sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
87c8514ae146f8fa729ae3f6bba78a1f27227dca5e6d348e9c6f033b8a1e8864 | Python | 11,812 | 299 | #!/usr/bin/env python
# Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import os
from typing import IO, TYPE_CHECKING, Any
from onnx import AttributeProto, defs, load
from onnx.backend.test.case import collect_snippets
from onnx.backend.test.loader ... |
aa3e905fc8ada3b30d35beb5e3ae21d78aa5e6498b80a5b50928057218f9f810 | Python | 11,812 | 305 | """Support vector classifier using time series kernels..
Direct wrap of sklearn SVC with added functionality that allows time series kernel to be
passed, and uses the sktime time series classifier interface.
"""
__author__ = ["fkiraly"]
__all__ = ["TimeSeriesSVC"]
from inspect import signature
from sklearn.svm impo... |
bbfeaa4b36ab3abcdeb1126bf8ecda18d05b8444aba4119901bbe303437348c3 | Python | 11,827 | 278 | """Residual Network (ResNet) for classification in PyTorch."""
__authors__ = ["srupat"]
__all__ = ["ResNetClassifierTorch"]
from collections.abc import Callable
import numpy as np
from sktime.classification.deep_learning.base import BaseDeepClassifierPytorch
from sktime.networks.resnet import ResNetNetworkTorch
c... |
44b2f9c6549280523e6f63046358080a7dd0e54be91a969185caaf16d51b891c | Python | 11,828 | 338 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
26ce68dc2d45970d06d6e2b9ced5c2350d7bd0896a88f94bb70078eede46c2f5 | Python | 11,832 | 375 | from __future__ import annotations
import warnings
from collections import Counter
from copy import deepcopy
from typing import Optional, Tuple, Union
from pathlib import Path
import numpy as np
import pandas as pd
from libpysal.weights import KNN
from libpysal.weights import W as libpysal_W
from . import cluster, d... |
66ebed5b4ae06b579646c298f8b6dc6dd54eaceeff35129e80f348a807d048e9 | Python | 11,836 | 353 | # SPDX-License-Identifier: LGPL-3.0-or-later
from typing import (
Any,
overload,
)
import ml_dtypes
import numpy as np
import torch
import torch.nn.functional as F
from deepmd.dpmodel.common import PRECISION_DICT as NP_PRECISION_DICT
from deepmd.pt.utils import (
env,
)
from .env import (
DEVICE,
... |
60184281f6f41ad86b978b08a454f32ee025340b2a669c025873535667ed593d | Python | 11,840 | 332 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
205c2ec13a052cfaed26111a54566721d2c6363276e61642da20c74bab141cea | Python | 11,845 | 290 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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... |
41f6f8583fdf374460ce986b3d91e9f3d3d453e9c6f4e1368bb04b48eb148615 | Python | 11,845 | 378 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
class Split(Base):
@staticmethod
def export_1d_opset13() -> None:
... |
55ad7529a91f0872f4a89e4702908895a768506d6f740a35179e10a6c11a88ff | Python | 11,846 | 335 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
import onnx
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
from onnx.reference.ops.op_causal_conv_with_state import (
CausalConvWithS... |
d04b41112dbcca7059999c2e7a6e5e96884955a5f0653d41cbf6a06ce38fa553 | Python | 11,847 | 282 |
import os.path as osp
import torch
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Parameter
from torch_geometric.nn import MessagePassing
from torch_geometric.utils import remove_self_loops, add_self_loops #, softmax
from torch_scatter import scatter
from torch_geometric.nn.inits import... |
c12fc8fd0a58a7e857854c642da8821a007515e20387afa1b98abe3da283cf56 | Python | 11,854 | 279 | # Copyright [2020] Luis Alberto Pineda Cortés, Rafael Morales Gamboa.
#
# 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 ... |
84d02dc0ac1c6b666a8d8ea7f5c3909cb51ff72f5f58a9f0223d449ce6f476b4 | Python | 11,860 | 282 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
efb02bb3da14d4146bbe0e4cbfb3f9d7b34be88fb359dc245ba519fdc94d11e2 | Python | 11,860 | 351 | # Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... |
52ce5a87934779c1b9c79b669b122127c7ed3d5a01d27d1c038335a3f539644e | Python | 11,876 | 364 |
import numpy as np
import rdkit
import rdkit.Chem as Chem
import networkx as nx
from build_vocab import WordVocab
import pandas as pd
import os
import torch.nn as nn
from dataset import DTADataset,Pre_DTADataset
from model import *
from utils import *
from torch_geometric.loader import DataLoader
fr... |
77015fa448d752135837ecde96da361608360890c130517d9a29b32049774e8d | Python | 11,877 | 210 | """
@file: rise_mobile_v3.py
Created on 21.11.19
@project: CrazyAra
@author: queensgambit
Upgrade of RISE architecture using mixed depthwise convolutions, preactivation residuals and dropout
proposed by Johannes Czech
Influenced by the following papers:
* MixConv: Mixed Depthwise Convolutional Kernels, Mingxing ... |
bb4abbafdf0afc7e9f0ccebd955e3cb13b71ca5b92fbe7cfc0d486b9fd8b0ca8 | Python | 11,889 | 312 | # Copyright (c) OpenMMLab. All rights reserved.
