sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
53ad083b48a3ce35493048e6eb720b5fb8cf7ebe14615ffd92ebbe5b2a7243ee | Python | 3,662 | 128 | import os
import imageio
import numpy as np
from .event2frame import EventSlicer
from .event2frame import rectify_events, cumulate_spikes_into_frames
import h5py
from tqdm import tqdm
def generate_files(root: str, sequence: str, num_frames_per_ts: int = 1):
flow_path = os.path.join(root, 'train', sequence, ... |
8cbe159bb5148c29b210ee8976f7fded894fc203f58f3c8bde3ca90d46411345 | Python | 3,663 | 112 | # 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... |
0160e30201decf02b2a5a583efd405d7c2f4e0b2d3c479e2438789a1ac922868 | Python | 3,665 | 109 | # coding=utf-8
# Copyright (C) 2022. 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
#
# ... |
3a987e6d239d015f99671d811d9b4af95152139ad114e1ec72eee80909357b6f | Python | 3,666 | 97 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
7860bfa8bdcb06131f0403342a1382782307d922a685d111b9105dd9ec401668 | Python | 3,666 | 100 | #!/usr/bin/env python3
'''
Created on Aug 9, 2017
@author: arnon
The MIT License (MIT)
Copyright (c) 2015 Acrisel
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including w... |
17c32e7b83b4eb4b8d85eee94b85249847e16ca27344ca3d551ad42fc1d55894 | Python | 3,668 | 101 |
import copy
import torch
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import grad
from torch.optim import Optimizer
import sys
import glob
import os
import numpy as np
from CloMu import *
#Prediction of causal relations on Simulation I-a
for R in r... |
1fcf2c107ebaee7ca8206b2229ec7923e48bdf61e6a559e2b1137ef0bec4f634 | Python | 3,668 | 98 | # Copyright (C) 2022-2025 Shijiazhuang Xianyu Digital Biotechnology Co., Ltd
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any la... |
39c12fa76ac02df24f3656e03657702f98f58a1108eb5998d1731ab35a76600e | Python | 3,668 | 100 | # 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... |
0cc7c3cc5f8e351297a9924376369f70a1fb3c1ce6e70d3a04d83ab915492f25 | Python | 3,669 | 102 | import os
import subprocess
import glob
import dxpy
import dx_utils
BIONANO_ROOT = '/Solve3.2.1_04122018/'
SCRIPTS_DIR = os.path.join(BIONANO_ROOT, 'PIPELINE', 'Pipeline')
HYBRID_DIR = os.path.join(BIONANO_ROOT, 'HybridScaffold', '04122018')
TOOLS_DIR = os.path.join(BIONANO_ROOT, 'RefAligner', '7437.7523rel')
os.env... |
ce539c410580e3d5c98806341b7c9b98584502a3ad6fa314b05745397ff96a8e | Python | 3,672 | 95 | """
This script generates figure S6d from the paper :
This is the decoding accuracy after movement onset
Internal notes:
"""
import pandas as pd
import pickle as pkl
import numpy as np
import os
import glob
import matplotlib.pyplot as plt
import matplotlib as mpl
from tqdm import tqdm
# Plotting
import sciplotlib.pol... |
d70f1c2b8353e4b1f08a8d5bb26c667cb2e42abbe83f480391d756761cafb9bd | Python | 3,676 | 101 | """Unit tests common to all catalogues."""
__author__ = ["jgyasu"]
__all__ = []
import pytest
from sktime.tests.test_all_estimators import BaseFixtureGenerator, QuickTester
class CatalogueFixtureGenerator(BaseFixtureGenerator):
"""Fixture generator for catalogue tests.
Fixtures parameterized:
--------... |
73e191213ea8bcb6e0fc317e86f6055094d9b28b1ac6f06b54d1a82231953b65 | Python | 3,677 | 99 | #-------------------------------------------------------------------------------
# elftools tests
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
import unittest
from io import BytesIO
from random import randint
fr... |
45f07fd2c637d111dae4f859a288b304f729f9623737bcc6dee72bcd9562e773 | Python | 3,680 | 100 | import pytest
import flair
from flair.data import Sentence
from flair.embeddings import TransformerWordEmbeddings
from flair.models import TARSTagger
from tests.model_test_utils import BaseModelTest
class TestTarsTagger(BaseModelTest):
model_cls = TARSTagger
train_label_type = "ner"
model_args = {"task_n... |
7311d3ecd83ba971cf9e5581bf05700b81e2de27734929fb84ca8592a2aff2da | Python | 3,680 | 116 | import logging
logger = logging.getLogger('DockOnSurf')
def tail(f, lines=20):
"""Returns the specified last number of lines of a file.
