sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
28493074033e91eb69fb2a2877f53afb27865f0361679f67a0d2d54a08ff3164 | Python | 8,872 | 225 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.nn import BatchNorm, LayerNorm, SGConv, SSGConv
import numpy as np
import math
from .module import MultiHopSGConv
class FourierPositionMapping(nn.Module):
def __init__(self, in_dim=2, num_frequencies=8, sigma=1.0):
sup... |
c7ee37d60ee7045d980728867a6d9288e91d58fb6d6cbac49d5bc16ebb2a70ca | Python | 8,872 | 265 | from typing import Literal
import numpy as np
import torch
from torch.distributions import NegativeBinomial, Normal
from scvi import REGISTRY_KEYS
from scvi.module.base import BaseModuleClass, LossOutput, auto_move_data
class RNADeconv(BaseModuleClass):
"""Model of scRNA-seq for deconvolution of spatial transcr... |
d1200332ddeea79aa01c59ae1641f442c0ff8cc8b5fe0d968afc7211a03ba0ff | Python | 8,872 | 266 | import math
from typing import Optional
import haiku as hk
import jax
import jax.numpy as jnp
from folx.experimental.pallas.attention import multi_head_self_attention
from .basic import Constructor, MultiDimLinear, PsiformerDense, param_free_ln
class MaskedMultiHeadSelfAttention(hk.Module):
def __init__(
... |
2ce5427b535ff87efc63d2f6bd591667d41af445c9591f58b34fc202af288f11 | Python | 8,885 | 151 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. 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 cop... |
d918af5ee4de0d8bbb1c9d127d3ef116bf417a1f4a815e26f6803f1911a6495f | Python | 8,886 | 152 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. 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 cop... |
fa4952dc8f13a56f23a6efea6a46eddd7a0d55d4adee7670186f7376e189a7b3 | Python | 8,889 | 223 | #!/usr/bin/env python
import argparse
import ast
import csv
import gc
import logging
import pathlib
from functools import lru_cache
from pprint import pformat
import torch
import torch._dynamo
from d3text import data, factory, runtime, tracking, utils
from d3text.cli.args import non_negative_limit
from d3text.datase... |
a7a44c8f99aa52124e11131b1c1d89077fd3e5ea8a71dd5952fa80b2b7b22807 | Python | 8,899 | 186 | import tkinter as tk
from tkinter import ttk
from src.window_utils import center_window_on_screen
class ExportOptionsContainer(ttk.Frame):
def __init__(self, parent,
file_path_var,
settings_manager,
extract_button_click_handler,
save_image,
... |
629f0a74860d34e7929d716549e8134ec7f0de187002ff9c2b9e5e202a9ce83e | Python | 8,900 | 213 | import theano
import theano.tensor as T
from theano import In
import numpy as np
from theano import config
def softp(x):
return np.log(1 + np.exp(x))
class GenerativeModel(object):
"""
Generative Model Interface Class
The generative model describes the fluorescence dynamics for given latent spikes: ... |
8bd10122e1a0b75aa5305f5729d651a65c10d84b5d4dfa3ef58fa191a2900c3d | Python | 8,900 | 216 | import os
import json
import subprocess
import sys
import tempfile
import unittest
from pathlib import Path
from scripts.validation.common import (
Case,
_generated_example_files,
apply_legacy_settings,
compare_csv,
csv_comparison_for_cases,
environment_for,
load_cases,
load_comparison_... |
5193517ce08d5a2120c029ac063547e7cefdc1e01b57074af96ffd156c541593 | Python | 8,903 | 216 | # -*- coding: UTF-8 -*-
"""
@Project: iDCF
@File : shap_utils.py
@IDE : PyCharm
@Author : hjguo
@Date : 2025/7/11 14:51
@Doc : SHAP interpretability analysis code
"""
import shap
import torch
import numpy as np
import os
import matplotlib.pyplot as plt
def explain_expression_genes(model, data_tensor, featur... |
c97fff7381aea8293db96b20ecb2658ce517709f4e0d41065152afc1ec5fc3bd | Python | 8,908 | 149 | from typing import Union, List
import numpy as np
import torch
from acvl_utils.cropping_and_padding.bounding_boxes import insert_crop_into_image
from batchgenerators.utilities.file_and_folder_operations import load_json, save_pickle
from nnunetv2.configuration import default_num_processes
from nnunetv2.training.datal... |
1a49ccec63fae37068cf5da4376f1fe701768d9ec78af04208f97c22b3833dc2 | Python | 8,909 | 174 | from typing import Dict, Optional
import torch
import torch.nn.functional as F
from dgr.utils.warp import grid_warp_x, tv_loss, jacobian_det_penalty_1d_x, grid_warp_2d
from dgr.utils.splat import softmax_splat_2d
class ReconLoss(torch.nn.Module):
def __init__(self, ssim_weight: float = 0.2):
super().__i... |
8979a9e70ff43c88dd7cbd748b50e0125ea1ace92a1ee8e4d5321ba003fc7331 | Python | 8,909 | 279 | #!/usr/bin/env python3
