sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
e474ee5b8efb2fab94795956b43a27f5459b10845fb4255028d29110d3c007c2 | Python | 12,643 | 321 | #
# \file generator.py
#
# \brief Generates the CUTLASS Library's instances
#
#
import enum
import os.path
import shutil
from library import *
###################################################################################################
#
class Conv3dOperation:
#
def __init__(self, conv_... |
8435adda58956d3af31d9e4e76b832c1f9a7206157827a4f20b6e37ee983783e | Python | 12,644 | 351 | import glob
import hashlib
import os
import h5py
import joblib
import numpy as np
import pandas as pd
import scipy.io
import torch
from numpy.random import Generator
from numpy.random import PCG64
from sklearn.decomposition import PCA
import sklearn.model_selection
import cebra.datasets
from . import pi_vae
class Syn... |
c04142abec388558e27620a7c6b6c07469f4abf0cbfc6d18dfec0231dc45219a | Python | 12,647 | 426 | # Copyright 2024 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, ... |
d3d262d76c8e7d9b11a6f467599034f6a2fe51a1e61534eaf70cd9f7fa2cfc8a | Python | 12,651 | 257 | import torch
import torch.nn as nn
import numpy as np
import scanpy as sc
import anndata as ad
from torch.optim.lr_scheduler import _LRScheduler, ReduceLROnPlateau
from tqdm import tqdm
from copy import deepcopy
from ..utils.eval import downstream_eval, aggregate_eval_results
from ..utils.data import XDict, Transcripto... |
f21a419625d10c7954ec89def9827e3792193268eec1932ce821016c4457e550 | Python | 12,655 | 369 | # @license
# Copyright 2017 Google 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 to in... |
30063b62d6a2ead9e072909b8783db45493fba41283913f5ac6f1b0340c82535 | Python | 12,657 | 347 | # Copyright 2026 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, ... |
264fe2ded0131f931af10f32aaadafd4960af9322d62de71f98dff2807d7bb81 | Python | 12,658 | 367 | import re
from dataclasses import dataclass
from pathlib import Path
from typing import Dict, List, Union
import flyvis
from flyvis.network.ensemble import model_paths_from_parent
@dataclass
class Status:
"""Status object from log files of model runs.
Attributes:
ensemble_name: Name of the ensemble.... |
36ea01af1062cfdc19a617205ada97f96c3d0bd49ed73f01b618b31d8674289d | Python | 12,662 | 312 | # -*- coding: utf-8 -*-
"""
PMLB was primarily developed at the University of Pennsylvania by:
- Randal S. Olson (rso@randalolson.com)
- William La Cava (lacava@upenn.edu)
- Weixuan Fu (weixuanf@upenn.edu)
- and many more generous open source contributors
Permission is hereby granted, free of charge, ... |
7392047a970b098ee51284833c1f83a4ee0d16e69700463a1c1d1df7705ac966 | Python | 12,667 | 353 | import rdkit
import rdkit.Chem as Chem
import numpy as np
import random
elem_list = ['C', 'N', 'O', 'S', 'F', 'Si', 'P', 'Cl', 'Br', 'Mg', 'Na', 'Ca', 'Fe', 'As', 'Al', 'I', 'B', 'V', 'K', 'Tl', 'Yb', 'Sb', 'Sn', 'Ag', 'Pd', 'Co', 'Se', 'Ti', 'Zn', 'H', 'Li', 'Ge', 'Cu', 'Au', 'Ni', 'Cd', 'In', 'Mn', 'Zr', 'Cr', 'Pt',... |
1b77104534a5b53413c36ac29ebf1b36c85da38fee4b149f211aba5e16f85632 | Python | 12,669 | 329 | # -*- coding: utf-8 -*-
### ------------------------ IMPORTS -------------------------------------- ###
import os
import json
import tables
import adi
from tqdm import tqdm
import numpy as np
from scipy import signal
from string import ascii_lowercase
from helper.array_helper import chunk_array
### -------------------... |
a054ac2cb407bb7dec14f0f7be62ce726f063f738b45242b423ac7713e2b9d56 | Python | 12,671 | 287 | import torch
from torch.utils.data import Dataset, DataLoader, SubsetRandomSampler, random_split
import pandas as pd
import numpy as np
import os
import random
from collections import defaultdict, Counter
from itertools import combinations
import json
import torch.nn as nn
import torch.nn.functional as F
from sklearn.m... |
b730c9cd5ffcee2dcc997ec26ba2a510ea4a5645e2f7e316907f4ea68587224e | Python | 12,673 | 316 | """MetaQ backend (Li et al., Nat Commun 2025)."""
from __future__ import annotations
import time
from typing import List, Optional
import numpy as np
from scipy import sparse
from .base import FitResult, MetaCellBackend
class MetaQBackend(MetaCellBackend):
name = "metaq"
capabilities = {"soft", "latent",... |
8b52ff1f2b9d0994609cb4f1bd1803c8f82738671a020058cc0b3ec80bea9789 | Python | 12,675 | 362 | # 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... |
075d5d1868d59ba843b2f7609d444cad03b6ec651d02d2ad9d03b179dc59e258 | Python | 12,676 | 357 | """
Ray Serve application: Video Embedding → Multi-Decoder.
