how extraction decision rules of random forest in python - machine-learning
I have one question though. I heard from someone that in R, you can use extra packages to extract the decision rules implemented in RF, I try to google the same thing in python but without luck, if there is any help on how to achieve that.
thanks in advance!
Assuming that you use sklearn RandomForestClassifier you can find the invididual decision trees as .estimators_. Each tree stores the decision nodes as a number of NumPy arrays under tree_.
Here is some example code which just prints each node in order of the array. In a typical application one would instead traverse by following the children.
import numpy
from sklearn.model_selection import train_test_split
from sklearn import metrics, datasets, ensemble
def print_decision_rules(rf):
for tree_idx, est in enumerate(rf.estimators_):
tree = est.tree_
assert tree.value.shape[1] == 1 # no support for multi-output
print('TREE: {}'.format(tree_idx))
iterator = enumerate(zip(tree.children_left, tree.children_right, tree.feature, tree.threshold, tree.value))
for node_idx, data in iterator:
left, right, feature, th, value = data
# left: index of left child (if any)
# right: index of right child (if any)
# feature: index of the feature to check
# th: the threshold to compare against
# value: values associated with classes
# for classifier, value is 0 except the index of the class to return
class_idx = numpy.argmax(value[0])
if left == -1 and right == -1:
print('{} LEAF: return class={}'.format(node_idx, class_idx))
else:
print('{} NODE: if feature[{}] < {} then next={} else next={}'.format(node_idx, feature, th, left, right))
digits = datasets.load_digits()
Xtrain, Xtest, ytrain, ytest = train_test_split(digits.data, digits.target)
estimator = ensemble.RandomForestClassifier(n_estimators=3, max_depth=2)
estimator.fit(Xtrain, ytrain)
print_decision_rules(estimator)
Example outout:
TREE: 0
0 NODE: if feature[33] < 2.5 then next=1 else next=4
1 NODE: if feature[38] < 0.5 then next=2 else next=3
2 LEAF: return class=2
3 LEAF: return class=9
4 NODE: if feature[50] < 8.5 then next=5 else next=6
5 LEAF: return class=4
6 LEAF: return class=0
...
We use something similar in emlearn to compile a Random Forest to C code.
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Isolation Tree algorithm question about classification
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Where can I get the pretrained word embeddinngs for BERT?
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-2.5461e-03, -3.1498e-01, 6.3761e-03, 4.8914e-02, -7.7636e-03, 6.0919e-02, 2.1346e-02, -3.9741e-02, 2.2853e-01, 2.6502e-02, -1.0144e-03, -7.8480e-03, -1.9995e-03, 1.7057e-02, -3.3270e-02, 4.5421e-03, 6.1751e-03, -1.0077e-01, -2.0973e-02, -1.4512e-04, -9.6657e-03, 1.0871e-02, -1.4786e-02, 2.6437e-04, 2.1166e-02, 1.6492e-02, -5.1928e-03, -1.1857e-02, -9.9159e-03, -1.4363e-02, -1.2405e-02, -1.2973e-02, 2.6778e-02, -1.0986e-02, 1.0572e-02, -2.5566e-02, 5.2494e-03, 1.5890e-02, -5.1504e-03, -7.5859e-03, 2.0259e-02, -7.0155e-03, 1.6359e-02, 1.7487e-02, 5.4297e-03, -8.6403e-03, 2.8821e-02, -7.8964e-03, 1.9259e-02, 2.3868e-02, -4.3472e-03, 5.5662e-02, -2.1940e-02, 4.1779e-03, -5.7216e-03, 2.6712e-02, -5.0371e-03, 2.4923e-02, -1.3429e-02, -8.4337e-03, 9.8188e-02, -1.2940e-03, 1.2865e-02, -1.5930e-03, 3.6437e-03, 1.5569e-02, 1.8620e-02, -9.0643e-03, -1.9740e-02, 1.0530e-02, -2.7359e-03, -7.5283e-03, 1.1492e-03, 2.6162e-03, -6.2757e-03, -8.6096e-03, 6.6221e-01, -3.2235e-03, -4.1309e-02, 3.3047e-03, -2.5040e-03, 