repo stringlengths 2 99 | file stringlengths 13 225 | code stringlengths 0 18.3M | file_length int64 0 18.3M | avg_line_length float64 0 1.36M | max_line_length int64 0 4.26M | extension_type stringclasses 1
value |
|---|---|---|---|---|---|---|
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/inference/auto_model.py | # -*- coding: utf-8 -*-
# Copyright 2020 The HuggingFace Inc. team and Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICEN... | 4,153 | 33.04918 | 110 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/inference/savable_models.py | # -*- coding: utf-8 -*-
# Copyright 2020 TensorFlowTTS Team
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | 2,870 | 35.807692 | 87 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/inference/auto_config.py | # -*- coding: utf-8 -*-
# Copyright 2020 The HuggingFace Inc. team and Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICEN... | 3,150 | 33.626374 | 109 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/inference/__init__.py | from tensorflow_tts.inference.auto_model import TFAutoModel
from tensorflow_tts.inference.auto_config import AutoConfig
from tensorflow_tts.inference.auto_processor import AutoProcessor
| 186 | 45.75 | 65 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/inference/auto_processor.py | # -*- coding: utf-8 -*-
# Copyright 2020 The TensorFlowTTS Team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | 3,111 | 33.197802 | 113 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/losses/stft.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 5,179 | 33.533333 | 97 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/losses/spectrogram.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,697 | 31.902439 | 83 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/losses/__init__.py | from tensorflow_tts.losses.spectrogram import TFMelSpectrogram
from tensorflow_tts.losses.stft import TFMultiResolutionSTFT
| 124 | 40.666667 | 62 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/trainers/base_trainer.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 36,562 | 35.165183 | 113 | py |
TensorFlowTTS | TensorFlowTTS-master/tensorflow_tts/trainers/__init__.py | from tensorflow_tts.trainers.base_trainer import GanBasedTrainer, Seq2SeqBasedTrainer
| 86 | 42.5 | 85 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_hifigan.py | # -*- coding: utf-8 -*-
# Copyright 2020 TensorFlowTTS Team
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | 3,900 | 29.960317 | 76 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_fastspeech.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,995 | 34.247059 | 86 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_tacotron2.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 5,329 | 34.533333 | 87 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_melgan_layers.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,965 | 30.892473 | 113 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_melgan.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,841 | 29.55914 | 84 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_mb_melgan.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,401 | 29.025 | 86 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_parallel_wavegan.py | # -*- coding: utf-8 -*-
# Copyright 2020 TensorFlowTTS Team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | 2,967 | 26.481481 | 82 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_fastspeech2.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 4,805 | 35.969231 | 88 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_auto.py | # -*- coding: utf-8 -*-
# Copyright 2020 Minh Nguyen (@dathudeptrai)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | 2,820 | 34.708861 | 79 | py |
TensorFlowTTS | TensorFlowTTS-master/test/test_base_processor.py | import pytest
from tensorflow_tts.processor.base_processor import BaseProcessor, DataProcessorError
import string
from dataclasses import dataclass