Processes entire videos by chunking into segments.
Videos are downloaded from S3 to temp file, then processed locally (faster than streaming).
Encoder refs are passed directly to decoder; Ray Serve resolves dependencies automatically.
Usage:
serve run a... |
85ac56e9420bdc6eda87c9730d93d2cb0c5887736bee0892349b8e0a7785b3c0 | Python | 12,677 | 331 |
import numpy
import gym
import pfrl
import torch
import functools
from torch import nn
def calc_shape(shape, layers):
"""
Calculates the shape of the tensor after the layers
:param shape: A `tuple` of the input shape
:param layers: A `list`-like of layers
:returns : A `tuple` of the output shap... |
34523d3231f0f7622ea39254dfb71d73c7ebda0aebf63bdcd9f77ca6c318fec5 | Python | 12,680 | 307 | import csv
import argparse
from pathlib import Path
import datetime
import json
import numpy as np
import os
from keras.layers import Embedding,Dense, Activation,TimeDistributed, GRU, Dropout, Input
import sys
sys.path.insert(0,str(Path(__file__).resolve().parents[1]))
from mothra_runtime import CompatibleGRU, Deduplic... |
7d2fd293a154b4ba4210f486a2242ea49ed892a703bba1a9e9ca6617d26e4716 | Python | 12,684 | 346 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# pylint: disable=invalid-name
# pylint: disable=line-too-long
# pylint: disable=multiple-statements
# pylint: disable=too-many-lines
# pylint: disable=wrong-import-position
#-------------------------------------------------------------------------------
'''
This program... |
1f74ad6db10088db447721e06e4be0f30f4fd778cd3c15f9e0924b1b2b62165e | Python | 12,687 | 306 | import torch
import torch.nn as nn
from collections import OrderedDict
from utils.kfac_utils import fetch_mat_weights
# from utils.common_utils import (tensor_to_list, PresetLRScheduler)
from utils.prune_utils import (filter_indices,
filter_indices_ni,
get_t... |
54b5beb8f52784fe87ec2b7334af6b447e52306a22b437f8018a1ce3299604ea | Python | 12,688 | 425 | """RuntimeEventEmitter — unified observability surface for OVAgent runtime.
Routes all runtime state through structured logger sinks and the harness
event stream. Print output is **not** part of this contract — it is
non-authoritative and optional.
Observability contract
----------------------
* Every dispatch, resu... |
f77c741f7f5d5b46db2a179a7842369aedde8ea34c9ec969a0e758e386913784 | Python | 12,689 | 293 |
# %%
import pandas as pd
import numpy as np
import os
import re
from icecream import ic
from scipy import stats
import math
import warnings
warnings.filterwarnings("ignore")
# Train set
nacc = pd.read_csv('training_cohorts/new_nacc_revised_selection.csv')
aibl = pd.read_csv('training_cohorts/aibl_revised.csv')
nifd =... |
0b49898c57cf9da117662bf559455c630a624a6b80f0c70c3764f9588a5ca54f | Python | 12,700 | 313 | #
# 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... |
3421b2a615404695d07a32b40f76f030aea8521ec2733020996e0d960202b4c1 | Python | 12,711 | 343 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# pylint: disable=abstract-method
"""High level analog tiles (analog)."""
from typing import Optional, Tuple, Any
from torch import Tensor
from aihwkit.simul... |
4ef780ef2b6196d04a18d3bce570c58c77eb7d481d4dfbf9785886bdb0255b92 | Python | 12,715 | 340 | # Ultralytics YOLO 🚀, GPL-3.0 license
import numpy as np
from ..utils import matching
from ..utils.kalman_filter import KalmanFilterXYAH
from .basetrack import BaseTrack, TrackState
class STrack(BaseTrack):
shared_kalman = KalmanFilterXYAH()
def __init__(self, tlwh, score, cls):
# wait activate
... |
6579a82fa272ac6be08e556f7fe60c46e8b0b6200143677a19fc84b0fb405125 | Python | 12,716 | 395 | import soft_rank_isotonic
import numpy as np
from scipy import special
def isotonic_l2(input_s, input_w=None):
"""Solves an isotonic regression problem using PAV.
Formally, it solves argmin_{v_1 >= ... >= v_n} 0.5 ||v - (s-w)||^2.
