sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
48f855ca9655f937c9e04bf57c424833b06122ceb8cc3901bec681c405997690 | Python | 10,736 | 263 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
# pyre-unsafe
import logging
import os
from collections import OrderedDict
from typing import List, Optional, Union
import torch
from torch import nn
from detectron2.checkpoint import DetectionCheckpointer
from detectron2.config import CfgNode
fr... |
3f0e82b479e6000ecff8ebddeaed9cfa3e680cbfc09908df832caa5ef6a7dd46 | Python | 10,739 | 272 | """Scoped glue between the ColabFold JAX runner and the shared RGI engine."""
from __future__ import annotations
import copy
import functools
import inspect
import json
from contextlib import contextmanager
from pathlib import Path
from colabfold.citations import write_rgi_citation
from colabfold.rgi import ALPHAFOL... |
172bd3ab0b3dc186c7096236eb1d4fec3bab5f4c483460b8594bf52ca950b203 | Python | 10,744 | 244 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import prl_preprocess_func
__all__ = ['prl_fictitious_rp_woa']
class PrlFictitiousRpWoa(TaskModel):
def __init__(self, **... |
7301f24c54eaf8f59eed97b69cf4e2619c38504b20d6ef25da3636c3fcf81f6e | Python | 10,745 | 281 | import warnings
from typing import Any
from typing import Callable
import torch
from torch import nn
import ptrnets
from ..utils.mlayer import clip_model
from ..utils.mlayer import hook_model_module
class Core(nn.Module):
def initialize(self) -> None:
raise NotImplementedError("Not initializing")
d... |
bb80584eef496565b32089dba50b7c11bd59c55cb92c347f689fc55ce5c245e1 | Python | 10,746 | 248 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import banditNarm_preprocess_func
__all__ = ['banditNarm_lapse_decay']
class BanditnarmLapseDecay(TaskModel):
def __init_... |
71d065bbbcf46ec634d044da351c2eb37bf80a4586d7831260f15cfc327aaa69 | Python | 10,758 | 299 | import keras
from keras.models import Sequential, Model, load_model
from keras.layers import Dense, Dropout, Activation, Flatten, Input, Lambda
from keras.layers import Conv2D, MaxPooling2D, Conv1D, MaxPooling1D, LSTM, ConvLSTM2D
from keras.layers import GRU, BatchNormalization, LocallyConnected2D, Permute
from keras.l... |
d4ce8bb5558fe7f740f9cec57eed54f4159aafcd1d6db82f2db07f7690354c33 | Python | 10,758 | 299 | import keras
from keras.models import Sequential, Model, load_model
from keras.layers import Dense, Dropout, Activation, Flatten, Input, Lambda
from keras.layers import Conv2D, MaxPooling2D, Conv1D, MaxPooling1D, LSTM, ConvLSTM2D
from keras.layers import GRU, BatchNormalization, LocallyConnected2D, Permute
from keras.l... |
4e77742885521d26e7870b45514722d0418ce11dd7e1a0f2ca38abc2bbbe949f | Python | 10,759 | 245 | # -*- coding: utf-8 -*-
"""
Created on Thu Apr 23 11:36:41 2020
@author: gritti
"""
import sys, time, tqdm, copy, os, glob
# sys.path.append(os.path.join('..'))
import pandas as pd
import numpy as np
from scipy.ndimage import map_coordinates
from skimage.io import imread, imsave
from skimage.filters import gaussian
f... |
e6a085e37279bb05f1d10f7e51db9f613d6c45227a05722a756da05a87f9e285 | Python | 10,764 | 246 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import prl_preprocess_func
__all__ = ['prl_fictitious_rp']
class PrlFictitiousRp(TaskModel):
def __init__(self, **kwargs)... |
bfb6f4725f7a40e6f73ef1883d929e7793556515bef4e06f8848f3b439d79e51 | Python | 10,768 | 271 | from collections import Counter
from argparse import ArgumentParser
from argparse import RawTextHelpFormatter
import sys, os
import re
from mantis_ml.modules.pre_processing.data_compilation.process_features_filtered_by_disease import ProcessFeaturesFilteredByDisease
from mantis_ml.config_class import Config
... |
4c2e8c806b576f9632d9351e4cd85d16c938fe8b67b82418951359996ace6f34 | Python | 10,773 | 254 | import pandas as pd
import numpy as np
import sys
import matplotlib.pyplot as plt
from sklearn.ensemble import (ExtraTreesClassifier, RandomForestClassifier, GradientBoostingClassifier)
from sklearn.svm import SVC
from sklearn.metrics import confusion_matrix, roc_curve, roc_auc_score
import xgboost as xgb
# fro... |
c57d762185dfaa914bb0022a8bc1bdb8d54ab928ed14c584d507dc49c8d3b3cd | Python | 10,775 | 254 | import pandas as pd
import numpy as np
import sys
import matplotlib.pyplot as plt
from sklearn.ensemble import (ExtraTreesClassifier, RandomForestClassifier, GradientBoostingClassifier)
from sklearn.svm import SVC
from sklearn.metrics import confusion_matrix, roc_curve, roc_auc_score
import xgboost as xgb
# fro... |
371d5140cee0a53d732a4df6d34ab480da22c532896dc3a89f6f941485837ab6 | Python | 10,781 | 304 | #!/usr/bin/env python3
# pylint: disable=line-too-long
"""
Various functions for generating machine learning models for genomes.
