sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
33e584d847febf2d800f7d2001c8f10036063288905abefd447d48aa95328b08 | Python | 7,448 | 176 | # 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.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... |
3222692818e8c7cc789a5caa5042f6e978367b7f4606ea404c4c0e18bb5f33e0 | Python | 7,453 | 234 | """Base API client with common functionality for all bioinformatics databases."""
import asyncio
import logging
import time
from abc import ABC, abstractmethod
from typing import Any, Dict, Optional, Union
from urllib.parse import urljoin
import httpx
import requests
from requests.adapters import HTTPAdapter
from url... |
d9ad7bc6093f64b33bced36fb204270a481aec0d22422116dc28fe7ccc82763f | Python | 7,453 | 151 | # Usage: python get_xy_data_cnn_combine_from_database.py bulk_gene_list.txt sc_gene_list.txt gene_pair_list data_separation_index_list bulk_expression_data sc_exprsssion_data flag (0, no label. 1, label)
# command line in developer's linux machine :
# python get_xy_label_data_cnn_combine_from_database.py bulk_gene... |
c04353045fdafde7db932585d0ec55a056dffbe4c57ac70695b6b81b7c9efe8e | Python | 7,454 | 217 | """
Mosaic for Horizontal Cells from (Keeley et al., 2020) Figure 8-1.
"""
from glob import glob
import numpy as np
import matplotlib.pyplot as plt
from OPIPP import *
CELLNAME = "Mouse Horizontal Cell"
EDGE_LEN = 300 # the length of two sides
scope = Scope(min_x=0, max_x=EDGE_LEN, # x-axis
min_y=0, ... |
0444ac961d9c39dd631887b9e4ef7c91d64923a44f44d7aeb86fad8fb1367a92 | Python | 7,455 | 225 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Read-only and placeholder tensor views for analog tile weights."""
from typing import Any, Callable, Optional
from torch import Tensor
from torch._C import ... |
6bab909fdc53d41795f98306ea906e4e703da8914844500c24cdd1da45256b95 | Python | 7,455 | 179 | ####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
# Eleftherios Zisis <eleftherios.zisis@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://githu... |
e364cf5a33b7c7214a53acd3e1c7bea8ec1c241390e24615a2673a3f4403f66d | Python | 7,456 | 157 | import os
os.environ['KMP_DUPLICATE_LIB_OK'] = 'True'
import numpy as np
import torch
from model import Circuit, Circuit2D
from utils import find_peaks, bin_traj
from cluster_finding import find_cluster, find_cluster_2d
from tqdm import trange
import matplotlib
import plt_config
import matplotlib.pyplot as ... |
0b212048cac7ca1f82ca5bf77cfaaa050805d30a37c2fc4ec0f6b67583070d58 | Python | 7,459 | 132 | from collections import defaultdict
from datetime import datetime
import pickle
from utils import str_to_datetime
import pandas as pd
def exclude(prescription_taken_by_patient, patient_dates, eligibility_criteria):
# interval, followup, baseline, min_prescription): # patient_1stDX_date, patient_start_date
# ... |
d2898c2915243072afdbeb235576bd7bb79ed29e5cac0e5c30d8f465c9f31522 | Python | 7,459 | 216 | # # Implement a a pipeline that re-tests significant associations but controlling for common variants
import pandas as pd
import pyranges as pr
from pyarrow.parquet import ParquetFile
import numpy as np
import zarr
from pathlib import Path
from numcodecs import Blosc
import logging
from deeprvat.utils import pval_corr... |
5d9a383282a1f0633ee5c4c8ffd070eb693a3f535bddc7e2bed75bc8017348c6 | Python | 7,460 | 161 | import matplotlib.pyplot as plt
import pickle
import numpy as np
import os
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
# define a function to calculate precision, recall, F1 score... |
e50cc1d7f6ddfbd0a86583c1b3bca607fc3c73153cbe23ebec9418c5726f8b9e | Python | 7,461 | 129 | __author__ = "Simon Andermatt"
__copyright__ = "Copyright (C) 2017 Simon Andermatt"
import logging
from copy import deepcopy
import tensorflow as tf
from tensorflow.python.ops import variable_scope as vs
from mdgru.helper import compile_arguments, generate_defaults_info
from mdgru.model import batch_norm
from mdgru.... |
67dae589d0f688c00b1cef1bb368355979a021bae621b39bbdea0de0c5a80399 | Python | 7,464 | 260 | """
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 os
from dataclasses import dataclass
import numpy as np
import torch
from ase import Atoms
from... |
530cdabeda9a16907530a104818bd6a3ac5e4247d48577135dc6a518a345df4e | Python | 7,467 | 224 | import numpy as np
import multiprocessing
import xarray as xr
from scipy.optimize import minimize
import pandas as pd
#from pybayesprism import process_input
from .process_input import norm_to_one
#from pybayesprism import references as rf
from .references import RefPhi, RefTumor
###################################... |
0a7091478a7f28cff55cc0445b514e3a5bf6f121051db587628095d3632c8b4f | Python | 7,469 | 176 | """
Uploaded August 2, 2023
"""
import csv
from itertools import zip_longest
import shutil
shutil.move("/PATH/inference_extraction.py", "/PATH/fastchat/serve/inference_extraction.py")
from prompt_toolkit import PromptSession
from prompt_toolkit.auto_suggest import AutoSuggestFromHistory
from prompt_toolkit.completi... |
b2b866ffdc55d796506392797ef1202f178a37f5a0a4ff4aac7b43ceb10fec6f | Python | 7,470 | 352 | # -*- coding: utf-8 -*-
### -------------- IMPORTS -------------- ###
import numpy as np
from numba import jit
from scipy.signal import welch, hilbert
from scipy.fftpack import fft
### ------------------------------------- ###
@jit(nopython = True)
def find_nearest(array, value):
"""
find_nearest(array, value... |
bcf915246d50e90ef055fe0563002e3b7003a76e9c3399362687d1c2f5dc0a58 | Python | 7,475 | 143 | import os
import math
import copy
import pickle
import numpy as np
import pandas as pd
from tqdm.auto import tqdm
import dgl
from .utils import preprocess_kg, create_split, process_disease_area_split, create_dgl_graph, evaluate_graph_construct, convert2str, data_download_wrapper
import warnings
warnings.filterwarnin... |
a9105ab4f4281dc00852fdf6fe4afe47264d185d1b29fe82ed86dd963e2d9385 | Python | 7,476 | 243 | # -*- 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.
