sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3ca47034ef2b1e92eb001b6c999a5d87d99bceb0816517b7ed735d4a3251d9d8 | Python | 4,163 | 161 | import numpy as np
alg = 'MPVNN'
ctype = 'OV'
basedir = '..\\Data\\'
outbasedir = "..\\Out\\"
topmax = 3
thrval1 = 0.85
thrval2 = thrval1
edges = []
pgenes = set()
with open(basedir+'pi3k-akt.txt', 'r') as f:
for line in f:
lineData = line.strip().split("\t")
pgenes.add(lineData[0])
p... |
58b617b492ff6d8bdcae8dc5cf3b7517815c17eef7cf8ee32ff195733fb1c701 | Python | 4,163 | 100 | import pandas as pd
from sklearn.base import clone
from sklearn.linear_model import LinearRegression
from sklearn.metrics import r2_score
from pgmpy.causal_discovery._base import BaseOrderDiscovery
class R2Sort(BaseOrderDiscovery):
r"""Causal discovery by sorting global R^2 values and regressing on predecessors.... |
7ec25a4fb1cc4115e1f48d32b096147aeac0c8f49f554f4c64cfe581434ce73e | Python | 4,163 | 129 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.
import os.path as osp
import loggi... |
04936a374981877bc3bfcd257d1e780192b777cc09d9cd1f5a5941dae47b8e94 | Python | 4,166 | 138 | from scipy.spatial import KDTree
import numpy as np
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, df, x0, x1, n_bins, n_boots):
"""Nearest neighbour PMF plot"""
# get data arrays
a = df.loc[df.Subtype == group + "a", ["Root_x", "Root_y", "Root_z"]]
b = df.loc[df.Subtype == ... |
244503b7528e57e5a5b4ff77f7e6e9510eb045d79f5343d3f788921b838a65af | Python | 4,166 | 98 | # 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/licenses/LICENSE-2.0
#
# Unless required by applicable law or agr... |
80497c8198798b2e1b70b49724f309b3b5fa948d9c1c15435b37440fcd3b5c82 | Python | 4,168 | 172 | ###############################################################################
#
# Import functions
#
###############################################################################
import glob
from pathlib import Path
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.font_m... |
08970778ddf38a65be05af6bf60f495db4721820a2c045cba61637ce81521cde | Python | 4,169 | 119 | import queue
import collections
import threading
__all__ = ['FutureResult', 'SlavePipe', 'SyncMaster']
class FutureResult(object):
"""A thread-safe future implementation. Used only as one-to-one pipe."""
def __init__(self):
self._result = None
self._lock = threading.Lock()
self._cond... |
4b9c4bc92659bd17f845e4b97014ecb6b3a4f0fe5e39593de597c04a4454a158 | Python | 4,170 | 106 | from argparse import ArgumentParser, BooleanOptionalAction
from pathlib import Path
import re
import nibabel as nib
import numpy as np
import pandas as pd
from scipy.stats import ttest_1samp
def parse_args(default_groups, default_invert, default_split, default_max):
parser = ArgumentParser()
parser.add_argum... |
b38a3ee6ea8dab3a8060cd007689f1bb58f1901f1c64a234828b803ca63952ca | Python | 4,170 | 115 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_test_desikan_main(gpu_index=0, subject=1):
'''
This function is to impleme... |
4d9da8a234afed444be227ae7df30891384d4f2719e3563d430f2cca9f1731e1 | Python | 4,172 | 107 | import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
from pathlib import Path
# Define paths
base_dir = Path('/egor2/egor/MovieProject2')
tonotopy_dir = 'tonotopy'
fd_file_pattern = 'motion_{subject_id}_enorm.1D'
plots_dir = base_dir / "bids_data/derivatives/group_analysis"
plots_dir.mkdir(parents=... |
7c42a3f07a13ada51c9473c0c5605bd1e27d05b1770383bc62919acf3b7ceadd | Python | 4,173 | 117 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_test_desikan_main(gpu_index=0, weight=1):
'''
This function is to implemen... |
d5e23ea27361a01e6b64008e5288eca33cc337b049d7f51b7c72efec806422d1 | Python | 4,173 | 117 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_test_desikan_main(gpu_index=0, weight=1):
'''
This function is to implemen... |
10ec6a380ef5410dd88fa0b96d76c660aa4dd354afae16920b708efe51c854fe | Python | 4,174 | 121 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from . import LegacyFairseqLRScheduler, register_lr_scheduler
import logging
import ast
logger = logging.getLogger(__name__)
logger.setLevel(... |
fb6e738f10eca62dbfdfdec709922716cf1ede4ae691e3c5b6633c140ac8bed0 | Python | 4,176 | 131 | from __future__ import annotations
from pathlib import Path
import pytest
from poetry.repositories.parsers.pypi_search_parser import Result
from poetry.repositories.parsers.pypi_search_parser import SearchResultParser
FIXTURES_DIRECTORY = Path(__file__).parent.parent / "fixtures" / "pypi.org" / "search"
@pytest.... |
0bb43b7a41745d58fac947cd3bef7dbcce80b8b8a846d595b0a5be7690c82951 | Python | 4,179 | 110 | import requests
import unittest
from unittest.mock import patch
from pyecharts import options as opts
from pyecharts.charts import Lines3D, Map3D
from pyecharts.globals import ChartType
class TestLines3DChart(unittest.TestCase):
@patch("pyecharts.render.engine.write_utf8_html_file")
def test_lines3d_base(sel... |
8d9ef4e5c446e43a5933995963d74b60625a13009c8574cdc5c7e7e72fedc00b | Python | 4,179 | 113 | #!/usr/bin/env python3
"""Check MPI prerequisites without confusing them with an app MPI gate.
