sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
a5febd740ebde30664a231d50044d2ce4ce5f97ed13b832614ebf18d970c3505 | Python | 15,282 | 519 | """Stimulus response functions with caching using xarray."""
from __future__ import annotations
from typing import Dict, Optional, Union
import numpy as np
import xarray as xr
import flyvis
from flyvis.datasets.datasets import StimulusDataset
from flyvis.datasets.dots import CentralImpulses, SpatialImpulses
from fl... |
90691b2c328f339cf7c4b18ccb1fe34c7073a5a30daa2a6ebaf1616604927ffa | Python | 15,283 | 473 | import random
from typing import List, Tuple, Union
import numpy as np
try:
from colormath.color_conversions import Lab_to_XYZ, XYZ_to_Luv, convert_color
from colormath.color_objects import LabColor, XYZColor, sRGBColor
except ImportError:
raise ImportError(
"The 'colormath' package is required for... |
574991fe89edc4c7994402d77daedb9591d9357bfe57181a90818fe827874fdd | Python | 15,290 | 377 | from imports import *
class TrimBase(common.BaseClass):
modulepath = 'ngs_mapper.trim_reads'
def setUp( self ):
super(TrimBase,self).setUp()
# Contains sanger, miseq and 454 fastq
self.read_dir = join( THIS, 'fixtures', 'trim_reads' )
# Only fastq files
self.se = [
... |
504dabdf761a70f7b99b0e70e21a6391be20ffb1ac2a1b713cf3403f54e74c17 | Python | 15,291 | 307 | import matplotlib.pyplot as plt
import pickle
import numpy as np
import os
from util import *
from sklearn.metrics import accuracy_score, confusion_matrix, roc_auc_score, roc_curve, precision_recall_curve, PrecisionRecallDisplay
def plot_scatter_plot(label_d, score_d, label_a, score_a, filename):
junc_prob = label... |
578d6c6ab5db16319c77c4615fc3592051cfaf9efef335ecb16eff90a26e89c5 | Python | 15,293 | 390 | from typing import Callable, Optional, Union
import torch
import torch.nn as nn
from sinabs.activation import MembraneSubtract, MultiSpike, SingleExponential
from . import functional
from .reshape import SqueezeMixin
from .stateful_layer import StatefulLayer
class LIF(StatefulLayer):
"""Leaky Integrate and Fir... |
7d2386513a99535087f7170f975a7fc17855a19fe6cd855471283b290f3ea71b | Python | 15,300 | 372 | # Ultralytics YOLO 🚀, GPL-3.0 license
import sys
from pathlib import Path
from ultralytics import yolo # noqa
from ultralytics.nn.tasks import (ClassificationModel, DetectionModel, SegmentationModel, attempt_load_one_weight,
guess_model_task, nn)
from ultralytics.yolo.cfg import ge... |
af937c8a8bec176fa32089981c4a7564c12fabd348f1649d08e0c1ab201ecbfc | Python | 15,313 | 382 | """
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 collections import Counter
from functools import partial
from typing import TYPE_CH... |
d0d32e9ed4504fa2e4d4178919a6373b82cd89460f99887c30074a6eb8ea9427 | Python | 15,315 | 531 | import os
import sys
from typing import List, Optional, Set, Tuple
import click
import yaml
from ci.ray_ci.configs import (
PYTHON_VERSIONS,
)
from ci.ray_ci.container import _DOCKER_ECR_REPO
from ci.ray_ci.linux_tester_container import LinuxTesterContainer
from ci.ray_ci.tester_container import TesterContainer
f... |
f5a9bc56f99ab7ebe5ebf14585e9adf4255b9d5258da3565c154e657f926915f | Python | 15,320 | 372 | import os
from datetime import datetime
import tensorboardX as tb
import torch
from torch.optim import SGD, Adam
from torch.optim.lr_scheduler import MultiStepLR
from torch.utils.data.dataloader import DataLoader
from tqdm import tqdm
from datasets.HumanPoseEstimation import HumanPoseEstimationDataset
from losses.los... |
6ab8d7a76203d59ae6d06dc18b35ff135eec687f8143cb7515b8efacb4bed301 | Python | 15,328 | 414 | import os
import sys
import unittest
from collections import defaultdict
from unittest.mock import MagicMock
# coding: utf-8
import pytest
from ray.autoscaler.v2.instance_manager.instance_manager import InstanceManager
from ray.autoscaler.v2.instance_manager.instance_storage import InstanceStorage
from ray.autoscaler... |
d2fa7fe3ccf3e98cfb00698170cf6b45fa6c7d62b3f080df2a0f3110f305cc7a | Python | 15,329 | 430 | 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',... |
6e4259efb13f7e2344c2f24238410e7bf2c62a1f1eaefe87b7bea00544147f03 | Python | 15,331 | 427 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Tile module base."""