@param f: The file to retrieve the last lines from.
@param lines: The number of lines to be retrieved.
@return str: The last number of lines
"""
total_lines... |
088e3a22b91719e522ae49684d06b361d1642e105cae113cb736188b718c5795 | Python | 3,681 | 114 | # 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... |
c4a80d50ae2fa3cee66cfb8427835db1a28a024b0f2abc5550a01fe3111fe3d6 | Python | 3,682 | 107 | #!/usr/bin/env python
# salsa 0.0.1
# Generated by dx-app-wizard.
#
# Basic execution pattern: Your app will run on a single machine from
# beginning to end.
#
# See https://wiki.dnanexus.com/Developer-Portal for documentation and
# tutorials on how to modify this file.
#
# DNAnexus Python Bindings (dxpy) documentation... |
03da48e16ebb01873b553afd9d51bd788118e8ce0ae5392dc6cd71e3bdd91cfd | Python | 3,684 | 92 | from copy import deepcopy
import sys, os
import torch
import torch.nn as nn
import numpy as np
from vp_suite.model_blocks import ConvLSTM as OurConvLSTM
from vp_suite.utils.models import state_dicts_equal
REFERENCE_GIT_URL = "https://github.com/Hzzone/Precipitation-Nowcasting.git"
REPO_DIR = "Precipitation-Nowcastin... |
44eef06d3d6993ce9903c00585e6fba6092696abf2f33a9d6d2e2981ee6eb57b | Python | 3,684 | 130 | from __future__ import annotations
from dataclasses import dataclass
from typing import ClassVar, Callable
import pandas as pd
from pandas import DataFrame
from seaborn._core.scales import Scale
from seaborn._core.groupby import GroupBy
from seaborn._stats.base import Stat
from seaborn._statistics import (
Estima... |
462639d3f7b28c2aedda98b42c837dcd718fa7d252ec34bba371e5e5e311e6d3 | Python | 3,685 | 113 | import pytest
from flair.data import Sentence
from flair.models.entity_mention_linking import (
Ab3PEntityPreprocessor,
BioSynEntityPreprocessor,
EntityMentionLinker,
load_dictionary,
)
from flair.nn import Classifier
def test_bel_dictionary():
"""Check data in dictionary is what we expect.
... |
6786d8b5199cfd8d73c04cfc791cb5152597d3881ceb509da3e811117e7fbb59 | Python | 3,685 | 110 | """
@file: input_representation.py
Created on 13.02.20
@project: CrazyAra
@author: queensgambit
Input representation for which is compatible to all available lichess variants and passed to the neural network
"""
import DeepCrazyhouse.src.domain.variants.input_representation as variants
from DeepCrazyhouse.src.domain.... |
afd8299afee7bb3d5f334dde2ea8586392511bdb91a418778b201edb9695a09a | Python | 3,687 | 104 | # Copyright 2022 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... |
74c9ef371932db410c4ebbb87eeafaf8cfe0265d329057d842650251eaa320f3 | Python | 3,689 | 114 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.utils.checkpoint as cp
from mmcv.cnn import ConvModule
from mmcv.runner import BaseModule
from .se_layer import SELayer
# class InvertedResidual(nn.Module):
class InvertedResidual(BaseModule):
"""Inverted Residual Block.