# 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 logging
from pathlib import Path
import shutil
from tempfile import NamedTemporaryFile
from typi... |
7a58c03f96d4c1b6a4522b185ff5d1bc5b41bb7206e15a581caa34f5ad3f3aaf | Python | 8,918 | 258 | from e3nn import o3
from nequip.data import AtomicDataDict
from nequip.model import model_builder
from nequip.nn import (
SequentialGraphNetwork,
AtomwiseReduce,
ForceStressOutput,
)
from nequip.nn.embedding import (
AddRadialCutoffToData,
PolynomialCutoff,
)
from nequip.nn.embedding... |
f3dfab08f8efbc851b0be79557963ccd2f4c3ffa371372167de28efab9243361 | Python | 8,919 | 245 | import logging
import os
import shutil
import subprocess
import sys
from typing import List, Dict, Optional, Set, Union
from types import SimpleNamespace
from .config import load_config, merge_namespaces
from .punchcards import PunchcardDeck, PunchcardSubset, PunchcardView
def is_task_complete(paths: SimpleNamespace... |
4ba486dbfdfe8c8e999608d6e9807b82da3612eabbfd14bf5b070c9d3d2db1b5 | Python | 8,922 | 227 | # 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 dynamicconv_cuda
import torch
import torch.nn.functional as F
from fairseq import utils
from fairseq.incremental_decoding_utils import ... |
319b96fcb97c8eba5075fc32dc56163c7f0f237a1aeb4c33add22961ca5e9ba1 | Python | 8,928 | 231 | # /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 time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init_para):
'''
Thi... |
1e8be41a26c9890edb37d912db0da8b923fb8ad5334f963c987214eb6eeec690 | Python | 8,931 | 200 | """Used to operate on a sub-graph of a larger GO DAG."""
__copyright__ = "Copyright (C) 2016-present, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import re
import collections as cx
from goatools.gosubdag.gosubdag import GoSubDag
from goatools.wr_tbl import wr_xlsx as wr_xl... |
00e6e60ddc817f7bf94402990705efa2b925cbb5c0b2fd7e34c1ac94828a91e8 | Python | 8,935 | 284 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from poetry.console.commands.update import UpdateCommand
from tests.helpers import get_package
if TYPE_CHECKING:
from pytest_mock import MockerFixture
from poetry.poetry import Poetry
from tests.helpers import DummyRepos... |
452409567afd91454a5f6d1114bf46de7119e0b5dea7441a20acc5cfcf0141f7 | Python | 8,936 | 228 | from collections.abc import Callable
from functools import partial
import click
import os
import zarr
import cv2
import dask.array as da
import joblib
import numpy as np
import xarray as xr
from skimage.feature import multiscale_basic_features
from skimage.morphology import binary_closing, binary_dilation, binary_erosi... |
7b479e9b64a077d6e511cb451a7edee65a424656e9d4176a25868584de2ca43c | Python | 8,936 | 275 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader
from typing import Optional
from abc import ABC, abstractmethod
from simulation_encoder.logger import Logger
class BaseRBM(ABC, nn.Module):
def __init__(self, logger: Optional[Logger] = None):
supe... |
5339f0ad1476572d5eb7302488a3537dab3ec0a2be679ef238a908cd4bd4a603 | Python | 8,940 | 211 | '''
Logic to simulate senescence response for various tau fractions, the results are stored on disk for
downstream processing by heatmapandrearange.py
Logic is seperated to support running the simulations on multiple processors
'''
import numpy as np
from scipy.integrate import solve_ivp
import os
from numba import n... |
1505b1d94e73b25bc4aa595364a26ea82ba79896aaf470f20c0af7b72495aa30 | Python | 8,946 | 225 | #!/usr/bin/env python3
"""Maintain RNAlysis contributor acknowledgments.
Two capabilities, both dependency-free (stdlib only) so the CI workflow needs no ``pip install``:
* ``--update-readme`` append any GitHub contributor missing from the contributor roster in
README.rst. Never re... |
af4534d58f98833d39cd08e67a10658a48c9913571ccabbb707bfe83242fc417 | Python | 8,950 | 181 | """Manage evidence codes as reported by the Gene Ontology Consortium."""
__copyright__ = "Copyright (C) 2016-2019, DV Klopfenstein, H Tang. All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import collections as cx
# pylint: disable=line-too-long
class EvidenceCodes(object):
"""From http://geneont... |
6b57666bfc769fbefcbaf47fa45a625bdcc52d22c5263d2e09de16f0c5eb71c2 | Python | 8,953 | 255 | # -*- coding: utf-8 -*-
import pdb
import os
import glob
from multiprocessing import Pool
import sys
import glob
import time
import subprocess, re
import numpy as np
import pandas as pd
def run_command(cmd):
"""Run command, return output as string."""
