sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
17843d9c1532c2d32c79a0903580c3d8d727d0b20641e737543ae3959205682e | Python | 6,207 | 129 | import os
import pandas as pd
import warnings
import torch
from torch.utils.data import DataLoader,TensorDataset
from modelClasses import *
from utilityFunctions import *
#torch.backends.cudnn.deterministic = True
warnings.filterwarnings("ignore")
# torch.backends.cudnn.benchmark = True
# os.environ['CUDA_LAUNCH_BLOCK... |
bbf21663ca257a6556157327bebaa0f9fc99fab7df447686ec1b6e6435481c52 | Python | 6,207 | 169 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
e0154964dd5b09f9e24720779204351beea00335aa1ff557a9f628220294f3f7 | Python | 6,207 | 189 | from abc import abstractmethod
from typing import Optional, Sequence, Tuple
from uuid import UUID
from chromadb.api.collection_configuration import (
CreateCollectionConfiguration,
UpdateCollectionConfiguration,
)
from chromadb.api.types import Schema
from chromadb.types import (
Collection,
CollectionA... |
ff3c2d519ce2b0e4120fb97ffbe407ae7ed5dd4ef0dd33a4fd9e2554a10e53ff | Python | 6,209 | 168 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
2ff11e8ccdefa2e9e34d1d9e6a75b48afc3d8855534f58c54caa77b4cc0fa1e9 | Python | 6,210 | 179 | """The stage-two loss weights are the ones the flags asked for.
`--swa_energy_weight` and its siblings only take effect after the stage-two swap,
which is why no end-to-end run pinned them: a short training either never swaps or
swaps into a loss nobody inspects. `get_swa` is where the flags become a loss, so
that is ... |
da82e4ad48cfd7c525d8c2bd2d8f6c7ffbc43199203d3dee59bad3ff4c1363bc | Python | 6,214 | 167 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import subprocess
import time
import traceback
import logging
import paramiko
log = logging.getLogger(__name__)
# Suppress paramiko logging
logging.getLogger('paramiko').setLevel(logging.CRITICAL+1)
def run_command_background(
cmd, r... |
0d9470f3f68dce38c0bed84a79e5bb80294f1846e3547edea0a4d66789e9368d | Python | 6,215 | 177 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from e3nn.o3._irreps import Irrep, Irreps
from nequip.data import AtomicDataDict
from typing import Optional
"""
Migrated from https://github.com/mir-group/pytorch_runstats
"""
def _broa... |
28ff41ba427ae8909f7a10ebaf33138fcc700a1603d6ce3d8993916b4403c795 | Python | 6,216 | 182 | """Online kmeans algorithm on Manifolds.
Lead author: Alice Le Brigant.
"""
import logging
from sklearn.base import BaseEstimator, ClusterMixin
import geomstats.backend as gs
class OnlineKMeans(BaseEstimator, ClusterMixin):
"""Online k-means clustering.
Online k-means clustering seeks to divide a set of ... |
29ee92e5c9fdef42353bf4313f4124e708cb14c09553e6a4c26e10f6b1fea8f3 | Python | 6,216 | 225 | r"""Integrator functions used when no closed forms are available.
Lead author: Nicolas Guigui.
These are designed for first order systems of ODEs written as a
spatial variable :math:`x` and a time variable :math:`t`:
.. math::
\frac{dx}{dt} = force(x, t)
where :math:`x` is called the state variable. It may rep... |
655888c7b1df82d2356cf2dd0e2acc66cd81bf2215ff33dc2720712d8af0af55 | Python | 6,219 | 185 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
"""Custom OmegaConf resolvers for nequip."""
import logging
from omegaconf import OmegaConf, ListConfig
from typing import Dict, Callable, Set, Any, Optional
from nequip.utils import get_project_root... |
485e96c693e6dee58e88f95e44ce8f10ff53a8db0a2361e9949a024f1fab14fa | Python | 6,223 | 159 | """The fragment `vdjdb-web` serves, produced by pandoc rather than by string surgery.
Any one of these failing silently blanks ``/overview``: the Scala side matches each image with a
regex that does not cross newlines, deletes nothing itself, and reads the fragment by a fixed
filename. They used to be properties of a ... |
8f6a55093f4f768f359586f645ce41f707b0807cc008868388efa6928d801fdb | Python | 6,223 | 124 | """
Parameter Sweeps
================
In this tutorial, you will learn how to use the :code:`pyrates.grid_search()` function, which allows you to
perform simulations of multiple parametrizations of a model in parallel. You will learn in which ways you can specify
your parameter grid, how you can customize your simulat... |
9910e5b3188516ad209d39fa7b12547674afccac6bd12a28f21a901f567916f1 | Python | 6,224 | 129 | import os
import sys
# supress warnings about having no GPU
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
import tensorflow as tf
import logging
# suppress warnings about tf retracing
tf.get_logger().setLevel('ERROR')
logging.getLogger('tensorflow').setLevel(logging.ERROR)
import pandas as pd
import numpy as np
import anarc... |
66f850319c1a310b0014287142144645e850c5cdcdc5dccb801d29cf49232c5e | Python | 6,229 | 121 | """Independent-study evidence: what counts as replication, and what does not."""