The probe launches the selected interpreter with ``mpirun`` and verifies that
the requested world size is visible to ``mpi4py``. It also records the
GROMACS build's MPI mode. A successful probe is runtime evidence for the
... |
cf0a09ffa8ffa1ecb24a80ba1d52914391e7d8cc7678b2776c7dfb184988d538 | Python | 4,179 | 104 | import cv2
import cmapy
from PIL import Image
import numpy as np
from msi_visual.utils import normalize_image_grayscale, image_histogram_equalization
class SegmentationAvgMZVisualization:
def __init__(self, segmentation_model):
self.segmentation_model = segmentation_model
self.k = self.s... |
0cc95ae45f1a930e2d980b48d15ab69b1ae9e536a77d13044efd3fa33e6bf44e | Python | 4,181 | 117 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_test_desikan_main(gpu_index=0, weight=1):
'''
This function is to implemen... |
38949d0709358516f0e13494a072ec78ee794758ab0bb49d0a1ea27294c059bf | Python | 4,182 | 141 | import argparse
import numpy as np
import gzip
import sys
import os
import yaml
import torch
import allel
import pysam
import pysam.bcftools
import textwrap
# put popgen-npe scripts in the load path
sys.path.insert(
0, os.path.join(os.path.dirname(__file__), "..", "..", "workflow", "scripts")
)
import ts_simulator... |
65972551e90812dbc89d410ae9aebbd7fc97b0ada0eeda259e73f75b76ef4f4a | Python | 4,182 | 119 | """Where the BRENDA data blobs live, independent of how this package installed.
The blobs are fetched from the Hugging Face Hub and never built into the
wheel, so their location cannot be package-relative. Under a non-editable
install a package-relative path resolves inside ``site-packages``, while the
downloader writ... |
2a1255bc08373a43a800c25cd4c599fe6f647108d846be9f491bbdb2e0459a90 | Python | 4,183 | 136 | """
dataset_fast.py
===============
Generate 4-state Markov input spike trains for the driven reservoir experiments.
For each combination of (seed, ε, v_on), produces a numpy array of Poisson spike
trains (4 channels), one per Markov state. Output files are named:
<outdir>/T{tbit}/e{eps*100:.0f}%_v{v}_s{seed}.npy... |
6f5a2eb6b6327a90651c534efc772aa620469d50495e3434775eeac984b0b45b | Python | 4,183 | 174 | from typing import List
import logging
from collections import OrderedDict
import numpy as np
logger = logging.getLogger(__name__)
IUPAC_CODES = OrderedDict([
('Ala', 'A'),
('Asx', 'B'),
('Cys', 'C'),
('Asp', 'D'),
('Glu', 'E'),
('Phe', 'F'),
('Gly', 'G'),
('His', 'H'),
('Ile', 'I'... |
e8a1276177a6b003bddd80d220cc9c24bd7b28418b09ef7980fe3cb1409d4aa6 | Python | 4,183 | 132 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import argparse
import gc
import logging
import os
import joblib
import soundfile as sf
import torch
from examples.textless_nlp.gslm.speech2u... |
b1a75db059d76dc28c02fe00eae5c185eaba33c401786e84a88ee1244c542ba1 | Python | 4,184 | 116 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
def CBIG_mfm_test_desikan_main(gpu_index=0, subject=1):
'''
This function is to impleme... |
1a1a0cb04426cd80574c1a78ffc1f8de61c8bcfc5adf7852edc7faa790f98ee0 | Python | 4,185 | 149 | import os, re, glob
import numpy as np
import matplotlib.pyplot as plt
from scipy.io import loadmat
from matplotlib.colors import Normalize
from matplotlib.lines import Line2D
plt.rcParams['figure.dpi'] = 400
# =========================================================
# USER SETTINGS
# ======================... |
b741e26169bbca05ea95e6125e74d94082a8af06b3e71f6d3d1c68d5dfd1ef28 | Python | 4,185 | 105 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use("TkAgg")
import pandas as pd
from cal_KL_div import calculate_kl_divergence
min_n = 100
max_n = 0
def get_model_bit_scores(model_name, min_n, max_n):
all_seq_score_list = []
all_list_left = []
all_list_right = []
... |
af13dd283339e276c15281b637eb40e06230be81b8d1e70d800236755d348687 | Python | 4,186 | 144 | # -*- coding: utf-8 -*-
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... |
846677fa4272820b49eedaf7259ecb2e523646cfe10ddae0a4c2bb2fb7edde52 | Python | 4,191 | 77 | """Offline regression checks for NSD output names and spherical atlases."""
import json
from pathlib import Path
import tempfile
import unittest
import nibabel as nib
import numpy as np
from utils.nsd_utils import NSDDataHandler, create_spherical_roi_atlas, encrypt_val
class NSDUtilsTests(unittest.TestCase):
de... |
b4f6942df021bb4efa50c3a0ad61901a68bcd56c86bc81a45fe05ca63cc882a1 | Python | 4,191 | 82 | #!/usr/bin/env python3
"""O OCE preve a DENSIDADE DE ESTADOS? Pergunta inedita no projeto.