Args:
input_s: input to isotonic regression, a 1d-array.
input... |
2767d0a117b8dbcfb4a051f6a1fcfe2e36cd88ffebebd06a03e0ebecf286752a | Python | 12,722 | 327 | r"""Interactive 3D visualization for :mod:`omicverse.mol`.
Built on **py3Dmol** (3Dmol.js): each view is a self-contained HTML/JS
block embedded in the notebook cell output, with no ``ipywidgets``
dependency, and **renders in nbconvert HTML / mkdocs** without a live
kernel.
The one caveat is Jupyter's **notebook-trus... |
0e5d612e801b5acb16c364d3e37d900cfa9a3c396d3b099b87b857d2090caebd | Python | 12,725 | 312 | import numpy as np
import os
import glob
import zipfile
import exputils
import re
def calc_repetition_statistics(statistics, load_experiment_data_func, *args, statistics_directory=None,
recalculate_statistics=False, verbose=False, repetition_directory_template=None,
... |
02b38bd61558fc01607aff504e2707f6ade3a08b21d754490b433b899e7babca | Python | 12,726 | 324 | import logging
import random
import threading
import time
from collections import defaultdict
from typing import Any, Dict, List, Optional
from ray.autoscaler._private.aliyun.config import (
PENDING,
RUNNING,
STOPPED,
STOPPING,
bootstrap_aliyun,
)
from ray.autoscaler._private.aliyun.utils import Ac... |
8cdcb8a5d32bfea0ebacc0a2fd98c7726f2049076089bfcbf3d87a76760e94b2 | Python | 12,726 | 412 |
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import copy
import glob, os
from poser.patients import Patient, PatientCollection
import re
import scipy.stats as st
import seaborn as sns
#from statannot import add_stat_annotation
#%% load patient data
directory = './data/' # put the DLC tr... |
1c0b6998e512626c646ec99f1cafb04ea6c1c08d7590d9078a50f758b7fa75d7 | Python | 12,729 | 345 | # 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... |
22ebe9a01ec1aaac0356de8d2d24b3d7a18a5ac6c059a7f54a19e9022fb3b633 | Python | 12,731 | 385 | import torch
from torch.utils.data import Dataset
import numpy as np
from functools import cached_property
from typing import Any, Type
from numpy.typing import NDArray
import random
from monai.utils.type_conversion import convert_to_tensor
import time
Tensor = Type[torch.Tensor]
from .masker import Masker
from . imp... |
94a62c31cf9c17c2fc41a1cf24db46449458a4e9591c45b47aeba4337fccf9e0 | Python | 12,731 | 346 | """
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
from pathlib import Path
from typing import Any
import numpy as np
import torch
from to... |
6ad4178080a120de6f71baaf304a4a8f06f011086f019377532eef7325e5cb45 | Python | 12,736 | 342 | # 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... |
fedda03650a03481c495110c12df0d958eb422262998c5d6684151ea8de1e812 | Python | 12,736 | 289 | import os
import torch
import torch.nn as nn
from torch.autograd import Variable
from torch.utils.data import DataLoader
import argparse
import time
import datetime
import numpy as np
from skimage import io
import math
if __name__ == '__main__':
############################################################ IMPOR... |
0ba72b2317ed757d4ae781ba209502844c29d01983837f61b6e4103442cabfa0 | Python | 12,739 | 415 | """
Usage examples for DataStateInspector Production API.
This module contains comprehensive examples demonstrating all features
of the DataStateInspector in real-world scenarios.
