phylokrr-dev 0.2.0__tar.gz

phylokrr_dev-0.2.0/PKG-INFO

@@ -0,0 +1,9 @@
+Metadata-Version: 2.4
+Name: phylokrr_dev
+Version: 0.2.0
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.5
+Requires-Dist: numpy
+Dynamic: classifier
+Dynamic: requires-dist
+Dynamic: requires-python

phylokrr_dev-0.2.0/README.md

@@ -0,0 +1,5 @@
+# KRGEE
+Kernel Ridge GEE
+
+
+Development repo

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/PKG-INFO

@@ -0,0 +1,9 @@
+Metadata-Version: 2.4
+Name: phylokrr_dev
+Version: 0.2.0
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.5
+Requires-Dist: numpy
+Dynamic: classifier
+Dynamic: requires-dist
+Dynamic: requires-python

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/SOURCES.txt

@@ -0,0 +1,13 @@
+README.md
+setup.py
+phylokrr_dev.egg-info/PKG-INFO
+phylokrr_dev.egg-info/SOURCES.txt
+phylokrr_dev.egg-info/dependency_links.txt
+phylokrr_dev.egg-info/not-zip-safe
+phylokrr_dev.egg-info/requires.txt
+phylokrr_dev.egg-info/top_level.txt
+src/__init__.py
+src/alpha_beta_weighting.py
+src/block_cross_validation.py
+src/phyloKPQL.py
+src/utils.py

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/not-zip-safe

@@ -0,0 +1 @@
+

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/requires.txt

@@ -0,0 +1 @@
+numpy

phylokrr_dev-0.2.0/phylokrr_dev.egg-info/top_level.txt

@@ -0,0 +1 @@
+phylokrr_dev

phylokrr_dev-0.2.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

phylokrr_dev-0.2.0/setup.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+
+import setuptools
+from distutils.core import setup
+
+dependencies = [
+    "numpy"
+]
+
+with open('README.md') as readme_file:
+    readme = readme_file.read()
+
+setup(name = "phylokrr_dev",
+      version = '0.2.0',
+    #   long_description = readme,
+    #   long_description_content_type = 'text/markdown',
+      packages = ['phylokrr_dev'],
+      package_dir = {'phylokrr_dev': 'src'},
+      python_requires='>=3.5',
+      install_requires = dependencies,
+      zip_safe = False,
+      include_package_data=True,
+      classifiers = [
+          'Programming Language :: Python :: 3',
+      ]
+    )

