From be2268e64c6a89c99866a1aaa42c4c3a29882122 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Fri, 20 Oct 2023 21:31:45 +0200 Subject: [PATCH 01/17] feat(export): make algorithm/pipeline info part of export + add in node ids --- README.md | 7 ++++--- causy/cli.py | 25 ++++++++++++++++++++----- causy/generators.py | 4 ++-- causy/graph.py | 38 ++++++++++++++++++++------------------ causy/interfaces.py | 3 ++- causy/utils.py | 2 +- tests/test_pc_graph.py | 8 ++++---- 7 files changed, 53 insertions(+), 34 deletions(-) diff --git a/README.md b/README.md index 34de638..83c765a 100644 --- a/README.md +++ b/README.md @@ -36,20 +36,21 @@ poetry run causy execute tests/fixtures/toy_data_larger.json --pipeline pc.json ### Usage via Code Use a default algorithm + ```python from causy.algorithms import PC -from causy.utils import show_edges +from causy.utils import retrieve_edges model = PC() model.create_graph_from_data( [ - {"a": 1, "b": 0.3}, + {"a": 1, "b": 0.3}, {"a": 0.5, "b": 0.2} ] ) model.create_all_possible_edges() model.execute_pipeline_steps() -edges = show_edges(model.graph) +edges = retrieve_edges(model.graph) for edge in edges: print( diff --git a/causy/cli.py b/causy/cli.py index 538ddab..6bdb12c 100644 --- a/causy/cli.py +++ b/causy/cli.py @@ -1,5 +1,6 @@ import importlib import json +from datetime import datetime from json import JSONEncoder import typer @@ -8,7 +9,7 @@ from causy.utils import ( load_pipeline_artefact_by_definition, load_pipeline_steps_by_definition, - show_edges, + retrieve_edges, ) app = typer.Typer() @@ -68,9 +69,17 @@ def execute( pipeline_config = load_json(pipeline) pipeline = create_pipeline(pipeline_config) model = graph_model_factory(pipeline_steps=pipeline)() + algorithm_reference = { + "type": "pipeline", + "reference": pipeline, # TODO: how to reference pipeline in a way that it can be loaded? + } elif algorithm: typer.echo(f"💾 Creating pipeline from algorithm {algorithm}") model = load_algorithm(algorithm)() + algorithm_reference = { + "type": "default", + "reference": algorithm, + } else: raise ValueError("Either pipeline_file or algorithm must be specified") @@ -83,7 +92,7 @@ def execute( typer.echo("🕵🏻‍♀ Executing pipeline steps...") model.execute_pipeline_steps() - edges = show_edges(model.graph) + edges = retrieve_edges(model.graph) for edge in edges: print( f"{edge[0].name} -> {edge[1].name}: {model.graph.edges[edge[0]][edge[1]]}" @@ -92,9 +101,15 @@ def execute( if graph_actions_save_file: typer.echo(f"💾 Saving graph actions to {graph_actions_save_file}") with open(graph_actions_save_file, "w") as file: - file.write( - json.dumps(model.graph.action_history, cls=MyJSONEncoder, indent=4) - ) + export = { + "name": algorithm, + "created_at": datetime.now().isoformat(), + "algorithm": algorithm_reference, + "steps": model.graph.action_history, + "nodes": model.graph.nodes, + "edges": edges, + } + file.write(json.dumps(export, cls=MyJSONEncoder, indent=4)) if render_save_file: # I'm just a hacky rendering function, pls replace me with causy ui 🙄 diff --git a/causy/generators.py b/causy/generators.py index 218ca5d..bd3a449 100644 --- a/causy/generators.py +++ b/causy/generators.py @@ -78,7 +78,7 @@ def generate( checked_combinations.add((node, neighbour)) if i == 2: - yield (node.name, neighbour.name) + yield (node.id, neighbour.id) continue other_neighbours = set(graph.edges[node]) @@ -87,4 +87,4 @@ def generate( continue for k in itertools.combinations(other_neighbours, i): - yield [node.name, neighbour.name] + [ks.name for ks in k] + yield [node.id, neighbour.id] + [ks.id for ks in k] diff --git a/causy/graph.py b/causy/graph.py index 9a2f068..2cb571c 100644 --- a/causy/graph.py +++ b/causy/graph.py @@ -1,10 +1,8 @@ -import importlib -import itertools -import json from abc import ABC from dataclasses import dataclass from typing import List, Optional, Dict, Set import multiprocessing as mp +from uuid import uuid4 from causy.interfaces import ( IndependenceTestInterface, @@ -33,10 +31,11 @@ @dataclass class Node(NodeInterface): name: str + id: str values: List[float] def __hash__(self): - return hash(self.name) + return hash(self.id) class UndirectedGraphError(Exception): @@ -62,9 +61,9 @@ def add_edge(self, u: Node, v: Node, value: Dict): :param v: v node :return: """ - if u.name not in self.nodes: + if u.id not in self.nodes: raise UndirectedGraphError(f"Node {u} does not exist") - if v.name not in self.nodes: + if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") if u not in self.edges: self.edges[u] = {} @@ -104,9 +103,9 @@ def remove_edge(self, u: Node, v: Node): :param v: v node :return: """ - if u.name not in self.nodes: + if u.id not in self.nodes: raise UndirectedGraphError(f"Node {u} does not exist") - if v.name not in self.nodes: + if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") if u not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any nodes") @@ -128,9 +127,9 @@ def remove_directed_edge(self, u: Node, v: Node): :param v: v node :return: """ - if u.name not in self.nodes: + if u.id not in self.nodes: raise UndirectedGraphError(f"Node {u} does not exist") - if v.name not in self.nodes: + if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") if u not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any nodes") @@ -148,9 +147,9 @@ def update_edge(self, u: Node, v: Node, value: Dict): :param v: v node :return: """ - if u.name not in self.nodes: + if u.id not in self.nodes: raise UndirectedGraphError(f"Node {u} does not exist") - if v.name not in self.nodes: + if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") if u not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any edges") @@ -167,9 +166,9 @@ def edge_exists(self, u: Node, v: Node): :param v: node v :return: True if any edge exists, False otherwise """ - if u.name not in self.nodes: + if u.id not in self.nodes: return False - if v.name not in self.nodes: + if v.id not in self.nodes: return False if u in self.edges and v in self.edges[u]: return True @@ -184,9 +183,9 @@ def directed_edge_exists(self, u: Node, v: Node): :param v: node v :return: True if a directed edge exists, False otherwise """ - if u.name not in self.nodes: + if u.id not in self.nodes: return False - if v.name not in self.nodes: + if v.id not in self.nodes: return False if u not in self.edges: return False @@ -238,16 +237,19 @@ def bidirected_edge_exists(self, u: Node, v: Node): def edge_value(self, u: Node, v: Node): return self.edges[u][v] - def add_node(self, name: str, values: List[float]): + def add_node(self, name: str, values: List[float], id: str = None): """ Add a node to the graph :param name: name of the node :param values: values of the node + :param id: id of the node :param : node :return: """ - self.nodes[name] = Node(name, values) + if id is None: + id = str(uuid4()) + self.nodes[id] = Node(name=name, id=id, values=values) def directed_path_exists(self, u: Node, v: Node): """ diff --git a/causy/interfaces.py b/causy/interfaces.py index 430fe52..ce15b57 100644 --- a/causy/interfaces.py +++ b/causy/interfaces.py @@ -32,10 +32,11 @@ def serialize(self): class NodeInterface: name: str + id: str values: List[float] def to_dict(self): - return self.name + return self.id class TestResultAction(enum.StrEnum): diff --git a/causy/utils.py b/causy/utils.py index 21b3e97..a64f311 100644 --- a/causy/utils.py +++ b/causy/utils.py @@ -134,7 +134,7 @@ def load_pipeline_steps_by_definition(steps): return pipeline -def show_edges(graph): +def