sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fe9c3d5596642e106051229635acea3d91468cb0df1e4149b59371b81b8b0ca3 | Python | 5,650 | 175 | """
File to define the entry point to Model Server
"""
import os
import re
import subprocess
import sys
import tempfile
from builtins import str
import psutil
from ts.version import __version__
from ts.arg_parser import ArgParser
def start():
"""
This is the entry point for model server
:return:
"""... |
6f2f7965f8ed3a8db0e1d0d73ae5095cec6c48058bc5e7e82fafa53a5d5fb09b | Python | 5,651 | 169 | """Time series Agglomerative Clustering."""
__author__ = ["Muhammad-Rebaal"]
__all__ = ["TimeSeriesAgglomerativeClustering"]
from scipy.cluster.hierarchy import fcluster, linkage
from scipy.spatial.distance import squareform
from sktime.clustering.base import BaseClusterer
from sktime.dists_kernels.base import Base... |
aad5498c5bb8454c8a0abeef9f043f7bab65e325362611de0183d6b65d79c671 | Python | 5,651 | 169 | #!/usr/bin/env python3
'''
Functions for manipulating matploblib and cv2 colormaps, as well as some functions for converting between rescaled to dfof values. On first import, loads defaults set by seas.defaults configuration into REGION_COLORMAP, DEFAULT_COLORMAP, and COMPONENT_COLORMAP.
Authors: Sydney C. Weiser
Dat... |
3db127f2f17a6b371d271e585c75aed5c1c792e8006c117f12a80451f46f2315 | Python | 5,656 | 154 | # 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... |
57b1f218bdcadbdffb406928a6edbcd9193ea4cbe9a74901172a66a3caad687b | Python | 5,664 | 152 | # 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... |
779438974cd2fd4e6ed2e6166a190513d4652b2c7f5f4bf2bf930b24a4c3eee3 | Python | 5,664 | 144 | from typing import Tuple
import torch
import torch.nn as nn
from .utils import get_p_polar, get_p_cartesian, get_polar_rel, check_p_dim
from scipy import optimize
class HungarianMSELoss(nn.Module):
"""Permutation invariant MSE Loss for jets using scipy.optimiz (Hungarian algorithm)."""
def __init__(self):
... |
506938143f92610069c33b802d17de159ec88d6e14932f8a89c84c7b8b42aba3 | Python | 5,665 | 179 | """
Utility methods for datasets.
"""
from __future__ import annotations
from typing import Set, List, Tuple, Union, Any
from numpy.typing import ArrayLike
import requests
import sys
import os
from os.path import exists
import numpy as np
import logging
def download_progress_bar(file_url: str, file_dest: str):
... |
c79a72174cd45225662378b897a065256d19b80d62f61dfcb7ed64f00f52f3a4 | Python | 5,665 | 202 | """MP distance."""
import numpy as np
def sliding_dot_products(q, t, q_len, t_len):
"""Compute the sliding dot products between a query and a time series.
Parameters
----------
q: numpy.array
Query.
t: numpy.array
Time series.
q_len: int
Length... |
43b54dcda71df954325a0023cf908ba625b4c12385e1536ee45d2eb24996b448 | Python | 5,669 | 152 | # 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... |
1ea6caadad8af1a58909bac11f9d5fb66bbd7584904d94083c008e5845bd9ee5 | Python | 5,672 | 187 | # 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... |
6df4412ed8c18733736ea48daceb54a3a14f0456242559e29bb91cb2b8982335 | Python | 5,673 | 129 | #!/usr/bin/env python
import sys
import os
import math
import re
from os.path import isfile, join, isdir
import imageio
import numpy as np
from kn_common import pipetools,pipedef
from kn_pipeline_class import CPipeError,CPipeStep
class CPipeStepHighResMap(CPipeStep):
matlab_tools=pipedef.maltab_tools
mat... |
c69599b4b617ccbe41b387c28ce20ac1be6482d5eeb1b5406bfb25ef8e51588a | Python | 5,673 | 158 | import cv2
import matplotlib.pyplot as plt
import numpy as np
import argparse
import glob
import time
import os
from tools import videoMetadata
from constants import *
import pdb
from scipy.stats import circmean
import matplotlib
from matplotlib import gridspec
import pandas as pd
from matplotlib import cm
from matplo... |
34d531561b7fae29112fb99240d6ed956c4dcf61e00c91c85a7f20924dbee00d | Python | 5,674 | 125 | #!/usr/bin/env python3
import subprocess
from pathlib import Path
from collections import defaultdict
import rdflib
from ttlser import natsort
from pyontutils.core import qname, makeGraph
from pyontutils.utils import TermColors as tc
from pyontutils.namespaces import NIFRID, ilxtr
from pyontutils.combinators import re... |
4e5eaf21a2a0a8152dcc37871349ba214a18e9a65f3a6bece122d458e6736fdd | Python | 5,675 | 217 | from sns_toolbox.networks import Network
from sns_toolbox.connections import NonSpikingSynapse, SpikingSynapse
from sns_toolbox.neurons import NonSpikingNeuron, SpikingNeuron
import time
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
# SNS Version
net_ns = Network()
net_s = Network()
neuron_... |
502ef354fbccc9d0144fa3e0eeb996e9ad77d6fecc93cc060c1aed3d91b5b1bd | Python | 5,677 | 175 | # 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
#
"""Data source identifier.