O registro tem uma pendencia declarada em varios lugares: **nenhuma densidade de
estados foi jamais ajustada com OCE em conjunto algum**. Agora ha o dado -- as
1.784 curvas de DOS das perovskitas SIESTA, calculadas dos .EIG e va... |
db6c6ee6c303f1aa2388e5f576cd83d9d22225191214b2305d238eb6a346398d | Python | 4,191 | 120 | """Tests for vak.prep.audio_dataset module."""
from pathlib import Path
import pandas as pd
import pytest
from ..fixtures.audio import (
AUDIO_DIR_CBIN, AUDIO_LIST_CBIN_ALL_LABELS_IN_LABELSET, AUDIO_LIST_CBIN_LABELS_NOT_IN_LABELSET
)
from ..fixtures.annot import LABELSET_NOTMAT
import vak.common.annotation
impor... |
976e1b8996783c453f6a86a0b733f775c6e5352c98fe39bc3cd06728aeba10f3 | Python | 4,193 | 112 | # -*- coding: utf-8 -*-
"""
@Time:Created on 2019/4/30 14:19
@author: LiFan Chen
@Filename: mol_featurizer.py
@Software: PyCharm
"""
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors
num_atom_feat = 34
def one_of_k_encoding(x, allowable_set):
if x not in allowable_set:
raise Exce... |
055c5d1b9ae988a0d510aef88e1d156cd02a54f77b41e3a671a09a33db051f40 | Python | 4,194 | 123 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
---
Script for calculating the scaling factors used to even out GemNet activation
scales. This generates the `scale_file` specified in the confi... |
7afeecf8712eed18feb1928d486fb333fa2aa231c1b20bb89d14330fd44b9c5a | Python | 4,196 | 113 | """Tests for the sparse-to-dense index mapping of FwdJacobian."""
import jax
import jax.numpy as jnp
import numpy as np
import pytest
from folx.api import FwdJacobian
from folx.utils import compact_repeated_dims_except, static_index_mask
jax.config.update('jax_enable_x64', True)
def _brute_force(mask: np.ndarray, ... |
f1d5566d79cedd05e800ca4d7cd42f842858c535bf55b0a8db73703131e09c54 | Python | 4,198 | 138 | import torch
import torch.nn.functional as F
def softmax_splat_2d(src: torch.Tensor, flow: torch.Tensor, temperature: torch.Tensor = 1.0) -> torch.Tensor:
"""
Softmax splatting (Niklaus & Liu) simplified 2D version.
Args:
src: [B,1,H,W] source intensities multiplied by mass m in [0,1]
flo... |
bcf9bdd6e1f712523091563f6e1b1aa2b4c50289dc9407a3d538ea1da3f6fc43 | Python | 4,200 | 150 | from __future__ import annotations
from copy import deepcopy
import pytest
from cleo.io.buffered_io import BufferedIO
from poetry.config.config_source import UNSET
from poetry.config.config_source import ConfigSourceMigration
from poetry.config.dict_config_source import DictConfigSource
@pytest.fixture
def config... |
d49abdccaacda0d521b51aaff49fb5a1eb303c92e9ed900c040779e9779f623c | Python | 4,200 | 160 | """CSS styling constant for Lossless Pipeline in Dash."""
# Author: Scott Huberty <seh33@uw.edu>
# Default Layout for individual scatter plots within timeseries
###############################################################
drawn_shapes_format = {
"drawdirection": "vertical",
"layer": "below",
"fillcolo... |
09dec6a08d0a3f238f4961b2cede8f3797377ae377eaf97c90cd381ff9daea6e | Python | 4,201 | 111 | docstring = """
Plot posterior coverage and concentration as a function of increasing numbers of training
samples, across misspecified priors.
