sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
98a8579af26bccde69ab42b8d7336df4a50b48539ac0140d31ed4598d3e1d3b9 | Python | 4,534 | 177 | from numbers import Number
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import puffbird as pb
import seaborn as sns
import proplot as pplt
from scipy.stats import norm
from chreyesees import utils
from chreyesees import WLS
import dreye
from scipy.spatial import convex_hull_plot_2d, ConvexHull... |
b9f55b8067627e542d2f8b45df0473d91e86fd6009c1c146b2a835b5e7e673be | Python | 4,534 | 122 | # Inspired by https://github.com/NVIDIA/NeMo/blob/main/nemo/collections/common/metrics/perplexity.py
# But we compute the perplexity correctly: exp(average(nll)), not average(exp(nll))
# Also adapted from https://github.com/Lightning-AI/metrics/blob/master/src/torchmetrics/text/perplexity.py
# But we pass in the loss t... |
674e2bf3adea2ea9de765805bccd40c529df478389ce7da30a8b308dc2efb71b | Python | 4,535 | 109 | # Copyright (c) MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, so... |
dac6a16324c31cd576c40946d1c85542ecc2f08da9d00cda48598437b17188ea | Python | 4,535 | 108 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
7a8fbc7874d10d8a8e345e6ac4409d1461b881380ab70604697b310c8681f6ea | Python | 4,538 | 116 | # Copyright (c) <2021> <University of Paderborn>
# Signal and System Theory Group, Univ. of Paderborn, https://sst-group.org/
# https://github.com/SSTGroup/independent_vector_analysis
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated d... |
fdb919b08ab2264c8cdf5ccb5b5213d2f0731aa9a95456c6dfeb78374aa086d0 | Python | 4,538 | 123 | # 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... |
075c75b810c0f95faed05fe620c147b9eb309a4b79d49c322164e6014e41381d | Python | 4,541 | 118 | # Copyright Generate Biomedicines, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to ... |
5ea0a9e489772d152b76a710ee9ff8b6d5c3b27c467ed1da13281c8780cdb3b1 | Python | 4,541 | 113 | #!/usr/bin/env python
"""Tests for `MRdataset` package."""
import shutil
import tempfile
from pathlib import Path
import hypothesis.strategies as st
import pytest
from hypothesis import given, settings, HealthCheck
from MRdataset import import_dataset
from MRdataset.tests.simulate import make_compliant_test_dataset... |
61737b928c43acb44ba27ae2f43c4531e4e3aabad41898b90e9291e51cbda113 | Python | 4,542 | 141 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
055ea54a78b9ff9531244cfff26e2fa7e0a45c6e506edcbcc1b83dfedc4c458a | Python | 4,543 | 141 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
9db83cfeda18280a12a46917f30939fdba1fca68db72f5abc22cd724dc8b8cc9 | Python | 4,544 | 113 | nameModelBase = 'MHATT_bonds_deeper_benchmark_clipping_weights'
logfile = open('Log_MHATT_bonds_deeper_benchmark_clipping_weights.txt','w')
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
import pandas as pd
import rdkit, rdkit.Chem, rdkit.Chem.rdD... |
c7c20e1588e7204688632b8627f2d4ce438c5c60fb075357f372ed7b16082863 | Python | 4,544 | 97 | import sys
sys.path.append('..')
from src.utils import set_random_seed
import argparse
import torch
from torch.utils.data import DataLoader
from torch.optim import Adam
from torch.nn import MSELoss, BCEWithLogitsLoss, CrossEntropyLoss
from torch.utils.tensorboard import SummaryWriter
from torch.utils.data.distributed ... |
44805942c4f50d5cc5da872a36beb36add0846133e019f9e34ceb5a3060d5075 | Python | 4,545 | 113 | nameModelBase = 'MHATT_bonds_deeper_benchmark_clipping_weights'
logfile = open('Log_MHATT_bonds_deeper_benchmark_clipping_weights.txt','w')
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
import pandas as pd
import rdkit, rdkit.Chem, rdkit.Chem.rdD... |
70cf61138d278420b4c0a1b282a40a3b2153159c1856ba2a74e618089abf12d0 | Python | 4,545 | 137 | from collections.abc import Sequence
import pytest
from langchain_core.chat_history import (
BaseChatMessageHistory,
InMemoryChatMessageHistory,
)
from langchain_core.messages import BaseMessage, HumanMessage
@pytest.mark.parametrize(
"history_class", [BaseChatMessageHistory, InMemoryChatMessageHistory]... |
9db6a97627418e4c8288a38fa3abf657d669984b49616f3aeb78d2f4c9c954c3 | Python | 4,545 | 113 | nameModelBase = 'MHATT_bonds_deeper_benchmark_clipping_weights'
logfile = open('Log_MHATT_bonds_deeper_benchmark_clipping_weights.txt','w')
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
import pandas as pd
import rdkit, rdkit.Chem, rdkit.Chem.rdD... |
e7104a2a36c1ed49a873877692eed649b83740c7f8690bf917dd9c555b7ecf4f | Python | 4,546 | 155 | from openff.toolkit.typing.engines.smirnoff.forcefield import ForceField
from openff.toolkit.typing.engines.smirnoff.parameters import (
ConstraintHandler,
ElectrostaticsHandler,
LibraryChargeHandler,
VirtualSiteHandler,
vdWHandler,
)
from openff.units import unit
from openff.units.elements import S... |
1a8f688212a510cff08f567885f7b877b4beb108043ad1fadafa2ede72f2342f | Python | 4,547 | 150 | import torch
import numpy as np
def calc_dmap(xyz, epsilon=1e-12, backend="torch"):
if backend == "torch":
B = torch
elif backend == "numpy":
B = np
else:
raise KeyError(backend)
if len(xyz.shape) == 2:
if xyz.shape[1] != 3:
raise ValueError(xyz.shape)
e... |
b7c217de02da79a25f86fe584729bf63cf7e50cea4fb70b620317aa5280e11f0 | Python | 4,547 | 141 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
34d33ba30b275e6941dfc7a72904ad50c8e4f97ccd6c99eae44d91147c31a91d | Python | 4,548 | 141 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
59f9d7feb57ced83a0cccf52bd09b4857fea6202e6f510c8610fc1a2b9638431 | Python | 4,548 | 89 | """Mask, resample and normalize scalar channels with reusable stage outputs."""