# pylint: disable=too-few-public-methods, abstract-method, bad-super-call
from typing import Dict, List, Optional, Union, Any, Callable... |
216d6bd21734a5d9299c6375e7b443c3d9d210b81c7972bbbd49fe62c2236f58 | Python | 15,334 | 352 | # Copyright 2023 Katherine Crowson, The HuggingFace Team and hlky. 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
#
# ... |
33a6d94eee55910ad5bfdfda90301d3a352c65376ad3841147da42e2a3102b79 | Python | 15,335 | 425 | """
Core data model and preprocessing functions for monocle2_py.
Operates on AnnData objects. Monocle2 metadata is stored in adata.uns['monocle'].
"""
import numpy as np
import pandas as pd
from scipy import sparse
from scipy.stats import gmean
def _init_monocle_uns(adata):
"""Initialize monocle namespace in ad... |
f6003dafd7871e050a21f784e46990736a9208314d2b61ecf8a395af74d223d8 | Python | 15,336 | 348 | #!/usr/bin/env python
# coding: utf-8
# author: Maruthi Mutnuri (maruthi2008@gmail.com)
# loading libraries
import pandas as pd
import numpy as np
import random
from sklearn.model_selection import PredefinedSplit, GridSearchCV, train_test_split
from sklearn.linear_model import LogisticRegression, Lasso
from imblear... |
486b27b3037125ff6fdf787cdcb0fee8238ba28023ce0cf29a820fd370b2d24a | Python | 15,341 | 331 | import os
import time
import argparse
import torch
import tqdm
import numpy as np
import matplotlib.pyplot as plt
from torch.utils.data import DataLoader
from torch import nn
from sklearn.utils import shuffle
from dataset import Dataset
from preprocessor import train_normalization, valid_normalization
from tester impo... |
8d153c0b3a0b4fea67dd4c86838015fc36098621fd68103a5f187620ae0d6420 | Python | 15,344 | 421 | # -*- 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=raise-missing-from
"""Tests for inference tiles."""
from typing import Optional, List, Type
from unittest import SkipTest
from parameterized... |
e22df15ff51502eb1357db070cccc0ed1ae8369de240dac21a401a8382cdf8cb | Python | 15,358 | 332 | import argparse
import pickle
from typing import Dict, List
import numpy as np
import torch
import tqdm
import visionloader as vl
from whitenoise import RandomNoiseFrameGenerator
from basis_functions.spatial_basis_functions import make_spatial_basis_from_hyperparameters
from lib.data_utils.matched_cells_struct impo... |
447016869d7117edea034532790906d565c071e2efe453e36261d16eb5954c0c | Python | 15,361 | 482 | import os
import gzip
import random
from csv import DictReader
from pathlib import Path
from typing import List, Dict, Set, Optional
from rich.progress import track
import tables as tb
import plyvel
from ppi_origami.sources.utils import upkb_query
import requests
from requests.adapters import HTTPAdapter, Retry
class... |
be641f37ffd250202209ddf9e42fdcf11f6311a7191d2e2fa58b211a605886bb | Python | 15,366 | 342 | # coding: utf-8
"""
# # SCRIPT: FIRST LEVEL GLM IN EEG-BASED TASK REPLAY
# # 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 warnings
import numpy as np
import pan... |
fd6bd85f4ab560e16546a967b0ee4cc37b97f042727164db361614217fc1ba87 | Python | 15,368 | 398 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Basic inferencing Experiment."""
# pylint: disable=too-many-locals
from typing import Any, Dict, Tuple, Type, Optional
from os import path, mkdir
from copy ... |
659f9b8b027d280218994629bb17e4a6aeab7edc0ca9e679a065a4daeae38105 | Python | 15,376 | 304 | import os
import exputils as eu
from glob import glob
import re
import numpy as np
import warnings
import collections
import importlib.util
# TODO: Feature - allow to load data from several campaigns
# TODO: allow to load single experiments by just providing the id
def load_experiment_descriptions(experiments_directo... |
c2da1384fd9c1a8bce158325ba7b2645e3751192462505dadc078ae2f59899e2 | Python | 15,389 | 426 | import asyncio
import hashlib
import json
import logging
import os
import re
import shutil
import sys
from asyncio import create_task, get_running_loop
from typing import Dict, List, Optional
from ray._common.runtime_env_uri import parse_uri
from ray._common.utils import try_to_create_directory
from ray._private.runti... |
8331fd40737f8206189ac2f2adb4d232e6d035588ba57ac7ca9d941c4c2690a7 | Python | 15,392 | 491 | # Copyright (C) 2019-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import inspect
import os
import os.path as osp
import re
import tempfile
import zipfile
from collections.abc import Callable, Generator, Iterable
from contextlib import contextmanager
from copy import deepc... |
9d80110050a71f6a941db69b22b5f578529e04dd52e5131e8bda82ab16afdbb8 | Python | 15,392 | 494 | import os
import numpy as np
import torch
import xarray as xr
from scipy import io
from torch.utils.data.dataset import Dataset
from ntd.utils.utils import standardize_array