"""
from anndata import AnnData
import numpy as np
import pandas as pd
def example_basic_validation():
"""Example 1: Basic validatio... |
4e0ec6719ebe6af50f733bcf2d2f11cd81243842a6273aaa2b18e5a7ad417dc6 | Python | 12,744 | 402 | from abc import abstractmethod
from discontinuous_galerkin.base.base_model import BaseModel
import numpy as np
from attr import dataclass
import pdb
import matplotlib.pyplot as plt
from tqdm import tqdm
import ray
from scipy.stats import norm
from data_assimilation.model_error import BaseModelError
from data_assimilat... |
2403e95afcb9987cf58974e0f3c65b91a1a641a9893848e0b095808aaa990391 | Python | 12,747 | 348 | from PIL import Image
import numpy as np
from ctypes import *
import ctypes
import copy
import torch
import torch.nn as nn
import torch.nn.functional as F
import os
import cv2
import time
import pdb
import socket
import pickle
import scipy
import scipy.ndimage
import matplotlib.pyplot as plt
from datas... |
7fe0405bbc197a1106685e38513f8b292b00039e0892a6b301d8ad900f8dd444 | Python | 12,747 | 173 | from argparse import ArgumentParser, ArgumentTypeError
from ruamel.yaml import YAML
import os, sys
from pathlib import Path
def str2bool(v):
if v.lower() in ('yes', 'true', 't', 'y', '1'):
return True
elif v.lower() in ('no', 'false', 'f', 'n', '0'):
return False
else:
raise Argumen... |
b44687ffd4adbda243a5418bb7879b99ef435e2993d51545ca54f549a246ca39 | Python | 12,749 | 282 | from typing import Optional
import os
from pathlib import Path
import pandas as pd
import numpy as np
from itertools import permutations, product
import scanpy as sc
import requests
from tqdm.auto import tqdm
zipfile_install = False
def check_zipfile():
global zipfile_install
try:
import zipfile
... |
0bd8986d669aa8cea05a00d6a58d00761a89dcc6ef3e9f7f59110c6d101b8973 | Python | 12,750 | 256 | import os
import torch
import torch.nn as nn
from torch.autograd import Variable
from torch.utils.data import DataLoader
import argparse
import time
import datetime
from torch.utils.tensorboard import SummaryWriter
import functools
import numpy as np
from DWonder.RMBG.utils import FFDrealign4, inv_FFDrealign4
from DWo... |
09f9cebae4bc57eaba6e92e559f304d500a11e141dd9026004f7c6ede0ce422f | Python | 12,751 | 346 | import logging
import os
from copy import deepcopy
from typing import TYPE_CHECKING, Dict, Optional
from packaging import version
from ray._private.dict import flatten_dict
if TYPE_CHECKING:
from mlflow.entities import Run
from mlflow.tracking import MlflowClient
logger = logging.getLogger(__name__)
class... |
259bbd24318229d5db0d5a019d38a2917284658859af58a059e6bf9c40aed478 | Python | 12,763 | 305 | # Copyright 2023 Stanford University Team 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-2.0
#
#... |
271ed4f2bf350d776f748d9f4b1cdfd5e608032c76c3b9fdbdd3d215a8d099ef | Python | 12,768 | 285 | from torch import nn
import torch
import math
class GCL(nn.Module):
def __init__(self, input_nf, output_nf, hidden_nf, normalization_factor, aggregation_method,
edges_in_d=0, nodes_att_dim=0, act_fn=nn.SiLU(), attention=False):
super(GCL, self).__init__()
input_edge = input_nf * 2... |
54579f0398b1d09a82af60cf7fc84d075f58d0f7bcb53bd2ac2baca4529ae087 | Python | 12,779 | 300 | import warnings
import torch
import torch.nn as nn
import sinabs.layers as sl
from sinabs.layers import NeuromorphicReLU
def spiking_hook(self, input_, output):
"""Forward hook meant for Sinabs/Exodus layers.
Calculates n_neurons (scalar), firing_rate_per_neuron (C,H,W) and average firing_rate (scalar).
... |
3bd03b980bac097b61301821fad4ba1ba8e2927b0c7d66446fddf06d378762cb | Python | 12,783 | 309 | import os
import time
from typing import Union
import bios
from FeatureCloud.app.engine.app import AppState, app_state, Role
from algo import Coordinator, Client
class States:
INITIAL = 'initial' # setup the app
LOCAL_TRAINING = 'local_training' # train the local model and send it to the coordinator
W... |
1b5c8aaff9394d05455934163e54c74e98498a214402d63e8a5826ac4b30ad62 | Python | 12,785 | 374 | import argparse
import inspect
import os
import sys
import warnings
from importlib import resources
from typing import Any, Dict, List, Optional, Union
import hydra
from colorama import Fore, Style, init
from datamate import Namespace, namespacify
from hydra.core.global_hydra import GlobalHydra
from omegaconf import D... |
fa9dc202fefdb43076e594487d8419ef98f386a0a27d757f827290f84a799e8e | Python | 12,790 | 310 | import torch
import random
from sklearn.metrics import accuracy_score, roc_auc_score, confusion_matrix, auc, precision_recall_curve, precision_score
import matplotlib.pyplot as plt
from torch.utils.data import DataLoader, Dataset
import calibration as cal
import logging
import yaml
import os
import pandas as pd
import ... |
5849125b9a5dbae1db45e93a057c824766f1f9a49d3c4a1e6413c29610ed1a08 | Python | 12,791 | 377 |
import numpy
import random
from scipy import optimize
from skimage import filters
from stedopt import defaults
from stedopt.create import create_microscope
class FluorescenceOptimizer():
"""
Optimizes the parameters of a fluorophore.
