compiled-knowledge 4.0.0a13__tar.gz → 4.0.0a14__tar.gz

{compiled_knowledge-4.0.0a13/src/compiled_knowledge.egg-info → compiled_knowledge-4.0.0a14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: compiled-knowledge
-Version: 4.0.0a13
+Version: 4.0.0a14
 Summary: A Python package for compiling and querying discrete probabilistic graphical models.
 Author-email: Barry Drake <barry@compiledknowledge.org>
 License-Expression: MIT
@@ -43,7 +43,7 @@ Refer to the project online documentation at
 The primary repository for the project is 
 [github.com/ropeless/compiled_knowledge](https://github.com/ropeless/compiled_knowledge). 
 
-The Python package is available on PyPi, see
+The Python package is available on PyPI, see
 [pypi.org/project/compiled-knowledge](https://pypi.org/project/compiled-knowledge/).
 
 For more information email

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/README.md

@@ -26,7 +26,7 @@ Refer to the project online documentation at
 The primary repository for the project is 
 [github.com/ropeless/compiled_knowledge](https://github.com/ropeless/compiled_knowledge). 
 
-The Python package is available on PyPi, see
+The Python package is available on PyPI, see
 [pypi.org/project/compiled-knowledge](https://pypi.org/project/compiled-knowledge/).
 
 For more information email

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "compiled-knowledge"
-version = "4.0.0a13"
+version = "4.0.0a14"
 description = "A Python package for compiling and querying discrete probabilistic graphical models."
 readme = "README.md"
 license = "MIT"

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/circuit_compiler/named_circuit_compilers.py

@@ -18,19 +18,19 @@ class NamedCircuitCompiler(Enum):
     Each member itself is callable, conforming to the CircuitCompiler protocol, delegating to the compiler function.
     """
 
-    LLVM_STACK: CircuitCompiler = (partial(llvm_compiler.compile_circuit, flavour=Flavour.STACK),)
-    LLVM_TMPS: CircuitCompiler = (partial(llvm_compiler.compile_circuit, flavour=Flavour.TMPS, opt=0),)
-    LLVM_VM: CircuitCompiler = (llvm_vm_compiler.compile_circuit,)
-    CYTHON_VM: CircuitCompiler = (cython_vm_compiler.compile_circuit,)
-    INTERPRET: CircuitCompiler = (interpret_compiler.compile_circuit,)
+    LLVM_STACK = (partial(llvm_compiler.compile_circuit, flavour=Flavour.STACK),)
+    LLVM_TMPS = (partial(llvm_compiler.compile_circuit, flavour=Flavour.TMPS, opt=0),)
+    LLVM_VM = (llvm_vm_compiler.compile_circuit,)
+    CYTHON_VM = (cython_vm_compiler.compile_circuit,)
+    INTERPRET = (interpret_compiler.compile_circuit,)
 
-    # The following circuit compilers were experimental but are not really useful
+    # The following circuit compilers were experimental but are not really useful.
     #
     # Slow compile and execution:
-    # LLVM_FUNCS: CircuitCompiler = (partial(llvm_compiler.compile_circuit, flavour=Flavour.FUNCS, opt=0),)
+    # LLVM_FUNCS = (partial(llvm_compiler.compile_circuit, flavour=Flavour.FUNCS, opt=0),)
     #
     # Slow compile and same execution as LLVM_VM:
-    # LLVM_VM_COMPILED_ARRAYS: CircuitCompiler = (partial(llvm_vm_compiler.compile_circuit, compile_arrays=True),)
+    # LLVM_VM_COMPILED_ARRAYS = (partial(llvm_vm_compiler.compile_circuit, compile_arrays=True),)
 
     def __call__(
             self,

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/example/pathfinder.py

@@ -2,25 +2,33 @@ from ck.pgm import PGM
 
 
 class Pathfinder(PGM):
+    """
+    This implementation of the Pathfinder PGM has 93 states for the "Fault" random
+    variable, and its factor has been normalised to be a CPT.
+    """
 
     def __init__(self):
         super().__init__(self.__class__.__name__)
 