from __future__ import annotations
import polars as pl
from vdjdb.assemble.evidence import build_evidence, independent_study, support_counts
from vdjdb.schema import EVIDENCE_TABLE_COLUMNS
def tables(*rows: tuple[str, str, str, str]) -... |
02f7eccaf7faa289a15f73e11719c36557219a980dc1559d7cec948740bdbbee | Python | 6,231 | 175 | import numpy as np
from scipy._lib._array_api import array_namespace, xp_capabilities
from scipy.interpolate._cubic import CubicHermiteSpline, prepare_input
@xp_capabilities(
cpu_only=True,
jax_jit=False,
skip_backends=[
("dask.array", "https://github.com/data-apis/array-api-extra/issues/488")
... |
577076b4003f53c9efbac832c6199aeb7ba27400cf510afb4f7bab55eb66f86a | Python | 6,232 | 225 | import logging
import scipy
import geomstats.backend as gs
from geomstats.exceptions import AutodiffNotImplementedError
from geomstats.numerics._common import result_to_backend_type
from ._optimization import Minimizer, RootFinder
class ScipyMinimize(Minimizer):
"""Wrapper for scipy.optimize.minimize.
Onl... |
9886f55861eeae2bbf2f597b5457bf46ce2faa945da1c6988c55086a7a3f14e0 | Python | 6,233 | 159 | #!/usr/bin/env python3
"""Render the canonical-kwarg vocabulary into the docs from one source.
`docs/_data/api-vocabulary.yml` is the single machine-readable source of truth for
the canonical-kwarg vocabulary. This script renders it into a hand-authored doc,
replacing the content between `<!-- AUTOGEN:api-vocabulary:<... |
2333775734ff6d314434c4588290f1002f0fbe16d7d6ca0fb2c0e570427e68da | Python | 6,234 | 192 | # Copyright (c) 2019 PaddlePaddle 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 appli... |
b2f0a23f3009ec32ffc27279c89b7cbc2646c49884b66b044fb4d3f4616f0d17 | Python | 6,235 | 174 | """
Select a region of interest (ROI) by thresholding the intensity signal.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import measure
import shapely.geometry as geo
import argparse
import neo
import os
from utils.io_utils import load_neo, write_neo, save_plot
from utils.parse import none_or_st... |
44c1d680b9298bddc660a4afba014c4ea5a34b4fb5caa9c6e4f43cbdb132e0a6 | Python | 6,236 | 154 | #*----------------------------------------------------------------------------*
#* Copyright (C) 2024 ETH Zurich, Switzerland *
#* SPDX-License-Identifier: Apache-2.0 *
#* *
... |
0c7cc63d53693ca8e41c744c121037f20b5f4068a766e4be0ea3e83368e3c225 | Python | 6,237 | 167 | # Copyright (c) 2020 PaddlePaddle 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
#
# Un... |
729c11207f9d3293eb9ae6fdb6eb5dc97f85df645cff86354c7e3d29be099fca | Python | 6,245 | 205 | """filter_remapped_reads
This is a rewrite of the official WASP code, which no longer requires
a .num.gz file. This code is compatable with the rewritten version of
the first step (find_intersecting_snps), which no longer generates the
.num.gz file. The bam file of remapped reads must be sorted by read name.
"""
from... |
c408f1bc240c04aadb4941f54ffe33846518e35c45a9cacb046113bbab1d6e76 | Python | 6,248 | 153 | import glob, numpy as np, matplotlib.pyplot as plt, cv2.cv2 as cv2, seaborn as sns
import keras.callbacks as cb
from keras.applications import ResNet50, DenseNet121, NASNetMobile, Xception
from keras.preprocessing.image import load_img, img_to_array, ImageDataGenerator
from keras.layers import Dense, Flatten, GlobalAve... |
3a5741038694bc23d6bffb72c87b7fc52350fafacf76e171733b82b475245645 | Python | 6,249 | 191 | # Copyright (C) 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
from openfl.experimental.workflow.interface.fl_spec import FLSpec
from openfl.experimental.workflow.interface.participants import Aggregator, Collaborator
from openfl.experimental.workflow.runtime import LocalRuntime
from openfl.experime... |
31167441b772e6858f5d9ff70ecebc75a9584cd33ee767f2b98b4d81b4dd0154 | Python | 6,252 | 211 | import sys
import json
from tqdm import tqdm
import pickle
import os
import pandas as pd
sys.path.append('../')
from utils import *
from processing import *
import numpy as np
import random
from joblib import Parallel, delayed
from pyimzml.ImzMLWriter import ImzMLWriter
from pyImagingMSpec.inMemoryIMS im... |
20fecaccad43150398c69a90b3ddef6f5c908c17eed98eb28ba157af4499d9d7 | Python | 6,253 | 161 | import importlib
import numpy as np
import torch
from mace.tools.torch_geometric.dataloader import DataLoader as _TgDataLoader
# --- Optional torch_geometric support ---
if importlib.util.find_spec("torch_geometric") is not None:
from torch_geometric.transforms import BaseTransform # pylint: disable=import-erro... |
7f87feaebbd014860e1553ffcf5418e2dd3a379b27786558fc8e1ce4a3f0bcc1 | Python | 6,254 | 198 | # ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.18.1
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
# name: python3
# ---
# %% [markdown]
# # REINVENT4 tutorial u... |
0a2e81f07a2ca008201e94843a2d48e44c0ef0483a9c30384ad3ac45995228fa | Python | 6,256 | 202 | import click
import six
from copy import deepcopy
from corgie import scheduling, argparsers, helpers, stack
from corgie.log import logger as corgie_logger
from corgie.layers import get_layer_types, DEFAULT_LAYER_TYPE, str_to_layer_type
from corgie.boundingcube import get_bcube_from_coords
from corgie.argparsers impo... |
a4e94a3ac32202128ae6b25e9f2b871cf9d586f16913a422825aa830b270186d | Python | 6,257 | 182 | from chromadb.api.types import (
Embeddings,
Embeddable,
EmbeddingFunction,
Space,
is_image,
is_document,
)
from typing import List, Dict, Any, Optional
import os
import numpy as np
from chromadb.utils.embedding_functions.schemas import validate_config_schema
import base64
import io
import impor... |
990e0a136362446b6642952ef2bcd8e8eb9df1198d34c5c04f8a727a44d9e924 | Python | 6,258 | 182 | # SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2020-2026, Christian Gaser. See LICENSE.
