sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
d56a9bc52bfb075b9055692f46989ea11927585a7358c3a4e787ad0ba9c808e1 | Python | 9,853 | 336 | import torch
from latent_time_stepping.special_loss_functions import MMD
from latent_time_stepping.time_stepping_training.optimizers import Optimizer
import pdb
import matplotlib.pyplot as plt
class LpLoss(object):
def __init__(self, d=2, p=2, size_average=True, reduction=True):
super(LpLoss, self).__init... |
4fa9862cc19c5dba72a09ed90a5adf45770ca26ea9012989d91863473c5c5077 | Python | 9,855 | 249 | from typing import List, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from mmcv.cnn import ConvModule
from mmdet.models.necks.fpn import FPN
from torch import Tensor
from lqit.registry import MODELS
from lqit.utils import ConfigType, MultiConfig, OptConfigType
@MODELS.register_module()
c... |
517636a71a862281721bdd42e3b309affcd1ef92aa3872d063b15e87119490f7 | Python | 9,855 | 245 | """Methods for reshaping raw ECG signal data for use in the pandas ecosystem."""
import os
import tempfile
from typing import Any, Dict, Optional, Tuple, Union
import numpy as np
import pandas as pd
from biosppy.signals.tools import filter_signal
import h5py
from ml4h.defines import ECG_BIKE_LEADS
from ml4h.defines im... |
839b46e57ace1788b4145d33794d04fa5193fba617aeee21ce0d99a4614d4d27 | Python | 9,857 | 280 | """
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
import tempfile
import importlib
from typing import TYPE_CHECKING
import numpy as np
import ... |
87e2c7b0d4f2129598a9f10a87594d365d54f9f295991f7c4a1dc1f9b6b8aa3e | Python | 9,857 | 328 | cd /mnt/d/Brain_region_project/SCENIC/
conda activate scenic_protocol
python
import scanpy as sc
import numpy as np
import pandas as pd
adata=sc.read_csv("Brain_region_raw_major_cell_counts_matrix.csv")
sc.pp.filter_genes(adata,min_cells=100)
adata.raw=adata
sc.pp.normalize_total(adata, target_sum=1e4)
sc.p... |
4b3d53fd9ec807e60f91d246564c036d761095c612c38dda2a5a7821340cb702 | Python | 9,859 | 297 | # built-in dependencies
import os
import json
import hashlib
import struct
import math
from typing import Any, Dict, Optional, List, Union
# project dependencies
from deepface.modules.database.types import Database
from deepface.modules.modeling import build_model
from deepface.commons.logger import Logger
logger = L... |
9c2793f8b3758684c1cf6be8100ce1612d005839c34ed6925eda8ced6d1771bb | Python | 9,859 | 316 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 18: resnet32 CNN with CIFAR10.
CIFAR10 dataset on a resnet inspired network based on the paper:
https://arxiv.org/abs/1512.03385
"""
# pylint... |
2104b8f9d95d327fee55bfff1706a52ca40e94fa430fbb857ec6cbfe03424d7d | Python | 9,864 | 223 | #!/usr/bin/env python
# Import required modules
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
from builtins import str
import os
import argparse
import subprocess
import ICA_AROMA_functions as aromafunc
import shutil
# Change to script directory
cwd = os.... |
aa23d4cab8cba7c2e49c1190740c42501ddbd1803a83642e5b4df045b6085ae9 | Python | 9,864 | 247 | """
class for handling manual settings
***
built as part of the Russell Ray Lab Breathing And Physiology Analysis Pipeline
***
Breathe Easy - an automated waveform analysis pipeline
Copyright (C) 2022
Savannah Lusk, Andersen Chang,
Avery Twitchell-Heyne, Shaun Fattig,
Christopher Scott Ward, Russell Ray.
This prog... |
d2dbb0ad89ea01ded4c64ccf03a0d4121a483511778682004a80a6a8fe09c62f | Python | 9,868 | 260 | # ML4H is released under the following BSD 3-Clause License:
#
# Copyright (c) 2020, Broad Institute, Inc. and The General Hospital Corporation.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
#... |
f97c6df0e87bd486cea91f1291b6617e612eb17cff42d535694332279734c5d2 | Python | 9,868 | 288 | import os
import signal
import time
import shutil
import numpy as np
import keras
from keras.callbacks import EarlyStopping, ModelCheckpoint
from nets import get_network
# force data format to "channels first"
keras.backend.set_image_data_format('channels_first')
def transform(Xb, yb):
"""
handle class for o... |
88d272a51368d0e7c25f1f227474d707334bc9ce19a959b41df4d8ddc6e4297c | Python | 9,871 | 310 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 4: analog CNN.