         pgm_rv0 = self.new_rv('Fault', (
-        'AIDS early', 'AILD', 'ALIP', 'Cat scratch disease', 'Dermatopathic laden', 'Florid follic hyperp',
-        'GLH hyaline vascular', 'GLH plasma cell', 'Granulomatous laden', 'Histiocytosis x', 'Infectious mono',
-        'Leprosy-lepromatous', 'Lymphangiographic', 'Mantle zone hyperpla', 'Necrotizing Kikuchi',
-        'Necrotiz non-Kikuchi', 'Rheumatoid arthritis', 'Sarcoidosis', 'SHML', 'Sinus histiocytosis', 'Syphilis',
-        'Toxoplasmosis', 'Tuberculosis', 'Viral NOS', "Whipple's disease", 'L&H nodular HD', 'L&H diffuse HD',
-        'Nodular sclerosis HD', 'Cellular phase NSHD', 'Syncytial NSHD', 'Mixed cellularity HD', 'Interfollicular HD',
-        'Diffuse fibrosis HD', 'Reticular-type HD', 'Small cleaved fol', 'Mixed fol', 'Large cell fol',
-        'Small noncleaved fol', 'Small lymphocytic', 'Plasmacytoid lyctic', 'Mantle zone lymphoma', 'Small cleaved dif',
-        'Mixed FCC dif', 'Large cell dif', 'B-immunoblastic', 'T-immunob mixed', 'AILD-like T-cell lym', 'Japanese ATL',
-        'Lymphoblastic', 'Small noncleaved dif', 'True histiocytic', 'Ki-1 LC anaplas T', 'Multiple myeloma',
-        'Mycosis fungoides', 'AML', 'Hairy cell leukemia', 'Carcinoma', 'Melanoma', 'EM plasmacytoma',
-        "Kaposi's sarcoma", 'Mast-cell disease', 'AIDS involutionary', 'T-immunob large', 'Monocytoid B-cell',
-        'Nasopharyngeal CA', 'Seminoma', 'SLE', 'Mycobact histiocytos', 'Mast-cell hyperplas', 'LGV', 'Histoplasmosis',
-        'Coccidioidomycosis', 'CMV', 'Brucellosis', 'Ki-1 LC anaplas B', 'Intermed lymphocytic'))
+            'AIDS early', 'AILD', 'ALIP', 'Cat scratch disease', 'Dermatopathic laden', 'Florid follic hyperp',
+            'GLH hyaline vascular', 'GLH plasma cell', 'Granulomatous laden', 'Histiocytosis x', 'Infectious mono',
+            'Leprosy-lepromatous', 'Lymphangiographic', 'Mantle zone hyperpla', 'Necrotizing Kikuchi',
+            'Necrotiz non-Kikuchi', 'Rheumatoid arthritis', 'Sarcoidosis', 'SHML', 'Sinus histiocytosis', 'Syphilis',
+            'Toxoplasmosis', 'Tuberculosis', 'Viral NOS', "Whipple's disease", 'L&H nodular HD', 'L&H diffuse HD',
+            'Nodular sclerosis HD', 'Cellular phase NSHD', 'Syncytial NSHD', 'Mixed cellularity HD',
+            'Interfollicular HD',
+            'Diffuse fibrosis HD', 'Reticular-type HD', 'Small cleaved fol', 'Mixed fol', 'Large cell fol',
+            'Small noncleaved fol', 'Small lymphocytic', 'Plasmacytoid lyctic', 'Mantle zone lymphoma',
+            'Small cleaved dif',
+            'Mixed FCC dif', 'Large cell dif', 'B-immunoblastic', 'T-immunob mixed', 'AILD-like T-cell lym',
+            'Japanese ATL',
+            'Lymphoblastic', 'Small noncleaved dif', 'True histiocytic', 'Ki-1 LC anaplas T', 'Multiple myeloma',
+            'Mycosis fungoides', 'AML', 'Hairy cell leukemia', 'Carcinoma', 'Melanoma', 'EM plasmacytoma',
+            "Kaposi's sarcoma", 'Mast-cell disease', 'AIDS involutionary', 'T-immunob large', 'Monocytoid B-cell',
+            'Nasopharyngeal CA', 'Seminoma', 'SLE', 'Mycobact histiocytos', 'Mast-cell hyperplas', 'LGV',
+            'Histoplasmosis',
+            'Coccidioidomycosis', 'CMV', 'Brucellosis', 'Ki-1 LC anaplas B', 'Intermed lymphocytic'))
         pgm_rv1 = self.new_rv('ACID', ('Negative', 'Positive'))
         pgm_rv2 = self.new_rv('F_CSA', ('No follicles', 'Absent', 'Present'))
         pgm_rv3 = self.new_rv('F_ISL', ('No follicles', 'Absent', 'Present'))
@@ -58,25 +66,27 @@ class Pathfinder(PGM):
                                ('Absent [0]', 'Rare [1-5]', 'Few [6-25]', 'Many [26-100]', 'Striking [>100]'))
         pgm_rv34 = self.new_rv('LH_NOD', ('Absent', 'Present'))
         pgm_rv35 = self.new_rv('LACUN', (
-        'Absent [0]', 'Rare [1-5]', 'Few [6-25]', 'Many [26 - 100]', 'Striking [>100]', 'Sheets [>50pc of section]'))
+            'Absent [0]', 'Rare [1-5]', 'Few [6-25]', 'Many [26 - 100]', 'Striking [>100]',
+            'Sheets [>50pc of section]'))
         pgm_rv36 = self.new_rv('LANG', ('Absent [0]', 'Present [1-5]', 'Prominent [>5]'))
         pgm_rv37 = self.new_rv('LEUK', ('Absent', 'Present'))
         pgm_rv38 = self.new_rv('LLC_CY', ('No LLCs', 'Scanty', 'Moderate-abundant clear', 'Moderate-abundant deep'))
         pgm_rv39 = self.new_rv('LLC_NS', (
-        'No LLCs', 'Multilobated [some]', 'Cerebriform/Mulberry [some]', 'Convoluted [some]', 'Irregular [most]',
-        'Round/slightly irregular [most]'))
+            'No LLCs', 'Multilobated [some]', 'Cerebriform/Mulberry [some]', 'Convoluted [some]', 'Irregular [most]',
+            'Round/slightly irregular [most]'))
         pgm_rv40 = self.new_rv('LLC', (
-        'Absent [0pc]', 'Sparse [<10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
+            'Absent [0pc]', 'Sparse [<10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
         pgm_rv41 = self.new_rv('F_POPU', (
-        'No follicles', '>80pc 6-12u', '>50pc 13-20u with nucleoli', '>50pc >20u with nucleoli', 'Other'))
+            'No follicles', '>80pc 6-12u', '>50pc 13-20u with nucleoli', '>50pc >20u with nucleoli', 'Other'))
         pgm_rv42 = self.new_rv('MAST', ('Absent [0]', 'Present [1-50]', 'Prominent [>50]'))
         pgm_rv43 = self.new_rv('MLC', (
-        'Absent [0pc]', 'Sparse [<10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
+            'Absent [0pc]', 'Sparse [<10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
         pgm_rv44 = self.new_rv('MELANOMA', ('Absent', 'Present'))