This module provides the main class and the support... |
db46c426c6f550b4ab9b8ebcfb7668cd10d60c22646577ed6385b78937a7dee6 | Python | 5,678 | 137 | # copyright: skpro developers, BSD-3-Clause License (see LICENSE file)
"""Base class for data types."""
__author__ = ["fkiraly"]
from sktime.datatypes._base import BaseDatatype
class ScitypeHierarchical(BaseDatatype):
r"""Hierarchical data type. Represents a hierarchical collection of time series.
The ``Hi... |
ee4eea6c19124337aa9c6d61d11ecace408c08f5ef6aba95eefe9960f29eb349 | Python | 5,679 | 133 | """
Parameters:
----------
ndl: neighbours of each vertex, read from the {h}.pial.neighbor.asc file for each hemisphere
nb: max number of neighbor for each vertex
Returns:
-------
{h}.pial.area.asc: surface area associated with each vertex for each hemisphere
{h}.pial.K.asc: Gaussian curvature (K) at ea... |
08e6fa4fb1721bf14fc9e1baabf78bbaf275fe55f965a42651ec5212afc930c5 | Python | 5,680 | 150 | # 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
#
# ... |
9c28c804d4078c2f929565713ed99580c8d3c2b384935a96a8266f52379a5193 | Python | 5,680 | 157 | # 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... |
4c3c9533291030aca61a2d4c3c85ca643301583c92f49812e4801343c82635cd | Python | 5,681 | 170 | import pandas as pd
from typing import Tuple, Optional, Dict, Any
from .src.validation.config_manager import ConfigManager
from .src.validation.input_validation import InputValidator
from .src.core.main import VarBayes
from .src.core.utils import write_data, pre_launch
from .src.viewer.run_flask import flask_app_start
... |
3de71645c0075abd665435685507a00b4ba1515c18d57a2f103afd17f12f65fb | Python | 5,683 | 186 | import itertools
from pathlib import PosixPath
from typing import Generator, List
import ants
import numpy as np
import torch
import torchio as tio
from omegaconf.dictconfig import DictConfig
from rich.progress import track
from hsf.augmentation import get_augmented_subject
from hsf.engines import InferenceEngine
d... |
d603479f341c3b2dd297304dc4d11e6e73dc3a5739d37d058963aba308e06735 | Python | 5,684 | 152 | patchseq_config = {
"train_batch_size": 16,
"finetune_batch_size": 16,
"transfer_batch_size": None,
"train_epochs": 20,
"finetune_epochs": 20,
"transfer_epochs": None,
"train_task": "cross_model_prediction_clus", # "cross_model_prediction_clus",
"finetune_task": "unsupervised_gr... |
d416ce15806257307e7635f153f1e36fe5cf7aa71d8182feaacbe3819a23c0fc | Python | 5,686 | 140 | # Copyright (c) ONNX Project Contributors
#
# SPDX-License-Identifier: Apache-2.0
from __future__ import annotations
import argparse
import json
import os
import shutil
import onnx.backend.test.case.model as model_test
from onnx import TensorProto, numpy_helper
TOP_DIR = os.path.realpath(os.path.dirname(__file__))
D... |
5d577082fc87633f2aa6977d0e72a02b52653aa20d80497c98b08c829b5c2a4b | Python | 5,687 | 162 | # 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... |
431e5522ec7914f81ac80029bc1031946de89a2540a6d28eebade60fbe0a912b | Python | 5,688 | 153 | # 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... |
ac33dd758d03220a32100d02525c5a009a29de9a4f192f5f54de60896189dbd8 | Python | 5,690 | 158 | import argparse
import json
import numpy as np
import os
import multiprocessing
import pickle
import sys
from collections import Counter
from rdkit import Chem
from tqdm import tqdm
sys.path.append('./util')
from rdchiral.template_extractor import extract_from_reaction
parser = argparse.ArgumentParser... |
c032e6dff915d150ba76624bf2b80d4ac4f03ab76c0865ca5dd36207c7ace452 | Python | 5,691 | 212 | # 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... |
7c8ec2491ba50213bc46939ce93f3041fdbfe0d0655a6bbdd38fc642b435fd81 | Python | 5,694 | 118 | # SAFE TEAM
