sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
121320c6d909c43f79393ba64bd5ea5af6cc44a1d8f2f1e7d127c8a5574e7cff | Python | 8,643 | 162 | import logging
import tensorflow as tf
import numpy as np
from .encoder import TransformerEncoder, GATEncoder
from .decoder import TransformerDecoder, SingleLayerDecoder, BilinearDecoder, NTNDecoder
from .critic import Critic
# Tensor summaries for TensorBoard visualization
def variable_summaries(name, var, with_max... |
22ae401bc9a3024fe979b13781726c4bc03475a0499c8f43df2bb7f34a4e12be | Python | 8,643 | 187 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
sys.path.extend(['/home/will'])
from e... |
2a767913bd31faf3314821f8c904f8856905fea6939c0ed32627d1e20b1a811f | Python | 8,647 | 316 | #!/usr/bin/env python
import click
from click_option_group import optgroup
import json
import numpy as np
import os
import pandas as pd
import re
from sklearn.metrics import average_precision_score, roc_auc_score
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
... |
8cfcb8de280bb55ba252fdf0b29defdc98834e118c2de7905c47e0a89c88f815 | Python | 8,652 | 332 | import random
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.transforms as TvT
from torch.autograd import Variable
from spikingjelly.clock_driven import functional
from spikingjelly.clock_driven import neuron
from poolingNet_cat_1res_mvsec import NeuronPool_Separ... |
c6505ddb98bcd481d7d27cd0673b9bd0f514ba6aba8831fb48b58b4ff0243410 | Python | 8,652 | 200 | '''
contains methods used in varipus components
.. codeauthor:: Nicholas Browning
'''
from __future__ import division
from builtins import str
from builtins import range
from past.utils import old_div
import math
import numpy
element2mass = {'Ru': 101.904348, 'Re': 186.955744, 'Rf': 261.10869, 'Ra': 226.025403,
... |
e87aac47bc8fcfe522f7d2cee1e82db440c0e33b491a301408d11b4c99073056 | Python | 8,654 | 213 | # -*- coding: utf-8 -*-
#
# Copyright © 2013 Charles E. Vejnar
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://www.mozilla.org/MPL/2.0/.
#
"""UCSC track hub."""
import os
class Node(ob... |
e3538aa155ed64e8b8836597f980cdb3e2be6c75be915c17c3fe7d9aa4e83e8b | Python | 8,655 | 213 | from typing import Iterator, List, Dict
import torch
import torch.optim as optim
from allennlp.data import Instance
from allennlp.data.fields import TextField, SequenceLabelField
from allennlp.data.dataset_readers import DatasetReader
from allennlp.common.file_utils import cached_path
from allennlp.data.token_indexers ... |
c9b616b3b89e7f2da8a905b72166e6373a3c079bd028804ba015906d33b88ee7 | Python | 8,657 | 207 | # 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... |
790f828559d4f3ca5dc42ca3f68d9fd806c7a5f8ff7e1fc79ab897719720f5e4 | Python | 8,659 | 261 | #!/usr/bin/python -u
import os
import math
import numpy
import random
import pandas
import matplotlib.pyplot as plt
from sklearn import *
#
if __name__ == '__main__':
numpy.random.seed(1)
random.seed(1)
predmatrix = pandas.read_csv("./tmp/prediction_matrix.tsv", sep="\t", ... |
81d0b80ee64d0321dd78cc9d4daf080e426263c995cd560c0ffab9456e3329f3 | Python | 8,661 | 250 | """Time series Kvisibility."""
__author__ = ["seigpe"]
import numpy as np
import pandas as pd
from sklearn.cluster import KMeans
from sktime.clustering.base import BaseClusterer
class TimeSeriesKvisibility(BaseClusterer):
"""Kvisibility for time series clustering.
kvisibility is a time series clustering t... |
8ec92485d5525b4744dad9a2015c75f17fc87946fd9b9fbed5364083e4f2f7a0 | Python | 8,661 | 261 | # 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... |
365454b2cf1b3c0de2f39b31975c5efb6cc1b3e3cf232f51738b0d2d37b20843 | Python | 8,668 | 245 | # -*- coding: utf-8 -*-
"""
Created on Tue May 31 11:11:16 2022
@author: tiagolab
"""
import matplotlib
#matplotlib.use('Qt5Agg')
from matplotlib import pyplot as plt
import os
import numpy as np
import glob
#from scipy import signal
#from scipy.signal import lfilter
#from scipy import stats
#import... |
e60d445dc8a70909ea2a6a847d1a8a20cf64da594979624e2fff66340c8723f0 | Python | 8,672 | 193 | """
Neurons are the computational nodes of an SNS, and can be either spiking or non-spiking.
