sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3810d10173c70e7e2b6b6e72b50a3f10c3a4d49d87b2b0a2c853d215fae76bc6 | Python | 8,541 | 352 | # flake8: noqa
# __reproducible_start__
import numpy as np
from ray import tune
def train_func(config):
# Set seed for trainable random result.
# If you remove this line, you will get different results
# each time you run the trial, even if the configuration
# is the same.
np.random.seed(config["... |
9965f36142af26853a9fe27d10fc71bd0be1268a829afce13010a8a7e1dd9e0e | Python | 8,541 | 214 | import time
from collections import defaultdict
from dataclasses import dataclass
from typing import Dict, List, Optional, Set
import ray
from ray.air.execution.resources.request import (
AcquiredResources,
RemoteRayEntity,
ResourceRequest,
)
from ray.air.execution.resources.resource_manager import Resourc... |
b19a880974610bad73fc5560af9bede4fb0c023d05ada1b1c834608ce18e7354 | Python | 8,541 | 265 | import torch
from torch import nn, optim
from torch.utils.data import DataLoader, Dataset
import numpy as np
from skimage.segmentation import clear_border
from skimage.morphology import closing
from skimage.measure import label
import os
import RS
from clean_pdb import clean_pdb
import pybel
import openbabel
import tf... |
793534b445f4b4a607349dc9096353b6aa87241cdffd85a054634ec4b217cf4c | Python | 8,543 | 238 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import functools
import sys
from contextlib import ExitStack
from dataclasses import dataclass
from io ... |
ddaf5c413ff22d1b85eefd021d0a7200e4c34ced6c24fdfcf6658e3261699259 | Python | 8,543 | 281 | import os
import numpy as np
import tensorflow as tf
import keras_tuner as kt
import matplotlib.pyplot as plt
from utils.constants import *
from utils.experiments_tools import *
from utils.regressor_tools import *
from utils.plot_tools import *
class TransformerTuner:
def __init__(
self,
output_dir... |
20881163f80a2b00f26ba980d40110370f8a88c2c04c040e2c98edcea875db09 | Python | 8,546 | 265 | import torch.nn as nn
import torch
import numpy as np
def flops_to_string(flops):
if flops // 10**9 > 0:
return str(round(flops / 10.**9, 2)) + 'GMac'
elif flops // 10**6 > 0:
return str(round(flops / 10.**6, 2)) + 'MMac'
elif flops // 10**3 > 0:
return str(round(flops / 10.**3, 2))... |
e816e4a43718de69e76ca85e31782cbe2f8fac277855043b621e4c8e15fd6b86 | Python | 8,547 | 208 | # built-in dependencies
from typing import Any, Dict, List, Union, Optional, Sequence, IO, cast
from collections import defaultdict
# 3rd party dependencies
import numpy as np
from numpy.typing import NDArray
# project dependencies
from deepface.commons import image_utils
from deepface.modules import modeling, detect... |
c312acf31d25b99636e105517b863054eeda10e188facc9c1fbdefb8ce089c2d | Python | 8,548 | 261 | from inspect import isfunction
import math
import torch
import torch.nn.functional as F
from torch import nn, einsum
from einops import rearrange, repeat
from stable_diffusion.ldm.modules.diffusionmodules.util import checkpoint
def exists(val):
return val is not None
def uniq(arr):
return{el: True for el i... |
58658fd0966cde68bc8b79eb0a17ae3f0fa4af1e76f170b9bc0bb4449b19a1fa | Python | 8,550 | 209 | import requests
from .__config import base_url
from .__aux_funcs import process_response
def get_samples_by_keyword(keyword=None, direction="ASC", pageNumber=0, pageSize=10000000, projection="SUMMARY", sortBy=None):
"""
Get all samples matching a keyword. \n
:param keyword: Search keyword that applies to t... |
643021677db809690b8554f45d79a5463e83dd58ea40124146ebd92eaa358225 | Python | 8,552 | 233 | import hashlib
import sys
import pytest
from ray._common.runtime_env_uri import Protocol, parse_uri
def _sha1_hex(s: str) -> str:
return hashlib.sha1(s.encode("utf-8")).hexdigest()
class TestParseUri:
@pytest.mark.parametrize(
"uri,protocol,package_name",
[
# GCS stays in the n... |
bee0b791642960fa4352734b90b9a44a7e839a12b419f5d5f7725a56ebc573c5 | Python | 8,553 | 290 | import random
import json
link_list = [
[0,0,0,0],
[0,0,0,1],
[0,0,1,1],
[0,0,1,2],
[0,0,1,3],
[0,1,1,1],
[0,1,1,2],
[0,1,2,2],
[0,1,2,3]
]
gnn_list = [
"gat", # GAT with 2 heads
"gcn", # GCN
"gin", # GIN
"cheb", # chebnet
"sage", # sage
"arma",
"graph", # k-GNN
"fc", # fully-co... |
a18a73fc94f51dcf47227e8f98e5db1cfb627c33d84573cc322c111f7bbbc934 | Python | 8,554 | 270 | import os
import pickle
import sys
from typing import List
from typing import Tuple
import pystow
import tensorflow as tf
import Transformer_decoder
if int(tf.__version__.split(".")[1]) <= 10:
import Efficient_Net_encoder
else:
raise ImportError("Please use tensorflow 2.10 when working with the checkpoints.")... |
ec1343a10c6b8efa5f40bfdd3ec42cb3e5af8f51a3ea38095664a98ff37983f0 | Python | 8,555 | 231 | # -*- coding: utf-8 -*-
"""
Alignment on simulated 2D data.