"""
# Imports
import pickle
import os
import logging
import numpy as np
from sklearn.ensemble import RandomForestRegressor, RandomForestClassifier
from sklearn.model_selection import train_te... |
90cdc9bce7fa3b4b1fd22d8de64d85babb5661c172f773786831b73adaee3ffd | Python | 10,785 | 317 | import re
from collections.abc import Sequence
from typing import Any
from langchain_core._api import deprecated
from langchain_core.agents import AgentAction
from langchain_core.callbacks import BaseCallbackManager
from langchain_core.language_models import BaseLanguageModel
from langchain_core.prompts import BasePro... |
f325d95e45f99624c26e4a5ea30df42f84663ed8296c95319fb45b0a12196176 | Python | 10,788 | 249 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import banditNarm_preprocess_func
__all__ = ['banditNarm_kalman_filter']
class BanditnarmKalmanFilter(TaskModel):
def __i... |
9b26c74432fe7a9f81bae8452c7abdae6e91f0f39035b27db33a82a7afb051de | Python | 10,790 | 241 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Publication figures for the arXiv preprint (English labels).
All values are read from the persisted result registries produced by the
campaign; none is hard-coded except the staircase amplitudes, which are read
back from the R2 registry for consistency.
"""
from __futu... |
c9e37e6787850f28efb3edea2b7d6b86a6af049a4f66ac348b5be7e07f0b6c1e | Python | 10,790 | 271 | import numpy as np
import nltk
import csv, os, re
import h5py, json, pickle
import pkg_resources
from symspellpy import SymSpell, Verbosity
import inflect
np.random.seed() # randomly initialize the seed
sym_spell = SymSpell(max_dictionary_edit_distance=2, prefix_length=7) # for correction of spelling mistakes
dictio... |
87bcdafdb421f42e1c1a6f4b50969d0e7c55ad8006cb72ca72682e9022d7a717 | Python | 10,801 | 239 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
import pdb
import torch
from torch import nn
from functools import partial
from .activations import ACTIVATION_REGISTRY
import numpy as np
import math
def fourier_embedding(timesteps: torch.Tensor, dim, max_period=10000):
r"""Create sinusoi... |
9f04479cc75383592c49909ff87acb4958006013c8d282e568e9e4dbd6822059 | Python | 10,802 | 315 | from __future__ import annotations
from typing import Annotated, Any, TypeVar
from langchain_core.exceptions import OutputParserException
from langchain_core.language_models import BaseLanguageModel
from langchain_core.output_parsers import BaseOutputParser, StrOutputParser
from langchain_core.prompt_values import Pr... |
7b4fbd4442cc6c0cc4b41228430cb741b7a1dc202177f861edadc16e911281a7 | Python | 10,805 | 225 | from collections.abc import Hashable
import numpy as np
import pandas as pd
from numpy.typing import ArrayLike
from pgmpy.parameterization._base import BaseParameter, _checked_evidence, _parent_order
from pgmpy.parameterization.distributions import NominalDistribution
from pgmpy.utils import build_state_names, encode... |
ef0a2d10c6c5f673cceb514739910ef1444cf7809b2c3290617837f200e2612d | Python | 10,808 | 284 | import warnings
import numpy as np
import matplotlib.pyplot as plt
from sklearn.decomposition import PCA
from pensa.preprocessing import merge_and_sort_coordinates
from .visualization import project_on_eigenvector_pca, sort_traj_along_projection
# --- METHODS FOR PRINCIPAL COMPONENT ANALYSIS ---
def calculate_pca(d... |
e5abb8ffb2a8d0060b4faedd267ac48a90fb6d5f5453fe686ba27c1a0f808d96 | Python | 10,809 | 279 | import numpy as np
from tqdm import tqdm
from rdkit import Chem, DataStructs
from rdkit.Chem import Descriptors, Crippen, Lipinski, QED
from analysis.SA_Score.sascorer import calculateScore
from analysis.molecule_builder import build_molecule
from copy import deepcopy
class CategoricalDistribution:
EPS = 1e-10
... |
ff11ec9d390cbf7cda6e6e0855ea53c871d8e8f0351a2f9b8886dfb354248406 | Python | 10,815 | 271 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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, either version 3 of... |
577b1ddbe117422be5b4e226407824113873295a141c05018295428731b415f7 | Python | 10,818 | 232 | """ OmicScope Module
OmicScope allows user to import data and perform statistical analysis
for differential gene/protein expression. This is the key module of
all OmicScope workflow, being the input for all other modules.