# distributed under license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode)
import argparse
import os
import sys
from subprocess import call
class Downloader:
def __init__(self):
parser = argparse.ArgumentParser(description='SAFE downloader')
parser.add... |
7053c716cc87a44d367de0c6690b2327671c654ab0c5fbec884c4430ae62aa0a | Python | 5,697 | 149 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import os
os.environ["CUDA_VISIBLE_DEVICES"]="1,6" # Choose which GPUs by checking current use with nvidia-smi
import tensorflow as tf
# import tensorflow_addons as tfa
from tensorflow import keras
from tensorflow.keras.applications import ResNet152V2
from tensorflow.ker... |
1f497aa481e276199d9407548dda38837652501d1bd4d296eda7360d710893ca | Python | 5,704 | 156 | import numpy as np
from keras.optimizers import *
import os
import pandas as pd
from scripts import models_util
from scripts_tl import training_util_tl
import scipy as sp
import keras
# Global dictionaries
name_to_optimizer_dict = {'Nadam': Nadam, 'SGD': SGD, 'RMSprop': RMSprop, 'Adagrad': Adagrad, 'Adadel... |
7990196023905cfc6541dceeca8383e43dc93396e9eca9021c2023e0e7effb91 | Python | 5,704 | 165 | #!/usr/bin/env python
__doc__ = """
Training Script
Put all the ugly things that change with every experiment here
Nicholas Turner, 2017-8
"""
import os, imp
import collections
import torch
import tensorboardX
import utils
import train
import loss
def main(**args):
#args should be the info you need to spec... |
c8bc892adc1343c8e45f9857536f9391d4f6a2b62c3ece38058c705e62cea4a5 | Python | 5,707 | 215 | import os
import sys
import yaml
import torch
import shutil
import argparse
import torch.nn as nn
from tqdm import tqdm
from operator import getitem
from functools import reduce
from torch.utils.data import DataLoader
from utils.const import regression_loss
def parse_config():
parser = argparse.ArgumentParser(... |
0b004d94ecde88c0ed4ba47cb3bb645bf8d7bb20f9107cfbefecf5f9e0e046ba | Python | 5,708 | 179 | """TSC Bake off 2017 catalogue."""
from sklearn.metrics import accuracy_score
from sklearn.model_selection import ShuffleSplit
from sktime.catalogues.base import BaseCatalogue
class BakeOffCatalogue(BaseCatalogue):
"""TSC Bake-off 2017 catalogue.
Catalogue of datasets, classifiers, metrics, and CV splitter... |
aca427cb1e108ea01510f78be3ecef3dbbf605a7f05fb945b693adbd731434a8 | Python | 5,711 | 165 | # 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... |
42a7abbabe414aac83903d83aef6d2db7c863db37f4a0f24aacd05e50465d0be | Python | 5,714 | 119 | # simple 2D unet from the previous 2D unet
# change the 2d conv into 2D conv
# add instance norm inside; deeper the model
from keras.models import Model
from keras.layers import Input, Conv2D, MaxPooling2D, concatenate, Conv2DTranspose, BatchNormalization, Dropout, Lambda
from tensorflow.keras.optimizers import Adam
f... |
78cfd74d4a9773b62254041a490634f2f8b99d97aaa549aabf051e345356fdf6 | Python | 5,715 | 179 | import json
import os
import shutil
from typing import Callable, List, Tuple
import numpy as np
import pandas as pd
from rdkit.Chem import MolFromInchi, MolFromSmiles, MolToInchi, MolToSmiles
from rdkit.Chem.Descriptors import MolWt
from rdkit.Chem.MolStandardize.rdMolStandardize import Cleanup
MW_THR = 800
MIN_P_DIF... |
e346a76c6cfefead14d899a488a4c95911d725d038d8039686a9e2fb451caa19 | Python | 5,717 | 110 | dbitseq_config = {'train_batch_size': 16,
'finetune_batch_size': 16,
'transfer_batch_size': None,
'train_epochs': 20,
'finetune_epochs': 10,
'transfer_epochs': None,
'train_task': 'cross_model_prediction_clus',
'finetune_task': 'unsupervised_group_identification',
... |
69b55da9587124e9bfe896f194b8cffa6a6a2d68e9cc6e7aa45bdbbb04fd95f7 | Python | 5,720 | 168 | """Hidden Markov Model with Poisson emissions.