retrieve_edges(graph): edges = [] for u in graph.edges: for v in graph.edges[u]: diff --git a/tests/test_pc_graph.py b/tests/test_pc_graph.py index 976fdb1..aa013fe 100644 --- a/tests/test_pc_graph.py +++ b/tests/test_pc_graph.py @@ -4,7 +4,7 @@ import numpy as np from causy.algorithms import PC -from causy.utils import show_edges +from causy.utils import retrieve_edges # TODO: generate larger toy model to test quadruple orientation rules. @@ -64,7 +64,7 @@ def test_with_rki_data(self): tst.create_graph_from_data(test_data) tst.create_all_possible_edges() tst.execute_pipeline_steps() - show_edges(tst.graph) + retrieve_edges(tst.graph) def test_with_minimal_toy_model(self): a, b, c, d, sample_size = 1.2, 1.7, 2, 1.5, 10000 @@ -73,7 +73,7 @@ def test_with_minimal_toy_model(self): tst.create_graph_from_data(test_data) tst.create_all_possible_edges() tst.execute_pipeline_steps() - show_edges(tst.graph) + retrieve_edges(tst.graph) def test_with_larger_toy_model(self): a, b, c, d, e, f, g, sample_size = 1.2, 1.7, 2, 1.5, 3, 4, 1.8, 10000 @@ -82,7 +82,7 @@ def test_with_larger_toy_model(self): tst.create_graph_from_data(test_data) tst.create_all_possible_edges() tst.execute_pipeline_steps() - show_edges(tst.graph) + retrieve_edges(tst.graph) if __name__ == "__main__": From 475942b9f7a1d1c2c1feb4b3f1c7eedd7971570d Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Fri, 20 Oct 2023 21:43:07 +0200 Subject: [PATCH 02/17] feat(output): show id + node name for easier readability --- causy/interfaces.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/causy/interfaces.py b/causy/interfaces.py index ce15b57..b99c601 100644 --- a/causy/interfaces.py +++ b/causy/interfaces.py @@ -36,7 +36,7 @@ class NodeInterface: values: List[float] def to_dict(self): - return self.id + return {"id": self.id, "name": self.name} class TestResultAction(enum.StrEnum): From ef673736c07392115c6c5c32561731c507190640 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Fri, 20 Oct 2023 21:48:17 +0200 Subject: [PATCH 03/17] replace name by id --- causy/independence_tests.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/causy/independence_tests.py b/causy/independence_tests.py index 3886475..416f273 100644 --- a/causy/independence_tests.py +++ b/causy/independence_tests.py @@ -29,6 +29,7 @@ # TODO: make tests configurable (choosing different generators for different algorithms) + class CalculateCorrelations(IndependenceTestInterface): GENERATOR = AllCombinationsGenerator( comparison_settings=ComparisonSettings(min=2, max=2) @@ -228,7 +229,7 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: other_neighbours.remove(graph.nodes[nodes[1]]) - if not set(nodes[2:]).issubset(set([on.name for on in list(other_neighbours)])): + if not set(nodes[2:]).issubset(set([on.id for on in list(other_neighbours)])): return covariance_matrix = [ From d0aedeb99618c08e5b1879533736eb074cc56e91 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Fri, 20 Oct 2023 21:51:36 +0200 Subject: [PATCH 04/17] update cli command for --output-file --- causy/cli.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/causy/cli.py b/causy/cli.py index 6bdb12c..5647fe1 100644 --- a/causy/cli.py +++ b/causy/cli.py @@ -59,7 +59,7 @@ def execute( data_file: str, pipeline: str = None, algorithm: str = None, - graph_actions_save_file: str = None, + output_file: str = None, render_save_file: str = None, log_level: str = "ERROR", ): @@ -98,9 +98,9 @@ def execute( f"{edge[0].name} -> {edge[1].name}: {model.graph.edges[edge[0]][edge[1]]}" ) - if graph_actions_save_file: - typer.echo(f"💾 Saving graph actions to {graph_actions_save_file}") - with open(graph_actions_save_file, "w") as file: + if output_file: + typer.echo(f"💾 Saving graph actions to {output_file}") + with open(output_file, "w") as file: export = { "name": algorithm, "created_at": datetime.now().isoformat(), From 651a587b6b984156b30cf0eac467364b6d44a40c Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Fri, 20 Oct 2023 23:36:16 +0200 Subject: [PATCH 05/17] feat(output): add edge value --- causy/cli.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/causy/cli.py b/causy/cli.py index 5647fe1..6661813 100644 --- a/causy/cli.py +++ b/causy/cli.py @@ -92,11 +92,18 @@ def execute( typer.echo("🕵🏻‍♀ Executing pipeline steps...") model.execute_pipeline_steps() - edges = retrieve_edges(model.graph) - for edge in edges: + edges = [] + for edge in retrieve_edges(model.graph): print( f"{edge[0].name} -> {edge[1].name}: {model.graph.edges[edge[0]][edge[1]]}" ) + edges.append( + { + "from": edge[0].to_dict(), + "to": edge[1].to_dict(), + "value": model.graph.edges[edge[0]][edge[1]], + } + ) if output_file: typer.echo(f"💾 Saving graph actions to {output_file}") From 11c56c39293b8718cad50c7d1b651fc0bf4432fd Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 11:26:07 +0200 Subject: [PATCH 06/17] feat(independence_tests): start migration to pytorch --- causy/graph.py | 6 +- causy/independence_tests.py | 48 +-- poetry.lock | 754 ++++++++++++++++++++++-------------- pyproject.toml | 1 + 4 files changed, 480 insertions(+), 329 deletions(-) diff --git a/causy/graph.py b/causy/graph.py index 2cb571c..ee30c7d 100644 --- a/causy/graph.py +++ b/causy/graph.py @@ -1,7 +1,9 @@ from abc import ABC from dataclasses import dataclass from typing import List, Optional, Dict, Set -import multiprocessing as mp + +import torch.multiprocessing as mp + from uuid import uuid4 from causy.interfaces import ( @@ -317,7 +319,7 @@ def __init__( ): self.graph = graph self.pipeline_steps = pipeline_steps or [] - self.pool = mp.Pool(mp.cpu_count() * 2) + self.pool = mp.Pool(round(mp.cpu_count() / 2)) def create_graph_from_data(self, data: List[Dict[str, float]]): """ diff --git a/causy/independence_tests.py b/causy/independence_tests.py index 416f273..3163a9b 100644 --- a/causy/independence_tests.py +++ b/causy/independence_tests.py @@ -1,15 +1,10 @@ import itertools -from statistics import correlation, covariance # , linear_regression +from statistics import correlation from typing import Tuple, List -import math from causy.generators import AllCombinationsGenerator, PairsWithNeighboursGenerator -# Use cupy for GPU support - if available - otherwise use numpy -try: - import cupy as np -except ImportError: - import numpy as np +import torch from causy.utils import get_t_and_critial_t, get_correlation @@ -212,7 +207,7 @@ class ExtendedPartialCorrelationTestMatrix(IndependenceTestInterface): comparison_settings=ComparisonSettings(min=4, max=AS_MANY_AS_FIELDS) ) CHUNK_SIZE_PARALLEL_PROCESSING = 200 - PARALLEL = False + PARALLEL = True def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: """ @@ -226,31 +221,26 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: return other_neighbours = set(graph.edges[graph.nodes[nodes[0]]]) - other_neighbours.remove(graph.nodes[nodes[1]]) if not set(nodes[2:]).issubset(set([on.id for on in list(other_neighbours)])): return - covariance_matrix = [ - [None for _ in range(len(nodes))] for _ in range(len(nodes)) - ] - for i in range(len(nodes)): - for k in range(i, len(nodes)): - if covariance_matrix[i][k] is None: - covariance_matrix[i][k] = covariance( - graph.nodes[nodes[i]].values, graph.nodes[nodes[k]].values - ) - covariance_matrix[k][i] = covariance_matrix[i][k] + covariance_matrix = [] + for node in nodes: + covariance_matrix.append(graph.nodes[node].values) + + inverse_cov_matrix = torch.inverse( + torch.cov(torch.tensor(covariance_matrix, dtype=torch.float64)) + ) + n = inverse_cov_matrix.size(0) + diagonal = torch.diag(inverse_cov_matrix) + diagonal_matrix = torch.zeros((n, n), dtype=torch.float64) + for i in range(n): + diagonal_matrix[i, i] = diagonal[i] - cov_matrix = np.array(covariance_matrix) - inverse_cov_matrix = np.linalg.inv(cov_matrix) - n = len(inverse_cov_matrix) - diagonal = np.diagonal(inverse_cov_matrix) - diagonal_matrix = np.zeros((n, n)) - np.fill_diagonal(diagonal_matrix, diagonal) - helper = np.dot(np.sqrt(diagonal_matrix), inverse_cov_matrix) - precision_matrix = np.dot(helper, np.sqrt(diagonal_matrix)) + helper = 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typing import List, Optional, Dict, Set +import torch import torch.multiprocessing as mp from uuid import uuid4 @@ -34,7 +35,7 @@ class Node(NodeInterface): name: str id: str - values: List[float] + values: torch.Tensor def __hash__(self): return hash(self.id) @@ -251,7 +252,9 @@ def add_node(self, name: str, values: List[float], id: str = None): """ if id is None: id = str(uuid4()) - self.nodes[id] = Node(name=name, id=id, values=values) + self.nodes[id] = Node( + name=name, id=id, values=torch.tensor(values, dtype=torch.float64) + ) def directed_path_exists(self, u: Node, v: Node): """ diff --git a/causy/independence_tests.py b/causy/independence_tests.py index 3163a9b..420a019 100644 --- a/causy/independence_tests.py +++ b/causy/independence_tests.py @@ -1,12 +1,10 @@ import itertools -from statistics import correlation from typing import Tuple, List -from causy.generators import AllCombinationsGenerator, PairsWithNeighboursGenerator - import torch -from causy.utils import get_t_and_critial_t, get_correlation +from causy.generators import AllCombinationsGenerator, PairsWithNeighboursGenerator +from causy.utils import get_t_and_critical_t, get_correlation, pearson_correlation import logging @@ -41,8 +39,10 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: x = graph.nodes[nodes[0]] y = graph.nodes[nodes[1]] edge_value = graph.edge_value(graph.nodes[nodes[0]], graph.nodes[nodes[1]]) - edge_value["correlation"] = correlation(x.values, y.values) - # edge_value["covariance"] = covariance(x.values, y.values) + edge_value["correlation"] = pearson_correlation( + x.values, + y.values, + ).item() return TestResult( x=x, y=y, @@ -71,7 +71,7 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: sample_size = len(x.values) nb_of_control_vars = 0 corr = graph.edge_value(x, y)["correlation"] - t, critical_t = get_t_and_critial_t( + t, critical_t = get_t_and_critical_t( sample_size, nb_of_control_vars, corr, self.threshold ) if abs(t) < critical_t: @@ -131,7 +131,7 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: # make t test for independency of x and y given z sample_size = len(x.values) nb_of_control_vars = len(nodes) - 2 - t, critical_t = get_t_and_critial_t( + t, critical_t = get_t_and_critical_t( sample_size, nb_of_control_vars, par_corr, self.threshold ) @@ -185,7 +185,7 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: par_corr = get_correlation(x, y, other_nodes) logger.debug(f"par_corr {par_corr}") # make t test for independence of a and y given other nodes - t, critical_t = get_t_and_critial_t( + t, critical_t = get_t_and_critical_t( sample_size, nb_of_control_vars, par_corr, self.threshold ) @@ -207,7 +207,7 @@ class ExtendedPartialCorrelationTestMatrix(IndependenceTestInterface): comparison_settings=ComparisonSettings(min=4, max=AS_MANY_AS_FIELDS) ) CHUNK_SIZE_PARALLEL_PROCESSING = 200 - PARALLEL = True + PARALLEL = False def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: """ @@ -226,12 +226,8 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: if not set(nodes[2:]).issubset(set([on.id for on in list(other_neighbours)])): return - covariance_matrix = [] - for node in nodes: - covariance_matrix.append(graph.nodes[node].values) - inverse_cov_matrix = torch.inverse( - torch.cov(torch.tensor(covariance_matrix, dtype=torch.float64)) + torch.cov(torch.stack([graph.nodes[node].values for node in nodes])) ) n = inverse_cov_matrix.size(0) diagonal = torch.diag(inverse_cov_matrix) @@ -244,11 +240,8 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: sample_size = len(graph.nodes[nodes[0]].values) nb_of_control_vars = len(nodes) - 2 - results = [] - - nodes_set = set([graph.nodes[n] for n in nodes]) - t, critical_t = get_t_and_critial_t( + t, critical_t = get_t_and_critical_t( sample_size, nb_of_control_vars, ( @@ -262,6 +255,7 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: logger.debug( f"Nodes {graph.nodes[nodes[0]].name} and {graph.nodes[nodes[1]].name} are uncorrelated given nodes {','.join([on.name for on in other_neighbours])}" ) + nodes_set = set([graph.nodes[n] for n in nodes]) return TestResult( x=graph.nodes[nodes[0]], y=graph.nodes[nodes[1]], @@ -273,8 +267,6 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: }, ) - return results - class PlaceholderTest(IndependenceTestInterface): NUM_OF_COMPARISON_ELEMENTS = 2 diff --git a/causy/utils.py b/causy/utils.py index a64f311..8907f41 100644 --- a/causy/utils.py +++ b/causy/utils.py @@ -1,6 +1,7 @@ import importlib import logging +import torch from sympy import transpose, Matrix, solve_linear_system, symbols, Symbol, shape from scipy import stats as scipy_stats import math @@ -97,14 +98,14 @@ def get_correlation(x, y, other_nodes): return corr -def get_t_and_critial_t(sample_size, nb_of_control_vars, par_corr, threshold): +def get_t_and_critical_t(sample_size, nb_of_control_vars, par_corr, threshold): # check if we have to normalize data deg_of_freedom = sample_size - 2 - nb_of_control_vars if abs(round(par_corr, 4)) == 1: return (1, 0) critical_t = scipy_stats.t.ppf(1 - threshold / 2, deg_of_freedom) - t = par_corr * math.sqrt((deg_of_freedom) / (1 - par_corr**2)) - return (t, critical_t) + t = par_corr * math.sqrt(deg_of_freedom / (1 - par_corr**2)) + return t, critical_t def serialize_module_name(cls): @@ -140,3 +141,10 @@ def retrieve_edges(graph): for v in graph.edges[u]: edges.append((u, v)) return edges + + +def pearson_correlation(x, y): + cov_xy = torch.mean((x - x.mean()) * (y - y.mean())) + std_x = x.std() + std_y = y.std() + return cov_xy / (std_x * std_y) From 69bc90e5909aa48af6ddd4a6e16269c58818f310 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 17:15:51 +0200 Subject: [PATCH 08/17] fix(torch): hack poetry so that our build pipelines work https://stackoverflow.com/questions/76327419/valueerror-libcublas-so-0-9-not-found-in-the-system-path --- poetry.lock | 344 ++++++++++++++++++++++++++++++++++++++++--------- pyproject.toml | 2 +- 2 files changed, 287 insertions(+), 59 deletions(-) diff --git a/poetry.lock b/poetry.lock index 7e3d253..d3cd1c8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -65,6 +65,35 @@ files = [ [package.dependencies] colorama = {version = "*", markers = "platform_system == \"Windows\""} +[[package]] +name = "cmake" +version = "3.27.7" +description = "CMake is an open-source, cross-platform family of tools designed to build, test and package software" +optional = false +python-versions = "*" +files = [ + {file = "cmake-3.27.7-py2.py3-none-macosx_10_10_universal2.macosx_10_10_x86_64.macosx_11_0_arm64.macosx_11_0_universal2.whl", hash = "sha256:d582ef3e9ff0bd113581c1a32e881d1c2f9a34d2de76c93324a28593a76433db"}, + {file = "cmake-3.27.7-py2.py3-none-manylinux2010_i686.manylinux_2_12_i686.whl", hash = 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a/pyproject.toml b/pyproject.toml index 0158fec..4ae558a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,21 +6,21 @@ authors = ["Sofia Faltenbacher ", "Lilith Wittmann readme = "README.md" [tool.poetry.dependencies] -python = ">=3.11,<3.13" +python = ">=3.10,<3.13" sympy = "^1.12" -numpy = "^1.26.0" scipy = "^1.11.2" -black = "^23.9.1" pre-commit = "^3.4.0" typer = "^0.9.0" networkx = "^3.1" matplotlib = "^3.8.0" -torch = ">=2.0.0, !