"""
import warnings
from .Input import Input
warnings.filterwarnings("ignore")
class Omicsc... |
64267e3ea677b16ecb5bae302f9271e702c8f086ac43b5427a3221654dc5cf35 | Python | 10,821 | 255 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Time : 2023/9/28 10:48
# @Author : zhangchao
# @File : transfer.py
# @Software: PyCharm
# @Email : zhangchao5@genomics.cn
import os
import os.path as osp
from typing import Union
import torch
import scanpy as sc
import numpy as np
import scipy.sparse as sp
impo... |
6d5dae03ec86e78f877ac95188815169c4ac6f86b5c73e7a8b8b709091ae4591 | Python | 10,824 | 325 | import pytest
import torch
import copy
from nequip.utils.unittests.model_tests_ase_integration import ASEIntegrationMixin
from nequip.utils.unittests.model_tests_train_time_compile import TrainTimeCompileMixin
from nequip.utils.unittests.model_tests_lammps import LAMMPSMLIAPIntegrationMixin
from nequip.utils.unittests.... |
52914160f062e13a224ad647552e6b4242e58e2446e9ae9bbeaccca8d772c2b3 | Python | 10,825 | 278 | # Copyright 2020 DeepMind Technologies Limited.
#
# 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... |
57eb678d1bae39971d457078d5c1320e8d3045932ac6131a7c2e63ced843fdea | Python | 10,827 | 320 | from datetime import datetime as dt
from datetime import timezone
from typing import Any, TypeVar
import pytest
from langchain_core.exceptions import OutputParserException
from langchain_core.output_parsers import BaseOutputParser
from langchain_core.prompt_values import PromptValue, StringPromptValue
from langchain_c... |
8ffc137e96c9d946c1c0a015963afa8f61a07741ef05f410dc319cf34abd1459 | Python | 10,834 | 254 | from __future__ import print_function
import numpy as np
from dipy.reconst import dti
from dipy.core.gradients import gradient_table_from_bvals_bvecs
from .utils import erode_mask
from .free_water_fit import grad_data_fit_tensor, clip_tensor_evals
from tqdm.notebook import tqdm
d = 3.0e-3
def estimate_tensor(dwi_da... |
37d59cb1c395aef13307e1a3a1227505e9178aa28cd93948ec334dc0b7318c79 | Python | 10,835 | 373 | """LLM Chains for evaluating question answering."""
from __future__ import annotations
import re
import string
from collections.abc import Sequence
from typing import Any
from langchain_core.callbacks import Callbacks
from langchain_core.language_models import BaseLanguageModel
from langchain_core.prompts import Pro... |
b3558a9b061216cdcfb31bed52f1c129cf29c311b32e1d88bf1e22ae3dfd0892 | Python | 10,836 | 279 | """Functions for clustering sequences before input.
This includes computing a distance matrix using MinHash, and
clustering that matrix.
"""
from collections import defaultdict
from collections import OrderedDict
import logging
import operator
import numpy as np
from scipy.cluster import hierarchy
from easyDesign.u... |
dc6a60494cae0467698144b0f0c34d4a9b8da12a184d6337ab9ec8e5942b9b65 | Python | 10,840 | 279 | # -*- coding: utf-8 -*-
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IMPORTS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# Standard library imports
from collections import OrderedDict, namedtuple, Counter
import gzip
# Third party imports
from tqdm import tqdm
import numpy as np
from pyfaidx import Fasta
# Local imports
from pycoMe... |
00c26824aad5a45b1dedb78acddacd54d83bceb6939153800bd757dac8406133 | Python | 10,843 | 267 | import sys
sys.path.append('../')
import os
import numpy as np
import matplotlib.pyplot as plt
import torch
from torch import nn
from torch.utils.data import DataLoader
import torch.nn.functional as F
from matplotlib.colors import LinearSegmentedColormap
import alg
from alg import alg
from utils.util import set_rando... |
f9dd90c6397932939b50fc80e5dd36ef5eaa39e4742a1c20863f1bb6a6cad3a8 | Python | 10,843 | 306 | '''
Author: Alexandra Fischbach
Github repo: https://github.com/AlexFischbach/local_csf_pipeline/tree/main
Date: 04-18-2025
Contact: fischbach.a@northeastern.edu
'''
def initialize_roi_dict(
roi_dir, subj
):
'''
Creates a dictionary of ROI NifTI mask file paths.
Key value corresponds to ROIs name... |
f55f85c8f6d4405ddbc5a83a163cee287676b9281a09522e8f00f886cb6b10ed | Python | 10,845 | 281 | import numpy as np
from pensa.comparison import \
relative_entropy_analysis, \
kolmogorov_smirnov_analysis, \
ssi_ensemble_analysis
from pensa.dimensionality import \
calculate_pca, get_components_pca
"""
Calculates the average and maximum Jensen-Shannon distance and the Kullback-Leibler divergenc... |
8375e8508759c034f28fa09b162a52af8c1689b072d0fb79ca2d9b1d9376058e | Python | 10,848 | 276 | """
Training ZephOD feature detection network
Usage:
train_zephod -h | --help
train_zephod -v | --version
train_zephod --index=<index> [options]
Options:
-h --help show this message and exit.
-v --version show version information and exit.