import argparse
from pathlib import Path
import shutil
import subprocess
import sys
if __package__ in (None, ''):
sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
import nibabel as nib
from preprocessing.cache import vali... |
a545d6b28033852ed04a7fd225e4345dd3159a0027db8440244dd041dd9844a4 | Python | 4,548 | 132 | # This file is a part of the `allegro` package. Please see LICENSE and README at the root for information on using it.
import torch
from ._contract import Contracter
import itertools
from typing import Dict
# we do lazy imports of cueq to allow `nequip-package` to pick this file up even if cueq is not installed
# s... |
f94471969dec58f9b8e5c1037ebf18e34965d79e906bdfef531087639f9e653d | Python | 4,548 | 76 | import torch
from .rk_common import _ButcherTableau, RKAdaptiveStepsizeODESolver
A = [ 1/18, 1/12, 1/8, 5/16, 3/8, 59/400, 93/200, 5490023248/9719169821, 13/20, 1201146811/1299019798, 1, 1, 1]
B = [
[1/18],
[1/48, 1/16],
[1/32, 0, 3/32],
[5/16, 0, -75/64, 75/64],
[3/80, 0, 0... |
ff11522840a7c6637a2d70dae69e018618011d9f5284926a410169a3924edb74 | Python | 4,548 | 65 | """Re-run the conformal variants affected by the audit fixes (run AFTER final_cpu.py finishes):
weighted : covariate-shift weighted conformal with CROSS-FITTED calibration weights
sm_weighted : shift-matched scores + cross-fitted weights
shift_matched_bal : shift-matched pool with each source da... |
9259a3fbceead0900fc939ab12c49587f9c21a095e66043de36183e94bd69d86 | Python | 4,549 | 113 | #nameModelBase = 'MHATT_bonds_deeper_benchmark_clipping_weights'
#logfile = open('Log_MHATT_bonds_deeper_benchmark_clipping_weights.txt','w')
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
from sklearn.neighbors import KernelDensity
import pandas as pd
import rdkit, rdkit.Chem, rdkit.Chem.r... |
bc342d74f6a45fad3c08a173c1760d30702229aa8a9f331e65974268b4b2e097 | Python | 4,549 | 165 | # adapted from https://github.com/papkov/noise2same.pytorch/blob/d65d5a10f35208f43aed92f3a750025cb9a03a39/noise2same/network.py
# translated from
# https://github.com/divelab/Noise2Same/blob/main/network.py
# https://github.com/divelab/Noise2Same/blob/main/resnet_module.py
from functools import partial
from typing impo... |
f4cf18a8f9b3d4e44f29796a380475f1380b8e425114b803c10306433c3f130c | Python | 4,551 | 144 | from typing import Dict, List, Sequence, Union
import arviz as az
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from hbayesdm.base import TaskModel
__all__ = ['rhat', 'print_fit', 'hdi', 'plot_hdi', 'extract_ic']
def rhat(model_data: TaskModel,
less: float = None) -> Dict[str, Uni... |
446dd0ca227742fb0e2790e478dcb0cbdb52102dbff9626bd16920c065ade32b | Python | 4,555 | 123 | import platform
from pathlib import Path
import numpy as np
import pytest
from astrocast.analysis import Events
from astrocast.detection import Detector
from astrocast.helper import EventSim, SampleInput
from astrocast.preparation import IO
class TestDetector:
@pytest.mark.parametrize("extension", [".h5"])
... |
b8ec7ce34c4d3ebd5d1352240e527267fe8a9ebd6f01d47af6758c1a54072132 | Python | 4,556 | 118 | from ..utils.utils import *
def build_annotations(
container,
annotation,
t_ref,
wlid_ref,
n_ref,):
"""Load and handle annotations from annotations.h5 file.
