sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b2857f0ee903dae1b9ec8865a5ecf02f1c4f69c193a180e827ee0d854f3e51db | Python | 9,171 | 239 | import logging
import warnings
import numpy as np
import pandas as pd
from keras.callbacks import Callback
# http://alexadam.ca/ml/2018/08/03/early-stopping.html
class FixedEarlyStopping(Callback):
"""Stop training when a monitored quantity has stopped improving.
# Arguments
monitors: quantities to be... |
c86a40504a1b3d4f994b039fb8e3f18bedb9ee00d4711510421cadef0429b59d | Python | 9,177 | 247 | import os
import h5py
import time
import numpy as np
import dask.array as da
from types import SimpleNamespace
from voluseg._steps.step4a import define_blocks
from voluseg._steps.step4b import process_block_data
from voluseg._steps.step4c import initialize_block_cells
from voluseg._steps.step4d import nnmf_sparse
from... |
06577b82279918d19310fa5f549a833e689a3dea402b2bffe30bbd8308267e61 | Python | 9,182 | 236 | from collections.abc import Hashable
import numpy as np
import pandas as pd
from scipy.stats import multivariate_normal
from pgmpy.structure_score._base import BaseStructureScore
class LogLikelihoodCondGauss(BaseStructureScore):
r"""
Log-likelihood score for Bayesian networks with mixed discrete and continu... |
b1ae7b256be306a24098bf1280e99ec0c912f3b3e5f6cf5d1ae7a2a28a79d6cd | Python | 9,182 | 238 | """Supplemental to Figure 2 — PhysMAP hyperparameter sweep on Hausser.
Grid (per preview_sweep.physmap_grid): 4 dimV × 3 metric × 3 nfeatures = 36 configs.
Each config's physmap_CV_results.csv contains 5 caret-CV folds (Fold1..Fold5).
Locked config (locked_configs.json): config_13, selection classifier KNN.
confi... |
42496814f276444dfcb534d7ebdf2b0c6098543a70bdfcee898b28cfc4678c90 | Python | 9,184 | 239 | # 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 logging
import math
from collections.abc import Collection
from dataclasses import dataclass, field
from typing import Any, List
impor... |
88102215f6d04a616a83e69bb75b391f09d796b287105096416d3d7f88eb4ee8 | Python | 9,186 | 286 | from typing import Dict, Optional, Tuple
import haiku as hk
import jax
import jax.numpy as jnp
from haiku import initializers
from nucleotide_transformer.types import SequenceMask
from nucleotide_transformer.utils import get_activation_fn
class DownSample1D(hk.Module):
"""
1D-UNET downsampling block.
""... |
9314bb2267b38c89b12c6e7bc24b57f8000476a20f8ad5d2319b5a84f8236e5e | Python | 9,187 | 222 | #!/usr/bin/env python3
"""
@file train_neural.py
@author Simon Yu
@date 02/15/2023
@brief Script for training neural models.
"""
import argparse
import dataset
import header
import logger
import math
import model
import test_neural
import torch
import tqdm
import utility
import wandb
def computeLoss(output, lab... |
fa60c2ac36b5e5079d02ab48e4c4669d1e5fdd345240784aba104bfc9945dd45 | Python | 9,191 | 216 | """
Compute the percentage of novel isoforms (structural_category != 'full-splice_match')
whose splice junctions are all supported by short-read RNA-seq (STAR SJ.out.tab files),
and whose 5' ends are within 100 bp of a CAGE-seq peak (refTSS).
"""
import sys
from pathlib import Path
import numpy as np
import polars as... |
698ee58a201979efac015b3d30ae40bbf3a78e5a85b972cf18add138d27012da | Python | 9,198 | 237 | """
scoring.py — cross-session CV scorers and score-mode dispatch.
Neutral home for the candidate-scoring strategies (kfold / loso / pairwise)
used by MAP, DWP and the BDP degrade path. These functions previously lived in
map_pipeline.py and were cross-imported by dwp_pipeline.py and bdp_pipeline.py;
centralizing them... |
8169db361fc3ba361b3c33658b8ea01486153811fe6790504e181bee53afdc3a | Python | 9,198 | 262 | # 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 copy
import logging
from fairseq.models import (
FairseqEncoderModel,
FairseqLanguageModel,
register_model,
register_m... |
ef876e90b66c19d47e50d92b27ff237dfe38e2076721bbe20417a601a42cba8e | Python | 9,203 | 167 | import os
import numpy
import numpy.testing
import pandas
from sqlalchemy import create_engine
import unittest
from metax import PredictionModel
from . import SampleData
def get_model_weights(path):
engine = create_engine('sqlite:///'+path)
return pandas.read_sql_table('weights', engine)
def get_weights_i... |
85077cdfcaad65199fe4ccbc46b44372d9fd6e9826d197899b8eb7c4ac29deaa | Python | 9,204 | 258 | """Analytic forces for OCE.
For each figure class F, we compute the partial derivatives ∂Π_F/∂r_a
of the correlation feature with respect to atomic positions r_a. The
total force on atom `a` is
F_a = -Σ_F J_F · ∂Π_F/∂r_a
with J_F obtained from a fitted ``oce.fit.OCEModel``.