"""
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
IMPORTS
"""
from typing import Dict, Any
import warnings
import numbers
from sns_toolbox.color_... |
c39a68e40327be3db5eae9fc66e0f03f32591dcff87356253552b0527defc2a7 | Python | 8,676 | 214 | from __future__ import annotations
from dataclasses import dataclass
from typing import Any, Callable
import numpy as np
from numpy import ndarray
import pandas as pd
from pandas import DataFrame
try:
from scipy.stats import gaussian_kde
_no_scipy = False
except ImportError:
from seaborn.external.kde impor... |
6212044026ed8e38e60a149ab664869125903b73723e3ec9f70397e7ec1a0ce5 | Python | 8,678 | 183 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# fr... |
19a0ecb9034d2d7518e62ce93ad5653041c5af5070f32c312b9b00e0dfa6a8c2 | Python | 8,696 | 236 | # 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... |
ab9787a11234a4963591d045bafbdbd43b7d0d8dd58f72163ca99af13cb59257 | Python | 8,696 | 274 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib import cm
import seaborn as sns
from scipy.spatial import Voronoi, voronoi_plot_2d
from sklearn.preprocessing import StandardScaler
from sklearn.cluster import KMeans, AgglomerativeClustering
from sklearn.metrics import silhouette_... |
76bddd21169dd35932f74fabbe6b1b85efb2e724a0dba0b22bc0a712fd52f45f | Python | 8,705 | 211 | __author__ = ["chrisholder", "TonyBagnall"]
from typing import Any
import numpy as np
from sktime.dists_kernels._numba_distances.base import (
DistanceAlignmentPathCallable,
DistanceCallable,
NumbaDistance,
)
class _EdrDistance(NumbaDistance):
"""Edit distance for real sequences (EDR) between two t... |
d57d6272963e2fd24e84b83af12baf9eeb23018b82e8b6264a6ed86b896d3602 | Python | 8,706 | 312 | """Machine type converters for Table scitype.
Exports conversion and mtype dictionary for Table scitype:
convert_dict: dict indexed by triples of str
1st element = convert from - str
2nd element = convert to - str
3rd element = considered as this scitype - str
elements are conversion functions of machine type (... |
fbac3d441e02f5fdd4fe420d2e419cf99b97c8b91c6908d4ff6444eeae1dd32a | Python | 8,709 | 197 | # Copyright 2007 Zachary Pincus
# This file is part of CellTool.
#
# CellTool is free software; you can redistribute it and/or modify
# it under the terms of version 2 of the GNU General Public License as
# published by the Free Software Foundation.
"""Tools for reading and writing delimited data files.
Files with v... |
d6e364dbca9ea447edc51d03ff8d8cc14db62043096d024b6ef82dcaea575509 | Python | 8,718 | 272 | #!/usr/bin/env python
# Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import argparse
import glob
import os
import re
import subprocess
from textwrap import dedent
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from collections.abc import I... |
c4b0e76561ad2e8aa18137973a9873cbd73b7ddd698387f113ff298fc0f9448c | Python | 8,720 | 263 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Sep 3 12:03:23 2021
Run gridsearch to fit SHJ
@author: robert.mok
"""
import os
import sys
import numpy as np
import torch
import itertools as it
import time
from scipy import stats
import pickle
location = 'cluster' # 'mbp' or 'cluster' (cbu clust... |
74cc5022dad93d71d0a23faf18417c1f91a2732245ffffc25178f40d49b48116 | Python | 8,725 | 211 | #!/usr/bin/env python
# blasr 0.0.1 test suite
# Generated by dx-app-wizard.
import os
import unittest
import time
import json
from uuid import uuid4
import dxpy
import dxpy.app_builder
from dxpy.exceptions import DXAPIError
src_dir = os.path.join(os.path.dirname(__file__), "..")
test_resources_dir = os.path.join(sr... |
49851c892eeddf9e42173495930b9de52399fac97cdf8144b0bcc0b90d6b3ca4 | Python | 8,728 | 302 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import pandas as pd
import matplotlib.pyplot as plt
import cv2 as cv
import numpy as np
from dataclasses import dataclass
import os
import random
from numba import njit, jit
from sklearn.utils import shuffle
import shutil
# In[2]:
## Read EMBED dataset metadata file... |
f2c894eb19517f73033f8340896fdac2f1f496114a189a9bdf03aa725de452c7 | Python | 8,731 | 192 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
b4b7f5d6a15c16e507bd3cc0ba6cc8e08471b0e464b030dd572dccb41a229b7a | Python | 8,736 | 250 | # 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... |
ddfbfbbac43facae07069347c64ed84feab716d989e7c22e39341c78eb926a5f | Python | 8,738 | 196 | from numba import jit, prange
import numpy as np
import numpy.typing as npt
from scipy.cluster.vq import kmeans2
from .run_gw import DistanceMatrix, Distribution, Matrix, gw
from scipy.spatial.distance import squareform, pdist
@jit(nopython=True, parallel=True)
def deformation(
A: npt.NDArray[np.flo... |
a47eeb7fb2be7feeb6e6dfbddee448d6a11d3db8282e63fd4b5f65e73997c03d | Python | 8,739 | 254 | #!/usr/bin/env python
# encoding: utf-8
"""
remap_hoc.py
Created by Paul Manis on 2013-01-04.