"""
Exact threshold-free cluster enhancement.
The TFCE of an element is the integral
TFCE(v) = int_0^{t_v} e_v(h)^E h^H dh
over the extent e_v(h) of the cluster containing v at height h. Implementations
normally appr... |
afddca3fda677ce8a76a7600f238084200d395e68940547e9ad002bdef254d76 | Python | 6,261 | 175 | """
Select a region of interest (ROI) by thresholding the intensity signal.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import measure
import shapely.geometry as geo
import argparse
import neo
import os
from utils.io_utils import load_neo, write_neo, save_plot
from utils.parse import none_or_st... |
62779323d4f7f281f253684039300bbec00cd7c57da1b2287824286e238ddb45 | Python | 6,263 | 157 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_scatter import scatter
from torch_geometric.nn import global_add_pool
from torch_geometric.nn.models import schnet
from torch_geometric.nn import radius_graph, MessagePassing
from ogb.graphproppred.mol_encoder import AtomEncoder, BondEncode... |
9e4ef276028230751854307688087a60ad049595c6f6d4b35fe99b30d9b8fe9c | Python | 6,263 | 210 | """
HRF Functions
=============
Various Hemodynamic Response Functions (HRFs) implemented by NiPy
Copyright (c) 2006-2017, NIPY Developers
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistr... |
a59d6a422b648ea599a2cc586a70eabf880ceec1d168d2ac393ee09300b2c671 | Python | 6,264 | 201 | import numpy as np
import pandas as pd
from neuron import h
from src.constants import DISTANCE_LABEL, SECTION_LABEL, TIME_LABEL, VOLTAGE_LABEL
from src.data import is_long_form, wide_to_long
from src.utils import nearest_idx, nearest_value
def calc_tail_current(ik_np: np.ndarray, t_np: np.ndarray, vclamp: h.SEClamp)... |
f96698341c612a6f5215a4ce42502cfad2d4dd20f138628f9484e3fafc85024e | Python | 6,264 | 167 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from dataclasses import dataclass, field
import torch
from fairseq import metrics, utils
from fairseq.criterions import FairseqCr... |
6a85dd995f9130ef84f01ae0e567c51c335fe51962834fd033257c1ee8992b07 | Python | 6,276 | 184 | import math
import numpy as np
from scipy.signal import butter, sosfilt, sosfilt_zi
BP_ORDER = 2
_BUFFER_DURATION = 30 # seconds
class _Scope:
"""
Class representing a base scope.
Parameters
----------
stream_receiver : neurodecode.stream_receiver.StreamReceiver
The connected stream r... |
51745468f80547c3205e9f0f9db42c30fdfd9dc6cb5020059650bec6d4d618ca | Python | 6,279 | 160 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
# from csbdeep.models import CARE
# from deeprest.rawDataClass import rawData
# from deeprest.modelClass import modelRest
# from deeprest.timeLapseClass import sampleTimeLapse
import time, os, glob
import shutil... |
900683830cdbc8f77e557eef8cf488d265a6087682c71df325e74a67a9e1eeb8 | Python | 6,280 | 155 | """The `vdjdb` command surface.
`cli.py` had no test at all: 173 statements, 0 % covered, while being the only way anyone runs this
build. These cover what can be exercised without a full build - argument handling, the projections
of the field registry, and the exit codes callers and workflows depend on.
The expensiv... |
50d20a3a1fc45ff421fa945781e16243763473b79b413232f9721a75a63a3b0a | Python | 6,281 | 207 | ###########################################################################################
# Statistics utilities
# Authors: Ilyes Batatia, Gregor Simm, David Kovacs
# This program is distributed under the MIT License (see MIT.md)
########################################################################################... |
880463521a618e2db1efd7ca71aec48a68d381a4cdb8145da0745377b9d41ded | Python | 6,282 | 148 | from PymoNNto.Exploration.Network_UI.Network_UI import *
from PymoNNto.Exploration.Network_UI.TabBase import *
class sidebar_neuron_grid_submodule(TabBase):
def __init__(self, add_color_dict):
self.add_color_dict = add_color_dict
self.compiled = {}
for param in self.add_color_dict:
... |
5ff3c524a34931d5d5ba323b5bd0ef2a5df35ff57e4a7b8c605b1b91c63ee27a | Python | 6,283 | 197 | """
This module contains an MQTTClient class that inherits from paho.mqtt.client.Client.