"""
FACTORS = {
"clusters" : 2.25, # CaMKII & PSD95
... |
6ea06bb55f5d89ff2956bd86c98810017e2d8629e09c0f93999f2a94b5b67dc8 | Python | 12,792 | 329 | import json
import logging
import os
import socket
from threading import RLock
from filelock import FileLock
from ray.autoscaler._private.local.config import (
LOCAL_CLUSTER_NODE_TYPE,
bootstrap_local,
get_lock_path,
get_state_path,
)
from ray.autoscaler.node_provider import NodeProvider
from ray.auto... |
a1593e6c7f7db03247453e0fd299532a323232bfc4f11e65ce2b9f789989c736 | Python | 12,793 | 332 | # Copyright (c) Facebook, Inc. and its affiliates.
# 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... |
127f4f12842fd5b4f9a5c77bea0735dcf3df8d3e62c155f121bb06536ed1ea36 | Python | 12,795 | 339 | # 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 to in writing, software
# distributed under th... |
80ea4f47587f623e53340c6bb63ac42791b32be0333ec25c6d9ba59c44f2879c | Python | 12,796 | 377 | # -*- 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.
#... |
d6066a68434c43496908b5dd0a2f97ebd4bdc057b0f3834fbd73fb2884c4ee22 | Python | 12,796 | 287 | # biolgca is a Python package for simulating different kinds of lattice-gas
# cellular automata (LGCA) in the biological context.
# Copyright (C) 2018-2022 Technische Universität Dresden, Germany.
# The full license notice is found in the file lgca/__init__.py.
"""
Interaction functions and helper functions for identi... |
6ab10005d404ca3e0b568fc3f57a529687f3e23ac777d370cf599e1d9936f47b | Python | 12,802 | 298 | import sys
import os
import numpy as np
import matplotlib.pylab as plt
import matplotlib as mpl
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
import torch.optim as optim
import matplotlib.pyplot as plt
from torch.utils.data.sampler import SubsetRandomSampler
from... |
2dbab15d1d734ff592f22ed9a074cb790879c07e48dd30b6bd40c1ad9c92f627 | Python | 12,814 | 241 | """SAMPLING ONLY."""
import torch
import numpy as np
from tqdm import tqdm
from functools import partial
from stable_diffusion.ldm.modules.diffusionmodules.util import make_ddim_sampling_parameters, make_ddim_timesteps, noise_like, \
extract_into_tensor
class DDIMSampler(object):
def __init__(self, model, s... |
3f2ac12c4804caeaf86bce3b68915219e4fd8aa2ff5ea20c0bd52bc1270d7e4e | Python | 12,815 | 284 | # Copyright 2023 Google Brain 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-2.0
#
# Unless requ... |
0ebc06272a554620e3620220d457480f4f65f278c5f8c90c3657482142170394 | Python | 12,817 | 290 | import torch
import numpy as np
import json
class PPM_extraction():
def __init__(self, train_instances, train_key, is_upper, is_lower, is_upper_lower_concat,
model_path, input_seq_len, padding_len, kernel_len,
ppm_file_name):
'''
:param train_instances: BS (posit... |
fa83ef40200568879fb2d3c86a6a2637b2fd4c036dc4cafeff02f0260b4affae | Python | 12,822 | 299 | ####################################################################################################
# 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... |
2269586f8692b07fa3af7588ab558c567f9f6f16087633b66f400628043d3c1f | Python | 12,827 | 268 | # 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... |
fc485fb2071e816adfaf2feb2c11055ae1a39007a46703db87cd4d2f62994614 | Python | 12,830 | 349 | # -*- 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.
#... |
2d141374b22f6e9628d52f5d0e9893d7b9bdea1e108dc91386715a403d59f331 | Python | 12,831 | 279 | #!/usr/bin/env python3
################################################################################
# -- Preprocessing and analysis of the simulation results
################################################################################
import numpy as np; import pylab as pl; import os, pickle
import matplotlib... |
7dde41c5a96947546da77b9d1629dcb0d8861599e060ea925d6a91ccf0e1ad16 | Python | 12,833 | 431 | """WoRMS (World Register of Marine Species) API client."""
from typing import Dict, List, Optional, Any
from .base import BaseAPIClient
class WoRMSClient(BaseAPIClient):
"""Client for WoRMS API - marine species taxonomy."""