Args:
in_channels ... |
d4495e84c66a0d1e8c43a0d79195bb16077fbd38f244f838ea3199b2d308e80d | Python | 3,689 | 129 | """ Test routine for pytest
Vector Strength routine testing
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R01 DC015901 (Spirou, Manis, Ellisman),
DC R01 DC004551 (Manis, 2013-2019, Early development)
DC R01 DC019053 (Manis, 2020-2025, Later development)
Copyright 2021- Paul B. Manis
Di... |
11aea5bb093d732629901f48824f63bc974bf39bba4a2bf73be1c9888778c853 | Python | 3,692 | 155 | """Figure 7 Supplement 1
Replot of VS-SAM-AN-BUcnmodel-test.pzfx
Just plot the ANF data, 100% modulation, all on one plot vs frequency
"""
import io
from pathlib import Path
import matplotlib.pyplot as mpl
import matplotlib.patches
import numpy as np
import pandas as pd
import seaborn as sns
import pylibrary.plottin... |
be5d156dd0acd71cb558201ce02782bf6c887c2bfb33c2c88ddb573a3a2b3e86 | Python | 3,692 | 112 | # -*- coding: utf-8 -*-
"""
Created on Thu Dec 15 17:48:41 2016
@author: daniel
"""
import pandas as pd
import json
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
def mg_block(mg, alpha, v, eta = 1/3.57, x_offset = 0):
block = 1 / (1 + mg * eta * np.exp(-alpha * (v + x_offset)) )
ret... |
df2947b3cd0f4eb4623afe014605a403617cd8189f160b17317abcf7b6cf4237 | Python | 3,693 | 122 | from __future__ import annotations
import json
from pathlib import Path
from typing import Any
import pyarrow as pyarrow
import pyarrow.parquet as pyarrow_parquet
from graynet.domain import RunConfig
RAW_EDGE_FILE_NAME = "edges_raw.parquet"
SUMMARY_EDGE_FILE_NAME = "edges_summary.parquet"
ROI_STATS_FILE_NAME = "roi... |
3245b28c24d4dc837ea887d9e61562f9526fb3c1182b8d522db75f3900fd6787 | Python | 3,694 | 99 | from flair.data import Sentence
from flair.models.prefixed_tagger import EntityTypeTaskPromptAugmentationStrategy, PrefixedSentence
def test_entity_type_task_prompt_augmentation_single_type():
strategy = EntityTypeTaskPromptAugmentationStrategy(["genes"])
sent = Sentence("This is a test sentence.")
aug_s... |
af502af4d3eba100eac78b8b69a9f9eb885916e2492f7568326c2e237d5784fb | Python | 3,695 | 108 | # 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... |
ac677c2c6c844780df6c953bd48268e37152c0ea057231741fb8f56f4b10cd66 | Python | 3,699 | 119 | from __future__ import annotations
from argparse import ArgumentParser
from multiprocessing import cpu_count
from pathlib import Path
from svgbit import load_10X, load_anndata_h5, load_table, run, plot
from svgbit.filters import low_variance_filter, quantile_filter
from svgbit.normalizers import logcpm_normalizer, cpm... |
161b9ca5de5e1cdb3796d329cce943466fa75d2e6e54bbe8f80ad7ee77ad1316 | Python | 3,701 | 114 | # 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
#
# ... |
fe089c02772a65b354fdb8541e49659b15c9585655b13e840f1bcbe2e96eac1d | Python | 3,702 | 110 | """
@file: input_representation.py
Created on 13.02.20
@project: CrazyAra
@author: queensgambit
Input representation for which is compatible to all available lichess variants and passed to the neural network
"""
import DeepCrazyhouse.src.domain.variants.input_representation as variants
from DeepCrazyhouse.src.domain.... |
7bdadfab5cb4b0318f3c699db45ec317b6160eb6561e9f11b5877c1724caae5f | Python | 3,703 | 110 | # 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... |
48edc68a8e92efbe278a60c30701df187b12d9715831a6ac4c1b9bd676774739 | Python | 3,704 | 124 | # 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... |
0e2f89eb15e382006a242628ec9c977e77c89bb1ac699df1a9f364fceeb532d0 | Python | 3,706 | 99 | """Test for distance path functionality."""
import numpy as np
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.dists_kernels._numba_distances._distance import (
_METRIC_INFOS,
distance,
distance_alignment_path,
)
from sktime.dists_kernels._numba_distances.tests._ut... |
dec533d0287109a8e18a5271491aab743180145b4c723213692c832c96e04450 | Python | 3,706 | 111 | # Copyright (c) OpenMMLab. All rights reserved.
from argparse import ArgumentParser, Namespace
from pathlib import Path
from tempfile import TemporaryDirectory
import mmcv
try:
from model_archiver.model_packaging import package_model
from model_archiver.model_packaging_utils import ModelExportUtils
except Imp... |
1403718ee5a5e027054b8b485877efcf964196ac08a604a2f713bdbf1cc07f2f | Python | 3,707 | 81 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
from mmcv.cnn import build_conv_layer, build_norm_layer
from ..builder import BACKBONES
from .resnet import ResNet
@BACKBONES.register_module()
class ResNet_CIFAR(ResNet):
"""ResNet backbone for CIFAR.