Annotations are loaded and sorted according to user arguments, and used to
populate an empty results array. This array will be f... |
de155473a985f389f4d0e7c39f404d587593829430c466ca8298232d53d7d4b7 | Python | 4,558 | 158 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
37d576c527563042c61164fd9c2755773587d5cddb2c7ae30789b647733bd5a9 | Python | 4,559 | 140 | ''' Example using BB-RBMs on the MNIST handwritten digit database.
:Version:
1.0
:Date:
06.06.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute i... |
c110c776ebdfa15dcd7386e8e9e0e00c8680c2d70c9d72c432555939dc25170f | Python | 4,559 | 158 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
e04b92049cf7f333506a22e21d376dffe19ab8bb2ff668ac3c358ff8a9a3f4de | Python | 4,561 | 110 | import os
import argparse
import numpy as np
import pandas as pd
import random
random.seed(49297)
from tqdm import tqdm
def process_partition(args, partition, sample_rate=1.0, shortest_length=4.0,
eps=1e-6, future_time_interval=24.0):
output_dir = os.path.join(args.output_path, partition)
... |
185ed9d1ea3765b8963ec05673f73935a63f418bbe0dd2a0160560512eac8586 | Python | 4,562 | 112 | """
Module to generate figures related to functional imaging during optogenetic stimulation of flies for which the VNC was cut.
Author: jonas.braun@epfl.ch
"""
import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.backends.backend_pdf impor... |
2c55d8370dbb9421238f02bf82b0040d20c137aa0dd1cebf15b137f87c2a471a | Python | 4,563 | 133 | import pytest
import torch
from e3nn import o3
from e3nn.util.test import assert_equivariant
from nequip.utils import torch_default_dtype, dtype_from_name
from nequip.utils.versions import _TORCH_GE_2_6
from allegro.nn._strided import Contracter
_TRITON_INSTALLED = False
_CUEQ_INSTALLED = False
if _TORCH_GE_2_6:
... |
6224b6795926be2f855e6a5c21e3c59d83ca280b1e9e6114b4ea44fe08e11587 | Python | 4,563 | 133 | from typing import Callable, Dict
import torch.nn as nn
from e3nn.nn import Gate
from e3nn.o3 import Irreps
from e3nn.util.jit import compile_mode
import hienet._keys as KEY
from hienet._const import AtomGraphDataType
@compile_mode('script')
class EquivariantGate(nn.Module):
"""
wrapper of e3nn.nn Gate (equ... |
6613d843fe67c9e6b46ac93538c1e32e1c39fbba4ba3d00884b046d8aa82d595 | Python | 4,564 | 117 | """
Implementation of Hao et al., 2018's method to obtain tissue-specific proteins
Hao, Y., Quinnies, K., Realubit, R., Karan, C., & Tatonetti, N. P. (2018). Tissue‐Specific Analysis of Pharmacological Pathways. CPT: Pharmacometrics & Systems Pharmacology, 7(7), 453–463. https://doi.org/10.1002/psp4.12305
"""
import ... |
c6021f8de833c469e6fb8444ccb570db3039f23b73d922676f73f32fc58743a9 | Python | 4,564 | 141 | import os
import time
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow.keras import backend as K
import numpy as np
'''
References:
github.com/eriklindernoren/Keras-GAN
https://www.tensorflow.org/tutorials/quickstart/advanced
https://www.tensorflow.org/tutorials/generative/dcgan
'''
BCE_... |
c7b4ae0cf123995f1d67dd18b21746fd2ffa9d32ab450868b6f616e7f9f84543 | Python | 4,564 | 121 | from torch.utils.data import DataLoader
import torch
import numpy as np
from torch import nn,optim
from bestmodel import MyModule
from Dataset import MyDataset
import sklearn.metrics as m
from tqdm import tqdm
import os
def RMSE(y_true, y_pred):
return np.sqrt(m.mean_squared_error(y_true, y_pred))
de... |
8b478fcb44ae5ea877848d65f64ff9aa65ef3b54e27d87b12dd7376495dfd903 | Python | 4,566 | 133 | from PyQt5.QtWidgets import QMessageBox
from sklearn.preprocessing import PolynomialFeatures
from sklearn.linear_model import LinearRegression
from enum import Enum
import json
import cv2 as cv
import numpy as np
def check_is_valid_int(n, err_msg, min_val=1, max_val=None):
show_err = False
if isinstance(n, flo... |
20130b131fdb00b04ab966cb35144aa99c5f869a42eccd5d20b2d517d2822ff4 | Python | 4,567 | 157 | # Read and write data from disk.
#
# A dataset is a single folder. To get data from the folder, you need to create
# a file called "getters.py" containing functions that return data and
# metadata.
#
# Authors: vivekv2@gmail.com
from functools import lru_cache, partial
import importlib.util
import json
from pathlib im... |
6fbcf10d7f0e2f61f20f0935d9e21bf41b48ce8590bcd8d606ee3cea4037d300 | Python | 4,569 | 152 | #!/usr/bin/env python3
"""
Calculate an optionally padded ROI for a single probabilistic label
Author
----
Mike Tyszka, Caltech Brain Imaging Center
License
----
This file is part of atlaskit.
atlaskit is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public Licens... |
77317dc2102b41746ba4431d40f5c794ef6ad7cc1d0815d52e8e9a837dfdf9ab | Python | 4,570 | 149 | """
Write OPC parameters into a SMIRNOFF force field.