=2.0.1, !=2.1.0" +torch = ">=2.0.0, !=2.0.1" [tool.poetry.group.dev.dependencies] mypy = "^1.5.1" pyinstrument = "^4.5.3" +black = "^23.9.1" +numpy = "^1.26.0" [build-system] requires = ["poetry-core"] From 4566d550f1d014f7386ad1b0b04d6e25a5174560 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 17:35:10 +0200 Subject: [PATCH 10/17] hmm --- poetry.lock | 2 +- pyproject.toml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1d8813b..a4b02fd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1199,4 +1199,4 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.13" -content-hash = "93ae8a7dcaab84a87faea695d1a67aa9bce6e0978adb59617ef535dd5aae55d5" +content-hash = "83d7e2fd2dd57d39a01e6803b63217bd397d90495c80f894f28950d57202b359" diff --git a/pyproject.toml b/pyproject.toml index 4ae558a..b25ee86 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -13,7 +13,7 @@ pre-commit = "^3.4.0" typer = "^0.9.0" networkx = "^3.1" matplotlib = "^3.8.0" -torch = ">=2.0.0, !=2.0.1" +torch = "^2.1.0" [tool.poetry.group.dev.dependencies] @@ -22,6 +22,7 @@ pyinstrument = "^4.5.3" black = "^23.9.1" numpy = "^1.26.0" + [build-system] requires = ["poetry-core"] build-backend = "poetry.core.masonry.api" From ea5940b2bb8b95eef6327be881b6831132bfd718 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 17:39:08 +0200 Subject: [PATCH 11/17] windows, osx --- .github/workflows/python-package.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 865377e..195f6b3 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -11,13 +11,12 @@ on: jobs: build: - - runs-on: ubuntu-latest strategy: fail-fast: false matrix: python-version: ["3.10", "3.11", "3.12"] - + platform: [macos-latest, windows-latest] # TODO: change add ubuntu-latest + runs-on: ${{ matrix.platform }} steps: - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} From b8fe11476c8687d310426e9e3656fe125b21db7f Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 17:44:06 +0200 Subject: [PATCH 12/17] windows, osx --- .github/workflows/python-package.yml | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 195f6b3..1daf24a 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -14,7 +14,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.10", "3.11", "3.12"] + python-version: ["3.11"] platform: [macos-latest, windows-latest] # TODO: change add ubuntu-latest runs-on: ${{ matrix.platform }} steps: diff --git a/pyproject.toml b/pyproject.toml index b25ee86..0efb2c8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ authors = ["Sofia Faltenbacher ", "Lilith Wittmann readme = "README.md" [tool.poetry.dependencies] -python = ">=3.10,<3.13" +python = ">=3.11,<3.12" # until torch is available for 3.12 sympy = "^1.12" scipy = "^1.11.2" pre-commit = "^3.4.0" From d8bb0229892328df76d21ea8e03a389549ba449e Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sat, 21 Oct 2023 21:20:12 +0200 Subject: [PATCH 13/17] add a properly working parallel implementation of the PC Algorithm --- causy/algorithms.py | 31 +++++++++++ causy/cli.py | 8 +-- causy/generators.py | 51 +++++++++++++++--- causy/graph.py | 102 +++++++++++++++++++----------------- causy/independence_tests.py | 15 +++--- causy/interfaces.py | 9 +++- causy/orientation_tests.py | 35 +++++++------ 7 files changed, 167 insertions(+), 84 deletions(-) diff --git a/causy/algorithms.py b/causy/algorithms.py index 17a93dc..1424f91 100644 --- a/causy/algorithms.py +++ b/causy/algorithms.py @@ -1,4 +1,5 @@ from causy.exit_conditions import ExitOnNoActions +from causy.generators import PairsWithNeighboursGenerator from causy.graph import graph_model_factory, Loop from causy.independence_tests import ( CalculateCorrelations, @@ -6,6 +7,7 @@ PartialCorrelationTest, ExtendedPartialCorrelationTestMatrix, ) +from causy.interfaces import AS_MANY_AS_FIELDS, ComparisonSettings from causy.orientation_tests import ( ColliderTest, NonColliderTest, @@ -32,3 +34,32 @@ ), ] ) + + +ParallelPC = graph_model_factory( + pipeline_steps=[ + CalculateCorrelations(), + CorrelationCoefficientTest(threshold=0.01), + PartialCorrelationTest(threshold=0.01), + ExtendedPartialCorrelationTestMatrix( + threshold=0.01, + chunk_size_parallel_processing=1000, + parallel=True, + generator=PairsWithNeighboursGenerator( + chunked=False, + shuffle_combinations=True, + comparison_settings=ComparisonSettings(min=4, max=AS_MANY_AS_FIELDS), + ), + ), + ColliderTest(), + Loop( + pipeline_steps=[ + NonColliderTest(), + FurtherOrientTripleTest(), + OrientQuadrupleTest(), + FurtherOrientQuadrupleTest(), + ], + exit_condition=ExitOnNoActions(), + ), + ] +) diff --git a/causy/cli.py b/causy/cli.py index 6661813..7ee16e9 100644 --- a/causy/cli.py +++ b/causy/cli.py @@ -95,12 +95,12 @@ def execute( edges = [] for edge in retrieve_edges(model.graph): print( - f"{edge[0].name} -> {edge[1].name}: {model.graph.edges[edge[0]][edge[1]]}" + f"{model.graph.nodes[edge[0]].name} -> {model.graph.nodes[edge[1]].name}: {model.graph.edges[edge[0]][edge[1]]}" ) edges.append( { - "from": edge[0].to_dict(), - "to": edge[1].to_dict(), + "from": model.graph.nodes[edge[0]].to_dict(), + "to": model.graph.nodes[edge[1]].to_dict(), "value": model.graph.edges[edge[0]][edge[1]], } ) @@ -127,7 +127,7 @@ def execute( n_graph = nx.DiGraph() for u in model.graph.edges: for v in model.graph.edges[u]: - n_graph.add_edge(u.name, v.name) + n_graph.add_edge(model.graph.nodes[u].name, model.graph.nodes[v].name) fig = plt.figure(figsize=(10, 10)) nx.draw(n_graph, with_labels=True, ax=fig.add_subplot(111)) fig.savefig(render_save_file) diff --git a/causy/generators.py b/causy/generators.py index bd3a449..874c3a0 100644 --- a/causy/generators.py +++ b/causy/generators.py @@ -1,3 +1,4 @@ +import copy import itertools import logging @@ -8,7 +9,7 @@ GraphModelInterface, AS_MANY_AS_FIELDS, ) - +from causy.utils import serialize_module_name logger = logging.getLogger(__name__) @@ -43,6 +44,24 @@ def generate( class PairsWithNeighboursGenerator(GeneratorInterface): + shuffle_combinations = True + chunked = True + + def __init__( + self, + comparison_settings: ComparisonSettings, + chunked: bool = None, + shuffle_combinations: bool = None, + ): + super().