Topology assumption
----------------... |
bbf31376720c83b3e940a5419ef16dd842489e9517e5f2ef4a0d443f6006655c | Python | 9,205 | 226 | import json
import os
import subprocess
import sys
from pathlib import Path
import pytest
from rnalysis.utils import param_typing
from rnalysis.utils.param_typing import DEFAULT_ORGANISMS
REPO_ROOT = Path(__file__).resolve().parent.parent
# param_typing getter -> the vocabulary key it reads out of the packaged snap... |
5425a2d516b294e6dde39af7cb982cda4e29248e33020b9fee5f20144fb4603c | Python | 9,209 | 222 | """
Usage:
This script is used to extract the embedding / logit for speech classification task.
1. Set fdir into your model checkpoint directory
2. Run the following command (preferrably on GPU machine to speed up the inference process)
CUDA_VISIBLE_DEVICES=0 python3 examples/wav2vec/gen_audio_embeddin... |
047241ceb99d0e6e65c967304f29ba3cd60bd533ea3efbd6f15efc21f7a3fea9 | Python | 9,213 | 338 | import os
import subprocess
import pytest
import torch
from mudata import MuData
import scvi
from scvi.model import MULTIVI, PEAKVI, TOTALVI, CondSCVI, LinearSCVI
@pytest.mark.multigpu
@pytest.mark.parametrize("unlabeled_cat", ["label_0", "unknown"])
def test_scanvi_from_scvi_multigpu(unlabeled_cat: str):
impor... |
1b23206fcf63c7dd10210a9561990d182968902aff9c01e0967fc3ca70bc1016 | Python | 9,215 | 225 | """Build the Nature Communications Source Data workbook.
Writes one sheet per manuscript panel containing the values plotted in that
panel. Nothing is recomputed from raw recordings: every sheet is a view of the
cached per-fold predictions and metrics that produced the figures.
Sheets sourced from ``figures/**/*_metr... |
c085227b9fa7d7ebf305a54c460b7412a96da2a291b3632a516a7465808db6d2 | Python | 9,225 | 218 | import configparser
import datetime
import sys
import os
import numpy as np
import pandas as pd
from scipy.stats import norm
from multiprocessing import Pool
def process_template_chr(c, template_dir, bfile_prefix, out_dir):
print(f"processing template chr {c}")
bim_file = os.path.join(template_dir, f"{bfile_p... |
7d0ed39f2b23f4f90d01377fa8dad304a1eb5c77caf52cd8c6ebd3b02bb25bef | Python | 9,228 | 319 | from docutils import nodes
from docutils.parsers.rst import Directive, directives
from sphinx.util.docutils import SphinxDirective
from docutils.statemachine import StringList
import os
import json
# Here we define the order of the model groups
# as they should appear in the list
GROUP_ORDER = [
"Quick start",
... |
d6a11d5e0e3729e23756ae7bfb5d89dc3f0af0b67b1650a1b667d2dfb8473303 | Python | 9,228 | 190 | """Sorts GO IDs or user-provided sections containing GO IDs."""
__copyright__ = "Copyright (C) 2016-2019, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import collections as cx
from goatools.wr_tbl import prt_txt
from goatools.grouper.sorter_nts import SorterNts
from goatool... |
3ed6d86e68d6a5659511a221fa6debfec8477b70d271e336dc6047e163e2e3ce | Python | 9,232 | 212 | from typing import Union, Tuple, List
import numpy as np
import torch
from batchgeneratorsv2.helpers.scalar_type import RandomScalar
from batchgeneratorsv2.transforms.base.basic_transform import BasicTransform
from batchgeneratorsv2.transforms.intensity.brightness import MultiplicativeBrightnessTransform
from batchgen... |
065182857e3e60ca0f274c86b8bf9d4b09c79dc3f3029f7bca32dd3e20c944a1 | Python | 9,234 | 261 | import numpy as np
from scipy.optimize import newton
import pandas as pd
from numba import jit
import os
import ast
import matplotlib.pyplot as plt
Lr = 0.013
gr = 1.
eps = 0.01 # perturbation rate for local sensitivity analysis (e.g., eps=0.01 means 1% perturbation)
rank = 1 # specify the rank of the parameters to u... |
57cb8aad5a9a7d4b7de00a27d8e6a548c356d7c618c81852b36e447ed04228ce | Python | 9,234 | 194 | """Functions to read text or tsv files containing GO IDs and sections of GO IDs."""
from __future__ import print_function
import os
import sys
import re
import pkgutil
import importlib
from goatools.gosubdag.go_tasks import chk_goids
from goatools.grouper.hdrgos import HdrgosSections
from goatools.grouper.grprobj imp... |
aa693f793a56e2d41bbe54c2c1ffc9b96d2f681a1ddb0f6d00eab6d6cf9a5725 | Python | 9,236 | 295 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# ecephys_spike_sorting documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present... |
fff7999b0ac93da58d1d122b8ed888231c17286c835fe986e08175ed728ec043 | Python | 9,239 | 239 | """Wave-1.5 OCE on perovskite SIESTA pool — full ablation.
Compares baseline (1F+2F), CT2F (Wave-1), and Wave-1.5 (CT2F_A + MADCT2F + CT3F)
variants on the n=243 SIESTA-PBE labelled pool, with per-kind and per-family
breakdown. Strain regime is the key target.