Please see the original library
(https://github.com/hmmlearn/hmmlearn/blob/main/lib/hmmlearn/hmm.py)
"""
from sktime.detection.hmm_learn import BaseHMMLearn
__author__ = ["klam-data", "pyyim", "mgorlin"]
__all__ = ["PoissonHMM"]
class PoissonHMM(BaseHMMLearn):
"""... |
93cd1def17853b4e3440ffc1042a9d9667e25514e82d1fd15c0e498a251c57f5 | Python | 5,724 | 129 | import numpy as np
import datetime
from parameterSetup import ParameterSetup
def linearFit(y):
x = np.array([i for i, _ in enumerate(y)])
X = np.c_[x, np.ones(len(x))]
beta = np.matmul(np.matmul(np.linalg.inv(np.matmul(X.transpose(), X)), X.transpose()), y)
# z = np.matmul(beta, X.transpose())
retu... |
47ebcb490966c8c9bd866fe127f4a6932dc3749e20737e1bbdc68d5e05d4c299 | Python | 5,726 | 157 | """
Base classes for JetNet datasets.
"""
import torch
from torch import Tensor
from typing import List, Optional, Tuple, Any, Callable
from .normalisations import NormaliseABC
from .utils import checkStrToList, checkListNotEmpty, firstNotNoneElement
class JetDataset(torch.utils.data.Dataset):
"""
Base cla... |
ccca3d806462fa1f6b354754ed60ec1b4e2bf75b1aa34479cab4c1c1a4cee64c | Python | 5,728 | 131 | 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... |
a8740ca95913bdefb3d1d2dfde96adee26db461efa296d63febc888ab2594c0a | Python | 5,729 | 149 | import torch.nn as nn
import torch
from vp_suite.base import VPModelBlock
class ConvLSTMCell(nn.Module):
r"""
This class implements a single ConvLSTM cell for the ConvLSTM
implemented in https://github.com/ndrplz/ConvLSTM_pytorch.
"""
def __init__(self, input_dim, hidden_dim, kernel_size, bias):
... |
4ac6bf9c44d8ad3a5677204a680e2613c8df58c80be60aed58d69bf827d0522b | Python | 5,731 | 124 | import numpy as np
import tensorflow as tf
# structure2vec
# DE-MF : discriminative embedding using Mean Field
# SAFE TEAM
#
#
# distributed under license: CC BY-NC-SA 4.0 (https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode.txt) #
#
class Network:
def __init__(self,
features_size,
embedd... |
7aaf08617132c7416c57085457ed5c387873444dcf8e115ca232021952f1a7de | Python | 5,732 | 151 | # SPDX-License-Identifier: LGPL-3.0-or-later
"""Register fake tensor implementations for deepmd custom tabulate ops.
These registrations enable torch.export and make_fx to trace through the
compressed forward path, which uses C++ custom ops (tabulate_fusion_se_*).
Without fake implementations, torch.export cannot dete... |
62f900002151b8c024b9699d820d5437a47718d315e2fcfb7e0bd86427ca9eaa | Python | 5,736 | 173 | # -*- coding: utf-8 -*-
import torch
import random
import inspect
from itertools import islice, repeat
import os
def split_corpus(path, shard_size, default=None):
"""yield a `list` containing `shard_size` line of `path`,
or repeatly generate `default` if `path` is None.
"""
if path is not None:
... |
22fae73370e0c990202b35d99e6bdb421c512b237b2b7a87d630173751c812e0 | Python | 5,740 | 166 | """Tests for source/odp_functions.py:check_species_input_legality.
This is the biggest single function in odp_functions and validates the
three input files for one species: genome FASTA, protein FASTA, and
.chrom. Each file has multiple failure modes that produce a multi-line
error message; we cover the happy path and... |
62315688d9034b592ae4d59a7689cc905093468e2c4582cf8e9c86582b000241 | Python | 5,746 | 178 | # Copyright (c) OpenMMLab. All rights reserved.
import numpy as np
import torch
from mmcls.models.utils.attention import ShiftWindowMSA, WindowMSA
def get_relative_position_index(window_size):
"""Method from original code of Swin-Transformer."""
coords_h = torch.arange(window_size[0])
coords_w = torch.ar... |
3c9197b452e65a6ecb4d9ed6883a8ee903428b8e57e70c3b0c1d1a438d090125 | Python | 5,747 | 200 | #!/usr/bin/env python
from Bio import SeqIO
import click
from click_option_group import optgroup
import json
import numpy as np
import os
import pandas as pd
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.... |
8623e42879c8ec31ebd13f564f2a60bc787c5d697f55ec17b25fbc3cf3ebeee0 | Python | 5,747 | 156 | """Find extrema for individual cycles."""
import numpy as np
from neurodsp.filt import filter_signal
from neurodsp.filt.fir import compute_filter_length
from bycycle.utils.checks import check_param_range
from bycycle.cyclepoints.zerox import find_flank_zerox
#########################################################... |
4f2e5a410d8d7eb66fd78915333fb034782dafad4799d338b8adbd4b46ef94a7 | Python | 5,750 | 206 | import json
import logging
import os
import random
import sys
from itertools import combinations
from pathlib import Path
from typing import Tuple
import numpy as np
import pandas as pd
import torch
from torch.utils.data import DataLoader
from transformers import HfArgumentParser
# Local imports
import training.pipel... |
31b42fcadbb8ddd4ddf8bd9352f918747b8039dcbe92e86ec1c02b2df3456730 | Python | 5,751 | 130 | """
Initialization of scCODA models.