Based on ambertools-22.0-py310h206695f.
Water Lennard-Jones parameters and geometry from $AMBERHOME/dat/leap/parm/frcmod.opc3
Water hydrogen charge from $AMBERHOME/dat/leap/lib/solvents.lib
Ion Lennard-Jones parameters from $AMBERHOME/dat/leap/parm/frcmod.ionslm_126... |
ad657efebb21dc31f6e552f0b8515deaded2af18f15eb5ee4daaacc9816926e4 | Python | 4,570 | 91 | import os
import argparse
import pandas as pd
from tqdm import tqdm
def is_subject_folder(x):
return str.isdigit(x)
def main():
n_events = 0 # total number of events
empty_hadm = 0 # HADM_ID is empty in events.csv. We exclude such events.
no_hadm_in_stay = 0 ... |
54f9a986716d0ce4dda8a306e028ebea6a27d5c2d4aee25bc40b87c97e097172 | Python | 4,572 | 137 | # Copyright (c) <2021> <University of Paderborn>
# Signal and System Theory Group, Univ. of Paderborn, https://sst-group.org/
# https://github.com/SSTGroup/independent_vector_analysis
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated d... |
6ea85b1471a6345faa9f9e11a925fe97a1872420c000712656248b74d0770357 | Python | 4,572 | 132 | from typing import Optional, List, Tuple
import numpy as np
from .fingerprints import (
create_RDKFingerprint,
merge_bit_fingerprints,
weight_sum_fingerprints,
reduce_fp_set,
apply_reduction_fp_set,
create_AtomicPairFingerprint,
)
from ._types import FingerprintFunction, PfpData
from .utils impo... |
b2798105d68d14f843f2c88be0fe5a34e1dc1026cf2bef61d49a93ff2ecc1578 | Python | 4,572 | 112 | import argparse
from pathlib import Path
from MRdataset import import_dataset, save_mr_dataset, logger
from MRdataset.utils import is_writable
def get_parser():
"""Parser for MRdataset"""
parser = argparse.ArgumentParser(
description='MRdataset : generates dataset for analysis',
add_help=Fals... |
c45cf0cf53ef7dd1ed6b2108a7ab9203ac7dda80805a6d780a5684bc0b7d4445 | Python | 4,572 | 129 | ''' Toy example using BB-RBMs on Bars and Stripes.
:Version:
1.0
:Date:
06.06.2016
:Author:
Jan Melchior
:Contact:
JanMelchior@gmx.de
:License:
Copyright (C) 2016 Jan Melchior
This program is free software: you can redistribute it and/or modify
... |
fd02dba2b768b5293b86498bf9cf947986fa7dd3f4710b74e434aa9096dba099 | Python | 4,573 | 114 | '''
concatenate all .rhd files into a single .mda
this line is inserted with vi. feels good
'''
import os
import gc
import warnings
from copy import deepcopy
import numpy as np
import pandas as pd
from scipy.io import loadmat, savemat
from load_intan_rhd_format import read_data, read_header, get_n_samples_in_data
fr... |
a946ac7ee3ac47c3e310fa7a4c45a02ab0c9c51c4d97493a2c7177f04732cbef | Python | 4,574 | 101 | '''
read channel info
8/31/2022 jz103
'''
import os
import gc
import warnings
from copy import deepcopy
from time import time
import re
import datetime
import json
import numpy as np
import matplotlib.pyplot as plt
SESSION_NAMING_PATTERN = r"[A-Za-z_ ]+_([0-9]+_[0-9]+)"
VALID_SESSION_LAMBDA = lambda x: (('_' in x) a... |
ea495f787b85e465a43bb284c9512bcd2a04696456051b8ccf2069180d4b32d9 | Python | 4,574 | 108 | import numpy as np
import torch
torch.set_printoptions(precision=4, sci_mode=False, threshold=5000)
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
plt.rc('savefig', format='pdf', bbox='tight')
plt.rc('font', size=8)
#plt.rc('legend', fontsize=8)
from data import generate_recog_data... |
36fbd060a407e2951295362f8567111961ed0dea8648f1cdab69c382e6e96548 | Python | 4,577 | 93 | import os
int_or_none = lambda x: int(x) if x is not None else None
str_list_or_none = lambda x: x.strip().split(',') if x is not None else None
int_list_or_none = lambda x: int(x.strip().split(',')) if x is not None else None
eval_if_str = lambda x: literal_eval(x) if isinstance(x, str) else x
class Config:
def __... |
ddfaf0be1e876652645efdd97cba073106d789cc76ad683ae4ee49c532d9337a | Python | 4,577 | 85 | import enum
import numpy as np
"""Parses the raycast observations from AnimalAI and returns a shortened version with only relevant objects"""
class RayCastObjects(enum.Enum):
"""Enum for the parsed objects from the raycast"""
ARENA = 0
IMMOVABLE = 1
MOVABLE = 2
GOODGOAL = 3
GOODGOALMULTI = 4
... |