from shutil import copyfile
@dataclass
class LJ(BaseProcessor):
def get_one_sample(self, item):
sample = {
"raw_text": None,
"text_ids... | 3,035 | 27.111111 | 85 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/setup.py | from setuptools import setup
config = {
'name': 'sgmcmc_ssm',
'version': '0.1',
'url': 'https://github.com/aicherc/sgmcmc_ssm_code',
'description': 'SGMCMC for SSM Code',
'author': 'Christopher Aicher',
'license': 'MIT License',
'packages': ['sgmcmc_ssm'],
}
setup(**config)
# Build Extensio... | 441 | 26.625 | 56 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/lgssm/driver.py | """ Experiment Driver
Call python <path_to_this_file>.py --help to see documentation
"""
import os
import sys
sys.path.append(os.getcwd()) # Fix Python Path
import numpy as np
import pandas as pd
import joblib
import time
import argparse
from tqdm import tqdm
import functools
import matplotlib
matplotlib.use('Agg')... | 57,938 | 38.657084 | 104 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/lgssm/demo_setup.py | """
Create Setup Script for Demo Experiment
Usage:
0. Change `project_root` in this file to match the directory of `sgmcmc_nonlinear_ssm`
1. Run this script, which will create a `setup.sh` script at `<experiment_folder>`
(default is `./scratch/<experiment_name>/scripts/setup.sh`)
This will generate... | 6,445 | 31.23 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/garch/driver.py | """ Experiment Driver
Call python <path_to_this_file>.py --help to see documentation
"""
import os
import sys
sys.path.append(os.getcwd()) # Fix Python Path
import numpy as np
import pandas as pd
import joblib
import time
import argparse
from tqdm import tqdm
import functools
import matplotlib
matplotlib.use('Agg')... | 53,197 | 38.729649 | 104 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/garch/demo_setup.py | """
Create Setup Script for Demo Experiment
Usage:
0. Change `project_root` in this file to match the directory of `sgmcmc_nonlinear_ssm`
1. Run this script, which will create a `setup.sh` script at `<experiment_folder>`
(default is `./scratch/<experiment_name>/scripts/setup.sh`)
This will generate... | 6,074 | 31.837838 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/svm/driver.py | """ Experiment Driver
Call python <path_to_this_file>.py --help to see documentation
"""
import os
import sys
sys.path.append(os.getcwd()) # Fix Python Path
import numpy as np
import pandas as pd
import joblib
import time
import argparse
from tqdm import tqdm
import functools
import matplotlib
matplotlib.use('Agg')... | 59,557 | 38.918231 | 104 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/svm/demo_setup.py | """
Create Setup Script for Demo Experiment
Usage:
0. Change `project_root` in this file to match the directory of `sgmcmc_nonlinear_ssm`
1. Run this script, which will create a `setup.sh` script at `<experiment_folder>`
(default is `./scratch/<experiment_name>/scripts/setup.sh`)
This will generate... | 5,924 | 32.100559 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/gradient_error_fig_scripts/svm_grad_compare.py | #!/usr/bin/python3
#This script is being used to test the particle gradient approximations (full data)
#######IMPORT RELEVANT MODULES######################
import numpy as np
import pandas as pd
import time
import joblib
import os
from sgmcmc_ssm.models.svm import ( SVMParameters,
SVMSampler,
SVMPrior... | 8,962 | 37.969565 | 107 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/gradient_error_fig_scripts/garch_grad_compare.py | #!/usr/bin/python3
#This script is being used to test the particle gradient approximations (full data)
#######IMPORT RELEVANT MODULES######################
import numpy as np
import pandas as pd
import time
import joblib
import os
from sgmcmc_ssm.models.garch import (
GARCHParameters,
GARCHSampler,
... | 9,330 | 38.041841 | 107 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/nonlinear_ssm_pf_experiment_scripts/gradient_error_fig_scripts/lgssm_grad_compare.py | #!/usr/bin/python3