#... |
aa63920e9fc41cd20eedd846096d49f0a8862ba2f1d002b5209c7fe2578bf445 | Python | 7,483 | 303 | from typing import List, Tuple, Union
import numpy as np
from matplotlib.colors import (
LinearSegmentedColormap,
ListedColormap,
hex2color,
to_rgba,
)
from flyvis.analysis.visualization.plt_utils import color_labels
from flyvis.utils.groundtruth_utils import polarity
ON = "#af0019" # red
OFF = "#00... |
ab301f606145652b2e155179ed46a018d8331d83d71d03e1aa05ab4cdd58c9e3 | Python | 7,483 | 218 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from collections import OrderedDict
from collections.abc import Callable
from datetime import datetime, timedelta, timezone
from typing import Any, TypeAlias, cast
import attrs
import cvat_sdk.auto_annotation as cvataa
import PIL.Image
from .agent_... |
d5fce6d3c109f57272c6cd6f4f178a172f16d1a19cd62741679d3e1bd1f977bd | Python | 7,485 | 170 | from collections import defaultdict
import logging
from random import Random
from typing import Dict, List, Set, Tuple, Union
import warnings
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
from tqdm import tqdm
import numpy as np
from .data import MoleculeDataset
def generate_scaffold(mol: U... |
cd9740a09f168a04cb2e6694fb46410447f94afd5fd1641cf5426d7ca2d89ee5 | Python | 7,488 | 204 | import importlib.util
from pathlib import Path
import pysam
import pytest
MODULE_PATH = Path(__file__).with_name("merge_stripy_vcfs.py")
MODULE_SPEC = importlib.util.spec_from_file_location("merge_stripy_vcfs", MODULE_PATH)
assert MODULE_SPEC is not None
assert MODULE_SPEC.loader is not None
merge_stripy_vcfs = impo... |
9bc64a1b2123361d30ec8923c0963f7b61da17ec6fef5484b5a1972db8a12cd4 | Python | 7,489 | 246 |
import numpy
import plotly.graph_objects as go
import matplotlib
from matplotlib import pyplot
from plotly.subplots import make_subplots
from plotly import express
from . import utils
COLOR = "#87cdde"
cmap = matplotlib.colors.LinearSegmentedColormap.from_list(
name="space",
# colors=["#45d7cd", "#ffc949"]... |
99bd16a9535f7addffc27eb382d3e8bb94c821ecf2cf6c19a3f2f531daece48a | Python | 7,490 | 248 | # -*- 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.
#... |
5d68f9c265c483132a82a8ebd18f05b0b9eb7ee07ed85c3bdcdc53f6d4dbe10a | Python | 7,493 | 231 | """Dataset utilities."""
from typing import List, Tuple
import numpy as np
from numpy.random import RandomState
from torch.hub import download_url_to_file
from torch.utils.data.sampler import Sampler
import flyvis
def random_walk_of_blocks(
n_blocks: int = 20,
block_size: int = 4,
top_lum: float = 0,
... |
b0888e2635855cbe54a89938c869dc86ee4e8f8571ff8e12459afbbbf0488c07 | Python | 7,493 | 224 |
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import time
from util import log
def initialize_weights(module):
if isinstance(module, nn.Conv2d):
nn.init.kaiming_normal_(module.weight.data, mode='fan_out')
elif isinstance(module, nn.ConvTranspose2d):
nn.init.kaiming_normal... |
e54a2c80369e7f20e01016ef8316c91853dbe0ee2217f879886af872c15169f1 | Python | 7,495 | 228 | # -*- coding: utf-8 -*-
"""
Created on Thu Apr 25 03:56:24 2024
@author: Leyang Xue
"""
import sys
import numpy as np
import matplotlib.pyplot as plt
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from utils import kcorePercolation as k... |
4d9b8beb49096d028c06347cae2e96e131684e8caddc251b255394fc4b9f4918 | Python | 7,497 | 168 | ###################################