Mnist dataset on a LeNet5 inspired network based on the paper:
https://www.frontiersin.org/articles/10.3389/fnins.2017.00538/f... |
9c96accaa373dd43e193eb26a211aaec509708cfa11da2a55717f4e9b4acf3aa | Python | 9,884 | 265 | """
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 math
import torch
from e3nn.o3 import FromS2Grid, ToS2Grid
class CoefficientMapping(torch.nn.... |
1d55dac539e260e686c80a1bfbb07701bafde45769cfc7490d71f9f83a3d1cb4 | Python | 9,886 | 268 | import torch
import numpy as np
from .. import nn
# from ..nn import ImagingModelWrapper
from .net_resnet3d import r3d_18
from typing import Any, Type
import math
Tensor = Type[torch.Tensor]
from icecream import ic
ic.disable()
class Transformer(torch.nn.Module):
''' ... '''
def __init__(self,
src_moda... |
98f8dc99c0e19bdd057da4cafd3b19dafd3c596085198b065b1f1a6b968b9f13 | Python | 9,886 | 312 | ####################################################################################################
# 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... |
95f1df393c7b027517085ced5f935dd827e0d064f2c1a13450581a264120c9af | Python | 9,890 | 256 | from sklearn.metrics.pairwise import cosine_distances, euclidean_distances
from sklearn.preprocessing import normalize
from sklearn.neighbors import NearestNeighbors
import numpy as np
import time
# import faiss
# from bonsai.bonsai_helpers import time_format
# from icecream import ic
# ic.configureOutput(prefix=time_... |
daa46afcb1da07cc091bdde8617ec3688e4cce23dcf02c34b3a35b8540f4d463 | Python | 9,890 | 258 | """ Main script for Segmentation Analysis of HRTEM images
Run this script to run the automated nanoparticle transmission electron
micrograph analyzer (ANTEMA)
Copyright (C) 2022 University of Duisburg-Essen
This program is free software: you can redistribute it and/or modify
it under the terms... |
0952370e0433926ab7a4afcec6189dab6658ecacdbf8adbdfbbd85f045441fe9 | Python | 9,895 | 261 | import os
import scipy.io
import numpy as np
#from tensorflow.keras.models import Model
from tensorflow.keras.layers import (Dense, Activation, Permute, Dropout, Conv2D,
MaxPooling2D, AveragePooling2D, SeparableConv2D,
DepthwiseConv2D, BatchNormali... |
acafe39b355d7e44181f1f2e05d91990c724e3e1bd6dacdfbb97439bacf95d0e | Python | 9,897 | 231 | from typing import Callable, Union
from torch_pgn.models.dimenet_utils import *
from torch_pgn.args import TrainArgs
import torch
from torch_geometric.utils.scatter import scatter
from torch_geometric.typing import SparseTensor
from torch_geometric.nn.resolver import activation_resolver
class DimeNet(torch.nn.Modu... |
7cea94c00a150e259ed28b4d2e31bedd12a7437e43e030892bbe736a802f62b9 | Python | 9,898 | 270 | #
# 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... |
d66aa28c8a5f176d6dd5ce9bbe854bae15ebe8cd80a5c959d5f757c5e37253c1 | Python | 9,900 | 307 | import pandas as pd
from pathlib import Path
import zarr
import numpy as np
from scipy.sparse import coo_matrix, spmatrix
from scipy import stats
import statsmodels.api as sm
import pickle
from deeprvat.data import DenseGTDataset
import sys
import os
import logging
logging.basicConfig(
format="[%(asctime)s] %(le... |
e10d8e462764e06efccbc8f3070e5aa9182db47a0bd92ca931fdd7e832427735 | Python | 9,904 | 204 | """
This script is used to threshold images with different methods and save the thresholded images.
The thresholded images are used to create the masks for the segmentation and naively analyse the data.
This makes it easier to preprocess whole folders with the same technique instead of having to use ImageJ.