### Datasets
# Macaque ECoG session times
# Session : 1
# time: 12.28 [s] : AwakeEyesOpened-Start
# time: 908.91 [s] : AwakeEyesOpened-End
# t... |
6d5486a9623e868f6722798087815111b9653445ad3cb2e0aac6beb2854580f1 | Python | 15,401 | 484 | import os
import gzip
import random
from csv import DictReader
from pathlib import Path
from typing import List, Dict, Set, Optional
from rich.progress import track
import tables as tb
import plyvel
from ppi_origami.sources.utils import upkb_query
import requests
from requests.adapters import HTTPAdapter, Retry
class... |
3d16f5234a7f6c084e328db1a87037fd2db045cd11eecdbe4a8082241cd46c71 | Python | 15,405 | 453 | # 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, ... |
0f569b94f03f376ff7b5a752f2cb7d9ed42a25649c5e43e24c8175fbea264e03 | Python | 15,412 | 440 | import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.patheffects as path_effects
import numpy as np
import pandas as pd
import seaborn as sns
from os import path
from matplotlib import rcParams
EXTRA_COLORSET = ["#797979","#000000","#505050","#FFFFFF","#B0B0B0",]
def apply_label(x, color, label,... |
8d2415b2a0a01ca71728b429615dd819300349356a0ca9af43634569f3d738c6 | Python | 15,412 | 346 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 18 14:53:08 2022
@author: Saad Idrees, Joel Zylberberg's Lab, York University
idrees.sa@gmail.com
This is a custom keras layer that converts light stimulus (R*/rod/s) into photoreceptor currents by using a biophysical model
of the photoreceptor by ... |
b366e4ef2ca022156e577d6906aad9c60f04e0d4abed7893f6a38af6c682aac0 | Python | 15,416 | 375 | 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 ... |
6054804b3199441972d7d490d6706fde448a60e1a36a094dbe4cd4920803d067 | Python | 15,417 | 433 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""High level analog tiles (inference)."""
# pylint: disable=too-many-ancestors
from typing import Optional, Union, Any, Tuple, List, Dict, TYPE_CHECKING
from... |
0893fa5be3a8be9b7c517bb38ed4f8d5dae5dbc5aee7a871eaf09b6b795afa38 | Python | 15,420 | 482 | import pdb,sys,os
import anndata
import scanpy as sc
import argparse
import copy
import torch
import numpy as np
import gc
import pandas as pd
import timeit
import scipy
import warnings
warnings.filterwarnings('ignore')
import faiss
from sklearn.cluster import KMeans
import sklearn
from scipy import stats
from sklearn.... |
d10a93c22e5c150032aaa259ed2ccd5885e615f6f3c6ca080b3960a01eac7b51 | Python | 15,423 | 404 | """
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 os
from glob import glob
from typing import TYPE_CHECKING, Any
import pandas as ... |
eefe12dba52a5d99720043e0b99e877547b39da4f7d1edfe7d36402079f82d2c | Python | 15,427 | 354 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
Calculate enrichment of clipped reads or discordant pairs at SV breakpoints.
"""
import argparse
import sys
import pysam
import pandas as pd
from svtk.pesr import SRTestRunner, PETestRunner, PETest, SRTest
def sr_test(argv):
parser = argparse.ArgumentParser(
... |
e308ec26b3af36feb76f3354cea7fad0d28a058da8b2a83ea839d21b17abda54 | Python | 15,430 | 462 | """
MemoryStore — SQLite-backed persistent memory for OmicVerse Jarvis.
Inspired by metabot's MemoryStorage design:
• Hierarchical folders (path-based)
• Markdown documents with tags
• FTS5 full-text search across title / content / tags
• Channel + session metadata for provenance
• Pure stdlib (sqlite3) — no... |
3d32f0e31813ac53c4dbacd4d2956d149b56d24e8c51cdac6acd65f888fe4020 | Python | 15,434 | 469 | import numpy as np
import scipy
import torch, h5py
import os
import argparse
from collections import defaultdict
parser = argparse.ArgumentParser()
parser.add_argument("--sample_list_file", type=str, help="path of dir storing original asm files")
parser.add_argument("--pred_pdb_dir", type=str, default="", hel... |
2cb8feecd782dc07cce5f9e4256af32cfe0b83465b39c722c17d2fb72794a49d | Python | 15,435 | 439 | # 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... |
ff11643316e636550e9228269a0d8fc23e3ad02ec23df3206ba270110fad451a | Python | 15,440 | 326 | import argparse
import pickle
from typing import Dict, List, Optional, 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_inverse_alg import noredu... |
b8c6f10e9b9302e9b2afd3de6fb01776d19be1adac08b36956828a1cbaa14e56 | Python | 15,458 | 539 | from __future__ import annotations
import typing
from typing import Literal, Union, overload, TYPE_CHECKING, cast
from . import fastcc3d
from .fastcc3d import (
DimensionError,
connected_components,
statistics,
each,
contacts,
region_graph,
voxel_connectivity_graph,
color_connectivity_graph,
estimat... |
784be613b9ff71c8143e4b3125290ee68f1adcfa8d627681ac9f2a8c7d1d9804 | Python | 15,461 | 500 | """
AutoPrerequisiteInserter - Automatic prerequisite insertion into generated code.