         pgm_rv45 = self.new_rv('MF10HP', ('0-5', '6-15', '16-50', '>50'))
         pgm_rv46 = self.new_rv('MLC_CY', ('No MLCs', 'Scanty', 'Moderate-abundant clear', 'Moderate-abundant deep'))
         pgm_rv47 = self.new_rv('MLC_NS', (
-        'No MLCs', 'Cerebriform [some]', 'Convoluted [some]', 'Irregular [most]', 'Round/slightly irregular [most]'))
+            'No MLCs', 'Cerebriform [some]', 'Convoluted [some]', 'Irregular [most]',
+            'Round/slightly irregular [most]'))
         pgm_rv48 = self.new_rv('MLC_NI', ('No MLCs', 'Absent to rare', 'Large central', 'Peripheral', 'Other'))
         pgm_rv49 = self.new_rv('MCC', ('Absent [0pc]', 'Present [<5pc]', 'Prominent [5-50pc]', 'Confluence [>50pc]'))
         pgm_rv50 = self.new_rv('MONO', ('Absent [0]', 'Rare [1-2]', 'Present [3-20]', 'Many [>20]'))
@@ -90,7 +100,8 @@ class Pathfinder(PGM):
         pgm_rv57 = self.new_rv('PAS', ('No', 'Yes'))
         pgm_rv58 = self.new_rv('PI', ('Absent', 'Present', 'Prominent'))
         pgm_rv59 = self.new_rv('PLASMA', (
-        'Absent [0pc]', 'Few [<5pc]', 'Moderate [6-20pc]', 'Marked [21-50pc]', 'Striking [51-90pc]', 'Sheets [>90pc]'))
+            'Absent [0pc]', 'Few [<5pc]', 'Moderate [6-20pc]', 'Marked [21-50pc]', 'Striking [51-90pc]',
+            'Sheets [>90pc]'))
         pgm_rv60 = self.new_rv('PC_TP', ('No plasma cells', 'Mature', 'Immature', 'Blastic', 'Pleomorphic', 'Mixed'))
         pgm_rv61 = self.new_rv('PLEO', ('Absent [0]', 'Rare [1-5]', 'Few [6-25]', 'Many [26-100]', 'Striking [>100]'))
         pgm_rv62 = self.new_rv('PFP', ('Absent', 'Present'))
@@ -101,10 +112,10 @@ class Pathfinder(PGM):
         pgm_rv67 = self.new_rv('S_RING', ('Absent', 'Present'))
         pgm_rv68 = self.new_rv('SLC_CY', ('No SLCs', 'Scanty', 'Moderate-abundant clear', 'Moderate-abundant deep'))
         pgm_rv69 = self.new_rv('SLC_NS', (
-        'No SLCs', 'Cerebriform [some]', 'Convoluted [some]', 'Moderate-mark irregular [most]',
-        'Round/slightly irregular [most]'))
+            'No SLCs', 'Cerebriform [some]', 'Convoluted [some]', 'Moderate-mark irregular [most]',
+            'Round/slightly irregular [most]'))
         pgm_rv70 = self.new_rv('SLC', (
-        'Absent [0pc]', 'Sparse [1-10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
+            'Absent [0pc]', 'Sparse [1-10pc]', 'Moderate [11-50pc]', 'Numerous [51-90pc]', 'Striking [>90pc]'))
         pgm_rv71 = self.new_rv('SINUSES', ('Distended', 'Patent', 'Part-greatly obliterated', 'Completely obliterated'))
         pgm_rv72 = self.new_rv('VASC_C', ('Absent', 'Present'))
         pgm_rv73 = self.new_rv('VASC_NS', ('Absent', 'Slight', 'Moderate', 'Marked', 'Pronounced'))
@@ -123,11 +134,12 @@ class Pathfinder(PGM):
         pgm_rv86 = self.new_rv('F_SS',
                                ('No follicles', 'Absent [0]', 'Slight [1-15]', 'Moderate [16-30]', 'Marked [>30]'))
         pgm_rv87 = self.new_rv('F_MZSTAT', (
-        'No follicles/no mantle zones', 'Mantle zones absent in most follicles', 'Most incompletely surround follicles',
-        'Most completely surround fol not thick', 'Most thick [>10 lymphocytes]'))
+            'No follicles/no mantle zones', 'Mantle zones absent in most follicles',
+            'Most incompletely surround follicles',
+            'Most completely surround fol not thick', 'Most thick [>10 lymphocytes]'))
         pgm_rv88 = self.new_rv('F_MZCM', ('No follicles/no mantle zones', 'Absent', 'Present'))
         pgm_rv89 = self.new_rv('F_DEF', (
-        'No follicles', 'Almost all well defined', 'Both well and poor defined', 'Almost all poor defined'))
+            'No follicles', 'Almost all well defined', 'Both well and poor defined', 'Almost all poor defined'))
         pgm_rv90 = self.new_rv('F_MITO', ('No follicles', '0-20', '21-50', '>50'))
         pgm_rv91 = self.new_rv('F_MZ', ('No follicles', 'Absent', 'Present'))
         pgm_rv92 = self.new_rv('F_CIO', ('No follicles', 'Most similar', 'Some similar', 'None similar'))
@@ -169,13 +181,14 @@ class Pathfinder(PGM):
         pgm_rv128 = self.new_rv('TB', ('Absent', 'Present', 'Prominent'))
         pgm_rv129 = self.new_rv('MELANIN', ('Absent to normal', 'Present', 'Prominent'))
         pgm_rv130 = self.new_rv('MC_SL_NS', (
-        'No follicles/no mantle zones', 'Round', 'Slightly irregular', 'Moderately irregular', 'Markedly irregular'))
+            'No follicles/no mantle zones', 'Round', 'Slightly irregular', 'Moderately irregular',
+            'Markedly irregular'))
         pgm_rv131 = self.new_rv('FMZ_FUS', (
-        'No thick mantle zones', 'No nodules no fusion', 'Nodules but no fusion', 'Fusion with or without nodules'))
+            'No thick mantle zones', 'No nodules no fusion', 'Nodules but no fusion', 'Fusion with or without nodules'))
         pgm_rv132 = self.new_rv('BH_NOS_L', ('No NOS benign histiocytes', 'Mainly interfollicular', 'Mainly sinusoidal',
                                              'Both interfollicular and sinusoidal'))
         pgm_rv133 = self.new_rv('SLC_NI', (
-        'No SLCs', 'None identifiable', '1 or more peripheral small', '1 central medium to large', 'Other'))
+            'No SLCs', 'None identifiable', '1 or more peripheral small', '1 central medium to large', 'Other'))
         pgm_rv134 = self.new_rv('HYALIN', ('Absent', 'Present', 'Prominent'))
         pgm_factor0 = self.new_factor(pgm_rv0)
         pgm_factor1 = self.new_factor(pgm_rv1, pgm_rv128)
@@ -315,22 +328,82 @@ class Pathfinder(PGM):
 