--ind... |
d8b10d29b6eb3c6e7f0460e14d7630db6dd42243612b17738aefe0f44da39a24 | Python | 10,851 | 375 | '''
Created on Oct 13, 2011
two normalization methods are supported.
sequence depth
bin correlation
@author: Ying Jin
'''
#from rpy2.robjects.packages import importr
#from rpy2.robjects import FloatVector
#import rpy2.robjects as robjects
#import rpy2.robjects.lib.ggplot2 as ggplot2
import subprocess
from array imp... |
07e30c5f6d974295c36bf0b1872f27daf051a5c975ae34776215ed1e48c72fe6 | Python | 10,855 | 300 | """
##############################################################################
#
# Filter ATtRACT database and save motifs in a MotEvo-compatible format
#
# AUTHOR: Maciej_Bak
# AFFILIATION: University_of_Basel
# AFFILIATION: Swiss_Institute_of_Bioinformatics
# CONTACT: wsciekly.maciek@gmail.com
# CREAT... |
e78782d7baa618e2fb45bfb5b10e8a48ce11d2d82134a6210b28413512280db7 | Python | 10,855 | 333 | # Adapted from OpenFold
# Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
#
# 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/l... |
ed6aa36aaee6d9d01d979bcc12000ac89e0655b3527b5b3ae745fa7217d59bb5 | Python | 10,857 | 179 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
757f45b2d09bfcf636c8da17621f9dba18f8bdac456263ce86747c47e1e908f5 | Python | 10,858 | 252 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import igt_preprocess_func
__all__ = ['igt_vpp']
class IgtVpp(TaskModel):
def __init__(self, **kwargs):
super()._... |
be270d5887e00ce939a702859b1953c8530b400adef151c5ffaddd37d1bea40f | Python | 10,867 | 273 | import enum
##
# Residue identities
non_standard_residue_substitutions = {
'2AS':'ASP', '3AH':'HIS', '5HP':'GLU', 'ACL':'ARG', 'AGM':'ARG', 'AIB':'ALA', 'ALM':'ALA', 'ALO':'THR', 'ALY':'LYS', 'ARM':'ARG',
'ASA':'ASP', 'ASB':'ASP', 'ASK':'ASP', 'ASL':'ASP', 'ASQ':'ASP', 'AYA':'ALA', 'BCS':'CYS', 'BHD':'ASP', '... |
90e175dc99ee03f130482afe28a8093b6a74eec4fe92a25748ef4da2d83d6db4 | Python | 10,868 | 297 | import copy
import logging
import os
import socket
import sys
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from configs.configs import get_config_dict
from helpers.hcp import get_human_connectome_project_subjects, rename_variables_for_plots
from helpers.figures import g... |
94e0ff1bac522084c87e03028699888201c1d29813cae8af51fa006f785d2e28 | Python | 10,868 | 267 | # Copyright (c) 2021, NVIDIA CORPORATION & AFFILIATES. 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 sof... |
3beffaaf9eab5da5a199644b991c645c5b3112a10215b4adb61ddabcfeb605ab | Python | 10,880 | 324 | """Script for preprocessing mmcif files for faster consumption.
- Parses all mmcif protein files in a directory.
- Filters out low resolution files.
- Performs any additional processing.
- Writes all processed examples out to specified path.
"""
import argparse
import dataclasses
import functools as fn
import multipr... |
e3c1b2699291f79aef69d88c892ffd896e5511f3d3c05ce8bef1fedce258aa4f | Python | 10,884 | 234 | # coding=utf-8
import os
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
from torch.cuda.amp import autocast
import torch.autograd as autograd
from torch.autograd import Variable
from torchmetrics import PeakSignalNoiseRatio as PSNR
from skimage.transform import resize
from alg.a... |
181981f057bd9505c7fdcebb5fea616d2fcc7ff6826d0d2a0db43a3889feadce | Python | 10,893 | 186 | # coding=utf-8
""" Defines test cases for tabular dataset """
import pytest
from vulcanai.datasets import tabular_data_utils
import os
import pandas as pd
import torch
import numpy as np
# noinspection PyMissingOrEmptyDocstring
class TestTabularDataset:
@pytest.fixture
def split_data(self):
pass
@... |
0b1f110389b704f9c20df8a8c83b37bfb4568fbdcba5aefaa059452b4d251276 | Python | 10,898 | 272 | import numpy as np
import random
import torch
import torch.nn as nn
from models.common import Conv, DWConv
from utils.google_utils import attempt_download
class CrossConv(nn.Module):
# Cross Convolution Downsample
def __init__(self, c1, c2, k=3, s=1, g=1, e=1.0, shortcut=False):
# ch_in, ch_out, kern... |
d26c91b5a72c1f6ddfe38fe1d50e67e4afaf90e74753dbb60f47741266c01aa6 | Python | 10,899 | 326 | import numpy
import cloudvolume
from cloudvolume.datasource.precomputed.mesh.unsharded import *
from pycilium.utils.skeleton_utils import *
def bb_included(bb1, bb2):
return (bb1.contains_bbox(bb2) or
bb2.contains_bbox(bb1) or
bb1.intersects(bb1, bb2))
def bbox_from_filename(fn, scale=... |
786117a9a699cf52d0613fc9719cc08348215a1dba84644b8aaafe95cb3bf9a4 | Python | 10,901 | 245 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import ts_preprocess_func
__all__ = ['ts_par4']
class TsPar4(TaskModel):
def __init__(self, **kwargs):
super().__... |
b0be730b6c6b39c7d63dc4d32b2dbd7ce56e20e22f885c504bd6cb346cf53f0c | Python | 10,905 | 208 | import matplotlib.pyplot as plt
import numpy as np
import yaml
import argparse
from collections import defaultdict
from src.utils import triu_inverse
from config.paths import GRADIENTS_PER_JOBS_PATH_TEMPLATE, CLASSIFICATION_PER_JOBS_PATH_TEMPLATE, FEATURE_IMPORTANCE_PATH_TEMPLATE, FEATURE_IMPORTANCE_FULL_MATRIX_PATH_TE... |
62a91ad11f319bcd30ecd437fe79f55e2a34ab03127d88fe6a1b74c7753094a4 | Python | 10,909 | 245 |
from ._base import register_transform
import torch
import math
from rde.utils.protein.dihedral_chi import AA_TO_INDEX, ALL_ATOMS, ALL_ATOM_POSNS,ONE_TO_THREE, CHI_PI_PERIODIC_LIST
from rde.utils.protein.constants import restype_to_heavyatom_names as restype_name_to_atom15_names
from rde.utils.protein.constants import ... |
f1ef61563160bf21134d0053a268f3bb5ae8d718ff61dbc5eae066a644d49e8b | Python | 10,914 | 191 | """CPU regression checks for label export and batched surface overlays."""