(c) 2024, M... |
4c6fc70ab9d4b9a88233124d47ba7f84430fddf6e13115fa708b9aa11abcb8d8 | Python | 9,909 | 287 | import os
import argparse
import time
from datetime import datetime, date
import random
import numpy as np
from scipy.sparse import load_npz
from sklearn.metrics import roc_auc_score, f1_score, precision_recall_curve, auc
from scipy.stats import pearsonr
import pandas as pd
import torch
import torch_geom... |
582b840cb1707b23bf25e8174c9d7e09064b41bc3e7733a10073f3726c7dab3a | Python | 9,915 | 279 | # 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... |
3017677ac9a1f621202d8c4cee7850eb5c560f3c467773af0acd967c16f86eaa | Python | 9,923 | 292 | # 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... |
bb362fb46a275db9eda1316f96c0314460f77b6c6e1e4791ba0e32e5debad99c | Python | 9,930 | 250 | import logging
import json
from agent.data.entities.config import BACKUPS_PATH, ROOT_LOGGER_ID
from agent.data.sql.sql_mgmt import get_connection, execute_query, execute_read_query, select_fields_where
logger = logging.getLogger(ROOT_LOGGER_ID)
def insert_crawled_item_instance(connection, item, crawl_date, review_l... |
6703b02e9946c70655103e034a42500f60384bc74564689a66e173dc259f8f32 | Python | 9,931 | 306 | """
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 warnings
from abc import ABC, abstractmethod
from typing import TYPE_CHECKING, An... |
727210b8982051e2a3f11846c035724c390d69bb14d7341518e81ecda3ddbdc1 | Python | 9,933 | 211 | #!/usr/bin/env python
# srnaLaunch.py 0.0.1
import argparse,os, sys, json
import dxpy
from launch import Launch
#from template import Launch # (does not use dxencode at all)
class SrnaLaunch(Launch):
'''Descendent from Launch class with 'small-rna-seq' methods'''
PIPELINE_NAME = "small-rna-seq"
''' This... |
25a923496bf44440df654d9523db3a5261dfd0be549187a2f29263a8c541bd56 | Python | 9,939 | 214 | import argparse
import pickle
from typing import List
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_inverse_alg import reinflate_cropped_glm_model, reinflat... |
5abe9903581de695731afec009a9392188b54f458844ff1fd8fc99548a399bf8 | Python | 9,939 | 248 | import nengo
import numpy as np
import nir
class IF(nengo.SpikingRectifiedLinear):
def step(self, dt, J, output, voltage):
voltage += J * dt
output[:] = (self.amplitude / dt) * np.where(voltage > 1, 1, 0)
voltage[output > 0] = 0
def nir_to_nengo(n, dt=0.001):
nengo_map = {}
pre_m... |
9145063c44a4e5f667923daf765d18109a842fb4bf51100584f0a57b4f095acc | Python | 9,941 | 333 | from sim_evaulation_functions import collect_all_results, get_maf_filter_var_explained
import sys
import os
import logging
import math
import itertools
import pickle
import pandas as pd
import numpy as np
import yaml
logging.basicConfig(
format="[%(asctime)s] %(levelname)s:%(name)s: %(message)s",
level="INFO",... |
7097c671a8fdacbf58855848b49bfec6ec18b2f7ab6825c55509bf5e0fe23131 | Python | 9,947 | 330 | # encoding: utf-8
"""
This module implements Git's wildmatch pattern matching which itself is
derived from Rsync's wildmatch. Git uses wildmatch for its ".gitignore"
files.
"""
from __future__ import unicode_literals
import re
import warnings
from .. import util
from ..compat import unicode
from ..pattern import Rege... |
b13e576d9337a673ff09c74f4e9d52b202682148ff46f41d0afc89ef8a63a219 | Python | 9,949 | 247 | import logging
from typing import TYPE_CHECKING, Optional
from .backpressure_policy import BackpressurePolicy
from ray._common.utils import env_float
from ray.data._internal.execution.resource_manager import (
_BLOCKING_MATERIALIZING_OPERATORS,
ResourceManager,
)
from ray.data.context import DataContext
if TY... |
27c6a95f1df0c70ee09db5cd31677daa0939c2f7e04f7f2b7d1a792145c81834 | Python | 9,951 | 225 | # -*- 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.
#... |
b921bbd156d7d78130e180368b3d8f35f42a2c1be829232239fb2677759b2b78 | Python | 9,951 | 218 | """
ModNN, first-generation architecture (released as 1.0.1): LSTM envelope module that also sees the time of
day, bounded internal-gain schedule, and an encoder that blends measured and predicted zone temperature to
initialise the thermal state. Select it with args["architecture"] = "v1".