Copyright (c) 2013 Paul B. Manis, Ph.D.. All rights reserved.
This function remaps a hoc file from 'axon[x]' to whatever is in the sectionLists.
It turns sections only found in the "section list" and replaces axon[k] with a... |
25afcb5e781ee2909aed2430fd2f11def47879a18bce931d62e845d91ab519a7 | Python | 8,740 | 220 | """BaseEstimator interface to sktime edit distances in distances module."""
__author__ = ["fkiraly"]
import numpy as np
from sktime.dists_kernels._numba_distances import pairwise_distance
from sktime.dists_kernels.base import BasePairwiseTransformerPanel
class EditDist(BasePairwiseTransformerPanel):
r"""Inter... |
f0cdaafb32073ce0ef85ec2e27298b90d7948ea2aa0b763b17248e26e3640ba5 | Python | 8,740 | 248 | """Random Interval Classifier.
Pipeline classifier using summary statistics extracted from random intervals and an
estimator.
"""
__author__ = ["MatthewMiddlehurst"]
__all__ = ["RandomIntervalClassifier"]
import numpy as np
from sktime.base._base import _clone_estimator
from sktime.classification.base import BaseCl... |
5ec30e1e45ee1eafef6ca88f893e9924dbf6491abe804923a7dd23aad8b76d7e | Python | 8,742 | 158 | """Perform GNN ensemble model training."""
import argparse
from os.path import exists, isdir
from os import mkdir
from copy import deepcopy
import time
import sys
sys.path.insert(0, "../src")
import random
import torch
import toml
from torch_geometric.loader import DataLoader
from gnn_eads.functions import create_l... |
a4296ba9434be38a1a3d0d12e14d4e0ba4325b4253dffbf8584f2ff1df28ec2b | Python | 8,743 | 204 | #!/usr/bin/env python
import os
import sys
import stat
from os.path import join as pjoin, exists as pexists, realpath
import numpy as np
"""#---------------------------------#---------------------------------#---------------------------------
The following script helps you generating job files for processing the lar... |
8efbf2533a7574c48ea1a13b990d42153f87e7b32f4cdf059c7caa5722eb37ae | Python | 8,745 | 251 | import copy
import os
from PIL import Image
import torch
import torch.utils.data
import torchvision
from pycocotools import mask as coco_mask
from pycocotools.coco import COCO
import custom_utils.transforms as T
class FilterAndRemapCocoCategories(object):
def __init__(self, categories, remap=True):
sel... |
53f0f455089a2e6b8d7cdde0ae6ef1ea4ca2de2cf26d38108be1d0c29573f1b0 | Python | 8,747 | 208 | from copy import deepcopy
from pprint import pformat
import rdflib
import networkx as nx # FIXME probably break this out into its own project to avoid scipy dep for deployment
from rdflib.extras import external_graph_libs as egl
from pyontutils.core import OntGraph, Edge
from pyontutils.utils import listIn, makeSimple... |
a76e1bc3a905dd6514b1a992f97efe55128d6f58ea515fcb82e71d9c1429bddb | Python | 8,751 | 233 | # Copyright (c) OpenMMLab. All rights reserved.
import warnings
from abc import ABCMeta, abstractmethod
from collections import OrderedDict
from typing import Sequence
import mmcv
import torch
import torch.distributed as dist
from mmcv.runner import BaseModule
from mmcls.core.visualization import imshow_infos
# TODO... |
245168c08d527bde09f584f9f2bc143e64c7dd5b3fe7e59ae88d0a29445a027f | Python | 8,759 | 244 | # -*-coding:utf-8-*-
# from __future__ import absolute_import
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
def conv1x1 (in_planes, out_planes, stride=1):
return nn.Conv2d(in_planes, out_planes, kernel_size=1, stride=stride, bias=False)
def conv3x3 (in_planes, out_planes, stri... |
e71c345cbeeb15ade8549b1ee1b109c100d5d20883c6d9521462eca947574abc | Python | 8,761 | 187 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# fr... |
f14c3dffe1bff7043afb386500419d51c6fd399bb9f212ffb7761c36435a6b95 | Python | 8,768 | 187 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# fr... |
30c0cf1548e8bed3b6daa4b644efcc06c7ee4b2f401e72aeae2802424008429a | Python | 8,772 | 274 | #!/usr/bin/env python
import click
from click_option_group import optgroup
import json
import numpy as np
import os
import pandas as pd
import shutil
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
os.pardir))
import time
import torch
from expl... |
4789051719eb2571bd019d9c584da287ab3e828d126d47001fdbf4370afad132 | Python | 8,774 | 207 | from os import listdir
from os.path import isdir, isfile, join
from pathlib import Path
from shutil import copy
from typing import Dict, List, Union
import numpy as np
import pandas as pd
import pydub.audio_segment
from pydub import AudioSegment
def code_with_extension(base_folder: str, code: str, extension: str) ->... |
f56bb72a507b37d769b5d5489507b7132f4bf8731c19cede13ca40b42f21f6c9 | Python | 8,774 | 350 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Do-nothing script for making a release.