import numpy as np
import torch.nn as nn
from mmcv.cnn import build_conv_layer, build_norm_layer
from ..builder import BACKBONES
from .resnet import ResNet
from .resnext import Bottleneck
@BACKBONES.register_module()
class RegNet(ResNet):
"""RegNet backbone.
M... |
ee0b744a5f4bb4807cc124f81862fc1803548c88161d8f4a74ffb8955b14f141 | Python | 11,889 | 315 | #-------------------------------------------------------------------------------
# elftools: dwarf/compileunit.py
#
# DWARF compile unit
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
from __future__ import annota... |
d5baeaa0bf5dec826949b88f11bdc44a423f2e75d235bc07116767aaa6aa1fad | Python | 11,906 | 320 | import logging
import numpy as np
from ray.rllib.models.modelv2 import ModelV2
from ray.rllib.models.tf.tf_modelv2 import TFModelV2
from ray.rllib.models.tf.misc import normc_initializer, get_activation_fn
from ray.rllib.models.catalog import ModelCatalog
from ray.rllib.policy.rnn_sequencing import add_time_dimension
... |
990507c209773ecdb90e6cac972e40267328842adb0010e59a2c613d88d7291a | Python | 11,910 | 314 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Compact canonical graph contract for compressed CUDA deployment."""
from __future__ import (
annotations,
)
from dataclasses import (
dataclass,
)
from typing import (
TYPE_CHECKING,
)
import torch
if TYPE_CHECKING:
from deepmd.dpmodel.utils.neighbor_g... |
2579cf95e121fbcdc1d110681ab5505deb8e3cb7e7d6790ccba82b181a11ffb6 | Python | 11,915 | 254 | from mprl.utility_services.real_time_payoff_tracker.protobuf.real_time_payoff_tracker_pb2 import PayoffTableKey, PolicyInfo, LivePolicyInfo, Confirmation, EvalMatchupResult
from mprl.utility_services.real_time_payoff_tracker.protobuf.real_time_payoff_tracker_pb2_grpc import RealTimePayoffTrackerServicer, \
add_Real... |
a68faafe5bcb2f5c97748a9f286214588fe4a2570f2063bd1ada7545a868c162 | Python | 11,918 | 309 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
c0666c6e11a07809cd92e091aa7bdd9f5d9e2856d407fb947ca96ff9b9f3d1ba | Python | 11,924 | 273 | #!/usr/bin/env python3
#!/usr/bin/env pypy3
import os
import sys
import gzip
from io import BytesIO
from pathlib import Path
from lxml import etree
import rdflib
import requests
from pyontutils.core import makeGraph, yield_recursive, qname, build
from pyontutils.core import Ont, Source, OntGraph, OntResIri
from pyontut... |
759e3e8352efe67b2a97c400f86c732597957f9cded945d660357a83e8b59164 | Python | 11,929 | 310 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
f9777b2b52640915d2d3990b630b7f44b90c826c2c649ee821dc5af8b98f135a | Python | 11,929 | 368 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
346dcd2924e35be40fe6f121c91e71640bc1ef7df43259d7f0bba5d1cd588a96 | Python | 11,932 | 352 | """Time Convolutional Neural Network (CNN) for classification."""
__all__ = [
"TapNetClassifier",
]
from copy import deepcopy
from sklearn.utils import check_random_state
from sktime.classification.deep_learning.base import BaseDeepClassifier
from sktime.networks.tapnet import TapNetNetwork
class TapNetClassi... |
8efcef36a24fd57651702c92d6cda5020d74c7763c4f3bce71278a2d88bdb75e | Python | 11,932 | 339 | """Tests that exercise heavy functions using real pipeline outputs.