The client is created in the mqtt.init function, and can be referenced at
mqtt.client.
mqtt.mqtt_json_callback is useful when the incoming message payload is a JSON string.
"""
import paho.mqtt.client as paho
import logging
impor... |
2af6291bbcff42a95cc25a7d91223044b53151b4394765972347e05626472341 | Python | 6,284 | 181 | # Author: Guoqing Bao
# School of Computer Science, The University of Sydney
# Date: 2019-12-12
# GitHub Project Link: https://github.com/guoqingbao/Pathofusion
# Please cite our work if you found it is useful for your research or clinical practice
# from IPython import get_ipython
import os
# os.environ["CUDA_VISIBLE... |
a44bcdef26805eeb199df5c5ea14e1b7815e7996a3d35326d0bd4e254c9fd17d | Python | 6,285 | 180 | import tensorflow as tf
class EEGNet(tf.keras.models.Model):
def __init__(self, num_channels, num_samples, dropout_rate=0.5):
super(EEGNet, self).__init__()
self.firstconv = tf.keras.layers.Conv2D(4, (3, 1), padding='valid', input_shape=(num_samples, num_channels, 1), use_bias=False)
self.d... |
f71a8184e326beab10644ec5f082c7bcd6bce3108c2ca965414714b32bcd5be6 | Python | 6,285 | 178 | """Convert the components dictionary into an internal data structure"""
__all__ = ["get_components"]
from dataclasses import dataclass
from collections import defaultdict
from typing import List, Dict, Optional, Tuple, Any
import logging
from .importer import get_registry
from .transforms.transform import get_transfo... |
13d9964213a191d2ecb175cffa00a8d64c926cbd52f4dc0f1cd126b755695d86 | Python | 6,286 | 182 | """
Based on:
https://github.com/hewittwill/ECGXMLReader
"""
import array
import base64
import os
from collections import OrderedDict
import numpy as np
import xmltodict
def find_substrings(substring_list, text):
res = [substring in text for substring in substring_list]
return int(any(res))
class ECGXMLRea... |
fab876f49aee88b97a54813945cbe81500f3873341e375b2e552961805c01c44 | Python | 6,295 | 151 | """
The GOOD-Motif dataset motivated by `Spurious-Motif
<https://arxiv.org/abs/2201.12872>`_.
"""
import os
import os.path as osp
import gdown
import torch
from munch import Munch
from torch_geometric.data import InMemoryDataset, extract_zip
class GOODMotif(InMemoryDataset):
r"""
The GOOD-Motif dataset motiv... |
3067a9cdcbe437d4f866bbec01bad4af78e051a7123ef32e1ce4877e08661d1f | Python | 6,297 | 187 | import torch
import torch.multiprocessing as mp
import torch.distributed as dist
import torch.nn as nn
from typing import List
from collections import namedtuple
import os
from model_angelo.utils.misc_utils import filter_useless_warnings
from model_angelo.utils.torch_utils import get_model_from_file, compile_if_possib... |
52b114262174e99690fc05fd22ec6ad2859abe62265d24c3d20d1d7282e9d575 | Python | 6,298 | 172 | """A training set smaller than one batch fails where the cause is, or trains.
`drop_last` throws away an incomplete final batch. When the set is smaller than
`--batch_size` that is the only batch, so the loader comes out empty and the run
cannot train. It used to say so several frames away, in
`compute_avg_num_neighbo... |
74c590a23e6ac82725838db0df986aaaa81699855b20fd52db5cb27e06ececf2 | Python | 6,298 | 207 | import utils
import torch
from torch.utils.data import DataLoader
import database
import glob
import argparse
import Networks
import collections
import train
import pickle
import calibration
import yaml
import subprocess as sp
functions_nn = {'gru2_bohb': Networks.gru2_bohb.gru,
'gru_bohb': Networks.gr... |
31266b5c1c59db5bc00cd7f435127e05809893ace52991f603a84125e87997d9 | Python | 6,300 | 204 | """Riemannian mean-shift clustering.
Lead author: Nina Miolane and Shubham Talbar.
"""
import joblib
from sklearn.base import BaseEstimator, ClusterMixin
import geomstats.backend as gs
from geomstats.learning.frechet_mean import FrechetMean
class RiemannianMeanShift(ClusterMixin, BaseEstimator):
"""Class for R... |
2849bef5761dd3c0ecec24c7e3e5fbd9996d19942e40782a9bb78e0461a05926 | Python | 6,303 | 163 | from pathlib import Path
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
import numpy as np
import os
palette = sns.color_palette("tab10")
saving_folder = os.path.abspath('results')
# Control separability for non-purified mAbs.
if True:
# Create an array with the colors you want to use
... |
4de06c081335bf5711c5b4e2b274c575f5184d80ccda58529cb2982895a3d2e3 | Python | 6,304 | 126 | import torch
from torch.utils.data import DataLoader,TensorDataset
import pandas as pd
from modelClasses import *
from utilityFunctions import *
# torch.backends.cudnn.deterministic = True
# torch.backends.cudnn.benchmark = False
os.environ['CUDA_LAUNCH_BLOCKING'] = '1'
if __name__ == "__main__":
# which session... |
530dddc4f02a93f5fd7147ece1a4e8b0be2d814037b776b3d40b2aff0d3d3559 | Python | 6,304 | 176 | """
Select a region of interest (ROI) by thresholding the intensity signal.