output = subprocess.Popen(cmd, stdout=subpr... |
7cc59466669ecd97c43653226a60078bdfc9da95a9694afe0833ada883f71083 | Python | 8,953 | 209 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Modifications by Roshan Rao
#
# 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:/... |
43458c6b18731364049dc325d30f939c3ca38fce8748319fba542cc9e4bb80d5 | Python | 8,954 | 226 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
import torch
import torch.nn as nn
from .AMPHelpers import aniso_features_qmmm, aniso_features, build_poles
from datastructures.Graphs import Graph
from modules.D4DispersionScaling import D4
from modules.Modules import AtomicEmbedding, Bes... |
57a0933a7c6c3c5795141f5a727a94a83df062b1a91a4b827d8c4300516b4b0c | Python | 8,955 | 179 | 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... |
1e030d9291c405940aac9abcb9c36e7b52dc399d2323d496a6cba92461999259 | Python | 8,957 | 159 | import numpy as np
import logging
import collections
from scipy.sparse import csr_matrix, coo_matrix, csc_matrix
import pytest
from gsa_mixer.utils import AnnotUnivariateParams
from .utils import UnivariateParametrization_natural_axis
from .utils import UnivariateParametrization_constPI
from .utils import UnivariateP... |
0896c059fed1e8f45c359204f46aa4a10eb4c8cec9c418ac15a19bbf0fe3df7f | Python | 8,959 | 218 | from src.utils import read_gtf, read_SJ
import polars as pl
from Bio import SeqIO
import os
import pyBigWig
from pathlib import Path
def gtf_to_SJ(gtf):
import numpy as np
assert gtf["feature"].unique().is_in(["exon", "CDS"]).all(), "GTF must only contain exon and CDS features"
return gtf\
.filte... |
b80fa43109a9c651e244262ec396fc0bbb3737c89b2db35b668988b45052950f | Python | 8,961 | 248 | from __future__ import annotations
from pathlib import Path
import pandas as pd
from st_risk.models.base import BaseSpatialModelOutput
from st_risk.models.io import save_base_model_output
from st_risk.reporting.anchored_validation import (
AnchoredModelSpec,
best_score_per_proxy_sample,
build_model_summa... |
caded74599b29cd51ce004cf37545d7991e836a5aa85438844efca6c458d412a | Python | 8,962 | 253 | # checking program
import math
import pandas as pd
from functools import reduce
import matplotlib.pyplot as plt
import glob, os
import numpy as np
import matplotlib.lines as mlines
import matplotlib as M
import json
import matplotlib.ticker as tkr # has classes for tick-locating and -formatting
# for cdci G... |
70728e1158f6e7a19ade21af77df8c691fbbaa7a04f5d1219694d3be83e034a9 | Python | 8,963 | 171 | import warnings
warnings.filterwarnings("ignore", category=DeprecationWarning)
warnings.filterwarnings("ignore", category=FutureWarning)
import joblib
from pathlib import Path
import numpy as np
import pandas as pd
from analysis.metrics import dPrime_model, dPrime_monkey, dPrime_model_RL
from sklearn.model_selection im... |
9dccb4825ede371fa260b13b565b96cc18d5f3828c80b6d01181a0bd11d18059 | Python | 8,967 | 226 | import qt, vtk, slicer
import numpy as np
from ..Widgets.ToolWidget import AbstractToolWidget
from ..Effects.DrawEffect import AbstractDrawEffect
from ..Helpers import GridNodeHelper
class DrawToolWidget(AbstractToolWidget):
def __init__(self):
toolTip = ''
AbstractToolWidget.__init__(self, 'Draw', t... |
1a669bc66159cfdbe8e02a8325fa0fdb23ef5a74ada44d19e3897a6dc93f4a87 | Python | 8,969 | 175 | #!/usr/bin/env python3
"""
EIF2S1 R3 REVISION - AD REPLICATION COHORT (Reviewer 4): GSE5281 superior frontal gyrus.
Author: Drake H. Harbert (D.H.H.) | ORCID 0009-0007-7740-3616 | Inner Architecture LLC.
Date: 2026-07-05
Reviewer 4 asked for the EIF2S1-PELO analysis in an additional disease dataset (frontal
cortex AD... |
2833d2ed1ade79e8114cd0e538c8b8aa8e9a69db6600405856b5b299abfba817 | Python | 8,970 | 258 | import typing
import math
import numpy as np
import sklearn.metrics
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.utils.weight_norm import weight_norm
from torch.utils.checkpoint import checkpoint
def Linear(in_features, out_features, bias=True):
m = nn.Linear(in_features, out... |
447adc0ab523aa598e65b5ae4ab8e7d1f8e69903d3f484235d6e1a6f9b5a2edb | Python | 8,971 | 274 | import sys
import os
import itertools
import numpy as np
from parcellate.constants import *
def stderr(s):
sys.stderr.write(s)
sys.stderr.flush()
def get_iterator_from_grid_params(grid_params):
_grid_params = {}
if grid_params:
for grid_param in grid_params:
_grid_params[grid_pa... |
5ad5bb8e55f2762cd9986d167f880072dda8ebb5f45c282a8ed430f5369cb2f4 | Python | 8,972 | 257 | from pathlib import Path
import os
import glob
import re
import numpy as np
import pandas as pd
import pickle
import argparse
# ibl specific imports
# from one.api import ONE
from celltypes_ibl.params.config import DATASETS_DIRECTORY
from deploy.iblsdsc import OneSdsc as ONE
from iblatlas.atlas import AllenAtlas
from... |
9f4423f2afaa3161cf56b475757fc42c126c2373647edf133fa48596fdf4b091 | Python | 8,985 | 272 | from __future__ import annotations
import collections.abc
import logging
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import pyro
import torch
from scvi._constants import REGISTRY_KEYS
from scvi.data import AnnDataManager
from scvi.data.fields import LayerField
from scvi.module import Amor... |
0d46eab5738f2055a12546f8455f4b55ae540630f08494cf612521ce6d7d95ef | Python | 8,991 | 205 | #!/usr/bin/env python3
"""Trains up a sequence-to-profile model in the BPNet style.