===============================
As we mentionned several times, we search for a transformation, let's call it
`R`, between the source subject data `X` and the target data `Y`. `X` and `Y`
are arrays of dimensions `(n_voxels, n_samples)` where each image is a... |
ecc409dd6a5d8b5bb4c8b73524352c17a1e93c0e0d6f774d1d0c7278aa70875b | Python | 8,555 | 241 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import logging
import math
import re
import readline
import sys
from itertools import islice
from pathl... |
5d9909b7e95bc6e06ca955a9a3b3a18185b59402ddebe401e215967dec69a07b | Python | 8,571 | 261 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
bffa94fdbfc7939ff8b7f54986cc2ccc2814162e7ceb4846848ca8c6ed0490df | Python | 8,571 | 211 | # -*- coding: utf-8 -*-
"""
Created on Fri Oct 29 18:09:15 2021
@author: Nikhil
"""
#Crossover analysis
#1. takes detrended timeseries as xov_df
#2. calculates 24 h rolling woindow average as xov_roll_avg
#3. takes difference of xov_df and xov_roll_avg
#4. looks for change in sign which indicates crossover
... |
128291e142dc6fd4c83df04ed8dee6323fad3f04a6aa43d2bd4cecd0c00bd813 | Python | 8,572 | 228 | import torch
from torch.nn import Module, BatchNorm1d, LeakyReLU, Conv1d, ModuleList, Softmax, Sigmoid, Flatten, Dropout2d, Linear
from torch.optim.lr_scheduler import LambdaLR
from torch.optim import Optimizer
from torch.utils.data import Dataset, DataLoader
import argparse
import math
import random
import numpy as n... |
bd8d9cea370032648ba80b1954aaaaa29d67dd0aab66a0e0ccf3a12e974492c4 | Python | 8,574 | 265 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import csv
import json
import os
import random
import sys
from itertools import product
NAME = "webhooks"
def read_rules(name):
rules = []
with open(os.path.join(sys.argv[1], f"{name}.csv")) as f:
reader = csv.DictReader(f)
... |
6b4cc1278aefad1d108fafe1bf0ac0f1788d9990a58319c9500ce61200518c25 | Python | 8,575 | 224 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
FastCSP Centralized Logging System
"""
from __future__ import annotations
import json
import logging
import sys
from datetime import datetime... |
89ce7dee4c81b297a922da25ad9952cbcdbf9e07de7fadda2ac777265fe21d59 | Python | 8,575 | 244 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import re
from unittest.mock import MagicMock, patch
from allauth.account.models import EmailAddress
from django.core import mail
from django.test import override_settings
from django.urls import re_path, reverse
from rest_framework import serialize... |
da3c59179fccda49d9408064b7b465f4ac081b2e1c61d24d33d41c15ae460b9a | Python | 8,577 | 255 | import random
from tkinter import W
import brainrender as b
import numpy as np
from brainrender.actors import Point
from brainrender import _utils
#Find cell coordinates
import csv as c
file = open("CN_neuron_coordinates_allcells.csv")
csvreader = c.reader(file)
# Skip first line to get to get to data
next(csvreade... |
2fbcc5ab54967da49b068a9cea954884d834bfad9afafef4cf8095cf598c42b6 | Python | 8,579 | 243 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------
# Created By : Kangjoo Lee (kangjoo.lee@yale.edu)
# Last Updated: 08/06/2024
# -------------------------------------------------------------------------
# =========================================... |
efceb68d0d88f89a95e8d31e6e6d0c618adc12ac2649d0727536a16b10e1b2f7 | Python | 8,580 | 244 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any modif... |
cba290848a900b8d9532c09f6fd3452947932b141394e1edd4d25cc531bd5f1a | Python | 8,587 | 221 | #!/usr/bin/env python
from scipy import stats
import numpy as np
from sklearn import mixture
# calculate the Del statistic given a FME combo in het files
def Deltest(F, M, E, length, crit=0.01, thres1=0.0005):
# if True:
thres1 = min(50 / length, thres1)
if F / length < thres1 and M / length < thres1 \
... |
6af6d28a8aa0459f4b40e3659d4abcd00b739397ed72d1d1d575da27c283a549 | Python | 8,589 | 211 | from typing import Callable, List, NamedTuple, Optional, Tuple
import pyarrow as pa
import pyarrow.compute as pc
def is_boolean_arrow_type(t: "pa.DataType") -> bool:
"""Whether ``t`` is boolean, including dictionary/run-end encoded booleans."""