Compared to standard ResNet, it uses... |
3a8641840c780e7c269089bf2684f4c76a8e9dacb47aac3a528b6c81fa12165b | Python | 3,707 | 102 | # 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... |
98006a1692dddd0bc78977e880c2bbb31a1d3ef79659fc8c1ed61a8b16680973 | Python | 3,707 | 108 | # Copyright (c) ONNX Project Contributors
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import numpy as np
from onnx.reference.op_run import OpRun
_MIN_REFLECT_AXIS_LENGTH = 2
def _pad_impl(data, raw_pads, mode, constant_values=0.0, axes=None):
input_rank = data.ndim
if axes is ... |
9ce59a16329957f3051e4c6a81e11e2942a8e214aa8f75b2bb5b1f9cdfdd95de | Python | 3,708 | 83 |
from collections import namedtuple
import pytest
from model_archiver.manifest_components.engine import EngineType
from model_archiver.manifest_components.manifest import RuntimeType
from model_archiver.model_packaging import generate_model_archive, package_model
from model_archiver.model_packaging_utils import Mode... |
ad93e87996eefdc2bcb5de49e0b571671b288e3c13a1dac77b8d8fd9d7b6f3f6 | Python | 3,708 | 105 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
298912292709480d5a844dfe202b51e8b74e89127bb127e4fc85d08c3eb2f2ab | Python | 3,709 | 119 | import numpy as np
from tqdm import tqdm
from sklearn.metrics import accuracy_score, sensitivity_score, specificity_score
from sklearn.metrics import confusion_matrix
from sklearn.model_selection import StratifiedKFold
import torch
from torch.utils.data import TensorDataset, DataLoader
from torch.autograd import Vari... |
8812c21e575b56cda9cd9bd12b33c3620e26e5ec01d924121738917c8b9e8667 | Python | 3,714 | 93 | # 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... |
af3fe6e89cb561d7bbd636b3e96d62f3440908cd582104dbcc9131698058342f | Python | 3,714 | 136 | # 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... |
e8d8ff2d4020e0b4c6e2e43a9ca7f7bc3330ea2073a544eb0950f08eb89cdd34 | Python | 3,715 | 111 | # 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... |
ae139c37061e15bcf5b878f154ad30c8823aa33a76b451d15c89a0cc8a771c15 | Python | 3,718 | 137 | """Hyperbolic distances implemented in pytorch.
This module was copied from the repository the following repository:
https://github.com/asappresearch/dynamic-classification
It contains the code from the paper "Metric Learning for Dynamic Text
Classification".
https://arxiv.org/abs/1911.01026
In case this file is mo... |
c55ce5d6c57bd277bcadf6591960c43678e537f2825c6ae50c0e6dafca215435 | Python | 3,719 | 90 | # 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 MelWeightMatrix(Base):
@staticmethod
def export() -> None:
... |
3c2e5976c1c93f30cf654915e8135026a2c4d8d2eb20b7686a15577cb7ce158c | Python | 3,720 | 111 | """
SNS-Toolbox version 1.5 has expanded the capabilities of Spiking Neurons and Synapses. This tutorial explores these new
features.
"""
"""Imports"""
# Import packages and modules for designing the network
from sns_toolbox.networks import Network
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.ne... |
3bfd61ed2bf9e7a05c37aabda036d2c231d0d74ebfdd035da8f64fd07f04c04b | Python | 3,721 | 98 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
5dd69a904072b0796e064f1ab8c4c410d8159754e3afd4daa843d10d383a225f | Python | 3,723 | 102 | from typing import List, Tuple
import numpy as np
from torch_geometric.data import HeteroData
from molucn.utils.utils import get_common_nodes, get_positions, get_substituents
EPS_ZERO = 1e-8
def get_imp_substituent(site, subs, pos_sub, color_pred):
"""Returns the importance of the substituent at the given site.... |
556d91cbc89f40b7e68810caa8876f68decad58ccc10d194f762e79b8c00f0fd | Python | 3,724 | 109 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
aaec9d9af45c4494065aad6863e02215f72b67f012593aca53ac4ec38f9c9b24 | Python | 3,725 | 84 | """ Converts owl or ttl or raw rdflib graph into a pandas DataFrame. Saved in .pickle format.