from pathlib import Path
import tempfile
import unittest
from unittest.mock import patch
import nibabel as nib
import numpy as np
from postprocessing.labels import read_regions, write_labels
from postprocessing.overlays import FIELDS, copy_fra... |
7d7679856527dbf4733c3043bcd11e8994fd9a2c401959dad9a80181ad3d3b37 | Python | 10,919 | 325 | '''
PipelineTranscriptDiffExpression.py - Utility functions for
pipeline_transcriptdiffexpression.py
==============================================================
:Author: Toms Smith
:Release: $Id$
:Date: |today|
:Tags: Python
Code
----
'''
import cgatpipelines.tasks.expression as Expression
import cgatpipelines.... |
130697e2fd7ace4aef789a18f4314a1b4e6d3c0529be83e4e2ec3532a99af183 | Python | 10,922 | 357 | '''
https://github.com/flatironinstitute/mountainsort/blob/master/packages/pyms/mlpy/mdaio.py
Modified by jiaaoZ 01/20/2022
'''
import numpy as np
import struct
class MdaHeader:
def __init__(self, dt0, dims0):
uses64bitdims=(max(dims0)>2e9)
self.uses64bitdims=uses64bitdims
self.... |
02b8fed955933441e94f63dc071a32cb436b633bec2bdd713ca765b8c80aad06 | Python | 10,932 | 300 | import numpy as numx
import pydeep.base.numpyextension as npExt
from pydeep.base.activationfunction import Sigmoid
import pydeep.rbm.model as MODEL
import pydeep.rbm.estimator as ESTIMATOR
import pydeep.misc.measuring as MEASURE
#import pydeep.misc.visualization as VIS
import pydeep.misc.io as IO
import pydeep.misc.toy... |
60b74b4e24a34d25e995d9455c9d6722cae4fa8ce08ef2c69c50c147ac29ffe2 | Python | 10,934 | 320 | """
Created by
@author Shengze Cai
Modified by
@author Mitchell Daneker
Contact Mitchell Daneker with any questions via mdaneker@seas.upenn.edu
"""
import os
os.environ["TF_CPP_MIN_LOG_LEVEL"] = "2"
import tensorflow as tf
if tf.__version__ >= "2.0.0":
import tensorflow.compat.v1 as tf
tf.disable_v2_beha... |
ea2bdcc93dffa29c143fa71bbc2d6754a2c0d11e90b75d07d8a8e653c1e8d61f | Python | 10,944 | 267 | from pathlib import Path
from typing import List, Union
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
import pandas as pd
from omegaconf import DictConfig, ListConfig
from scipy import linalg
from libs.function.function import Log, Standardize
from libs.function.utils import pca
from libs.u... |
e0f7debf2902b7fdd8e47d0848a49fb533c07024c7f9c6fc5d4f7fa695c8df41 | Python | 10,947 | 312 | """Prompt schema definition."""
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING, Any
from pydantic import BaseModel, model_validator
from typing_extensions import override
from langchain_core.prompts.string import (
DEFAULT_FORMATTER_MAPPING,
PromptTemplateFormat... |
99a5a37e85bc0760275a8250d86ec27b836ef095e637a2a611281900a0c02389 | Python | 10,948 | 249 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import ts_preprocess_func
__all__ = ['ts_par6']
class TsPar6(TaskModel):
def __init__(self, **kwargs):
super().__... |
a3802a81a1b2749396fdd6b989a4f349bb3fdea8dd0cba88578177229d7dffdb | Python | 10,948 | 239 | import random
import re
import torch
import nibabel as nib
from data import create_dataset
from .helpers import *
import pandas as pd
import numpy as np
from .util import mkdir
from .metrics import SSIM3D
from monai.metrics import RMSEMetric, PSNRMetric
class PhaseNotDefinedError(Exception):
pass
class NIIVisua... |
22071b33f2d0889357fd84adc510b54f82b897f38d11028fa444d3f8a891df90 | Python | 10,950 | 281 | import math
from e3nn import o3
from typing import Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import Tensor
from torch_sparse import SparseTensor
import torch.nn as nn
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.typing import Adj, OptTensor, PairTensor
f... |
2d34da2afeaa295fcdd2dc7235f340e164d7a6232c6304783e092512d3ce5d7c | Python | 10,953 | 301 | # Copyright 2023 DeepMind Technologies Limited.