def __init__(self):
super().__init__(
base_url="https://www.... |
9d0f204c2b31568b4bc93b21f7e6e03f8db0c75da8b0020091ca5eaed52f0c13 | Python | 12,834 | 334 | ####################################################################################################
# Copyright (c) 2021, 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... |
8ecbce6e952dc22320fa9c828e0a9d34d67963af82d8cf4ed7f5685a4ba30a2a | Python | 12,837 | 373 | import csv
import gzip
import json
import os
from csv import DictWriter, DictReader
from csv import reader as csv_reader
from pathlib import Path
from typing import Iterable
from typing import Optional, List
import plyvel
from . import utils, uniprot
from .string import load_upkb_aliases, update_secondaries
def par... |
8fef62c2ab60e113847fb68dde80eefda603b3b1390fdb8e4cd034267d97033d | Python | 12,840 | 314 | #! /usr/bin/env python3
import logging
from collections import defaultdict
import numpy as np
import torch
import tqdm
from sklearn.preprocessing import StandardScaler, normalize
from ..utils import common_functions as c_f
from ..utils import stat_utils
from ..utils.accuracy_calculator import AccuracyCalculator
cl... |
dbe252eca4868a61aad6f07c3501ac98afa95c0d61be68bba3531c74e2bdb5aa | Python | 12,840 | 372 | import json
import logging
import os
import secrets
import subprocess
import sys
from contextlib import contextmanager
from typing import Optional, Tuple
import pytest
import ray
logger = logging.getLogger(__name__)
@pytest.fixture
def shutdown_only():
yield None
# The code after the yield will run as tear... |
36097197eaafe951a009db29c3c6b047416ab68f9cc8c2647638a0cddf2195af | Python | 12,848 | 270 | """
Context-belief- and/or history-based agent
by Aditya Gilra, Sep-Oct-Nov 2021
"""
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import scipy.io as scipyio
import scipy.stats
import sys
from exp_data_analysis import get_exp_reward_around_transition, \
mouse_behaviour_data,mouse_be... |
edee19bf7bae695fbccb38db575800158c0c290df97874f09120caf4103379d3 | Python | 12,848 | 279 | import os
import time
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
import importlib
import copy
import ... |
c8c9f7db60b5769be1a6b1f8b848551fa212bfa3992703136fef35688b163baf | Python | 12,856 | 318 | import cv2
import math
import numpy as np
import os
import queue
import threading
import torch
from basicsr.utils.download_util import load_file_from_url
from torch.nn import functional as F
ROOT_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
class RealESRGANer():
"""A helper class for upsampl... |
4d1242b538f22a71f3bc24d9e60bdb809114ce38bf4a9f9a162d9430c429f671 | Python | 12,858 | 316 | import os
import torch
import torch.utils.model_zoo
import torchvision.models as models
from src.model.snn import *
from src.model.cann import CANN
from src.tools.utils import *
os.environ['CUDA_VISIBLE_DEVICES'] = "3"
device = torch.device('cuda' if torch.cuda.is_available() else "cpu")
class MHNN(nn.Module):
de... |
ebcf74979f4faa41bdca6e73ee6ff445e619e0a6b630a60987bec4aac9d32a38 | Python | 12,860 | 352 |
import numpy as np
from collections import Counter
from scipy import sparse
class BadRegionError(Exception):
pass
class NotInGenomeError(BadRegionError):
pass
class Region:
@classmethod
def read_bedfile(cls, path):
regions = []
with open(path, 'r') as f:
for line in f:
... |
6d2373d33e438dc3df89a95da125feba84e399bd990c362f0276cbce68b7f235 | Python | 12,863 | 355 | # 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... |
5550a98f1489072384c7f7585829ff8ad3e71c04fa16a2998fb4aa508e28bdeb | Python | 12,864 | 292 | import numpy as np
import pandas as pd
from plotnine import *
import glob
import yaml
import pickle
import os
SAMPLING_COLORS_LIST_10 = ['#c6dbef','#9ecae1', '#99CCCC', '#6baed6','#3182bd',
'#08519c', '#8B4513', '#CD853F', '#D2691E', '#DEB887']
ANNO_COLOR_INDV_LIST = ['#3182bd', '#6baed6',
... |
98c60987c3ba7dda545ebdc3d64aa5b14503f3c3972dcab934511c5bba19c560 | Python | 12,864 | 267 | r"""Real measured datasets, for when a demonstration needs data it did not invent.
Every function here downloads a **published measurement** and caches it. Nothing
is simulated. That distinction is the whole point: a design tool shown only on
data generated by its own assumptions has not been shown to work on anything... |
a5ee5ad2ece7ed8304342718ebff4ccd02e43fb15bd3b490deafc4d33fefe948 | Python | 12,864 | 266 | import os
import numpy as np
import matplotlib.pyplot as plt
project_root = "/ccb/cybertron/khchao/splam-analysis-results/"
# albation_study_root=f'{project_root}results/albation_study/MODEL/subset_10000/'
albation_study_root=f'{project_root}results/albation_study/MODEL/subset_10000/'
output_dir = f'{albation_study_ro... |
95bac8dc6621898f3dc8719709607246c72e02bfcf08ef74c8077e6d8f0f46f5 | Python | 12,871 | 379 | # 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... |
ebb75bf50478cf1529414b7825f7b08e46f34ea7ff7888511ea38e3727b3bf26 | Python | 12,872 | 428 | """WoRMS (World Register of Marine Species) API client."""