The fixtures used here live in `tests/test_odp_basic/odp/` and
`tests/testdb/`, products of prior smoke-test runs. The .D.FET.rbh
files carry the full column set (FET, D, ix, breakchrom, break_ix) that
the plotting + statistics functions expect; the .... |
6e2bed84b4607daa3604365b6ff1e9b621be968c0c7396a220c32207bf1fee15 | Python | 11,938 | 423 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jun 21 15:25:48 2021
Plotting examples showing double-update (Fig 1D, 2A)
@author: robert.mok
"""
import os
import sys
import numpy as np
import torch
from scipy.stats import multivariate_normal
import matplotlib.pyplot as plt
import imageio
sys.path... |
a19ba20f553f7d424c712acf744e086d85506af0a0bcc6f573fec53ab7ec6d90 | Python | 11,948 | 335 | import xml.etree.ElementTree as ET
from akkadian.data import from_key_to_line_number, from_key_to_text_and_line_numbers
def parse_word(sentence, word):
"""
Add all parts of word to sentence (include punctuation marks as well for example)
:param sentence: sentence of words being built as we proceed
:pa... |
8581e09546b462ada16356b2c0bb07a6604c9a1b0e4ee02bdc8c96e771939357 | Python | 11,950 | 385 | """ClaSP (Classification Score Profile) Segmentation.
Notes
-----
As described in
@inproceedings{clasp2021,
title={ClaSP - Time Series Segmentation},
author={Sch"afer, Patrick and Ermshaus, Arik and Leser, Ulf},
booktitle={CIKM},
year={2021}
}
"""
from sktime.detection.base import BaseDetector
__author__ = [... |
023f51871d92eb4bdda7b98f0e5f07cf00fca7f44652632c132be92cb798f424 | Python | 11,954 | 203 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Sep 13 17:05:41 2019
@author: wanglab
"""
path_to_lighsheet_folder = '/home/kellyms/wang/seagravesk/toms_lightsheet_software_20190104/lightsheet'
import os, sys, shutil, numpy as np, pandas as pd
import datetime
from collections import Counter
sys.pa... |
a45a7b42b05b233655a98f5fceff10543801db2fb045078248bdf827517b6663 | Python | 11,957 | 319 | from akkadian.data import increment_count, compute_vocab_count, compute_accuracy
from akkadian.build_data import preprocess
TEST_DATA_SIZE_FOR_LAMBDAS = 3
def hmm_preprocess(train_sents):
"""
train the HMM model
:param train_sents: train sentences for the model
:return: counts of unigrams, bigrams and... |
e830a6f79c159a0a2c195ed094db83f9ed293476af3edb98f4545ee089205aac | Python | 11,966 | 466 | """ Light weight functions for generating html
and working with the rest of the unholy trinity. """
__version__ = '0.0.4'
# chars
nbsp = '\xA0'
# html
def tag(_tag, n=False):
nl = '\n' if n else ''
s = f'<{_tag}{{extra}}>{nl}'
e = f'{nl}</{_tag}>'
def tagwrap(*value, **kwargs):
if 'class_' ... |
5b10c4cc9fe15694d4d6f71ae1c72cba66f87de0a6c75b3e6564dcee7c9e2619 | Python | 11,967 | 317 | # Copyright 2020 by Gongfan Fang, Zhejiang University.
# All rights reserved.
import torch
import torch.nn.functional as F
def _fspecial_gauss_1d(size, sigma):
r"""Create 1-D gauss kernel
Args:
size (int): the size of gauss kernel
sigma (float): sigma of normal distribution
... |
8fa274831e9b7bf6446b442159679b0e4542e7cf339e580961f9fcb659ca434a | Python | 11,967 | 336 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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... |
12860e9c7351c0e2f1c4aa616f802514175d6925c0df81bfff775f787dacda55 | Python | 11,972 | 300 |
# Copyright 2019-2026 The AmpliGraph Authors. All Rights Reserved.
#
# This file is Licensed under the Apache License, Version 2.0.
# A copy of the Licence is available in LICENCE, or at:
#
# http://www.apache.org/licenses/LICENSE-2.0
#
"""
Train KGE model on benchmark datasets:
Usage:
predictive_performance.py ... |
97cf821abf74c61c29d056a7b27ca38d26162a5cd6f34bc7d4b4ef4751d59d96 | Python | 11,973 | 323 | #!/usr/bin/env python3
# SPDX-License-Identifier: LGPL-3.0-or-later
"""Generate the DPA4C long-range .pt2 test models and reference values.
A latent-charge long-range module sums over every pair of atoms of a complete
non-periodic system, and over the images of the cell of a periodic one when
it serves periodic system... |
0a8eb40e3ee9e90d3d0c80a1d48d2a419ea0a96e5fc1df8ec78aea0166141ac9 | Python | 11,982 | 290 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
4886620b4f145bfc510e000bc112a6cbfc9530c8bc796a2efc5562cb622f3ec3 | Python | 11,988 | 378 | # Copyright [2020] Luis Alberto Pineda Cortés, Gibrán Fuentes Pineda,
# Rafael Morales Gamboa.
#
# 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.... |
bac2094405edf5f9887280ba0780d03ca8ab6feb5da5cefcdad2b1994919d58d | Python | 11,990 | 316 | """Time Series Forest (TSF) Classifier.