#This script is being used to test the particle gradient approximations (full data)
#######IMPORT RELEVANT MODULES######################
import numpy as np
import pandas as pd
import time
import joblib
import os
from sgmcmc_ssm.models.lgssm import (
LGSSMParameters,
LGSSMSampler,
... | 10,036 | 39.800813 | 107 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/lgssm_quick_start.py | import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
np.random.seed(12357)
###############################################################################
# Generate Synthetic Data
###############################################################################
from sgmcmc_ssm.models.lgssm import (
... | 7,617 | 33.008929 | 79 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/exchange_rate/exchange_rate_full_demo.py | import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
from sgmcmc_ssm.models.svm import SeqSVMSampler
from tqdm import tqdm
np.random.seed(12345)
####################################################... | 5,954 | 33.622093 | 79 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/exchange_rate/exchange_rate_subset_demo.py | import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
from sgmcmc_ssm.models.svm import SeqSVMSampler
from tqdm import tqdm
np.random.seed(12345)
####################################################... | 5,815 | 33.414201 | 79 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/exchange_rate/exchange_rate_single_demo.py | import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from pandas.plotting import register_matplotlib_converters
register_matplotlib_converters()
from sgmcmc_ssm.models.svm import SeqSVMSampler, SVMSampler
from tqdm import tqdm
np.random.seed(12345)
########################################... | 5,702 | 33.355422 | 79 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/exchange_rate/process_exchange_data.py | import pandas as pd
import numpy as np
import os
###############################################################################
# Process Raw Exchange Rate Data Pulled From Finam.RU
###############################################################################
path_to_raw_data = './data/EURUS_data.csv'
path_to_outpu... | 2,209 | 39.181818 | 122 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/synthetic/lgssm_demo.py | import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import joblib
import logging
import os
from tqdm import tqdm
from sgmcmc_ssm.models.lgssm import (
generate_lgssm_data,
LGSSMParameters,
LGSSMPrior,
LGSSMPreconditioner,
LGSSMHelper,
L... | 5,352 | 30.674556 | 83 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/synthetic/hmm_demo.py | import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import joblib
import logging
import os
from tqdm import tqdm
from sgmcmc_ssm.models.gauss_hmm import (
generate_gausshmm_data,
GaussHMMParameters,
GaussHMMPrior,
GaussHMMPreconditioner,
Gauss... | 6,538 | 33.597884 | 83 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/synthetic/slds_demo.py | import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import joblib
import logging
import os
from tqdm import tqdm
from sgmcmc_ssm.models.slds import (
generate_slds_data,
SLDSParameters,
SLDSPrior,
SLDSPreconditioner,
SLDSHelper,
SLDSSam... | 6,876 | 33.557789 | 105 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/ion_channel/ion_channel_subset_demo.py | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sgmcmc_ssm.models.gauss_hmm import GaussHMMSampler
from tqdm import tqdm
np.random.seed(12345)
# Load and Scale Data
from scipy.io import loadmat
ion_data = loadmat('data/alamethicin.mat')
from sklearn.preprocessing import RobustScaler
scal... | 4,577 | 31.013986 | 83 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/ion_channel/ion_channel_downsample_demo.py | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sgmcmc_ssm.models.gauss_hmm import GaussHMMSampler