         pgm_function0 = pgm_factor0.set_dense()
         pgm_function0.set_flat(
-            20.0, 1.5, 5.0, 5.0, 25.0,
-            25.0, 5.0, 5.0, 15.0, 4.0,
-            2.0, 2.0, 5.0, 12.5, 8.0,
-            12.8, 2.0, 2.0, 3.0, 20.0,
-            2.0, 5.0, 4.0, 15.0, 0.5,
-            15.0, 2.5, 90.0, 8.0, 8.0,
-            70.0, 5.0, 3.0, 3.0, 110.0,
-            55.0, 20.0, 5.0, 40.0, 8.0,
-            10.0, 5.0, 6.0, 110.0, 20.0,
-            20.0, 12.0, 2.0, 10.0, 80.0,
-            1.0, 15.0, 2.0, 3.0, 5.0,
-            0.1, 20.0, 8.0, 5.0, 8.0,
-            2.0, 20.0, 25.0, 20.0, 5.0,
-            2.0, 2.0, 2.0, 2.0, 2.0,
-            2.0, 2.0, 5.0, 0.25, 4.0,
-            8.0
+            0.018279029,
+            0.001370927,
+            0.004569757,
+            0.004569757,
+            0.022848787,
+            0.022848787,
+            0.004569757,
+            0.004569757,
+            0.013709272,
+            0.003655806,
+            0.001827903,
+            0.001827903,
+            0.004569757,
+            0.011424393,
+            0.007311612,
+            0.011698579,
+            0.001827903,
+            0.001827903,
+            0.002741854,
+            0.018279029,
+            0.001827903,
+            0.004569757,
+            0.003655806,
+            0.013709272,
+            0.000456976,
+            0.013709272,
+            0.002284879,
+            0.082255632,
+            0.007311612,
+            0.007311612,
+            0.063976603,
+            0.004569757,
+            0.002741854,
+            0.002741854,
+            0.100534662,
+            0.050267331,
+            0.018279029,
+            0.004569757,
+            0.036558059,
+            0.007311612,
+            0.009139515,
+            0.004569757,
+            0.005483709,
+            0.100534662,
+            0.018279029,
+            0.018279029,
+            0.010967418,
+            0.001827903,
+            0.009139515,
+            0.073116118,
+            0.000913951,
+            0.013709272,
+            0.001827903,
+            0.002741854,
+            0.004569757,
+            9.13951E-05,
+            0.018279029,
+            0.007311612,
+            0.004569757,
+            0.007311612,
+            0.001827903,
+            0.018279029,
+            0.022848787,
+            0.018279029,
+            0.004569757,
+            0.001827903,
+            0.001827903,
+            0.001827903,
+            0.001827903,
+            0.001827903,
+            0.001827903,
+            0.001827903,
+            0.004569757,
+            0.000228488,
+            0.003655806,
+            0.007311612,
         )
 