Interval based TSF classifier, extracts basic summary features from random intervals.
"""
__author__ = ["kkoziara", "luiszugasti", "kanand77"]
__all__ = ["TimeSeriesForestClassifier"]
import numpy as np
import pandas as pd
from sklearn.tree import DecisionTreeClassifier
from... |
7755994272c7e54d73bd4d01eccacb7afd4cd79de7520abeeb6c0e1f9fce1fe5 | Python | 11,992 | 335 | import xml.etree.ElementTree as ET
from akkadian.data import from_key_to_line_number, from_key_to_text_and_line_numbers
def parse_word(sentence, word):
"""
Add all parts of word to sentence (include punctuation marks as well for example)
:param sentence: sentence of words being built as we proceed
:pa... |
9b3a13641f2b4f8593e2b1f8bee66c6bf4152bba9e579388674272dc8eff6ea6 | Python | 11,996 | 373 | import unittest
from unittest.mock import patch, MagicMock
from siibra.volumes.parcellationmap import (
Map, space, parcellation, MapType, MapIndex
)
from siibra.exceptions import (
ExcessiveArgumentException, ConflictingArgumentException,
NonUniqueIndexError, NoVolumeFound
)
from siibra.commons import Spec... |
869a07d48748ad4aab86d12d5988480953cc76a404c55a3b438f9c4354280c63 | Python | 12,000 | 349 | import json
import tempfile
import numpy as np
import copy
import time
import torch
import torch._six
from pycocotools.cocoeval import COCOeval
from pycocotools.coco import COCO
import pycocotools.mask as mask_util
from collections import defaultdict
import utils
class CocoEvaluator(object):
def __init__(self... |
eb550018ecbf51ebe81bfa94dac276c62dba81ceb019922acc79cabe49ffbd21 | Python | 12,006 | 345 | # Helper functions for plotting ASR results,
# adapted from the Topiary library
# See https://topiary-asr.readthedocs.io/en/latest/topiary.draw.html
import topiary
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import numpy as np
from matplotlib import pyplot as plt
import matplotlib.patches a... |
6239f230b7dcba742122769877cc34301cfd83cceaedc5b6f01a410101e56968 | Python | 12,012 | 244 | # -*- coding: utf-8 -*-
"""
Code used for binary discrimination and discrimination in clutter results.
As with all other ***_runSFA code meant to be used with a batch wrapper module
that feeds in the vocalizations to compare.
@author: ronwd
"""
import numpy as np
import soundfile as sf
import pyfilterbank.gammatone... |
e70d25d66244284df1d7e88776370de6d2f2db45aa92b1dcbcd01a6d481e1e9e | Python | 12,016 | 317 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
ff9c814246948544466069268f435f144866b865ff0589ec039905eabc98609f | Python | 12,036 | 354 | # -*- coding: utf-8 -*-
"""! @file calibrate.py
@brief Script to do calibration of visual stimulus monitors.
@author Perry Hargrave, Jay Borseth, Derric Williams
@copyright Allen Institute for Brain Science
This works to adjust gamma and luminance so the response of the monitor is
roughly a straight line ... |
43b0643763a01542b50532caa089dd8191af0d13f5cdc03dc92e2c50a596d982 | Python | 12,046 | 328 | """AxialTAD — Wilcoxon rank-sum post-hoc filter for trained models.
The filter (window_size=8, p<0.05) operates on:
- dense Hi-C matrix (KR-balanced .txt)
- per-bin model predictions (binary 0/1)
It (a) standardises the matrix per anti-diagonal, (b) finds "gap regions" via
zero-row windows, (c) on each non-gap pr... |
569de872ea0a9785ab258372ad421f9451a0694b2d54a72000d95e82669d9ef2 | Python | 12,058 | 450 | DATASET_TAGS = {
"m1_yearly_dataset": {
"n_instances": 181,
"n_panels": 1,
"n_hierarchy_levels": 0,
"is_univariate": True,
"is_one_series": False,
"n_splits": 0,
},
"m1_quarterly_dataset": {
"n_instances": 203,
"n_panels": 1,
"n_hierarc... |
eda9ef5836413b6fc18516a5980284a96e63fc7c62422793709c894a023fdafc | Python | 12,066 | 328 | import torch
import math
import numpy as np
from models.se3transformer_layers.from_se3cnn.SO3 import irr_repr, torch_default_dtype
from models.se3transformer_layers.from_se3cnn.cache_file import cached_dirpklgz
from models.se3transformer_layers.from_se3cnn.representations import SphericalHarmonics
####################... |
152f65d817f27d05ea514f0257c0b93b1e0778f179e0d0b21b7a171bfd13ffa4 | Python | 12,069 | 342 | import matplotlib.pyplot as plt
import mmcv
import numpy as np
from matplotlib.backend_bases import CloseEvent
# A small value
EPS = 1e-2
def color_val_matplotlib(color):
"""Convert various input in BGR order to normalized RGB matplotlib color
tuples,
Args:
color (:obj:`mmcv.Color`/str/tuple/int... |
2dcb843eb921f61868e93dcb617ff2870ccc5e420361d189d990f046e00d5021 | Python | 12,072 | 306 | from __future__ import annotations
import math
from typing import Any
from typing import TYPE_CHECKING
import numpy as np
from optuna.distributions import CategoricalDistribution
from optuna.distributions import FloatDistribution
from optuna.distributions import IntDistribution
if TYPE_CHECKING:
from optuna.di... |
c026fea090e98f33f670d20f63e34f1b6349f68ab3f37db78192bb3199ad0e13 | Python | 12,072 | 315 | """
CTULIP: Canine TUmor CLassIfication Predictor
This tool predicts the primary tumor type (17 or 32 types) based on RNA-seq Canine data.