from tqdm import tqdm
np.random.seed(12345)
# Load and Scale Data
from scipy.io import loadmat
ion_data = loadmat('data/alamethicin.mat')
from sklearn.preprocessing import RobustScaler
scal... | 4,961 | 31.860927 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/ion_channel/ion_channel_full_demo.py | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sgmcmc_ssm.models.gauss_hmm import GaussHMMSampler
from tqdm import tqdm
np.random.seed(12345)
# Load and Scale Data
from scipy.io import loadmat
ion_data = loadmat('data/alamethicin.mat')
from sklearn.preprocessing import RobustScaler
scal... | 4,127 | 32.024 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/hmm_long_demo.py | import numpy as np
from sgmcmc_ssm.models.gauss_hmm import (
generate_gausshmm_data,
GaussHMMParameters,
GaussHMMPrior,
GaussHMMPreconditioner,
GaussHMMHelper,
GaussHMMSampler,
)
np.random.seed(12345)
# Parameters
## Define Gaussian HMM Parameters
logit_pi = np.array([[... | 8,623 | 30.246377 | 101 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/slds_long_demo.py | import numpy as np
from sgmcmc_ssm.models.slds import (
generate_slds_data,
SLDSParameters,
SLDSPrior,
SLDSPreconditioner,
SLDSHelper,
SLDSSampler,
)
np.random.seed(12345)
# Parameters
## Define SLDS Parameters
alpha = 0.05
delta=np.pi
b = np.pi/2
pi = np.array([
... | 11,414 | 31.991329 | 107 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/arhmm_long_demo.py | import numpy as np
from sgmcmc_ssm.models.arphmm import (
generate_arphmm_data,
ARPHMMParameters,
ARPHMMPrior,
ARPHMMPreconditioner,
ARPHMMHelper,
ARPHMMSampler,
)
np.random.seed(12345)
# Parameters
## Define ARPHMM Parameters
logit_pi = np.array([[2, 0], [0, 2]])*2
D =... | 8,407 | 30.02583 | 101 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/lgssm_pf_demo.py | import numpy as np
from sgmcmc_ssm.models.lgssm import (
generate_lgssm_data,
LGSSMParameters,
LGSSMPrior,
LGSSMPreconditioner,
LGSSMHelper,
LGSSMSampler,
)
from tqdm import tqdm
np.random.seed(12345)
# Parameters
## Define LGSSM Parameters
A = np.eye(1)*0.95
C = np.eye... | 7,269 | 28.673469 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/garch_long_demo.py | import numpy as np
from sgmcmc_ssm.models.garch import (
generate_garch_data,
GARCHParameters,
GARCHPrior,
GARCHHelper,
GARCHSampler,
)
from tqdm import tqdm
np.random.seed(12345)
# Parameters
## Define GARCH Parameters
alpha = 0.1
beta = 0.8
gamma = 0.05
tau = 0.3
log_mu, lo... | 8,081 | 29.383459 | 82 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/svm_long_demo.py | import numpy as np
from sgmcmc_ssm.models.svm import (
generate_svm_data,
SVMParameters,
SVMPrior,
SVMHelper,
SVMSampler,
)
from tqdm import tqdm
np.random.seed(12345)
# Parameters
## Define SVM Parameters
A = np.eye(1)*0.95
Q = np.eye(1)*1.0
R = np.eye(1)*1.0
LQinv = np.lina... | 7,747 | 29.868526 | 103 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/demo/api_demos/lgssm_long_demo.py | import numpy as np
from sgmcmc_ssm.models.lgssm import (
generate_lgssm_data,
LGSSMParameters,
LGSSMPrior,
LGSSMPreconditioner,
LGSSMHelper,
LGSSMSampler,
)
np.random.seed(12345)
# Parameters
## Define LGSSM Parameters
A = np.eye(2)*0.9
Q = np.eye(2)*0.1
C = np.eye(2)
R... | 7,933 | 29.633205 | 101 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/driver_utils.py | import numpy as np
import pandas
import contextlib
import os
import joblib
import io
import time
from tqdm import tqdm
import logging # For Logs
logger = logging.getLogger(name=__name__)
def script_builder(
script_name,
python_script_path,
python_script_args,
path_to_shell_script,
... | 6,683 | 31.926108 | 146 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/trace_metric_functions.py | """
Metric Functions for full parameter traces
(e.g. Kernel Stein Divergence)
"""
import numpy as np
import pandas as pd
from tqdm import tqdm
from itertools import product
import logging
LOGGING_FORMAT = '%(levelname)s: %(asctime)s - %(name)s: %(message)s ...'