#
# 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... |
46a8caa8b8c0ee6a4438699744c06e2f1331c9b5d7fd648bc4379cce659863c2 | Python | 10,956 | 320 | import argparse
from pathlib import Path
from datetime import datetime
import logging
import quantities as pq
import neo
from neo.utils import get_events, cut_segment_by_epoch, add_epoch
from elephant.signal_processing import butter
from elephant.spectral import welch_psd
import numpy as np
import matplotlib.pyplot... |
c00834bc9fd546354abde75bead22c653551b8658326fe83243837ca6ce31ade | Python | 10,959 | 277 | import json
from logging import Logger
import os
from typing import Dict, List
import numpy as np
import pandas as pd
from tensorboardX import SummaryWriter
import torch
from tqdm import trange
from .evaluate import evaluate, evaluate_predictions
from .predict import predict
from .train import train
from HMSA.args impo... |
f2be4e596350e1db79477a4268370fa19e615f359dcb368defc8883b1d78c25c | Python | 10,962 | 312 | from ChipseqReport import *
import Motifs
##########################################################################
##########################################################################
##########################################################################
# Base class for mast analysis
#####################... |
76f4b3d55024361f4e87d6f42d2033927b6fd7f762b5401047bed3f466cb5636 | Python | 10,964 | 357 | """Asynchronous iterator utilities.
Adapted from
https://github.com/maxfischer2781/asyncstdlib/blob/master/asyncstdlib/itertools.py
MIT License.
"""
from collections import deque
from collections.abc import (
AsyncGenerator,
AsyncIterable,
AsyncIterator,
Awaitable,
Callable,
Iterator,
)
from c... |
9e6cdc90aa81091efe3594469dd2aaeb2c95aea2ac26817471b17ebf1e9ae4a6 | Python | 10,966 | 297 | from sklearn.svm import SVC
from sklearn.metrics import accuracy_score
from sklearn.model_selection import StratifiedKFold
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader, TensorDataset
import os
from sklearn.metrics import confusion_mat... |
33076fb443f64b05ec3b0e84894e6aedceb0cdfeb9a6e7a6655938ab3f580ec6 | Python | 10,969 | 294 | r"""A project configuration module that reads config argument from a file; set automatic generated arguments; and
overwrite configuration arguments by command arguments.
"""
import copy
import sys
import typing
import warnings
from os.path import join as opj
from pathlib import Path
import os
import torch
from munch ... |
5e752b1e7afa38a65ccbf1479342251c2147f17a9ce5ea9e38c31b60b7d13fca | Python | 10,973 | 250 | import logging
import os
import random
import time
import numpy as np
import torch
import h5py
from lightning.pytorch.callbacks import Callback
from lightning.pytorch import seed_everything
from lightning.pytorch.utilities import rank_zero_only # don't log twice while training on multiple GPUs
from predmoter.utilitie... |
025689be34b02025bb0d438a0c42c15426d3c26baa12019c9de143f85d828d85 | Python | 10,979 | 259 | import torch
from torch import nn
class NNRELoss(nn.Module):
"""wrapper of loss function for PU learning"""
def __init__(self, prior=None, loss=(lambda x, y: torch.sigmoid(-x*y)), gamma=1, beta=0, transform=True):
super(PULoss,self).__init__()
self.prior = prior
self.gamma = gamma
... |
7449d9c0045205be9265174862352596670c16d66c92a4480796493098257f9f | Python | 10,981 | 182 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
a033505d9d0c4b0b6a6435fc3e1597cb4db173b4828e9bf995ab29242058a82b | Python | 10,981 | 244 | """non-rigid ICP (Amberg et al. 2007), scipy-only.
