import os from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter from collections import namedtuple import pathlib import numpy as np import pandas as pd import sympy from sympy import sympify, Symbol, lambdify sympy_mappings = { 'div': lambda x, y : x/y, 'mult': lambda x, y : x*y, 'plus': lambda x, y : x + y, 'neg': lambda x : -x, 'pow': lambda x, y : sympy.sign(x)*sympy.Abs(x)**y, 'cos': lambda x : sympy.cos(x), 'sin': lambda x : sympy.sin(x), 'tan': lambda x : sympy.tan(x), 'cosh': lambda x : sympy.cosh(x), 'sinh': lambda x : sympy.sinh(x), 'tanh': lambda x : sympy.tanh(x), 'exp': lambda x : sympy.exp(x), 'acos': lambda x : sympy.acos(x), 'asin': lambda x : sympy.asin(x), 'atan': lambda x : sympy.atan(x), 'acosh':lambda x : sympy.acosh(x), 'asinh':lambda x : sympy.asinh(x), 'atanh':lambda x : sympy.atanh(x), 'abs': lambda x : sympy.Abs(x), 'mod': lambda x, y : sympy.Mod(x, y), 'erf': lambda x : sympy.erf(x), 'erfc': lambda x : sympy.erfc(x), 'logm': lambda x : sympy.log(sympy.Abs(x)), 'logm10':lambda x : sympy.log10(sympy.Abs(x)), 'logm2': lambda x : sympy.log2(sympy.Abs(x)), 'log1p': lambda x : sympy.log(x + 1), 'floor': lambda x : sympy.floor(x), 'ceil': lambda x : sympy.ceil(x), 'sign': lambda x : sympy.sign(x), 'round': lambda x : sympy.round(x), } def pysr(X=None, y=None, weights=None, procs=4, populations=None, niterations=100, ncyclesperiteration=300, binary_operators=["plus", "mult"], unary_operators=["cos", "exp", "sin"], alpha=0.1, annealing=True, fractionReplaced=0.10, fractionReplacedHof=0.10, npop=1000, parsimony=1e-4, migration=True, hofMigration=True, shouldOptimizeConstants=True, topn=10, weightAddNode=1, weightInsertNode=3, weightDeleteNode=3, weightDoNothing=1, weightMutateConstant=10, weightMutateOperator=1, weightRandomize=1, weightSimplify=0.01, perturbationFactor=1.0, nrestarts=3, timeout=None, extra_sympy_mappings={}, equation_file='hall_of_fame.csv', test='simple1', verbosity=1e9, maxsize=20, fast_cycle=False, maxdepth=None, variable_names=[], threads=None, #deprecated julia_optimization=3, ): """Run symbolic regression to fit f(X[i, :]) ~ y[i] for all i. Note: most default parameters have been tuned over several example equations, but you should adjust `threads`, `niterations`, `binary_operators`, `unary_operators` to your requirements. :param X: np.ndarray, 2D array. Rows are examples, columns are features. :param y: np.ndarray, 1D array. Rows are examples. :param weights: np.ndarray, 1D array. Each row is how to weight the mean-square-error loss on weights. :param procs: int, Number of processes (=number of populations running). :param populations: int, Number of populations running; by default=procs. :param niterations: int, Number of iterations of the algorithm to run. The best equations are printed, and migrate between populations, at the end of each. :param ncyclesperiteration: int, Number of total mutations to run, per 10 samples of the population, per iteration. :param binary_operators: list, List of strings giving the binary operators in Julia's Base, or in `operator.jl`. :param unary_operators: list, Same but for operators taking a single `Float32`. :param alpha: float, Initial temperature. :param annealing: bool, Whether to use annealing. You should (and it is default). :param fractionReplaced: float, How much of population to replace with migrating equations from other populations. :param fractionReplacedHof: float, How much of population to replace with migrating equations from hall of fame. :param npop: int, Number of individuals in each population :param parsimony: float, Multiplicative factor for how much to punish complexity. :param migration: bool, Whether to migrate. :param hofMigration: bool, Whether to have the hall of fame migrate. :param