logging.basicConfig(
level = logging.INFO,
... | 3,870 | 31.805085 | 85 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/_utils.py | """
Utilities functions
"""
import numpy as np
import pandas as pd
import logging
import scipy
import scipy.linalg.lapack
from copy import deepcopy
logger = logging.getLogger(name=__name__)
# Random Categorical
def random_categorical(pvals, size=None):
out = np.random.multinomial(n=1, pvals=pvals, size=size).d... | 5,978 | 31.318919 | 138 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/plotting_utils.py | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import logging
logger = logging.getLogger(name=__name__)
def plot_metrics(evaluator, full_trace=True, burnin=None,
x='iteration'):
df = evaluator.get_metrics()
df['variable:metric'] = df['variable']+':'+df['me... | 7,187 | 38.065217 | 91 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/base_parameters.py | """
Base Parameters
"""
import numpy as np
from copy import deepcopy
# Param and ParamHelper Class
class BaseParameters(object):
""" Base Class for Parameters """
# List of ParamHelpers
_param_helper_list = []
# Set Attributes (must be copied in each subclass)
for param_helper in _param_helper_l... | 10,720 | 29.807471 | 80 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/evaluator.py | import numpy as np
import pandas as pd
import logging
import time
logger = logging.getLogger(name=__name__)
class BaseEvaluator(object):
""" Evaluator Base Class """
def __init__(self, sampler, metric_functions=None, sample_functions=None):
# Set Sampler
self.sampler = sampler
# Check ... | 28,263 | 36.735648 | 85 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/metric_functions.py | """
Sampler Metric Function Generators
"""
import numpy as np
def sample_function_parameter(parameter_name, return_variable_name=None):
""" Returns sample function that extracts a parameter from current state
Args:
parameter_name (string): atrribute in sampler.parameters
(e.g. A, C, LRin... | 17,322 | 36.577007 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/__init__.py | from .sgmcmc_sampler import SGMCMCSampler, SGMCMCHelper
from .evaluator import SamplerEvaluator
| 96 | 31.333333 | 55 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/sgmcmc_sampler.py | import numpy as np
import pandas as pd
import time
from datetime import timedelta
import logging
from .evaluator import BaseEvaluator
logger = logging.getLogger(name=__name__)
NOISE_NUGGET=1e-9
# SGMCMCSampler
class SGMCMCSampler(object):
""" Base Class for SGMCMC with Time Series """
def __init__(self, **kwa... | 82,434 | 39.789213 | 86 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/hmm_helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ..sgmcmc_sampler import SGMCMCHelper
from .._utils import random_categorical
class HMMHelper(SGMCMCHelper):
""" HMM Helper
forward_message (dict) with keys
prob_vector (ndarray) dimension num_states
l... | 22,130 | 37.894552 | 127 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/__init__.py | 0 | 0 | 0 | py | |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/arphmm/sampler.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import ARPHMMParameters, ARPHMMPrior, ARPHMMPreconditioner
from .helper import ARPHMMHelper
class ARPHMMSampler(SGMCMCSampler):
# Note d = m*p
def __init__... | 8,279 | 34.084746 | 103 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/arphmm/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ..hmm_helper import HMMHelper
from .parameters import stack_y
from ..._utils import random_categorical
class ARPHMMHelper(HMMHelper):
""" ARPHMM Helper
forward_message (dict) with keys
prob_vector (ndarray) dimen... | 13,187 | 38.8429 | 82 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/arphmm/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
TransitionMatrixParamHelper, TransitionMatrixPriorHelper,
TransitionMatrixPrecondHelper,
RectM... | 5,128 | 32.522876 | 88 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/arphmm/__init__.py | from .parameters import (
ARPHMMParameters,
ARPHMMPrior,
ARPHMMPreconditioner,
generate_arphmm_data,
stack_y,
)
from .helper import ARPHMMHelper
from .sampler import ARPHMMSampler, SeqARPHMMSampler