Constraints available: "hvac"... |
35b6c98b2e8e0909f55c76fb8d785671d98f56e6c693551ec602451691471930 | Python | 9,952 | 299 |
import torch.utils.model_zoo
import time
from src.model.mhnn import *
from src.tools.utils import *
from src.config.config_utils import *
import argparse
import logging
logging.basicConfig(level=logging.INFO)
log = logging.getLogger()
setup_seed(0)
parser = argparse.ArgumentParser(description='mhnn', argument_defau... |
e1096e9bba6bc13196c2d86f9b57150f45fa02ef2bf676709fc2feac2b5477b9 | Python | 9,953 | 283 | # built-in dependencies
from typing import List, Tuple, Union, cast
# 3rd party dependencies
import torch
from torch import nn, Tensor
import torch.nn.functional as F
# project dependencies
from deepface.commons import weight_utils
from deepface.models.facial_recognition.pytorch.TorchFacialRecognition import (
To... |
82f8b91e3d7ef7b41d98d6b929ed90baec25aa21319cb8de90474f4c572e5d8b | Python | 9,956 | 222 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import os
import os.path
import glob
import json
from jinja2 import Environment, FileSystemLoader, Undefined
import logging
# This script generates input files (for example JSON inputs to be passed to cromwell, but also
# potentially tsv files for Terra im... |
62aeaeb57fdd9e896cab31c920831c7816f2e3418b9632985d749408e506cd48 | Python | 9,958 | 244 | import numpy as np
import pandas as pd
from scipy.interpolate import interp1d
from lib5c.util.lowess import lowess
from hic3defdr.util.printing import eprint
def lowess_fit(x, y, logx=False, logy=False, left_boundary=None,
right_boundary=None, frac=0.3, delta=0.01):
"""
Opinionated convenienc... |
acc6f405c9adcbf694746f62b0d1b263c99d07f2ef7949554ab282eff8af406c | Python | 9,958 | 271 | """Keep normalization, distance, threshold and confidence in the same space."""
from copy import deepcopy
import numpy as np
import pandas as pd
import pytest
from deepface.modules import datastore, verification
class MemoryDatabase:
"""Deterministic storage boundary; real search/identify logic runs above it."... |
b341fe6d061e2387ea1619e338c92d79ba91e93c7fe9078653c6ac6f5e82ecdd | Python | 9,962 | 264 | import re
import nibabel as nib
import numpy as np
from lib.qc import QCResult
from lib.qc_report import QCReport, fig_to_png
from lib.qc_surface import (
COMPARE_METRICS,
DEFAULT_THRESHOLDS,
DEFECT_MAP_CAPTION,
DEFECT_TYPES,
STAGE_DESCS,
STAGE_LABELS,
defect_panel,
defect_table,
fa... |
5ba3e5e21e40e17799d4faaedb798925e4ae4bc789337b3d20dc8ff1799aa143 | Python | 9,963 | 243 | # -*- 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 model conversions."""
from unittest import SkipTest
from torch import Tensor, manual_seed, randn
from torch.nn import Sequential, Linear, Conv2d, ... |
4f4fa919cec162868c5f42fa260e90ef2aeab34001659afadb651fa6092abccc | Python | 9,964 | 199 | from typing import Union, List, Tuple
from nnunetv2.configuration import ANISO_THRESHOLD
from nnunetv2.experiment_planning.experiment_planners.default_experiment_planner import ExperimentPlanner
from nnunetv2.experiment_planning.experiment_planners.residual_unets.residual_encoder_unet_planners import \
nnUNetPlann... |
a8f716e8de67d874b93ebfbc713548d721398aa40c2c28a01fea01427f147d7e | Python | 9,964 | 230 | """PyTorch implementation of R CellChat ``computeCommunProb`` (sc/snRNA-seq mode).
For every LR pair ``i`` and sender/receiver groups ``(s, r)``::
avg = triMean of data.signaling / max(data.signaling) per group
L, R = ligand / receptor expression (complex = geometric mean of subunits)
R = ... |
ba2b966363023b06d2e0a172a7d7c4f5d40b9dc32ebd512f4c146c2058a416a5 | Python | 9,968 | 297 | # 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... |
f86578151ba7f81c86c0ab0a93fe1924f7ec9be5e775f1e6a8cf1dea0362ab05 | Python | 9,971 | 266 | # -*- 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.