1.2838e-04, -6.8073e-03, 6.0291e-03, -9.8468e-03, 8.0641e-03, -1.9815e-03, 2.5801e-02, 5.7429e-03, -1.0712e-02, 2.9176e-02, 5.9414e-03, 2.4795e-02, -1.7887e-02, 7.3183e-01, 1.0964e-02, 5.9942e-03, -4.6157e-02, 4.0131e-02, -9.7481e-03, -8.9496e-01, 1.6385e-02, -1.9816e-03, 1.4691e-02, -1.9837e-02, -1.7611e-02, -4.5263e-04, -1.8605e-02, -1.5660e-02, -1.0709e-02, 1.8016e-02, -3.4149e-03, -1.2632e-02, 4.2877e-03, -3.9169e-01, 1.0016e-02, -1.0955e-02, 4.5133e-03, -5.1150e-03, 4.9968e-03, 1.7852e-02, 1.1313e-02, 2.6519e-03, 3.3658e-01, -1.8168e-02, 1.3170e-02, 7.3927e-03, 5.2521e-03, -9.6230e-03, 1.2844e-02, 4.1554e-01, -9.7247e-03, -4.2439e-03, 5.5287e-04, 1.8271e-02, -1.3889e-03, -2.0502e-03, -8.1946e-03, -6.5979e-06, -7.2764e-04, -1.4625e-03, -6.9872e-03, -6.9633e-03, -8.0701e-03, 1.9936e-02, 4.8370e-03, 8.6883e-03, -4.9246e-02, -2.0028e-02, 1.4124e-03, 1.0444e-02, -1.1236e-02, -4.4654e-03, -2.0491e-02, -2.7654e-02, -3.7079e-02, 1.3215e-02, 6.9498e-02, 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1.6709e-02, 1.6860e-03, -3.3842e-03, 8.6805e-03, 7.1340e-03, 1.5147e-02], grad_fn=<EmbeddingBackward>)
To get context-sensitive word embedding for given input sentence/text, here is the code, import numpy as np import torch from transformers import AutoTokenizer, AutoModel def get_word_idx(sent: str, word: str): return sent.split(" ").index(word) def get_hidden_states(encoded, token_ids_word, model, layers): """Push input IDs through model. Stack and sum `layers` (last four by default). Select only those subword token outputs that belong to our word of interest and average them.""" with torch.no_grad(): output = model(**encoded) # Get all hidden states states = output.hidden_states # Stack and sum all requested layers output = torch.stack([states[i] for i in layers]).sum(0).squeeze() # Only select the tokens that constitute the requested word word_tokens_output = output[token_ids_word] return word_tokens_output.mean(dim=0) def get_word_vector(sent, idx, tokenizer, model, layers): """Get a word vector by first tokenizing the input sentence, getting all token idxs that make up the word of interest, and then `get_hidden_states`.""" encoded = tokenizer.encode_plus(sent, return_tensors="pt") # get all token idxs that belong to the word of interest token_ids_word = np.where(np.array(encoded.word_ids()) == idx) return get_hidden_states(encoded, token_ids_word, model, layers) def main(layers=None): # Use last four layers by default layers = [-4, -3, -2, -1] if layers is None else layers tokenizer = AutoTokenizer.from_pretrained("bert-base-cased") model = AutoModel.from_pretrained("bert-base-cased", output_hidden_states=True) sent = "I like cookies ." idx = get_word_idx(sent, "cookies") word_embedding = get_word_vector(sent, idx, tokenizer, model, layers) return word_embedding if __name__ == '__main__': main() More details can be found here.
Getting the column names chosen after a feature selection method
Given a simple feature selection code below, I want to know the selected columns after the feature selection (The dataset includes a header V1 ... V20) import pandas as pd from sklearn.feature_selection import SelectFromModel, SelectKBest, f_regression def feature_selection(data): y = data['Class'] X = data.drop(['Class'], axis=1) fs = SelectKBest(score_func=f_regression, k=10) # Applying feature selection X_selected = fs.fit_transform(X, y) # TODO: determine the columns being selected return X_selected data = pd.read_csv("../dataset.csv") new_data = feature_selection(data) I appreciate any help.