fe6c6a52c810adc100d3f2b117bb2f5db68c8bb4070f1a5079abb01ee766fe06 | Python | 4,577 | 112 | #! /usr/bin/env python2
import subprocess, time, os, sys
LOCAL_DIR = '/Users/danil/My/School/Columbia/Research/ongoing_plasticity/'
REMOTE_SYNC_SERVER = 'dt2586@habaxfer.rcs.columbia.edu' #must have ssh keys set up
REMOTE_SERVER = 'dt2586@habanero.rcs.columbia.edu'
REMOTE_PATH = '/rigel/home/dt2586/ongoing_plast... |
5167d261e1f0b23c24099da3e2ae8e0f2406fb6abbdfdabad8c63fb1dc3b9477 | Python | 4,583 | 118 | import sys
import os
import numpy as np
import torch
import torch.utils.data as du
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import util
from util import *
from DrugGene_Network import *
import argparse
from sklearn.preprocessing import MinMaxScaler
def predict_drugGene... |
77550925eed8a002460dbd1f2c538ad41944bf19e1d706062938c6e6df575ac5 | Python | 4,583 | 148 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import os, sys
import numpy as np
import pandas as pd
from bed_reader import open_bed
# sys.path.append('/u/home/z/zhengton/project-sriram/wes/scripts/gene_h2/')
# sys.path.append('/u/project/sriram/zhengton/wes/scripts/gene_h2/')
from regional_her import RegionalHer
... |
25e34f043dc14b9745115086d8dd79fe3505850a1a1f512f429a5cb17ba563fa | Python | 4,584 | 93 | """
Find the optimal combination of hyperparameters
"""
import numpy as np
from hyperopt import fmin, tpe, hp, STATUS_OK, Trials
from keras.models import Sequential
from keras.layers import Dense, GRU, Dropout
from keras.layers.embeddings import Embedding
from keras.layers.core import SpatialDropout1D
from keras.opti... |
5978b2800b01f71dee1f6509a412f4ea0e50a94e2937fc53423cddf863f35c4a | Python | 4,587 | 135 | import msgpack
# import h5py
import os
import numpy as np
import torch
from torch.utils.data import BatchSampler, DataLoader, Dataset, SequentialSampler
import argparse
def batch_stack(props):
"""
Stack a list of torch.tensors so they are padded to the size of the
largest tensor along each axis.
Para... |
de00879503aac638f3e3e119db623b1838614b095752041ee85643ec1f65c182 | Python | 4,587 | 135 | import contextlib
from typing import Any
from langchain_core.callbacks import (
UsageMetadataCallbackHandler,
get_usage_metadata_callback,
)
from langchain_core.language_models import GenericFakeChatModel
from langchain_core.messages import AIMessage
from langchain_core.messages.ai import (
InputTokenDetai... |
1df77504705a765bfbbad5ef666b4f13fa62af3f0c5e8c69b6917985d965a912 | Python | 4,588 | 133 | # Load in data of Birds Dataset (CUB_200_2011)
import scipy.io
import numpy as np
from os import listdir
from os.path import isfile, join
from PIL import Image
# Paths to files, change if necessary.
LABELS_PATH = '../../data/data_birds/CUB_200_2011/image_class_labels.txt'
TRAIN_TEST_SPLIT_PATH = '../../data/data_bir... |
42d32f634a4f91a515416eab102f3f127d2f4eb747858c0d51fd2b1076cd1936 | Python | 4,588 | 114 | #!/usr/bin/env python
import gzip
import glob
import sys
import os
import tempfile
import subprocess
import math
from joblib import Parallel, delayed
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot
import matplotlib.font_manager
def dformat(xxl):
x = xxl if type(xxl) is str else xxl[0]
xx =... |
95f0cb84669503a385162c40c332391852f354a3949f40a30997ed8c30cbc568 | Python | 4,589 | 122 | # -*- coding: utf-8 -*-
"""
Created on Thu May 30 23:46:20 2019
@author: Iluva
"""
import matplotlib.pyplot as plt
import collections
def plot_curve(curve, xs, ys_mean, ys_upper, ys_lower, ax, color, hatch, alpha, line, title, **kwargs):
title = 'ADNI test' if title=='test' else title
assert curve in ['roc',... |
0e92943f6880b2600a75022cdac72530bf9b104c40865c4ab1956dfd1b571aee | Python | 4,592 | 129 | # FCN model
# when tuning start with learning rate->mini_batch_size ->
# momentum-> #hidden_units -> # learning_rate_decay -> #layers
import tensorflow.keras as keras
import numpy as np
from sklearn.model_selection import train_test_split
import time
import tensorflow as tf
from utils.utils import save_logs
from utils.... |
42bac5cb2b50a67ed9d3217e27938197c026a062e9d854ef3f438ed21b605d7d | Python | 4,592 | 81 | """Printed font size of text inside figures, measured in the compiled PDFs.