__init__(comparison_settings, chunked) + if shuffle_combinations is not None: + self.shuffle_combinations = shuffle_combinations + + def to_dict(self): + result = super().to_dict() + result["params"]["shuffle_combinations"] = self.shuffle_combinations + return result + def generate( self, graph: BaseGraphInterface, graph_model_instance_: GraphModelInterface ): @@ -71,20 +90,36 @@ def generate( for i in range(start, stop): logger.debug(f"PairsWithNeighboursGenerator: i={i}") checked_combinations = set() - for node in graph.edges: - for neighbour in graph.edges[node]: + local_edges = copy.deepcopy(graph.edges) + for node in local_edges: + for neighbour in local_edges[node]: if (node, neighbour) in checked_combinations: continue checked_combinations.add((node, neighbour)) if i == 2: - yield (node.id, neighbour.id) + yield (node, neighbour) continue other_neighbours = set(graph.edges[node]) - other_neighbours.remove(neighbour) + if neighbour in other_neighbours: + other_neighbours.remove(neighbour) + else: + continue if len(other_neighbours) + 2 < i: continue - - for k in itertools.combinations(other_neighbours, i): - yield [node.id, neighbour.id] + [ks.id for ks in k] + combinations = itertools.combinations(other_neighbours, i) + if self.shuffle_combinations: + combinations = list(combinations) + import random + + random.shuffle(combinations) + + if self.chunked: + chunk = [] + for k in combinations: + chunk.append([node, neighbour] + [ks for ks in k]) + yield chunk + else: + for k in combinations: + yield [node, neighbour] + [ks for ks in k] diff --git a/causy/graph.py b/causy/graph.py index 0604a3a..b285726 100644 --- a/causy/graph.py +++ b/causy/graph.py @@ -1,6 +1,6 @@ from abc import ABC from dataclasses import dataclass -from typing import List, Optional, Dict, Set +from typing import List, Optional, Dict, Set, Tuple import torch import torch.multiprocessing as mp @@ -47,8 +47,8 @@ class UndirectedGraphError(Exception): class UndirectedGraph(BaseGraphInterface): nodes: Dict[str, Node] - edges: Dict[Node, Dict[Node, Dict]] - edge_history: Dict[Set[Node], List[TestResult]] + edges: Dict[str, Dict[str, Dict]] + edge_history: Dict[Tuple[str, str], List[TestResult]] action_history: List[Dict[str, List[TestResult]]] def __init__(self): @@ -68,16 +68,16 @@ def add_edge(self, u: Node, v: Node, value: Dict): raise UndirectedGraphError(f"Node {u} does not exist") if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") - if u not in self.edges: - self.edges[u] = {} - if v not in self.edges: - self.edges[v] = {} + if u.id not in self.edges: + self.edges[u.id] = {} + if v.id not in self.edges: + self.edges[v.id] = {} - self.edges[u][v] = value - self.edges[v][u] = value + self.edges[u.id][v.id] = value + self.edges[v.id][u.id] = value - self.edge_history[(u, v)] = [] - self.edge_history[(v, u)] = [] + self.edge_history[(u.id, v.id)] = [] + self.edge_history[(v.id, u.id)] = [] def retrieve_edge_history( self, u, v, action: TestResultAction = None @@ -90,14 +90,14 @@ def retrieve_edge_history( :return: """ if action is None: - return self.edge_history[(u, v)] + return self.edge_history[(u.id, v.id)] - return [i for i in self.edge_history[(u, v)] if i.action == action] + return [i for i in self.edge_history[(u.id, v.id)] if i.action == action] def add_edge_history(self, u, v, action: TestResultAction): - if (u, v) not in self.edge_history: - self.edge_history[(u, v)] = [] - self.edge_history[(u, v)].append(action) + if (u.id, v.id) not in self.edge_history: + self.edge_history[(u.id, v.id)] = [] + self.edge_history[(u.id, v.id)].append(action) def remove_edge(self, u: Node, v: Node): """ @@ -110,18 +110,18 @@ def remove_edge(self, u: Node, v: Node): raise UndirectedGraphError(f"Node {u} does not exist") if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") - if u not in self.edges: + if u.id not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any nodes") - if v not in self.edges: + if v.id not in self.edges: raise UndirectedGraphError(f"Node {v} does not have any nodes") - if v not in self.edges[u]: + if v.id not in self.edges[u.id]: return - del self.edges[u][v] + del self.edges[u.id][v.id] - if u not in self.edges[v]: + if u.id not in self.edges[v.id]: return - del self.edges[v][u] + del self.edges[v.id][u.id] def remove_directed_edge(self, u: Node, v: Node): """ @@ -134,14 +134,14 @@ def remove_directed_edge(self, u: Node, v: Node): raise UndirectedGraphError(f"Node {u} does not exist") if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") - if u not in self.edges: + if u.id not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any nodes") - if v not in self.edges: + if v.id not in self.edges: raise UndirectedGraphError(f"Node {v} does not have any nodes") - if v not in self.edges[u]: + if v.id not in self.edges[u.id]: return - del self.edges[u][v] + del self.edges[u.id][v.id] def update_edge(self, u: Node, v: Node, value: Dict): """ @@ -154,13 +154,13 @@ def update_edge(self, u: Node, v: Node, value: Dict): raise UndirectedGraphError(f"Node {u} does not exist") if v.id not in self.nodes: raise UndirectedGraphError(f"Node {v} does not exist") - if u not in self.edges: + if u.id not in self.edges: raise UndirectedGraphError(f"Node {u} does not have any edges") - if v not in self.edges: + if v.id not in self.edges: raise UndirectedGraphError(f"Node {v} does not have any edges") - self.edges[u][v] = value - self.edges[v][u] = value + self.edges[u.id][v.id] = value + self.edges[v.id][u.id] = value def edge_exists(self, u: Node, v: Node): """ @@ -173,9 +173,9 @@ def edge_exists(self, u: Node, v: Node): return False if v.id not in self.nodes: return False - if u in self.edges and v in self.edges[u]: + if u.id in self.edges and v.id in self.edges[u.id]: return True - if v in self.edges and u in self.edges[v]: + if v.id in self.edges and u.id in self.edges[v.id]: return True return False @@ -190,9 +190,9 @@ def directed_edge_exists(self, u: Node, v: Node): return False if v.id not in self.nodes: return False - if u not in self.edges: + if u.id not in self.edges: return False - if v not in self.edges[u]: + if v.id not in self.edges[u.id]: return False return True @@ -238,7 +238,7 @@ def bidirected_edge_exists(self, u: Node, v: Node): return False def edge_value(self, u: Node, v: Node): - return self.edges[u][v] + return self.edges[u.id][v.id] def add_node(self, name: str, values: List[float], id: str = None): """ @@ -265,8 +265,8 @@ def directed_path_exists(self, u: Node, v: Node): """ if self.directed_edge_exists(u, v): return True - for w in self.edges[u]: - if self.directed_path_exists(w, v): + for w in self.edges[u.id]: + if self.directed_path_exists(self.nodes[w], v): return True return False @@ -280,8 +280,8 @@ def directed_paths(self, u: Node, v: Node): if self.directed_edge_exists(u, v): return [[(u, v)]] paths = [] - for w in self.edges[u]: - for path in self.directed_paths(w, v): + for w in self.edges[u.id]: + for path in self.directed_paths(self.nodes[w], v): paths.append([(u, w)] + path) return paths @@ -310,7 +310,6 @@ def unpack_run(args): class AbstractGraphModel(GraphModelInterface, ABC): - pipeline_steps: List[IndependenceTestInterface] graph: BaseGraphInterface pool: mp.Pool @@ -456,14 +455,23 @@ def execute_pipeline_step(self, test_fn: IndependenceTestInterface): result = [result] actions_taken.extend(self._take_action(result)) else: - iterator = [ - unpack_run(i) - for i in [ - [test_fn, [*i], self.graph] - for i in test_fn.GENERATOR.generate(self.graph, self) + if test_fn.GENERATOR.chunked: + for chunk in test_fn.GENERATOR.generate(self.graph, self): + iterator = [ + unpack_run(i) + for i in [[test_fn, [*c], self.graph] for c in chunk] + ] + actions_taken.extend(self._take_action(iterator)) + else: + iterator = [ + unpack_run(i) + for i in [ + [test_fn, [*i], self.graph] + for i in test_fn.GENERATOR.generate(self.graph, self) + ] ] - ] - actions_taken.extend(self._take_action(iterator)) + actions_taken.extend(self._take_action(iterator)) + self.graph.action_history.append( {"step": type(test_fn).