This module provides automatic insertion of simple prerequisites into generated
code, creating complete executable workflows with proper dependency ordering.
Main Components:
AutoPrerequisiteInserter: Automatic prerequisite inser... |
85fbebef1baa77bbc744ae5d6d478663ac9898ea89b55cba08f608e07bcd05c2 | Python | 15,461 | 322 | import sys
import json
import datetime
import numpy as np
from tqdm import tqdm
from spiking_readout.snn import forward
from spiking_readout.train import stdp, get_winners
from spiking_readout.utils import weight_norm, Logger, EarlyStopper, decision_making
# Class storing all the parameters for training the readout
#... |
ad5dbced6b3f0a57d86fbcd4a54819816366745f42e5b789906a9435890bcd0f | Python | 15,463 | 352 | # -*- coding: utf-8 -*-
# Development work, e.g. for higher level functions.
# These functions are not intended to work on any machine or pass the tests.
# They are early drafts (e.g. of higher level workflows) intended to be shared among select collaborators or multiple machines of one collaborator.
# Please don't ed... |
b3c6ff4c71efe06159ef2ec2a5f561b09aff605df8e848ada954a0225cbb69a4 | Python | 15,474 | 386 | from scipy.stats import mode
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import os
from scipy.sparse import issparse
from .dp_related import rotate_by_theta
def bin_data(counts_mat, gaston_labels, gaston_isodepth,
cell_type_df, gene_labels, num_bins=70, num_bins_per_domain=... |
3c3edfc07e4311f9f1571b788e469e9d6861f33f5a962560c63dde09f35519ce | Python | 15,478 | 324 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
pandas version: 1.5.0
numpy version: 1.23.3
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 R... |
dae2bc442330a429737b1312447776439b361520ad4472b12dc46751b0d07cbf | Python | 15,479 | 429 | """ Module matching %GC compo distribution b/w fg and bg w/i a sliding win. """
import sys
import random
import numpy
from utils import GC
from Bio import SeqIO
from GC_compo_matching import print_in_bg_dir, get_bins_from_bg_dir
from GC_compo_matching import get_bins_len_from_bg_dir
def GC_info(seq, win_len, step):... |
732511149206f75c20b40ea65da9f75142924d419d990508e63d890eb99effe5 | Python | 15,491 | 428 | """
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 pytest
import torch
import torch.nn as nn
from fairchem.core.models.uma.outputs import (
co... |
20a3abc21e08936857783784aaa78c44c5625b7d946b282723ad2f2b314e749d | Python | 15,498 | 417 | import sys
import numpy as np
import os
# os.environ['CUDA_DEVICE_ORDER'] = 'PCI_BUS_ID'
# os.environ['CUDA_VISIBLE_DEVICES'] = '0'
import keras
from keras.datasets import mnist
from keras.models import Sequential
from keras.layers import Dense, Flatten, Add, Input
from keras.layers import Conv2D, MaxPooling2D, BatchN... |
0fe5816f2e06da6c25fcfb04b12b6b8b2592de1e8f02a904c0cfd297dca9f213 | Python | 15,499 | 399 | from __future__ import annotations
import asyncio
import collections
from typing import TYPE_CHECKING, Deque, Iterator, Optional
import ray
from ray.exceptions import GetTimeoutError, ObjectRefStreamEndOfStreamError
from ray.util.annotations import DeveloperAPI, PublicAPI
if TYPE_CHECKING:
from ray._private.work... |
199da599921dced82c00d629f136fa6fea59a6b9b335df3e6272b00822fe5a40 | Python | 15,499 | 330 | """
Script for computing the effective rank, stable rank, number of dormant neurons, and average weight magnitude of the
models trained during the incremental cifar experiment.
"""
# built-in libraries
import time
import os
import argparse
# third party libraries
from tqdm import tqdm
import torch
from torch.utils.da... |
e20b62adf08605f5708bcaeb1de8230270b207df0f5e658f2f04fe7fc8d703f0 | Python | 15,506 | 386 | ####################################################################################################
# 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... |
ce0fd9a980f1ec7e7a9b900f3882fc2f0edfeb2ba835c5777f1fcb0156823fc5 | Python | 15,519 | 326 | # Location for utility functions that are used at various stages during the model training and validation process
import torch
import numpy as np
import time
import os
import Dataset_Generator
# load the full dataset into RAM
class Full_Load_Dataset(torch.utils.data.Dataset):
def __init__(self, inpu... |
78850f3c45027e9b5562d51567fd3d8cf06afdc92d27a15b45c076622bc30d6b | Python | 15,523 | 325 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# mypy: disable-error-code=attr-defined
"""Quantization configuration parameters"""
from dataclasses import dataclass, field
from typing import Any, Dict, List... |
9c0bc0597e02eafaed36f4bad7a417d1b0075f3961fa3c8a63b2729ffb5bfd5d | Python | 15,526 | 332 | r"""``pyMetabo`` — AnnData-native lifecycle class for metabolomics QC/stats.
