sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
197e8a735f7c42e93ff27d163ecb7a2847bb0539e9238238b203a1aa7216d6ba | Python | 37,762 | 826 | r"""Can it actually be made? — the missing dimension of layer B.
``predict_structure`` / ``inverse_design`` / ``variant_effect`` / ``enzyme_kcat``
form a complete *design* loop: they answer whether a protein folds, what to
mutate, and how fast it turns over. None of them answers the question that kills
most industrial... |
b097f56047216cf3833effa9a4b996e9987e36fa3ed83f3ec4da816a1bf76539 | Python | 37,775 | 866 | from typing import List, Tuple, Dict, Callable
import numpy as np
import torch
from torch.nn import functional as F
from lib.data_utils import dynamic_data_util as ddu
from lib.data_utils.dynamic_data_util import LoadedBrownianMovieBlock, interpolate_frame_transition_times2
from lib.data_utils.matched_cells_struct im... |
f3f2842b355d2d3c1918de6b56a691587dbe04af4f9534148026cf81cb3ef7f4 | Python | 37,856 | 878 | from copy import deepcopy
from pprint import pformat
from typing import Callable, Dict, Iterable, List, Optional, Set, Tuple, Type, Union
import nirtorch
import torch
import torch.nn as nn
from sinabs import layers as sl
from sinabs.utils import get_new_index
from .connectivity_specs import (
LAYER_TYPES_WITH_MU... |
07ca96d82c43c8e228c2798aeb2e86dbe7678b231bc9e3190aaf73aead6b2acb | Python | 37,892 | 1,034 |
from itertools import cycle, islice
import numpy as np
import operator
import random
import scipy
from scipy.sparse import csc_matrix, csr_matrix, vstack
from sklearn.manifold import TSNE
from sklearn.metrics.pairwise import rbf_kernel, euclidean_distances
from sklearn.neighbors import NearestNeighbors
from sklearn.pr... |
17f3457c4fd0ce627919278f24387323f6b8aa22ec10db4c3564a337e743dfef | Python | 37,910 | 702 | import inspect
from itertools import repeat
from typing import Callable, List, Optional, Union
import torch
from transformers import CLIPImageProcessor, CLIPTextModel, CLIPTokenizer
from ...models import AutoencoderKL, UNet2DConditionModel
from ...pipeline_utils import DiffusionPipeline
from ...pipelines.stable_diffu... |
8bbbb9b1f1f377323fa06ad302c06121bdffbb920e4ab9cf5948e20985ae9d80 | Python | 37,964 | 892 | import torch
from torch import nn
from . import Module
from contextlib import ExitStack
from .esmfold_openfold.tri_self_attn_block import TriangularSelfAttentionBlock
from .utils_train_valid import return_predcadist_plddt
class RelativePosition(nn.Module):
def __init__(self, bins, pairwise_state_dim):
sup... |
b3b39038bd8ec14b2e2e3a3d271b8ac945e9d7c643c46677f739da5142b75b06 | Python | 38,006 | 846 | #!/usr/bin/env python3.7
"""Defines Simulation class.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing
instructions. The source code can be found on the following GitHub
repository: https://github.com/wmglab-duke/ascent
"""
import copy
import... |
bddfd56a77d200f70b27a7c7e6c9217cfb3f28809a4eb36b2c3f0d63b3d677c7 | Python | 38,059 | 1,307 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Feb 14 02:44:59 2016
@author: leyangx
"""
import numpy as np
import os
import pickle as pk
import random
import networkx as nx
import itertools as itert
import matplotlib.pyplot as plt
def load(filename):
'''
This function can load some data ... |
ca58fe14eff12048652625ca123c6ed22977be217740f8c07ec3cd08545d38f3 | Python | 38,087 | 1,101 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
Tests: Ray Serve inference server in three modes:
1. Ray remote tasks (typical usage — submit as Ray tasks).
2. External clien... |
fb22af8c8c1f3f2df096763f10401d02562444e879f7deb90d709cbd847bfa7c | Python | 38,100 | 856 | from __future__ import print_function, division
import pandas as pd
import torch
import torch.nn as nn
import torch.optim as optim
from torch.optim import lr_scheduler
import torch.backends.cudnn as cudnn
import numpy as np
from torch.utils.data.sampler import SubsetRandomSampler
from timm.data.constants import IMAGENE... |
ba424f02378db80514296c4f329434cbe8b0d1d75328c594b08f3ef1934f853d | Python | 38,151 | 783 | # import gpytorch
# from gpytorch.constraints import Positive, GreaterThan
# from gpytorch.lazy import DiagLazyTensor,BlockDiagLazyTensor,MatmulLazyTensor, InterpolatedLazyTensor, PsdSumLazyTensor, RootLazyTensor, KroneckerProductLazyTensor, lazify
# from gpytorch.utils.broadcasting import _mul_broadcast_shape
# from g... |
e7cadc53a1d80379fe3826726c8a686c26e4a184c2a54504f5a57381374491e1 | Python | 38,169 | 1,028 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
a1b75c55deb7fa466d9d599e5d92c96013f3b7d78cde828e07dc873b02371e67 | Python | 38,187 | 730 | import matplotlib
import matplotlib.pyplot as plt
import networkx as nx
import seaborn as sns
import scanpy as sc
import numpy as np
import pandas as pd
from typing import Union, Sequence, List, Tuple, Optional, Iterable
from matplotlib.axes import Axes
palette_network = list(sns.color_palette("tab20") \
... |
0b58ca0d5507455df31d602d5fe2d06787fe49ca07811d082247ce53a10c13e1 | Python | 38,203 | 824 | # --------------------------------------------------------
# Swin Transformer MoE
# Copyright (c) 2022 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ze Liu
# --------------------------------------------------------
import torch
import torch.nn as nn
import torch.nn.functional as F
i... |
5e2d05af8042e860848bbafd6d11d5ac2cec272e03dcf5e9ac69d4879ef500fe | Python | 38,241 | 1,050 | """
Interactive setup wizard for Jarvis.