__name__, "actions": actions_taken} ) diff --git a/causy/independence_tests.py b/causy/independence_tests.py index 420a019..2f15e72 100644 --- a/causy/independence_tests.py +++ b/causy/independence_tests.py @@ -154,8 +154,8 @@ class ExtendedPartialCorrelationTestLinearRegression(IndependenceTestInterface): GENERATOR = AllCombinationsGenerator( comparison_settings=ComparisonSettings(min=4, max=AS_MANY_AS_FIELDS) ) - CHUNK_SIZE_PARALLEL_PROCESSING = 1 - PARALLEL = False + CHUNK_SIZE_PARALLEL_PROCESSING = 1000 + PARALLEL = True def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: """ @@ -206,7 +206,7 @@ class ExtendedPartialCorrelationTestMatrix(IndependenceTestInterface): GENERATOR = PairsWithNeighboursGenerator( comparison_settings=ComparisonSettings(min=4, max=AS_MANY_AS_FIELDS) ) - CHUNK_SIZE_PARALLEL_PROCESSING = 200 + CHUNK_SIZE_PARALLEL_PROCESSING = 1000 PARALLEL = False def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: @@ -217,13 +217,14 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: :param nodes: the nodes to test :return: A TestResult with the action to take """ + if not graph.edge_exists(graph.nodes[nodes[0]], graph.nodes[nodes[1]]): return - other_neighbours = set(graph.edges[graph.nodes[nodes[0]]]) - other_neighbours.remove(graph.nodes[nodes[1]]) + other_neighbours = set(graph.edges[nodes[0]]) + other_neighbours.remove(graph.nodes[nodes[1]].id) - if not set(nodes[2:]).issubset(set([on.id for on in list(other_neighbours)])): + if not set(nodes[2:]).issubset(set([on for on in list(other_neighbours)])): return inverse_cov_matrix = torch.inverse( @@ -253,7 +254,7 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: if abs(t) < critical_t: logger.debug( - f"Nodes {graph.nodes[nodes[0]].name} and {graph.nodes[nodes[1]].name} are uncorrelated given nodes {','.join([on.name for on in other_neighbours])}" + f"Nodes {graph.nodes[nodes[0]].name} and {graph.nodes[nodes[1]].name} are uncorrelated given nodes {','.join([graph.nodes[on].name for on in other_neighbours])}" ) nodes_set = set([graph.nodes[n] for n in nodes]) return TestResult( diff --git a/causy/interfaces.py b/causy/interfaces.py index b99c601..608630d 100644 --- a/causy/interfaces.py +++ b/causy/interfaces.py @@ -63,7 +63,7 @@ def to_dict(self): class BaseGraphInterface(ABC): nodes: Dict[str, NodeInterface] - edges: Dict[NodeInterface, Dict[NodeInterface, Dict]] + edges: Dict[str, Dict[str, Dict]] @abstractmethod def retrieve_edge_history(self, u, v, action: TestResultAction) -> List[TestResult]: @@ -128,6 +128,7 @@ def execute_pipeline_step(self, step): class GeneratorInterface(ABC): comparison_settings: ComparisonSettings + chunked: bool = False @abstractmethod def generate(self, graph: BaseGraphInterface, graph_model_instance_: dict): @@ -138,15 +139,19 @@ def serialize(self) -> dict: "name": serialize_module_name(self), "params": { "comparison_settings": self.comparison_settings.serialize(), + "chunked": self.chunked, }, } - def __init__(self, comparison_settings: ComparisonSettings): + def __init__(self, comparison_settings: ComparisonSettings, chunked: bool = None): if type(comparison_settings) == dict: comparison_settings = load_pipeline_artefact_by_definition( comparison_settings ) + if chunked is not None: + self.chunked = chunked + self.comparison_settings = comparison_settings diff --git a/causy/orientation_tests.py b/causy/orientation_tests.py index a1ebaab..793cb1d 100644 --- a/causy/orientation_tests.py +++ b/causy/orientation_tests.py @@ -43,13 +43,14 @@ def test( return TestResult(x=x, y=y, action=TestResultAction.DO_NOTHING, data={}) # if x and y are NOT adjacent, store all shared adjacent nodes - potential_zs = set(graph.edges[x].keys()).intersection( - set(graph.edges[y].keys()) + potential_zs = set(graph.edges[x.id].keys()).intersection( + set(graph.edges[y.id].keys()) ) # if x and y are not independent given z, safe action: make z a collider results = [] for z in potential_zs: + z = graph.nodes[z] actions = graph.retrieve_edge_history( x, y, TestResultAction.REMOVE_EDGE_UNDIRECTED ) @@ -57,9 +58,9 @@ def test( separators = [] for action in actions: if "separatedBy" in action.data: - separators += action.data["separatedBy"] + separators += [a.id for a in action.data["separatedBy"]] - if z not in separators: + if z.id not in separators: results += [ TestResult( x=z, @@ -103,12 +104,13 @@ def test( return # if x and y are NOT adjacent, store all shared adjacent nodes - potential_zs = set(graph.edges[x].keys()).intersection( - set(graph.edges[y].keys()) + potential_zs = set(graph.edges[x.id].keys()).intersection( + set(graph.edges[y.id].keys()) ) # if one edge has an arrowhead at z, orient the other one pointing away from z. # It cannot be a collider because we have already oriented all unshielded triples that contain colliders. for z in potential_zs: + z = graph.nodes[z] breakflag = False if graph.only_directed_edge_exists(x, z) and graph.undirected_edge_exists( z, y @@ -161,12 +163,13 @@ def test( x = graph.nodes[nodes[0]] y = graph.nodes[nodes[1]] - potential_zs = set(graph.edges[x].keys()).intersection( - set(graph.edges[y].keys()) + potential_zs = set(graph.edges[x.id].keys()).intersection( + set(graph.edges[y.id].keys()) ) results = [] for z in potential_zs: + z = graph.nodes[z] if ( graph.undirected_edge_exists(x, y) and graph.only_directed_edge_exists(x, z) @@ -216,14 +219,14 @@ def test( x = graph.nodes[nodes[0]] y = graph.nodes[nodes[1]] - potential_zs = set(graph.edges[x].keys()).intersection( - set(graph.edges[y].keys()) + potential_zs = set(graph.edges[x.id].keys()).intersection( + set(graph.edges[y.id].keys()) ) results = [] for zs in itertools.combinations(potential_zs, 2): - z = zs[0] - w = zs[1] + z = graph.nodes[zs[0]] + w = graph.nodes[zs[1]] if ( not graph.undirected_edge_exists(x, y) and graph.only_directed_edge_exists(x, z) @@ -279,14 +282,14 @@ def test( x = graph.nodes[nodes[0]] y = graph.nodes[nodes[1]] - potential_zs = set(graph.edges[x].keys()).intersection( - set(graph.edges[y].keys()) + potential_zs = set(graph.edges[x.id].keys()).intersection( + set(graph.edges[y.id].keys()) ) results = [] for zs in itertools.combinations(potential_zs, 2): - z = zs[0] - w = zs[1] + z = graph.nodes[zs[0]] + w = graph.nodes[zs[1]] if ( not graph.undirected_edge_exists(x, y) and graph.only_directed_edge_exists(x, z) From 539137562c2b4062a5e68467ae7ab8326e74260b Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sun, 22 Oct 2023 07:30:12 +0200 Subject: [PATCH 14/17] feat(algorithms): configuration of ParallelPC + cleanup --- causy/algorithms.py | 4 +++- causy/cli.py | 3 +-- causy/generators.py | 1 - causy/graph.py | 27 ++++++++++++--------------- causy/independence_tests.py | 31 ++++++++++++++++++------------- causy/interfaces.py | 27 ++++++++++++++------------- causy/utils.py | 11 ++++++++--- 7 files changed, 56 insertions(+), 48 deletions(-) diff --git a/causy/algorithms.py b/causy/algorithms.py index 1424f91..3dfd76f 100644 --- a/causy/algorithms.py +++ b/causy/algorithms.py @@ -40,7 +40,9 @@ pipeline_steps=[ CalculateCorrelations(), CorrelationCoefficientTest(threshold=0.01), - PartialCorrelationTest(threshold=0.01), + PartialCorrelationTest( + threshold=0.01, parallel=True, chunk_size_parallel_processing=10000 + ), ExtendedPartialCorrelationTestMatrix( threshold=0.01, chunk_size_parallel_processing=1000, diff --git a/causy/cli.py b/causy/cli.py index 7ee16e9..959047c 100644 --- a/causy/cli.py +++ b/causy/cli.py @@ -2,18 +2,17 @@ import json from datetime import datetime from json import JSONEncoder +import logging import typer from causy.graph import graph_model_factory from causy.utils import ( - load_pipeline_artefact_by_definition, load_pipeline_steps_by_definition, retrieve_edges, ) app = typer.Typer() -import logging def load_json(pipeline_file: str): diff --git