         pgm_function1 = pgm_factor1.set_dense()

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/in_out/parse_ace_lmap.py

@@ -108,7 +108,7 @@ class Parser(ABC):
         except ParseError as e:
             raise e
         except Exception as e:
-            input_stream.raise_error(e)
+            input_stream.raise_error(str(e))
 
     @abstractmethod
     def comment(self, raise_f, message: str) -> None:

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/in_out/parse_ace_nnf.py

@@ -64,10 +64,20 @@ def read_nnf_with_literal_map(
         check_header=check_header,
         optimise_ops=optimise_ops,
     )
+    circuit = top_node.circuit
+
+    # Build the slot map from indicator to slot.
+    # Some indicators may not be in `literal_slot_map` because they were not needed
+    # for the arithmetic circuit in the NNF file. For those indicators, we create
+    # dummy circuit vars.
+    def _get_slot(_literal_code: int) -> int:
+        _slot: Optional[int] = literal_slot_map.get(_literal_code)
+        if _slot is None:
+            _slot: int = circuit.new_var().idx
+        return _slot
 
-    # Build the slot map from indicator to slot
     slot_map: Dict[SlotKey, int] = {
-        indicator: literal_slot_map[literal_code]
+        indicator: _get_slot(literal_code)
         for literal_code, indicator in literal_map.indicators.items()
     }
 