This tool takes expression data of 14,761 genes, that is common to Canine-to-Human 1 to 1 mapped and Human protein coding genes
Authors: Satish RG, Sara Jones
"""
from __future__... |
da9c17fcabdef32b496aa4677a12fe87967cc385a8a9d2914617f74940e5f4c0 | Python | 12,076 | 302 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Fri Dec 23 14:11:22 2016
@author: tpisano
"""
import numpy as np, SimpleITK as sitk, sys
import tifffile
import itertools
import matplotlib.pyplot as plt
####################################################################################################
... |
89086adf42de32053806917e0027850b0457fad26184371f76236c941ae90d5c | Python | 12,080 | 299 | import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
import gensim
from gensim.models import Word2Vec
import os
import pickle
def save_model_here(model_name, model_object, object_name):
directory = './models/' + model_name
if not os.path.isdir(directory):
os.make... |
8b9dbe8badd668d3867bb3c85b41b5ace71794a3f5bac2846497c55f069af18a | Python | 12,081 | 295 | import logging
import pickle
import re
import shutil
import sqlite3
from pathlib import Path
from typing import Union
import numpy as np
import torch
from tqdm import tqdm
import flair
from flair.embeddings import WordEmbeddings
# this is the default init size of a lmdb database for embeddings
DEFAULT_MAP_SIZE = 100... |
66454a551a9a36a77a9109cf3b8976f94da278d567fe8c628321977e199508a0 | Python | 12,085 | 341 | #!/usr/bin/env python3
# CBDA validation and training set creation.
# This script defines multiple trainig sets for a CBDA project.
#
# Inputs:
# File name of original data file.
# The following assumptions are made about the contents of the file:
# It is a text file with standard Unix style e... |
fb90c9f930ff5f89a0d1624403073325c7c5de05383f454c509c1ea01684226c | Python | 12,094 | 371 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
108ea38fb71ba0b1b834816fe23272a7a5333cd9ddd2d9d7e98fb0c465d4d7e7 | Python | 12,095 | 309 | from flair.data import Label, Relation, Sentence, Span
def test_token_tags():
# example sentence
sentence = Sentence("I love Berlin")
# set 4 labels for 2 tokens ('love' is tagged twice)
sentence[1].add_label("pos", "verb")
sentence[1].add_label("sentiment", "positive")
sentence[2].add_label(... |
dac36ea5ceed6d18f1d581f1103a6bd392b8453ba689862bec8798144ae8a9aa | Python | 12,096 | 350 | # Copyright 2022 Diagnostic Image Analysis Group, Radboudumc, Nijmegen, The Netherlands
#
# 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... |
2c888b070cd0338f9cfb79f11082054db211cbf1b8c84e0782d1983b2b746bdc | Python | 12,100 | 277 | import os
import logging
import numpy as np
import scipy as sp
import scipy.spatial
import pandas as pd
import torch
from torch.utils.data import Dataset, DataLoader
from atom3d.datasets import LMDBDataset, extract_coordinates_as_numpy_arrays
from utils import batch_stack, drop_zeros
class CormorantDatasetMSP(Dataset... |
3128700c0d8f639d346350b2758a759b2ef14ca11918c1df9f88ffd16db0e8d7 | Python | 12,101 | 321 | """
Analysis tools for VarBayes algorithm results.
This module provides diagnostic and analysis capabilities for examining the results
of the VarBayes spatial transcriptomics algorithm.
