I am trying to use the GluonTS implementation of deepAR to train deepAR on multiple time series(using the m5 dataset). However, when I train deepAR on a single time series in the data set, the training takes just as little time as it does to train the model on 100(or more) time series. I have spend hours trying to understand what could be going wrong but I haven't found any potential solution. Here is code replicating the issue, assuming you have the m5 dataset downloaded:
from gluonts.mx import Trainer
from gluonts.evaluation import make_evaluation_predictions
from gluonts.model import deepar
from gluonts.mx.distribution.neg_binomial import NegativeBinomialOutput
import numpy as np
import pandas as pd
########################
##### PREPARING THE DATA
########################
prediction_length = 28
freq = "D"
start = pd.Timestamp("29-01-2011")
# load data
ste = pd.read_csv("sales_train_evaluation.csv")
# pandas Series of item 2
eva = ste.iloc[1,6:]
# 1-dimensional array containing time series data of item 2
item = np.array(ste.iloc[1,6:])
# Convert item to GluonTS-compatible ListDataset object
train_1 = ListDataset(
[{'target': item[:-prediction_length], 'start':start}],
freq=freq
)
# 2-dimensional array, containing time series data of 100 items
items = np.array(ste.iloc[1:101,6:])
# Convert to GluonTS-compatible ListDataset object
# train_100 contains 100 dictionaries, each corresponding to a given time series
train_100 = ListDataset(
[{'target': ts, 'start':start} for ts in items[:, :-prediction_length]],
freq=freq
)
########################
##### TRAINING THE MODEL
########################
nbo = NegativeBinomialOutput()
trainer = Trainer(epochs=5)
# train deepAR on 1 time series
estimator1 = deepar.DeepAREstimator(
freq="D", prediction_length=28, trainer=trainer, distr_output=nbo
)
estimator1.train(training_data=train_1)
# train deepAR on 100 time series
estimator100 = deepar.DeepAREstimator(
freq="D", prediction_length=28, trainer=trainer, distr_output=nbo
)
estimator100.train(training_data=train_100)
Yes for 100 time series it will take time, are you using the gpu or cpu?
In my I am using GPU so it works fine for me
estimator = SimpleFeedForwardEstimator(
num_hidden_dimensions=[10],
prediction_length=custom_ds_metadata['prediction_length'],
context_length=2*custom_ds_metadata['prediction_length'],
freq=custom_ds_metadata['freq'],
trainer=Trainer(
ctx="gpu",
epochs=5,
learning_rate=1e-3,
hybridize=False,
num_batches_per_epoch=100
)
)`enter code here`
Related
can I use the y-hat variance, the bounds, and the point estimate from the forecast data frame to calculate the confidence level that would contain a given value?
I've seen that I can change my interval level prior to fitting but programmatically that feels like a LOT of expensive trial and error.
Is there a way to estimate the confidence bound using only the information from the model parameters and the forecast data frame?
Something like:
for level in [.05, .1, .15, ... , .95]:
if value_in_question in (yhat - Z_{level}*yhat_variance/N, yhat + Z_{level}*yhat_variance/N):
print 'im in the bound level {level}'
# This is sudo code not meant to run in console
EDIT: working prophet example
# csv from fbprohets working examples https://github.com/facebook/prophet/blob/master/examples/example_wp_log_peyton_manning.csv
import pandas as pd
from fbprophet import Prophet
import os
df = pd.read_csv('example_wp_log_peyton_manning.csv')
m = Prophet()
m.fit(df)
future = m.make_future_dataframe(periods=30)
forecast = m.predict(future)
# the smallest confidence level s.t. the confidence interval of the 30th prediction contains 9
## My current approach
def __probability_calculation(estimate, forecast, j = 30):
sd_residuals = (forecast.yhat_lower[j] - forecast.yhat[j])/(-1.28)
for alpha in np.arange(.5, .95, .01):
z_val = st.norm.ppf(alpha)
if (forecast.yhat[j]-z_val*sd_residuals < estimate < forecast.yhat[j]+z_val*sd_residuals):
return alpha
prob = __probability_calculation(9, forecast)
fbprophet uses the numpy.percentile method to estimate the percentiles as you can see here in the source code:
https://github.com/facebook/prophet/blob/0616bfb5daa6888e9665bba1f95d9d67e91fed66/python/prophet/forecaster.py#L1448
How to inverse calculate percentiles for values is already answered here:
Map each list value to its corresponding percentile
Combining everything based on your code example:
import pandas as pd
import numpy as np
import scipy.stats as st
from fbprophet import Prophet
url = 'https://raw.githubusercontent.com/facebook/prophet/master/examples/example_wp_log_peyton_manning.csv'
df = pd.read_csv(url)
# put the amount of uncertainty samples in a variable so we can use it later.
uncertainty_samples = 1000 # 1000 is the default
m = Prophet(uncertainty_samples=uncertainty_samples)
m.fit(df)
future = m.make_future_dataframe(periods=30)
# You need to replicate some of the preparation steps which are part of the predict() call internals
tmpdf = m.setup_dataframe(future)
tmpdf['trend'] = m.predict_trend(tmpdf)
sim_values = m.sample_posterior_predictive(tmpdf)
The sim_values object contains for every datapoint 1000 simulations on which the confidence interval is based.