#... |
329501ceffc6db9d7ab2942bca43b2f7bffc98a28964eac987a17e2700629df6 | Python | 9,972 | 319 | import numpy as np
import sys, tqdm
import torch
import torch.nn.functional as F
from numpy import interp
from collections.abc import Sequence
from collections import defaultdict
from sklearn.metrics import confusion_matrix, roc_curve, roc_auc_score, auc
from sklearn.metrics import precision_recall_curve, average_preci... |
d9f56807d28ffb3443e062c96411800865df58e30d1c66759a2b49e2e7861dfd | Python | 9,977 | 156 | import numpy as np #Numpy for numerical 'ala Matlab' computations
import pymc as pm #pymc will be doing most of our heavy lifting for Bayesian calculations
import matplotlib.pyplot as plt #This works as our plotting tool
import arviz as az # arviz is a visualization packag... |
e6264e430c01456999c537de240e952d000e90a3de142a6769cd51d8844ee3c4 | Python | 9,977 | 279 | # 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... |
bd12c805d385aa9af45d0b6685332b118877de704c2888174b19afe2b3fb50ac | Python | 9,985 | 198 | import argparse
from utils.utils import load_data, define_logger, tokenize_gen, evaluate_gpt2, gpt2_evaluate, compute_ppl
import random
import numpy as np
import torch
from model.generatively_model import gpt2_generate, bart_generate
from transformers import AdamW, GPT2LMHeadModel
import sys
import torch.nn as nn
impor... |
6c21c4991798afbd35ec805cdb58e24ea5683c9546360b475614ec615d7b3e46 | Python | 9,986 | 335 | # flake8: noqa
# fmt: off
from typing import List
# __textbot_setup_start__
import asyncio
import logging
from queue import Empty
from fastapi import FastAPI
from starlette.responses import StreamingResponse
from transformers import AutoModelForCausalLM, AutoTokenizer, TextIteratorStreamer
from ray import serve
lo... |
496adc5b9bf9a6d9b75e4a52d02fe618c1600ab17fd3fbe35baa90f89b5bd299 | Python | 9,988 | 148 | #-------------------------------------------------------------------------------------------------------------------------------------
# Author: Brandon S Coventry Wisconsin Institute for Translational Neuroengineering
# Date: 08-17-2022
# Purpose: This calculates a simple linear regression (Bayesian Formulation... |
a18165977494d39175c49d36a01178b58facbb80f47e788a14eea0cf23c10f90 | Python | 9,989 | 301 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Digital/analog model conversion utilities.
This module includes tools for converting a given torch model to a
model containing analog layers.
"""
from typin... |
8ca9d8eab09fa57240095a0b13c0dcb236a6bf22942d6ee75c80006f77dce606 | Python | 9,991 | 356 | """Helper functions for quick command line interfaces with skorch and
fire.
"""
from functools import partial
from importlib import import_module
from itertools import chain
import re
import shlex
import sys
from sklearn.base import BaseEstimator
from sklearn.pipeline import FeatureUnion
from sklearn.pipeline import... |
f043545f7e8efbcde17a3e55550f2b1385a588857e6f6e14650c0c7cf9306814 | Python | 9,991 | 272 | import dataclasses
from dataclasses import asdict, fields
from typing import Awaitable, Callable, List, Tuple
import aiohttp.web
from ray.dashboard.optional_utils import rest_response
from ray.dashboard.runtime_env_redaction import (
redact_state_rows,
should_redact_runtime_env,
)
from ray.dashboard.utils imp... |
753e4d62bfc9e1bf9382abfaaf1030a566b1abaae8b489a5adfaf0e28588559d | Python | 9,993 | 299 | # 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... |
fe993595d32e0a8b6be7f78b34da7040926b5c2c6131b208489d7605f3490815 | Python | 9,995 | 261 | import json
import logging
import pathlib
import random
import string
import threading
from datetime import datetime
from enum import Enum
from typing import Union
from ray._private import ray_constants
from ray._private.protobuf_compat import message_to_dict
from ray.core.generated.export_dataset_metadata_pb2 import ... |
37f855886dd8297a9fad8f5a200b8ff45d50eb18efa2a13cf9758a0ee8552588 | Python | 9,996 | 285 | from abc import ABC, abstractmethod
from dataclasses import dataclass, field
from typing import List, Optional
from ray import ObjectRef
from ray.actor import ActorHandle
from ray.data._internal.execution.interfaces.common import NodeIdStr
from ray.data._internal.execution.interfaces.execution_options import Execution... |
a03011887fa5eea0fa4dbf4d78e2969a7d9bb1aff8e42d3b22440e758dae18c7 | Python | 9,998 | 289 | """
Do clustering analysis
"""
import warnings
warnings.filterwarnings('ignore')
import pandas as pd
import numpy as np
import copy
import pickle as pkl
import os
import matplotlib.pyplot as plt
import seaborn as sns
from sklearn import mixture
from sklearn import cluster
from sklearn.manifold import TSNE
import ... |
f97b4ff34d6e56b6a052505ffba3e347950763a0747dccb5a5483433a42540aa | Python | 9,999 | 316 | import math
import os
from itertools import groupby
from multiprocessing import Process
from typing import Dict, List, Tuple
import numpy as np
import samna
import samnagui
import torch
from .utils import parse_device_id, standardize_device_id
# A map of all device types and their corresponding samna `device_name`
d... |
caf5b2ba2248863cd0bbf9b81eb56a8d491d5f592713246c5a69cfafa40cfbbd | Python | 10,002 | 164 | ####################################################################################################
# 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... |
fe3927cbfc5463abf2dfefd590b8b628a7f3be11c9a079a6bd0de70d5241dae6 | Python | 10,004 | 630 | """Groundtruth data structures for fly visual system cell types.