# This python script plots the average score plot for the donors / acceptors
# and their surrounding regions.
###################################
import matplotlib.pyplot as plt
import sys
import numpy as np
import os
import pickle
from sklearn.metrics import accuracy_score, confus... |
2413c059aea127c2117a4a6da283e768d19e7d79fe1d8f5118e811de98547736 | Python | 7,498 | 291 | import numpy as np
from numba import jit
from tqdm import tqdm
import pandas as pd
from scipy.stats import norm
from scipy.sparse import issparse
from statsmodels.stats.multitest import multipletests
import multiprocessing
from . import danb_model
from . import bernoulli_model
from . import normal_model
from . import ... |
3bceea91ef1e9140c213a245184be086dbbb27211c3ea89b6b2e3758123712ec | Python | 7,498 | 183 |
import gym
import numpy
import random
import os
from gym import error, spaces, utils
from gym.utils import seeding
from matplotlib import pyplot
from collections import OrderedDict
import gym_sted
from gym_sted import rewards, defaults
from gym_sted.utils import SynapseGenerator, MicroscopeGenerator, get_foreground,... |
d0a09a0b9a89acd03f094794ae6149141170596b667020340006019d06e03053 | Python | 7,498 | 223 | import os
from os.path import join
import pickle
import argparse
import numpy as np
import pandas as pd
from tqdm import tqdm
from pyplink import PyPlink
from util import LATENT_DIR, get_latent_pkl, get_latent_bolt
def main():
parser = argparse.ArgumentParser()
parser.add_argument('geno_temp', type=str, ... |
cf8b1df3687d256cc97a2ccda92a12b60b2ce8ab1efc00b2c42451f3a3d32324 | Python | 7,500 | 197 | import asyncio
import io
import logging
import os
import sys
from concurrent.futures import ThreadPoolExecutor
import ray
import ray._private.ray_constants as ray_constants
import ray.dashboard.consts as dashboard_consts
from ray._common.utils import run_background_task
from ray._raylet import GcsClient
from ray.dashb... |
cef3d9d4711e9b2b16e019b175972747bf08ce5f4e3548fae44e2fa5faaf89e8 | Python | 7,503 | 136 | # coding: utf-8
"""
# # SCRIPT: IDENTIFY EEG-BASED REACTIVATION ONSETS IN REST
# # PROJECT: FMRIREPLAY
# # WRITTEN BY QI HUANG 2022
# # CONTACT: STATE KEY LABORATORY OF COGNITIVE NEUROSCIENCE AND LEARNING, BEIJING NORMAL UNIVERSITY
"""
# In[1]: import relevant packages
import os
import sys
import warnings
import numpy... |
47f5800b0300fcc94acb0e92d514051dc1d5637ec31d00ae8795c01710483981 | Python | 7,506 | 226 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from enum import StrEnum
from typing import cast
from django.conf import settings
from rest_framework.exceptions import PermissionDenied, ValidationError
from cvat.apps.engine.models import Job, Project, Task
from cvat.apps.engine.permissions impor... |
9602ddce65434a5084184dab88ad851170ead3617b2310096ce94e3bfcaa96c7 | Python | 7,506 | 240 | import warnings
import tempfile
import torch
import numpy as np
from rdkit import Chem
from rdkit.Chem.rdForceFieldHelpers import UFFOptimizeMolecule, UFFHasAllMoleculeParams
import openbabel
import utils
from constants import bonds1, bonds2, bonds3, margin1, margin2, margin3, \
bond_dict
def get_bond_order(ato... |
973e7ea66402a9c63e39e2b441748becbbc50b8952b5c6b9c87e073346f0adcb | Python | 7,511 | 215 | #!/usr/bin/env python
from __future__ import print_function
import re
import argparse
import logging
# 3rd party
import networkx as nx
from networkx.algorithms.dag import descendants
from networkx.algorithms.lowest_common_ancestors import lowest_common_ancestor
from networkx.algorithms.shortest_paths.unweighted import ... |
c769d911116ebc72cc339cba24915b190d3237071a157ca189b348a5e2c2b661 | Python | 7,514 | 154 | ####################################################################################################
# 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... |
595dc0db23f325a7bea7794caeb46b5920b12da3af193851b96820c01eeda580 | Python | 7,516 | 207 | ####################################################################################################