Now you can call the scipy.stats.percentileofscore method with any target value
target_value = 8
st.percentileofscore(sim_values['yhat'], target_value, 'weak') / uncertainty_samples
# returns 44.26
To prove this works backwards and forwards you can get the output of the np.percentile method and put it in the scipy.stats.percentileofscore method.
This works for an accuracy of 4 decimals:
ACCURACY = 4
for test_percentile in np.arange(0, 100, 0.5):
target_value = np.percentile(sim_values['yhat'], test_percentile)
if not np.round(st.percentileofscore(sim_values['yhat'], target_value, 'weak') / uncertainty_samples, ACCURACY) == np.round(test_percentile, ACCURACY):
print(test_percentile)
raise ValueError('This doesnt work')
My problem is as follow:
I have several datasets (900K, 1M7 and 1M7 entries) in csv format which I load into multiple Dask Dataframe.
Then I concatenate them all in one Dask Dataframe that I can feed to my Snorkel Applier, which applies a bunch of Labeling Function to each row of my Dataframe and return a numpy array with as many rows as there are in the Dataframe and as many columns as there are Labeling Functions.
The call to Snorkel Applier seems to take forever when I do that with 3 datasets (more than 2 days...). However if I just run the code with only the first dataset, the call takes around 2 hours. Of course I don't do the concatenation step.
So I was wondering how can this be ? Should I change the number of partitions in the concatenated Dataframe ? Or maybe I'm using Dask badly in the first place ?
Here is the code I'm using:
from snorkel.labeling.apply.dask import DaskLFApplier
import dask.dataframe as dd
import numpy as np
import os
start = time.time()
applier = DaskLFApplier(lfs) # lfs are the function that are going to be applied, one of them featurize one of the column of my Dataframe and apply a sklearn classifier (I put n_jobs to None when loading the model)
# If I have only one CSV to read
if isinstance(PATH_TO_CSV, str):
training_data = dd.read_csv(PATH_TO_CSV, lineterminator=os.linesep, na_filter=False, dtype={'size': 'int32'})
slices = None
# If I have several CSV
elif isinstance(PATH_TO_CSV, list):
training_data_list = [dd.read_csv(path, lineterminator=os.linesep, na_filter=False, dtype={'size': 'int32'}) for path in PATH_TO_CSV]
training_data = dd.concat(training_data_list, axis=0)
# some useful things I do to know where to slice my final result and be sure I can assign each part to each dataset
df_sizes = [len(df) for df in training_data_list]
cut_idx = np.insert(np.cumsum(df_sizes), 0, 0)
slices = list(zip(cut_idx[:-1], cut_idx[1:]))
# The call that lasts forever: I tested all the code above without that line on my 3 datasets and it runs perfectly fine
L_train = applier.apply(training_data)
end = time.time()
print('Time elapsed: {}'.format(timedelta(seconds=end-start)))
If you need more info I will try to get them to you as much as I can.
Thank in you advance for your help :)
It seems that by default applier function is using processes, so does not benefit from additional workers you might have available:
# add this to the beginning of your code
from dask.distributed import Client
client = Client()
# you can see the address of the client by typing `client` and opening the dashboard
# skipping your other code
# you need to pass the client explicitly to the applier
# after launching this open the dashboard and watch the workers work :)
L_train = applier.apply(training_data, scheduler=client)
How do I interpret following results? What is the best possible algorithm to train based on autogluon summary?
*** Summary of fit() ***
Estimated performance of each model:
model score_val fit_time pred_time_val stack_level
19 weighted_ensemble_k0_l2 -0.035874 1.848907 0.002517 2
18 weighted_ensemble_k0_l1 -0.040987 1.837416 0.002259 1
16 CatboostClassifier_STACKER_l1 -0.042901 1559.653612 0.083949 1
11 ExtraTreesClassifierGini_STACKER_l1 -0.047882 7.307266 1.057873 1
...
...