This idea comes from here:
- https://blog.danslimmon.com/2019/07/15/do-nothing-scripting-the-key-to
-gradual-automation/
The script is adapted from:
- https://github.com/alan-tu... |
4f1dc66fb4ea718c396c009a66c104e5a9a549b84b3fab499eea888e5896f777 | Python | 8,775 | 187 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# fr... |
dc4fff97032e9e27f3e1ef7f4bda5fdd7d6d88358fb7b192efab09b1de7dafc8 | Python | 8,780 | 174 | import numpy as np
import torch
import random
from tqdm import tqdm
from vp_suite.base import VPModel
from vp_suite.model_blocks.enc import DCGANEncoder, DCGANDecoder
from vp_suite.model_blocks.phydnet import K2M, DecoderSplit, EncoderSplit, PhyCell, SingleStepConvLSTM
class PhyDNet(VPModel):
r"""
This clas... |
63ad6dfd8511983d077260a5405aea65146dea7ea38594437db6afcf18bccf83 | Python | 8,781 | 219 | # -*- coding: utf-8 -*-
"""
Created on Thu December 10 11:41:02 2022
@author: Pawan Panwar, Quanpeng Yang, Ashlie Martini
PyL3dMD: Python LAMMPS 3D Molecular Dynamics/Descriptors
Copyright (C) 2022 Pawan Panwar, Quanpeng Yang, Ashlie Martini
This file is part of PyL3dMD.
PyL3dMD is free software: you ... |
f0f91348fa5252df507f32a63334846172ed47a8f9f88857071aa0af9d40440e | Python | 8,789 | 284 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# face_recognition documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in t... |
5e49a016a326af3c557d7ce53eaf0602142a103aa19108738853cee1f5f4b2db | Python | 8,792 | 205 | import copy
from functools import partial
from pathlib import Path
import pandas as pd
import numpy as np
def create_binary_diagnoses_df(
abcd_data_path: Path
):
subindicators_table = pd.read_csv(abcd_data_path / 'subindicators_table.csv')
# aggregate diagnoses via OR rule and remove '_or_rule' suffix
... |
c900551ffab657bf1a104921097322b65d5247757d1495f3386b029778400db8 | Python | 8,793 | 186 | import torch
import torch.nn as nn
class BANet(nn.Module):
def __init__(self, in_channels=4, out_channels=1, init_features=8):
super(BANet, self).__init__()
# Common
self.activation = nn.ReLU(inplace=True)
scale = 2
# ENCODER
# Layer 1
in_features_1 = in_c... |
0c073071bcb3874b0f0a2bc6a06dfbf378a28df12b4817bb5ebea796477df540 | Python | 8,795 | 245 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Exercise magnetic-force conventions through the registered LAMMPS adapter.
Generate the CPU graph fixture with ``source/tests/infer/gen_dpa4c_spin_lmp.py``.
PyTorch-enabled LAMMPS CI sets DPA4SPIN_LMP_REQUIRED=1 so missing fixtures,
Python bindings, or plugin registratio... |
1632bc2cabb14b2562fc69e977059fa298f796682e7d103021d676493e7c08e3 | Python | 8,798 | 229 | """
This script will upload data to the designated VGP upload bucket in AWS
and create a link to a corresponding file object in DNAnexus.
