├── jtms-ex.lisp │ ├── jtms-ex.rkt │ ├── jtms.lisp │ ├── jtms.rkt │ ├── jtre.lisp │ ├── jtre.rkt │ ├── logic.rkt │ ├── match.lisp │ ├── match.rkt │ ├── my.lisp │ ├── pjtms-ex.rkt │ ├── pjtms.rkt │ ├── simplify.lisp │ ├── simplify.rkt │ ├── sudoku-rule.lisp │ ├── sudoku.lisp │ ├── tinytms-ex.rkt │ ├── tinytms.rkt │ ├── unify.lisp │ ├── unify.rkt │ └── utils.rkt ├── ltms │ ├── abduction-ex.lisp │ ├── abduction-simple.lisp │ ├── abduction.lisp │ ├── carnival-ex.dot │ ├── carnival-ex.lisp │ ├── carnival-ex.png │ ├── carnival-from-dot.py │ ├── carnival-load.lisp │ ├── carnival-ltre.lisp │ ├── carnival-play.lisp │ ├── carnival-test.dot │ ├── carnival-test.lisp │ ├── carnival-test.png │ ├── carnival.lisp │ ├── cltms.lisp │ ├── cltms.rkt │ ├── counterfactual.lisp │ ├── cwa.lisp │ ├── dds.lisp │ ├── explain.lisp │ ├── forward-abduction.lisp │ ├── funify.lisp │ ├── indirect.lisp │ ├── interactive-ex.lisp │ ├── laccept.lisp │ ├── ldata.lisp │ ├── linter.lisp │ ├── lrules.lisp │ ├── ltms-ex.lisp │ ├── ltms-ex.rkt │ ├── ltms.lisp │ ├── ltms.rkt │ ├── ltre.lisp │ ├── marx.lisp │ ├── marxdata.lisp │ ├── my.lisp │ ├── mystery.lisp │ ├── setrule.lisp │ ├── sudoku.lisp │ ├── unify.lisp │ └── unsat.lisp ├── relax │ ├── allen.lisp │ ├── cube.lisp │ ├── jcatalog.lisp │ ├── my.lisp │ ├── scene.lisp │ ├── stack.lisp │ ├── sudoku.lisp │ ├── sudoku.rkt │ ├── sudoku_puzzles.lisp │ ├── timedb.lisp │ ├── ttest.lisp │ ├── waltzer.lisp │ ├── waltzer.rkt │ └── wedge.lisp ├── smt │ ├── load.lisp │ └── use.lisp ├── tcon │ ├── condef.lisp │ ├── debug.lisp │ ├── intex.txt │ ├── motion-ex.lisp │ ├── motion.lisp │ ├── my.lisp │ ├── polybox.lisp │ ├── sudoku-prototype.lisp │ ├── sudoku.lisp │ ├── suspend.lisp │ └── tcon.lisp ├── tgizmo │ ├── debug.lisp │ ├── defs.lisp │ ├── ex1.lisp │ ├── ex2.lisp │ ├── ex3.lisp │ ├── ex4.lisp │ ├── ex5.lisp │ ├── ex6.lisp │ ├── ex7.lisp │ ├── ineqs.lisp │ ├── laws.lisp │ ├── mi.lisp │ ├── mlang.lisp │ ├── psvs.lisp │ ├── resolve.lisp │ ├── states.lisp │ ├── tgizmo.lisp │ └── tnst.lisp ├── tre │ ├── data.lisp │ ├── rules.lisp │ ├── tinter.lisp │ ├── tre.lisp │ ├── treex1.lisp │ └── unify.lisp └── utils │ ├── bps-init.lisp │ ├── gen.sh │ ├── loader.lisp │ ├── lst.lisp │ └── my.lisp ├── GPT4-synthesis ├── .ipynb_checkpoints │ └── Untitled-checkpoint.ipynb ├── 0-synthesize-program.rkt ├── 1-metacognition.rkt ├── 2-self-improvement.rkt ├── 3-context-awareness.rkt ├── 4-incremental-synthesis.rkt ├── 5-collaboration.rkt ├── 6-explanation-and-justification.rkt ├── 7-transfer-learning.rkt ├── 8-dynamic-strategy-selection.rkt ├── Untitled.ipynb ├── Untitled.rkt └── synthesize-program.orig.rkt ├── NOTES.md ├── README.md ├── coverage ├── README.txt ├── ccoverage.lisp ├── check-growth-rules.lisp ├── check-growth.lisp ├── check-growth.txt ├── coverage-rules.lisp ├── coverage.lisp ├── coverage2-debug-rules.lisp ├── coverage2-rules.lisp ├── coverage2.lisp ├── ex.lisp ├── gen.sh ├── jcoverage-debug-rules.lisp ├── jcoverage-rules.lisp ├── jcoverage.lisp ├── lcoverage-debug-rules.lisp ├── lcoverage-rules.lisp ├── lcoverage.lisp ├── organism-ex.lisp ├── organism-l.lisp ├── real-ex.lisp ├── real-not-produced-j.lisp ├── real-not-produced-l.lisp ├── real-not-produced.lisp ├── stats.txt └── universal-ex.lisp ├── metabolizer ├── adj.lisp ├── atoms.lisp ├── biotransformation.lisp ├── functional-spec.txt ├── meta-cpd-classes.lisp ├── meta-cpds.lisp ├── smiles-gen.lisp └── smiles.lisp ├── network-debugger ├── API.txt ├── README.txt ├── configure ├── loader.lisp ├── nd-extended-rules.lisp ├── nd-inter.lisp ├── nd-pathway-rules.lisp ├── nd-rules.lisp ├── nd.lisp ├── presentation │ ├── demo-experiments.lisp │ ├── demo-false-negative.lisp │ ├── demo-false-positive.lisp │ ├── demo-negative.lisp │ ├── demo-network.lisp │ ├── demo-positive.lisp │ ├── demo.dia │ ├── demo.png │ ├── outline.txt │ ├── system.dia │ └── system.png ├── spec.txt ├── stats.txt ├── tests │ ├── ecoli-experiments.lisp │ ├── ecoli-extended.lisp │ ├── ecoli-pathways.lisp │ ├── ecoli-stats.lisp │ ├── knock.lisp │ ├── lessons.lisp │ ├── pathways.lisp │ ├── reversible.lisp │ ├── simple-stats.lisp │ ├── simple.lisp │ ├── unknown-enzyme.lisp │ └── unknown.lisp └── utils.lisp ├── ptools ├── README.md ├── biolog-experiments.lisp ├── biolog-model-comp.txt ├── biolog-pm1.txt ├── biolog-pm2.txt ├── biolog-pm3.txt ├── data │ ├── biolog-experiments.lisp │ ├── ecoli-experiments.lisp │ ├── ecoli-network.lisp │ └── 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