0 RandomForestClassifierGini_STACKER_l0 -0.291987 9.871649 1.054538 0
The code to generate the above results:
import pandas as pd
from autogluon import TabularPrediction as task
from sklearn.datasets import load_digits
digits = load_digits()
savedir = "otto_models/" # where to save trained models
train_data = pd.DataFrame(digits.data)
train_target = pd.DataFrame(digits.target)
train_data = pd.merge(train_data, train_target, left_index=True, right_index=True)
label_column = "0_y"
predictor = task.fit(
train_data=train_data,
label=label_column,
output_directory=savedir,
eval_metric="log_loss",
auto_stack=True,
verbosity=2,
visualizer="tensorboard",
)
results = predictor.fit_summary() # display detailed summary of fit() process
Which algorithm seems to work in this case?
weighted_ensemble_k0_l2 is the best result in terms of validation score (score_val) because it has the highest value. You may wish to do predictor.leaderboard(test_data) to get the test scores for each of the models.
Note that the result shows a negative score because AutoGluon always considers higher to be better. If a particular metric such as logloss prefers lower values to be better, AutoGluon flips the sign of the metric. I would guess a val_score of 0 would be a perfect score in your case.
Update 1
I’m thinking that it might be the mistake in my detector code.
So, here is my code for using the trained learner/model to predict images.
import requests
import cv2
bytes = b''
stream = requests.get(url, stream=True)
bytes = bytes + stream.raw.read(1024) # I have my mobile video streaming to this url. the resolution for the video streaming is: 2048 x 1080
a = bytes.find(b'\xff\xd8')
b = bytes.find(b'\xff\xd9')
if a != -1 and b != -1:
jpg = bytes[a:b+2]
bytes = bytes[b+2:]
img = cv2.imdecode(np.fromstring(jpg, dtype=np.uint8), cv2.IMREAD_COLOR)
processedImg = Image(pil2tensor(img, np.float32).div_(255))
predict = learn.predict(processedImg)
self.objectClass = predict[0].obj
and I read the document of imdecode() method, it returns image in B G R order.
Could it because of different channel data used when in training and detecting?
Or
Could it because that I trained with image size 299 x 450, but when detecting the input image size from the video streaming is 2048 x 1080 without resizing it?
new to FastAi, ML and Python. I trained my “Birds Or Not-Birds” model. The train_loss, valid_loss and error_rate were improving. If I only trained 3 epochs, then the model worked(meaning it can recognize whether there are birds or no birds in images), then I increased to 30 epochs, all metrics look very good, but the model does not recognize things anymore, whatever images I input, the model always return Not-Birds.
here is the training output:
Here are the plots of learn.recorder
Here is my code:
from fastai.vision import *
from fastai.metrics import error_rate
from fastai.callbacks import EarlyStoppingCallback,SaveModelCallback
from datetime import datetime as dt
from functools import partial
path_img = '/minidata'
train_folder = 'train'
valid_folder = 'validation'
tunedTransform = partial(get_transforms, max_zoom=1.5)
data = ImageDataBunch.from_folder(path=path_img, train=train_folder, valid=valid_folder, ds_tfms=tunedTransform(),
size=(299, 450), bs=40, classes=['birds', 'others'],
resize_method=ResizeMethod.SQUISH)
data = data.normalize(imagenet_stats)
learn = cnn_learner(data, models.resnet50, metrics=error_rate)
learn.fit_one_cycle(30, max_lr=slice(5e-5,5e-4))
learn.recorder.plot_lr()
learn.recorder.plot()
learn.recorder.plot_losses()
Here is my dataset folder structure:
minidata
train
birds (7500 images)
others (around 7300 images)
validation
birds (1008 images)
others (around 872 images)
Your learning rate schedule is sub-optimal for this dataset. Try to first figure out the best learning rate for this network and dataset with
LRFinder. This can be done by exploring the loss behavior for different learning rates with
learn.lr_find()
learn.recorder.plot()
Edit:
It looks like you are re-training the last layer in your network. Instead try training more layers from scratch. as:
learn.unfreeze(2)
I have a final project in my first degree and I want to build a Neural Network that gonna take the first 13 mfcc coeffs of a wav file and return who talked in the audio file from a banch of talkers.
I want you to notice that:
My audio files are text independent, therefore they have different length and words
I have trained the machine on about 35 audio files of 10 speaker ( the first speaker had about 15, the second 10, and the third and fourth about 5 each )
I defined :
X=mfcc(sound_voice)
Y=zero_array + 1 in the i_th position ( where i_th position is 0 for the first speaker, 1 for the second, 2 for the third... )
And than trained the machine, and than checked the output of the machine for some files...