The directory structure created in S3 will be as follows:
s3://bucketname/
|--species
| |-- <species_name>
| | |-- <species_id>
| | | |-- genomic_data
| | | | |... |
499b79b141c843bc2ea3d371dd87ee7880e0a9b934c3cf636a1a04d1646f5f34 | Python | 8,798 | 231 | import torch
from torch import nn
torch.cuda.empty_cache()
import datasets
import transformers
from transformers import activations
import pandas as pd
import numpy as np
from transformers import DistilBertTokenizer, \
DistilBertForSequenceClassification, DistilBertModel, DistilBertPreTrainedModel, Trainer, TrainingArg... |
b484bb65c869a908eb9eb0ace7858687a8a28a9cf49efaaec5272185511c3df8 | Python | 8,798 | 185 | import sys
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import NonSpikingNeuron
from sns_toolbox.connections import NonSpikingSynapse
from sns_toolbox.networks import Network
# # Personal stuff to send an email once data collection is finished
# sys.path.extend(['/home/will'])
# ... |
2ab16030618ea2a7e27eaa5aa7986b7e74098aeca8361fec1805b6e9e018fe54 | Python | 8,808 | 220 | # Copyright 2019-2021 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... |
590dfad665be8d5f911474ed1ce8151bc3b4da562b1ec1dd1cbd61f3a3d93c41 | Python | 8,809 | 257 | # 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... |
8b3271018ed2fd542c72b29976fae772053625b402c575a11b768dfd67649987 | Python | 8,810 | 358 | #%%
import pandas as pd
filename = "bgm/data/elife-24838-fig1-figsupp4-data1-v1.csv"
adj_df = pd.read_csv(filename, index_col=0)
adj_df
# %%
from graspologic.plot import heatmap
heatmap(adj_df.values, transform="binarize")
#%%
heatmap(adj_df.values[5:, 5:], transform="binarize")
#%%
orn_adj_df = adj_df.iloc[5:, 5:]... |
97cbb591fefb423f822022ab158a81412bd4db0e1a4b47da6b4afa546051372b | Python | 8,816 | 329 | #%% [markdown]
# # Connectome data
#%%
import datetime
import time
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from pkg.data import load_split_connectome
from pkg.io import OUT_PATH
from pkg.io import glue as default_glue
from pkg.io import sa... |
128cb21fe187aedeb551ccde398a06ee0f6290f3c3a6802fc2ad254a7848da73 | Python | 8,823 | 304 | import random
import torch
import torch.nn as nn
import torchvision.transforms as TvT
from spikingjelly.clock_driven import functional
from spikingjelly.clock_driven import neuron
from network_3d.poolingNet_cat_1res import NeuronPool_Separable_Pool3d
from tqdm import tqdm
from data.dsec_dataset_lite... |
48489c04b71cb6e1ab626173349aa0e4cf0c40a8ff75e0470b64fa5a54f80dc4 | Python | 8,824 | 232 | import dolfin as df
class Solver():
""" Class for solving the zero-flow model used in Sætra et al. 2023
with unknowns w = (k_r, phi_r) where:
k_r - concentration of ion species k in compartment r
phi_r - potential in compartment r """
def __init__(self, model, dt_value, Tstop):... |
40a73321328a8f1a20cc357b3bdd1b65df902db8be63f4f1eb5515cb87f650ad | Python | 8,827 | 273 | import os
import torch
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader
import sys
import shutil
from train import train
import time
import math
from read_input_data import *
device=torch.device('cuda:0')
# torch.cuda.set_device(device)
torch.backends.cuda.matmul.allow_tf32 = False
torch.backends... |
1e221c8e579590c2403fff48bffc0dd9e6b5f923fa2e0697db1579a9f006f36a | Python | 8,831 | 212 |
#import re, sys, string
import regex as re, sys, string
###########################
#Generic_G4_g = re.compile(r'G{3,}([ATCG]{1,3}G{3,}){3,}', re.I)
#Generic_G4_c = re.compile(r'C{3,}([ATCG]{1,3}C{3,}){3,}', re.I)
Generic_G4_g = re.compile(r'(?=(G{3,}[ATCG]{1,7}?G{3,}[ATCG]{1,7}?G{3,}[ATCG]{1,7}?G{3,}))', re.I)
Gener... |
de97ecc231d216635b1b92a5da0fcb5bc8eca8035c4ee2b3b32896a3a33e59e8 | Python | 8,831 | 240 | # 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... |
5010f1372ee1d58cfecc6db79bb727d43f95a3f46c63d0b00584d40bf466dcc4 | Python | 8,834 | 204 | # SAFE TEAM
#
#
# distributed under license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode.txt) #
#
import tensorflow as tf
# structure2vec
# DE-MF : discriminative embedding using Mean Field
class NetworkLSTM:
def __init__(self,
features_size,
e... |
233b77c37d6c2ca05edd4f53ef709adaa9af39d8b420e57e7ce44416b6887b2e | Python | 8,837 | 258 | """Residual Network (ResNet) for classification."""