"""
from __future__ import annotations
import json
import... |
9b8091d4062983ee7636f7ece07143093e42bc91237124a129d872ca6f7f4f9f | Python | 9,240 | 259 | import pytest
from pgmpy.independencies import IndependenceAssertion, Independencies
@pytest.fixture
def assertion():
return IndependenceAssertion()
@pytest.fixture
def eq_assertions():
return {
"i1": IndependenceAssertion("a", "b", "c"),
"i2": IndependenceAssertion("a", "b"),
"i3":... |
3287c5daf9bba5d974466354db314aeb3e86512fe052159b1a72e13832b478df | Python | 9,243 | 216 | from functools import partial
from typing import Callable
import jax
import jax.numpy as jnp
from jax import random, vmap
from ..geom import masked_pairwise_distance
from ..types import (
ElectronConfiguration,
ModelDimensions,
MolecularConfiguration,
ParallelElectrons,
RandomKey,
)
from ..utils i... |
dc73cb28beeebfd66c1a1a64f98904b3cbae6fc06002f13250a5c97da3143d57 | Python | 9,248 | 280 | """Manage optional GO-DAG attributes."""
__copyright__ = (
"Copyright (C) 2015-present, DV Klopfenstein, H Tang, All rights reserved."
)
__author__ = "DV Klopfenstein"
import re
import collections as cx
from ..base import logger
class OboOptionalAttrs:
"""Manage optional GO-DAG attributes."""
optional... |
4bbf7bb02ee3d8b4555fea852a6867d26c9d825dbe26e90ce12bcdf3388a6fca | Python | 9,256 | 190 | # 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... |
53f1f9feb7be7657d40d7dc47bfeeda90187efd147f32630721ae88adcb3f692 | Python | 9,259 | 208 | # Ranger deep learning optimizer - RAdam + Lookahead + Gradient Centralization, combined into one optimizer.
# https://github.com/lessw2020/Ranger-Deep-Learning-Optimizer
# and/or
# https://github.com/lessw2020/Best-Deep-Learning-Optimizers
# Ranger has been used to capture 12 records on the FastAI leaderboard.... |
dd0a5847dfef9627f1638509058c22d892625656e571d6a337d69c63f2f3757b | Python | 9,259 | 211 | #!/usr/bin/env python3
"""
@file train_blackbox.py
@author Simon Yu
@date 01/26/2023
@brief Script for training blackbox models.
"""
import argparse
import dataset
import header
import logger
import model
import test_blackbox
import torch
import tqdm
import utility
import wandb
def processArguments():
parse... |
d3ac536d7c1e2c7276c4128b3d9941d3b87957e14c3e03bb818fc5a2b700755f | Python | 9,260 | 251 | from __future__ import annotations
import numpy as np
from skbase.base import BaseEstimator
from pgmpy.base import DAG
from pgmpy.models import DiscreteBayesianNetwork, LinearGaussianBayesianNetwork
from pgmpy.utils import build_state_names, preprocess_data
class BaseParameterEstimator(BaseEstimator):
"""
T... |
fa1d12377606eceeac65a08d1a3743613052709460d04659c333224d632b2430 | Python | 9,261 | 186 | #!/usr/bin/env python
# PYTHON_ARGCOMPLETE_OK
"""Fit one of the models to the given data.
This function can use two kinds of noise standard deviation, a global or a local (voxel wise).
If the argument -n / --noise-std is not set, MDT uses a default automatic noise estimation which
may be either global or local. To use... |
3b687fe4abb4f1c960eef6190225356ee686f6ea62e2c6ff2d16da1cb8e3b3ae | Python | 9,262 | 312 | import os
import time
import sys
import traceback
from PyQt5 import QtCore
from contextlib import contextmanager
from functools import wraps
from PyQt5.QtCore import QObject, pyqtSignal
from PyQt5.QtCore import QTimer
from PyQt5.QtWidgets import QApplication
from mdt.__version__ import __version__
from mdt.lib.log_... |
aaa20dc927f6f23d0b2aa9e10e72ad13b19f3cb87faa5ceb8f5227a6363be926 | Python | 9,262 | 254 | import numpy as np
from scipy.stats import ttest_ind, pearsonr
from sklearn.model_selection import StratifiedKFold
class CounterbalancedStratifiedSplit(object):
def __init__(self, X, y, c, n_splits=5,
c_type='categorical', metric='corr', use_pval=False,
threshold=0.05, verbose=F... |
50d2c003d53ffd72dbe68cfa8663185a189d61cddece0fe98089d3c3e2e60f36 | Python | 9,264 | 173 | import numpy as np
import logging
from scipy.sparse import csr_matrix
from .utils import AnnotUnivariateParams
from .utils import AnnotUnivariateParametrization
def get_null_params(libbgmg):
return AnnotUnivariateParams(libbgmg=libbgmg, s=0, l=0, sig2_zeroL=0)
def get_params(libbgmg):
return get_null_params(... |
52add9ae12174cf84e06a84cd81479cc2d9ca154cd41f819e5f85a401c30e5a0 | Python | 9,267 | 242 | """Classifier and relation heads used by the models in this package.
Also holds `PermutationBatchNorm1d`, the hidden-block normalisation layer
`base.py` builds into its hidden layers and runs through
`base._run_hidden_layer` — not a head, but placed here rather than moved
next to its only caller.