from typing import Dict, List, Optional, Any
from ..base import BaseAPIClient
class WoRMSClient(BaseAPIClient):
"""Client for WoRMS API - marine species taxonomy."""
def __init__(self):
super().__init__(
base_url="https://www... |
9bd2c2947a18883ac12c3e32dff09652e2627cd43a61b056215ebf95a8f23982 | Python | 12,881 | 273 | ####################################################################################################
# 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... |
1ac5369d31e852b9e7a33a6912a18f74f9c3e5a6b85586a171e6b51fd34d6b15 | Python | 12,882 | 353 | 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... |
c96bf5c02747754f1cff100e73a8e18404a647fb49a67f19d7c7fa843ab9d217 | Python | 12,882 | 292 | import numpy as np
import torch,os,pickle
import time
from tqdm import tqdm
from torch.nn import DataParallel as DP
from mne.io import read_raw_edf
np.set_printoptions(suppress=True)
import warnings
warnings.filterwarnings("ignore")
import multiprocessing
multiprocessing.set_start_method('spawn', True)
im... |
ceb642941b1565e34218a2fb07b3666eb3ce7928f0b1a7d73d54dd58d320b0e5 | Python | 12,885 | 222 | import multiprocessing
import os
from time import sleep
from typing import List, Type, Union
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import load_json, join, save_json, isfile, maybe_mkdir_p
from tqdm import tqdm
from nnunetv2.imageio.base_reader_writer import BaseReaderWriter
from... |
a4d4de00c0f1cde33580111822116bd0ceb9bd38221646f9c9d1cb4f3f97ef86 | Python | 12,897 | 338 | # 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... |
5925911c0260379ce05d84a710d508e7b010a139504722ad405b99b20ac47aa6 | Python | 12,907 | 378 | '''
Train an S4 model on sequential CIFAR10 / sequential MNIST with PyTorch for demonstration purposes.
This code borrows heavily from https://github.com/kuangliu/pytorch-cifar.
This file only depends on the standalone S4 layer
available in /models/s4/
* Train standard sequential CIFAR:
python -m example
* Train ... |
2075906413f30f528a75435fcf0d4f86bbbfd1a66aac046726e8f5804b93b076 | Python | 12,908 | 243 | from collections import OrderedDict
from copy import deepcopy
from typing import Union, Tuple, List
import numpy as np
import torch
from batchgenerators.augmentations.utils import resize_segmentation, SEG_TIEBREAKS
from scipy.ndimage import map_coordinates
from skimage.transform import resize
from nnunetv2.configurati... |
4c85e41d787f2d5b27353b01fe72e2804b5e513c37b03aecac08d6c2adfa0ede | Python | 12,908 | 343 | import functools
import logging
import sys
import time
from contextlib import contextmanager
def silence_logger(name):
"""Given a logger name, silence it completely.
:param name: name of the logger
:type name: str
"""
package_logger = logging.getLogger(name)
package_logger.setLevel(logging.CR... |
a673337074f684bdc2132fb87770888131efaf01453a435385c50c628b97acb5 | Python | 12,913 | 481 | """
This script creates a plot which compares the heading dependent firing rates
when numerically simulating equation 8 versus using the analytical derivation
in equation 32 of the manuscript. The plot was not ued in the final version
of the manuscript.
"""
import numpy as np
import matplotlib
import matplotlib.pyplot ... |
aaf3198bdcad69da8720d5e5e73ee655105b54cdef8dd03d589209c04e5a39ba | Python | 12,913 | 366 | # Copyright (C) 2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import csv
import json
import uuid
from collections import Counter
from datetime import datetime, timedelta, timezone
from http import HTTPStatus
from io import StringIO
from time import sleep
import pytest
im... |
b199bd5ec1bea42362d4c76301a12eb14e482662430c6529e654efb3c4b58326 | Python | 12,913 | 278 | import argparse
import pickle
from collections import namedtuple
from typing import Dict, List, Any, Iterator
import numpy as np
import torch
import lib.data_utils.data_util as du
import lib.data_utils.dynamic_data_util as ddu
import lib.dataset_config_parser.dataset_config_parser as dcp
from denoise_inverse_alg.glm_... |
ebeb0a565300e1ac2f82bc32e372c8bccfc30536a17563a5528064c6085f2022 | Python | 12,917 | 270 | import datetime
from datetime import timedelta
import torch
from tqdm import trange
from torch import nn
import matplotlib.pyplot as plt
import matplotlib.dates as dates
from soft_dtw_cuda import SoftDTW
import os
import pickle
from sklearn.metrics import mean_absolute_error, mean_absolute_percentage_error
class Early... |
7dc8bda6487c30a5c549a4ae5aee091aa54888926b33a0433ab49710b67fec2d | Python | 12,919 | 376 | import asyncio
import logging
import os
import shutil
import subprocess
import sys
from datetime import datetime
from pathlib import Path
from typing import Tuple, Union
from ray._private.ray_constants import (
VALID_CPU_PROFILING_FORMATS,
VALID_MEMORY_PROFILING_FORMATS,
)
logger = logging.getLogger(__name__)... |
bee6264a1a4de7b0fc0ac160b9462e3e3ff01519fdf1794f2f95f8da2df75804 | Python | 12,922 | 327 | """NCBI BLAST API client."""