if pa.types.is_dictionary(t) or pa.types.is_run_end_encoded(t):
... |
8ce33621d35379f18b10a287a6f026629640fb7c7bf38bafb82e69e3d35e3f88 | Python | 8,592 | 270 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
from dataclasses import dataclass
from typing import TYPE_CHECKING
import numpy as np
from fairchem.c... |
6064187abecdb76433ec86b1f06915e13ad2b739c11ab4b604a74c84ea371610 | Python | 8,598 | 240 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------
# Created By : Kangjoo Lee (kangjoo.lee@yale.edu)
# Last Updated: 08/06/2024
# -------------------------------------------------------------------------
# =========================================... |
b9e191b97a98198efb223d0fb248735aadc1cf918b355261bd5a8a6aaa10a454 | Python | 8,600 | 241 | import argparse
import numpy as np
from tqdm import tqdm
import torch.multiprocessing
import torch
from torch import nn
from torch import optim
from data import build_retina_dataset
from models import SpatialDecoder, FlattenLayer, ResNetFeatures
WANDB = False
if WANDB:
import wandb
PROJECT_NAME = 'Multi-ta... |
df9fb1fa58475b4cde4be7c58ac7b2f590dcebd70391687a0c79daed3f9e4734 | Python | 8,600 | 296 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 20 13:49:57 2016
@author: agiovann
"""
from builtins import range
from past.utils import old_div
import logging
import numpy as np
import scipy
try:
import numba
except:
pass
#%%
def mode_robust_fast(inputData, axis=None):
"""
R... |
832c6328626e94539c565af1f9049d0213058bea9f6156d7d954577bdba68106 | Python | 8,601 | 298 | import numpy as np
import pandas as pd
import scanpy as sc
from scipy import stats
from sklearn.linear_model import Lasso, LassoCV
from sklearn.metrics import mean_squared_error, r2_score
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import StandardScaler
from tqdm.auto import tqdm
#... |
8ade3fb0c366505b7571c9263032579f4876f0f69048711c0b1cf686b0c7d2c9 | Python | 8,601 | 184 | import torch
import torch.nn as nn
from .transformer import AbstractTrasnformerLayer
from ..utils import create_norm
## Core code for Flow-Attention, Please refer to each folder for corresponding experiments
class Flow_Attention(nn.Module):
# flow attention in normal version
def __init__(self, d_model, n_head... |
9da1a18b33c5dceb4415bbdbb7ea1b574bb51bd542fcf3359c0067d7b1c7275f | Python | 8,603 | 232 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 27 10:15:17 2021
@author: sam
"""
#Parse inputs
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("file", help="path to video file")
parser.add_argument("-intenseSample",type=float,
default=40, help="minutes... |
42b055b2a7d8067a58c7a499056b3f85250677374e9499c968c8bec946ec71fc | Python | 8,605 | 256 | import pandas as pd
import pathlib
import subprocess
from collections import Counter
TARGET_NAME = 'target'
# these are words that yaml doesn't like you to use
protected_feature_names = ['y','Y','yes','Yes','YES','n','N','no','No','NO',
'true','True','TRUE','false','False','FALSE',
... |
3174283f9e93165a87cdfdbbe369d71f1c19d9f12a590da3e9033393f3941b18 | Python | 8,611 | 314 | """HTML rendering for the AnnData report.
Single-file output: all plots are inlined as base64 PNGs and the CSS is
inlined too, so the report can be emailed or hosted from any static
file server with no asset directory.
Style: warm cream background, dark warm-grey text, single accent in
muted terracotta — keeps the re... |
7207a3f317162f2176193f2a2ef88d555983dab049c299cb10bb81c99da3d244 | Python | 8,611 | 244 | # coding=utf-8
# Copyright 2023 HuggingFace Inc.
#
# 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 ag... |
4935670160fced9136cadd08e43d51c976fce0b90d2cbf9b1fda5556e74e4749 | Python | 8,612 | 262 | import torch.nn as nn
import math
import torch.utils.model_zoo as model_zoo
import torch
def conv3x3(in_planes, out_planes, stride=1):
"""3x3 convolution with padding"""
return nn.Conv1d(in_planes, out_planes, kernel_size=3, stride=stride,
padding=1, bias=False)
def conv5x5(in... |
d68c93ed62715ddaa8e1d4a0c8e2773adecc8e74d84705db3742b8610a98eddc | Python | 8,612 | 270 | #!/usr/bin/env python
import os, sys
sys.path = [os.path.dirname(os.path.abspath(__file__))] + sys.path
from liblinear import *
from liblinear import __all__ as liblinear_all
from ctypes import c_double
__all__ = ['svm_read_problem', 'load_model', 'save_model', 'evaluations',
'train', 'predict'] + libline... |
8c09bfb8bc0263f6ca147314fd996b10fb53020a98a7709b14a84a96d86aba5e | Python | 8,617 | 255 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import json
import logging
import os
import shutil
import time
from abc import ABC, ABCMeta, abstractme... |
fb47c6c0c234b059c8748cc042681aa166df27abffb4bd768f2aaa3378e50326 | Python | 8,617 | 197 | import argparse
import multiprocessing
import os
from time import sleep
from typing import Union
import numpy as np
import torch
from batchgenerators.dataloading.multi_threaded_augmenter import MultiThreadedAugmenter
from batchgenerators.utilities.file_and_folder_operations import load_json, save_pickle, join, maybe_m... |
e56901239b7454730feebe8b3d9f904286bd829d2d6566171ff56cf74427de3e | Python | 8,620 | 261 | """
Performs size simulations for all hypotheses.