# 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... |
b8519eba170af269e8858588a601373084f0280c2624af3cf11d2a51ebb06033 | Python | 7,516 | 151 | from pathlib import Path
import argparse
import json
import os
import random
import signal
import pickle
import sys
import warnings
warnings.filterwarnings('ignore') # "error", "ignore", "always", "default", "module" or "once"
import time
import urllib
import numpy as np
from datetime import datetime
from torch import... |
1ce18ad0060ee2b8a0d00fe8f508e2ef07b0d530e0fa739ca111056796dc0d7c | Python | 7,518 | 211 | # -*- coding: utf-8 -*-
"""
Created on Sun Jul 1 17:15:00 2019
@author: ju-bar
Cluster recognition tools
This code is part of the 'emilys' repository
https://github.com/ju-bar/emilys
published under the GNU General Publishing License, version 3
"""
import numpy as np
# %%
class cluster:
'''
class cluste... |
fc5f73ebbcae8e078649dc11d68cf32eade9084d0676b0015612ce15ae16757a | Python | 7,518 | 167 | import torch
import numpy as np
import h5py
import pandas as pd
from scipy import signal as sgn
from src.dataset.batchdataloader import BatchDataloader
from src.dataset.utils import compute_weights, remove_baseline_filter
MIN_TRAIN_SET_SIZE = 1000 # the minimum size of the dataset before weight computation could beco... |
7868eba08cbcf8816ac8d53a2b0d65cfcc7b7cd20a7b3b0cc5f644e586f06b04 | Python | 7,520 | 202 | #!/bin/python
import pysam
import sys
from collections import defaultdict
from operator import attrgetter
from itertools import combinations
import svtk.utils as svu
# Inputs
VCF_PATH = sys.argv[1]
BOTHSIDE_PASS_PATH = sys.argv[2]
BACKGROUND_FAIL_PATH = sys.argv[3]
DROPPED_RECORD_OUTPUT_VCF_PATH = sys.argv[4]
if len... |
4a699aa97c7ba2782514e0ae45ce6a9cef4287fde2a2284d6b31b32b3acb08a1 | Python | 7,528 | 208 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
59af865ae6a3e06a749ca061ce4fa87963b4660873a3f5e3059a6429ef8bb184 | Python | 7,529 | 235 | # coding=utf-8
# Copyright 2022 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... |
1814ef2d8ccf7d65fa117b62e4b6e65c9c2aaa86b9d18ad3f705e0551511f367 | Python | 7,533 | 176 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Complete pipeline for online processing using CaImAn Online (OnACID).
The demo demonstates the analysis of a sequence of files using the CaImAn online
algorithm. The steps include i) motion correction, ii) tracking current
components, iii) detecting new components, iv... |
0bf024ac0652e0bbff23d0bbb0bd9c2e1ca9b1754aec58ffa1e1f71797fc9e0b | Python | 7,535 | 201 | """
Memory(i.e.History)-based agent
by Aditya Gilra, Sep 2021
"""
import gym
import numpy as np
import gym_tasks
import matplotlib as mpl
import matplotlib.pyplot as plt
# reproducible random number generation
seed = 1
np.random.seed(seed)
# if history, then store current and previous observations as state
# else j... |
2ff2a888c2a43e773e016a6d355c9c4a8ec15d9a6921d16903b09364c20ab27f | Python | 7,537 | 206 | import argparse
import logging
import os
import os.path as osp
import warnings
from mmengine.config import Config, DictAction
from mmengine.logging import print_log
from mmengine.registry import RUNNERS
from mmengine.runner import Runner
from lqit.common.utils.lark_manager import (context_monitor_manager,
... |
98929f971969e3cdca9619a27df6d3a3303588349b30cd6c0333a5cb607998d5 | Python | 7,537 | 223 | import numpy as np
from ml4h.TensorMap import TensorMap, Interpretation
def _read_dataset(hd5, path):
if path not in hd5:
raise KeyError(f"Missing dataset '{path}' in {hd5.filename}")
return hd5[path]
def _read_ecg_2500_12(hd5):
x = np.array(_read_dataset(hd5, "ecg/waveform"), dtype=np.float32)... |
feae00679b4c1c20ddd4387657bd6e914bb6b9728111c897f7e49d16c5e03d75 | Python | 7,540 | 201 | import nengo
import numpy as np
import nir
model = nengo.Network(seed=3)
with model:
model.config[nengo.Ensemble].neuron_type = nengo.LIF(tau_rc=0.02, tau_ref=0)
x = nengo.Ensemble(n_neurons=600, dimensions=3, radius=30)
synapse = 0.1
def lorenz(x):
sigma = 10
beta = 8.0 / 3
... |
74665d50ea6a6ee9e9683e752a427a97f8f75f372e39630a0e2dfdcec1cd7684 | Python | 7,541 | 188 | """
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.