So that’s what I did... but unfortunately it’s look like the results are completely random...
Can you help me understand why?
This is my code in python -
from sklearn.neural_network import MLPClassifier
import python_speech_features
import scipy.io.wavfile as wav
import numpy as np
from os import listdir
from os.path import isfile, join
from random import shuffle
import matplotlib.pyplot as plt
from tqdm import tqdm
winner = [] # this array count how much Bingo we had when we test the NN
for TestNum in tqdm(range(5)): # in every round we build NN with X,Y that out of them we check 50 after we build the NN
X = []
Y = []
onlyfiles = [f for f in listdir("FinalAudios/") if isfile(join("FinalAudios/", f))] # Files in dir
names = [] # names of the speakers
for file in onlyfiles: # for each wav sound
# UNESSECERY TO UNDERSTAND THE CODE
if " " not in file.split("_")[0]:
names.append(file.split("_")[0])
else:
names.append(file.split("_")[0].split(" ")[0])
names = list(dict.fromkeys(names)) # names of speakers
vector_names = [] # vector for each name
i = 0
vector_for_each_name = [0] * len(names)
for name in names:
vector_for_each_name[i] += 1
vector_names.append(np.array(vector_for_each_name))
vector_for_each_name[i] -= 1
i += 1
for f in onlyfiles:
if " " not in f.split("_")[0]:
f_speaker = f.split("_")[0]
else:
f_speaker = f.split("_")[0].split(" ")[0]
(rate, sig) = wav.read("FinalAudios/" + f) # read the file
try:
mfcc_feat = python_speech_features.mfcc(sig, rate, winlen=0.2, nfft=512) # mfcc coeffs
for index in range(len(mfcc_feat)): # adding each mfcc coeff to X, meaning if there is 50000 coeffs than
# X will be [first coeff, second .... 50000'th coeff] and Y will be [f_speaker_vector] * 50000
X.append(np.array(mfcc_feat[index]))
Y.append(np.array(vector_names[names.index(f_speaker)]))
except IndexError:
pass
Z = list(zip(X, Y))
shuffle(Z) # WE SHUFFLE X,Y TO PERFORM RANDOM ON THE TEST LEVEL
X, Y = zip(*Z)
X = list(X)
Y = list(Y)
X = np.asarray(X)
Y = np.asarray(Y)
Y_test = Y[:50] # CHOOSE 50 FOR TEST, OTHERS FOR TRAIN
X_test = X[:50]
X = X[50:]
Y = Y[50:]
clf = MLPClassifier(solver='lbfgs', alpha=1e-2, hidden_layer_sizes=(5, 3), random_state=2) # create the NN
clf.fit(X, Y) # Train it
for sample in range(len(X_test)): # add 1 to winner array if we correct and 0 if not, than in the end it plot it
if list(clf.predict([X[sample]])[0]) == list(Y_test[sample]):
winner.append(1)
else:
winner.append(0)
# plot winner
plot_x = []
plot_y = []
for i in range(1, len(winner)):
plot_y.append(sum(winner[0:i])*1.0/len(winner[0:i]))
plot_x.append(i)
plt.plot(plot_x, plot_y)
plt.xlabel('x - axis')
# naming the y axis
plt.ylabel('y - axis')
# giving a title to my graph
plt.title('My first graph!')
# function to show the plot
plt.show()
This is my zip file that contains the code and the audio file : https://ufile.io/eggjm1gw
You have a number of issues in your code and it will be close to impossible to get it right in one go, but let's give it a try. There are two major issues:
Currently you're trying to teach your neural network with very few training examples, as few as a single one per speaker (!). It's impossible for any machine learning algorithm to learn anything.
To make matters worse, what you do is that you feed to the ANN only MFCC for the first 25 ms of each recording (25 comes from winlen parameter of python_speech_features). In each of these recordings, first 25 ms will be close to identical. Even if you had 10k recordings per speaker, with this approach you'd not get anywhere.
I will give you concrete advise, but won't do all the coding - it's your homework after all.
Use all MFCC, not just first 25 ms. Many of these should be skipped, simply because there's no voice activity. Normally there should be VOD (Voice Activity Detector) telling you which ones to take, but in this exercise I'd skip it for starter (you need to learn basics first).
Don't use dictionaries. Not only it won't fly with more than one MFCC vector per speaker, but also it's very inefficient data structure for your task. Use numpy arrays, they're much faster and memory efficient. There's a ton of tutorials, including scikit-learn that demonstrate how to use numpy in this context. In essence, you create two arrays: one with training data, second with labels. Example: if omersk speaker "produces" 50000 MFCC vectors, you will get (50000, 13) training array. Corresponding label array would be 50000 with single constant value (id) that corresponds to the speaker (say, omersk is 0, lucas is 1 and so on). I'd consider taking longer windows (perhaps 200 ms, experiment!) to reduce the variance.