"""
import numpy as np
import matplotlib.pyplot as plt
from skimage import measure
import shapely.geometry as geo
import argparse
from pathlib import Path
import neo
import os
from utils.io_utils import load_neo, write_neo, save_plot
from util... |
1513d61433e7665b09deedd6ca5e581c31367ac09c4e3d4ca7b4173157a91285 | Python | 6,306 | 179 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
3c8cd56d5e5c5623273e82cdf524e6ba974a783f34ab69e546d97f01bf8726fd | Python | 6,308 | 119 | """The reference diff between two releases: the database changelog (#432).
Not a code changelog. A reader of a VDJdb release wants to know which studies arrived, how many
records each brought, and what the totals now are.
The publication years are already a committed input: :mod:`vdjdb.summary.references` resolved th... |
5a350a9ac72a7390de4cc4fb4e5d408646370a54a925eb05243a58a2589f3c37 | Python | 6,309 | 156 | # Copyright © 2023 German Cancer Research Center (DKFZ), Division of Medical Image Computing
#
# SPDX-License-Identifier: Apache-2.0
from radtract.features import load_features
from sklearn.model_selection import LeaveOneOut, StratifiedKFold
from sklearn.feature_selection import SelectKBest, f_regression
from sklearn.... |
e179a1b9f3c54d7f19aa097dc8618c78c115f3b149f1f2b89fe91fd8d4bee4db | Python | 6,309 | 171 | """`torch_tools.default_dtype` puts the process default back, exception or not.
The default dtype is process-wide, and this scope guards code that raises.
`MACECalculator.calculate` runs inside it, in nine places across the two
calculator classes, and so does every converter entry point -- which sets the
default from ... |
c06f74310a6c35b154ac526f160073ccc537dd7fed402011f9dd71fcb2206129 | Python | 6,310 | 122 | import tensorflow as tf
import tensorflow.keras.backend as K
def get_loss(pred_train,
model_configuration,
y_pred_names,
other_outputs,
pos_weights):
global_pooling = model_configuration["global_pooling"]
if "loss_type" in model_configuration.keys():
... |
6dbaf2a096f417d5eefb95102123a929e09aa6677246e53faa9944b96e78ee23 | Python | 6,311 | 163 | #### make_local_connectivity_ones.py
# Copyright (C) 2010 R. Cameron Craddock (cameron.craddock@gmail.com)
#
# This script is a part of the pyClusterROI python toolbox for the spatially
# constrained clustering of fMRI data. It constructs a spatially constrained
# connectivity matrix from a fMRI dataset, where then con... |
f1e6b911ed9f9725616626e865a60855c9a9fd0e140579fd6b48a43c3860b625 | Python | 6,313 | 196 | """Compute various scores with RDKit"""
import itertools
from typing import List, Callable
import logging
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem as Chem, Crippen, Descriptors, Lipinski
from ..component_results import ComponentResults
logger = logging.getLogger(__name__)
def num_s... |
dfceea11495cc409762a3f12dd840e8d9bdbe253ea737fc8b3cabb20134daa4b | Python | 6,315 | 204 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# OS stuff
import os
import sys
import warnings
from pathlib import Path
# Computational stuff
import numpy as np
import matplotlib as mplb
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
from matplotlib import font_manag... |
84dd4742adaf61189d3541e72d4736495a12ace809a40f0e5dd8597638e08226 | Python | 6,317 | 180 | """GNC backend dispatch. Each backend module implements GncBackend."""
from pathlib import Path
from typing import Protocol
import nibabel as nib
import numpy as np
from lib.gnc.backends import gradunwarp, tortoise
from lib.utils import force_remove
class GncBackend(Protocol):
"""Interface every backend module... |
24e88757e7ad1c06d5afbd5dd7f1f51a505fd41cb82279e17ba222c5b1e990b3 | Python | 6,321 | 195 | import pytest
from pathlib import Path
import torch
from reinvent.runmodes.RL.run_staged_learning import run_staged_learning
from reinvent.runmodes.utils.helpers import set_torch_device
SCORING = {
"type": "custom_product",
"parallel": 1,
"component": [
{
"custom_alerts": {
... |
5c190daa39cb3687fb07d1aef7de331a5d02756cae3631c79220cc5ad8f4109e | Python | 6,324 | 151 | """Which ``les`` produced a number, and whether it is the one installed now.
The LES goldens are the only ones in this directory whose value depends on a
package outside this repository. ``MACELES`` predicts latent multipoles and
then hands them to ``les.Les``, which does the Ewald sum and the Born-charge
derivative; ... |
dafb091c1c0988b333fa98ddf044be234e8a7e0fde49ea0c07f0cf207610a264 | Python | 6,325 | 111 | """Render the release dashboard and verify the fragment `vdjdb-web` will serve.