"""
import math
from... |
6ad2a9c95e09d843dfdf553a4350c1d15d238fb3f390f58cae1619fc4ca7e061 | Python | 9,272 | 258 | from functools import partial
from typing import Callable, Literal, Optional, Protocol, Tuple, Type, Union
import jax
import jax.numpy as jnp
import jax.numpy.linalg as jnp_linalg
import numpy as np
import scipy
from pyscf.dft import numint
from oneqmc.density_models.analysis import DensityModel, get_dft_grid
from .... |
dd6cb72fff9dfbba9137c56b8128e80fbe18bf8423bc2bbcd27f374f775c10f0 | Python | 9,275 | 251 | import numpy as np
from ClusterWrap.decorator import cluster as cluster_constructor
from bigstream.align import alignment_pipeline
from bigstream.transform import apply_transform
from bigstream.piecewise_align import distributed_piecewise_alignment_pipeline
from bigstream.piecewise_transform import distributed_apply_tr... |
758fb064594fc945fa79c9874f0a1d5c7401f932a6fdebd8e2c2058aec0f5301 | Python | 9,280 | 181 | import sys
sys.path.append("../utils")
import torch
import torch.nn as nn
from utils import utils_basic
import config.cfg_lodet as cfg
#处理类别不平衡问题，使得模型更关注难分类的样本，从而提高性能
class FocalLoss(nn.Module):
def __init__(self, gamma=2.0, alpha=1.0, reduction="mean"):
super(FocalLoss, self).__init__()
s... |
a7ae26d7af4bc8ddda058bb948dda51789e40e6823c5c8a713d558ce6a4998ab | Python | 9,281 | 292 | # 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 required by applicable law or a... |
6667ee47cede72f80e62200ac683d032b84d13c459ca7e915a2c7bb6164e83d7 | Python | 9,283 | 191 | #!/usr/bin/env python3
"""Análise da DOS das 1.784 perovskitas: o que ela responde para o artigo.
Consome `dos_perovskitas.npz` (curvas em grade relativa a E_F + escalares),
produzido por `dos_remoto.py`.
AS PERGUNTAS, em ordem de importância para o manuscrito do gap:
1. VALIDAÇÃO nas 1.784 (não em amostra): o gap... |
d472833446987c6ca4eb659b168401c78ea28f69e06629be0c8226da8d964256 | Python | 9,285 | 201 | #%%
import os
import numpy as np
import pandas as pd
from tqdm import tqdm
import itertools
from scipy.stats import mannwhitneyu
from statsmodels.stats.multitest import multipletests
from utils import compute_ccc, combat_correction, bca_bootstrap_ci
BIAS_CORRECTION = ["none", "default", "brain", "gwm"]
ZNORM_ROI = [... |
c32aca77e589f5c37f629f23d28b778bb9fda6f43afb6a75260a9f2e40771728 | Python | 9,289 | 254 | # 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
import torch
import torch.nn.functional as F
from fairseq.models.nat import (
_apply_del_words,
_apply_ins_masks,
_ap... |
04821328d01da8ed76a999b8678d5b2549ebc5953c5f8d578d74e67d5d59fe8c | Python | 9,292 | 247 | # 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 contextlib
import logging
import unittest
from io import StringIO
from unittest.mock import MagicMock, patch
import torch
from fairseq... |
fa8f2fa776ec87656f40dbaf96c5dfac863453926c86278400e3a7703cbe506d | Python | 9,292 | 321 | import os
import csv
import math
import re
from pathlib import Path
PROJECT_ROOT = Path(__file__).resolve().parent
INDEX_2016_PATH = PROJECT_ROOT / "dataset" / "index" / "v2016" / "INDEX_general_PL_data.2016"
INDEX_2020_PATH = PROJECT_ROOT / "dataset" / "index" / "v2020.R1" / "INDEX_general_PL.2020R1.lst"
CASF_2013_... |
771ce812372a88753fd58401ff1aabb67f3505a7d96ad185d54634570851ac10 | Python | 9,296 | 273 | import plotly.graph_objects as go
import networkx as nx
import matplotlib.pyplot as plt
import json
import os
def get_traces(G, adj_mode="color"):
edge_x = []
edge_y = []
for edge in G.edges():
x0, y0 = G.nodes[edge[0]]['pos']
x1, y1 = G.nodes[edge[1]]['pos']
edge_x.append(x0)
... |
afb693b51676dbe3f09305d70a9d0b7d85873e50f79379860d1982ab7f18a07d | Python | 9,305 | 251 | """Module providing queries into the document database."""