:authors: Johannes Ostner
"""
import numpy as np
import patsy as pt
from anndata import AnnData
from sccoda.model import scCODA_model as dm
from typing import Union, Optional
class CompositionalAnalysis:
"""
Initializer class for scCODA models. This class is called when ... |
726ea81909bd5f5f64ac9cd1bd05c436b5f7f8ca90183fe4a5bb2ac06fe4a377 | Python | 5,751 | 158 | #-------------------------------------------------------------------------------
# elftools: common/utils.py
#
# Miscellaneous utilities for elftools
#
# Eli Bendersky (eliben@gmail.com)
# This code is in the public domain
#-------------------------------------------------------------------------------
from __future__ ... |
b4eb7da3265eacf86514394ad697b95ca6dc4570ab38137ba02ae9bb9a281061 | Python | 5,753 | 126 | from mprl.rl.common.util import set_policies_to_train_in_trainer
# def get_ed_fixed_scheduler(best_response_iterations, equilibrium_policy_iterations,
# trainable_tmp_policy_key, static_tmp_policy_key):
#
# def ed_fixed_scheduler(trainer, eval_data):
# if 'is_training_best_respo... |
f445008e15ce5d20462db6ddb6d95e8714325c8a03364b17aeb211a9965fbbc9 | Python | 5,753 | 170 | # 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... |
edf6b40232a7eb53f0b389d4a6c941f4071286a5b7b61b9e9195b0a90110c651 | Python | 5,754 | 131 | # 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... |
b1755923ac2f6b7f42258bd12f967e33baa9fe9c1b4c867c9ef08a74f8e79a30 | Python | 5,756 | 137 | import torch
import torch.nn as nn
import torch.nn.functional as F
import sys
class EncoderDecoder(nn.Module):
def __init__(self, in_seq_len, out_seq_len, in_feat_len, out_feat_len, static_feat_len,
hidden_size, num_layers, enc_dropout, dec_dropout, arch, device):
super().__init__()
... |
33ea07f5999ff1b84407681ddd8e45d43fe91c032cf6a5d886b036fb7f122b43 | Python | 5,757 | 196 | """NIfTI orientation utilities: query, reorient, and swap axes."""
import os
from pathlib import Path
from typing import List, Optional, Tuple, Union
import nibabel as nib
from tqdm import tqdm
from bcblib.imaging._types import NiftiLike
from bcblib.imaging.io import load_nifti
# ----------------------------------... |
edc1849adc4792f30ed242562d884c88531f96c77c8d76b710b2763903d288a0 | Python | 5,757 | 148 | # 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... |
0a20cbbb0a5b54c7da98f7cd8cdcf9b8c5d8ea26356b2622f0a7739f97bf78a6 | Python | 5,758 | 110 | """
@file: preact_resnet_se.py
Created on 01.05.21
@project: CrazyAra
@author: queensgambit
Descirption of a preactivation resnet with se layers
"""
import mxnet as mx
from DeepCrazyhouse.src.domain.neural_net.architectures.builder_util_symbol import value_head, policy_head, get_se_layer
def preact_residual_block(da... |
3e4c22f7ab81994c3e431b46680a3f50a38106da489b56bf4a4da5edcca2b1d2 | Python | 5,758 | 160 | import torch
import torch.nn as nn
from torch.utils import data
import torch.nn.functional as F
import pickle
import numpy as np
class RawDataset(data.Dataset):
def __init__(self, dataset, window_size, train=True):
self.dataset = dataset
self.window_size = window_size
self.train = train
... |
c7b39d2946dd8e1f21f69e06c7be6a5654f22f94088e5e9f07a5ad38b1d6126f | Python | 5,759 | 161 | """
common.py -- Shared model, tilt dynamics, pass@k, sign-variation utilities.
Paper 2: "Pass@k Can Cross Twice" (working title). Solvable model of RLVR as
exponential tilting of a policy over strategies SHARED across prompts.