Figures are embedded as vector PDFs, so their text survives as real text spans whose size in the compiled document is the size a
reader sees. This script finds every figure image block on each page, collects the text spans that lie inside it, ... |
68fb3da59a5e66bce8920203a52804cca83c4edd6bfab0166b6bc465c33266e0 | Python | 4,593 | 143 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
cb44c29d656027002b613776e4286c909d29b1956c0a8717ce153c05fda36180 | Python | 4,594 | 143 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
fd097379e9895d337672103f5aa5f629ef9a45eb98b1a691b59371834a21bd0a | Python | 4,595 | 145 | 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.data import reorder_ica_components
from helpers.hcp import scan_id_to_scan_name
def plot_brain_state_cluster_centroi... |
11f8581609ebdb7867b4abfa3bddc9dbd782fda7f8d8e4b14926f6f84f047b6e | Python | 4,596 | 140 | """Test groq block translator."""
from typing import cast
import pytest
from langchain_core.messages import AIMessage
from langchain_core.messages import content as types
from langchain_core.messages.base import _extract_reasoning_from_additional_kwargs
from langchain_core.messages.block_translators import PROVIDER_... |
e6a1128ddc62a866921db044fd71b73776718270a272b5879ed6c833ca06918a | Python | 4,596 | 128 | # coding=utf-8
from pyexpat import features
import torch
import torch.nn as nn
import torch.nn.functional as F
from alg.modelopera import get_fea
from network import common_network
from alg.algs.base import Algorithm
import numpy as np
import re
from torch.cuda.amp import autocast
class Vanilla(Algorithm):
"""
... |
ebd9401b22b65e26301590a668b4fe5ebd018ba6c0551704f33116233ee8a197 | Python | 4,597 | 115 | """unit tests for api/sessions.py's Session.snapshot_target/restore_target/
switch_active_target - the per-target scene snapshot that lets the frontend
switch between cranial and facial without re-running align/clip/run against
whichever target it switches back to. pure dataclass-field tests, no
FastAPI/pipeline needed... |
a8eebce509c36e713e8f6c1b19fb42f253efe3652de3e4b35a93182a7ee38016 | Python | 4,601 | 138 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
a83ba1254c7307cff0b038ce067bfd034c037b7c414917d262196aaa85cdb69d | Python | 4,602 | 138 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
dcfc4c6c4cef3d458de0e5da3d36a789e9564e6806eb5f67e2a9b0c83273ffc6 | Python | 4,602 | 193 | """Pydantic model for default configuration and validation."""
"""Implementation based on the template of ALIGNN."""
import subprocess
from typing import Optional, Union
import os
from pydantic import root_validator
# vfrom pydantic import Field, root_validator, validator
from pydantic.typing import Literal
from matf... |
22e3284f218a008475d2d1fe9672391bf78f1a059c03a5ddfb89a1fdac4c1833 | Python | 4,604 | 138 | """
This script summarized DE results.
"""
import numpy as np
import pandas as pd
import session_info
from pyhere import here
from functools import lru_cache
@lru_cache()
def get_annotation(feature):
"""
Get the annotation file based on feature.
"""
feat_lt = {"genes": "gene", "transcripts": "tx",
... |
503386eaf93d46da4a2e2352c81a3edc7c6eed583a5015c550277d645c7a25fb | Python | 4,610 | 117 | # Copyright (c) <2021> <University of Paderborn>
# Signal and System Theory Group, Univ. of Paderborn, https://sst-group.org/
# https://github.com/SSTGroup/independent_vector_analysis
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated d... |
2055331e8f3991431cf8366593ef4b29f605985b8bb4ecfef87bb63623de3480 | Python | 4,611 | 155 | """SSRF Protection - thin wrapper raising ValueError for internal callers.
Delegates all validation to `langchain_core._security._policy`.
"""
import os
import socket
from typing import Annotated, Any
from urllib.parse import urlparse
from pydantic import (
AnyHttpUrl,
BeforeValidator,
HttpUrl,
)
from l... |
ffd0b695d29a43c01555083bfd2f4ae67fbe57ef68ce23215c2f7699c9d4fdd1 | Python | 4,612 | 107 | """tests for io.py.
test_strip_uninteresting_vertex_colors_* cover a real bug: some .ply files
carry an explicit but uniform vertex-color array (every vertex literally
[255, 255, 255, 255]) rather than no color data at all. trimesh treats that
as real per-vertex color (visual.kind == "vertex"), which round-trips into
... |
865df8fb2bd3bd3482c1bfb1273f558469f1bb67bbef5b7c9999eb5a90b7b0fa | Python | 4,618 | 83 | """C5: stimulated vs unstimulated, SHARED-GENES-ONLY, on Kang 2018 (GSE96583 batch 2).
GSM2560248 (2.1) = control, GSM2560249 (2.2) = IFN-beta stimulated.