"""
import matplotlib.pyplot as plt
import pickle
import argparse
import numpy as np
from matplotlib.ticker import ScalarFormatter
plt.rcParams["figure.dpi"] = 300
plt.rcParams... |
7a5103f5b1aecd2380324eeef3cf140d75c02755ec8a460255cf593127f958be | Python | 4,202 | 88 | #! /usr/bin/env python
import os
import logging
import pandas
import gzip
from timeit import default_timer as timer
from metax import __version__
from metax import Logging
from metax import Exceptions
from metax import PredictionModel
from metax import Utilities
from metax import MatrixManager
from metax.genotype imp... |
c53e5e6ff0ae203950721f4b25fba39d146bc18326ed5bb8ba78342c650b7b27 | Python | 4,203 | 136 | from __future__ import annotations
import tempfile
from pathlib import Path
from tempfile import TemporaryDirectory
from typing import TYPE_CHECKING
from poetry.core.packages.utils.utils import splitext
from poetry.utils.helpers import extractall
from poetry.utils.isolated_build import isolated_builder
if TYPE_CH... |
8580c2afb5489c0f8df84dfa3c79fe1fc48b15f1eef0630426dc36367c612b63 | Python | 4,205 | 103 | import numpy as np
def Surr_PseudoPeriodic(y,tau,dim,rho):
"""
inputs - y, time series
- tau, time lag for phase space reconstruction
- dim, embedding dimension for phase space reconstruction
- rho, noise radius
outputs - ys, surrogate time series
- yi, sele... |
91d6e8ee3033b18a1a0a6d943f6abdb8c3e0535977067f410109095e17982bce | Python | 4,206 | 111 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from typing import Any, Optional
import torch
import torch.onnx.operators
from fairseq import utils
from torch import nn, Tensor
... |
804c8ea80e22b8ef14d45b557fa98eaf335324f09082a2b6cfb1460b475220dc | Python | 4,207 | 100 | ## create model RDMs
#
# written by S-C. Baek
# update: 16.12.2024
#
import os
import scipy.io
from scipy.spatial import distance
import numpy as np
import pandas as pd
from utils import get_main_dir
# path settings
MAINDIR = get_main_dir()
DATADIR = MAINDIR + os.sep + 'data/'
def create_model_rdms(subjects, elem... |
d8e19fce136728a7060d69f261ffe4317f854b634905bdd546c450def10f9438 | Python | 4,207 | 106 | from pymatgen.core import Element
from pymatgen.entries.compatibility import Compatibility, CompatibilityError
from pymatgen.entries.computed_entries import (
ComputedEntry,
ComputedStructureEntry,
EnergyAdjustment,
)
class IdentityCorrectionScheme(Compatibility):
"""Perform no energy correction."""
... |
7fa9d57cc7ae7e86991812123e6a928bb73a8fdccfd436fad2256a9ea50ec181 | Python | 4,209 | 119 | import logging
import math
from typing import Any, Literal, Optional
import numpy as np
from pydantic import BaseModel, Field, root_validator
class MOJOConfig(BaseModel):
name: Literal["MOJO"]
alphabet_size: dict[str, int] = Field(default_factory=dict)
token_embed_dim: int
conv_init_embed_dim: int
... |
743008b175340fa98ae77d2a0f7cf578faaad9e34e23b22fd4649ab01843f9ce | Python | 4,211 | 114 | import numpy as np
from scvi import REGISTRY_KEYS
from scvi.data import AnnDataManager
from scvi.data._utils import get_anndata_attribute
from ._ann_dataloader import AnnDataLoader
from ._concat_dataloader import ConcatDataLoader
class SemiSupervisedDataLoader(ConcatDataLoader):
"""DataLoader that supports semi... |
42e6b7eb65d1f505b4500c0b1608b90ae12915cde87035774df0dfda062b6405 | Python | 4,212 | 143 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
from contextlib import redirect_stdout
from fairseq import options
from fairseq_cli import generate
from examples.noisychannel imp... |
f04856f79d8bc55fd892d5889cdbba6ec7a167c15fc43a6ecb90c0caa47d1b18 | Python | 4,213 | 124 | """Reclassify organisms in the `other_organisms` fields of the doc database.
When one of those organisms is a bacteria in the NCBI taxonomy, move it to the
bacteria field of the document and add an entry for it in the `bacteria` table
of the database.
Similarly, if one of those organisms is a bacterial strain, move i... |
feafa4aafaf481edca84fb20df9a66dcf8d85159116e4f626a74669792b57656 | Python | 4,213 | 122 | import pandas as pd
import numpy as np
import torch
from torch.utils.data import Dataset
class HTPDataset(Dataset):
def __init__(self, data_path, max_seq_length, encode_fn_name=None):
self.max_seq_length = max_seq_length
if data_path:
self.data_df = pd.read_csv(data_path)
... |
a61f232458dc546bc3c311c3fdefe40b7c6e9d709b2067eb8fe9bc06358d3cf5 | Python | 4,216 | 110 | """The tracked scripts that write `config.toml` must write one that loads.
Experiment drivers generate the repo-root `config.toml` wholesale, so a
key renamed in Python alone leaves them writing a file every `train`,
`evaluate` and `tune` then dies on in `machine_config()` — and regenerating it
is how the breakage rep... |
4165f94818a27df3596d0d6af39352f4c58a77214695cf184673695f0c738774 | Python | 4,217 | 116 | """Guards on where the data blobs are looked for.
The blobs ship through the Hugging Face Hub, so the directory holding them
has to be the same one whether this package is installed editable or copied
into `site-packages`. A package-relative answer is not: it moves with the
install, the downloader keeps writing to the... |
8ddbd9448bdfaff29a598f8592813617c4e3b7023c4a26f48a6b129e850c09d3 | Python | 4,220 | 111 | """The document id is what identifies a document to the embedding caches.