Same lifecycle as ``omicverse.pp._scdblfinder.ScDblFinder`` and
``omicverse.single.Milo`` — a class that holds the AnnData, exposes
chainable methods for each pipeline stage, and stashes intermediate
artifacts on ``self`` for later inspection... |
8a9f99a7e9930261267c77d9b8939886462b9d6a18c268b8bc301757774bfacf | Python | 15,532 | 480 | """An example of training DQN, with Optuna-powered hyperparameters tuning.
An example script of training a DQN agent with
[Optuna](https://optuna.org/)-powered hyperparameter tuning.
To keep this script simple, the target environment (``--env``) must have:
- 1d continuous observation space
- discrete action space
T... |
9a5dcb4a4fb274fc85bb510178fb95ffa478d6c0d72d80ca1c16d39afa948527 | Python | 15,533 | 455 | #!/usr/bin/env python
# HiC-Pro
# Copyleft 2015 Institut Curie
# Author(s): Nicolas Servant, Eric Viara
# Contact: nicolas.servant@curie.fr
# This software is distributed without any guarantee under the terms of the
# GNU General
# Public License, either Version 2, June 1991 or Version 3, June 2007.
"""
Script to kee... |
4a76f19605086b921626fcf5c3efc6ce58a039646f08bebad328908f6c632613 | Python | 15,534 | 389 | import torch
from torch import Tensor
import torch.nn as nn
from typing import Type, Any, Callable, Union, List, Optional
from torchvision.models.utils import load_state_dict_from_url
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152', 'resnext50_32x4d', 'resnext101_32x8d',
... |
b51f89f1a4060f0f856f399b3e5edda4e696ad131e6487eb41d20cff67f09718 | Python | 15,534 | 459 | import json
import os
import numpy as np
import snntorch as snn
from snntorch import functional as SF
from snntorch import surrogate
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, TensorDataset
# NIR stuff
import nir
# NOTE: this requires snntorch/nir (PR) and nirtorch/master (unreleased)... |
6e87ba5839f0d56f13bd73fe39e22f80600f961ab963bc2d2d3775e0457792a8 | Python | 15,541 | 430 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------
# Created By : Kangjoo Lee (kangjoo.lee@yale.edu)
# Last Updated: 08/06/2024
# -------------------------------------------------------------------------
# =========================================... |
e8d353aed50adc894048fbb3bc6c0ca1063066d392f3e8cdb4d37a7f36db20ad | Python | 15,545 | 299 | import numpy as np
from typing import Dict
from basis_functions.time_basis_functions import make_cosine_bump_family, backshift_n_samples, \
trim_basis_reduce_condition_number, trim_basis_by_cond_index, basis_shift_forward
from lib.dataset_specific_hyperparams.glm_hyperparameters import GLMModelHyperparameters
... |
fe65779544059417aa7a6964e94ab1fd0372045caad67754fddc83aa8fbe9f80 | Python | 15,552 | 325 | #!/usr/bin/env python3
################################################################################
# -- Preprocessing and analysis of the simulation results
################################################################################
import numpy as np; import pylab as pl; import os, pickle
import matplotlib... |
9836469bc216b7253cb62f2c0e70720921e6961a5e960d5bd3218bea78372f1f | Python | 15,561 | 429 |
# 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:
#
... |
7da93c67dcf0b0e44d8205d2d6b91e56b7629ded1776852ffbb7abef30320a1a | Python | 15,565 | 319 | # taken from Github, yjkimnada/ns_decoding
# Original Author: Young Joon Kim
# Original License
'''
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTI... |
fdc8467a95a636f3deba9e7c83b7eae6c29ee22102c0d6234e2c77ba41a0f59b | Python | 15,566 | 294 | import sys
sys.path.insert(1,'../src_simulation/')
sys.path.insert(1,'../src_VI/')
sys.path.insert(1,'../src_MCMC/')
import pandas as pd
import torch
from torch.utils.data import Dataset, DataLoader
import data_sim
from full_slab_spike_model_constructor import *
from training_func import *
from sklearn.preprocessing im... |
d2ff4d13db47c698a1d8ca50c3cf5f8a1ec40439617dd7114088bff23f50eab5 | Python | 15,573 | 307 | import tifffile as tiff
import cv2
import numpy as np
from skimage import io
import time
import datetime
import scipy.io as scio
import multiprocessing as mp
import math
import os
from DWonder.MN.utils import Split_Neuron, listAddtrace
from DWonder.MN.utils import Neuron_List_Initial, list2mask, listAddtrace, centroi... |
63c19aad744ae588ee72b438aca6f436492986aa73d0be784af4d57bae92c4a4 | Python | 15,584 | 475 | """
Chefer et al., CVPR 2021 — "Transformer Interpretability Beyond Attention Visualization"
Gradient-weighted attention rollout for encoder-only transformers.