phylokrr_dev-0.2.0/src/alpha_beta_weighting.py

@@ -0,0 +1,252 @@
+
+import numpy as np
+from phylokrr.treeio import parseNewickTree, is_leaf
+
+def split_leaves(sorted_leaves, folds):
+
+    n = len(sorted_leaves)
+    fold_size = n//folds
+    myfolds = []
+    for i in range(folds):
+        test_idx = list(range(i * fold_size, (i + 1) * fold_size))
+        train_idx = list(set(range(n)) - set(test_idx))
+        test_l = sorted_leaves[test_idx] 
+        train_l = sorted_leaves[train_idx]
+        myfolds.append([train_l, test_l])
+
+    return myfolds
+
+def tree_postorder(root):
+
+    L = []
+    S = [root]
+    while S:
+        v = S.pop()
+        L.append(v)
+
+        if is_leaf(v):
+            continue   
+
+        l = v.left
+        r = v.right
+        S.append(l)
+        S.append(r)
+
+    return L
+
+# tree = "((4,5),(6,7));"
+def alpha_weighting(tree, alpha=1/4):
+    """
+    Weight the leaves of a phylogenetic tree based on 
+    on the number of decendents using an alpha parameter. 
+
+    Since it uses a hash table to store the weights, 
+    the order of the leaves is not guaranteed 
+    to be the same as in the input tree.
+
+    """
+    _, root = parseNewickTree(tree)
+
+    L = tree_postorder(root)
+
+    while L:
+        v = L.pop()
+        if is_leaf(v):
+            v.branch_length = 1
+            continue
+
+        l = v.left
+        r = v.right
+        v.branch_length = l.branch_length + r.branch_length
+
+    # alpha = 1/4
+    A = {}
+    # S = [(root, math.log(1))]
+    S = [(root, 1)]
+    while S:
+        pa,p = S.pop()
+
+        if is_leaf(pa):
+            # store only leaves probabilities
+            A[pa.name] = p
+            continue
+
+        nl = pa.left.branch_length
+        nr = pa.right.branch_length
+        
+        pr = (nr/(nl+nr))**alpha
+        pl = 1 - pr
+        # S.append((pa.left, math.log(pl) + p))
+        # S.append((pa.right, math.log(pr) + p))
+        S.append((pa.left, pl * p))
+        S.append((pa.right, pr * p))
+
+    return A
+
+def sample_mChoice(P, rng, Fz):
+    """
+
+    Return a set of indices sampled according to P, without replacement, and with size Fz
+    """
+    S_idx = rng.choice(len(P), size=Fz, p=P, replace=False)
+    P[S_idx] = 0
+    P /= np.sum(P)
+
+    return set(S_idx)
+
+def split_data_idx(num_test, P, rng): # type: ignore
+    """
+
+    Return two lists of indices, one for test and one for train
+    """
+    all_idx = set(range(len(P)))
+    test_idx = sample_mChoice(P, rng, num_test)
+    return list(test_idx), list(all_idx - test_idx)
+
+def getT2(P, rng, n, folds = 5):
+    """
+    Return a list of sets
+    """
+    T = []
+    Fz = n//folds
+    # O(k * n)
+    for _ in range(folds - 1):
+        T.append(
+            sample_mChoice(P, rng, Fz)
+        )
+
+    last_S = []
+    for i in range(n):
+        if P[i] != 0.0:
+            last_S.append(i)
+    T.append(set(last_S))
+
+    return T
+
+
+def weighted_sample(P, rng, folds=5): # type: ignore 
+
+    n = len(P)
+    all_idx = set(range(n))
+    T = getT2(P, rng, n, folds)
+
+    myfolds = []
+    for test_idx in T:
+        myfolds.append([
+            list(all_idx - test_idx), 
+            list(test_idx)
+        ])
+    return myfolds
+
+# region: Testing
+
+# tree_file = "test_tree_v5.txt"
+# with open(tree_file, 'r') as f: 
+#     tree = f.read().strip()
+
+# from phylokrr.treeio import get_vcv
+
+# rng = np.random.default_rng(seed=12038)
+# V, leaves = get_vcv(tree,  process = "OU", sigma2 = 1, alpha = 1)
+
+# # P = np.linalg.inv(V) @ np.ones(len(leaves))
+# # P /= np.sum(P)
+
+
+
+
+# A = alpha_weighting(tree, alpha = 1e2)
+# P = np.array([A[leaf] for leaf in leaves])
+# # print(A)
+# print(P)
+
+# n = len(leaves)
+# test_idx, train_idx = split_data_idx(num_test=int(n*0.25), P=P, rng=rng)
+
+# P_train = P[train_idx]
+# myfolds = weighted_sample(P_train, rng, folds=5)
+
+# # for a,b in myfolds:
+# #     print(a,"-------",b)
+# # print(P[list(myfolds[3][1])])
+
+# test_leaves = [leaves[i] for i in test_idx]
+# with open("test_leaves.txt", 'w') as f:
+#     f.write(",".join(test_leaves) + "\n")
+# # print("Test Leaves: ", test_leaves)
+
+# # # # # myfolds
+# with open("folds.txt", 'w') as f:
+# # with open("folds_random.txt", 'w') as f:
+#     for train_idx_f, test_idx_f in myfolds:
+
+#         train_leaves_f = []
+#         for idx in train_idx_f:
+#             train_leaves_f.append(leaves[train_idx[idx]])
+
+#         test_leaves_f = []
+#         for idx in test_idx_f:
+#             test_leaves_f.append(leaves[train_idx[idx]])
+
+#         f.write(",".join(train_leaves_f) + "\n")
+#         f.write(",".join(test_leaves_f) + "\n")
+
+# endregion
+
+
+# region: Old code
+
+# def updateP(S, P):
+#     # mark those taken as 0
+#     P[S != 0] = 0
+#     # P[S] = 0
+#     # adjust the probabilities
+#     P /= np.sum(P)
+#     # print("Updated P: ", P)
+
+
+# def multi_sample(P, rng, Fz):
+#     # P = P.copy()
+#     # S_idx = rng.choice(len(P), size=Fz, p=P, replace=False)
+#     # S = np.zeros(len(P), dtype=int)
+#     # S[S_idx] = 1
+
+#     S = rng.multinomial(n=Fz, pvals=P, size=1)[0]
+#     updateP(S, P)
+#     NZ = sum(S != 0)
+#     while Fz > NZ:
+#         Si = rng.multinomial(n=Fz - NZ, pvals=P, size=1)[0]
+#         # Just update with the recently taken 
+#         # samples, not the whole S
+#         updateP(Si, P)
+#         S += Si
+#         NZ = sum(S != 0)
+    
+#     return S
+
+# def getT(P, rng, n, folds = 5):
+#     # P = P.copy()
+#     T = []  
+#     Fz = n//folds
+#     # O(k * n)
+#     for _ in range(folds - 1):
+#         S = multi_sample2(P, rng, Fz)
+#         T.append(S)
+
+#     S = np.zeros(n, dtype=int)
+#     S[P != 0] = 1
+#     T.append(S)
+#     return T
+
+# def split_sample(t):
+#     test_idx = []
+#     train_idx = []
+#     for k, v in enumerate(t):
+#         if v != 0:
+#             test_idx.append(k)
+#         else:
+#             train_idx.append(k)
+
+#     return test_idx, train_idx
+
+# endregion