import logging
from collections.abc import Callable, Iterable, Mapping, MutableMapping
from pathlib import Path
from types import TracebackType
from typing import Any, Literal, Self
from apiadapters.ncbi.parser import is_scanned
from lpsn_interface import lps... |
87b6cdbb8dc03898018f4381b5db783ba67011e36161798efeeb2412e3f52616 | Python | 9,307 | 244 | from math import e
import time
from matplotlib.pylab import f
import scipy
import pandas as pd
import numpy as np
import pingouin as pg
import matplotlib.pyplot as plt
from scipy.stats import pearsonr
import seaborn as sns
from sklearn import metrics
# durations
egestive_priming_data = scipy.io.loadmat("data_folder/Eg... |
916c08f988843e744d3e76a62324ba3f0c9f54975296dabe4af86a50941b5ed0 | Python | 9,308 | 236 | """Unit tests for vak.prep.frame_classification.make_splits"""
import json
import pathlib
import shutil
import crowsetta
import numpy as np
import pandas as pd
import pytest
import vak.prep.frame_classification.make_splits
@pytest.mark.parametrize(
'annots, expected_sort_inds',
[
(
[
... |
5d20b91b872da434b59ae85efbf0d9c232f5ceebc02f4db5675a7fa6b90dbbb6 | Python | 9,311 | 270 | import os
import warnings
from pathlib import Path
import anndata as ad
import numpy as np
from anndata import AnnData
from scvi import settings
from scvi.utils import dependencies
@dependencies("readfcs")
def read_fcs(
path: str,
return_raw_layer: bool = True,
include_hidden: bool = False,
remove_m... |
06763765eab7786586fec9625ab69a8f05018e0567aee0a3df057bb0de362467 | Python | 9,312 | 268 | # 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 logging
import os
from dataclasses import dataclass, field
from typing import Optional
import numpy as np
from omegaconf import II
fro... |
305cef45c6dc034bdf72fd91aba1e89e1c6b5d222c3d6baffff5acdfd9b3873e | Python | 9,312 | 220 | #!/usr/bin/env python
#
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list o... |
f728aba8677e22bd4f467206504c9063e2a6699255a5988dfc49e71269d7f73c | Python | 9,315 | 281 | #!/usr/bin/env python3
"""Train a fully connected BM, writing results directly to disk."""
import argparse
from itertools import product
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
import yaml
from neuralsampling import utils
from neuralsampling.network import GradDescent, NeuralSamp... |
62313378bf5b1ea7a87affca1ff857cf38b0382677ef92867b178589bc22b16b | Python | 9,321 | 283 | """Utilities used in Gene Ontology Enrichment Analyses."""
import bz2
import gzip
import io
import logging
import os
import os.path as op
import sys
import tempfile
import traceback
import zlib
from os.path import isfile
from subprocess import PIPE, Popen
from urllib.request import urlopen
import requests
from ftpr... |
028cc15ddeccab9f1f671a176ed1d9eda7294c42311bb05ede0dc39296b214f2 | Python | 9,324 | 317 | # -*- coding: utf-8 -*-
"""
Created on Thu Mar 6 14:00:52 2025
@author: hanna
"""
"""
[Figure 4A, 4B] changes in preferred of individual BCI neurons from example sessions
"""
import os
import pickle
import numpy as np
import pandas as pd
from tqdm import tqdm
import seaborn as sb
import matplotlib as mpl
im... |
144b299a115edb3e3fb6ea18d226d86e6841f79ce4254ee861dac53c5a337d72 | Python | 9,324 | 265 | """Sequence encoders for Bayesian Optimization.
Supports one-hot encoding, physicochemical property encoding, and Boltz2
remote API embeddings.
"""
import hashlib
import os
import numpy as np
import requests
import time
from concurrent.futures import ThreadPoolExecutor, as_completed
AAS = "ILVAGMFYWEDQNHCRKSTP"
# P... |
4b4ef729c34322b7edbecebae0fbf0a35c41f534837dd70aaa05ca6673532fcb | Python | 9,325 | 252 | """Module providing queries into the document database."""
import logging
from collections.abc import Callable, Iterable, Mapping, MutableMapping
from pathlib import Path
from types import TracebackType
from typing import Any, Literal, Self
from apiadapters.ncbi.parser import is_scanned
from d3types import Document, ... |
5f7d26a7eb6970ce9b3615dd16fbac9adf1711ab83400b0f0e95aa9ac53060a7 | Python | 9,327 | 289 | from typing import Tuple, List, Dict, Optional, Sequence
from collections import defaultdict
import string
from pathlib import Path
from Bio import SeqIO
import subprocess
from .typed import PathLike
from .constants import IUPAC_CODES
from .dataset import ThreadsafeFile
import numpy as np
from scipy.spatial.distance im... |
24f2ee742e965c91e1b49b4f9e257cebd79239719ef71300d3855b0c9f667120 | Python | 9,328 | 300 | # Copyright 2026 Hongyu Sun
# Licensed under the Apache License, Version 2.0
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
import pytorch_lightning as pl
from torch_geometric.nn import MessagePassing
class Feedforward(nn.Module):
def __init__(self, channel_size: int, hidden... |
6bc69cb0eff0c490b27afb8f0a73c4769f52c8999b3c906b013fc6b1a1524a0f | Python | 9,329 | 300 | # Copyright 2026 Hongyu Sun
# Licensed under the Apache License, Version 2.0
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
import pytorch_lightning as pl
from torch_geometric.nn import MessagePassing
class Feedforward(nn.Module):
def __init__(self, channel_size: int, hidden... |
75e4b15d26782edda38d5bb171bc264c2035b68f26bf9ba8dadeb19d898b5b99 | Python | 9,332 | 256 | import cProfile
import pstats
import time
import os
from simulation_encoder.runner import Runner