All randomness goes through a seeded numpy Generator. Every script fixes its
own seed so e... |
013bb6d3fa366b6f555f74cfd13bbd1461fa298a948386e0a4b0addb90ebbdaa | Python | 5,760 | 87 | """
Data structures for model_run
XM13 with nabu channels
"""
# nabu _vshift 4.3 [1] 4.3 [1] 4.3 [1] 4.3 [1] 4.3 [1]
ChannelData = u"""
This table describes the REFERENCE ion channel densities (and voltage shifts if necessary)
for different cell types based on the Xie and ... |
d2a50a9c1e845aac85d83b182a2930db0f9a74387beb47e91d4005d2ad467324 | Python | 5,760 | 110 | """
@file: preact_resnet_se.py
Created on 01.05.21
@project: CrazyAra
@author: queensgambit
Descirption of a preactivation resnet with se layers
"""
import mxnet as mx
from DeepCrazyhouse.src.domain.neural_net.architectures.builder_util_symbol import value_head, policy_head, get_se_layer
def preact_residual_block(da... |
5042552f54798357fe0248d38f365b1f5355852ac643f362fe4b96c5db44a7d0 | Python | 5,765 | 128 | import typing
import torch
import flair.embeddings
import flair.nn
from flair.data import Corpus, Sentence, TextPair, _iter_dataset
class TextPairClassifier(flair.nn.DefaultClassifier[TextPair, TextPair]):
"""Text Pair Classification Model for tasks such as Recognizing Textual Entailment, build upon TextClassif... |
7d10193528641d5942965cbaa60b56bf3c9ef9ad03247166f3ad251d746aa5c1 | Python | 5,769 | 199 | """librdf parser for rdflib"""
__version__ = '0.0.1'
try:
import RDF
except ImportError as e:
print('WARNING: librdf bindings not found. You will have runtime errors.')
import rdflib
from pathlib import Path
def Literal(string, language=None, datatype=None):
datatype = datatype if datatype is None else ... |
a314ccd11c349b838e42e4ccd95bcf5eb0b8b5751c68e0d644c422a7e80c139a | Python | 5,773 | 111 | import unittest
import yaml
import pandas as pd
from hbip.predict import read_seqs
def load_data(base_path, data_name):
config_path = base_path + data_name + "_config.yml"
with open(config_path, "r") as file:
config = yaml.safe_load(file)
data_path = config["path"]
return pd.read_csv(data_p... |
a5e8b947137ca3c34e3e689dfe13c9c7a0ce8f61eddde82edb508e7702189af3 | Python | 5,773 | 123 | import requests
import base64
import json
import sys
import os
import pandas as pd
from tqdm import tqdm
import time
SLEEP_DURATION = 5 # in seconds
# cloud_function_url = 'https://jivjy5pgt3.execute-api.us-east-2.amazonaws.com/covid/oraquicktestpredict'
# cloud_function_url = 'https://jivjy5pgt3.execute-api.us-east... |
def4f262810c2760728846ef92aa331eff7be4079abe777273bd2337dc33699d | Python | 5,774 | 179 | """Tests for KNeighborsTimeSeriesClassifier."""
import numpy as np
import pandas as pd
import pytest
from sktime.alignment.dtw_python import AlignerDTW
from sktime.classification.distance_based._time_series_neighbors import (
KNeighborsTimeSeriesClassifier,
)
from sktime.datasets import load_unit_test
from sktime... |
8efd8e401777cdd45ca5c03111455c9ae56ca3be27498c89b28e0cfe6f82b5b3 | Python | 5,775 | 135 | import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from sklearn.metrics import classification_report, roc_curve, roc_auc_score
from hbip.preprocess import train_test
wuhan = {
"Accession": "YP_009724390",
"Sequence": "MFVFLVLLPLVSSQCVNLTTRTQLPPAYTNSFTRGVYYPDKVFRSSVLHSTQDLFLPFFSNVTWFHA... |
8b01289730ddb3565ee243ba46c32d9fb46df2c7f351da5a3a2d37696568e087 | Python | 5,780 | 188 | from utils import *
import pandas as pd
import numpy as np
import torch.utils.data
import torch
import pickle
import h5py as h5
import os
from model import *
from torch.autograd import Variable
import h5py
import time
#wandb.init()
class Chip2HiCDataset(torch.utils.data.Dataset):
def __init__(self, chipseq_path... |
ae8e0e75f0a0b8cf7c64c2069fac7d764adb8373f3c9315fb0f9800a0bae6293 | Python | 5,782 | 149 | """Methods to extract protein interface labels pair."""