@@ -193,7 +203,7 @@ class Parser(ABC):
         except ParseError as e:
             raise e
         except Exception as e:
-            input_stream.raise_error(e)
+            input_stream.raise_error(str(e))
 
     @abstractmethod
     def comment(self, raise_f, message: str) -> None:

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/pgm_compiler/ace/ace.py

@@ -101,16 +101,13 @@ def compile_pgm(
             node_names: List[str] = render_bayesian_network(pgm, file, check_structure_bayesian=False)
 
         # Run Ace
-        ace_result: subprocess.CompletedProcess = subprocess.run(ace_cmd, capture_output=True, text=True)
-        if print_output:
-            print(ace_result.stdout)
-            print(ace_result.stderr)
+        ace_result: subprocess.CompletedProcess = subprocess.run(ace_cmd, capture_output=(not print_output), text=True)
         if ace_result.returncode != 0:
             raise subprocess.CalledProcessError(
                 returncode=ace_result.returncode,
                 cmd=' '.join(ace_cmd),
-                output=ace_result.stdout,
-                stderr=ace_result.stderr,
+                output=None if print_output else ace_result.stdout,
+                stderr=None if print_output else ace_result.stderr,
             )
 
         # Parse the literal map output from Ace

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/pgm_compiler/factor_elimination.py

@@ -21,7 +21,7 @@ def compile_pgm(
         *,
         algorithm: JoinTreeAlgorithm = MIN_FILL_THEN_DEGREE,
         limit_product_tree_search: int = DEFAULT_PRODUCT_SEARCH_LIMIT,
-        pre_prune_factor_tables: bool = True,
+        pre_prune_factor_tables: bool = False,
 ) -> PGMCircuit:
     """
     Compile the PGM to an arithmetic circuit, using factor elimination.
@@ -60,7 +60,7 @@ def compile_pgm_best_jointree(
         const_parameters: bool = True,
         *,
         limit_product_tree_search: int = DEFAULT_PRODUCT_SEARCH_LIMIT,
-        pre_prune_factor_tables: bool = True,
+        pre_prune_factor_tables: bool = False,
 ) -> PGMCircuit:
     """
     Try multiple elimination heuristics, and use the join tree that has
@@ -114,7 +114,7 @@ def join_tree_to_circuit(
         join_tree: JoinTree,
         const_parameters: bool = True,
         limit_product_tree_search: int = DEFAULT_PRODUCT_SEARCH_LIMIT,
-        pre_prune_factor_tables: bool = True,
+        pre_prune_factor_tables: bool = False,
 ) -> PGMCircuit:
     """
     Construct a PGMCircuit from a join-tree.