Three steps, each able to fail the build on its own:
1. ``rmarkdown::render`` on ``summary/vdjdb_summary.Rmd``, pointed at the legacy projection of this
build, with ``clean = FALSE`` so knitr's intermediate survives. The render makes n... |
2a9866bedc2d325bb59d382bb21ed48d636352cc38e08a52e0f6b586984bddd7 | Python | 6,326 | 189 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import torch
from torch import nn
from typing import Optional
from utils import logger
import math
from .identity import Identity
from .normalization import (
BatchNorm1d,
BatchNorm2d,
SyncBatchNorm,
... |
c63fab2c982c9ccd9b153d6291c2e5c024a31d3cf17b8178e684be1d5ef35f8c | Python | 6,326 | 178 | """
This module is responsible for correcting the distortion of the camera lens using existing functions from Open-CV.
As the camera is located close to the target, and captures a relatively wide angle frame, the barrel distortion is
significant. The function get_distortion_matrix analyzes images that contain a checker... |
0f96d7f8be60411f77a558fd4b2692e0ed4105dbec5d9ace10128d381061814a | Python | 6,333 | 210 | """The Visualization Package."""
import matplotlib
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # NOQA
import geomstats.backend as gs
from geomstats.visualization.hyperbolic import (
KleinDisk,
PoincareDisk,
PoincareHalfPlane,
)
from geomstats.visualization.hypersphere import C... |
0e925cd9ee1539c6514cd1e2df3245d80b746d00b37837f74e2cd7d3bb498330 | Python | 6,334 | 204 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
import random
import argparse
from typing import Optional
import numpy as np
from common import DEFAULT_IMAGE_WIDTH, DEFAULT_IMAGE_HEIGHT
from . import register_sampler, BaseSamplerDDP, BaseSamplerDP
@register_... |
4a96ab7ad0d59c7044a356b6f55f7179936afef0493c97b36eb16de34f257f1e | Python | 6,334 | 126 | # -*- coding: utf-8 -*-
#%%
import functions.rate_coding
import numpy as np
import functions.Graphs
import matplotlib.pyplot as plt
import pandas as pd
import functions.statistics_test as st
#%% Load data
data = np.load('/datapath/dataset.npy', allow_pickle=True).item()
#%% 1C Behavioral performance
pe... |
c1611053c084f390d048098d4e6315ac51dd9ac7b40a8b77db4ad9d3881622b2 | Python | 6,335 | 152 | import os
import torch
import numpy as np
from tqdm import tqdm
from torch_geometric.data import DataLoader
from .utils import generate_xyz
class Mol3DTrainer():
def __init__(self, train_dataset, val_dataset, configs, device):
self.configs = configs
self.train_dataset = train_dataset
self.... |
43d3338922e2a1336ed7856e312c1cbfe0aaf2eba3b8f3ddfabd60741a19cfbd | Python | 6,338 | 125 | # Copyright 2020 Forschungszentrum Jülich GmbH and Aix-Marseille Université
# "Licensed to the Apache Software Foundation (ASF) under one or more contributor license agreements; and to You under the Apache License, Version 2.0. "
import nest
import nest.raster_plot
import matplotlib.pyplot as plt
from nest_elephant_t... |
25c3080a104fec61fbb81d581f6bfdc8fa6af73ca0d0a9f0535871a902973a55 | Python | 6,340 | 190 | """Inception makes use of SMILES to speed-up optimization
Inception is the idea that an initial set of SMILES will guide optimization
towards wanted structures and so speed-up learning. The SMILES will be kept in
memory depending on their score. Only the N most high scoring SMILES will be
retained. This typically m... |
d35599f62a4c36d454b94c31e293e0f1af157f99d8f86c6eb2a15eec3291a11a | Python | 6,342 | 140 | from typing import Callable, Sequence, Union
from functools import partial
from jax import vmap
from jax.tree_util import tree_map, tree_transpose, tree_structure
from jax._src.api_util import check_callable, argnums_partial, _ensure_index
from jax._src.util import wraps
from jax._src import linear_util as lu
from jax.... |
7322373a2302675424e45e4759289cfcc1cf356a02b1685b3d995ce254fa55cb | Python | 6,346 | 200 | import torch.nn as nn
import torch.nn.functional as F
import torch
from scipy.io import savemat
class Down3d(nn.Module):
def __init__(self, in_channels, out_channels):
super().__init__()
self.conv = nn.Sequential(
nn.Conv3d(in_channels, out_channels, kernel_size=3, stride=2, ... |