The paper's claim: removing genes exclusive to one condition (the trivial split), the conditions are
still separable by a coordinated shift across SHARED genes. We ... |
97459b099d46b7f2e1fa8a8d276fc66be0c8972fdd936186d7bf1d9cf177cc5f | Python | 4,623 | 150 | import glob
import sys
import matplotlib.pyplot as plt
import numpy as np
# Define grid dimensions globally
ROWS = 28
COLS = 28
def plotGrids(gridData):
if gridData.shape[0] % ROWS != 0 or gridData.shape[1] != COLS:
raise ("Incompatible grid dimensionality: check data and assumed dimensions.")
grid... |
2deb565708af3e0892ad4aca34705ac0aa9c3243aa4bb7cc97deefa7b8da2218 | Python | 4,625 | 121 | from torch.utils.data import DataLoader
import torch
import numpy as np
from torch import nn,optim
from bestmodel import MyModule
from Dataset import MyDataset
import sklearn.metrics as m
from tqdm import tqdm
import os
def RMSE(y_true, y_pred):
return np.sqrt(m.mean_squared_error(y_true, y_pred))
de... |
786a6246fe0b0f3b0871e328a97104399479c58ac7efa63a19e8d3eb6073f005 | Python | 4,625 | 131 | """
Author: Anna M. Puszkarska
SPDX-License-Identifier: Apache-2.0
"""
import keras
import numpy as np
from keras.layers import (Dense, Dropout, Conv1D,
BatchNormalization, MaxPool1D, Flatten, Input)
from keras.models import Sequential, Model
from keras.models import load_model
from keras.reg... |
38fdc8c5508512fa80092a1ddafabbb82558e2aba22ca3f336fd6a6bafca5bfe | Python | 4,628 | 131 | # builtin modules
import subprocess
import os
# pnabind modules
from .data import data
def getAtomChargeRadius(structure, source="AMBER", min_radius=0.6):
""" Assign atomic parameters to every atom in a protein chain. Values are stored in atom.xtra
dictionary. The following keys are used
----------------... |
ad9d432b691b49f693da4a3ff6dbed7d2edd76428218f0ebbd832f49ec6a58dd | Python | 4,628 | 82 | # Sconda conda activate TensorFlow_CPU_01; cd /mnt/BioAdHoc/Groups/RaoLab/Edahi/Projects/09.TimeCourse5hmC/ForFerhatGit/FCDNN/results/gene_expression_distribution; python
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import os
# Calculate the mean and standard deviation of the TPM values
def p... |
4fb79d9e9264635bc71b8e0fec7a8a9d276c8f20d543f60e5d2d5f9c04a6bc08 | Python | 4,635 | 110 | """Test rate limiter."""
import time
import pytest
from freezegun import freeze_time
from langchain_core.rate_limiters import InMemoryRateLimiter
@pytest.fixture
def rate_limiter() -> InMemoryRateLimiter:
"""Return an instance of InMemoryRateLimiter."""
return InMemoryRateLimiter(
requests_per_seco... |
0a2a4f630cb7fb5d8251c3e2152fb303398aa482b8c0bf35ae8dba6996f1394b | Python | 4,636 | 106 | """ Statistic Module comprises all statistical tests performed
by OmicScope for differential expression analysis.
Returns:
DataFrame: DataFrame with recommended statistical
analysis performed
"""
import os
import pandas as pd
def perform_static_stat(self):
"""log2 transformation for express... |
a5b8016b6c2d1b6bff9a7a72a540236ef54045cbca192deaf8a60df968650166 | Python | 4,636 | 98 | """shared reshaping helper: craniumpy_core.cohort.GroupMeasurements (the
dataclass measure_mean_shape returns) -> CohortMeanShapeMeasurementsResponse
(the same per-metric response models ResultsResponse uses). factored out of
api/routers/cohort.py's own get_mean_shape_measurements so
api/routers/longitudinal.py can reu... |
c04f512e6cc0160deab3fac1eaf714fd0462f41928ec6e1ef31b3b8a1dfaffb9 | Python | 4,638 | 96 |
from copy import copy
import pandas as pd
class Input:
def __init__(self, Table, pdata,
quant_strategy='LFQ intensity'):
""" MaxQuant output
MaxQuant output is composed by a ProteinGroup.txt file and it contains
several parameters that can be used to filter the data.
... |
ac5ea15b4391713875c56d5e89a1d4cd465744b6b721a890359c3d87f28aec8f | Python | 4,640 | 142 | #!/usr/bin/env python3
"""
Merge cortical and subcortical Harvard-Oxford atlas labels into single image
- 1 mm spatial resolution
- Deterministic threshold p > 0.25
- Split cortical labels into LH and RH
AUTHOR
----
Mike Tyszka, Ph.D.