__all__ = ["ResNetClassifier"]
from copy import deepcopy
from sklearn.utils import check_random_state
from sktime.classification.deep_learning.base import BaseDeepClassifier
from sktime.networks.resnet import ResNetNetwork
class ResNetClassifier(BaseDeepClassifi... |
9d5624a941829ae3ae1745b86052f1f4e535dde5fa757bffbaf3bf59b3b3ef19 | Python | 8,842 | 228 | #!/usr/bin/env python
# coding: utf-8
import os
from scipy import sparse
import argparse
import logging
import pandas as pd
import numpy as np
import anndata
from robustlink import utils
from robustlink import enhancer_gene_utils
logger = utils.create_logger()
def pipe_corr_analysis_atac(
common_modx_cells,... |
a2dead361675aa26a6e1bee4a235bcf76071a97c83b28b2c3c1b743e5e0cb102 | Python | 8,845 | 285 | from __future__ import annotations
from dataclasses import dataclass
from typing import ClassVar
import numpy as np
import matplotlib as mpl
from seaborn._marks.base import (
Mark,
Mappable,
MappableFloat,
MappableString,
MappableColor,
resolve_properties,
resolve_color,
document_prope... |
7a602808b2c4719c872cc42afdb658b2d55985076f2715fe5cf4a7041ccf023a | Python | 8,847 | 271 | import os
import sys
import numpy as np
from sklearn.cluster import KMeans
import numpy as np
from sklearn.cluster import KMeans
import glob
from torch_geometric.data import InMemoryDataset, DataLoader
from torch_geometric import data as DATA
import torch
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
imp... |
0be83256838735a5346f1b2b8c4ec93770a6caa17e7c48ef9c8bbbb48dc86b9a | Python | 8,848 | 272 | import os
import sys
import numpy as np
from sklearn.cluster import KMeans
import numpy as np
from sklearn.cluster import KMeans
import glob
from torch_geometric.data import InMemoryDataset, DataLoader
from torch_geometric import data as DATA
import torch
from rdkit import Chem
from rdkit.Chem import MolFromSmiles
imp... |
1590ac0d0377352ee7cf71f285339f8e5a76acfceb3046fbab190641f6fe1434 | Python | 8,851 | 191 | #------------------------------------------------------------------------------
# elftools tests
#
# Maxim Akhmedov (max42@yandex-team.ru)
# This code is in the public domain
#------------------------------------------------------------------------------
import os
import unittest
from elftools.elf.elffile import ELFFi... |
f923c1c531965c34bb2b9b76b71240ef28b88cbad3202bf416e258d4a5e38be2 | Python | 8,852 | 220 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import warnings
from ..builder import CLASSIFIERS, build_backbone, build_head, build_neck
from ..heads import MultiLabelClsHead
from ..utils.augment import Augments
from .base import BaseClassifier
warnings.simplefilter('once')
@CLASSIFIERS.register_module... |
6c09503604d7130045cfb3997890ad482bfe9a46609b9e66aab6e4a1a1e4cca3 | Python | 8,853 | 216 | # 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... |
b6c2917ed88150c09ed18bceef61d77a4b19a2681e459e7f86abe4fbe868f26c | Python | 8,855 | 193 | """
@file: dataset_loader.py
Created on 22.10.18
@project: crazy_ara_refactor
@author: queensgambit
Please describe what the content of this file is about
"""
import glob
import logging
import numpy as np
import zarr
from DeepCrazyhouse.configs.main_config import main_config
from DeepCrazyhouse.src.domain.util import ... |
7c2b0c6a4429b678f34f3b803ec4087828bdb54de96ca501e2d3e461990d571b | Python | 8,859 | 231 | # -------------------------------------------------------------------------------
# elftools: ehabi/ehabiinfo.py
#
# Decoder for ARM exception handler bytecode.
#
# LeadroyaL (leadroyal@qq.com)
# This code is in the public domain
# -------------------------------------------------------------------------------
from __f... |
fe412fec7d4585f584f6605f959fd7985905eddf3763aaf6cde827fba004f971 | Python | 8,862 | 193 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
73c66b158c074050fe294ed245f3c90edc0aace98614c5d61450085fcd30d869 | Python | 8,864 | 202 | #Plot BoostMEC trees
#This code is modified from the lightgbm source code for plotting/create_tree_digraph()
#https://lightgbm.readthedocs.io/en/latest/pythonapi/lightgbm.create_tree_digraph.html
#https://lightgbm.readthedocs.io/en/latest/_modules/lightgbm/plotting.html
import os
import matplotlib
import pydot
... |
7d9fe8f104e0850389d0b9f9c2fbe895eca4ca6f1291ac25f495d959650b13a6 | Python | 8,864 | 190 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
0335b80656f89d82d145aa8ff288f14847454009db3f9bdcde866c57528d05df | Python | 8,865 | 260 | import os
import redis
import pickle
from sys import platform
from pciSeq.src.viewer.utils import get_pciSeq_install_dir
import pciSeq.src.diagnostics.config as config
import getpass
import subprocess as sp
import logging
du_logger = logging.getLogger(__name__)
class RedisDB:
def __init__(self, flush=False):
... |
c8e8aaf7af6df0ac6d11195873364a3b8b252f7a7e5c0498c43e5f3002f9016d | Python | 8,866 | 239 | import os
import pickle
import subprocess
from pathlib import Path
from typing import Union
import numpy as np
import SimpleITK as sitk
from evalutils import SegmentationAlgorithm
from evalutils.validators import (UniqueImagesValidator,
UniquePathIndicesValidator)
from picai_baseline.... |
067edb9fee46918c49446914a8b749b0372d3a80ea61f788287c6a0f9c828f52 | Python | 8,867 | 257 | """Machine type checkers for Alignment scitype.