Usage:
allen_transgenic_lines [options]
Options:
-h --help Display this help message
-v --version Current version of file
-r --refresh Update local copy
-i ... |
12ad37f3436eaa4c97e8f0a2afb986c9287f86eeebfc83ba34a77e71ca94d466 | Python | 3,726 | 124 | import random
import matplotlib.pyplot as plt
import numpy as np
import torch
from gpytGPE.gpe import GPEmul
from gpytGPE.utils.metrics import R2Score
from Historia.history import hm
from Historia.shared.design_utils import get_minmax, lhd
SEED = 8
def f(x): # elliptic paraboloid: y = x1^2/a^2 + x2^2/b^2, a=b=1
... |
22cb9b83a1fb7f12adff81d68653e566d8a37505250232eef15b26364fbc3b8d | Python | 3,728 | 100 | # 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... |
36cddacbf2e9a49ba623d9945cb06ab5c01a6e5dde6e19754b31a637a7fa5f41 | Python | 3,728 | 86 | # 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... |
3ca2cce01c957fbe555e8a34d6c6023cff089d8621128e430ef0ec62742dcd8c | Python | 3,728 | 112 | import numpy as np
import pandas as pd
from sklearn.cross_decomposition import CCA
from sklearn.utils import check_array
from sklearn.utils.validation import check_is_fitted, FLOAT_DTYPES
from sklearn.metrics import silhouette_samples
class CCA_extended(CCA):
def __init__(self,*args,**kwargs):
super().... |
5154bc9bce2b41aa80d9aa0e4d2ab0c58f3d392bd3b098525e453699274b482f | Python | 3,729 | 108 | # 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... |
2f05affaf4455e295d684b7e1e9994c35d9481d1485692adc54536ac78dc9307 | Python | 3,731 | 111 | # copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
# Ported from skchange (BSD-3-Clause), original authors: johannvk
"""Rank-based multivariate cost function."""
__author__ = ["johannvk"]
import numpy as np
from sktime.detection.costs._base import BaseCost
def _rank_cost(segment_starts, segmen... |
9c765365ed71baabbd2c010c360a842ba24688a2d511ef43220c2fed09294804 | Python | 3,735 | 91 | import matplotlib.pyplot as mpl
import numpy as np
from pathlib import Path
from scipy.io import loadmat
from lmfit.models import LinearModel
from scipy.stats import linregress
import pylibrary.plotting.plothelpers as PH
# sns.set_style(rc={"pdf.fonttype": 42})
mpl.style.use("~/.matplotlib/figures.mplstyle")
diskpath... |
f54dd2788ea0b72b792ccec78bdfa99c703d9ffc50d7c493ade5b462c7d75581 | Python | 3,738 | 129 | # Copyright 2019-2020 The ASReview 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 appl... |
b594141079d9ad47a2dab917173b5c8f22a8370eae288e6b7dca98cf669d102c | Python | 3,739 | 94 | import argparse
from biom import load_table
import pandas as pd
import numpy as np
from q2_matchmaker._stan import _case_control_single
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument(
'--biom-table', help='Biom table of counts.', required=True)
parser.add_argumen... |
c87583da2751c91e4f4ca5624e3eaf700142337d26e71b6d2c0f3982f31de33a | Python | 3,739 | 118 | from __future__ import annotations
import logging
import time
from typing import TYPE_CHECKING
from optuna.artifacts.exceptions import ArtifactNotFound
_logger = logging.getLogger(__name__)
if TYPE_CHECKING:
from typing import BinaryIO
from optuna.artifacts._protocol import ArtifactStore
class Backoff:... |
9d26e3b6c12a9c1242f60332f8961e4de7e2c67e5dba44e1437fac80d3c4a9a1 | Python | 3,740 | 101 | # 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... |
d8e49480127f5a5dfd1bdd6b79f1f601e745f97cb7084d212af997e1e9e89b1e | Python | 3,744 | 127 | #!/usr/bin/env python
import click
from functools import partial
import gzip
from multiprocessing import Pool
import os
import pandas as pd
import re
from sklearn.preprocessing import quantile_transform
import subprocess as sp
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
... |
ed4de428cd163274a0aeb32d91d4cc0ac13bf98701ace822591cd70b47122c36 | Python | 3,744 | 111 | """
Author: Yifan Jiang (yifanyifan.jiang@mail.utoronto.ca) and Peidi Xu (peidi@di.ku.dk)
Description: Given a bifurcation, finds the optimal position of the branching point
and the optimal radii.