f0502d0c026c6aa53f02ea7cbb8780a979351b31088409fe74f7531bcbe74da2 | Python | 6,346 | 170 |
import string
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import torch
from matplotlib import cm
from scipy.ndimage import rotate, shift
import mlspm.preprocessing as pp
from mlspm.datasets import download_dataset
from mlspm.models import EDAFMNet
# # Set matplotlib font rendering to... |
30abf53c736128d75377ba3378c645e22ccce13d91051bae1d647ad5ada8ee50 | Python | 6,355 | 185 | import torch
import torch.nn as nn
import torch.nn.functional as F
import rdkit.Chem as Chem
from .nnutils import *
from .chemutils import get_mol
ELEM_LIST = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na',
'Ca', 'Fe', 'Al', 'I', 'B', 'K', 'Se', 'Zn', 'H', 'Cu', 'Mn', 'unknown']
ATOM_FDIM = ... |
9179aecc3b35adf7ea902de4aa804dedb96918376f19d303ac6f6c4c1948640d | Python | 6,355 | 180 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
import torch
import torch.nn.functional as F
from fairseq import metrics, utils
from fairseq.criterions import FairseqCriterion, ... |
bf9b0cc00f98b617e177a5cbebf0688c1278f75cac7958845016b78dc73664a9 | Python | 6,358 | 168 | from math import pi as PI
import torch
import torch.nn.functional as F
from torch.nn import Embedding, Sequential, Linear
from torch_scatter import scatter
from torch_geometric.nn import radius_graph
class update_e(torch.nn.Module):
def __init__(self, hidden_channels, num_filters, num_gaussians, cutoff):
... |
c557a79dab3c64b767a96f51562314459064d75cbe95a15d496f7048f1dadc89 | Python | 6,359 | 176 | from typing import Optional
from torch_geometric.typing import Adj, OptTensor
import torch.nn.functional as F
from torch.nn import ModuleList, Linear, BatchNorm1d
from torch_geometric.nn import GCN2Conv
import torch
from torch import Tensor
from torch_sparse import SparseTensor
from ..models import ScalableGNN
cla... |
890a937157be562c7d529987529f3d13e044d3271ad6bef2e02a998568e9c9f3 | Python | 6,361 | 242 | import tensorflow as tf
def lrelu(inputs, leak=0.1):
with tf.variable_scope('lrelu') as scope:
return tf.maximum(inputs, leak * inputs, name=scope)
def fc(
name,
inputs,
n_hiddens,
bias=None,
):
# Weight initializer
weight_initializer = tf.variance_scaling_initializer(
sc... |
d97110403ab8ac589a6d539c47279494a05209aad0309b915ac4181a419f145e | Python | 6,363 | 210 | import click
from corgie import scheduling, helpers, stack
from corgie.log import logger as corgie_logger
from corgie.layers import get_layer_types, DEFAULT_LAYER_TYPE, str_to_layer_type
from corgie.boundingcube import get_bcube_from_coords
from corgie.argparsers import (
LAYER_HELP_STR,
create_layer_from_spe... |
4447642e1e7162acf666c3f5a1afc42b69f7aa2776c7fe8915b5685bf89fd2aa | Python | 6,364 | 207 | import logging
import numpy as np
import torch
import yaml
from matplotlib import pyplot as plt
from scipy.stats import truncnorm
from typing import Optional, Tuple, Union, Iterable
def get_deg2pix_coeff(run_params: dict) -> float:
view_angle = run_params['view_angle']
resolution = run_params['resolution']
... |
42ffb06eb22fa29358b74bfe9f1fbfc0f9ad8686ce19c33965439f6a86717a20 | Python | 6,365 | 181 | import os
import argparse
import warnings
warnings.simplefilter(action="ignore", category=FutureWarning)
import pandas as pd
import tensorflow as tf
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
import brainscore.benchmarks as bench
from brainscore.metrics.regression import linear_regression, ridge_r... |
fec08bc99bb3975b409d89668933a6eac213630e2cb7b86a90775b333dfc7966 | Python | 6,365 | 115 | ########################################################################
class Basic:
"""
Contains the basic parameters for the online modality of Motor Imagery protocol
"""
#-------------------------------------------
# PATH TO SAVE DATA
#-------------------------------------------
params0 ... |
7bdbe08e031ae2567fdcc45da5240313245ce54d695fb804c6852753d4b17cce | Python | 6,367 | 151 | """
Detect trigger times (i.e., state transition / local wavefronts onsets)
by finding crossing of a set phase-value in the channel signals.