Exports checkers for Alignment scitype:
check_dict: dict indexed by pairs of str
1st element = mtype - str
2nd element = scitype - str
elements are checker/validation functions for mtype
Function signature of all elements
check_dict[(mtype, scitype)]
Parameters
--... |
7839d92329fb8023a2d7bce6e52e71670e5339b68679c8a86a2e11f392acca8e | Python | 8,867 | 316 | """Tests for source/odp_polarity_plot.py.
The polarity plotter is mostly rendering code, so these tests use tiny
in-memory-style TSV fixtures and inspect the matplotlib objects it adds.
"""
from __future__ import annotations
import math
import pandas as pd
import pytest
@pytest.fixture(scope="module")
def pp(sourc... |
969161cb8a8fd71930e55d35fd9e13880b56f039112da560f6f771f6e9d0bfe9 | Python | 8,868 | 238 | from typing import Any, Optional
import pytest
import flair
from flair.data import Dictionary, Sentence
from flair.embeddings import TransformerEmbeddings
from flair.models import FewshotClassifier
from flair.nn import Model
from flair.trainers import ModelTrainer
class BaseModelTest:
model_cls: type[Model]
... |
9b8e1d00174a66727864baf40964c6f3da5d4e3a72858f0ee34589990b14e9dc | Python | 8,868 | 264 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
from typing import Any
import numpy as np
import onnx
from onnx import NodeProto
from onnx.backend.test.case.base import Base
from onnx.backend.test.case.node import expect
class TfIdfVectorizerHelp... |
a84240f7c1f7d6c2fd1a9644952a632226b1ce8c35c881b7f5b19804ef4d95cc | Python | 8,869 | 193 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
6dce1a3878f0185377ea79f7efba002049b8886db9cdfb374714f4c48e6cba53 | Python | 8,879 | 159 | """Recover shared splice chains before intersecting study-specific identifiers.
This creates a separate data version; it never modifies the original benchmark.
No target-domain count is consulted when constructing the shared catalogue.
The catalogue still uses both studies' released annotations (closed catalogue,
not ... |
05b314656e1035730db643342e279957cce8988428614dac1797f8affddbd1c5 | Python | 8,880 | 193 | """
Compare the simulation speed of the different backends
William Nourse
September 9 2021
The correct term is Babes, sir
"""
import numpy as np
import torch
import time
import pickle
from sns_toolbox.neurons import SpikingNeuron
from sns_toolbox.connections import SpikingSynapse
from sns_toolbox.networks import Netw... |
b57f5f717496a1dcca67601d52471249593424c114b01a05097297d8abf9a245 | Python | 8,890 | 232 | import torch
import torch.nn as nn
import math
#from math import round
import torch.utils.model_zoo as model_zoo
def conv3x3(in_planes, out_planes, stride=1):
"3x3 convolution with padding"
return nn.Conv2d(in_planes, out_planes, kernel_size=3, stride=stride,
padding=1, bias=False)
clas... |
104f1470c5768e78b0ff7744a9bd4bbcc7fe40cbcc04ba4935f24f71b9ecc823 | Python | 8,894 | 277 | """
Test and compare different cross-correlation methods.
We test our "local" calculation in reverse_correlation.py with a reference
package in elephant. The Brian package (in spikestatistics.py) makes different
assumptions, and is not comparable.
This module is part of *vcnmodel*.
Support::
NIH grants:
DC R... |
6b553b064daacbb810a77490a22737d563d53f8ee41d2a2d6a52178e7db01b77 | Python | 8,897 | 248 | # Copyright (c) OpenMMLab. All rights reserved.
from typing import Sequence
import torch.nn as nn
from mmcv.cnn import build_norm_layer
from mmcv.cnn.bricks.transformer import FFN
from mmcv.runner.base_module import BaseModule, ModuleList
from ..builder import BACKBONES
from ..utils import PatchEmbed, to_2tuple
from ... |
e60214c7e3b77c2bbd0b5bcf6d1795eb4b14f43b9e2e2799573cc02551fce7ce | Python | 8,897 | 291 | # Mocapy: A parallelized Dynamic Bayesian Network toolkit
#
# Copyright (C) 2004 Thomas Hamelryck
#
# This library is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License... |
dedd9bacdf39e7268db17d46c5237cd1cb16844ab6e49a538d879415fd32754c | Python | 8,898 | 167 | #!/usr/bin/env python
"""
This takes in a list of RBH files from multiple species and constructs a rbh database file.
This is useful in the case where we have limited .rbh files that only have a few columns.