"""
import numpy as np
from scipy.optimize import minimize
class GD_OptimizerUnit:
def __init__(self, locs, rad... |
d0dba2c56ec9817580f30cfd96dfaf33e28378491b0b61cf56122097d462eff2 | Python | 3,747 | 116 | # 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.defs import AI_ONNX_PREVIEW_TRAINING_DOMAIN
def apply_adagrad(r, t... |
ad1afd3ee809fed0ecabddaef0b0eb4d324d80420ddd5a6757881838c0f8bb44 | Python | 3,750 | 94 | from docopt import docopt
from IPython import embed
from ilxutils.cli import Client
import json
import os
import requests as r
from sys import exit
import time
import unittest
VERSION = '0.0.2'
# ILX:0108124 == "Organ" | term
# ILX:0101431 == "brain" | term
# ILX:0107497 == "Neuron" | term
# ILX:0112772 == "Afferent pr... |
1e81e7f46d889cc2662ea9f30128b5cdc921303c0a1c94fd4095e903b48f82e9 | Python | 3,753 | 121 | # 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... |
2b42f14fb346dd4c22e353fe827d76fb1b4b90e9e508010f0a33db91e1973fc2 | Python | 3,756 | 122 | # 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... |
b4c0b87bf4c8e8221e1a58f60e79a78dc5d3600ffcddfc24b6bb12b2e058d833 | Python | 3,756 | 103 | '''
Pure-python implementation of UCSC "liftover" genome coordinate conversion.
LiftoverChain test.
Copyright 2013, Konstantin Tretyakov.
http://kt.era.ee/
Licensed under MIT license.
'''
import os
import sys
if sys.version_info < (3, 0):
from cStringIO import StringIO
else:
from io import BytesIO as StringIO... |
b9d53956425c2fcd1c1f1d2d4bee4f91e48e49f1d8e6edb61907c47c2e60382a | Python | 3,757 | 100 | #-------------------------------------------------------------------------------
# elftools example: dwarf_lineprogram_filenames.py
#
# In the .debug_line section, the Dwarf line program generates a matrix
# of address-source references. This example demonstrates accessing the state
# of each line program entry to retr... |
0c7b6965f499167ad25c8f51769bd0dbabcd57cca255356dc0c775a95f665369 | Python | 3,758 | 87 | # Copyright 2023 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... |
902997654fb160ea28dc18aa24fa8702ee25c14fe396a7ef839f78da344e7018 | Python | 3,759 | 107 | import h5py
import numpy as np
import os
class anidataloader(object):
''' Contructor '''
def __init__(self, store_file):
if not os.path.exists(store_file):
exit('Error: file not found - '+store_file)
self.store = h5py.File(store_file)
''' Group recursive iterator (iterate thr... |
85d8841aa996bfd58b40e7b8bd434b18e6d9a4ccdbe95991a417becaa19e634a | Python | 3,760 | 108 | """ Functions to extract the cell boundaries """
import pandas as pd
import numpy as np
from multiprocessing import Pool, cpu_count
from multiprocessing.dummy import Pool as ThreadPool
# All that below is to avoid diplib to show a welcome msg on import. If hasattr(sys,'ps1') return True, then
# import diplib will prin... |
300df905a53f81492b548fcb148dfcf8923815f880704265586f982e158db680 | Python | 3,761 | 116 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Dec 12 13:56:45 2017
@author: tpisano
"""
import numpy as np
from math import sqrt, exp
from skimage.morphology import disk, dilation, binary_dilation, ball
from tools.imageprocessing.target_arrays import generate_target_array_selem, apply_dilation
#... |
4bea19a8f4bd10c0707d32742d4d16f676f8b089e8e2503e0d65eeec136c0942 | Python | 3,761 | 94 | from genomic_benchmarks.data_check import is_downloaded
from genomic_benchmarks.loc2seq import download_dataset
from genomic_benchmarks.utils.paths import CACHE_PATH
from torch.utils.data import Dataset
class GenomicClfDataset(Dataset):
"""
A class to represent generic genomic classification pytorch dataset.