compiled_knowledge-4.0.0a14/src/ck/pgm_compiler/named_pgm_compilers.py

@@ -0,0 +1,63 @@
+from enum import Enum
+
+from ck.pgm import PGM
+from ck.pgm_circuit import PGMCircuit
+from ck.pgm_compiler import variable_elimination, factor_elimination, recursive_conditioning, ace
+from .pgm_compiler import PGMCompiler
+from .support.named_compiler_maker import get_compiler_algorithm as _get_compiler_algorithm, \
+    get_compiler as _get_compiler
+
+
+class NamedPGMCompiler(Enum):
+    """
+    A standard collection of named compiler functions.
+
+    The `value` of each enum member is tuple containing a compiler function (PGM -> PGMCircuit).
+    Wrapping in a tuple is needed otherwise Python erases the type of the member, which can cause problems.
+    Each member itself is callable, confirming to the PGMCompiler protocol, delegating to the compiler function.
+    """
+    # @formatter:off
+
+    VE_MIN_DEGREE = _get_compiler_algorithm(variable_elimination, 'MIN_DEGREE')
+    VE_MIN_DEGREE_THEN_FILL = _get_compiler_algorithm(variable_elimination, 'MIN_DEGREE_THEN_FILL')
+    VE_MIN_FILL = _get_compiler_algorithm(variable_elimination, 'MIN_FILL')
+    VE_MIN_FILL_THEN_DEGREE = _get_compiler_algorithm(variable_elimination, 'MIN_FILL_THEN_DEGREE')
+    VE_MIN_WEIGHTED_DEGREE = _get_compiler_algorithm(variable_elimination, 'MIN_WEIGHTED_DEGREE')
+    VE_MIN_WEIGHTED_FILL = _get_compiler_algorithm(variable_elimination, 'MIN_WEIGHTED_FILL')
+    VE_MIN_TRADITIONAL_WEIGHTED_FILL = _get_compiler_algorithm(variable_elimination, 'MIN_TRADITIONAL_WEIGHTED_FILL')
+
+    FE_MIN_DEGREE = _get_compiler_algorithm(factor_elimination, 'MIN_DEGREE')
+    FE_MIN_DEGREE_THEN_FILL = _get_compiler_algorithm(factor_elimination, 'MIN_DEGREE_THEN_FILL')
+    FE_MIN_FILL = _get_compiler_algorithm(factor_elimination, 'MIN_FILL')
+    FE_MIN_FILL_THEN_DEGREE = _get_compiler_algorithm(factor_elimination, 'MIN_FILL_THEN_DEGREE')
+    FE_MIN_WEIGHTED_DEGREE = _get_compiler_algorithm(factor_elimination, 'MIN_WEIGHTED_DEGREE')
+    FE_MIN_WEIGHTED_FILL = _get_compiler_algorithm(factor_elimination, 'MIN_WEIGHTED_FILL')
+    FE_MIN_TRADITIONAL_WEIGHTED_FILL = _get_compiler_algorithm(factor_elimination, 'MIN_TRADITIONAL_WEIGHTED_FILL')
+    FE_BEST_JOINTREE = factor_elimination.compile_pgm_best_jointree,
+
+    RC_MIN_DEGREE = _get_compiler_algorithm(recursive_conditioning, 'MIN_DEGREE')
+    RC_MIN_DEGREE_THEN_FILL = _get_compiler_algorithm(recursive_conditioning, 'MIN_DEGREE_THEN_FILL')
+    RC_MIN_FILL = _get_compiler_algorithm(recursive_conditioning, 'MIN_FILL')
+    RC_MIN_FILL_THEN_DEGREE = _get_compiler_algorithm(recursive_conditioning, 'MIN_FILL_THEN_DEGREE')
+    RC_MIN_WEIGHTED_DEGREE = _get_compiler_algorithm(recursive_conditioning, 'MIN_WEIGHTED_DEGREE')
+    RC_MIN_WEIGHTED_FILL = _get_compiler_algorithm(recursive_conditioning, 'MIN_WEIGHTED_FILL')
+    RC_MIN_TRADITIONAL_WEIGHTED_FILL = _get_compiler_algorithm(recursive_conditioning, 'MIN_TRADITIONAL_WEIGHTED_FILL')
+
+    ACE = _get_compiler(ace)
+
+    # @formatter:on
+
+    def __call__(self, pgm: PGM, const_parameters: bool = True) -> PGMCircuit:
+        """
+        Each member of the enum is a PGMCompiler function.
+
+        This implements the `PGMCompiler` protocol.
+        """
+        return self.compiler(pgm, const_parameters=const_parameters)
+
+    @property
+    def compiler(self) -> PGMCompiler:
+        return self.value[0]
+
+
+DEFAULT_PGM_COMPILER: NamedPGMCompiler = NamedPGMCompiler.FE_BEST_JOINTREE

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/pgm_compiler/recursive_conditioning.py

@@ -28,7 +28,7 @@ def compile_pgm(
         const_parameters: bool = True,
         *,
         algorithm: ClusterAlgorithm = MIN_FILL_THEN_DEGREE,
-        pre_prune_factor_tables: bool = True,
+        pre_prune_factor_tables: bool = False,
 ) -> PGMCircuit:
     """
     Compile the PGM to an arithmetic circuit, using recursive conditioning.

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/pgm_compiler/support/factor_tables.py

@@ -269,40 +269,48 @@ def _pre_prune_factor_tables(factor_rows: Sequence[_FactorRows]) -> None:
     will be formed, which may eliminate rows. This method identifies and removes
     such rows.
     """
+    # Find all pairs of factors that have at least one common random variable.
     pairs_to_check: List[_FactorPair] = [
         _FactorPair(f1, f2)
         for f1, f2 in pairs(factor_rows)
         if not set(f1.rv_indexes).isdisjoint(f1.rv_indexes)
     ]
 
-    pairs_done: List[_FactorPair] = []
-
-    while len(pairs_to_check) > 0:
-        pair = pairs_to_check.pop()
-        x = pair.x
-        y = pair.y
-
-        x_size = len(x)
-        y_size = len(y)
+    # Simple version.
+    for pair in pairs_to_check:
         pair.prune()
 