This module contains various dictionaries and lists that represent groundtruth
information from literature about different cell types in the fly visual system.
The data includes polarity, pathway classification, layout, direction selectivity,
and other p... |
e39f8ee1c2d28d1d27a2939990bcc5f1edc726654ac913eeb7e314d2ca1cd6ae | Python | 10,005 | 288 | #
# 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... |
3d43ca9e9beef86b7a4cf86041ac2e5caaaf98003233eabaf787d406bed4c2e7 | Python | 10,006 | 248 | import requests
from .__config import base_url
from .__aux_funcs import process_response
def get_muts_in_mol_prof_by_sample_list_id(molecular_profile_id, sample_list_id, entrez_gene_id=None,
projection="SUMMARY", direction="ASC", pageNumber=0, pageSize=10000000, sortBy=None)... |
3f5cc9b02a9b6afc1d20467683a8ec067699f4ed7a941510b1b488cd17660a52 | Python | 10,009 | 247 | #!/usr/bin/env python
"""
Complete demo pipeline for motion correction, source extraction, and
deconvolution of two-photon calcium imaging data using the CaImAn package.
Demo is also available as a jupyter notebook (see demo_pipeline.ipynb)
Dataset couresy of Sue Ann Koay and David Tank (Princeton University)
This d... |
fb4629e1b59381bb9c4c9ed58e367930bdc1759fd62701c48854f1950ad3461a | Python | 10,012 | 281 | import json
import os
from pathlib import Path
from typing import Optional, Union
import numpy as np
import scanpy as sc
import torch
from anndata import AnnData
from torch.utils.data import DataLoader, SequentialSampler
from tqdm import tqdm
from .. import logger
from ..data_collator import DataCollator
from ..model... |
11013d6b6a5bfd2695fff6da285f3cdeb40952f923e94bd48e5d11da7e57c0ac | Python | 10,014 | 260 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Helper for generating presets."""
from typing import Union, Type, Callable, Any
from copy import deepcopy
from aihwkit.exceptions import ArgumentError
from ... |
d6733e0bdc6662f5be9a7264671b9f52bf1551ae017b09c00d2d6e0cebea52c0 | Python | 10,016 | 302 | """
Analysis of responses to flash stimuli.
Info:
Relies on xarray dataset format defined in `flyvis.analysis.stimulus_responses`.
"""
from typing import List, Optional, Tuple
import matplotlib.pyplot as plt
import numpy as np
import xarray as xr
from flyvis.utils import groundtruth_utils, nodes_edges_utils
fro... |
849bd1bcdc77ca8610ce3c116ce449a76372ae5c21269f64cfe3bca4dce9e61b | Python | 10,021 | 221 | import multisensory as ms
import matplotlib.pyplot as plt
from matplotlib import cm
import json
import os
import numpy as np
from scipy.optimize import fsolve
from collections import defaultdict
plt.style.use('./style_sheet.mplstyle')
def get_ideal_data_classical_comod():
fname = 'figdata/ideal_data_classical_com... |
f465fa75a657fd7d5553a16e6712190f64d64e4e7a44c318e7f0c41561acf3e9 | Python | 10,021 | 268 | #*
# @file Different utility functions
# Copyright (c) Zhewei Yao, Amir Gholami
# All rights reserved.
# This file is part of PyHessian library.
#
# PyHessian is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... |
b39f429fd02c99e680cda5f06cead95fa02c3d7befa9f9997463c9e27adf918d | Python | 10,022 | 245 | ####################################################################################################
# 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... |
11032749123e88c654b960a02d3035e8ae3addeef96d6c4f371bcc16592b122e | Python | 10,023 | 297 | ####################################################################################################
# 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... |
0bbd9a0de1262a56afe312791db450e2ef65c51b036adc45fab95c6bbccaeeac | Python | 10,026 | 341 | #!/usr/local/bin/python
"""
***********************************************
- PROGRAM: smoothMatrix.py
- CONTACT: Bryan lajoie (bryan.lajoie@umassmed.edu)
***********************************************
"""
from __future__ import print_function
import argparse
import logging
import os.path
import sys
import gzip
impo... |
4db468efc7bba9d0c776cc3b28f5c3998f7b4e85a29405af02758477c4c2ed2b | Python | 10,030 | 223 | """Test utils"""
import unittest
import pandas as pd
from rdkit import Chem
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers
from lefshift import utils
from lefshift.fp import LEFFingerprint
class UtilsTests(unittest.TestCase):
"""Test utils"""
def test_smiles_nof_unique_fingerprints(se... |
972ba2343013054071fe0d815ded53f5335f3aa2e0e38e1da12a9cbe1ed6c322 | Python | 10,031 | 278 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Utilities for resistive processing units configurations."""