from simulation_encoder.writer import Writer
from simulation_encoder.plotter import Plotter
from simulation_encoder.logger import Logger
from simulation_encoder.dataclass.param_sets import DatasetParams, ModelParams
from ... |
a488215e53c5c0338b7d1a5c85d76fd4f5af81013a23e1b98bc34c199fe95ea3 | Python | 9,338 | 289 | import os
import re
import sys
import logging
import time
from nipype import config
from nipype import logging as nlogging
from nipype.interfaces.base import CommandLine
import subprocess
# Use Nipype's concurrent rotating handler if available (multi-proc safe)
try:
from nipype.external.cloghandler import (
... |
e956605d5b8aced0e8a1f056002ef14914e0496d19b478e9ffc2019ad10e760a | Python | 9,340 | 232 | from ryp import r, to_r, to_py
import polars as pl
import polars.selectors as cs
def read_gtf(file, attributes=["transcript_id"], keep_attributes=True):
if keep_attributes:
return pl.read_csv(file, separator="\t", comment_prefix="#", schema_overrides = {"seqname": pl.String}, has_header = False, new_column... |
eeca74593efbf62b04eb17728122f43a888be5fe3594b93cd1b57088db6fcb2b | Python | 9,341 | 238 |
"""
Xception is adapted from https://github.com/Cadene/pretrained-models.pytorch/blob/master/pretrainedmodels/models/xception.py
Ported to pytorch thanks to [tstandley](https://github.com/tstandley/Xception-PyTorch)
@author: tstandley
Adapted by cadene
Creates an Xception Model as defined in:
Francois Chollet
Xceptio... |
7dacb79f88dda492ccfdc219883db75fde24a249c11c44a7a2060bf504673ef9 | Python | 9,347 | 369 | import re
import pytest
from skbase.lookup import all_objects
from pgmpy.base import DAG
from pgmpy.example_models import list_models, load_model
from pgmpy.example_models._base import BaseExampleModel
from pgmpy.models import (
DiscreteBayesianNetwork,
FunctionalBayesianNetwork,
LinearGaussianBayesianNet... |
f5dbce99372cb323a1462962bfa216a7da26d792e4c4447495eeb8824522838f | Python | 9,350 | 229 | #!/usr/bin/env python3
"""Build the per-sample bulk-RNA sex table that the sex-adjusted sensitivity analysis consumes.
WHY THIS EXISTS. sex_adjusted_sensitivity_rna.R reads Methylation_Data/rna_sex_persample.csv, and
that file was never deposited - it was written to a session temp directory and lost, so the
sensitivit... |
6dd4b4dca7c7b55e4ed3cabfc75acf8d1bf08a4b9b0a68b7f7e55e3c38b8f921 | Python | 9,358 | 274 | # Copyright (c) Facebook, Inc. All Rights Reserved
import numpy as np
import os
import torch
class Processor(object):
"""
A generic processor for video (codec, feature etc.) and text.
"""
def __call__(self, **kwargs):
raise NotImplementedError
class MetaProcessor(Processor):
"""
A ... |
d1ffdeab48419d8f4c2bc2e1799f680bb5faee91f169863afd8c87a13dc061b9 | Python | 9,358 | 359 | #!/usr/bin/env python
# ENCODE DCC common functions
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import re
import csv
import logging
import subprocess
import math
import signal
import time
import argparse
logging.basicConfig(
format='[%(asctime)s %(levelname)s] %(message)s',
stream=sys.stdout)
... |
33aa7d61681c15023a5e9953ab3bb16566987f79d43519259437d51db103a490 | Python | 9,365 | 153 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'optimization_extra_data_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.10.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_OptimizationExtraDataDialog(object):
def set... |
d9e8f1a6b21f81c9a4c12b4e3adfd5f1faa603dde2d11600afc80e6797077e9d | Python | 9,367 | 278 | # Simulate uniform rotations and translation of the whole sensor array
#%% Imports
import numpy as np
import matplotlib.pyplot as plt
from bfieldtools import sphtools as sph
import functions
font = { 'size' : 20}
plt.rc('font', **font)
#%% Plot parameters
legendfontsize = 15
linewidth = 2.5
#%% Define paramete... |
9c17ea0eb4a96c8cc2d2e92279caba3febd7718fc05d0ac83d10ff799fa71eb4 | Python | 9,368 | 356 | # 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 required by applicable law or a... |
a8175682b19964f0123852de27d4f31460f023c0cb0c376f291b405e55058868 | Python | 9,368 | 273 | import json
import os
import pathlib
import shutil
import tarfile
import urllib.request
import nox
DIR = pathlib.Path(__file__).parent.resolve()
VENV_DIR = pathlib.Path('./.venv').resolve()
with pathlib.Path('./tests/vak.tests.config.json').open('rb') as fp:
VAK_TESTS_CONFIG = json.load(fp)
nox.options.sessi... |
4409ed7d62268011d94ffd0a2df1d9674fb59d13bd1d2ace001c6384b734f65a | Python | 9,372 | 185 | """
VGG 16 model without Predify
"""
import torch
import torch.nn as nn
from torchvision.models import vgg16_bn
class VGG16Baselin... |
f7aba24d8529fe755e63ad44b26f6365f7da99334c0f63301c304a9f6935b4a5 | Python | 9,373 | 351 | # 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 bisect
import time
from collections import OrderedDict
from typing import Dict, Optional
try:
import torch
def type_as(a, b):... |
6502f38ed6b9e8f831bab978d13a9bf176ecd6110263bab79eba808f8c2a8378 | Python | 9,375 | 205 | """tests for vak.config.learncurve module"""
import pytest
import vak.config.learncurve
class TestLearncurveConfig:
@pytest.mark.parametrize(
'config_dict',
[
{
'standardize_frames': True,
'batch_size': 11,
'num_... |
e5c050ca5bbf40c6bccde806a8ef0ab332f19a141d925d0a7a098306760a9f45 | Python | 9,379 | 218 | import numpy as np