"""
from utils.grid_funcs import (
gridpop_clustering,
gridpop_conj,
gridpop_repsupp,
gen_offsets,
traj
)
from utils.utils import (
convert_to_rhombus,
get_hexsym,
get_pathsym
)
import numpy as np
import pickle
import os
import settings
i... |
172a1c3439b460f94dcbe3a9cf49a57a69f139c90cc728193d9e504b9351e944 | Python | 8,621 | 174 | import os
import numpy as np
import matplotlib.pyplot as plt
import ivim
root = '/path/to/root'
input_root = os.path.join(root,'data')
results_root = os.path.join(root,'results')
subs = [sub for sub in os.listdir(results_root) if sub.startswith('sub')]
runs = ['run-{}'.format(r+1) for r in range(2)]
scans = ['sIVIM'... |
338d7916a8dda880ebbef2b2c5c760d77216774454eabbd3bed0e0b0eded8072 | Python | 8,621 | 219 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import gzip
import io
import json
import os
from glob import glob
from typing import TYPE_CHECKING, Any... |
0af70b59d65d798f076ef25d7f7f0c519d7cf6ff67424ed048ce2c0531637278 | Python | 8,622 | 230 | import json
import re
from typing import (
Any,
Dict,
List,
Optional,
)
import yaml
import ray._private.ray_constants as ray_constants
# Regex patterns used to validate that labels conform to Kubernetes label syntax rules.
# https://kubernetes.io/docs/concepts/overview/working-with-objects/labels/#sy... |
4530c9781d25fe0315929a702ebbb2312c090be5f0c86c1a41dc9622dfdab315 | Python | 8,622 | 285 | import os
import numpy as np
import tensorflow as tf
import keras_tuner as kt
import matplotlib.pyplot as plt
from utils.constants import *
from utils.experiments_tools import *
from utils.regressor_tools import *
from utils.plot_tools import *
class InformerTuner:
def __init__(
self,
output_direct... |
5670398129a16603ca610ac8f56432c944e1e45db57a06636c464bbae5e0ff4a | Python | 8,622 | 174 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
acb576adae1479f91e3fcd7b523bde7f25057fa12f83cec5e3b9b52e45e793c8 | Python | 8,622 | 263 | import os
import torch
import time
import argparse
import numpy as np
import pandas as pd
import torch.nn as nn
from tqdm import tqdm
from sklearn.metrics import mean_absolute_error
from torch.utils.data import DataLoader, Dataset, random_split
import torch.nn.functional as F
parser = argparse.ArgumentParser()
masks... |
b529ebe354a1a27c8035e84d453e5fc327b289f7071293e1cb637b5117e3c5a4 | Python | 8,622 | 259 | import abc
import json
from copy import deepcopy
from dataclasses import dataclass
from inspect import signature
from typing import Dict, List, Union
import ray
from ray.util import placement_group
from ray.util.annotations import DeveloperAPI
RemoteRayEntity = Union[ray.remote_function.RemoteFunction, ray.actor.Acto... |
a5dca14da775177c6295e65a1efa1b7db33b176c5d8b27fd1381387c55d85c90 | Python | 8,625 | 197 | r"""Biomolecular complex structure & binding affinity — Boltz-2.