import logging
import time
import xml.etree.ElementTree as ET
from typing import Any, Dict, List, Optional
from ..base import BaseAPIClient
from ...config import settings
logger = logging.getLogger(__name__)
class BLASTClient(BaseAPIClient):
"""Client for NCBI BLAST API.
... |
38f2af92f9dbc108d1050c8e2c03f4e1a55a2c5de112d62ff0e44f11948e3f3c | Python | 12,924 | 327 | """NCBI BLAST API client."""
import logging
import time
import xml.etree.ElementTree as ET
from typing import Any, Dict, List, Optional
from .base import BaseAPIClient
from config.config import settings
logger = logging.getLogger(__name__)
class BLASTClient(BaseAPIClient):
"""Client for NCBI BLAST API.
... |
a954f965c4efefd51a381ea51707f84ccdc2f832801ba98c065eab62d06d1057 | Python | 12,925 | 332 | r"""
This module contains wrapper for the neo Segment, that add extra functionality to the class.
Within mozaik the data are stored and passed in this format.
Most of the included functionality should in future be provided directly by neo.
When this happens most of this code should become irrelevant and the rest shoul... |
4197f845cc7bd73c4d15d505e6505276a0a7d7b5493dda971a9c2e058cb68c29 | Python | 12,927 | 347 | '''
Copyright 2023 Tashreque Mohammed Haq
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 ... |
cdb3e0984f784102a42dfd3fc02e89ae79e4fcb0164ed6b6639da0db2ee10512 | Python | 12,929 | 496 | """Configuration for the package."""
from enum import Enum
from pathlib import Path
from typing import Any, Dict, List, Optional, Tuple, Union
import yaml
from pydantic.v1 import BaseModel, BaseSettings, Field, PrivateAttr
def _merge_dictionaries(dict1: dict, dict2: dict) -> dict:
"""
Recursive merge diction... |
938743d77c735bee3b4820a5e28883dad3252dadcf71e8b4e89610827e5e7243 | Python | 12,932 | 282 | # -*- coding: utf-8 -*-
# File : batchnorm.py
# Author : Jiayuan Mao
# Email : maojiayuan@gmail.com
# Date : 27/01/2018
#
# This file is part of Synchronized-BatchNorm-PyTorch.
# https://github.com/vacancy/Synchronized-BatchNorm-PyTorch
# Distributed under MIT License.
import collections
import torch
import torc... |
c0a99753042e22ed44e7e97378680eba082d9dca3be142f19a4151542e46d1ea | Python | 12,934 | 411 | import logging
import os
import tempfile
from pathlib import Path
from time import sleep
from typing import Any, Iterable, Literal, Optional, Union
import ffmpeg
import matplotlib
from IPython import display
__all__ = ["Animation", "AnimationCollector", "convert"]
TESTING = os.getenv("TESTING", "False").lower() == "... |
58c342e3c20d0a9c56b8184c97d82acd7dd24250224b6f4bd682e920c1004902 | Python | 12,941 | 437 | # -*- 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.
#... |
4dc4d8a09573f214996cb9dd0b6c6063f9fe3c5587df249717e81273e0465454 | Python | 12,942 | 363 | '''
Created on 03.18.2014
@author: Dorjee Tamang
'''
import os
import tempfile
class MethodScores(object):
@property
def scale_dict(self):
return dict(zip(self._dict['residue'], self._dict['score']))
@scale_dict.setter
def scale_dict(self, val):
self._dict = val
... |
0e66e04d049f700833bf52526ab7059a995a45ff54a5a97af3e20a1b85391644 | Python | 12,945 | 337 | #!/usr/bin/env python3.7
"""Defines the Deformable class.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing
instructions. The source code can be found on the following GitHub
repository: https://github.com/wmglab-duke/ascent
"""
import sys
fro... |
4764d8730e7635aab67818ee25e5a8ae2e353ae67ac3e90778d95b4d66ee859a | Python | 12,948 | 376 | import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
mpl.rcParams['axes.spines.right'] = False
mpl.rcParams['axes.spines.top'] = False
import seaborn as sns
from matplotlib.colors import ListedColormap
import matplotlib.pyplot as plt
def sort_refs(refs):
idx = np.argsort(... |
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