This program generates a neural network that maps genomic sequence to
experimental readout.
In cases where you don't need to regress out a bias track, this is the only
training program you'll use.
The required input files are two hdf5... |
7f46fad9fa1d72f3a97f7c41ef3460f9c3bd70b46504d86c6c013693a237b4ab | Python | 8,992 | 261 | # extract_timeseries_c1.py
# C1 extraction using Cambridge/BASC atlas (3mm), FIXED to:
# - use BASC scale064 explicitly
# - extract ONLY run-1
# - feed ONLY preprocessed SPM bolds (prefer wrsub-* then wsub-*)
# - NEVER use raw (skip if no wr/w exists)
#
# Tasks kept: encoding, similarity, rest.
import... |
ffbf9ade2adc673d52a6820c2fa881934c0dbe4d9b9adc6e2b54f8ffc1aab9ac | Python | 8,992 | 237 | # /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 time
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def get_init(myelin_data, gradient_data, highest_order, init_para):... |
b3846507da2e620f8e17014a1c042b3092e3d93b71bb7ab5c8a5630d314d7f40 | Python | 8,995 | 281 | # Copyright 2026 Hongyu Sun
# Licensed under the Apache License, Version 2.0
import argparse
from pathlib import Path
import h5py
import numpy as np
import torch
import matplotlib
import matplotlib.pyplot as plt
from model_eval import QNO
from utils import set_seed
matplotlib.rcParams.update({
"font.size": 12,
... |
51043dd1c228520c157421a97cd2f0e7886c44aa7cf91c03150bae34d3ec2217 | Python | 9,002 | 242 | #!/usr/bin/env python3
"""Execute the calculation-combination matrix in isolated external copies."""
from __future__ import annotations
import argparse
import json
import time
from datetime import datetime, timezone
from pathlib import Path
from typing import Any
try:
from .common import (
DEFAULT_EXAMPL... |
65166005049710d44e6a03a65c7d8df4acb24fb6b3a2477cae3ffb2f243b1db2 | Python | 9,007 | 185 | """Page 9: Prediction Error Analysis."""
import streamlit as st
import plotly.express as px
import plotly.graph_objects as go
import pandas as pd
import numpy as np
from utils import PIPE_ORDER, PIPE_COLORS, style_figure
def render(store, dataset):
st.header("Error Analysis")
st.markdown(
"Go beyond ... |
4f5b304b60d0d03e5201845472969687c52e66a7de7db06859fa8db4d4143f14 | Python | 9,008 | 231 | # 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, field
from typing import List, Optional
import torch
import torch.nn.functional as F
from fair... |
ac0915c6e66c0380e426f1afb794975a968dc492db894c15c9d8fbb02967d556 | Python | 9,008 | 229 | from typing import Dict, Type, Callable, Optional, Union
from torch.utils.data import Dataset
from .models.modeling_utils import ProteinModel
from pathlib import Path
PathType = Union[str, Path]
class TAPETaskSpec:
"""
Attributes
----------
name (str):
The name of the TAPE task
dataset (T... |
b2162315b45ea3890863c24aace91bc278aaef9686e02be92051881a5a829830 | Python | 9,008 | 311 |
import os
import argparse
import sys
import torch.optim as optim
import torch
import pandas as pd
import yaml
import ast
# ---- Training ----
if __name__ == "__main__":
project_root = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
sys.path.append(project_root)
# Simulate ... |
0925abcba8f87d84819921ae661fdafa5c871226a5dbceca61e9947e63acad98 | Python | 9,019 | 203 | from collections import OrderedDict
from copy import deepcopy
from typing import Union, Tuple, List
import numpy as np
import pandas as pd
import torch
from batchgenerators.augmentations.utils import resize_segmentation
from scipy.ndimage import map_coordinates
from skimage.transform import resize
from nnunetv2.config... |
26ab0409df7419f888a87f1917a2f5aeb9a17bfdea9cbf85e0405608e30019a3 | Python | 9,028 | 239 | """
hippie-wf3dacg — C4 H5 Dataset Loader
=====================================
Reads C4-database H5 files (Beau et al., 2024) and returns the arrays needed
to construct a HippieWF3DACGDataset.
Per-dataset conditioning metadata (source / super-region / technology /
layer) follows the same vocabulary used by the rest ... |
5425e623968c59e1ac4007d5c0c9e17d0845cb1e782785f2fde6c3fbb36d29f6 | Python | 9,028 | 259 | from collections.abc import Iterable
from dataclasses import dataclass, field
import numpy as np
import pandas as pd
from rich import print
from sklearn.gaussian_process import GaussianProcessClassifier
from scvi.utils import dependencies
@dataclass
class DifferentialExpressionResults:
"""Dataclass for storing ... |
281cf3939cabba172f26dd2814eed93429d0a59daec5f843d30d06145f8ff8ee | Python | 9,031 | 238 | """
Cross-validate all forecasting models on the training split.