`Boltz-2 <https://github.com/jwohlwend/boltz>`_ (Passaro *et al.* 2025) is an
open, AlphaFold3-class model that co-folds proteins, nucleic acids and small
molecules **and** predicts binding affinity — the first open model to approach
FEP-level affinity a... |
e91d31cedcdd6c0c6b3da83d3d511699c3b107f12cc2a6167af6df30d9def5ed | Python | 8,627 | 197 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
aa0e30a352ebbdc860aecdd9f3713d4e31f9bde895796d31af30de48d3dc093c | Python | 8,632 | 193 | import optuna
import Training_Utility_Functions as Training_Utils
import os
import Dataset_Generator
import torch
import numpy as np
import logging
import ML_Models
logging_file_name = "optuna_logs.txt" # file name for where the hyperparameter optimisation output logs will be saved
base_path = "/app" # t... |
1cb1b5b64c8a4513339da05d781f19a00665cb63294ce405fcd6cc942b52f923 | Python | 8,635 | 255 | import torch
import numpy as np
import torch.nn as nn
import torch.nn.functional as F
class Quantizer(nn.Module):
def __init__(self, entry_num, entry_dim):
super().__init__()
self.entry_num = entry_num
self.entry_dim = entry_dim
self.decay = 0.9
self.entry = nn.Embedding(s... |
fea44c09d705cb529dcf94caf5439d8f71f4960e2eadbdc217f6583536644822 | Python | 8,641 | 193 |
import numpy
import json
import os
from matplotlib import pyplot
from scipy.spatial import distance
from .user import select
from .prefnet import PrefNet
from .pareto import find_dominating
OBJ_NAMES = {
"FWHM (nm)" : "Resolution",
"Signal Ratio" : "SNR",
"Bleach" : "Bleach",
"Squirrel" : "Squirrel"... |
8c0276919a0d93f853b5e562ebeb145f25be3e2278aa84e8bfd3350de5b20aa1 | Python | 8,644 | 239 | # built-in dependencies
import io
import cv2
import pytest
import numpy as np
import pytest
# project dependencies
from deepface import DeepFace
from deepface.commons.logger import Logger
logger = Logger()
def test_standard_represent():
img_path = "dataset/img1.jpg"
embedding_objs = DeepFace.represent(img_p... |
9581a7c2aa314855f760f31ea5b3cefa48c91fcc53d996f3789737fe9930bd55 | Python | 8,646 | 227 | import numpy as np
import matplotlib.pyplot as plt
from scipy.integrate import odeint
import torch
class CANN():
"""
Generic CANN modules for rapid testing
"""
def __init__(self, data, num = 128, tau = 0.02, Inh_inp = -.1, I_dur = 0.5, dt = 0.05, A = 20, k = 1):
self.num = num
self.tau... |
6fd3abc9a3afe57e593b118e11985a6c765fde3668ca40ee076f796b699ede9c | Python | 8,647 | 281 | from typing import Optional, Tuple
import torch.nn as nn
from sinabs.layers import SumPool2d
from sinabs.utils import expand_to_pair
from .crop2d import Crop2d
from .flipdims import FlipDims
class DVSLayer(nn.Module):
"""DVSLayer representing the DVS pixel array on chip and/or the pre-processing. The order of
... |
8fd58159f55216b6f1768fdb4d2495ab5c89683c009d3ef7e1bc352126020c76 | Python | 8,647 | 224 | """Parquet helpers shared by the V2 Parquet datasource, scanner, reader and
footer indexer.
These used to live in the legacy
``ray.data._internal.datasource.parquet_datasource`` module. They moved here so
that ``datasource_v2`` does not depend on the legacy package; the legacy module
imports them from here instead. It... |
c3f407a936d6662c4d7beabbdf4e45bb6fc0a6a6d2a8b079c7dae4a08e7a428c | Python | 8,648 | 194 | from dataclasses import dataclass
from typing import Optional, Union
import torch
import torch.nn.functional as F
from torch import nn
from ..configuration_utils import ConfigMixin, register_to_config
from ..utils import BaseOutput
from .attention import BasicTransformerBlock
from .embeddings import TimestepEmbedding... |
eaaec798642c19534b2ba04462dc0c2f8bc411555084c03f5728f325d65bc5be | Python | 8,649 | 189 |
####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fr... |
2949e7d4c50c8b9f0e7177730310d3f00fa4d652bd183a7118c19df3eb035bd2 | Python | 8,650 | 219 | from __future__ import print_function
import argparse
import glob
import sys
import os
def parse_args():
parser = argparse.ArgumentParser("Consolidates output logs for chunked marginPhase run")
parser.add_argument('--log_dir', '-l', dest='log_dir', default='.', type=str,
help='Location w... |
d77f53cd0c6d8631f6cf2b36145f8c2077db8230872baf0f1c509bf449289293 | Python | 8,650 | 265 |
import imageio
import os
import glob
from skimage import io, transform
import matplotlib.pyplot as plt
from scipy import ndimage
from skimage import color
import numpy as np
starts = {'bold': [3330, 3753, 4175, 4602, 5026],
'vaso': [996, 1420, 1842, 2269, 2693]}
SF = 2400/1000
template = f'/Users/sebas... |
e285d63ab97ae669f780ef7f4893d9af464855fc6dac3900a9334fbb4c95f095 | Python | 8,650 | 246 | """STRING API client."""
import logging
from typing import Any, Dict, List, Optional
from urllib.parse import urlencode
from .base import BaseAPIClient
from ..config import settings
logger = logging.getLogger(__name__)
class STRINGClient(BaseAPIClient):
"""Client for STRING database API.
STRING (Sear... |
1801e8bdd316321986812d3690539a4bbfcbabd009993c6b0590b4544947c014 | Python | 8,657 | 210 | # Copyright 2022 The Music Spectrogram Diffusion Authors.