The CellAnalyzer class provides methods for:
- Analyzing gene expression patterns within cells
- Examining spatial relations... |
5f97114070ea6bfd7eb3fdb9e5b1f33ad09aab8c5dfcdc1d791cde88b3f99a3e | Python | 12,102 | 306 | import os
from pathlib import Path
import statistics
from .bilstm import prepare1, prepare2, LstmTagger, PosDatasetReader
from akkadian.build_data import preprocess, break_into_sentences
from akkadian.hmm import hmm_train, hmm_viterbi, hmm_compute_accuracy
from akkadian.data import load_object_from_file, logits_to_tran... |
f2326ec4ba4f761658bae6dfa09d20ebd99718e8cf65535728d2d618180f55b7 | Python | 12,112 | 213 | """
@file: rise_mobile_v3.py
Created on 21.11.19
@project: CrazyAra
@author: queensgambit
Upgrade of RISE architecture using mixed depthwise convolutions, preactivation residuals and dropout
proposed by Johannes Czech
Influenced by the following papers:
* MixConv: Mixed Depthwise Convolutional Kernels, Mingxing ... |
ccda2bff44c36557ea72cad45bff2623df2f04112121021c991f0e45ad6b813e | Python | 12,113 | 346 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
65667a8e27e5621da6b3be38377a0d09547c8b306dd41e9f8d64259249996be0 | Python | 12,115 | 336 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
f9cd4cb1741d272bbf881a65db58b9b286774bc3ddab4025a3418812a78b86d0 | Python | 12,122 | 318 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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... |
7e24ae46ad2cd66d45a6d0797aec0aa3db3a84e0c7f41a98f5dd7c251302f4f4 | Python | 12,140 | 302 | """Multi-scale Attention Convolutional Neural Network (MACNN) Classifier in PyTorch."""
__authors__ = ["Faakhir30"]
__all__ = ["MACNNClassifierTorch"]
from collections.abc import Callable
import numpy as np
from sktime.classification.deep_learning.base import BaseDeepClassifierPytorch
from sktime.networks.macnn imp... |
4260a1e2d3aafbc4ac62cbd70dfadd38b35a24e226cf5fd4f9dc27cfcc10446b | Python | 12,141 | 307 | """Operations to perform comparisons between two different molecule systems."""
import numpy as np
from scipy.spatial.distance import cdist
from scipy.optimize import linear_sum_assignment
from scipy.linalg import svd
def molecule_compare(mol1, mol2, options='vacuum',
excluded=False, threshold=0.... |
60671a486e14956e225699d9723c125e5e5355b8dae362064b96c927eb5fb147 | Python | 12,148 | 360 | """
@file: input_representation.py
Created on 26.05.21
@project: CrazyAra
@author: queensgambit
Input representation for chess v2.8.
This presentation avoids potential overfitting and bias, e.g. no color information, no move counter, no progress counter
and adds features which are hard for the CNN to extract, e.g. mat... |
1efe743816affa49321acc6e268fb7148092f7db2557cba745a175cf22c6f22b | Python | 12,152 | 360 | """
@file: input_representation.py
Created on 26.05.21
@project: CrazyAra
@author: queensgambit
Input representation for chess v2.8.
This presentation avoids potential overfitting and bias, e.g. no color information, no move counter, no progress counter
and adds features which are hard for the CNN to extract, e.g. mat... |
31fbd413ad37a2071e3c79a5fc948f0b3687679c79e7280adeb4bb85ea7cde2f | Python | 12,155 | 304 | # coding=utf-8
# Copyright (C) 2021. Huawei Technologies Co., Ltd. All rights reserved.
#
# 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
#
# ... |
6ac8520195c7db4652c9ff63ee26ece22f8b35ec2ba0c0d7f91aed0017ba523a | Python | 12,155 | 238 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 26 10:35:25 2017
@author: tpisano
see: tools.conv_net.mem_map for example usage
"""
from tools.utils.io import chunkit
import multiprocessing as mp
import pandas as pd
import numpy as np
from math import sqrt
import sys, os, cv2, gc, time
clas... |
67b226023c584dc5a8535d8f8d35d95b32010dffeec13ab71fa36ad2db33a161 | Python | 12,160 | 364 | import numpy as np
import torch
from typing import Union, Iterable
def p4_polar_from_p4_cartesian_massless(
p4: Union[np.ndarray, torch.Tensor]
) -> Union[np.ndarray, torch.Tensor]:
"""
Transform 4-momenta from Cartesian coordinates to polar coordinates for massless particle features.
Args:
p... |
359dcb608a7a05703d88e2686abca6f532c35a006aa7e0f48fb8edc14b654d75 | Python | 12,163 | 412 | """Utilities for loading datasets."""