-        # See if any pairs need re-checking
-        rvs_affected: Set[int] = set()
-        if x_size != len(x):
-            rvs_affected.update(x.rv_indexes)
-        if y_size != len(y):
-            rvs_affected.update(y.rv_indexes)
-        if len(rvs_affected) > 0:
-            next_pairs_done: List[_FactorPair] = []
-            for pair in pairs_done:
-                if rvs_affected.isdisjoint(pair.all_rv_indexes):
-                    next_pairs_done.append(pair)
-                else:
-                    pairs_to_check.append(pair)
-            pairs_done = next_pairs_done
-
-        # Mark the current pair as done.
-        pairs_done.append(pair)
+    # Earlier version.
+    # This version re-checks processed pairs that may get benefit from a subsequent pruning.
+    # Unfortunately, this is computationally expensive, and provides no practical benefit.
+    #
+    # pairs_done: List[_FactorPair] = []
+    # while len(pairs_to_check) > 0:
+    #     pair: _FactorPair = pairs_to_check.pop()
+    #     x: _FactorRows = pair.x
+    #     y: _FactorRows = pair.y
+    #
+    #     x_size = len(x)
+    #     y_size = len(y)
+    #     pair.prune()
+    #
+    #     # See if any pairs need re-checking
+    #     rvs_affected: Set[int] = set()
+    #     if x_size != len(x):
+    #         rvs_affected.update(x.rv_indexes)
+    #     if y_size != len(y):
+    #         rvs_affected.update(y.rv_indexes)
+    #     if len(rvs_affected) > 0:
+    #         next_pairs_done: List[_FactorPair] = []
+    #         for pair in pairs_done:
+    #             if rvs_affected.isdisjoint(pair.all_rv_indexes):
+    #                 next_pairs_done.append(pair)
+    #             else:
+    #                 pairs_to_check.append(pair)
+    #         pairs_done = next_pairs_done
+    #
+    #     # Mark the current pair as done.
+    #     pairs_done.append(pair)
 
 
 def _make_factor_table(

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck/pgm_compiler/variable_elimination.py

@@ -25,7 +25,7 @@ def compile_pgm(
         const_parameters: bool = True,
         *,
         algorithm: ClusterAlgorithm = MIN_FILL_THEN_DEGREE,
-        pre_prune_factor_tables: bool = True,
+        pre_prune_factor_tables: bool = False,
 ) -> PGMCircuit:
     """
     Compile the PGM to an arithmetic circuit, using variable elimination.

{compiled_knowledge-4.0.0a13 → compiled_knowledge-4.0.0a14}/src/ck_demos/pgm_compiler/compare_pgm_compilers.py

@@ -9,6 +9,14 @@ from ck_demos.utils.compare import compare
 
 # @formatter:off
 
+# =========================================
+#  Experiment configuration
+# =========================================
+
+CACHE_CIRCUITS: bool = True
+BREAK_BETWEEN_PGMS: bool = True
+COMMA_NUMBERS: bool = True
+
 PGMS: Sequence[PGM] = [
     example.Rain(),
     example.Cancer(),
@@ -19,20 +27,20 @@ PGMS: Sequence[PGM] = [
     example.Child(),
     example.Alarm(),
 
-    # example.Hailfinder(),
-    # example.Insurance(),
-    # example.Pathfinder(),
-    # example.Mildew(),
+    example.Hailfinder(),
+    example.Insurance(),
+    example.Pathfinder(),
+    example.Mildew(),
 ]
 
-CCT_COMPILERS: Sequence[NamedCircuitCompiler] = [DEFAULT_CIRCUIT_COMPILER]
-
 PGM_COMPILERS: Sequence[NamedPGMCompiler] = [
     named_compiler
     for named_compiler in NamedPGMCompiler
     if named_compiler.name.startswith('FE_') and 'WEIGHTED' not in named_compiler.name
 ] + [NamedPGMCompiler.ACE]
 
+CCT_COMPILERS: Sequence[NamedCircuitCompiler] = [DEFAULT_CIRCUIT_COMPILER]
+
 # @formatter:on
 
 
@@ -41,6 +49,9 @@ def main() -> None:
         pgms=PGMS,
         pgm_compilers=PGM_COMPILERS,
         cct_compilers=CCT_COMPILERS,
+        cache_circuits=CACHE_CIRCUITS,
+        break_between_pgms=BREAK_BETWEEN_PGMS,
+        comma_numbers=COMMA_NUMBERS,
     )
     print()
     print('Done.')