The script first reserves a subject-level holdout split, then runs LOSO-CV only
over the train subjects. Torch model checkpoints are written under
``saves/checkpoints`` under the parent ``fmri_connectivity`` project root.
"""
from __future__ import anno... |
358fa8a8bcbd89ebefecd8b5deb30a08fde1f2051f20684987593f89d4086f7f | Python | 9,032 | 234 | # 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 pathlib import Path
import torch
from fairseq import checkpoint_utils
from fairseq.data.data_utils import le... |
03a23122f76ee3af891289f6bd5c92196c9d2dc1ebf8168eed0437ef173d5ade | Python | 9,037 | 319 | from reproducible_ephys_functions import (
filter_recordings,
labs,
BRAIN_REGIONS,
query,
get_insertions,
)
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from fig_ephysfeatures.ephysfeatures_functions import get_brain_boundaries, plot_probe
from mpl_toolkits.axes_grid1.inset... |
582fe5562afbe123f1a61550479978c8d0d961383166bdb37f4ecbd923f08154 | Python | 9,040 | 230 | import numpy as np
import pandas as pd
from collections import OrderedDict
from ...common.utils import printProgressBar
def remove_double_counted_spikes(spike_times, spike_clusters, spike_templates, amplitudes, channel_map, templates, pc_features, pc_feature_ind, sample_rate, params, epochs = None):
""" Remove p... |
ddd4c46372d054331defefd03e241ea736a70613e2465f50443e94b565af7cc0 | Python | 9,049 | 254 | """The bridge table's on-disk contract and its two-way reading.
The table is the only thing standing between an evaluation and a 176 MB NCBI
dump, so what it says has to survive a round trip and refuse to be read as
identifiers of another kind.
"""
import collections
import pathlib
import pytest
from d3text.datasets... |
8749d53b79d94235b5ce295a4045100fbb348fb0fc5030bfb7d8fd4a2f35746a | Python | 9,067 | 270 | import logging
from typing import Optional
import anndata
import numpy as np
import pandas as pd
import scanpy as sc
from sklearn.cluster import KMeans
from sklearn.metrics import silhouette_score
from sklearn.mixture import BayesianGaussianMixture
from sklearn.neighbors import KNeighborsClassifier
from tqdm import tq... |
ed284bb23aae35c52a57a379963ef669a2929de5cd096725a56f12b4496a8e65 | Python | 9,068 | 270 | """End-to-end shape-contract smoke tests for `ETEBrendaModel`.
A real model with a tiny random BERT injected for the frozen base, so there is
no download. Parametrized over the `device` fixture, so on a GPU machine these
also exercise device placement of the heads, buffers and pooled tensors.
"""
import pytest
import... |
e6d2628243834230a7858a114c242f1fb3c55c55d6617cf5024ddc2e23522e20 | Python | 9,070 | 176 | import json
import os
from pathlib import Path
import sys
import tempfile
import unittest
from unittest.mock import patch
import zipfile
import nibabel as nib
import numpy as np
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
os.environ.setdefault("SEGREF3D_DISABLE_SAM2", "1")
MODULE_DIR = Path(__file__).resol... |
a1d1acd78c658d5803880005cfec10f63f3f904b2262854da5a255d92fb0d5aa | Python | 9,075 | 301 | import os
import anndata as ad
import numpy as np
import pytest
from scvi.criticism import PosteriorPredictiveCheck
from scvi.criticism._constants import METRIC_CV_GENE
from scvi.data import synthetic_iid
from scvi.external import cytovi
RAW_LAYER_KEY = "raw"
SCALED_LAYER_KEY = "scaled"
NAN_LAYER_KEY = "_nan_mask"
R... |
593661523b1c309f26cffa297c78f37cebfca837b807c0c1c4cab72903eacbdf | Python | 9,076 | 270 | """Base neural network components for DIAGVI model."""
from __future__ import annotations
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import Normal
from scvi.utils import dependencies
EPS = 1e-8
class DecoderSinglePathway(nn.Module):
"""Single-pathway decoder fo... |
7aaf8c604fe117783a5897120789104a8c81693cbf74ace1d9098f7d78dd5501 | Python | 9,076 | 255 | # sam2_interface.py
import os
import sys
import numpy as np
from PIL import Image
from PyQt6.QtGui import QPainterPath
from PyQt6.QtWidgets import QApplication
# # sam2pkg/sam2 をパスに追加
# BASE_DIR = os.path.dirname(os.path.abspath(__file__))
# SAM2_DIR = os.path.join(BASE_DIR, "sam2pkg", "sam2")
# if SAM2_DIR n... |
4e5ef1cd73fdb31f31c8afee93fc5a04435be1110025291bf0a7c6e0f8da2318 | Python | 9,083 | 275 | from __future__ import annotations
import logging
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from collections.abc import Iterable
from typing import Literal
from anndata import AnnData
from mudata import MuData
import numpy as np
from scvi import REGISTRY_KEYS
from scvi.data import AnnDataM... |
c9deb8d9af936fbc3b92d69da078e6e9565e4f538a4211c54f48687b25487ef3 | Python | 9,086 | 267 | import math
import torch as th
from torch import nn, Tensor
from dataclasses import dataclass
from typing import Tuple, NamedTuple
from einops import rearrange, repeat
from utils import M2H
from config_base import BaseConfig
from .nn import conv_nd, linear, timestep_embedding
from .MBAblocks import ResBlockConfig, At... |
7201219a51a4a0fff87bb4d3f847938715d403b0d9d0daf909676899b1ecc131 | Python | 9,088 | 265 | """Functions for creating splits of datasets used with neural network models,
such as the standard train-val-test splits used with supervised learning methods."""