LICENSE
----
MIT License
Copyright (c) 2019 Mike Tyszka
Permission is hereby gra... |
ea56afec7576632be9076e8885f8e7ac58dc7fd4cc4113b18c4827effd421543 | Python | 4,640 | 156 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2023 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for d... |
2efa19f11e778d63660523a083c0583fd512b9e3169a6e22679b1b33e0430162 | Python | 4,641 | 156 | ####################################################################################
#
# STEPS - STochastic Engine for Pathway Simulation
# Copyright (C) 2007-2026 Okinawa Institute of Science and Technology, Japan.
# Copyright (C) 2003-2006 University of Antwerp, Belgium.
#
# See the file AUTHORS for detai... |
38e93793de3b9f82187c779d743733106a8fdd377a60813a7e43b8281796e8ef | Python | 4,641 | 95 | import torch
import torch.nn as nn
from .utils import prod
import e3nn.o3 as o3
class Expansion(nn.Module):
def __init__(self, irrep_in, irrep_out_1, irrep_out_2):
super(Expansion, self).__init__()
self.irrep_in = irrep_in
self.irrep_out_1 = irrep_out_1
self.irrep_out_2 ... |
eaf87d7d42a07a6d3c70a2f987fc53801485b66b5eda9f2cfe1b00b33671fb2b | Python | 4,642 | 151 | """
Test the methods in cwas.core.common
"""
import cwas.core.common as common
import numpy as np
import pytest
def test_cmp_two_arr():
# Empty arrays
arr1 = np.array([])
arr2 = np.array([])
assert common.cmp_two_arr(arr1, arr2)
# Different lengths
arr1 = np.array([1, 2, 3, 4, 5])
arr2 = ... |
e7d3eb982b79b182136fa85941664a219eb4b8999c8e42fb916aa47e1437694f | Python | 4,644 | 130 | import glob
import os
import logging
LOG = logging.getLogger(__name__)
def get_versioned_dir(output_dir, version=None, resume=False):
"""version gets dir for specific version, resume gets dir for last version."""
if version is None:
current_versions = glob.glob(os.path.join(output_dir, "version*"))
... |
ed4d266259fa6d8367c1dedc644a9e4ea4072b11cfdd6600ece0ba42985ad0b5 | Python | 4,645 | 180 | # These are tools to be used along with Python dataclasses.
#
# Author: vivekv2@gmail.com
from dataclasses import asdict
from datetime import datetime
from pathlib import Path
from typing import Type, TypeVar
import pandas as pd
import numpy as np
import h5py
def add_backup_timestamp(path: Path) -> Path:
timest... |
d540065a242673d3c4cff91105cfa561d024ed1cd3fcc9f0e3a86fcef3441bd8 | Python | 4,648 | 122 | # -*- coding: utf-8 -*-
"""
Created on 20 may 22
@author: degano
"""
import matplotlib.pyplot as plt
import numpy as np
import mne
from scipy import stats
outfile = 'decoding_results_nested_LeftDepProsody_final_classes_logistic_full_slideF_NCfull_sel_cv10.npz'
npzfile = np.load(outfile)
Ttimes = npzfi... |
5180d8c3bca435f61a047531aeac2b3d5677c9dafd60bffedc8d115d48daa2d1 | Python | 4,649 | 157 | import sys
import uuid
from typing import Any
from uuid import UUID
import pytest
from langchain_core.callbacks import AsyncCallbackHandler, BaseCallbackHandler
from langchain_core.callbacks.manager import (
adispatch_custom_event,
dispatch_custom_event,
)
from langchain_core.runnables import RunnableLambda
f... |
6566956c1c84e793578997768c7e1762a3307241ace8586982818bac51c18874 | Python | 4,649 | 133 | ## Tensorflow models and callbacks
import math
import numpy as np
from contextlib import redirect_stdout
import tensorflow as tf
from tensorflow.keras.layers import (
Dense,
Conv1D,
Activation,
SpatialDropout1D,
BatchNormalization,
Flatten,
Dropout,
Input,
GRU,
LSTM,
Bidirec... |
8f8941427d7eee0122b5460996ee407e6247a0849bc1242f00801e55d9b5a033 | Python | 4,650 | 110 | # Our proposed model CNN + LSTM
import tensorflow.keras as keras
import tensorflow as tf
import tensorflow_addons as tfa
import numpy as np
import time
from utils.utils import save_logs
from utils.utils import calculate_metrics
class Classifier_ENCODER:
def __init__(self, output_directory, input_shape, nb_classe... |
f2ed38b82d78e0e2ba9942657c8e36797ca23c06990aeadf67b6550dcfa2088d | Python | 4,651 | 117 | """Interface with the [LangChain Hub](https://smith.langchain.com/hub)."""
from __future__ import annotations
from collections.abc import Sequence
from typing import Any
from langchain_core._api.deprecation import deprecated
from langsmith import Client as LangSmithClient
@deprecated(
since="1.0.6",
remova... |
d660c28cf6d3d55bccba7ca9589e305476b4ad5bcf1ea33296e0f9889a53225a | Python | 4,653 | 106 | """ Import PatternLab Output
PatternLab V allows user to export Excel file with filtered identified
proteins, sample information, biological and technical replicates.
Here, we advise users to export data with at least 1 unique peptide/protein
and protein abundance normalized by XIC.
@author: Reis-de-Oliveira G <gu... |
94cf4c2bd36538cf395348994b8d1d5cd983839883f8ee7f8994310e463b0f66 | Python | 4,655 | 134 | from collections.abc import Callable
from typing import Any
from langchain_core.documents import Document
from typing_extensions import override
from langchain_classic.retrievers.multi_vector import MultiVectorRetriever, SearchType
from langchain_classic.storage import InMemoryStore
from tests.unit_tests.indexes.test... |
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