__author__ = [
"ericjb",
]
__all__ = [
"load_fpp3",
"_load_fpp3",
]
import os
import shutil
import tarfile
import tempfile
import warnings
import pandas as pd
# import zipfile
# from urllib.error import HTTPError, URLError
# from warnings import warn
# from sktim... |
a3f57a335fc7df61889f31b1f1f6065e0ed098f13c640236cbdb95cf11e5947d | Python | 12,164 | 289 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from sparemax import Sparsemax
def init_weights_lstm(m):
"""权重初始化"""
classname = m.__class__.__name__
if classname.find('Conv2d') != -1 or classname.find('ConvTranspose2d') != -1:
... |
4b5cca63c0ed40eb5d81270dd24091cd9f53c942475412f6c6712f396ff0aedb | Python | 12,170 | 427 | """This module implements gammatone filters and a filtering routine.
A filterbank is coming soon [Hohmann2002]_.
.. plot::
import gammatone
gammatone.example()
TODO:
- Tests,
- nice introduction with example,
- implementing the filterbank class
References
----------
.. [Hohmann2002]
Hohman... |
e54fc0ad00c9e4a459a692bc41d97c724f9a7fc1fd8d5b831d39dbeab5edd3b3 | Python | 12,185 | 357 | """Tests for the grid search engine shared by the classification and regression tuners.
The engine is tested directly here, the tuner classes in their own test modules.
"""
__author__ = ["yash-sangwan"]
import numpy as np
import pytest
from sklearn.metrics import accuracy_score, log_loss, mean_squared_error, r2_scor... |
dea37225a1ed20e752703af73798aac820862b39306c12f745c31344cddc6e5c | Python | 12,190 | 315 | # Copyright 2019 DeepMind Technologies Ltd. All rights reserved.
#
# 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... |
9e12cc6083a533025b0d1259b1b481727e2a5812186106418d1bfc127048a266 | Python | 12,195 | 384 | #!/usr/bin/env python3
'''
Functions used for loading and finding files for brain analysis.
Authors: Sydney C. Weiser
Date: 2017-07-28
'''
import os
import re
import sys
import time
from subprocess import call
import yaml
from typing import List
def find_files(folder_path: str,
match_string: str,
... |
5d4be6404e60db8b1722df4b532b6175932e76a9897dc8efc4c283b48d8f365d | Python | 12,201 | 326 | """Compute shape features for individual cycles."""
import numpy as np
import pandas as pd
from neurodsp.timefrequency import amp_by_time
from bycycle.utils import rename_extrema_df, check_param_range
from bycycle.features.cyclepoints import compute_cyclepoints
######################################################... |
5f3314bbce4166e9326b61bdf7798991e0afa783cabd6fdca66cc5a208349b00 | Python | 12,203 | 333 | import cv2
import numpy as np
import os
import pandas as pd
import matplotlib.pyplot as plt
# Replace with the path to your video file
video_path_directory = '/Volumes/BET lab/BET Lab/Science/BET lab in Sheffield/Projects/Active Decison-making/pythonProject/Videos/'
output_dir = '/Volumes/BET lab/BET Lab/Science/BET ... |
e62539c395c9f6209b094e2169bda453b08ebf5e765f26b475c897acce6ccabe | Python | 12,203 | 308 | from typing import Union, List, Dict, Tuple
import numpy as np
import pandas as pd
import scanpy as sc
from anndata import AnnData
import warnings
from . import config
def _validate_obsm_key(ad, key, as_df=True):
"""
Validates and retrieves the data associated with a specified key from the provided AnnData o... |
db9f41212fd63c091a1e2df22ac20a437da9109a68471d3eda021e3efda1f2ac | Python | 12,211 | 333 | # code copied from https://github.com/torchmd/torchmd-net/blob/main/torchmdnet/models/utils.py
import math
from typing import Optional
import torch
from torch import nn
import torch.nn.functional as F
from torch_geometric.nn import MessagePassing
from torch_cluster import radius_graph
import warnings
def visualize_b... |
98a1a93f732b0276e147c5199a036ab7a35ed4c2c17ce348bf60930a1349054b | Python | 12,221 | 309 | from __future__ import annotations
from copy import copy
from typing import Callable
import numpy as np
from .dataset import JetDataset
from .normalisations import NormaliseABC
from .utils import (
checkConvertElements,
checkDownloadZenodoDataset,
checkListNotEmpty,
checkStrToList,
getOrderedFeat... |
005d80d4ceba6654a232da5477d64b470c6cfb00858ccbba4338eb241e416d1e | Python | 12,226 | 380 | # Copyright 2023 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
904270c68770fe61cb37e4487659ff1771302e7f40788f85498711fa2b3336cd | Python | 12,231 | 339 | # Copyright (c) OpenMMLab. All rights reserved.