# Copyright 2023 The HuggingFace Team. 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... |
8223a64dfc81d68ba4ccd2fe1f9018284cde5b0e38752cde002d69f02703c08f | Python | 8,657 | 113 | # Tensor maps for the CelebA Dataset
# https://mmlab.ie.cuhk.edu.hk/projects/CelebA.html
import os
import sys
import gzip
import pickle
import logging
from typing import Dict
import h5py
import numpy as np
from skimage.transform import resize
from ml4h.normalizer import ZeroMeanStd1
from ml4h.TensorMap import Tensor... |
472886e3752037172bb2838aa9c7af75e9e9401d15d52005edfae1564d196575 | Python | 8,661 | 247 | import numpy as np
import pytest
import torch
import torch.nn as nn
from sinabs.layers import ALIF, ALIFRecurrent
def test_alif_basic():
batch_size, time_steps = 10, 100
tau_mem = torch.as_tensor(30.0)
alpha = torch.exp(-1 / tau_mem)
input_current = torch.rand(batch_size, time_steps, 2, 7, 7) / (1 - ... |
b90eebb061da195dcd57ccc24761b6aa49439ac0fd59950f27ae5d6056e58085 | Python | 8,664 | 202 | # Copyright (c) DP Technology.
# 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
import pandas as pd
import numpy as np
from unicore import metrics
from unicore.losses import UnicoreLoss, ... |
ac71f66099d83d873ac7575d831f019e986b19b3588baf753110c1b5252261b7 | Python | 8,665 | 132 | import os
import argparse
import easygrid
import pdb # DFR add 8-31-21
# Stages
MAKE_TEMPLATE_FILES = 'make_template_files'
TRAIN_MODELS = 'train_models'
SCORE_SUMSTATS = 'score_sumstats'
GATHER_SUMSTATS = 'gather_sumstats'
if __name__ == '__main__':
parser = argparse.ArgumentParser('Script to generate LD score r... |
f29ccb5af16fe2b2dce09c2f1033b670f73de28043f094c92f27953a22692064 | Python | 8,666 | 211 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
42b38676413f218254da1a0493295ef6fa041f83c29652c64a66d05c71ebaee1 | Python | 8,668 | 267 | '''test our simple memory mechanism on meta scene vectors
using a encoding-recall temporal generalization test
assume:
- the model encode at time t, where t can be some early time points or at the end of each event
- the model recall LC (context classification) at time t
- for both retrieval and encoding, the model use... |
465aa11c4e73b50a7e217a966bcb863bfdeb62ea84addf2973bc8800ec5a459b | Python | 8,669 | 204 | import os,time,pickle
import numpy as np
import torch
from timm import scheduler as schedulers # do not delete!
from os.path import join
from tqdm import tqdm
from tensorboardX import SummaryWriter
from torch.nn import DataParallel as DP
from tools import *
from sleep_models import build_model
import w... |
dfc0a39bf3b29135024dc72cec83c24e7afaafb03308cdebd68304dacea56094 | Python | 8,670 | 227 | from sklearn.model_selection import train_test_split
import torch,os, pickle, threading
from torch import nn
import numpy as np
import matplotlib.pyplot as plt
class MedianAge(nn.Module):
def __init__(self, *args, **kwargs) -> None:
super().__init__(*args, **kwargs)
def forward(self, x):
... |
b08d062a1d8593272260526eb822c2722b4ece51237c41046d21bf3a2257202c | Python | 8,683 | 231 | from collections import deque
from copy import deepcopy
from dataclasses import dataclass
from typing import Dict, List, Optional, Tuple, Union
import sinabs
from .dvs_layer import DVSLayer
from .dynapcnn_layer import DynapcnnLayer
from .exceptions import InvalidModel
@dataclass
class LayerConstraints:
kernel_m... |
9c70c54789d390550f6211d6c7a6b5e758a6f1968f98b308dfe7ea4007cfde0d | Python | 8,684 | 255 | """Tests for dashboard token authentication."""
import sys
import pytest
import requests
import ray
from ray._common.test_utils import wait_for_condition
from ray._private.test_utils import reset_autoscaler_v2_enabled_cache
from ray.autoscaler.v2.utils import is_autoscaler_v2
from ray.experimental.internal_kv import... |
0659dd71455d6dbfd0047369ec627664bf5f6808c55e2476a021c79787bbd2fd | Python | 8,687 | 257 | """Compositional preprocessing for microbiome AnnData.
All functions operate on a ``samples × features`` AnnData with int counts in
``X``. Most write the result back into ``X`` (returning a new AnnData is not
default; pass ``copy=True`` to avoid in-place modification).