... |
f0b2c0528427ec315b4c906dbdfcfe572c8b29e1c1acfecdd0f0c936c15bbd54 | Python | 3,763 | 133 | # 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... |
5e2f4620c0c491b8a5dbb6f568b48359b49af61821a5ffdf51f04fddf494e166 | Python | 3,764 | 113 | # 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... |
981c5ee47f7220139082ac48e8315c03558cb4e7e7d90b8e206f9fe3c3212f09 | Python | 3,765 | 101 | # 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... |
cd6062970ad76839e199ab1b482e826396757eddb29669b043e01cb833ef026a | Python | 3,765 | 112 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Description:
# Testing code of DIAM-CNN
#
# Copyright @ Yanqiu Feng
# Laboratory for Medical Imaging and Diagnostic Technology
# Southern Medical University
# email: foree@163.com
#
import sys
sys.path.append("/public/siwenbin/DLQSM_YH/")
from utils import *
from c... |
11dde09fd58980675da0f799c9960dcf365bef125ecdeb079dc1a748368d1030 | Python | 3,766 | 74 | """
@file: mixture_net.py
Created on 17.02.20
@project: CrazyAra
@author: queensgambit
Experimental network which combines the output of multiple singular networks
by a weighted sum of a learnable weighting parameters.
Proposed by Arseny Skryagin and Johannes Czech
"""
import mxnet as mx
from DeepCrazyhouse.src.doma... |
431c92723d0aa2f2991a968c0dc1e0785048046d7f2990fc789ef9f8236ed11c | Python | 3,766 | 118 | # 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... |
bf075d589f1da4a64d7ebf370e90018122bae782c6485cb0342bb1b57e634ec0 | Python | 3,767 | 74 | """
@file: mixture_net.py
Created on 17.02.20
@project: CrazyAra
@author: queensgambit
Experimental network which combines the output of multiple singular networks
by a weighted sum of a learnable weighting parameters.
Proposed by Arseny Skryagin and Johannes Czech
"""
import mxnet as mx
from DeepCrazyhouse.src.doma... |
d37ad85fb61dfd0f8b3199299b2e572b1a754262b87f9492698bdeb62f58d214 | Python | 3,768 | 98 | from IPython.core.debugger import set_trace
import numpy as np
import tensorflow as tf
from src.utilities.findiff.findiff_general import solver_arguments
from src.solvers.findiff.findiff_solver import fd_solve
########################################################
"""
Common along with testcase specific arguments... |
42006f29c19027c264464aa94ec2b56328d16864be17108f39cc6ddcc7618730 | Python | 3,769 | 114 | # coding=utf-8
# Copyright (C) 2022. 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
#
# ... |
fefe1902e12c31833b064697feb098ec35350389501480eac6c614104fbdf6ee | Python | 3,769 | 131 | import pandas as pd
import numpy as np
import joblib
import seaborn as sns
import matplotlib.pyplot as plt
# Need this line so text is text in svg export
plt.rcParams['svg.fonttype'] = 'none'
import wrangle_data as wd
import rf_auxililary_functions as rf_aux
# Utilities
from sklearn.model_selection import train_test... |
8f712346aa069220827d1fc57f3483356acdff4c40a4e24159acfbed364a49c0 | Python | 3,771 | 160 | import torch
import torchvision.transforms as TvT
import random
import numpy as np
class Random_horizontal_flip:
def __init__(self, p = 0.5):
self.p = p
def __call__(self, x):
events, flow, mask = x
if torch.rand(1).item() <= self.p:
events = TvT.functional.hflip(ev... |
0edf0a7ec44aa2eac308c11bb20da87f3a3b005d3de7d3c538c6ad501b172a27 | Python | 3,772 | 111 | # 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... |
2de82ef40188d6cb447a2e584ce45467dc0712f3c64ac83cc2838968deef839a | Python | 3,772 | 110 | """Compact GA minimal implementation"""
from __future__ import division, print_function
import numpy as np # to replace 'inf' with np.inf and vice versa
class CompactGA(object):
"""Randomized search on the binary domain {0,1}^n.
cGA samples two different solutions per iteration.