phylokrr_dev-0.2.0/src/block_cross_validation.py

@@ -0,0 +1,256 @@
+import sys
+import time
+from collections import deque
+
+import numpy as np
+
+from phylokrr_dev.alpha_beta_weighting import weighted_sample
+from phylokrr_dev.utils import progressbar
+
+
+def sample_hyperParams(params, seed, sample, verbose):
+    """
+    Random search for hyperparameter tuning using k-fold cross-validation
+
+    Parameters
+    ----------
+    params : dict
+        hyperparameters to sample from
+
+    seed : int
+        random seed
+
+    sample : int
+        number of samples
+
+    verbose : bool
+        print number of unique hyperparameters
+
+    Returns
+    -------
+    np.ndarray
+        sampled hyperparameters
+
+    dict
+        index of hyperparameters
+
+    list
+        names of hyperparameters
+    """
+
+    np.random.seed(seed=seed)
+    # make random choice from the grid of hyperparameters
+    P_n = params.keys()
+    P_r = np.zeros((sample, len(P_n))) # random hyperparameters
+
+    P_index = {}
+    for n,k in enumerate(P_n):
+        P_r[:,n] = np.random.choice(params[k], sample, )
+        P_index[k] = n
+
+    if verbose:
+        # check tested_params are unique
+        P_r = np.unique(P_r, axis=0)
+        print("Number of unique hyperparameters: ", P_r.shape[0])
+
+    return  P_r, P_index, P_n
+
+def pick_init_index(P_index, P_r, seed):
+    """
+    Pick the initial index for the hyperparameters
+    """
+
+    np.random.seed(seed=seed)
+    # get the lambda index
+    lam_idx = ""
+    if "lambda" in P_index:
+        lam_idx = P_index["lambda"]
+
+    if "lam" in P_index:
+        lam_idx = P_index["lam"]
+
+    if lam_idx:
+        init_idx = np.argmax(P_r[:,lam_idx])
+        # ave = np.mean(P_r[:,lam_idx])
+        # init_idx = np.argmin(np.abs(P_r[:,lam_idx] - ave))
+    else:
+        init_idx = np.random.randint(P_r.shape[0])
+        
+    return init_idx
+
+def init_model(X_train, y_train, vcv_train, model, 
+                    param_init, i):
+    """
+    Initialize the model.
+    This initialization of the model is used at the beginning of every
+    fold. This set the inverse of the inverse of the correlation matrix
+    and the initial alpha.
+    
+    if it is the first fold iteration, the alpha is calculated
+    from the initial hyperparameters. Otherwise, the previous
+    solution is used as the initial alpha.
+
+    For a given fold, the correlation matrix is the same
+    for all the hyperparameters, then inverse of the correlation
+    matrix is calculated only once at the beginning of the fold.
+    """
+    # for the initial model, R inv should be calculated
+    model.copy_R_inv = False
+
+
+    # for the initial model, initial params should be random
+    # when it is the first fold iteration. Otherwise
+    # we can use the previous solution as the initial
+    # i is the fold index
+    # model.warm_start = False if i == 0 else True
+    model.warm_start = False
+
+    # set the initial hyperparameters
+    model.set_params(**param_init)
+    # model fit, while also setting the R_inv matrix
+    time_start = time.time()
+    model.fit(X_train, y_train, vcv_train)
+    time_end = time.time()
+    print(f"Initial model fit time: {time_end - time_start:.2f} seconds")
+
+    # for the next iteration alpha is used
+    model.warm_start = False
+
+    # for the next iteration R_inv is used
+    model.copy_R_inv = True 
+
+
+def sort_P_r(P_r, P_index):
+
+    if "lambda" in P_index: 
+        lam_index = P_index["lambda"]
+
+    elif "lam" in P_index:
+        lam_index = P_index["lam"]
+
+    else:
+        lam_index = None
+
+    if lam_index:
+        P_r = P_r[np.argsort(P_r[:,lam_index])[::-1],]
+
+    return P_r
+
+
+def k_fold_cv_weigthed(X, y, vcv, model, W,
+                       params,