Tests: ASE vs LAMMPS energy/force agreement for a fairchem-backed
calculator running NVE, NPT, and Langevin molecular dynamics
... |
93e66665530baad0c7a25ba14e71cee1d26b520f68534e8ff9f1c5bd3c73f37c | Python | 7,545 | 225 | import argparse
import time
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from models import GNN
from torch_geometric.data import DataLoader
from torch_geometric.nn import global_mean_pool
from datasets import MoleculeDataset_graphcl
class graphcl(nn.Module):
def __init__(sel... |
50f41eb8ebeb0dea99f793d4c3239880b2cd847f37ce1c9957810f4c25ac2366 | Python | 7,547 | 234 | import os
import subprocess
import spinnaker2.hardware
from spinnaker2.configuration import (
Experiment,
ExperimentConfig,
MemoryRegion,
PEConfig,
)
from spinnaker2.coordinates import (
PE,
ByteAddr,
WordAddr,
align_addr_to_next_multiple_of_other,
)
from spinnaker2.helpers import read_... |
b14e51395435466f937e2f671395ddb875760d4815ead11498afeed60f509333 | Python | 7,547 | 230 | from pathlib import Path
from typing import TYPE_CHECKING, Any
import numpy as np
import xarray as xr
from numpy.typing import NDArray
from PIL import Image
from siapy.core.exceptions import InvalidInputError
from siapy.entities.images.interfaces import ImageBase
if TYPE_CHECKING:
from siapy.core.types import Xa... |
840df1bd81204362b648a5921546f01b4986645c51cf8bc8d7ce767b07b9b37e | Python | 7,548 | 291 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# Copyright (c) 2021 Qualcomm Technologies, Inc.
# All Rights Reserved.
# mypy: disable-error-code=attr-defined
"""Functions to manipulate the quantization sta... |
3e7e2bc371e945d5b607e1cee085deab7064b74a70255aa6d5a6d5ab26979fd9 | Python | 7,549 | 194 | import logging
import platform
import subprocess
from typing import Dict, List, Optional, Tuple
from ray._private.accelerators.accelerator import AcceleratorManager
logger = logging.getLogger(__name__)
class AppleGPUAcceleratorManager(AcceleratorManager):
"""Apple Silicon GPU (MPS) accelerator manager.
Unl... |
77925090d5d74432a3be2d24b15d914b646766dd9e683656b6c18166622713f1 | Python | 7,555 | 238 | import unittest
import numpy as np
from neuron_morphology.morphology import Morphology
from neuron_morphology.constants import (
AXON, APICAL_DENDRITE, BASAL_DENDRITE, SOMA
)
from neuron_morphology.feature_extractor.data import Data
from neuron_morphology.features.branching import bifurcations as bf
from neuron_m... |
f115205d5b1f25e4d43c7a6f0e6cfa8547a2bc8c93dce8c3760e1b89bdc4491d | Python | 7,555 | 174 | #!/usr/bin/env python
#!/usr/bin/env python
'''
Example of a single-layer bidirectional long short-term memory network trained with
connectionist temporal classification to predict character sequences from nFeatures x nFrames
arrays of Mel-Frequency Cepstral Coefficients. This is test code to run on the
8-item data se... |
027b363f1f129826846c4053f6e60919753a80fa79e33383a9006e8131458a95 | Python | 7,556 | 207 | import logging
from json import loads
from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Tuple
from urllib.parse import urlparse
from urllib.request import getproxies
import numpy as np
import pyarrow as pa
from ray.data._internal.object_extensions.arrow import raise_on_pickle_object_columns
from ... |
a59dce72f43718e52aa7fdf885ce72dcbda0baeec77396c181b7cf8b33ca840b | Python | 7,557 | 177 | import math
import torch
from torch import nn
# from torch.nn import TransformerEncoderLayer, TransformerEncoder
# from torch_cluster import knn_graph, radius_graph
# from torch_geometric.nn import MetaLayer, voxel_grid, global_max_pool, max_pool, avg_pool
# import torch.nn.functional as F
# from torch_geo... |
a3845ca44927ca669778ca7489a522f4f5138e8303c7efe6818a193e1b15d376 | Python | 7,559 | 299 | # isort: skip_file
from ray._private import log # isort: skip # noqa: F401
import logging
import os
import sys
from typing import TYPE_CHECKING
log.generate_logging_config()
logger = logging.getLogger(__name__)
def _configure_system():
import os
import platform
import sys
"""Wraps system configurat... |
a91b040b5991f21add7acdcaf61668fa5037715926bc607565ed58d1e0c146ec | Python | 7,561 | 227 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Tests for general functionality of layers."""