Minimal example::
... |
047ff8981fe15a1686978146bc95ce31f2f1289717ac7293a37b6aa56034987e | Python | 3,773 | 106 | """Interpolated phase, using cyclepoints."""
import numpy as np
###################################################################################################
###################################################################################################
def extrema_interpolated_phase(sig, peaks, troughs, r... |
0935f4821fca909ce99b4184bf320ce3bdc282929905efd2b04bbe0431440fde | Python | 3,774 | 117 | # 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... |
743a755653d6ce7d843c80b133d79d34162b22b6486ac603d91a8a040a4a06b2 | Python | 3,775 | 102 | #!/usr/bin/env python
# show traces from simulation run (current-voltage - IV)
#
from __future__ import print_function
import os
import sys
from pathlib import Path
import pickle
import matplotlib.pyplot as mpl
import toml
def main():
with open("wheres_my_data.toml", "r") as fh:
config = toml.load(fh)
... |
180d2238dac1beae5062c7a95d2f15acdf65b4c7d9890e2d33cb20cf07f4d830 | Python | 3,777 | 108 | import dataclasses
from typing import Dict, List
import numpy as np
import pandas as pd
import torch
from torch.utils.data import Dataset
from preprocessing.features import AudioFeatures
from utils.arguments import AudioArguments
class AudioDataset(Dataset):
def __init__(
self,
samples_df: pd.Da... |
ae6dacf71dd614cd2428d441ba53d6ade65be6346098cfcf0c1be26520f24910 | Python | 3,777 | 79 | # Copyright 2018-2025
# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
# 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/LICE... |
d0f1c56fe775f2609ad4fa612d783ca45a7dca72b972e41725c4a19837f5541f | Python | 3,777 | 81 | from __future__ import print_function
from freqAnalysisTools import band
from os import listdir
from os.path import isfile, join, splitext
import sys
import pickle
import math
import numpy as np
from sklearn import linear_model, svm, ensemble, neural_network
from parameterSetup import ParameterSetup
from evaluationCrit... |
e982ef3b39954dce87ba41971405e70bdbbabac68d538200cddd37b721f0fedf | Python | 3,779 | 107 | # 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... |
dad7b0ff314a11fc391a1b12c116842e600c3051b9a3a77b797b0081feb4e5b2 | Python | 3,781 | 104 | """
@file: change_onnx.py
Created on 30.10.21
@project: CrazyAra
@author: queensgambit
Allows changing the batch size of an already existing ONNX-model.
Based on https://github.com/onnx/keras-onnx/issues/605
https://github.com/sitting-duck/stuff/blob/32b77388c54c5ca5f5039365824b15483fc22fc2/ai/onnxruntime/edit.py
""... |
8b206891061427a405b705ec187bbc5efc861e0b7af7c33b630dc3f365320122 | Python | 3,782 | 98 | """
This script generates figure S6c from the paper :
This is the decoding accuracy before movement onset, removing unreliable trials (movement before main movement onset)
Internal notes:
"""
import pandas as pd
import pickle as pkl
import numpy as np
import os
import glob
import matplotlib.pyplot as plt
import matplo... |
53b1035883f6f6a3a5844ae8127cd144d9a1ec4faad8a79e397ab36d6814bb19 | Python | 3,783 | 118 | # 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... |
97165ef65e3fc01f2b9663a77bd710dd527d1f8fa78137a221bb64de739e9a36 | Python | 3,783 | 98 | import numpy as np
def rolling_window(a, window, step):
"""
Make an ndarray with a rolling window of the last dimension with a given step size.
Parameters
----------
a : array_like
Array to add rolling window to
window : int
Size of rolling window
step : int
Size o... |
e0536813d1a7573f8ec033fff072506c4d88d9920d53a4a8d3eaedf135676864 | Python | 3,783 | 102 | # ----------------------------------------------------------------------------
# Copyright (c) 2017-2026, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... |
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