"""
from __future__ import annotations
from typi... |
a193a3f6a2516b401b07e3054e15ffb441ca3bdf8378661d14da503d5b055d15 | Python | 8,691 | 309 | import gzip
import logging
import re
import tempfile
from pathlib import Path
import numpy as np
from Bio.PDB import (PDBIO, NeighborSearch, PDBParser, Polypeptide, Select,
Selection)
from pokeformer.consts import PDB_SET_DIR
logger = logging.getLogger(__name__)
_hydrogen = re.compile("[123 ]*[... |
eb0add0c74250b9f73b17425e0285b5a39d9bd9ac811601f9788b1ad5afcd303 | Python | 8,692 | 219 | from torch import nn
from abc import ABC, abstractmethod
from torch import Tensor
from torch.nn import functional as F
from torch.nn.modules import Module
from torch.nn.modules.activation import MultiheadAttention
from torch.nn.modules.container import ModuleList
from torch.nn.init import xavier_uniform_
from torch.nn.... |
07d9390bf426feb6bc9b25bdcf60897fa9963e07cf28a07748e7e1f65d720cca | Python | 8,695 | 206 | import matplotlib.pyplot as plt
import pickle
import numpy as np
import os
import pandas as pd
from util import *
from sklearn.metrics import auc, accuracy_score, confusion_matrix, roc_auc_score, roc_curve, precision_recall_curve, PrecisionRecallDisplay
from sklearn import svm
POS_NUM = 250
NEG_NUM = 25000
def plot_pr... |
16ab790f8d5041226170a10650be9c6065e013e79bf9f653fe812ce9f41fafe4 | Python | 8,701 | 182 | # -*- coding: utf-8 -*-
#Written in Python 3.7
#Python 2 compliant as of 6/16/17
#Most recently updated/tested in openpyxl 2.6
"""
Python functions for the Factorial Mass ERP Univariate Toolbox
AUTHOR: Eric Fields
VERSION DATE: 18 April 2019
"""
import sys
import re
import openpyxl
from openpyxl.styl... |
a4d4afa40dc319dc726f27dc35f9f469d1e8516f5bc1b0c3f8ffd77477ef475a | Python | 8,701 | 228 | import os
import time
import datetime
from subprocess import call
import numpy as np
import pandas as pd
import seaborn as sns
from scipy import stats
import seaborn as sns
import matplotlib.pyplot as plt
import scipy as sc
from matplotlib.colors import ListedColormap
import scipy.sparse as sparse
from scipy.stats imp... |
ea3bbc88b26273aa71940207683ba1059e137c1bef45e65ee15229512bbd49ad | Python | 8,704 | 253 | import sys
import random
import networkx as nx
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from utils import kcorePercolation as kp # Import custom utility functions
def kcorepercolationPlateau(G, rm_nodes, kcore, dp, p, zeta, simu,... |
ed2a9b03162d24bf3549012638c3b2904e0100f4550a268306bc882fb6206f2c | Python | 8,707 | 230 | import os
import re
import shutil
import logging
import datetime
import argparse
import xmltodict
from timeit import default_timer as timer
def _format_date(input_date, day_flag, sep_char='-'):
'''Format input date from `mm-dd-yyyy` into `yyyy-mm`, or `yyyy-mm-dd`
This is the ISO 8601 standard for date'''
... |
47ba675fcf7995a34a39acb10df71d9bdf6fc68f667e3cd38ae0ff1614eea5a0 | Python | 8,709 | 287 | # -*- coding: utf-8 -*-
"""
Created on Wed Nov 17 11:53:51 2021
@author: mmall
"""
CODE_DIR = 'C:/Users/mmall/Documents/github/'
SAVE_DIR = 'C:/Users/mmall/Documents/uni/columbia/assignment_errors/fits/'
import socket
import os
import sys
import pickle as pkl
import numpy as np
import scipy as sp
import matplotlib... |
e425aadef79bcfe7b6866a67b05a7b21ddf5948d8bf9ff1a61f4baf187aee685 | Python | 8,710 | 253 | import sys
import random
import networkx as nx
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from utils import kcorePercolation as kp # Import custom utility functions
def kcorepercolationPlateau(G, rm_nodes, kcore, dp, p, zeta, simu,... |
1dbffbc941b707a565987daf6de79f10fa27687afe500d2da87e0bab0e40947b | Python | 8,711 | 258 | import matplotlib.pyplot as plt
import nir_reference_impl
import norse
import numpy as np
import snntorch as snn
import torch
# NOTE: this requires snntorch Pull-Request #246 and nirtorch/feature-state
from snntorch import export_nirtorch
from torch import nn
def compare_spike_counts(results):
n_spikes_st = np.c... |
789116a9c4425a4044e0df5932936fa899d253235a17d7c94591866cf12c1d02 | Python | 8,713 | 387 | import numpy as np
import nir
from .test_readwrite import factory_test_graph
from tests import mock_affine
def test_sequential():
a = mock_affine(2, 2)
b = nir.Delay(np.array([0.5, 0.1, 0.2]))
c = nir.LIF(
tau=np.array([10, 20, 30]),
r=np.array([1, 1, 1]),
v_leak=np.array([0, 0, 0... |
98686747f2785560586bc2b9ef356e57d2ad37a3fc809871b7f8c9b63b7ba3b7 | Python | 8,714 | 285 | """Databricks credential providers for Ray Data.
This module provides credential abstraction for Databricks authentication,
supporting static tokens with extensibility for future credential sources.