deforms a template (source) mesh onto a target mesh while preserving the
template's own topology, so every registered patient ends up with the exact
same vertex count/connectivity as the template - useful for a cohort where
you want point-to-point correspondence acros... |
ebb4df53da3b436b18f2ff9c087d6ee870949b5427e976bb5c3fe4e56e055fcd | Python | 10,983 | 229 | import torch.nn.functional as F
import torch
import torch.nn as nn
import math
import escnn
import timeit
# ----------------------------------------------------------------------------------------------------------------------
# GFNO2d
# ---------------------------------------------------------------------------------... |
c3a32755256fb7925c012520df311a0d641af72a9190e91cc151cca157271ef2 | Python | 10,989 | 318 | import hashlib
import logging
import json
import os
from typing import Any, Dict, List, Optional
from pathlib import Path
import hydra
import lightning.pytorch as pl
import omegaconf
import torch
import wandb
from lightning.pytorch import Callback
from omegaconf import DictConfig, ListConfig
from lightning.pytorch im... |
fc92d60b5a42a5532c0133b98a38f0ceaa5c2609612e02153e39d2b746a268a1 | Python | 10,994 | 306 | # This file uses sklearn library to setup ML model comparison experiment with cross validation
# It will write out files to an 'out' directory that it will try to create
import time
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.preprocessing import PolynomialFeatures, F... |
8d95ec0ae02d3a36f8269232e0c4fa7b74e5632e00c52118599d7d30ae6fbc22 | Python | 11,000 | 323 | import os, glob, sys
from collections import defaultdict
import openfold.np.protein as protein
import openfold.np.residue_constants as rc
import torch
import openfold.data.data_transforms as dt
import openfold.data.data_pipeline as dp
import openfold.data.input_pipeline as ip
import openfold.data.feature_pipeline as Fp... |
1d23f719ffd4fc55a69a0bbee1c9d113e4c088db689f73633573f63bdf1a50a8 | Python | 11,003 | 287 | import torch
import numpy as np
import torch.nn as nn
from timm.models.layers import trunc_normal_
from pdearena.models.transolver.model.Embedding import timestep_embedding
from pdearena.models.transolver.model.Physics_Attention import Physics_Attention_Structured_Mesh_2D
from pdearena.configs.config import CFDConfig
f... |
38b69aba290240d45dd91541fff6fa42e2899a1193045ddaebcae7a1eae58c8f | Python | 11,003 | 394 | """
pipeline_expression.py - analysis of expression data
====================================================
Purpose
-------
This pipeline predicts gene that are differentially expressed.
This pipeline uses the bioconductor package.
Usage
-----
Type::
python <script_name>.py --help
for command line help.
C... |
4d7cf66f5566815775df97c52066d4430ed54c51c564bb7663504d2f3b971a39 | Python | 11,006 | 324 | #
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.parameter import Parameter
from torch.nn.modules.module import Module
from functools import partial
def sce_loss(x, y, alpha=3):
x = F.normalize(x, p=2, dim=-1)
y = F.normalize(y, p=2, dim=-1)
# loss = - (x *... |
94091a84a546f4cbc63afa412055d32719106b93b17e0c2e72f2c2f9300a4aa6 | Python | 11,007 | 328 | #!/usr/bin/env python3
from collections.abc import Hashable, Iterable
from pgmpy.utils.types import Self
__all__ = ["_GraphRolesMixin"]
class _GraphRolesMixin:
"""Mixin class for handling roles in a causal graph."""
def get_role(self, role: str):
"""Return list of nodes in graph G with a specific r... |
a1a0fdd0aae58bf26ed54832c0f8f7f573e6ef55f7b400bc2d820afe4a12676c | Python | 11,007 | 229 | import pandas as pd
import argparse
from utils import set_seed
import numpy as np
import wandb
import os
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from torch.nn import functional as F
from torch.cuda.amp import GradScaler
from model import GPT, GPTConfig
from trainer import Trainer, Tra... |
ea74b7edb308f6957c4df26e512eef315e02a97b2430e9d4be2641dea6e5892e | Python | 11,011 | 258 | # MIT License
#
# Copyright (c) 2022 Matthieu Kirchmeyer & Yuan Yin
import torch
from torch import nn
from .utils import *
from functools import partial
import torch.nn.functional as F
from torch.quasirandom import SobolEngine
import copy
import numpy as np
nls = {'relu': partial(nn.ReLU),
'sigmoid': partial(... |
8b28a745ba19821d0a0894b5482926fb280e5305d0bb832e0e5d44faa50464b5 | Python | 11,013 | 252 | # Copyright 2019 DeepMind Technologies Limited. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... |
3404e21f170a7a27b15adfc8163b7443f0e8dd3fb096a744429a3264512c600d | Python | 11,016 | 294 | """The script to test all layers and SELU activation properties hold."""
import pytest
import numpy as np
import math
import copy
from functools import reduce
import torch
import torch.nn as nn
from torch.nn import modules
from vulcanai.models.layers import BaseUnit, ConvUnit, DenseUnit
from vulcanai.models.utils impor... |
9a1c110cdd1aca88650d8512356ad00fb15e369343988ea59f75caf6a3286f7e | Python | 11,025 | 249 | from typing import Sequence, Union, Any
from collections import OrderedDict
from numpy import inf, exp
import pandas as pd
from hbayesdm.base import TaskModel
from hbayesdm.preprocess_funcs import pstRT_preprocess_func
__all__ = ['pstRT_ddm']
class PstrtDdm(TaskModel):
def __init__(self, **kwargs):
sup... |
96509c4b99500559eaa8d8d46e645fab4516fda9114a1994c553ab5870ab098d | Python | 11,026 | 217 | import os
from copy import deepcopy
from collections import OrderedDict
from itertools import groupby
import warnings
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import matplotlib.font_manager
from matplotlib.colors import ListedColormap
from matplotlib.cm import get_cmap
import scipy.stats as... |
bbd65c9fb63b1d960b4b64f3510daf0fd54cebe619ab72649fbe4bc45dbbe0c7 | Python | 11,032 | 343 | ###########################
# Latent ODEs for Irregularly-Sampled Time Series
# Author: Yulia Rubanova
###########################
import numpy as np
import torch
import torch.nn as nn
from torch.nn.functional import relu
import lib.utils as utils
from lib.encoder_decoder import *
from lib.likelihood_eval import *
f... |
0dd148f935c0434a67cc29e5a0ff9f37a7fec33768244536e37f9997b74345da | Python | 11,035 | 291 | """
Analyze the information gain afforded by a single outcome
in different studies previously conducted.