from torch import randn
from aihwkit.inference import (
PCMLikeNoiseModel,
ReRamCMONoiseModel,
Cus... |
976edfa5fde971b125cb20480140abac51785e19f862d7a17f348f8664f37b17 | Python | 7,565 | 208 | ####################################################################################################
# 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... |
391a7aef4bc6bf31716b1c265f935aa7e187eea9640233b799181152fcd569ef | Python | 7,567 | 204 |
import h5py
import numpy as np
import pandas as pd
import sys
from optparse import OptionParser
import json
from scipy.sparse import csr_matrix, isspmatrix_csr, issparse
from concurrent.futures import ThreadPoolExecutor
from tqdm import tqdm
from .._registry import register_function
# Small number for checking intege... |
c0d8a22b60fadb306839b71fa420fe2598d8d38beb5ce6eaeb2bb1c9c1bd7abc | Python | 7,567 | 213 | from itertools import cycle
from datetime import datetime, timedelta
import pytest
import numpy as np
from torch.utils.data import DataLoader
import tensorflow as tf
from ml4ht.data.data_description import DataDescription
from ml4ht.data.sample_getter import DataDescriptionSampleGetter
from ml4ht.data.data_loader imp... |
8757d7f0956eb204d457b1d914f9335573314c54566ee106b1417d3383c25f2c | Python | 7,568 | 235 | """
Implementing "two networks with merging outputs" in https://github.com/synsense/sinabs/issues/181
"""
import torch
import torch.nn as nn
from sinabs.activation.surrogate_gradient_fn import PeriodicExponential
from sinabs.layers import IAFSqueeze, Merge, SumPool2d
class SNN(nn.Module):
def __init__(self, bat... |
d5735780d2a983c5b3cbd8bf583a35f0ab0114e9e85ea5709665ef1f9111be9e | Python | 7,568 | 214 | from torch_pgn.data.dmpnn_utils import BatchProxGraph
from torch_pgn.models.model import PGNNetwork
from torch_pgn.args import TrainArgs
from argparse import Namespace
import torch
import torch.nn.functional as F
from scipy.stats import pearsonr
from sklearn.metrics import r2_score
from tqdm import tqdm
import nump... |
89296c26df3530c6c4ce082c19ef88fbb1e52313bfd968ccce8f445731ee9b91 | Python | 7,570 | 189 | import torch
from torch.utils.data import DataLoader, TensorDataset
from transformers import AutoImageProcessor, AutoModelForImageClassification
import torch.nn as nn
import numpy as np
def calculate_accuracy(outputs, labels):
_, predicted = torch.max(outputs.logits, 1)
correct = (predicted == labels).sum().i... |
e494943c51051ae27ffd4536e39fd374f4414a50b42a5a5c073939a479eb7120 | Python | 7,571 | 206 | """Get event-related averages per stimulus duration"""
import os
import glob
import nibabel as nb
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
ROOT = '/Users/sebastiandresbach/data/neurovascularCouplingVASO/Nifti'
# Define data dir
DATADIR = '/Users/sebastiandresbach/d... |
642c749d8b19e82a8a0df0e035005e0e8f5a5fc3b72a073a6e913b3073b66151 | Python | 7,572 | 241 | """File-backed analysis run store for OVAgent."""
from __future__ import annotations
from dataclasses import asdict, dataclass, field
import json
import logging
from pathlib import Path
import time
import uuid
from typing import Any, Optional
logger = logging.getLogger(__name__)
from .workflow import WorkflowDocume... |
c6034c65e0ec1a7d0cb74dba8dd9361c082689e23e5f14c97b9cbd0de901c08b | Python | 7,572 | 264 |
import gym
import numpy
import random
import os
import queue
import pysted.base
from gym import error, spaces, utils
from gym.utils import seeding
from matplotlib import pyplot
from collections import OrderedDict
import gym_sted
from gym_sted import rewards, defaults
from gym_sted.utils import SynapseGenerator, Micr... |
3602e620eb716e7565b7c840f77adfc298e9c5d589a45743da0739501b3cdd76 | Python | 7,574 | 207 | """Tests for fairchem.core.models.uma.compat — UMA generation classifier
and in-place ``model_id`` back-fill.
"""
from __future__ import annotations
import pytest
from fairchem.core.models.uma.compat import (
UMA_1P1_MODEL_ID,
apply_uma_compat_fixups,
get_uma_version,
)
from fairchem.core.units.mlip_unit... |
43277a0a2e4485c5713c211c00e58bc387d1bf7eedc8a193ace1071a6eff73bb | Python | 7,575 | 241 | import os
import tempfile
import numpy as np
import pytest
import torch
from torch import distributions, nn
import pfrl
from pfrl.envs.abc import ABC
from pfrl.experiments import (
train_agent_batch_with_evaluation,
train_agent_with_evaluation,
)
from pfrl.experiments.evaluator import (
batch_run_evaluati... |
b90c0d85cc30759e3e5b0e786c7266996de74571c2747fabaa214179967b8cc6 | Python | 7,576 | 188 | import os
import numpy as np
import pandas as pd
import opensim as osim
from tqdm import tqdm
from NeuroMotion.MSKlib.pose_params import RANGE_DOF
class MSKModel:
def __init__(self, model_path='/home/msh/git/NeuroMotion/NeuroMotion/MSKlib/models/ARMS_Wrist_Hand_Model_4.3.2', model_name='Tenodesis_Model_moreDoF.o... |
bf7e997f1efef7238148e0dce3ab82c65fe30dba8c4cd4f76990e6848ba774cd | Python | 7,578 | 228 | """Functions necessary for aggregating temporal features into single values."""