`get_token_embeddings` keys a cache that lives as long as the process on a
batch item's id, and checks nothing behind that id but the entry's row count,
so two documents of one token count handed one id are served each other's
activations with n... |
3789a7f037db20468c1ee0cfb6a8994d961ff9967a74e337c709489381d542f7 | Python | 4,221 | 143 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
# The code in this file is adapted from the BeiT implementation which can be found here:
# https://github.com/microsoft/unilm/tree/master/beit... |
3fb631cdc73fcc2261ccff5a815879d9e5c18fc5a61fdf6be5bc58534963dc99 | Python | 4,228 | 121 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from os.path import join
from tractseg.data import dataset_specific_utils
from tractseg.libs.system_config import SystemConfig as C
class Config:
"""
Settings and hyperparameters
"""
# inpu... |
62904860dfb6e7cb971e17b330a1274a2f2ee3140860f05df7d94228dadbcf74 | Python | 4,228 | 119 | from collections.abc import Hashable
import pandas as pd
import pytest
from pgmpy.structure_score import (
BIC,
K2,
BaseStructureScore,
BICCondGauss,
BICGauss,
)
from pgmpy.structure_score._base import get_scoring_method
class CountingScore(BaseStructureScore):
def __init__(self, data):
... |
db4bf308783fe6c7a2e1251663f418a20fd7191797865044b8a95852a2c446d0 | Python | 4,230 | 128 | import logging
from typing import Dict, List, Union
import numpy as np
import scipy.cluster.hierarchy as hc
from scipy.spatial.distance import pdist
import loompy
from cytograph.annotation import AutoAnnotator, AutoAutoAnnotator
from cytograph.enrichment import Enrichment, Trinarizer
from cytograph.manifold import Grap... |
e04221d2532ca3591e60f67f9e81d6931afffa41f81520862e18a4394f2dc42e | Python | 4,230 | 116 | """Plot the SIESTA-PBE vs Mannodi-VASP-HSE06 decomposition-energy parity
on the 18 F-free endmembers, partitioned by A-cation (Cs vs K).
"""
from __future__ import annotations
import json
from pathlib import Path
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
from scipy.sta... |
44f38e7b95ebe277d9ecd2436867f6214bb6b91de721e5337f7a2751b538badf | Python | 4,231 | 119 | """
This module contains metrics to evaluate the Garfield model training.
"""
from typing import Optional, Union
import matplotlib.pyplot as plt
import numpy as np
import sklearn.metrics as skm
import torch
from matplotlib.ticker import MaxNLocator
def eval_metrics(
edge_recon_probs: Union[torch.Tensor, np.ndar... |
2c42729690c03c7b8f7064d27f65d2d242c29c53f891edaed1575eaae458b667 | Python | 4,234 | 90 | """Plot a GoSubDag.
GO Terms in a plot contain text. The first two lines appear by default:
GO:0015618 L07 D13 p2 c2 d3
potassium-transporting ATPase activity
GO:0015618 => GO ID
First line:
LNN => The "level" of the go term.
The length of the shortest path(s) fr... |
570d0bec2a77bbcda943b33654c9b16959f9cac0c0b09e865f35d4bcfc30aeab | Python | 4,236 | 137 | import sys
from os.path import dirname, realpath
current_dir = dirname(dirname(realpath(__file__)))
sys.path.insert(0, dirname(current_dir))
import pandas as pd
from matplotlib import pyplot as plt
from os.path import join
import numpy as np
import itertools
from sklearn.metrics import confusion_matrix
from mpl_tool... |
7e1f0317ce0bf395b84591f817729e57b91c940e29d503ca800289f7c734cfdc | Python | 4,236 | 128 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
from fairseq.modules import Fp32GroupNorm
class KmeansVectorQuantizer(nn.Module):
def __init__(
... |
6516da5083fd4fb61d5d2b26cb7018bff15b02efc279204824e88a26008a6d6c | Python | 4,237 | 121 | import os
import time
import json
import numpy as np
import re
import sys
sys.path.append(".")
# Get structural seqs from pdb file
def get_struc_seq(foldseek,
path,
chains: list = None,
process_id: int = 0,
plddt_mask: bool = False,
... |
bab7ecf223ea20b21c5a5d3ed447b30466d586a126ffc623633a18e8eed90175 | Python | 4,237 | 93 | import torch
import torch.nn as nn
import numpy as np
import torch.nn.functional as F
from collections import OrderedDict
class _SimpleSegmentationModel(nn.Module):
def __init__(self, backbone, classifier):
super(_SimpleSegmentationModel, self).__init__()
self.backbone = backbone
self.class... |
24f22affe5868ac2d64a9524decdcaabb989b8bf78d2cf90f717ef6bd4ad59a7 | Python | 4,238 | 88 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/PretrainUI.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def setupUi(self, Form):
Form.setObjectN... |
32b0a5a04cdb2501788641a66c93d18c608689e039d7ddc170650779fc6fe0db | Python | 4,238 | 143 | """fixtures relating to array files containing spectrograms"""
import pytest
import vak.common.files.spect
from .annot import (
ANNOT_LIST_NOTMAT,
ANNOT_LIST_YARDEN,
LABELSET_NOTMAT,
LABELSET_YARDEN,
)
from .test_data import GENERATED_TEST_DATA_ROOT, SOURCE_TEST_DATA_ROOT
SPECT_DIR_MAT = SOURCE_TEST... |
37f079eaf3c21d6e1a917e9e58ee1c8e1015d146c0447384af9b453380b13ba4 | Python | 4,238 | 83 | # This extension template provides instructions to add new example models to pgmpy.