| 222 | 21.3 | 52 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/gauss_hmm/sampler.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import GaussHMMParameters, GaussHMMPrior, GaussHMMPreconditioner
from .helper import GaussHMMHelper
class GaussHMMSampler(SGMCMCSampler):
def __init__(self, nu... | 7,485 | 34.478673 | 100 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/gauss_hmm/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ..hmm_helper import HMMHelper
from ..._utils import random_categorical
class GaussHMMHelper(HMMHelper):
""" GaussHMM Helper
forward_message (dict) with keys
prob_vector (ndarray) dimension num_states
... | 8,999 | 37.961039 | 78 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/gauss_hmm/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
TransitionMatrixParamHelper, TransitionMatrixPriorHelper,
TransitionMatrixPrecondHelper,
Vecto... | 3,793 | 33.490909 | 94 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/gauss_hmm/__init__.py | from .parameters import (
GaussHMMParameters,
GaussHMMPrior,
GaussHMMPreconditioner,
generate_gausshmm_data,
)
from .helper import GaussHMMHelper
from .sampler import GaussHMMSampler, SeqGaussHMMSampler
| 223 | 23.888889 | 56 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/lgssm/kernels.py | import numpy as np
from scipy.special import expit, logsumexp
from ...particle_filters.kernels import LatentGaussianKernel
# LGSSMKernels:
# Prior Kernel
class LGSSMPriorKernel(LatentGaussianKernel):
""" Prior Kernel for LGSSM
K(x_{t+1} | x_t) = Pr(x_{t+1} | x_t, parameters)
"""
def rv(self, x_t, *... | 7,345 | 34.487923 | 82 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/lgssm/sampler.py | import numpy as np
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import LGSSMPrior, LGSSMPreconditioner
from .helper import LGSSMHelper
class LGSSMSampler(SGMCMCSampler):
def __init__(self, n, m, observations=None, prior=None, parameters=None,
forward_message=None, back... | 3,592 | 34.574257 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/lgssm/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCHelper
from .kernels import (
LGSSMPriorKernel,
LGSSMOptimalKernel,
LGSSMHighDimOptimalKernel,
)
from ...particle_filters.buffered_smoother import (
buffered_pf_wrappe... | 52,767 | 37.629575 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/lgssm/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
SquareMatrixParamHelper, SquareMatrixPriorHelper,
SquareMatrixPrecondHelper,
RectMatrixParamHe... | 4,433 | 32.590909 | 86 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/lgssm/__init__.py | from .parameters import (
LGSSMParameters,
LGSSMPrior,
LGSSMPreconditioner,
generate_lgssm_data,
)
from .helper import LGSSMHelper
from .kernels import (
LGSSMPriorKernel,
LGSSMOptimalKernel,
LGSSMHighDimOptimalKernel,
)
from .sampler import LGSSMSampler, ... | 337 | 21.533333 | 50 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/slds/sampler.py | import numpy as np
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import SLDSPrior, SLDSParameters, SLDSPreconditioner
from .helper import SLDSHelper
class SLDSSampler(SGMCMCSampler):
def __init__(self, num_states, n, m,
observations=None, prior=None, parameters=None,
... | 29,068 | 39.206086 | 86 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/slds/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCHelper
from ..._utils import random_categorical, lower_tri_mat_inv
class SLDSHelper(SGMCMCHelper):
""" LGSSM Helper
forward_message (dict) with keys
x (dict):
log_c... | 53,484 | 39.153904 | 103 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/slds/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
TransitionMatrixParamHelper, TransitionMatrixPriorHelper,
TransitionMatrixPrecondHelper,
Squar... | 5,953 | 34.023529 | 88 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/slds/__init__.py | from .parameters import (
SLDSParameters,
SLDSPrior,
SLDSPreconditioner,
generate_slds_data,
)
from .helper import SLDSHelper
from .sampler import SLDSSampler
| 179 | 19 | 32 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/garch/kernels.py | import numpy as np
from ...particle_filters.kernels import Kernel
# GARCH Kernel:
class GARCHPriorKernel(Kernel):
# n = 2, first dimension is x_t, second is sigma2_t
def sample_x0(self, prior_mean, prior_var, N, **kwargs):
""" Initialize x_t