shouldOptimizeConstants: bool, Whether to numerically optimize constants (Nelder-Mead/Newton) at the end of each iteration. :param topn: int, How many top individuals migrate from each population. :param nrestarts: int, Number of times to restart the constant optimizer :param perturbationFactor: float, Constants are perturbed by a max factor of (perturbationFactor*T + 1). Either multiplied by this or divided by this. :param weightAddNode: float, Relative likelihood for mutation to add a node :param weightInsertNode: float, Relative likelihood for mutation to insert a node :param weightDeleteNode: float, Relative likelihood for mutation to delete a node :param weightDoNothing: float, Relative likelihood for mutation to leave the individual :param weightMutateConstant: float, Relative likelihood for mutation to change the constant slightly in a random direction. :param weightMutateOperator: float, Relative likelihood for mutation to swap an operator. :param weightRandomize: float, Relative likelihood for mutation to completely delete and then randomly generate the equation :param weightSimplify: float, Relative likelihood for mutation to simplify constant parts by evaluation :param timeout: float, Time in seconds to timeout search :param equation_file: str, Where to save the files (.csv separated by |) :param test: str, What test to run, if X,y not passed. :param maxsize: int, Max size of an equation. :param maxdepth: int, Max depth of an equation. You can use both maxsize and maxdepth. maxdepth is by default set to = maxsize, which means that it is redundant. :param fast_cycle: bool, (experimental) - batch over population subsamples. This is a slightly different algorithm than regularized evolution, but does cycles 15% faster. May be algorithmically less efficient. :param variable_names: list, a list of names for the variables, other than "x0", "x1", etc. :param julia_optimization: int, Optimization level (0, 1, 2, 3) :returns: pd.DataFrame, Results dataframe, giving complexity, MSE, and equations (as strings). """ if threads is not None: raise ValueError("The threads kwarg is deprecated. Use procs.") if maxdepth is None: maxdepth = maxsize # Check for potential errors before they happen assert len(unary_operators) + len(binary_operators) > 0 assert len(X.shape) == 2 assert len(y.shape) == 1 assert X.shape[0] == y.shape[0] if weights is not None: assert len(weights.shape) == 1 assert X.shape[0] == weights.shape[0] if len(variable_names) != 0: assert len(variable_names) == X.shape[1] if populations is None: populations = procs local_sympy_mappings = { **extra_sympy_mappings, **sympy_mappings } rand_string = f'{"".join([str(np.random.rand())[2] for i in range(20)])}' if isinstance(binary_operators, str): binary_operators = [binary_operators] if isinstance(unary_operators, str): unary_operators = [unary_operators] if X is None: if test == 'simple1': eval_str = "np.sign(X[:, 2])*np.abs(X[:, 2])**2.5 + 5*np.cos(X[:, 3]) - 5" elif test == 'simple2': eval_str = "np.sign(X[:, 2])*np.abs(X[:, 2])**3.5 + 1/(np.abs(X[:, 0])+1)" elif test == 'simple3': eval_str = "np.exp(X[:, 0]/2) + 12.0 + np.log(np.abs(X[:, 0])*10 + 1)" elif test == 'simple4': eval_str = "1.0 + 3*X[:, 0]**2 - 0.5*X[:, 0]**3 + 0.1*X[:, 0]**4" elif test == 'simple5': eval_str = "(np.exp(X[:, 3]) + 3)/(np.abs(X[:, 1]) + np.cos(X[:, 0]) + 1.1)" X = np.random.randn(100, 5)*3 y = eval(eval_str) print("Running on", eval_str) pkg_directory = '/'.join(__file__.split('/')[:-2] + ['julia']) def_hyperparams = "" # Add pre-defined functions to Julia for op_list in [binary_operators, unary_operators]: for i in range(len(op_list)): op = op_list[i] if '(' not in op: continue def_hyperparams += op + "\n" # Cut off from the first non-alphanumeric char: first_non_char = [ j for j in range(len(op)) if not (op[j].isalpha() or op[j].isdigit())][0] function_name = op[:first_non_char] op_list[i] = function_name def_hyperparams += f"""include("{pkg_directory}/operators.jl") const binops = {'[' + ', '.join(binary_operators) + ']'} const unaops = {'[' + ', '.join(unary_operators) + ']'} const ns=10; const parsimony = {parsimony:f}f0 const alpha = {alpha:f}f0 const maxsize = {maxsize:d} const maxdepth = {maxdepth:d} const fast_cycle = {'true' if fast_cycle else 'false'} const migration = {'true' if migration else 'false'} const hofMigration = {'true' if hofMigration else 'false'} const fractionReplacedHof = {fractionReplacedHof}f0 const shouldOptimizeConstants = {'true' if shouldOptimizeConstants else 'false'} const hofFile = "{equation_file}" const nprocs = {procs:d} const npopulations = {populations:d} const nrestarts = {nrestarts:d} const perturbationFactor = {perturbationFactor:f}f0 const annealing = {"true" if annealing else "false"} const weighted = {"true" if weights is not None else "false"} const useVarMap = {"false" if len(variable_names) == 0 else "true"} const mutationWeights = [ {weightMutateConstant:f}, {weightMutateOperator:f}, {weightAddNode:f}, {weightInsertNode:f}, {weightDeleteNode:f}, {weightSimplify:f}, {weightRandomize:f}, {weightDoNothing:f} ] """ if X.shape[1] == 1: X_str = 'transpose([' + str(X.tolist()).replace(']', '').replace(',', '').replace('[', '') + '])' else: X_str = str(X.tolist()).replace('],', '];').replace(',', '') y_str = str(y.tolist()) def_datasets = """const X = convert(Array{Float32, 2}, """f"{X_str})"""" const y = convert(Array{Float32, 1}, """f"{y_str})" if weights is not None: weight_str = str(weights.tolist()) def_datasets += """ const weights = convert(Array{Float32, 1}, """f"{weight_str})" if len(variable_names) != 0: def_hyperparams += f""" const varMap = {'["' + '", "'.join(variable_names) + '"]'}""" with open(f'/tmp/.hyperparams_{rand_string}.jl', 'w') as f: print(def_hyperparams, file=f) with open(f'/tmp/.dataset_{rand_string}.jl', 'w') as f: print(def_datasets, file=f) with open(f'/tmp/.runfile_{rand_string}.jl', 'w') as f: print(f'@everywhere include("/tmp/.hyperparams_{rand_string}.jl")', file=f) print(f'@everywhere include("/tmp/.dataset_{rand_string}.jl")', file=f) print(f'@everywhere include("{pkg_directory}/sr.jl")', file=f) print(f'fullRun({niterations:d}, npop={npop:d}, ncyclesperiteration={ncyclesperiteration:d}, fractionReplaced={fractionReplaced:f}f0, verbosity=round(Int32, {verbosity:f}), topn={topn:d})', file=f) print(f'rmprocs(nprocs)', file=f) command = [ f'julia -O{julia_optimization:d}', f'-p {procs}', f'/tmp/.runfile_{rand_string}.jl', ] if timeout is not None: command = [f'timeout {timeout}'] + command cur_cmd = ' '.join(command) print("Running on", cur_cmd) os.system(cur_cmd) try: output = pd.read_csv(equation_file, sep="|") except FileNotFoundError: print("Couldn't find equation file!") return pd.DataFrame() scores = [] lastMSE = None lastComplexity = 0 sympy_format = [] lambda_format = [] sympy_symbols = [sympy.Symbol('x%d'%i) for i in range(X.shape[1])] for i in range(len(output)): eqn = sympify(output.loc[i, 'Equation'], locals=local_sympy_mappings) sympy_format.append(eqn) lambda_format.append(lambdify(sympy_symbols, eqn)) curMSE = output.loc[i, 'MSE'] curComplexity = output.loc[i, 'Complexity'] if lastMSE is None: cur_score = 0.0 else: cur_score = np.log(curMSE/lastMSE)/(curComplexity - lastComplexity) scores.append(cur_score) lastMSE = curMSE lastComplexity = curComplexity output['score'] = np.array(scores) output['sympy_format'] = sympy_format output['lambda_format'] = lambda_format return output[['Complexity', 'MSE', 'score', 'Equation', 'sympy_format', 'lambda_format']]