from sys import version_info
from typing import Any, List, Optional, Type
from dataclasses import ... |
df1dbdae3921f447a06edc22213f2733ed01d6f838aa663205dacc5e1301b318 | Python | 10,035 | 238 | # camera-ready
# NOTE! OS: output stride, the ratio of input image resolution to final output resolution (OS16: output size is (img_h/16, img_w/16)) (OS8: output size is (img_h/8, img_w/8))
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.models as models
def make_layer(block, in... |
f93b6085982d6b4c2b8ed78f63b526b98326b6141eeb19505c3f19cb6b9cb975 | Python | 10,035 | 281 | """
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.
"""
"""
Driver script to evaluate the performance of ML models on predicting
experimental products for HER and CO2RR in the OCx24 dataset.
"""
... |
403e5d2938109862e33fc7c8cffbe55c5a527a6f19faafbdcd379ba9df712737 | Python | 10,036 | 294 | from collections import defaultdict, deque
from copy import deepcopy
from typing import TYPE_CHECKING, List, Optional, Set, Tuple, TypeVar, Union
import torch
import torch.nn as nn
import warnings
import sinabs.layers as sl
from .crop2d import Crop2d
from .dvs_layer import DVSLayer
from .exceptions import InputConfi... |
f8c6c0358a3e6678dce41f569b283dd8d0ca330c0f4a532bd4aa623d9e496f43 | Python | 10,036 | 216 | import numpy as np
import pandas as pd
from scipy.sparse import csr_matrix
def compute_weighted_average_around_target(
adata,
target_cell_type_quantile: float = 0.995,
source_cell_type_quantile: float = 0.95,
normalisation_quantile: float = 0.95,
distance_bin: list = None,
sample_key: str = "s... |
05966e8af10bbe1d9407a85a644af1e0db1834b8a28088c5e7b4cac45fb17e2d | Python | 10,037 | 293 | # -*- 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=no-name-in-module, import-error, too-few-public-methods
"""Mappings for version 1 of the AIHW Composer format."""
from collections import nam... |
bae6c79ab045d132e9e2de3c2bfe175f7f97a465d013c5fecbd8eca54158b843 | Python | 10,042 | 313 | # -*- 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.
#... |
4db4a4b906081835f496337716ca2aa31dc1a53237cd4cf693aecc201c1e2728 | Python | 10,044 | 254 | ####################################################################################################
# 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... |
5b24a69e0c2739ad8ccb64594a7f2f486f1d3c792bd87e30159aea0d8c0ee566 | Python | 10,047 | 256 | # Copyright (c) 2020-2021, NVIDIA CORPORATION. All rights reserved.
#
# NVIDIA CORPORATION and its licensors retain all intellectual property
# and proprietary rights in and to this software, related documentation
# and any modifications thereto. Any use, reproduction, disclosure or
# distribution of this software... |
7a2ed5fa0859aece70105717b0673d079a3edd6ef746d0200ba1e33e99bb72a2 | Python | 10,047 | 294 | 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... |
835f9d25c0ba47cfff3a2a3c63171b7cd789bdc61aaf103770833d27f28b2fae | Python | 10,047 | 289 | ####################################################################################################
# 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... |
27aea0806b13a45605faebf8f04e09aaf239fb0b9bd10695c3ea7b3dd631855f | Python | 10,049 | 255 | ####################################################################################################
# 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... |
8d80d1ba2238108be9fcc82cd1c97cb293e0b27ceb0c6838ed23261ef1552513 | Python | 10,050 | 254 | import exputils as eu
import numpy as np
import plotly.subplots
def plotly_meanstd_bar(data=None, config=None, **kwargs):
"""
param repetition_ids: Either scalar int with single id, list with several that are used for each experiment, or a dict with repetition ids per experiment.