from __future__ import annotations
import logging
import pathlib
import numpy as np
import pandas as pd
from ...common.labels import from_df as labels_fr... |
919431f936b198f68338a2f1e9e6f8eb78f0da5689e4e4a98887e32cbec6c561 | Python | 9,088 | 261 | from abc import abstractmethod
from itertools import combinations
from math import prod
import networkx as nx
from tqdm.auto import tqdm
from pgmpy import config
from pgmpy.models import DiscreteBayesianNetwork, DiscreteMarkovNetwork
class BaseEliminationOrder:
"""
Base class of the greedy elimination-order... |
17bed1309507cda69fdee29e95d18c3be524d3053294fe2f443022dcbbf6d158 | Python | 9,101 | 187 | #!/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... |
6a9f2e5278c0d84ee85d240a706595841e7e32edb45a3ae765003ff401103eb6 | Python | 9,102 | 202 | import theano.tensor as T
from lasagne import init
from lasagne import nonlinearities
from .conv import Conv2DLayer
__all__ = [
"LocallyConnected2DLayer",
]
class LocallyConnected2DLayer(Conv2DLayer):
"""
lasagne.layers.LocallyConnected2DLayer(incoming, num_filters, filter_size,
stride=(1, 1), pad... |
cb1916ffc92a44ef148c96e58cfecb15963c79240c4b7b909433ba36f46b33f7 | Python | 9,103 | 226 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 8 09:32:26 2020
@author: Muammer
"""
import numpy as np
from sklearn.model_selection import cross_validate
from sklearn.model_selection import cross_val_predict
from sklearn.metrics import matthews_corrcoef
from sklearn.metrics import classification_report
from sklearn.... |
8ad445ae2745ef2a84ee067209e4a328707bd74f347a1a17b16542363c182506 | Python | 9,106 | 226 | import numpy as np
import theano.tensor as T
from lasagne import init
from lasagne import nonlinearities
from .base import Layer
__all__ = [
"DenseLayer",
"NINLayer",
]
class DenseLayer(Layer):
"""
lasagne.layers.DenseLayer(incoming, num_units,
W=lasagne.init.GlorotUniform(), b=lasagne.init.Co... |
73a4d5de382427fc19bcf0a81560cf2803a64a17f50582a016ca0cd30627ba86 | Python | 9,107 | 196 | # 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... |
1b41e6afc98b9d65052b26ba5fecafc9ba9e9723fc4d67e2542ed774cf53b062 | Python | 9,108 | 227 | import torch
from torch import nn
import math
from rinalmo.model.rope import RotaryPositionEmbedding
from flash_attn import flash_attn_varlen_qkvpacked_func, flash_attn_qkvpacked_func
from flash_attn.layers.rotary import RotaryEmbedding
from flash_attn.bert_padding import unpad_input, pad_input
from einops import ... |
49b4ae32f9e88bb3638a960743192c0d0040bda2f0ee0b86c87403124640b06d | Python | 9,108 | 216 | import numpy as np
import json
import os
import sys
import copy
def estimate_bilateral_weights(estim_w_rh_json, estim_w_lh_json, target_profiles, fixed_symptom_weights):
""" Find bilateral symptoms and estimate bilateral weights accounting for possible asymmetry in fiber values
Parameters
----------
... |
37a910963f0e6c40edc13df01b89f4cc54004aa3962a6a0d444deb95860de21a | Python | 9,110 | 277 | from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from poetry.core.constraints.version import Version
from poetry.packages import Locker
from tests.helpers import get_package
if TYPE_CHECKING:
from cleo.testers.command_tester import CommandTester
f... |
bd0f6fd523bc62d49ecbe2b9472987f8f63dbe663ab1029575994ebb148bf888 | Python | 9,110 | 206 | import unittest
import numpy as np
from pgmpy.factors.discrete import DiscreteFactor
from pgmpy.models import ClusterGraph
from pgmpy.tests import help_functions as hf
class TestClusterGraphCreation(unittest.TestCase):
def setUp(self):
self.graph = ClusterGraph()
def test_add_single_node(self):
... |
02d17024385ef3baad8a4c6473af1ed207ad59ce7396ceab1a31bb991b2a30d2 | Python | 9,115 | 171 | import numpy as np
import torch
from tqdm import tqdm
from joblib import Parallel, delayed
from torch.optim import Adam
data_dir = 'PCA_then_ICA' # 1024 patches per video, 20000 iterations
stationary_responses_nonrandom = np.load(data_dir + "/stationary_responses_nonrandom_multi_dist_FastICA.npy")
moving_responses_no... |
cf8b43b81b1182834e9e7627a678c15e9dbbc7f06e5d26ec86e8267dd0cd4cd3 | Python | 9,116 | 235 | # Form implementation generated from reading ui file 'GUI/main_dialog.ui'
#
# Created by: PyQt5 UI code generator 5.12.1 and edited by IBP
#
# To implement:
# * Cache last selected folder
# * Batch mode for multiple input folders and a single output
# * Uncaugth exception handling
from PyQt5 import QtCore, QtWid... |
cbce7e918e7bc642d60009306be04ef2a2246ea6808796b6ef7e5a8afae9a92f | Python | 9,117 | 241 | """
Naive Adjustment Regressor in sklearn Compatible Design.