from scvi import settings
from scvi.data import AnnDataManager
from scvi.dataloaders import DataSplitter
from scvi.dataloaders._data_splitting import (
validate_data_split,
validate_data_split_with_external_indexing,
)
from ._contrastive_dataloader import ContrastiveDataLoader
class Contr... |
18a6685c37474e2371481e70e35cc22dbd51e88b59660831e9670bbd67cbde5d | Python | 9,382 | 253 | import numpy as np
import pandas as pd
import os, six, sys, subprocess, time
def prob_output(pred_data, pred_path):
"""
INPUT: a tuple of (predict, label)
output prob_file
"""
pred_label = pred_data
for id, seq, y_pred in pred_label:
y_pred = y_pred.cpu().numpy() # GPU data to CPU
... |
ae24e6199228e5da17d84dd1fcfcd448b79f7783985655cdee00866be94bbfb0 | Python | 9,383 | 253 | import numpy as np
import pandas as pd
import os, six, sys, subprocess, time
def prob_output(pred_data, pred_path):
"""
INPUT: a tuple of (predict, label)
output prob_file
"""
pred_label = pred_data
for id, seq, y_pred in pred_label:
y_pred = y_pred.cpu().numpy() # GPU data to CPU
... |
bbb2f4aa6db2e822f6abc89a54e21755674d2612e44be0df23ae95feaf44fd5a | Python | 9,384 | 274 | import os
import glob
import re
from pathlib import Path
import pickle
import numpy as np
import pdb
from celltype_ibl.params.config import DATASETS_DIRECTORY
from torch.utils.data import Dataset
import torch
SAVE_DIR = DATASETS_DIRECTORY
def find_files(directory: str, filename: str):
"""
Find files with a s... |
4a8b4f464d4bb0f21cb3f69d20ef99e5fa84accf401d68222c176d2b57ceb05f | Python | 9,389 | 228 | #Line 1-190 is from https://github.com/phbradley/alphafold_finetune/blob/main/predict_utils.py
from alphafold.common import residue_constants
from alphafold.data import templates
import numpy as np
#this is from alphafold/data.templates.py
from typing import Any, Dict, Mapping, Optional, Sequence, Tuple, Union, List
i... |
aecc2079edf9249fb33d458832a0e9a9954f78319f9f3095dff0735edceb38ac | Python | 9,392 | 219 | """Phase 2: KAN interpretability on tahini.
Produces (into results_phase1/paper/): the symbolic equation (txt + LaTeX), an accuracy-vs-complexity
table, KAN response curves overlaid on the linear PLS effect (where they differ = KAN's added value),
and PLS-component-to-chemistry loadings. Run: python -m kanfood.interpre... |
22268ce7f1c86961d987699c12f9c5f25b1c8e30ff4b916065384da21a482fae | Python | 9,394 | 231 | from typing import Callable, List, Optional, Tuple, Union
import numpy as np
import torch
import ttach as tta
from pytorch_grad_cam.activations_and_gradients import ActivationsAndGradients
from pytorch_grad_cam.utils.image import scale_cam_image
from pytorch_grad_cam.utils.model_targets import ClassifierOutputTarget
... |
d2da92e0f66a06b756740f64acec15e9f9f2413e8bdd5c12732c1a49317c5281 | Python | 9,399 | 313 | """
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.
"""
# Copyright (c) Facebook, Inc. and its affiliates.
# Borrowed from https://github.com/facebookresearch/pythia/blob/master/pythia/common/regis... |
78b94f58b3d729395c3a0ee9769309138afb2989f73880b1e254ea03ef33207a | Python | 9,402 | 210 | import os
import fcntl # For Unix-like systems (including Ubuntu)
'''
By properly implementing file locking mechanisms like using fcntl for Unix-like systems,
one can ensure that the Optuna optimization process runs smoothly without encountering
race conditions or file locking issues, even when using multiple proces... |
0331e58fb87d2060f70a72fc6eebc881ff6a08f7bbe9cee4491afe2726533598 | Python | 9,403 | 267 | # Copyright (c) 2021-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 logging
import math
from ty... |
a8fa1bcc2615475120de1b3205e12473ad85b9df1313dd36e8100f823c1cce57 | Python | 9,404 | 264 | import os
import sys
from pathlib import Path
from sklearn import metrics
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, TensorDataset, Dataset
from tqdm import tqdm
from sklearn.metrics import accuracy_score, recall_score, precision_score, f1_score, m... |
ae10ea9585e3080e4455ba3d10758b48602b796933bc6c9c4ac1b0bb2045a14f | Python | 9,410 | 245 | import os
import json
from typing import Optional, Callable, Any
from abc import ABC, abstractmethod
import numpy as np
import torch
from torch.utils.data import DataLoader, Subset, TensorDataset
from simulation_encoder.logger import Logger
from simulation_encoder.loaders.dataset_utils.augmentation import Augmentatio... |
b8f3fe9dde0e8184076aed64d2e2df60786e963942758d7f9febef31f2380ba2 | Python | 9,412 | 289 | import sys
from PyQt5.QtWidgets import QApplication, QWidget, QPushButton, QGridLayout, QFileDialog
import PyQt5.QtWidgets as QtWidgets
from PyQt5.QtGui import QIcon, QKeyEvent
from PyQt5.QtCore import pyqtSlot, Qt
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as... |
f3214ad483667e5647ea903d371be054cbb2b873ab8f36fb509cd2cc2c503a3d | Python | 9,414 | 274 | import os
import glob
import re
from pathlib import Path
import pickle
import numpy as np
import pdb
from celltype_ibl.params.config import DATASETS_DIRECTORY
from torch.utils.data import Dataset
import torch
SAVE_DIR = DATASETS_DIRECTORY
def find_files(directory: str, filename: str):
"""
Find files with a s... |
8929f4b6cfa19d37ac8f524fb74f428a1f6af4dbe90b5bbc91f4382c7d3a376f | Python | 9,420 | 247 | """Build a perovskite structure library for OCE feature evaluation.