"""
default_config = ... |
9fb624ea264d76845d49264e6efd1b2cb705534fdda61f7dffec1ac42ef88819 | Python | 10,052 | 304 | # built-in dependencies
import os
import json
import hashlib
import struct
import math
from typing import Any, Dict, Optional, List, Union
# project dependencies
from deepface.modules.database.types import Database
from deepface.modules.modeling import build_model
from deepface.commons.logger import Logger
logger = L... |
93d11d5c830513d7369dffb5a8d7b31a7db1864a449490edc37d77c2566424c4 | Python | 10,061 | 273 | # 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, ... |
e54e9c5448b6ff95bd1c9302d73d2f4ff3a8f85fa25b85fe32b24696d84a8274 | Python | 10,062 | 251 | # -*- coding: utf-8 -*-
# @Time :2024/6/6 14:56
# @Author :MENGLong Li
# @File :MachineLearning.py
# @Software:PyCharm
import numpy as np
import matplotlib.pyplot as plt
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import train_test_split
import tensorflow as tf
from tensorflow.... |
060f1f46259d3c94feeb28e8d99f7aba2b4d816f7b28d289d736336db9273c82 | Python | 10,063 | 269 | import math
import warnings
from functools import partial
import torch
import torch.nn as nn
def softmax(x, dim, inplace=False):
if inplace:
torch.exp(x, out=x)
else:
x = torch.exp(x)
s = torch.sum(x, dim=dim, keepdim=True)
x /= s
return x
def _no_grad_trunc_normal_(tensor, mean,... |
a52a919d225533ae628648b4f58ec7db6302cbbb5b4896a766bc12378d777c1f | Python | 10,063 | 246 | """
Top-level functions.
"""
import pandas as pd
from distributed import Client, LocalCluster
from arboreto.core import create_graph, SGBM_KWARGS, RF_KWARGS, EARLY_STOP_WINDOW_LENGTH
def grnboost2(expression_data,
gene_names=None,
tf_names='all',
client_or_address='local',
... |
8685748a32158344ee8541f3686e2bea70098a20067068501681229ed8e5aa6c | Python | 10,064 | 291 | import logging
import math
import pickle
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import torch
import datasets
from datasets.utils.logging import disable_progress_bar, enable_progress_bar
from sklearn import preprocessing
from sklearn.metrics... |
a9ba09100f8faf79d3a06914b95d3a5eeda4bdee0daa29d38662469a8dc1822e | Python | 10,066 | 233 | import numpy as np
from spinnaker2.neuron_models.application import BaseApplication
from spinnaker2.mapper import SynapseWordSize, SynapseWordSpec
from spinnaker2.configuration import PEConfig, MemoryRegion
from spinnaker2.neuron_models.common import (add_log_memory_region,
collect_routing_targets, format_rout... |
c63da3196cb7b505633c4d87937aa991011e4355a390bc59f28ab75ef6569825 | Python | 10,067 | 247 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Constrained Nonnegative Matrix Factorization
A similar CNMF class that will output data that are not usually present in the regular CNMF process
Created on Fri Aug 26 15:44:32 2016
@author: agiovann
"""
from builtins import str
from builtins import object
from pa... |
78c7d031a49bf00e483833c026aed940771bd8030c9027bb78e7d1848751de4c | Python | 10,070 | 301 | # 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... |
91a087e34f3f675eb976dbd38f9dcd34af3232afdbc213080b91593a0f42ff7a | Python | 10,070 | 292 | """Exceptions for SiaPy library.
This module defines custom exceptions used throughout the SiaPy library to handle
errors related to file handling, input validation, processing, and configuration.
"""
from pathlib import Path
from typing import Any
__all__ = [
"SiapyError",
"InvalidFilepathError",
"Inva... |
f9fac9cd89796e78690dbf8dab89a42a94323d0a54802865d9a0c7c0b73ae114 | Python | 10,072 | 218 | import os
import sys
import argparse
import ast
import cv2
import time
import torch
from vidgear.gears import CamGear
import numpy as np
sys.path.insert(1, os.getcwd())
from SimpleHRNet import SimpleHRNet
from misc.visualization import draw_points, draw_skeleton, draw_points_and_skeleton, joints_dict, check_video_rota... |
b19dece69b13bf9f54b43a828255de8cf7d3f02fe5298a485684bc4acb7a1793 | Python | 10,073 | 264 | import torch
import torch.nn as nn
import torch.utils.data as torch_data
import torch.optim as optim
from torch.utils.tensorboard import SummaryWriter
import numpy as np
import matplotlib.pyplot as plt
from typing import Callable, Tuple
import os
class Neurips2017_Encoder(nn.Module):
'''
Benchmark for the H... |
091a7ba200bb518504aaf220319f2756ed038ffddcafc9aa1a05edac5a10386c | Python | 10,084 | 326 | """ This module contains utilities for running snap_polygons directly from the
Allen Institute's internal Laboratory Information Management System.
Example Usage
-------------
python -m neuron_morphology.snap_polygons
--host <lims host>
--port <lims port>
--user <username>
--password <password>
... |
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