a/causy/generators.py b/causy/generators.py index 874c3a0..08cbb74 100644 --- a/causy/generators.py +++ b/causy/generators.py @@ -9,7 +9,6 @@ GraphModelInterface, AS_MANY_AS_FIELDS, ) -from causy.utils import serialize_module_name logger = logging.getLogger(__name__) diff --git a/causy/graph.py b/causy/graph.py index 932b73d..086a772 100644 --- a/causy/graph.py +++ b/causy/graph.py @@ -1,16 +1,15 @@ from abc import ABC from dataclasses import dataclass from typing import List, Optional, Dict, Set, Tuple +from uuid import uuid4 +import logging import torch import torch.multiprocessing as mp -from uuid import uuid4 - from causy.interfaces import ( IndependenceTestInterface, ) - from causy.interfaces import ( BaseGraphInterface, NodeInterface, @@ -20,9 +19,6 @@ LogicStepInterface, ExitConditionInterface, ) - -import logging - from causy.utils import ( load_pipeline_artefact_by_definition, load_pipeline_steps_by_definition, @@ -258,20 +254,20 @@ def bidirected_edge_exists(self, u: Node, v: Node): def edge_value(self, u: Node, v: Node): return self.edges[u.id][v.id] - def add_node(self, name: str, values: List[float], id: str = None): + def add_node(self, name: str, values: List[float], id_: str = None): """ Add a node to the graph :param name: name of the node :param values: values of the node - :param id: id of the node + :param id_: id_ of the node :param : node :return: """ - if id is None: - id = str(uuid4()) - self.nodes[id] = Node( - name=name, id=id, values=torch.tensor(values, dtype=torch.float64) + if id_ is None: + id_ = str(uuid4()) + self.nodes[id_] = Node( + name=name, id=id_, values=torch.tensor(values, dtype=torch.float64) ) def directed_path_exists(self, u: Node, v: Node): @@ -317,7 +313,8 @@ def inducing_path_exists(self, u: Node, v: Node): for i in range(1, len(path) - 1): r, w = path[i] if not self.bidirected_edge_exists(r, w): - return False + # TODO: check if this is correct (@sof) + return True return False @@ -546,11 +543,11 @@ def __init__( ): super().__init__() # TODO check if this is a good idea - if type(exit_condition) == dict: + if isinstance(exit_condition, dict): exit_condition = load_pipeline_artefact_by_definition(exit_condition) # TODO: check if this is a good idea - if len(pipeline_steps) > 0 and type(pipeline_steps[0]) == dict: + if len(pipeline_steps) > 0 and isinstance(pipeline_steps[0], dict): pipeline_steps = load_pipeline_steps_by_definition(pipeline_steps) self.pipeline_steps = pipeline_steps or [] diff --git a/causy/independence_tests.py b/causy/independence_tests.py index 2f15e72..a8965ea 100644 --- a/causy/independence_tests.py +++ b/causy/independence_tests.py @@ -1,15 +1,11 @@ import itertools -from typing import Tuple, List +from typing import Tuple, List, Optional +import logging import torch from causy.generators import AllCombinationsGenerator, PairsWithNeighboursGenerator from causy.utils import get_t_and_critical_t, get_correlation, pearson_correlation - -import logging - -logger = logging.getLogger(__name__) - from causy.interfaces import ( IndependenceTestInterface, BaseGraphInterface, @@ -20,7 +16,7 @@ ComparisonSettings, ) -# TODO: make tests configurable (choosing different generators for different algorithms) +logger = logging.getLogger(__name__) class CalculateCorrelations(IndependenceTestInterface): @@ -58,7 +54,7 @@ class CorrelationCoefficientTest(IndependenceTestInterface): CHUNK_SIZE_PARALLEL_PROCESSING = 1 PARALLEL = False - def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: + def test(self, nodes: List[str], graph: BaseGraphInterface) -> Optional[TestResult]: """ Test if x and y are independent and delete edge in graph if they are. :param nodes: list of nodes @@ -83,8 +79,6 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: data={}, ) - return - class PartialCorrelationTest(IndependenceTestInterface): GENERATOR = AllCombinationsGenerator( @@ -93,7 +87,9 @@ class PartialCorrelationTest(IndependenceTestInterface): CHUNK_SIZE_PARALLEL_PROCESSING = 1 PARALLEL = False - def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: + def test( + self, nodes: Tuple[str], graph: BaseGraphInterface + ) -> Optional[List[TestResult]]: """ Test if nodes x,y are independent given node z based on a partial correlation test. We use this test for all combinations of 3 nodes because it is faster than the extended test (which supports combinations of n nodes). We can @@ -104,6 +100,7 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: TODO: we are testing (C and E given B) and (E and C given B), we just need one of these, remove redundant tests. """ results = [] + already_deleted_edges = set() for nodes in itertools.permutations(nodes): x: NodeInterface = graph.nodes[nodes[0]] y: NodeInterface = graph.nodes[nodes[1]] @@ -112,6 +109,10 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: # Avoid division by zero if x is None or y is None or z is None: return + + if not graph.edge_exists(x, y) or (y, x) in already_deleted_edges: + continue + try: cor_xy = graph.edge_value(x, y)["correlation"] cor_xz = graph.edge_value(x, z)["correlation"] @@ -139,6 +140,7 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: logger.debug( f"Nodes {x.name} and {y.name} are uncorrelated given {z.name}" ) + results.append( TestResult( x=x, @@ -147,6 +149,7 @@ def test(self, nodes: Tuple[str], graph: BaseGraphInterface) -> TestResult: data={"separatedBy": [z]}, ) ) + already_deleted_edges.add((x, y)) return results @@ -157,7 +160,9 @@ class ExtendedPartialCorrelationTestLinearRegression(IndependenceTestInterface): CHUNK_SIZE_PARALLEL_PROCESSING = 1000 PARALLEL = True - def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: + def test( + self, nodes: List[str], graph: BaseGraphInterface + ) -> Optional[List[TestResult]]: """ Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using linear regression and a correlation test on the residuals. We use this test for all combinations of more than 3 nodes because it is slower. @@ -209,7 +214,7 @@ class ExtendedPartialCorrelationTestMatrix(IndependenceTestInterface): CHUNK_SIZE_PARALLEL_PROCESSING = 1000 PARALLEL = False - def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: + def test(self, nodes: List[str], graph: BaseGraphInterface) -> Optional[TestResult]: """ Test if nodes x,y are independent given Z (set of nodes) based on partial correlation using the inverted covariance matrix (precision matrix). https://en.wikipedia.org/wiki/Partial_correlation#Using_matrix_inversion diff --git a/causy/interfaces.py b/causy/interfaces.py index da621cd..6aa3cf6 100644 --- a/causy/interfaces.py +++ b/causy/interfaces.py @@ -2,7 +2,7 @@ import multiprocessing from abc import ABC, abstractmethod from dataclasses import dataclass -from typing import List, Dict +from typing import List, Dict, Optional import logging from causy.utils import serialize_module_name, load_pipeline_artefact_by_definition @@ -12,7 +12,6 @@ DEFAULT_THRESHOLD = 0.01 AS_MANY_AS_FIELDS = 0 -import sys @dataclass @@ -52,7 +51,7 @@ class TestResult: x: NodeInterface y: NodeInterface action: TestResultAction - data: Dict = None + data: Optional[Dict] = None def to_dict(self): return { @@ -145,7 +144,7 @@ def serialize(self) -> dict: } def __init__(self, comparison_settings: ComparisonSettings, chunked: bool = None): - if type(comparison_settings) == dict: + if isinstance(comparison_settings, dict): comparison_settings = load_pipeline_artefact_by_definition( comparison_settings ) @@ -157,29 +156,29 @@ def __init__(self, comparison_settings: ComparisonSettings, chunked: bool = None class IndependenceTestInterface(ABC): - NUM_OF_COMPARISON_ELEMENTS = 0 - GENERATOR: GeneratorInterface = None + NUM_OF_COMPARISON_ELEMENTS: int = 0 + GENERATOR: Optional[GeneratorInterface] = None - CHUNK_SIZE_PARALLEL_PROCESSING = 1 + CHUNK_SIZE_PARALLEL_PROCESSING: int = 1 - PARALLEL = True + PARALLEL: bool = True def __init__( self, threshold: float = DEFAULT_THRESHOLD, - generator: GeneratorInterface = None, + generator: Optional[GeneratorInterface] = None, num_of_comparison_elements: int = None, chunk_size_parallel_processing: int = None, parallel: bool = None, ): if generator: - if type(generator) == dict: + if isinstance(generator, dict): self.GENERATOR = load_pipeline_artefact_by_definition(generator) else: self.GENERATOR = generator if num_of_comparison_elements: - if type(num_of_comparison_elements) == dict: + if isinstance(num_of_comparison_elements, dict): self.NUM_OF_COMPARISON_ELEMENTS = load_pipeline_artefact_by_definition( num_of_comparison_elements ) @@ -195,7 +194,7 @@ def __init__( self.threshold = threshold @abstractmethod - def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: + def test(self, nodes: List[str], graph: BaseGraphInterface) -> Optional[TestResult]: """ Test if x and y are independent :param x: x values @@ -204,7 +203,9 @@ def test(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: """ pass - def __call__(self, nodes: List[str], graph: BaseGraphInterface) -> TestResult: + def __call__( + self, nodes: List[str], graph: BaseGraphInterface + ) -> Optional[TestResult]: return self.test(nodes, graph) def serialize(self) -> dict: diff --git a/causy/utils.py b/causy/utils.py index 8907f41..6a264cd 100644 --- a/causy/utils.py +++ b/causy/utils.py @@ -2,7 +2,7 @@ import logging import torch -from sympy import transpose, Matrix, solve_linear_system, symbols, Symbol, shape +from sympy import transpose, Matrix, Symbol, shape from scipy import stats as scipy_stats import math from statistics import correlation @@ -25,7 +25,7 @@ def backward_substituion(R, b, n): :param n: int, dimension :return: Matrix, n-dimensional regression coefficient vector """ - + # TODO: rewrite this function with torch or remove it # Define the symbolic variables my_symbols = [] for z in range(n + 1): @@ -53,6 +53,7 @@ def get_regression_coefficients(x, Z): :param Z: list of lists (length of outer list = # of samples, length of inner list = # of variables in Z) :return: sympy matrix, regression coefficients from regressing x on Z """ + # TODO: rewrite this function with torch or remove it z_matrix = Matrix(Z) (n, m) = shape(z_matrix) logger.debug(f"(n,m)={(n, m)}") @@ -61,7 +62,7 @@ def get_regression_coefficients(x, Z): "Z must have at most as many rows as columns. (Otherwise you have more variables than samples - which seems to be the case here)" ) Q, R = z_matrix.QRdecomposition() - if not shape(R) == (m, m): + if shape(R) != (m, m): raise Exception("The matrix of data we regress on (Z) must have full rank.") q_transposed = transpose(Q) logger.debug(f"Q_transposed shape = {shape(q_transposed)}") @@ -85,12 +86,15 @@ def get_residuals(x, Z): CAUTION: Z must have full rank TODO: add optional check """ + # TODO: rewrite this function with torch or remove it + n = len(x) res_x = Matrix(n, 1, x) - Matrix(Z) @ get_regression_coefficients(x, Z) return list(res_x) def get_correlation(x, y, other_nodes): + # TODO: rewrite this function with torch or remove it other_nodes_transposed = [list(i) for i in zip(*other_nodes)] residuals_x = get_residuals(x.values, other_nodes_transposed) residuals_y = get_residuals(y.values, other_nodes_transposed) @@ -99,6 +103,7 @@ def get_correlation(x, y, other_nodes): def get_t_and_critical_t(sample_size, nb_of_control_vars, par_corr, threshold): + # TODO: rewrite this function with torch # check if we have to normalize data deg_of_freedom = sample_size - 2 - nb_of_control_vars if abs(round(par_corr, 4)) == 1: From 1cb066a52b982c76bca68b4b328015f7c847e6a9 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sun, 22 Oct 2023 07:40:13 +0200 Subject: [PATCH 15/17] chore(docs): add sphinx build --- .github/workflows/python-package.yml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml index 1daf24a..ef659d4 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-package.yml @@ -36,3 +36,8 @@ jobs: - name: Test with pytest run: | poetry run python -m unittest + - name: Publish to GitHub Pages + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/build From d12076220e9ee726f688cef5ed9edc8dcc0f332d Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sun, 22 Oct 2023 07:49:22 +0200 Subject: [PATCH 16/17] chore(pipeline): add black + doc generation --- .github/workflows/create-docs.yml | 32 +++++++++++++++++++ .../{python-package.yml => python-tests.yml} | 12 +++---- 2 files changed, 37 insertions(+), 7 deletions(-) create mode 100644 .github/workflows/create-docs.yml rename .github/workflows/{python-package.yml => python-tests.yml} (85%) diff --git a/.github/workflows/create-docs.yml b/.github/workflows/create-docs.yml new file mode 100644 index 0000000..efe34a6 --- /dev/null +++ b/.github/workflows/create-docs.yml @@ -0,0 +1,32 @@ +# This workflow will install Python dependencies, run tests and lint with a variety of Python versions +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python + +name: Python package + +on: + push: + branches: [ "main" ] + +jobs: + build: + strategy: + fail-fast: false + matrix: + python-version: ["3.11"] + platform: [macos-latest] # TODO: change add ubuntu-latest + runs-on: ${{ matrix.platform }} + steps: + - uses: actions/checkout@v3 + - name: Set up Python ${{ matrix.python-version }} + uses: actions/setup-python@v3 + with: + python-version: ${{ matrix.python-version }} + - name: Install dependencies + run: | + python -m pip install --upgrade pip poetry flake8 + poetry install + - name: Publish to GitHub Pages + uses: peaceiris/actions-gh-pages@v3 + with: + github_token: ${{ secrets.GITHUB_TOKEN }} + publish_dir: docs/build diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-tests.yml similarity index 85% rename from .github/workflows/python-package.yml rename to .github/workflows/python-tests.yml index ef659d4..627901d 100644 --- a/.github/workflows/python-package.yml +++ b/.github/workflows/python-tests.yml @@ -5,9 +5,9 @@ name: Python package on: push: - branches: [ "main" ] + branches: [ "*" ] pull_request: - branches: [ "main" ] + branches: [ "*" ] jobs: build: @@ -33,11 +33,9 @@ jobs: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics + - uses: rickstaa/action-black@v1 + with: + black_args: ". --check" - name: Test with pytest run: | poetry run python -m unittest - - name: Publish to GitHub Pages - uses: peaceiris/actions-gh-pages@v3 - with: - github_token: ${{ secrets.GITHUB_TOKEN }} - publish_dir: docs/build From a15df71562d1be17c32ff04256f4c97d952f01a7 Mon Sep 17 00:00:00 2001 From: Lilith Wittmann Date: Sun, 22 Oct 2023 07:52:53 +0200 Subject: [PATCH 17/17] chore(pipeline): remove black again --- .github/workflows/python-tests.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml index 627901d..1de0a48 100644 --- a/.github/workflows/python-tests.yml +++ b/.github/workflows/python-tests.yml @@ -33,9 +33,6 @@ jobs: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics - - uses: rickstaa/action-black@v1 - with: - black_args: ". --check" - name: Test with pytest run: | poetry run python -m unittest