#
# Please follow the following steps:
# 1. Copy this file to the appropriate subdirectory in `pgmpy/example_models` (e.g.,
# `pgmpy/example_models/bnlearn/my_model.py`). If adding a new model source, create a new subdirectory in
# ... |
a3cf5e7bfa653e19bf9aa1c5ad0f3470aa5afbdb4dcb20694eb8fb8a73e44de0 | Python | 4,238 | 127 | from typing import Protocol
import jax
import jax.numpy as jnp
import jax.numpy.linalg as jnp_linalg
from .density_models.forces import coulomb_force_nuclei
from .physics import local_energy
from .types import ElectronConfiguration, ModelDimensions, RandomKey, Stats
class Observable(Protocol):
def __call__(
... |
9d283b07a48f8a28e30c20809be01a9d57fdd9db827fca96a14c3aeba08bcdf0 | Python | 4,239 | 140 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, df, x0, x1, n_bins, n_boots):
"""Nearest neighbour PMF plot"""
# get data arrays
a = df.loc[df.Subtype == g... |
21eba90471761da0dadc04f4484c0adec1b6cf827e04a6ea99117fcb91bf574d | Python | 4,245 | 132 | #!/usr/bin/env -S uv run --script
# /// script
# requires-python = ">=3.11"
# dependencies = [
# "icechunk",
# "zarr>=3",
# ]
# ///
import asyncio
import json
import os
import pathlib
import shutil
import icechunk
import numpy as np
import zarr
import zarr.core.buffer
SCRIPT_DIR = os.path.abspath(os.path.dir... |
358c61a818992ee6c871fd3e30983f0e750b71f00112e08138046fde2e00faf0 | Python | 4,245 | 115 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.modules.utils import _pair
class PQConv2... |
76dc28be79051d6d3aaa6d361c20633e3b2c7933ddb2434a5c891a765b523ace | Python | 4,246 | 91 | """Defines the Multinomial NLL loss and the adaptive counts loss.
These are derived from the basepairmodels repository, which is licensed under
an MIT license. You can find a copy at ``etc/basepairmodels_license.txt``.
"""
from collections.abc import Callable
from bpreveal.internal import disableTensorflowLogging # p... |
eaff743e3111af8cd179006eeb9b0fc9cf7aa19bd7c7617da239b9fd01e103c4 | Python | 4,249 | 108 | """Tests for the AdditiveNoiseModel (ANM) simulator dataset."""
import numpy as np
import pytest
from skbase.utils.dependencies import _check_soft_dependencies
from pgmpy.base import DAG
from pgmpy.datasets import list_datasets, load_dataset
def test_load_anm_dataset():
ds = load_dataset("anm", seed=42)
ass... |
4eaee1bfc548564cdb7da53e7ffc776c5eb60472e65c4be13510aa5f0db1cdcc | Python | 4,250 | 137 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from glob import glob
from vlpp.utils import add_suffix, nfmap2dict, warn, run_shell, gzipd, run_matlab, TPL_PATH
from vlpp.registration import applyWarpImageMultiTransform, estimatePet2Anat
def main():
transitional = "${transitional}"
mode = "${config... |
6186379a88269be4c7ab3f75c47e780ea8c92ac3d962371e3463ecf7a5a8ce4b | Python | 4,251 | 115 | # Copyright 2020 The Lucent Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... |
3abee3d17a29184a177d7c3f1c5564f05c8dce8ce425f47d0a8b297b0b0c3746 | Python | 4,253 | 147 | """Central registries for dataset / model / task plugins (see ``dlbase/plugin_bootstrap``)."""
from __future__ import annotations
from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import Any, Callable, Type
from omegaconf import DictConfig
class TaskModule(ABC):
"""Abstract task... |
432bef58eed978f3b36b02631b3e042223ce67614b431d3a173c9b98fa76ca1d | Python | 4,253 | 114 | """
This module contains dataloaders for the training of Garfield model.
"""
from typing import Optional
from torch_geometric.data import Data
from torch_geometric.loader import LinkNeighborLoader, NeighborLoader
def initialize_dataloaders(
node_masked_data: Data,
edge_train_data: Optional[Data] = None,
... |
7da8528466fea9c91f0293e3c51dbd60486b51efc9b5d979f6dd5c61a4246eb1 | Python | 4,254 | 117 | import vtk, qt, slicer
class AbstractEffect():
"""
One instance of this will be created per-view when the effect
is selected. It is responsible for implementing feedback and
label map changes in response to user input.