The reason for writing this script was to accommodate alternative ways of introducing homologous loci into var... |
b02fc28717d42954f15dad87277894d7a2f7cc6af7b80b2dfac827d0c1903d35 | Python | 8,901 | 280 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# PyFilterbank documentation build configuration file, created by
# sphinx-quickstart on Sun Jun 1 13:01:31 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this... |
fbc2ed7ae81b05f87ce2f45603bf6185eddc3f796819adef2f083bb2df976a87 | Python | 8,909 | 200 |
import os
import numpy as np
import matplotlib.pyplot as plt
from PIL import Image
from numpy.lib.function_base import flip
import pandas as pd
from math import *
import pandas as pd
import torch
import torchvision.transforms.functional as TF
from skimage.segmentation import disk_level_set
torch.cuda.e... |
a3906a41b1f38ba536ba32fe34b0bd024257a2395a5fb2d578b8be1fbc97f11f | Python | 8,920 | 225 | import json
from multiprocessing import Queue
import networkx as nx
from networkx import json_graph
import numpy as np
from scipy import sparse
import sqlite3
from threading import Thread
from binary_similarity.utils import __padAndFilterLSTM as padAndFilterLSTM
from binary_similarity.utils import __padAndFilter as pad... |
15f762f6f070d87a3206afe75c535ba02f30f5f62ee9a2ef0fa57596cebc9038 | Python | 8,922 | 289 | """
iterio from werkzug.contrib since it was deprecated and remove
ideally we can get rid of this in idlib
werkzug@2b2c4c3dd3cf7389e9f4aa06371b7332257c6289
"""
def _mixed_join(iterable, sentinel):
"""concatenate any string type in an intelligent way."""
iterator = iter(iterable)
first_item = next(iterator... |
5b9d53b6383ba365ebd5bda4576565942208b50795d87c645d508a0a1e1cc1ab | Python | 8,923 | 230 | """
@file: lr_schedules.py
Created on 30.09.18
@project: crazy_ara_refactor
@author: queensgambit
This file contains the description of the common Advanced Learning rates.
Code is based on:
https://mxnet.incubator.apache.org/tutorials/gluon/learning_rate_schedules_advanced.html
"""
import copy
import math
import matp... |
5747b8a4db4eb86656f67399544d5434963bf9ba6f273a00cad5d7ea59017569 | Python | 8,926 | 268 | #!/usr/bin/env python
import click
from click_option_group import optgroup
import json
import numpy as np
import os
import pandas as pd
import shutil
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
os.pardir))
sys.path.insert(0, os.path.join(os.... |
3d650b9964cdba83c58246304e0331932ec83bdf834240ae814cb4e292ce3fba | Python | 8,927 | 268 | #!/usr/bin/env python
import click
from click_option_group import optgroup
import json
import numpy as np
import os
import pandas as pd
import shutil
import sys
sys.path.insert(0, os.path.join(os.path.abspath(os.path.dirname(sys.argv[0])),
os.pardir))
import time
import torch
from expl... |
1776656a36ee2642d22105328123ac145b386d04fa9f0260329a13e6e5d9b4e4 | Python | 8,928 | 196 | import tensorflow as tf
from tensorflow.contrib.rnn import LSTMCell, GRUCell, MultiRNNCell, DropoutWrapper
from tensorflow.contrib import distributions as distr
from .encoder import Attentive_encoder
# RNN decoder for pointer network
class Pointer_decoder(object):
def __init__(self, encoder_output, config):
... |
8a68da44056d41a869e3b0033e64e719089c23bb32afac93950caacf2ece38da | Python | 8,928 | 215 | import glob
import os
import numpy as np
import torch
from nn_common_modules import losses as additional_losses
from torch.optim import lr_scheduler
import utils.common_utils as common_utils
from utils.log_utils import LogWriter
CHECKPOINT_DIR = 'checkpoints'
CHECKPOINT_EXTENSION = 'pth.tar'
class Solver(object):
... |
60849740595e2467cccafb444cdc0164d341437b7001615a544921ede2054629 | Python | 8,938 | 269 | # 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... |
45518bcb4da8f7eaac0dc9e1973dd838dd2ea7e216b37d4a63977d1bb1f0ea30 | Python | 8,940 | 266 | #%% [markdown]
# # Maggot connectome subset
#%%
import datetime
import logging
import time
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
import pymaid
import seaborn as sns
from graspologic.plot import adjplot
from pkg.data import DATA_PATH
from pkg.io import glue as defa... |
6c9f21d4cafb084a1ec237c1955d67d067effa185d771344abca9085a1d916e6 | Python | 8,950 | 249 | """Checks that the GIFT-Eval evaluation script runs off a safetensors snapshot.
``benchmarks/forecasting/gift_eval/evaluate.py`` is a script rather than an
importable package, so it is loaded here by path. Its ``build_model`` is the
whole checkpoint-facing surface: it resolves ``--pretrain_ckpt``, wraps the
backbone ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.