"""
import numpy as np
from sklearn.base import BaseEstimator, clone
from sklearn.linear_model import LinearRegression
from sklearn.utils.validation import (
check_is_fitted,
validate_data,
)
from pgmpy.prediction._base import BaseCausalPrediction
... |
d61db262a27c08b2c131b797954a45273b91765f2c0155fc4354311eadc3dc08 | Python | 9,121 | 237 | # ##############################################################################
# GPLv3 LICENSE INFO #
# #
# Copyright (C) 2020 Mario S. Valdés-Tresanco and Mario E. Valdés-Tresanco ... |
3da3477fae87d909a0086daf4c6dbb0e385121e044929a9eedbb60e3a05b28d4 | Python | 9,123 | 211 | import os
import numpy as np
import pandas as pd
from currentscape_calculator.CurrentscapeCalculator import CurrentscapeCalculator
from simulator.ModelSimulator import ModelSimulator
from preprocessor.Preprocessor import Preprocessor
from currentscape_visualization.currentscape import plot_currentscape
class Current... |
7bad9c548cdbf575e4076745e6d4978972a32f15616255cd4a79c245a4d3b8fc | Python | 9,123 | 267 | # This Python script creates a full set of C++ C header files that
# are missing on some platforms.
#
# Usage:
# mkdir cpp_c_headers
# cd cpp_c_headers
# python generate_cpp_c_headers.py
#
# The files created by this script are in the directory:
# root/boost/compatibility/cpp_c_headers
#
# Supported platforms:
... |
cd752723bcf126ab94ebaea197674a56f6a578a5d6b98b75cd4d2baec11514e8 | Python | 9,124 | 218 | """Internal CLI parsing helpers used by GOATOOLS."""
from __future__ import print_function
__copyright__ = "Copyright (C) 2016-present, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import argparse
import shlex
import sys
from goatools.godag.consts import NS2GO
from goatools.gosubdag... |
697e513ab3503df9646b0c0b4742d269da57a13e887f7d642684c232f33a97f5 | Python | 9,125 | 271 | """The psycholinguistics noise pool: disjoint per split, stable per process.
These pin a `brenda_references` function from d3text's own gated suite on
purpose. The pool is drawn once per split inside `brenda_dataset`, so a
regression here does not raise — it silently changes which documents a run
trains and evaluates ... |
da4cc2054646d4f0dbf1cae231785c66f7a00738c3b3e1229c06d995e9b1b789 | Python | 9,129 | 243 | """Calculates read level embeddings, then pools by averaging embeddings."""
import warnings
import torch
import medaka.architectures.base_classes as base_classes
import medaka.architectures.read_level_modules as read_level_modules
import medaka.features
class ReversibleLSTM(torch.nn.Module):
"""A wrapper around... |
94ed027b88878d0c27d1c5c65338fdd34b82a548e2ec4ebd7dc008e21637687c | Python | 9,131 | 211 | import os
import numpy as np
import pandas as pd
from currentscape_calculator.CurrentscapeCalculator import CurrentscapeCalculator
from simulator.ModelSimulator import ModelSimulator
from preprocessor.Preprocessor import Preprocessor
from currentscape_visualization.currentscape import plot_currentscape
class Current... |
3d51a38a4d8699c4c793eaf45cabc50b245aa9a3819812d338aa936b3a82a3f9 | Python | 9,132 | 241 | #!/usr/bin/env python
from itertools import combinations
import networkx as nx
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from tqdm.auto import tqdm
from pgmpy import config
from pgmpy.causal_discovery._base import BaseCausalDiscovery, _TreeSearchMixin
class TAN(_TreeSearchMixin, B... |
4de998e7b7bc877f62a436c1d6c363642f4703c45b542d09520be5deaede7192 | Python | 9,132 | 224 | """
Study Preprocessor for NeuroVFM
Loads and preprocesses medical imaging studies for inference.