"""
import argparse
import neo
import numpy as np
import quantities as pq
from scipy.signal import hilbert
from scipy.stats import zscore
import matplotlib.pyplot as plt
import ... |
079005fb5e774fca92425ad01cf1d0fa9f3e00a07dcd80b68fa6b24e33359f80 | Python | 6,374 | 167 | import cv2
import os
import json
from tqdm import tqdm
import numpy as np
provinces = [
"皖", "沪", "津", "渝", "冀", "晋", "蒙", "辽", "吉", "黑", "苏", "浙", "京", "闽", "赣",
"鲁", "豫", "鄂", "湘", "粤", "桂", "琼", "川", "贵", "云", "藏", "陕", "甘", "青", "宁",
"新", "警", "学", "O"
]
alphabets = [
'A', 'B', 'C', 'D', 'E', 'F', ... |
64aeb443621967724a40dbade6be56d255f0e7af94d89eca59e38a47643f033f | Python | 6,374 | 182 | import collections
import numpy as np
import renderapi
from ..schemas import *
from ..utils import make_dbconnection, get_matches
import time
import matplotlib
matplotlib.use('Agg')
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.collections import LineCollection
import matplotlib.pyplot as plt
imp... |
17237c3d2555bc63a7969f1be38cec3c73034b58331d5d2b446e70473a66047b | Python | 6,376 | 198 | import os
from os import path
import numpy as np
import xml.etree.ElementTree as ET
import re
from tqdm import tqdm
import pickle
import requests
import io
import matplotlib.pyplot as plt
import pandas as pd
import sys
sys.path.insert(0, './')
from pyImagingMSpec.inMemoryIMS import inMemoryIMS
def loa... |
b09556c6d8921af1cf09e6442257d3aa0c4b52278dad10fa156a4122cf03ea6e | Python | 6,377 | 138 | import torch
import torch.nn.functional as F
from torch import nn
from torch_geometric.nn import MessagePassing
from torch_geometric.nn.aggr import Set2Set
from torch_geometric.utils import scatter
from torch_geometric.nn.pool import global_add_pool, global_mean_pool, global_max_pool
from torch.nn import Sequential as ... |
ee0b1350e2eb2da14b1886fcd74857f302c307dd45fc71a235aa1516d90fa623 | Python | 6,378 | 162 | # -*- coding: utf-8 -*-
import os
import argparse
import logging
import glob
import numpy as np
from data_functions import load_data, TwoPopAlignmentFormatter, load_data_slim, read_slim_out
from mpi4py import MPI
import h5py
import time
from collections import deque
# use this format to tell the parsers
# where to ... |
49facb8b71236dfb1c19a96cbed4ce802bc32a280a656f222f4c7654a4ac890f | Python | 6,380 | 178 | from copy import deepcopy
from math import log
from corgie.log import logger as corgie_logger
from corgie import scheduling, helpers
from corgie.stack import PyramidDistanceFieldSet
class BroadcastJob(scheduling.Job):
def __init__(
self,
block_field,
stitching_fields,
output_field,... |
740010041a90aabc9b7e1ef8c196b8aa2d869603dae14de788c759e61170f526 | Python | 6,380 | 192 | # This coded was modified from the cuequivariance library: https://github.com/NVIDIA/cuEquivariance/blob/main/cuequivariance/cuequivariance/group_theory/experimental/mace/symmetric_contractions.py
# SPDX-FileCopyrightText: Copyright (c) 2024 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifie... |
19515ef597fe866974924993028eeed13e10dc2236bb1f5ea4dd5472926ff01e | Python | 6,381 | 113 | ########################################################################
class Basic:
"""
Contains the basic parameters to train the Motor Imagery algorithm
"""
#-------------------------------------------
# Data
#-------------------------------------------
params1 = dict()
params1.upd... |
56196708fe9a3b3058e57974b42c26b66a60c1671437e1921b82d6bbd57a0a36 | Python | 6,382 | 184 | import tensorflow as tf
import numpy as np
import keras
import pandas as pd
import matplotlib.pyplot as plt
from scipy.sparse.linalg import lsmr
from Bio.Align import substitution_matrices
import matplotlib.gridspec as gs
def get_norm_prob(scores, t=1):
# getting boltzmann probabilities using scores as energies.
... |
95fd5e9767caa8844019838e158179c033d6f32ac60e26bc3ce0ecfc68ee94b3 | Python | 6,386 | 161 | # R squared calculator from sklearn.metrics This has been isolated from sklearn so the App using it can be successfully compiled without the full sklearn package
# due to hidden import errors
# Modified for simple linear regression
# BSD 3-Clause License
# Copyright (c) 2007-2023 The scikit-learn developers.
# All ri... |
e752e02be8c7dfc198800190d198ebdde2e26b23052eef4665cfb00e3a81ac62 | Python | 6,388 | 173 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
from math import sqrt, exp
import lightning
from lightning.pytorch.callbacks import Callback
from nequip.data import AtomicDataDict
from nequip.train import NequIPLightningModule
from typing import List... |
4995d7c98f0bedd7c0177704ed9dddcfa1c084d1fce25e8dd7e8ca12373498bb | Python | 6,389 | 184 | import tensorflow as tf
import numpy as np
import keras
import pandas as pd
import matplotlib.pyplot as plt
from scipy.sparse.linalg import lsmr
from Bio.Align import substitution_matrices
def get_norm_prob_log(scores, t=1):
# getting boltzmann probabilities using scores as energies.
# assumes that all scores... |
6872a1847893947e75e8e7a1480b1685801400cafacbd50c9bbee36d6160a526 | Python | 6,390 | 162 | """
gathering the accuracy as a function of the weight quantization
ideally, this script would be run the various results obtained with the trainig_task.py script
"""
from SHIP import ListHauler,lS_1o
from torch import (tensor,
arange,
zeros,
normal,
... |
2bed58ac9f9d88d966453143b545d66ccedca25493de597b24cbbe3a94f80b8b | Python | 6,391 | 140 | import sys
import argparse
import tensorflow as tf
import flammkuchen as fl
import numpy as np
from deepd3.core.analysis import Stack, ROI2D_Creator, ROI3D_Creator
parser = argparse.ArgumentParser()
parser.add_argument('stack', type=argparse.FileType('r', encoding='UTF-8'), help='File to be segmented')
parser.add_argu... |
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