import click
import numpy as np
import pandas as pd
import scipy.spatial as spa
import atom3d.util.log as log
logger = log.get_logger('neighbors')
index_columns = \
['ensemble', 'subunit', 'structure', 'model', 'chain', 'residue']
def neighbors_from_ense... |
31f604e46f6dc87c53752fe894c946cb0408b8e1103bd8e5171b5d65b4758bd6 | Python | 5,783 | 159 | import numpy as np
from keras.optimizers import *
import os
import pandas as pd
from scripts import models_util
from scripts import training_util
import scipy as sp
# Global dictionaries
initializer_dict = {'0': 'he_uniform', '1': 'lecun_uniform', '2': 'normal', '3': 'he_normal'}
optimizer_dict = {'0': Nad... |
dfb952675d1c100cc6a2b03c8f1749bcc700219be4948477568ef960fcfb38d0 | Python | 5,783 | 148 | # 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... |
644c2639a7ba2f214618b6afa984cad41294d0deb61590a461937fc3b2de1a6d | Python | 5,784 | 200 | #!/usr/bin/env python
# coding: utf-8
#Code to generate the figure from the paper
import pytest
import numpy as np
import matplotlib.pyplot as plt
from scipy import optimize
from scipy import sparse
from time import time
from fnnls.fnnls import fnnls
class nnls_comparison():
def __init__(self):
ret... |
41ea25d318d71b2f028d51946c5e5cf49071b9f6a4b4a8f1fac59894160bd33a | Python | 5,786 | 207 | # 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... |
886155f3b8df50ff1ad374ad4ae3027346314987e7174d5dbfe64821c66dc40c | Python | 5,789 | 129 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 3 08:32:28 2020
@author: sam
"""
from detectron2.data import MetadataCatalog, DatasetCatalog
from detectron2.utils.logger import setup_logger
setup_logger()
import os
import numpy as np
import cv2
import random
import pandas as pd
from tqdm impor... |
a2743f4f9a2f78485a30f9cc8775bda7942ecc8eb9e19cb306535071ee3075bf | Python | 5,793 | 173 | # 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... |
b9a87f8a72bc387622e35d198b09ada701a813fb3d73b4e5e04e770ee865f015 | Python | 5,793 | 184 |
import cv2
import matplotlib
import numpy as np
from matplotlib import pyplot as plt
# * syn where to set this
# must use 'Agg' to plot out onto image
matplotlib.use('Agg')
####
def fig2data(fig, dpi=180):
"""
Convert a Matplotlib figure to a 4D numpy array with RGBA channels and return it
Args:
... |
18ce8161e224008c9a2ec7a672794db76004e743c414653de0b2e783f425e28e | Python | 5,795 | 68 | r"""
This module contains the Settings class, which contains constants;
and pre-set program configurations, such as default run config parameters.
"""
import json
from pathlib import Path
from vp_suite.utils.utils import get_public_attrs, timed_input
class _PackageSettings:
r"""
This class contains package c... |
6c5ddce1c7f95acca58ac696380fa653e11467398d9f3b035355db491d261928 | Python | 5,802 | 220 | # code in this file is adpated from
# https://github.com/ildoonet/pytorch-randaugment/blob/master/RandAugment/augmentations.py
# https://github.com/google-research/fixmatch/blob/master/third_party/auto_augment/augmentations.py
# https://github.com/google-research/fixmatch/blob/master/libml/ctaugment.py
import logging
i... |
989bd74be1dc93db7c492c0baf1f6a710b62c2c64fce9e06ebf336e6c1b19f6e | Python | 5,807 | 125 | # Copyright 2019 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... |
0706a5a37f30e9380b6a81a15dd92ac6a1eb0900611cef063efac6628dd298fb | Python | 5,810 | 156 | '''
optimise.py
@author: Nicholas Browning
'''
import numpy as np
import matplotlib.pyplot as plt
'''
general, gly, prepro, pro
'''
import os
import sys
def get_script_path():
return os.path.dirname(os.path.realpath(sys.argv[0]))
def loadold():
# 0 : GEN
# 1 : GLY
# 2 : PREPRO
# 3 : PRO
... |
481d345da3762c6d14e8b73f9125048fc3b03ffff34c574f257b6b6d97877e58 | Python | 5,814 | 168 | """UCR UEA Datasets."""
__author__ = ["jgyasu"]
__all__ = ["UCRUEADataset"]
from inspect import signature
from sktime.datasets import load_UCR_UEA_dataset
from sktime.datasets.classification._base import BaseClassificationDataset
from sktime.datasets.classification.ucr_uea_archive._tags import DATASET_TAGS
from skti... |
48cae547fede2664212551946af25f7f6b4057fe36a84ba34865bf19c2d5c0ef | Python | 5,814 | 115 | """
@file: rl_training.py
Created on 20.11.19
@project: CrazyAra
@author: queensgambit
Functionality for conducting a single NN update within the reinforcement learning loop
"""
import sys
import glob
import logging
from pathlib import Path
import torch
sys.path.append("../../../")
from DeepCrazyhouse.configs.train_... |
015bbe4aa32409d2922833937d5df1823aac756c384ec87a5ccf96be2c4ba705 | Python | 5,816 | 157 | """
Controller component of the MVC pattern for pciSeq diagnostics.
This module implements the Controller layer, responsible for:
1. Coordinating between Model and View components
2. Managing dashboard lifecycle (start/stop)
3. Handling data flow from algorithm to diagnostics
4. System initialization and shutdown
The... |
81367dda74f4c81f259d048832e2994ea43d62b3e65b1ffb06ca745ed0e18ffb | Python | 5,817 | 124 | # -*- 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/.