+                       folds = 3, 
+                       sample = 100,
+                       verbose = True,
+                       seed = 12038):
+    """
+    """
+    
+    model.verbose = False
+    np.random.seed(seed=seed)
+    rng = np.random.RandomState(seed=seed)
+    
+    # X = X_train
+    P_r, P_index, P_n = sample_hyperParams(params, seed, sample, verbose)
+    
+    # if lambda is present, then sort by lambda
+    P_r = sort_P_r(P_r, P_index)
+
+    # a random index if lambda is not present. 
+    # otherwise (most typical), the index with the highest lambda
+    init_idx = pick_init_index(P_index, P_r, seed)
+    param_init = dict(zip(P_n, P_r[init_idx,:]))
+
+    n, _ = X.shape
+    # linked list to store all the errors
+    all_errors = deque([])
+    myfolds = weighted_sample(W, rng, folds=folds)
+
+    # O(n^3*folds*sample)
+    for i, (train_idx, test_idx) in enumerate(myfolds):
+        print("Fold: ", i)
+        # print(test_idx)
+        X_train, X_test = X[train_idx, :], X[test_idx, :]
+        y_train, y_test = y[train_idx], y[test_idx]
+
+        is_vcv =  isinstance(vcv, np.ndarray)
+        vcv_train = None
+        vcv_test_12 = None
+
+        if is_vcv and model.add_extraK:
+            model.Rnn = vcv[train_idx,:][:,train_idx]
+            model.Rzn = vcv[test_idx,:][:,train_idx]
+
+        elif is_vcv and not model.add_extraK:
+            vcv_train = vcv[train_idx,:][:,train_idx]
+            vcv_test_12 = vcv[test_idx,:][:,train_idx]
+
+        elif not is_vcv and model.add_extraK:
+            raise ValueError("Missing correlation structure at Cross validation")
+        
+        else:
+            # everything is None
+            pass
+
+        # inverse of the correlation is calculated only once
+        # This is used to test all the rest of hyperparameters
+        # An initial alpha is calculated from a previously 
+        # specified hyperparameter. This initial alpha is
+        # used for all the folds
+        init_model(X_train, y_train, vcv_train,
+                   model, param_init, i)
+        
+        # init_err1 = model.score(X_test, y_test, vcv_test_12)*len(y_test)
+        # init_err2 = model.score(X_test, y_test, None)*len(y_test)
+        # init_err = max(init_err1, init_err2)
+
+        init_err = model.score(X_test, y_test, None)*len(y_test)
+
+        all_errors.append([init_idx, init_err])
+
+        j = 0
+        for p_j in progressbar(P_r, prefix = "Testing hyperparameters: ", size=60):
+            
+            if j == init_idx:
+                continue
+
+            tmp_param = dict(zip(P_n, p_j))
+            
+            model.set_params(**tmp_param)
+            # vcv and spps are already copied
+            # from init_model
+            model.fit(X_train, y_train, vcv_train)
+
+            # tmp_err1 = model.score(X_test, y_test, vcv_test_12)*len(y_test)
+            # tmp_err2 = model.score(X_test, y_test, None)*len(y_test)
+            # tmp_err = max(tmp_err1, tmp_err2)
+
+            tmp_err = model.score(X_test, y_test, None)*len(y_test)
+
+            all_errors.append([j, tmp_err])
+            j += 1
+
+    # O(sample*folds)
+    out = {}
+    for pi, err in all_errors:
+        if pi in out:
+            out[pi] += (err/n)
+        else:    
+            out[pi] = (err/n)
+    
+    # out = lkrgee_best_params # for testing
+    # print("Time taken: ", time.time() - start)
+    
+    # O(sample * log sample)
+    best_pi,best_err = sorted(out.items(), key=lambda kv: kv[1], reverse=False)[0]
+    best_ = dict(zip(P_n, P_r[best_pi,:]))
+
+    if verbose:
+        print("CV score: ", best_err)
+
+    # This let model fit with another correlation matrix
+    model.copy_R_inv = False
+    # let the model start with new alpha
+    model.warm_start = False
+    
+    return best_