This class observes the editor parameter node to configure itself
and queries the curr... |
1f367ad7adf80d69136d709dee0dfd7086b74bcea157eb7948ab1b4d13bd986d | Python | 4,255 | 100 | import cv2
import cmapy
from PIL import Image
import numpy as np
from msi_visual.utils import normalize_image_grayscale, image_histogram_equalization
class SegmentationUMAPVisualization:
def __init__(self, UMAP_model, segmentation_model):
self.UMAP_model = UMAP_model
self.segmentation_... |
3fb399dc483fdd4258949c966cc5927177f9f80ec2cecd775d50b274463d3175 | Python | 4,259 | 126 | """script to download sample data for vak autoannotate tutorial
Adapted from
https://github.com/NickleDave/bfsongrepo/blob/main/src/scripts/download_dataset.py
"""
from __future__ import annotations
import argparse
import pathlib
import shutil
import sys
import time
import urllib.request
import warnings
DATA_TO_DOW... |
733c0814737decb73f1127b75b8323e6d6d45980b04d7cccb2ae4199345bd93f | Python | 4,260 | 107 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import math
from dataclasses import dataclass
import torch.nn.functional as F
from fairseq import utils
from fairseq.logging import metrics
f... |
b5f6b938a31d51150ebf2698c6a117b743eb613918d3d68f9b7d9d769b09c96c | Python | 4,261 | 130 | import numpy as np
import itertools
from mdt.lib.post_processing import DTIMeasures, DKIMeasures
from mdt.model_building.parameter_functions.priors import AlwaysOne, UniformWithinBoundsPrior
from mdt.component_templates.parameters import FreeParameterTemplate, ParameterBuilder
from mdt.component_templates.compartment... |
00788409425336ea490542ba172917ffe4893dde3a458f55e5ac67a215c48dfd | Python | 4,263 | 118 |
try:
from importlib.metadata import version
except ModuleNotFoundError:
from pkg_resources import get_distribution
version = lambda name: get_distribution(name).version
from . import train, pre, scKANFormer_model
from .train import fit_model
from .pre import prediect
import os
name = "scKANFormer"
__vers... |
1cb89692356f4aab15a9641f0566eada20e70de1ca7776621f7b2616dd8a641f | Python | 4,265 | 105 | import torch
from torch import nn
from torch.nn import functional as F
class GroundTrans(nn.Module):
def __init__(self, in_channels, inter_channels=None, mode='dot', dimension=2, bn_layer=True):
super(GroundTrans, self).__init__()
assert dimension in [1, 2, 3]
if mode not in ['gaussian', 'em... |
08f3f9760d2f95c1ffd32e91a9dbd36123c4168ed2bded8d0ab35852236269a3 | Python | 4,266 | 143 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import TypeVar
import pytest
from cleo.testers.application_tester import ApplicationTester
from poetry.console.application import Application
if TYPE_CHECKING:
from pathlib import Path
from poetry.utils.cache import FileCache... |
f79d3da5c08290ebcfc64bccb1780778ccee4f901cdc9a6365b99ed9a1751fc4 | Python | 4,268 | 121 | import logging
# from lifelines.utils import concordance_index
from sklearn import metrics
from sklearn.metrics import accuracy_score
def evalualte(y_test, y_pred, y_pred_score=None):
accuracy = accuracy_score(y_test, y_pred)
# score_train = accuracy_score(y_train, y_pred_train)
if y_pred_score is None:
... |
2f9941853d82817cd5d434bcf29e4b5bfc9bb1e2a5681bc2c96e6cb6a9404ec6 | Python | 4,269 | 120 | import numpy as np
import scipy.signal
from scipy.linalg import sqrtm
import cv2 as cv
def Extend_Spatial_Decorrelation(v,xdim,ydim,dx,dy,dr): ##xdim是heigh,ydim是width
stacktmp = []
n,m = v.shape
##对数组做调整
s = np.zeros((xdim*ydim,n))
for i in range(n):
tmp = v[i, :]
tmp_... |
6352739fbe76834c9f25bfdc906ab7d5f04b370e96e6108bbb60e16239934898 | Python | 4,269 | 108 | #!/usr/bin/env python3
"""Encode all Hausser (mouse) and Lisberger (macaque) cells into 16-D latent
space, then save per-cell z vectors for latent-space flow visualisation.
Output NPZ keys:
{ct}_z_mouse (N_mouse, z_dim) float32
{ct}_z_macaque (N_mac, z_dim) float32
{ct}_wave_mouse (... |
0b711c6feb102ccd2295250f45bc9417ed9d33cfb9cf5c714f2a87698f75b1b4 | Python | 4,271 | 183 | import os
from jinja2 import Environment, FileSystemLoader
from pyecharts.commons.utils import JsCode
class _RenderType:
CANVAS: str = "canvas"
SVG: str = "svg"
class _Locale:
EN: str = "EN"
ZH: str = "ZH"
class _FileType:
SVG: str = "svg"
PNG: str = "png"
JPEG: str = "jpeg"
HTML... |
9f5cde90f3053484c70ae32bdfca14a0efcacfe5fc076b70e2bb72bab094ee72 | Python | 4,271 | 132 | #!/usr/bin/env python3
# Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license.
import logging
import os
import platform
from collections.abc import Iterator
from itertools import groupby
def setup_logging() -> logging.Logger:
"""Configure logging for the script.