Usage (inference only — model weights are never modified):
relevancy = compute_relevancy_scores(
model=trained_model,
inputs=batch_inputs_... |
ca1f848c8181a878162041b4e6a3a0bf9435d82baac164c6a39dfb815d8aa9ea | Python | 15,591 | 416 | from __future__ import annotations
import warnings
from contextlib import contextmanager, suppress
from datetime import datetime
from typing import TYPE_CHECKING
import importlib.util
import numpy as np
import pandas as pd
from natsort import natsorted
if TYPE_CHECKING:
from collections.abc import Generator, It... |
82191737c67f54e3f3f1eabcd52e0fed3defe2d6865032c5273d28b9334a0a22 | Python | 15,600 | 368 | import logging
import math
from typing import TYPE_CHECKING, Any, Callable, Dict, Iterable, List, Optional, Tuple
from ray.data._internal.object_extensions.arrow import raise_on_pickle_object_columns
from ray.data._internal.util import _check_import
from ray.data.block import Block, BlockAccessor, BlockMetadata
from r... |
8fd2cb5605a6cadd225721e4b0a2f9cd6dcf18bc9959663e6402c8f276d3fdde | Python | 15,600 | 409 | from typing import Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
from lqit.registry import MODELS
from lqit.utils import OptConfigType
@MODELS.register_module()
class StructureFFTLoss(nn.Module):
"""`FFT-based Structure Loss.
<https://link.springer.com... |
c30edadf1d3baabdcc62f83bea3c2aea25b68aee0283806e544cecc8c6460977 | Python | 15,605 | 453 | """
Taken from https://github.com/tugstugi/pytorch-speech-commands and modified
by Karan Goel.
"""
import argparse
import os
import torch
import numpy as np
from functools import reduce
from natsort import natsorted
from scipy import linalg
from scipy.stats import norm, entropy
from sklearn.cluster import KMeans
fro... |
1da4dda1b12cd1b43edc00d577ad0fab2db3f00d89f517d9b3937656587bf7c7 | Python | 15,622 | 381 |
#!/usr/bin/env python
# Python Version: 3.10
# Author: Reese Wilkinson, Nick Souter
# Institution: University of Sussex
# Last Update: 01/11/2023
# Version 0.2.2
## Example 1:
# -bash$ qacct -j 3744147 | python3 calc_carbon.py
# Job ID: 3744147
# 1:
# kWh: 0.000000
# ... |
8a74eb48f4336807f1e625412c44d6984095f50b33d2ffd857000bc62c6e6042 | Python | 15,625 | 405 | # data generator code for training CNN
import sys
import numpy as np
import tensorflow as tf
import msprime
import tskit
from attrs import define,field
from read_input import *
from process_input import coords2array
import gc # garbage collect
@define
class DataGenerator(tf.keras.utils.Sequence):
"Generates data ... |
b9f6a301634122c1fa0d28503ba9b7be42a127e89cb8c46778905fb8191dd9bf | Python | 15,625 | 450 | # -*- coding: utf-8 -*-
import numpy as np
from pathlib import Path
from vtkplotlib._get_vtk import vtk
try:
# Doing this allows the current figure to be remembered if vtkplotlib gets
# re-imported.
_figure
except NameError:
_figure = None
_auto_fig = True
def auto_figure(auto=None):
"""Enable... |
9a34f65908bbb5de68d5dd90439654db17de995eb55c941ee0462551ca9afb85 | Python | 15,632 | 470 | import h5py
import numpy as np
import datetime
from ml4h.TensorMap import TensorMap, Interpretation, str2date
from ml4h.defines import StorageType
from ml4h.metrics import weighted_crossentropy
from ml4h.tensormap.ukb.demographics import prevalent_tensor
DAYS_IN_5_YEARS = 365 * 5
DAYS_IN_10_YEARS = 365 * 10
def _sur... |
7cb74e7f94271aac97e35bfbd470f150032ac2d45a729213269ef4570230546b | Python | 15,633 | 356 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# --------------------------------------------------------
# References:
# DeiT: https://github.com/facebookresearch/deit
#... |
d18df784aa6c9110723f013c4a610a300265f4be97762a770e85a6bf71c2a568 | Python | 15,636 | 426 | #
# 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... |
ffe21303826f40a961661d6365e3702ce56349c1197fc374e8e3fceae4cf7e11 | Python | 15,638 | 356 | from imports import *
from ngs_mapper import compat
class Base(BaseClass):
modulepath = 'ngs_mapper.run_bwa'
class TestUnitBWAMem(Base):
functionname = 'bwa_mem'
def test_bwa_mem_nonpaired(self):
with patch('ngs_mapper.run_bwa.BWAMem', return_value=Mock( run=Mock( return_value=0 ) ) ) as b:
... |
b7860a26359785ce137a33cdab5e978e4818cd38ba21b71216fd5c160abf94ea | Python | 15,644 | 370 | """Prompt construction for OVAgent agentic and subagent loops.