I have used the iris dataset for my example but you can probably easily modify your code to match your use case. The SelectKBest method has the scores_ attribute I used to sort the features. Feel free to ask for any clarifications. import pandas as pd import numpy as np from sklearn.feature_selection import SelectFromModel, SelectKBest, f_regression from sklearn.datasets import load_iris def feature_selection(data): y = data[1] X = data[0] column_names = ["A", "B", "C", "D"] # Here you should use your dataframe's column names k = 2 fs = SelectKBest(score_func=f_regression, k=k) # Applying feature selection X_selected = fs.fit_transform(X, y) # Find top features # I create a list like [[ColumnName1, Score1] , [ColumnName2, Score2], ...] # Then I sort in descending order on the score top_features = sorted(zip(column_names, fs.scores_), key=lambda x: x[1], reverse=True) print(top_features[:k]) return X_selected data = load_iris(return_X_y=True) new_data = feature_selection(data)
I don't know the in-build method, but it can be easily coded. n_columns_selected = X_new.shape[0] new_columns = list(sorted(zip(fs.scores_, X.columns))[-n_columns_selected:]) # new_columns order is perturbed, we need to restore it. We use the names of the columns of X as a reference new_columns = list(sorted(cols_new, key=lambda x: list(X.columns).index(x)))
How to get class labels from TensorFlow prediction
I have a classification model in TF and can get a list of probabilities for the next class (preds). Now I want to select the highest element (argmax) and display its class label. This may seems silly, but how can I get the class label that matches a position in the predictions tensor? feed_dict={g['x']: current_char} preds, state = sess.run([g['preds'],g['final_state']], feed_dict) prediction = tf.argmax(preds, 1) preds gives me a vector of predictions for each class. Surely there must be an easy way to just output the most likely class (label)? Some info about my model: x = tf.placeholder(tf.int32, [None, num_steps], name='input_placeholder') y = tf.placeholder(tf.int32, [None, 1], name='labels_placeholder') batch_size = batch_size = tf.shape(x)[0] x_one_hot = tf.one_hot(x, num_classes) rnn_inputs = [tf.squeeze(i, squeeze_dims=[1]) for i in tf.split(x_one_hot, num_steps, 1)] tmp = tf.stack(rnn_inputs) print(tmp.get_shape()) tmp2 = tf.transpose(tmp, perm=[1, 0, 2]) print(tmp2.get_shape()) rnn_inputs = tmp2 with tf.variable_scope('softmax'): W = tf.get_variable('W', [state_size, num_classes]) b = tf.get_variable('b', [num_classes], initializer=tf.constant_initializer(0.0)) rnn_outputs = rnn_outputs[:, num_steps - 1, :] rnn_outputs = tf.reshape(rnn_outputs, [-1, state_size]) y_reshaped = tf.reshape(y, [-1]) logits = tf.matmul(rnn_outputs, W) + b predictions = tf.nn.softmax(logits)
A prediction is an array of n types of classes(labels). It represents the model's "confidence" that the image corresponds to each of its classes(labels). You can check which label has the highest confidence value by using: prediction = np.argmax(preds, 1) After getting this highest element index using (argmax function) out of other probabilities, you need to place this index into class labels to find the exact class name associated with this index. class_names[prediction] Please refer to this link for more understanding.
You can use tf.reduce_max() for this. I would refer you to this answer. Let me know if it works - will edit if it doesn't.
Mind that there are sometimes several ways to load a dataset. For instance with fashion MNIST the tutorial could lead you to use load_data() and then to create your own structure to interpret a prediction. However you can also load these data by using tensorflow_datasets.load(...) like here after installing tensorflow-datasets which gives you access to some DatasetInfo. So for instance if your prediction is 9 you can tell it's a boot with: import tensorflow_datasets as tfds _, ds_info = tfds.load('fashion_mnist', with_info=True) print(ds_info.features['label'].names[9])
When you use softmax, the labels you train the model on are either numbers 0..n or one-hot encoded values. So if original labels of your data are let's say string names, you must map them to integers first and keep the mapping as a variable (such as 0 -> "apple", 1 -> "orange", 2 -> "pear" ...). When using integers (with loss='sparse_categorical_crossentropy'), you get predictions as an array of probabilities, you just find the array index with the max value. You can use this predicted index to reverse-map to your label: predictedIndex = np.argmax(predictions) // 2 predictedLabel = indexToLabelMap[predictedIndex] // "pear" If you use one-hot encoded labels (with loss='categorical_crossentropy'), the predicted index corresponds with the "hot" index of your label. Just for reference, I needed this info when I was working with MNIST dataset used in Google's Machine learning crash course. There is also a good classification tutorial in the Tensorflow docs.