"""
import logging
import os
from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import C... |
86b0ad01dc7aee77355bd398fe5b5cc8f426386f5ec56006cd13c69a92a1a91c | Python | 8,716 | 217 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import logging
import math
import time
from typing import TYPE_CHECKING, Iterator
import numba as nb
i... |
90d5da3c3f069bd79ffdf261ecede5afabd890b49805dbbb51f636b2388d8ea7 | Python | 8,716 | 259 | import argparse
import os
import numpy as np
import pytorch_lightning as pl
import torch
import torch.nn.functional as F
import torchaudio
import hydra
from omegaconf import OmegaConf
from torch.distributions import Categorical
from tqdm.auto import tqdm
from src import utils
from src.dataloaders.audio import mu_law... |
63b5ad5882832ba1665c56eeb5e421a04ae531e950fdce164883eb7ad9a5552e | Python | 8,717 | 233 | # built-in dependencies
import base64
# 3rd party dependencies
import cv2
import numpy as np
import pytest
# project dependencies
from deepface import DeepFace
from deepface.commons import image_utils
from deepface.commons.logger import Logger
logger = Logger()
detectors = ["opencv", "retinaface"]
# opencv 5 droppe... |
d60ac834b14d110fc03ed548838c1374e1c583c22c2bab3c7bf597b728d89b66 | Python | 8,717 | 266 | # Copyright 2021 Google LLC
# 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, sof... |
52f4349520658dd4c9a531305bb6517de7251b0d3254ba7454884a1401e52043 | Python | 8,719 | 198 | from lisa.core.lisa_core import LISA_Core
from lisa.lisa_public_data.genes_test import FromGenes
from lisa.core.data_interface import PACKAGE_PATH, REQURED_DATASET_VERSION, INSTALL_PATH
from lisa.core.lisa_core import CONFIG_PATH as base_config_path
import numpy as np
from scipy import sparse
from lisa.core import geno... |
b10492d32eeab60ffe96ae0227bbca63bba36ec40e07ceb80ed293d7bc514106 | Python | 8,719 | 221 | ####################################################################################################
# Copyright (c) 2022, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
9d29470edfcc3ccd8c90b95c5098a64b56399447403958efb659493aedb7fa85 | Python | 8,720 | 113 | """
DATA COLLECTION FOR BENCHMARKING
@date: 02/09/2023
@author: dimiboeckaerts
"""
import pandas as pd
from Bio import SeqIO, Entrez
absolute_path = '/Users/dimi/Documents/GitHub/PhageDEPOdetection/data/Benchmarking/'
# 1 - NCBI DATA COLLECTION, FASTAS, DATAFRAME
# ------------------------------------------
# collec... |
73e40a60db2247bb75d9768cc9573937f60c671d04f689d6517ca2b654fcf193 | Python | 8,723 | 197 | # Copyright (c) 2017-present, Facebook, Inc.
#
# 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 agreed... |
aa3e240dc99ae83a3caa4bcc320493fdecc4cb31bf45c7e61df821ce6bd0297f | Python | 8,723 | 243 | #!/usr/bin/env python
from __future__ import print_function
import argparse
import glob
import sys
import numpy as np
import pysam
import time
import tempfile
import os
from subprocess import run
from contextlib import closing
from multithread import *
import subprocess
FORWARD="FORWARD"
BACKWARD="BACKWARD"
FILE_LOCAT... |
0542787812d1354e7907006ebf382482e2fd3a053df147f7d9faf1daca438910 | Python | 8,724 | 187 | import torch
import utility
import loss
from trainer import Trainer
torch.backends.cudnn.enabled = False
import argparse
from div2k import DIV2K
from torch.utils.data import dataloader
import model
def options():
parser = argparse.ArgumentParser(description='EDSR and MDSR')
parser.add_argument('--model', defa... |
f5635d73e6605aca824a59c24348c48497651bf3f9c802fc60147c5d95c3f61b | Python | 8,724 | 174 | import torch.nn as nn
import torch
from pytorch3dunet.unet3d.buildingblocks import DoubleConv, ExtResNetBlock, create_encoders, \
create_decoders
from pytorch3dunet.unet3d.utils import number_of_features_per_level, get_class
class Abstract3DUNet(nn.Module):
"""
Base class for standard and residual UNet.
... |
210a373d125255d093557966be18652d8ef698f8891793511d025c63e8730d6d | Python | 8,725 | 218 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#... |
8d90ef773fb5de1d6c8729885bd2288b1a820eb1d0a6c5288a26a7bb0cd606e1 | Python | 8,725 | 158 | # Copyright 2021 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
# and Applied Computer Vision Lab, Helmholtz Imaging Platform
#
# 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 L... |
d85e089bc8d575c0ce226dd0a8f0a3268bcc88cbd42f6b55618f9ad7c10b42d0 | Python | 8,725 | 187 | from lisa.core.utils import LoadingBar
from lisa.core.assays import LISA_RP_Assay, delta_RP_wrapper, transform_RP
from multiprocessing import Pool
import numpy as np
from scipy import stats, sparse
import os
from collections import defaultdict
class PeakRP_Assay(LISA_RP_Assay):
def __init__(self, **kwargs):
... |
130d0ef77ace0cb688dbb553996e7bfcd2a40f23839336884e532c4ee78d949f | Python | 8,726 | 139 | #!/usr/bin/env python
# coding: utf-8
# author: Maruthi Mutnuri (maruthi2008@gmail.com)
# loading libraries
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn.experimental import enable_iterative_imputer
from sklearn.impute import IterativeImputer
from sklearn.lin... |
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