Returns:
x_t (N by n ndarray)
""... | 5,770 | 30.535519 | 78 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/garch/sampler.py | import numpy as np
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import GARCHPrior, GARCHParameters
from .helper import GARCHHelper
class GARCHSampler(SGMCMCSampler):
def __init__(self, n=1, m=1, observations=None, prior=None, parameters=None,
forward_message=None, nam... | 2,499 | 30.25 | 80 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/garch/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCHelper
from .kernels import GARCHPriorKernel, GARCHOptimalKernel
from ...particle_filters.buffered_smoother import (
buffered_pf_wrapper,
average_statistic,
)
class GARCHHelper(SGMCM... | 15,844 | 35.425287 | 84 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/garch/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
CovarianceParamHelper, CovariancePriorHelper,
)
from ...variables.garch_var import (
GARCHPara... | 4,397 | 29.971831 | 74 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/garch/__init__.py | from .parameters import (
GARCHParameters,
GARCHPrior,
generate_garch_data,
)
from .helper import GARCHHelper
from .kernels import GARCHPriorKernel, GARCHOptimalKernel
from .sampler import GARCHSampler, SeqGARCHSampler
| 248 | 23.9 | 57 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/svm/kernels.py | import numpy as np
from ...particle_filters.kernels import LatentGaussianKernel
# SVM Kernels:
class SVMPriorKernel(LatentGaussianKernel):
def set_parameters(self, parameters):
self.parameters = parameters
if np.abs(parameters.A) > 1:
raise ValueError("Current AR parameter is |A| = {0} ... | 2,117 | 31.090909 | 76 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/svm/sampler.py | import numpy as np
from ...sgmcmc_sampler import SGMCMCSampler, SeqSGMCMCSampler
from .parameters import SVMPrior, SVMParameters
from .helper import SVMHelper
class SVMSampler(SGMCMCSampler):
def __init__(self, n, m, observations=None, prior=None, parameters=None,
forward_message=None, name="SVMSampler... | 2,745 | 32.487805 | 76 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/svm/helper.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...sgmcmc_sampler import SGMCMCHelper
from .kernels import SVMPriorKernel
from ...particle_filters.buffered_smoother import (
buffered_pf_wrapper,
average_statistic,
)
from ..lgssm.helper import gaussian_sufficient... | 14,913 | 36.472362 | 82 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/svm/parameters.py | import numpy as np
import logging
logger = logging.getLogger(name=__name__)
from ...base_parameters import (
BaseParameters, BasePrior, BasePreconditioner,
)
from ...variables import (
SquareMatrixParamHelper, SquareMatrixPriorHelper,
SquareMatrixPrecondHelper,
RectMatrixParamHe... | 4,148 | 29.065217 | 78 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/models/svm/__init__.py | from .parameters import (
SVMParameters,
SVMPrior,
generate_svm_data,
)
from .helper import SVMHelper
from .kernels import SVMPriorKernel
from .sampler import SVMSampler, SeqSVMSampler
| 214 | 20.5 | 46 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/variables/covariance.py | import numpy as np
import scipy.stats
import logging
from ..base_parameters import (
ParamHelper, PriorHelper, PrecondHelper,
get_value_func, get_hyperparam_func, get_dim_func,
set_value_func, set_hyperparam_func,
)
from .._utils import (
array_wishart_rvs,
pos_def_mat_in... | 28,228 | 39.384835 | 82 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/variables/matrices.py | import numpy as np
import scipy.stats
from ..base_parameters import (
ParamHelper, PriorHelper, PrecondHelper,
get_value_func, get_hyperparam_func, get_dim_func,
set_value_func, set_hyperparam_func,
)
from .._utils import (
normal_logpdf,
matrix_normal_logpdf,
pos... | 57,109 | 39.417551 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/variables/__init__.py | from .matrices import (
VectorParamHelper,
VectorPriorHelper,
VectorPrecondHelper,
VectorsParamHelper,
VectorsPriorHelper,
VectorsPrecondHelper,
SquareMatrixParamHelper,
SquareMatrixPriorHelper,
SquareMatrixPrecondHelper,
SquareMatricesPara... | 1,077 | 28.135135 | 38 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/variables/probweight.py | import numpy as np