#
"""Interface with the `Bowtie2 <https://github.... |
714886bb7b7fae38ee5cbc60ca1d6c29af35239b9a31fe0864a653c903a81575 | Python | 5,818 | 169 | import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import os
import argparse
parser = argparse.ArgumentParser(
'Visualize the distribution of learned edges between residues.')
parser.add_argument('--num-residues', type=int, default=77,
help='Number of r... |
7202a6d091b22a6d7e815ffbe6553b8afc136a8075b869037048359d0f246288 | Python | 5,818 | 150 | import argparse
import logging
import os
import time
import datetime
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import pandas as pd
import torch
import torch.nn.functional as F
from torch_geometric.data import DataLoader
from model import GNN_SMP
from data import GNNTransformSMP
from atom... |
ae0da30fdb8345344af30106968b13c8efd086022dbcc56c87ac8761f1610389 | Python | 5,820 | 175 | # 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... |
a520c67d9470e61840609066ffb8d7f02aca45bb1f203423b9a206df623b7723 | Python | 5,823 | 144 | import sys
import pickle
import numpy as np
import math
from parameterSetup import ParameterSetup
#--------------
# print in the format of a latex table
params = ParameterSetup()
pickledDir = params.pickledDir
paramDir = params.pickledDir
args = sys.argv
if args[1] == 'test':
datasetType = 'test'
groupIDs = ... |
39b757f5d9dfd6c62901a496a21b56545e87cf9284bee4ea6392cac09015745d | Python | 5,824 | 191 | #!/usr/bin/env python3 -u
# copyright: sktime developers, BSD-3-Clause License (see LICENSE file)
"""Utility class for plotting functionality."""
import numpy as np
from skbase.utils.dependencies import _check_soft_dependencies
from sktime.utils.validation.forecasting import check_X
__all__ = [
"plot_time_series... |
c2b9a61eaf2c5c76dbfea261896f1e40cb968637ab09df184a3ee72be75cd496 | Python | 5,824 | 147 | import numpy as np
import os
import pickle
# My Scripts
from scripts import models_util
from scripts import training_util
from scripts import testing_util
def concantenate_test_data(config, X, X_biofeat, y, DataHandler):
if config.enzyme == 'multi_task':
a=0 # TODO
else:
X = np.... |
899c591a13fdc66fbdb9aa66fb0efa8235edd40667008d33d820494c42bef60f | Python | 5,827 | 110 | dbitseq_config = {'train_batch_size': 16,
'finetune_batch_size': 16,
'transfer_batch_size': None,
'train_epochs': 20,
'finetune_epochs': 10,
'transfer_epochs': None,
'train_task': 'cross_model_prediction_clus',
'finetune_task': 'unsupervised_group_identification',... |
4f10e5021203a74d03d23d33f5ad7e73f379cca8490d0ab7797339c01d399154 | Python | 5,832 | 114 | # 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.
"""Extract contours from images, optionally rescaling and resampling... |
b6db213f4b83b5fd7af3c994640635037ca44f03f0db7a4f22ddabf5a9f90948 | Python | 5,834 | 194 | #!/usr/bin/env python3
# SPDX-License-Identifier: LGPL-3.0-or-later
"""Evaluate a charge-density model on validation/test datasets.
Usage
-----
python dptest_density_script.py model.pt /path/to/data --ratio 0.1 --output result.txt
"""
import argparse
import glob
import math
import os
import random
import sys
import ... |
204e852292a70148a29f5c85a5d3d80134684009f130f893c4a62e6f81ed17e0 | Python | 5,835 | 137 | """
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... |
0cc22caeee3f51930026e3ddc164e3cd6fdd8a19137f0b918e136b8c5fa94927 | Python | 5,836 | 142 | # 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... |
9846bee54a8aae9930e89abfc7f3981396adbee5b262d991044c6504f79af2e0 | Python | 5,840 | 200 | #!/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 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.path.abspath(o... |
ad172fd4f06be0c0d8b18006dee0840a33ee190f3bdd65e5dfc38a6c114eb21d | Python | 5,840 | 155 | """
Module for all things voxelwise and volumetric
"""
import sys
import traceback
import warnings
import hiwenet
import networkx as nx
import nibabel
import numpy as np
from graynet import config_graynet as cfg
from graynet.parcellate import get_atlas_path
from graynet.utils import (
import_features,
is_i... |
46136daa5eb626a0582436076acac58ac60c16f04418a6b7c6e517810b099994 | Python | 5,841 | 128 | """Testing machine type converters for scitypes - convert_to utility."""
__author__ = ["fkiraly"]
import pytest
from sktime.datatypes._convert import convert_to
from sktime.datatypes._examples import get_examples
from sktime.tests.test_switch import run_test_module_changed
from sktime.utils.deep_equals import deep_e... |
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