Don't forget to split your data for training, validation and test. You will have more than enough data. Also, for this exercise I'd watch for not feeding too much of data for any single speaker - ot taking steps to make sure algorithm is not biased.
Later, when you make prediction, you will again compute MFCCs for the speaker. With 10 sec recording, 200 ms window and 100 ms overlap, you'll get 99 MFCC vectors, shape (99, 13). The model should run on each of the 99 vectors, for each producing probability. When you sum it (and normalise, to make it nice) and take top value, you'll get the most likely speaker.
There's a dozen of other things that typically would be taken into account, but in this case (homework) I'd focus on getting the basics right.
EDIT: I decided to take a stab at creating the model with your idea at heart, but basics fixed. It's not exactly clean Python, all because it's adapted from Jupyter Notebook I was running.
import python_speech_features
import scipy.io.wavfile as wav
import numpy as np
import glob
import os
from collections import defaultdict
from sklearn.neural_network import MLPClassifier
from sklearn import preprocessing
from sklearn.model_selection import cross_validate
from sklearn.ensemble import RandomForestClassifier
audio_files_path = glob.glob('audio/*.wav')
win_len = 0.04 # in seconds
step = win_len / 2
nfft = 2048
mfccs_all_speakers = []
names = []
data = []
for path in audio_files_path:
fs, audio = wav.read(path)
if audio.size > 0:
mfcc = python_speech_features.mfcc(audio, samplerate=fs, winlen=win_len,
winstep=step, nfft=nfft, appendEnergy=False)
filename = os.path.splitext(os.path.basename(path))[0]
speaker = filename[:filename.find('_')]
data.append({'filename': filename,
'speaker': speaker,
'samples': mfcc.shape[0],
'mfcc': mfcc})
else:
print(f'Skipping {path} due to 0 file size')
speaker_sample_size = defaultdict(int)
for entry in data:
speaker_sample_size[entry['speaker']] += entry['samples']
person_with_fewest_samples = min(speaker_sample_size, key=speaker_sample_size.get)
print(person_with_fewest_samples)
max_accepted_samples = int(speaker_sample_size[person_with_fewest_samples] * 0.8)
print(max_accepted_samples)
training_idx = []
test_idx = []
accumulated_size = defaultdict(int)
for entry in data:
if entry['speaker'] not in accumulated_size:
training_idx.append(entry['filename'])
accumulated_size[entry['speaker']] += entry['samples']
elif accumulated_size[entry['speaker']] < max_accepted_samples:
accumulated_size[entry['speaker']] += entry['samples']
training_idx.append(entry['filename'])
X_train = []
label_train = []
X_test = []
label_test = []
for entry in data:
if entry['filename'] in training_idx:
X_train.append(entry['mfcc'])
label_train.extend([entry['speaker']] * entry['mfcc'].shape[0])
else:
X_test.append(entry['mfcc'])
label_test.extend([entry['speaker']] * entry['mfcc'].shape[0])
X_train = np.concatenate(X_train, axis=0)
X_test = np.concatenate(X_test, axis=0)
assert (X_train.shape[0] == len(label_train))
assert (X_test.shape[0] == len(label_test))
print(f'Training: {X_train.shape}')
print(f'Testing: {X_test.shape}')
le = preprocessing.LabelEncoder()
y_train = le.fit_transform(label_train)
y_test = le.transform(label_test)
clf = MLPClassifier(solver='lbfgs', alpha=1e-2, hidden_layer_sizes=(5, 3), random_state=42, max_iter=1000)
cv_results = cross_validate(clf, X_train, y_train, cv=4)
print(cv_results)
{'fit_time': array([3.33842635, 4.25872731, 4.73704267, 5.9454329 ]),
'score_time': array([0.00125694, 0.00073504, 0.00074005, 0.00078583]),
'test_score': array([0.40380048, 0.52969121, 0.48448687, 0.46043165])}
The test_score isn't stellar. There's a lot to improve (for starter, choice of algorithm), but the basics are there. Notice for starter how I get the training samples. It's not random, I only consider recordings as whole. You can't put samples from a given recording to both training and test, as test is supposed to be novel.
What was not working in your code? I'd say a lot. You were taking 200ms samples and yet very short fft. python_speech_features likely complained to you that the fft is should be longer than the frame you're processing.
I leave to you testing the model. It won't be good, but it's a starter.