Extracted from ``smart_agent.py`` to keep prompt assembly in one place.
All methods are pure string construction with no side effects.
Since task-034, the heavy lifting is delegated to the
``PromptTemplateEngine`` in ``prompt_templates.py``; this module
r... |
e65bbd30460f52556b50ca1968da18448e77d9b4abfcf6b89532b5a95ebcda72 | Python | 15,650 | 361 | #
# 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... |
f71b0776e0bd0bb7c4a9e762b3793ca5edf70db848f0df0b0082e157a096f043 | Python | 15,680 | 442 | import os
import shutil
import sys
import tempfile
import unittest
from collections import namedtuple
from unittest.mock import MagicMock, patch
import pytest
from mlflow.tracking import MlflowClient
import ray
from ray._private.dict import flatten_dict
from ray.air._internal.mlflow import _MLflowLoggerUtil
from ray.... |
341bb36dbf5ccf05101a3567bf888a13c30584fe9fbebe2de965b6dec2545685 | Python | 15,687 | 375 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 12 20:50:03 2021
@author: irisstone
"""
import numpy as np
import autograd.numpy as npa
from autograd import hessian
from glmhmm.hmm import HMM
from glmhmm.init_params import init_transitions, init_states, init_weights
from glmhmm import glm
from g... |
657ab50c37a582d0044336c10997b23dc87ddb146ef3c10e4536e2053f307c1f | Python | 15,696 | 397 | #!/usr/bin/env python
from __future__ import print_function
import subprocess
import os
import shutil
import math
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from matplotlib import rcParams
rcParams.update({'font.size': 16})
rcParams.update({'figure.autolayout': True})
COVERAGE_BEDS = [
... |
08e3b6e3766c27668829f6da8f98afb1c1f31695e7621e61aa437bd933ef4864 | Python | 15,703 | 383 | """Self library
author: Ting-Ting Gao"""
import pandas as pd
import numpy as np
import itertools as it
def elementary_functions_name(dimensionList,order):
Combination_func = list(it.combinations_with_replacement(dimensionList,order))
Num_of_func = len(Combination_func)
Name_of_func = []
for i in ra... |
2da0956d60b514d0228f3ac5e99fc23675f9b06d32b63dfaa13e9bdc87b03df7 | Python | 15,703 | 423 | """Implementation of scoring methods."""
import numpy as np
import pandas as pd
from typing import Dict, List, Union
from scipy import stats
import warnings
def aucell_score(
expression: np.ndarray,
pathways: Dict[str, List[str]],
gene_names: List[str],
ncores: int = 1,
aucMaxRank: int = None,
) ... |
d6e87a6b4c1767472c30ad8c3971554ee9d5518a93763f72505028a23372b2de | Python | 15,703 | 404 | # -*- 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.
#... |
3a1077bcbb523e6278ae1bf9c4fca175b8ddd126c7a59262dc9b876b617c94d6 | Python | 15,706 | 511 | import cv2 # noqa: F401 — preload libtiff before HIPT/torchvision shadows it (omicverse vendored patch)
import os
from time import time
import argparse
from einops import rearrange, reduce, repeat
import numpy as np
import skimage
import torch
from utils import load_image
from hipt_model_utils import eval_transforms... |
fb698d0dc7d6aa733d9f842cef2cf6bbb18f84b33b569dd464ac1d95a2ba711d | Python | 15,712 | 448 | from typing import Optional, Sequence, Tuple, Union, Callable, Any
from jaxtyping import Key
import jax
import jax.lax as lax
import jax.numpy as jnp
from jax.nn import initializers
import jax.random as jrandom
import jax.tree_util as jtu
import equinox as eqx
from .initializers import lecun_normal
from ..global_defs i... |
b5f8266d1766091992dfad017acc7ce7f0e71bc6a13b09ff55716616dd80573b | Python | 15,714 | 411 | import numpy as np
import random
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.patches import FancyArrowPatch
from ._palette import palette_112
from .._registry import register_function
def curved_line(x0, y0, x1, y1, eps=0.8, pointn=30):
r"""
Generate poin... |
8e48715905f1cc921c2892a0e5dce79899a75e1354e6f3f3c764744287fa7012 | Python | 15,719 | 439 | """DADA2 backend for 16S ASV inference.
Wraps the pure-Python re-implementation `pydada2`
(https://github.com/omicverse/py-dada2) — no R / rpy2 dependency.