... |
c74b5c90f342822615a329bcbd7feb418fe76922ac5e17182ad2504369b5d211 | Python | 4,272 | 119 | import warnings
from importlib.util import find_spec
from beartype.typing import Any, Callable, Dict, Optional, Tuple
from omegaconf import DictConfig
from src.utils import pylogger, rich_utils
log = pylogger.RankedLogger(__name__, rank_zero_only=True)
def extras(cfg: DictConfig) -> None:
"""Applies optional u... |
c7a199711718c90349554d01fb2714918ff2682f2acb5cad8ded1eb5ae213669 | Python | 4,272 | 136 | from layers import *
from utils import *
flags = tf.app.flags
FLAGS = flags.FLAGS
class Model(object):
def __init__(self, **kwargs):
allowed_kwargs = {'name', 'logging'}
for kwarg in kwargs.keys():
assert kwarg in allowed_kwargs, 'Invalid keyword argument: ' + kwarg
name = kwa... |
fdd65454f5ccc538a5ab3ffef72a2e619a1318f5c001deff5a58ba48128a9097 | Python | 4,272 | 122 | """
This code is to create a upper triangular cosine similarity matrix for all pmids.
author: Vishnu Vardhan Dadi
credits: [Leyla Jael Castro, Dietrich Rebholz-Schuhmann]
copyright: GENERAL PUBLIC LICENSE Version 3, 29 June 2007
"""
import argparse
import numpy as np
import pandas as pd
from tqdm import tqdm
from n... |
c8323d149c55f8ab4acb92f0b6c6cbdeec4f8b02d8fc1cd37a3c9afc8f9d2ddd | Python | 4,273 | 97 | import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from GMXMMPBSA.test_manifest import (
ManifestError,
build_help_text,
load_manifest,
verify_outputs,
)
class TestManifest(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.manifest = load_manifest... |
442616e7ce0a58b8213c871d2c0e0364cd25e151596af106e5cc72e8e6ec8a22 | Python | 4,274 | 91 | """Robustness of the Paper-#2 benchmark to the data split: refit every model with its canonical
tuned configuration across N independent group hold-out splits (different seeds) and report the
hold-out R² distribution per model per food. Answers the reviewer question "does the headline depend
on one lucky split?" at thi... |
052c91287754aa1b61ef02957e6f36e1e887e4f13786697de6ddf85654cd541d | Python | 4,278 | 139 | import argparse
import json
import pathlib
import webbrowser
import neuroglancer
import neuroglancer.cli
class Tool:
def __init__(
self,
viewer: neuroglancer.Viewer,
paths: list[pathlib.Path],
num_to_prefetch: int,
) -> None:
self.viewer = viewer
self.paths = p... |
7bbaee0b1d709d84a0a57ebce76b4e09ac3dd63fd4b5287075796c8128a956fd | Python | 4,278 | 190 | import math
import torch
import torch.nn.functional as F
import numpy as np
class MSELoss(torch.nn.Module):
'''
mean squared error loss function
'''
def __init__(self,
is_tensor=False):
super().__init__()
self.is_tensor = is_tensor
... |
fb0b6801c9188980d60dd63676917bb7549ef6e57f397af7b7d50e2dfa27040f | Python | 4,279 | 121 | import os
import anndata
import numpy as np
import pandas as pd
from scvi.data._built_in_data._dataset_10x import _load_dataset_10x
from scvi.data._download import _download
def _load_purified_pbmc_dataset(
save_path: str = "data/",
subset_datasets: list[str] = None,
) -> anndata.AnnData:
url = "https:/... |
544f2de4d011693105202bbd26002a344f8f4077e53dfdd1e4353a3df7138ba4 | Python | 4,281 | 88 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'UI/SimpleGNGUI.ui'
#
# Created by: PyQt5 UI code generator 5.5.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Form(object):
def setupUi(self, Form):
Form.setObject... |
854ba3080c52b62401defb82dabb6162654d3bbf904d09329d95893b919c5607 | Python | 4,283 | 93 | from mdt import CompartmentTemplate
import numpy as np
__author__ = 'Robbert Harms'
__date__ = '2018-08-27'
__maintainer__ = 'Robbert Harms'
__email__ = 'robbert@xkls.nl'
__licence__ = 'LGPL v3'
class Racket(CompartmentTemplate):
"""Computes the Racket model from [1].
As in the original paper, we optimize "... |
44816b4cd2807349ea6cc46422db4be22e1a9cf0c35c768e1ce073d4194adbc5 | Python | 4,285 | 107 | import numpy as np
from sklearn.metrics import (r2_score, mean_absolute_error, mean_squared_error,
f1_score, accuracy_score, precision_score, recall_score)
def normalize_to_100(pred: np.ndarray) -> np.ndarray:
pred = np.clip(pred, 0, None)
s = pred.sum(axis=1, keepdims=True)
s... |
e83ea429a536dac7cec8a885cd3249dbdde94e92daadabc512b6a3a2f48b8b59 | Python | 4,286 | 119 | """Options for calculating uncorrected p-values."""
__copyright__ = (
"Copyright (C) 2016-2018, DV Klopfenstein, H Tang et al., All rights reserved."
)
__author__ = "DV Klopfenstein"
import collections as cx
import sys
class PvalCalcBase(object):
"""Base class for initial p-value calculations."""
def _... |
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