"""
import torch
from typing import Dict, List, Optional, Union
from pathlib import Path
import logging
from neurovfm.data.io import load_image
from neurovfm.data.preprocess import prepare_for_inference, tokenize_volume... |
8fe9888fb53a499d5df8a909eabf4e23b722a1c675d1142640357e8f616e52ea | Python | 9,132 | 301 | # 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 typing import Optional
import torch
from fairseq.modules import (
ESPNETMultiHeadedAttention,
LayerNorm,
MultiheadAttentio... |
d4b1c449072fc2217b7e7f20097ad7169766405ff78e4ea19f4833ec6f0d79ae | Python | 9,133 | 279 | """
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 json
import torch
from torch_scatter import segment_csr
def read_json(path):
""""""
if not path.endswith(".json"):
... |
0fd8863656fa6c9b069569343eed823977cfcc87b5a3f8e12ae8e54a2451c4db | Python | 9,134 | 274 | # 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... |
5e1b8926617309e2e77256c4aad925a72e642059b5cf5b4a472f2fd66a254a35 | Python | 9,141 | 253 | # Copyright (c) 2024, Shenghao Cao & Ye Yuan. Shanghai Jiao Tong University, Shanghai 200240, China
# Some classes and functions are modified from scGPT (https://github.com/bowang-lab/scGPT), copyright (c) 2022 suber
# Some classes and functions are modified from scFoundation (https://github.com/biomap-research/scFound... |
dbed9b8fb13c8513850e848e4865fa4fbd3e2ec390ac8ae7521b0555c6d022e0 | Python | 9,148 | 244 | """Unit tests for packaging/snapshot_api_payload.py (pure logic; no live network).
The script lives in ``packaging/`` (which is *not* a Python package and would shadow the PyPI
``packaging`` distribution if imported by name -- see ``tests/test_contributors.py`` for the same
pattern), so it is loaded directly from its ... |
f6a0da726a8bcdd40640fab39c0814a56d6188531b44a3ce6e7e7137755c9a02 | Python | 9,149 | 270 | import logging
import typing
import torch
import torch.nn as nn
from torch.nn.utils import weight_norm
from .modeling_utils import ProteinConfig
from .modeling_utils import ProteinModel
from .modeling_utils import ValuePredictionHead
from .modeling_utils import SequenceClassificationHead
from .modeling_utils import Se... |
30154f906a18e8700f35984ffb3c83537bd0e727f830786f85c006d405a3c666 | Python | 9,156 | 258 | import pickle
import numpy as np
import os
import json
import scipy.io
import scipy.spatial.distance as ssd
import scipy.cluster.hierarchy as sch
from scipy.stats import pearsonr
from helper_functions_egestive_priming import *
from helper_functions_image import plot_group_neurons
from collections import Counter
from sc... |
09c1afc1eba2fd10dece757ddb05724de3d95d647f2068c5b7df71155d4eec1a | Python | 9,160 | 286 | # encoding: utf-8
"""
@author: LiFan Chen
@contact: s18-chenlifan@simm.ac.cn
@software: pycharm
@file: utils.py
@time: 2019/7/19 15:29
@desc:
"""
from collections import defaultdict
import copy
import importlib.util
import math
import os
import sys
from typing import Callable, List
import warnings
import torch
import ... |
c91cb255a6ab0ba8d1d79fd9ddce223e15dbb0bf0a3c78355343c11165a6c310 | Python | 9,161 | 180 | from PyQt5.QtWidgets import *
import os
from PyQt5.QtGui import *
from PyQt5.QtCore import *
import sys
import cv2 as cv
import numpy as np
class Data_Postprocess(QWidget):
def __init__(self):
super(Data_Postprocess, self).__init__()
self.setFixedSize(400, 275)
self.setWindowTit... |
c477f66b742490f0cb148800723939f7a4bd3411694ff9293bf5f9e885b9ade3 | Python | 9,162 | 244 | from __future__ import annotations
import math
from typing import TYPE_CHECKING
import torch
from torch import nn
if TYPE_CHECKING:
from typing import Any
class StackedLinearLayer(nn.Module):
"""A parallel stacked linear layer that applies multiple linear transformations in parallel.
This layer applie... |
5597f7a429688d4a09267ef11ce35fccfd2589cdfaaf628627eadfe6fb18ee0b | Python | 9,166 | 205 | import scipy.stats as ss
import numpy as np
from scipy.stats import norm
import cmmcost_omp as cmmcost
import argparse
import sys
import time
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument("--no-precision", action="store_true",
help="Don't measure precision")
... |
969d2c714c6645efd6fb6f82b73d5a2eb4d3a9ab63da23ef0162ce9b57b08888 | Python | 9,166 | 269 |
# Source code:
# https://github.com/zbmed-semtec/doc2vec-doc-relevance-training/blob/main/code/train_model/utilities.py
# This file includes the modifications to the source codes according to this project!
import tqdm
import gensim
import logging
import numpy as np
import pandas as pd
from gensim.models.word2vec imp... |
994b47578331cb2b3002872777a046c202f4efeae61d0be0e9503c136e2dc31b | Python | 9,168 | 197 | from time import localtime, strftime
import pandas as pd
import numpy as np
import argparse
from collections import namedtuple
from multiprocessing import Pool
import scipy.io as sio
annotation_categories = ["transcript", "exon", "intron", "utr5", "utr3",
"coding", "upstream_1kb", "downstream_1kb"]
v... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.