import logging
import time
from collections import defaultdict
from functools import partial
from importlib import import_module
from pathlib import Path
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn import pre... |
5f604c7dfda9da964204d2235cdd8f56a39989afe4c18aa49061aa278001c546 | Python | 7,579 | 223 | import matplotlib.pyplot as plt
import nir_reference_impl
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.count_nonzero(... |
af0c8de0cf4643bff72fe7e1d970eee26090f5820abbfcef1f43cf79bcd3acc1 | Python | 7,580 | 194 | import logging
from datetime import datetime
from transformers import BertForSequenceClassification
from agent.data.entities.config import DEV_LABEL, TEST_LABEL, EXTERNAL_LABEL, CTT3_LABEL, CTT3FR_LABEL, CTT3HEALTH_LABEL
from agent.classifiers.tr_ffnn_ensemble_classifier import tr_ffnn
from agent.classifiers.data.wra... |
d9613fb8666b7b285074a69e153d32dd254861f9415a2905a898ca6b27d118a8 | Python | 7,581 | 196 | import argparse
import datetime
import pickle
import sys
import time
import numpy as np
import os
import pandas as pd
from torch.utils.data import DataLoader, Dataset
from torchnet import meter
import torch
from sklearn.model_selection import train_test_split
from model import AIMP
from preprocess impo... |
8287339f92bf2ac53078259f1b5eb32bdcc3276dc8e5f9cdec6eb845aed5f6dc | Python | 7,582 | 156 | import torch
from torch import flatten
from torch import nn
import torch.nn.functional as F
# Training augments with the functions test-time augmentation uses, which live with the inference code (the built app predicts without PyTorch)
from candycrunch.inference import transform_mz, transform_rt
class SimpleDataset(t... |
90dd3ae6d4938151843fcf9a7daa0def446b517abcb211c32915cab1f91de8f0 | Python | 7,583 | 232 | import numpy as np
import os
from pynwb import NWBFile, NWBHDF5IO, image
from pynwb.ophys import TwoPhotonSeries, OpticalChannel, ImageSegmentation, ImagingPlane
from pynwb.file import Subject
from pynwb.device import Device
import math
import statistics
import pandas as pd
import h5py #Provides methods to supplement ... |
fd5b814def49c36f3b6b520f5d45e9ceafafa38901d82a77552221f32bd849a5 | Python | 7,584 | 192 | import subprocess
import argparse
from tempfile import NamedTemporaryFile
from collections import OrderedDict
import gzip
############################################################################
# Functions for calling liftover to remap SNP coordinates from HG19 to MM9
#############################################... |
036494b30e42ff059927ce6179c8cdf76793718911aaad1cd83b6f8c6d2abeef | Python | 7,585 | 246 | """KEGG API client."""
import logging
from typing import Any, Dict, List, Optional
from .base import BaseAPIClient
from ..config import settings
logger = logging.getLogger(__name__)
class KEGGClient(BaseAPIClient):
"""Client for KEGG REST API.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a datab... |
c67af8f8db4e5d3966149460a6322b6beda2737b7a6ff14d5cb322f8f5c11ad3 | Python | 7,587 | 246 | """KEGG API client."""
import logging
from typing import Any, Dict, List, Optional
from ..base import BaseAPIClient
from ...config import settings
logger = logging.getLogger(__name__)
class KEGGClient(BaseAPIClient):
"""Client for KEGG REST API.
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a dat... |
178e76c11b4081ceed4f6ba27aa56a0e08ab8fcfce6858aa04ebe39c4f88531b | Python | 7,588 | 219 | # Vendored from `decoupler` (https://github.com/scverse/decoupler) by
# omicverse for in-tree GPU acceleration work. Original copyright by
# the decoupler authors, redistributed under decoupler's GPL-3.0
# license. Cross-module imports rewritten from `decoupler.*` to
# `omicverse.es.*` (see scripts/vendor_decoupler.py)... |
cbda6dfac4372be7f34a6f3eea44c6c39b86df3b1bfdc73ae5bc96ab0d706655 | Python | 7,591 | 156 | import h5py
import glob
import os.path
import numpy as np
import pandas as pd
import argparse
import glob
import pdb
def minimal_qtl_processing(QTL_Dir, OutputDir, writeToOneFile=True, compressed = False, overWrite=True, minimalPValue = 1, minimalFeaturePValue = 1, topMode = False, debugMode = False):
qtl_results_... |
8bd4c550a53879c31123f010a8666ef1f8f2bf5f79222c539b9b6447cdee28f5 | Python | 7,592 | 171 | # Copyright 2023 ETH Zurich Computer Vision Lab and 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.org/licenses/LICENSE-2... |
26ca2c037a37118480e165efd0aedfb3f720ead9a311fe218fcc8e4023618d0c | Python | 7,593 | 195 | import torch.nn as nn
import torch
from spikingjelly.clock_driven import layer
__all__ = [
'PreActResNet', 'spiking_resnet18', 'spiking_resnet34'
]
class PreActBlock(nn.Module):
'''Pre-activation version of the BasicBlock.'''
expansion = 1
def __init__(self, in_channels, out_channels, stride, dropou... |
7243bcb8dbdf190f4aff0c0618812b2d923c4d17e1067c6a791fe7f86d1629a6 | Python | 7,597 | 219 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
"""
import sys
import numpy as np
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.preprocessing import LabelEncoder
from sklearn.metrics import roc_curve
def rf_classify(metrics, trainable, testable, features, labeler, cutoffs,... |
d6f0ea38a9dca7ba73eef4300fb329a0705254d7f311c1fefcd51c5aaa302365 | Python | 7,597 | 253 | from dataclasses import dataclass
from typing import Any
import numpy as np
from .node import NIRNode
@dataclass(eq=False)
class CubaLI(NIRNode):
r"""Current based leaky integrator model.