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as cp
from mmcv.cnn import build_conv_layer, build_norm_layer
from ..builder import BACKBONES
from .resnet import Bottleneck as _Bottleneck
from .resnet import ResLayer, ResN... |
d5106c929e67251ee9e3362ab2ca49d8809424bd1958e3c976f5e1391b3740e3 | Python | 12,237 | 332 | # -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: real_time_payoff_tracker.proto
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflection
from google.protobuf import symbol_data... |
ad6bc96bc2102c935a982a4a1cbfda0da41f7afd1361cce0c387ecc0fae0a1c6 | Python | 12,239 | 363 | """
@file: util.py
Created on 09.06.18
@project: DeepCrazyhouse
@author: queensgambit
Utility functions which are use by the converter scripts
"""
import copy
import numpy as np
from DeepCrazyhouse.src.domain.variants.constants import (
LABELS_XIANGQI,
CHANNEL_MAPPING_CONST,
CHANNEL_MAPPING_POS,
MAX_N... |
a5ed3741c741ad65bfed0d3189ca4fda46b7116bb12ce04287f1a5e0dd12941f | Python | 12,242 | 334 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import pytest
from shape_inference_test_utils import TestShapeInferenceHelper
import onnx.parser
from onnx import TensorProto
from onnx.helper import make_node, make_tensor, make_tensor_value_info
cl... |
e93c468e9b7c374262e7bdf605e66055171670d505555ee452cfd591d09eadc1 | Python | 12,248 | 346 | # Copyright 2019 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
fe8a93bd82f3dd9423e3c7ab37bc66f5b4a8f6e94876e6bea15308c3035ccdf3 | Python | 12,253 | 340 | import numpy as np
import pandas as pd
import argparse
import os
import re
import pickle
from rdkit import Chem
from tqdm import tqdm
parser = argparse.ArgumentParser()
parser.add_argument('--dataset',
type=str,
default='USPTO50K',
help='dataset: USPTO50K or... |
cda65a1b36d90c11682f83b132dbe07c20ece0b3145d50d45d9970e6eeb2db9d | Python | 12,277 | 250 | """
@file: rl_loop.py
Created on 12.10.19
@project: crazy_ara
@author: queensgambit
Main reinforcement learning for generating games and train the neural network.
"""
import os
import sys
import logging
import argparse
from rtpt import RTPT
import dataclasses
from multiprocessing import Process, Queue
assert os.getc... |
732bfed9a3b8d454bd6eeba570f5e72322baad97c870d9300c4c9f9768071d6c | Python | 12,282 | 296 | from __future__ import annotations
import itertools
from numbers import Real
from typing import Any
from typing import TYPE_CHECKING
from typing import Union
import numpy as np
from optuna._warnings import optuna_warn
from optuna.logging import get_logger
from optuna.samplers import BaseSampler
from optuna.samplers.... |
60dd9cd90fc121f516718ebb0f1f008ef448c0e774e2891abe45a0a0754a00f1 | Python | 12,298 | 302 | import logging
import random
import typing
from pathlib import Path
from typing import Any, Optional, Union
import torch
import flair.nn
from flair.data import DT, Corpus, Sentence
from flair.file_utils import cached_path
from flair.nn import Classifier
from flair.training_utils import Result
log = logging.getLogger... |
f5c0edead6b8d1c56d1876cb1d0eadb743022fbf3ab7e69abffe64710aedfd7b | Python | 12,306 | 277 | ##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
## Created by: Yaoyao Liu
## Tianjin University
## liuyaoyao@tju.edu.cn
## Copyright (c) 2019
##
## This source code is licensed under the MIT-style license found in the
## LICENSE file in the root directory of this source tree
##++++++++++++++... |
f45b8091fa450fded5a45942169f03a74b105fbbfa438be7cfbaf632e2d25672 | Python | 12,325 | 326 | from typing import Callable, Iterable, List, Union
import warnings
import torch
import torch.nn as nn
import torch.nn.functional as F
import logging
from utils.const import DEFAULT_DEVICE, DEFAULT_DTYPE, EPS
class GraphNet(nn.Module):
def __init__(
self,
num_nodes: int,
input_node_size: i... |
688b38d41cd80bb0e5573e32af094a23e9cf0c9e6e7d902721ae0d8582ea0fd0 | Python | 12,337 | 324 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
5aebff3402fd85e23bfe2a2cb6cbb1562cc4295ca53688d3510b505a2c4c7731 | Python | 12,349 | 238 | import pandas as pd
import os
import glob
def load_choice_decoding_results(files_folder_path='/Users/timothysit/Dropbox/msi-key-data/active-m2-choice-init-decoding/decodeChoiceThreshDir/'):
"""
Load choice decoding results used in the main figure for Coen 2022
INPUT
--------
files_folder_path : (s... |
7cf91d3e087d7b0fa76dffcfeb2e90ad2cb181c8821fc277ff04d3b9d3b97fa6 | Python | 12,349 | 346 | # Copyright 2026 DeepMind Technologies Limited
#
# 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 applicable law or agr... |
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