Submodule-style layout (like ``ov.alignment.vsearch``): each function is a
thin wrapper around the corresponding pydada2 call, plus one orchestrator
:func:`dada2_... |
194b99d1b6bf88f9c25e72c3b2e6e73bfbfc2a0642935de22b7039a66030d422 | Python | 15,723 | 438 |
# 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:
#
... |
afa03bc351aaa09e470a9aab719e667a4234a45851b402fc4e30e94c065e3bcc | Python | 15,729 | 311 | import os
import pandas as pd
import numpy as np
from sklearn.preprocessing import StandardScaler
def load_subjectiid(inputtxt):
'''
Load the sujectID file from the RPN output to easily pair the indices(RPNID) with the appropriate participants' id (subjid):
create a dictionary in which the keys are the s... |
983d9ee3194ce3c63eb4f24c25e4e9d0df04b9e117baa740a45ffec9a116ed09 | Python | 15,735 | 298 | """Matching and evaluation, including ports of the supplied MATLAB helpers."""
from collections import Counter
import numpy as np
from scipy import sparse
def pairwise_distances(x, y=None, metric="euclidean", max_pairs=25_000_000):
same_input = y is None
x = sparse.csr_matrix(x, dtype=np.float64)
y = x if... |
40901748ebcc448fbc7fad7e6cb47e8d8f2365418ba98d0a1182702d5713c796 | Python | 15,738 | 353 | import os
import csv
import logging
import operator
import h5py
import numpy as np
import pandas as pd
from typing.io import TextIO
from typing import List, Tuple
from ml4h.metrics import sparse_cross_entropy, weighted_crossentropy
from ml4h.TensorMap import TensorMap, Interpretation
from ml4h.DatabaseClient import B... |
90e43535f4b0256a051d60ab728bd335f5255cbd255ac0b1a060172ca332e66c | Python | 15,739 | 436 | # built-in dependencies
import os
import json
import struct
import hashlib
from typing import Any, Dict, Optional, List, Union
# 3rd party dependencies
import numpy as np
# project dependencies
from deepface.modules.modeling import build_model
from deepface.modules.database.types import Database
from deepface.modules... |
ce4b47a9743a7685352d369f5a547c29cf9d64f2567ba62d3e07aa47584b9962 | Python | 15,744 | 407 | from fractions import Fraction
import numpy as np
import pytest
from stl import mesh
from .test_mesh_mass_sliver import _unit_cube, sliver
def mixed_components(zero_volume_subset=False, ordinary_sign=1):
ordinary, volume, cog, inertia = _unit_cube()
ordinary = subdivide(ordinary)
ordinary['vectors'] +=... |
805ae0efe340bce3688a704c729373af9a5ff86669a799a6b95b22716e85f61f | Python | 15,745 | 467 | """plotting functions."""
import logging
import os
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import shap
import pandas as pd
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.gridspec import GridSpec
from mpl_toolkits.axes_grid1.inset_locator import ... |
1148c9080ad0012eaa65a6c43c6bf8b00b96ad52919951fc88921cd88a38b016 | Python | 15,749 | 519 | # -*- coding: utf-8 -*-
"""Module implementing alignment estimators on ndarrays."""
import warnings
import ot
import numpy as np
import scipy
from joblib import Parallel, delayed
from scipy import linalg
from scipy.optimize import linear_sum_assignment
from scipy.sparse import diags, csr_matrix
from scipy.spatial.dist... |
82a12c966c3b42b45b6074f3358724aa8c88978f2135d951a1d90a3efcfaed24 | Python | 15,749 | 379 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
The functions used to do selective recruitment analysis
Authors: Ladan Shahshahani, Joern Diedrichsen
"""
import os
import numpy as np
import deepdish as dd
import pandas as pd
from scipy import stats as sps # to calcualte confidence intervals, etc
import Functional... |
964c8e5cf6b5b0fe29f640f796094e4e1b7b20f753a31380f7a6ff1ce2b3541d | Python | 15,767 | 434 | # built-in dependencies
import os
import json
import hashlib
import struct
from typing import Any, Dict, Optional, List, Union, cast
# 3rd party dependencies
import numpy as np
# project dependencies
from deepface.modules.database.types import Database
from deepface.modules.exceptions import DuplicateEntryError
from ... |
83fba1661d1f922a5f3611961fbfb858fe5ea85d2c781f5805cfe318061d0826 | Python | 15,783 | 256 | import logging
from datetime import datetime
from agent.classifiers.utils.device_mgmt import get_gradient_accumulation_steps
from agent.classifiers.transformer_classifier import transformer_classifier
from agent.classifiers.ffnn_classifier import ffnn
from agent.classifiers.tr_ffnn_ensemble_classifier import tr_ffnn
... |
bbc9da4b9703a40be66436067cbee4fd633276863df526d24e6d2ccae2347053 | Python | 15,784 | 359 | """
This file evaluate the testing dataset for the SPLAM model.
Parameters:
MODEL_VERSION : the version of the model.
Input directory : "./INPUTS/"+SEQ_LEN+"bp/input_pos/"
Output directory: "../src_tools_evaluation/splam_result/"+MODEL_VERSION+"/"
"""
import os, sys
sys.path.append(os.path.dirname(os.p... |
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