import scipy.stats
from scipy.special import logit, expit, logsumexp
from ..base_parameters import (
ParamHelper, PriorHelper, PrecondHelper,
get_value_func, get_hyperparam_func, get_dim_func,
set_value_func, set_hyperparam_func,
)
import logging
logger = logging.getLo... | 21,332 | 39.099624 | 101 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/variables/garch_var.py | import numpy as np
import scipy.stats
from scipy.special import expit, logit
from ..base_parameters import (
ParamHelper, PriorHelper, PrecondHelper,
get_value_func, get_hyperparam_func, get_dim_func,
set_value_func, set_hyperparam_func,
)
from .._utils import (
normal_logpdf,
... | 6,592 | 33.518325 | 81 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/particle_filters/custom_kernels.py | """
Advanced Kernels for particle filters
"""
from .kernels import *
from scipy.optimize import root_scalar
from scipy.special import logsumexp, roots_hermitenorm
class SVMLaplaceKernel(LatentGaussianKernel):
def __init__(self, **kwargs):
self.approx_param=dict(mean=0, var=1)
super().__init__(**kw... | 14,606 | 36.841969 | 103 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/particle_filters/kernels.py | """
Kernels for particle filters
"""
import numpy as np
from scipy.special import expit, logsumexp
# Kernel
class Kernel(object):
def __init__(self, **kwargs):
self.parameters = kwargs.get('parameters', None)
self.y_next = kwargs.get('y_next', None)
return
def set_parameters(self, par... | 4,159 | 27.888889 | 74 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/particle_filters/buffered_smoother.py | """
Wrapper Helper Class around PaRIS
"""
import numpy as np
import functools
from .pf import (
paris_smoother, nemeth_smoother, poyiadjis_smoother,
pf_filter,
log_normalize,
)
def pf_wrapper(
observations, parameters, N,
kernel, smoother,
additive_statistic_func... | 7,476 | 34.268868 | 80 | py |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/particle_filters/__init__.py | 0 | 0 | 0 | py | |
sgmcmc_ssm_code | sgmcmc_ssm_code-master/sgmcmc_ssm/particle_filters/pf.py | """
Bootstrap Particle Filter
"""
import numpy as np
import functools
def pf(particles, log_weights, kernel):
""" Algorithm 1 of PaRIS
{particles_t, weights_t} -> {particles_{t+1}, weights_{t+1}}
Args:
particles (ndarray): N by n, latent states (xi_t)
log_weights (ndarray): N, log importa... | 14,308 | 36.360313 | 121 | py |
Retrieving-Top-Weighted-Triangles-in-Graphs | Retrieving-Top-Weighted-Triangles-in-Graphs-master/src/print_table.py | import os
import numpy as np
files = [
'tags-stack-overflow',
'threads-stack-overflow',
'wikipedia',
'eth',
'aminer',
'temporal-reddit-reply',
'MAG',
'spotify'
]
datasets = [
'tags-stack-overflow',
'threads-stack-overflow',
'Wikipedia-clickstream',
'Ethereum',
'Aminer',
'reddit-reply',
... | 6,198 | 35.251462 | 107 | py |
Retrieving-Top-Weighted-Triangles-in-Graphs | Retrieving-Top-Weighted-Triangles-in-Graphs-master/src/plot_static_hl_tradeoff.py | import matplotlib.pyplot as plt
import numpy as np
def make_plot(thresholds, accs, times, k, dataset):
thresholds = [0] + thresholds
times = [0] + times
accs = [0] + accs
fig, ax = plt.subplots()
# plt.subplot(2, 1, 1)
plt.yticks(fontsize=18)
plt.xticks(fontsize=18)
for y in np.arange(0, 1, 0.2):
... | 2,327 | 32.73913 | 102 | py |
Retrieving-Top-Weighted-Triangles-in-Graphs | Retrieving-Top-Weighted-Triangles-in-Graphs-master/src/plot_edge_weights.py | import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
import numpy as np
import powerlaw
from scipy.stats import binned_statistic
def drop_zeros(a_list):
return [i for i in a_list if i>0]
# https://stackoverflow.com/questions/16489655/plotting-log-binned-network-degree-distributions
def log_bi... | 3,021 | 38.246753 | 155 | py |
Retrieving-Top-Weighted-Triangles-in-Graphs | Retrieving-Top-Weighted-Triangles-in-Graphs-master/src/print_parallel_edge_times.py | import argparse
import os
files = [
'tags-stack-overflow',
'threads-stack-overflow',
'wikipedia',
'eth',
'aminer',
'temporal-reddit-reply',
'MAG',
'spotify'
]
parser = argparse.ArgumentParser()
parser.add_argument('-k')
args = parser.parse_args()
for fname in files:
path = os.path.join('../output/c... | 1,123 | 25.139535 | 81 | py |
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