Information gain is measured by the KL divergence between the prior and
the posterior (having observed a single outcome),
using the prior as reference distirbution.
Note that this is a standard way of measuring in... |
93c20c0036f0c393d1d0e7d36d21e4a345622547aab99e784182749dd1ce7b83 | Python | 11,036 | 305 | """Compute conn (PID | II) + stats across condition in the time domain.
This script can :
- Compute connectivity metrics like conn_pid and conn_ii
- Perform RFX-contacts on ii (two-tailed), redu | syn | redu - syn | syn - redu
(one-tailed)
- Computations are performed within conditions (i.e. rew | pun)
- Significanc... |
d8d20f5e0fdfd65a706840e68a48ca86ec724bcebea57f0cc146f7de6611ff83 | Python | 11,041 | 293 | import os
import sys
import re
import types
import itertools
import matplotlib.pyplot as plt
import numpy
import scipy.stats
import numpy.ma
import Stats
import Histogram
from cgatReport.Tracker import *
from cpgReport import *
##########################################################################
class UniqueIn... |
056bf4406a77ac38d514ecf920ad8bda7e48a80806e840c467cee5cf2364a9a5 | Python | 11,047 | 290 | import os
import time
import pickle
import numpy as np
import torch
from torch.optim import lr_scheduler
from torch.nn.init import xavier_normal,xavier_normal_
from torch import nn
import torch.utils.data.sampler as sampler
from config_PPI import DefaultConfig
from model_PPI import DGCNN
import data_generator_PPI
fr... |
07b31581f9b2c40aad76af0d69656bb16eee42ecebcff928327ee9154d69b1db | Python | 11,054 | 336 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from opt_einsum import contract as einsum
import copy
import dgl
from rfdiffusion.util import base_indices, RTs_by_torsion, xyzs_in_base_frame, rigid_from_3_points
def find_breaks(ix, thresh=35):
# finds positions in ix where th... |
466009cac9a281fb50e1a1c554a132f73307f94476675dc11bed3221c68f82a3 | Python | 11,055 | 328 | '''tasks for running a trained model on new data.
'''
import logging
import os
import luigi
from luigi.util import requires
import pandas
import numpy as np
from retchat.models import load_model
from keras.backend import clear_session
from .ioutils import imread_raw
from .predutils import Preprocessor
from .preduti... |
d58d1a07244e427d712ac002ab95fd7b9da368706016d17667add5564eb3129c | Python | 11,056 | 328 | '''tasks for running a trained model on new data.
'''
import logging
import os
import luigi
from luigi.util import requires
import pandas
import numpy as np
from retchat.models import load_model
from keras.backend import clear_session
from .ioutils import imread_raw
from .predutils import Preprocessor
from .preduti... |
8bac1ae5a03da74be32beb3fbb98d83f8e139ee286c54a8349fe39b5c70e8851 | Python | 11,057 | 328 | '''tasks for running a trained model on new data.
'''
import logging
import os
import luigi
from luigi.util import requires
import pandas
import numpy as np
from retchat.models import load_model
from keras.backend import clear_session
from .ioutils import imread_raw
from .predutils import Preprocessor
from .preduti... |
a0aa77bcc8a8ecf0f957102fbacebdf6d0b7c3613c013075d09d806b769fb668 | Python | 11,061 | 137 | from OCC.Core.BRepAlgoAPI import BRepAlgoAPI_Cut, BRepAlgoAPI_Fuse
from single_feature import (BaseSheet, FlangHole, Swelling, BendGroove, Rib, Rip, CommonHole, CommonGroove, Vent,
Array, ProfiledGroove, ProfiledArray, Bend, Roll, EarPlate)
class Compound(object):
def __init__(self, fl... |
dcd6dc964f4066f293a39e81ef8f32f85f9d576c01c294875f9b456bcc1a42f0 | Python | 11,061 | 382 | from pdearena import utils
from pdearena.modules.twod_resnet import DilatedBasicBlock
from pdearena.modules.conditioned.twod_resnet import (
FourierBasicBlock as CondFourierBasicBlock,
DilatedBasicBlock as CondDilatedBasicBlock
)
MODEL_REGISTRY = {
## sinenet: zeros
"sinenet1-dual-128": {
"cla... |
3befe7a47e1d5f9a26382f19373dd4f8151af969a1188d6e56319b58f527cef7 | Python | 11,066 | 256 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
23602d73a8df4f799d874fff05b4e4e1a5deb137d60cf53deb28225d50c8c948 | Python | 11,067 | 216 | # -*- coding: utf-8 -*-
# @title Hodgkin & Huxley parameters
# @file Hhparam.py
# @author Romain Beaubois
# @date 05 Dec 2022
# @copyright
# SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief Class to generates HH n... |
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