The current based leaky integrator neuron model
is defined by the following equations:
.. math::
\tau_... |
29e8a8e84cc312c5bbac7f1f023199444ceddfade04f105ab8faf2e5af166470 | Python | 7,600 | 222 | # Copyright 2021 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
#
# 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
#... |
50921bb868acc3f8958654c18c17674a6f4b82c2e64db35b38fa0753aa1fda33 | Python | 7,601 | 185 | # coding=utf-8
# Copyright 2023 The HuggingFace Inc. team.
#
# 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... |
e363899ade1924394c60964cf97ff9e86096de0f6e2f184cd4e3d6a5f59c953e | Python | 7,601 | 209 | """Clustering of EV subpopulations for single-EV proteomics.
EV-subpopulation discovery is the core of single-EV analysis: an EV x protein
AnnData is partitioned into vesicle subpopulations that share a surface-marker
profile.
This module keeps only the EV-specific routines:
* :func:`flowsom` — a native, pure-Python... |
c6321e0d000500ef04a2c75f7b180ee33ef3dfda0d17fb063b3a64767923e9fc | Python | 7,602 | 186 | import numpy as np
import torch
import torch.nn as nn
from typing import Union, Tuple, Optional
from torch_geometric.typing import (OptPairTensor, Adj, Size, NoneType,
OptTensor)
from torch import Tensor
import torch.nn.functional as F
from torch.nn import Parameter
from torch_g... |
3b1e5bf804b8f5afbe45d99fc91a77d40c212b0c929c8bb8dc983b349618da99 | Python | 7,603 | 212 | """Screen frames follow recorded presentations, with one synthetic endpoint."""
import json
from pathlib import Path
import numpy as np
import pytest
import yaml
from mozaik.tools.experanto_export import MozaikScreenExporter
IMAGE_META = dict(
condition_hash="image",
image_size=[144, 144],
modality="ima... |
a88135e63879e2adc79d13938e9c73460d71dc65c274545e02b4170c09272112 | Python | 7,604 | 176 | # hypertuning.py
# Imports
import logging
from timeit import default_timer as timer
import numpy as np
import tensorflow as tf
import kerastuner as kt
import kerastuner.engine.trial as trial_module
from tensorflow.keras.callbacks import EarlyStopping
from kerastuner.tuners import RandomSearch, BayesianOptimization, H... |
6f41b71b37236690e17d799f52ad1babc48ae6bff18207ee529f75e4e546e5d1 | Python | 7,606 | 166 | import logging
from datetime import datetime
from agent.classifiers.tree_classifiers import tree_classifier
from agent.classifiers.data.wrappers.count_features_fd_dataset_dev import get_raw_datasets as get_datasets_dev
from agent.classifiers.data.wrappers.count_features_fd_dataset_test import get_raw_datasets as get_... |
78f6921000f8a06e2c8190b7f70a46d9efeec822715f23a645c7a42be1032354 | Python | 7,606 | 171 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Python version: 3.10.9
pandas version: 1.5.0
seaborn version: 0.11.0
matplotlib version: 3.6.3
pingouin version: 0.5.3
"""
#%% Import Modules
import pandas as pd
import seaborn as sns
import matplotlib.pylab as plt
import pingouin as pg
from matplotlib.patches import ... |
c0943decdcbf34edb1b75e56ab7ec57c05662cbcd4d53faf11718982b268600b | Python | 7,610 | 200 | # Copyright 2023 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... |
173cb1bb266b87faa7f56821cf734786db6df2fbf5a8804548508c052e1118f3 | Python | 7,612 | 168 | import argparse
import pickle
from typing import List
import numpy as np
import torch
from lib.data_utils.matched_cells_struct import OrderedMatchedCellsStruct
import lib.dataset_config_parser.dataset_config_parser as dcp
from lib.dataset_config_parser.dataset_config_parser import read_config_file
import lib.data_uti... |
745d644af465c3521038c92d0c765f06ac8217dc5aa0328bd2973bbb4180a780 | Python | 7,612 | 192 | import numpy as np
import torch
import torch.nn.functional as F
from typing import List, Tuple, Dict, Callable
import lib.data_utils.dynamic_data_util as ddu
from lib.data_utils.matched_cells_struct import OrderedMatchedCellsStruct
FrameRateLNPSpikeTrains = List[torch.Tensor]
def frame_rate_lnp_multidata_bin_spike... |
abd4d1fec117554fba2b4b09579a182221ccb0fc789a2f304019979e787c674f | Python | 7,612 | 220 | """
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 argparse
import os
import numpy as np
import torch
from fairchem.core.calculate.ase_calculato... |
2fdd48d168882fb2efc56fa0b132518463b27147aae6f150aad2fde8eb191c99 | Python | 7,613 | 248 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
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