Inorganic ABX3 perovskites with A in {Cs,K}, B in {Pb,Sn,Ge}, X in {I,Br,Cl,F}.
Three families:
(a) endmembers — 5-atom cubic Pm-3m primitive cells, 24 ABX3 combinations
(b) mixed-X — 2x2x2 supercells (40 atoms) with 1-12 halide substitutions
... |
b4300553a02342eb8050cb6a9bca1a38c7f3247c964938a4f02825d2c7309c6a | Python | 9,423 | 270 | from typing import Tuple
from dataclasses import dataclass
import math
import torch as th
from torch import nn
from config_base import BaseConfig
from .blocks import Upsample, AttentionBlock
from .nn import conv_nd
from einops import rearrange
from utils import M2H
def exists(x):
return x is not None
class Si... |
ded9971904a3d98143de16f78bde7851253f1beb1388e5544dab9b0a0ce90153 | Python | 9,426 | 255 | import numpy as np
import torch
import torch.nn as nn
from sklearn.cross_decomposition import PLSRegression
from sklearn.ensemble import RandomForestRegressor
from sklearn.multioutput import MultiOutputRegressor
from sklearn.preprocessing import StandardScaler, MinMaxScaler
from sklearn.svm import SVR
from kan import K... |
0b04edc261c9ef030093e70a03d35a20b848c06b66cf67742dd3eb39dd491fd5 | Python | 9,429 | 259 | #!/usr/bin/env python
"""Provide a command line tool to validate and transform tabular samplesheets."""
import argparse
import csv
import logging
import sys
from collections import Counter
from pathlib import Path
logger = logging.getLogger()
class RowChecker:
"""
Define a service that can validate and t... |
3da02344ae52ae1a51d9f3fd174304af38e3a249abd3210c351cc961ede301da | Python | 9,429 | 241 | from __future__ import annotations
from typing import List, Literal
import torch
from .functional import precision_recall_fscore_rval, BOUNDARY_DETECTION_IR_METRICS, BoundaryDetectionIRMetric
class PrecisionRecallFScoreRVal:
r"""Compute information retrieval metrics for boundary detection:
precision, recal... |
e028a52f396b87c4fc5a31034305ae352032a3b289869c8f3351d5c83fb89840 | Python | 9,433 | 283 | """PyTorch module for methylVI for single cell methylation data."""
from collections.abc import Iterable
from typing import Literal
import torch
import torch.nn as nn
from torch.distributions import Binomial, Normal
from torch.distributions import kl_divergence as kl
from scvi import REGISTRY_KEYS
from scvi.distribu... |
4da53217a98c6d5917cabeb29033b9a10715a8d203480b8fc8a7edba16199567 | Python | 9,435 | 227 | """Phase 7 — focused coordination study.
Re-samples small subsets of percolation clusters (L = 32, 64) for both
materials × 3 lattices, runs LAMMPS optimisation, and stores BOTH the
relaxed positions AND the post-relaxation coordination distribution.
Goal: directly correlate post-relaxation ⟨z⟩ and the fraction of
4-... |
9c4526ad093033e9664dcba6e1da94f47c4e9de5c8d7181fa76cfc96dab9faf1 | Python | 9,440 | 256 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
#
# 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://ww... |
a8df99540fc4ce8a092980cff9f7f3f2d259c96d706159d72c3f0f4eb39be418 | Python | 9,441 | 257 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
#
# 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://ww... |
9a5b691e5ba51ba40d358c92148cedd9a4361812d2e0017d0da05eecf3408386 | Python | 9,443 | 291 | import argparse
import os
import random
from concurrent.futures import ProcessPoolExecutor
from copy import deepcopy
import h5py
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from sklearn.model_selection import KFold
from torch.utils.data import DataLoader, Dataset
from torchdiffeq ... |
fbc31d872242a88215290f9dad0ce1354f5d91597ce6c5071700a65dfb2bf119 | Python | 9,449 | 220 | import logging
import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from GMXMMPBSA.commandlineparser import (
AMBER_TRAJECTORY_FORMATS,
amber_parser,
amber_trajectory,
parser,
trajectory,
testparser,
validate_output_paths,
)
from GMXMMPBSA.exceptions import MMPBS... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.