"""
from __future__ import annotations
import getpass
import os
import shutil
import sys
from typing import Any, Dict, List, Optional, Sequence, Tuple
from .config import load_auth, save_auth
from .model_registry import (
discover_provider_models,
model_description,
... |
b0a2126f2eeb14cfe6abe6d1df3b8bde46bf834e569863eabb987f317c5bdf73 | Python | 38,243 | 869 | from typing import Optional, Union
import sys
import anndata
import numpy as np
import pandas as pd
import scanpy as sc
import networkx as nx
from matplotlib import cm
import matplotlib.pyplot as plt
import plotly
from scipy import sparse
from scipy.spatial import distance_matrix
from scipy.stats import spearmanr, pear... |
b03c8bee80d2a03ce5e449a8d8e553e6290b5026966588ffee6ea24188843fbc | Python | 38,282 | 892 | """
Assorted utility functions used throughout
"""
import scanpy as sc
import scvelo as scv
import numpy as np
import scipy as scp
import torch as th
import anndata as ad
import gc
from .velocity_genes import compute_velocity_genes
from ...pp import highly_variable_genes, umap, pca, neighbors, scale
from ...pp._norma... |
410d987e3ce870ac7e6e06409a4a5567dafdc876640ca7708a2a93f925b0e59a | Python | 38,294 | 749 | # Copyright 2023 The InstructPix2Pix Authors and The HuggingFace Team. 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
... |
7c74d682abf8bb139b0eca9c87ab87e6183faf6e4d7a11e53d2cf98a27fa14cc | Python | 38,420 | 734 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
d7dde579766d6acd202ed34b7348e2eac22928053b5bcfd1bfa2ecdc418a78ff | Python | 38,434 | 1,060 | """Provides helper class SkorchDoctor that assists understanding and debugging
the neural net training
"""
from collections.abc import Mapping
from functools import partial
import numpy as np
from sklearn.base import BaseEstimator
from sklearn.exceptions import NotFittedError
from sklearn.utils.validation import che... |
f2c8982d361009022c8b82a703afa81c42465643c0c8802a0e72a20e1660839a | Python | 38,461 | 945 | import copy
import logging
import os
import pickle
import sys
from typing import Any, Dict, List, Optional, Set, Tuple, Union
import dask.dataframe as dd
import h5py
import numpy as np
import pandas as pd
import torch
import zarr
from torch.utils.data import Dataset
import deeprvat.data.rare as rare_embedders
from de... |
3005dcd6f7f585a4e679280895217b4c64e3f7ce2496ff8134e646169020dc88 | Python | 38,464 | 1,083 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract neural activity from a fluorescence trace using a constrained deconvolution approach
Created on Tue Sep 1 16:11:25 2015
@author: Eftychios A. Pnevmatikakis, based on an implementation by T. Machado, Andrea Giovannucci & Ben Deverett
"""
from builtins import ... |
6e3d900976ee0a88578edf6670adaa149c9e223c523c9a394aeea06766160f49 | Python | 38,464 | 713 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
47fe289f9e36349b8587b61a84191594cbefd46e3a67ad913afe5d8ac1109fcb | Python | 38,556 | 742 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
189a443c22ea7dc25bb2d0b16ceeebf69fa2a7c1afb145603cf88430fc1330cd | Python | 38,678 | 706 | from copy import deepcopy
import logging
import time
from urllib import parse
from utils.TasksManager import Queue, Task
from utils.Typing import CompressFrameworkOpt, ReproducOpt, SingleTaskOpt
import shutil
import sys
from typing import Any, Dict, List, Tuple, Union
from tqdm import tqdm
from utils.misc import alloc_... |
79fa5cdb26865d64552a853106d73468d436b906dbb7d685b812d89ed2844e99 | Python | 38,682 | 539 | """
Context-belief- and/or history-based agent
by Aditya Gilra, Sep-Oct-Nov 2021
"""
import gym
import numpy as np
import gym_tasks
import matplotlib as mpl
import matplotlib.pyplot as plt
import scipy.io as scipyio
import sys
from BeliefHistoryTabularRL import BeliefHistoryTabularRL
from plot_simulation_data import... |
44e06493eedd5591e86fa761b3c777f5292c5596cea067cefbdc9557b62d9b69 | Python | 38,693 | 753 | import math
import sys
import numpy as np
# for linux env.
sys.path.insert(0, '..')
import time
from dataset import *
import pickle
import argparse
from torch.utils.data.sampler import SubsetRandomSampler
from evaluation import *
import torch.nn.functional as F
import os
from utils import save_model, l... |
ac3a543cba587b040a0808f9b8b1aa1e6e1561035926421fc3835ea4d18daf7d | Python | 38,694 | 820 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
c223d5f5ad1b1673d02e0a2f2308e0198ae8c3b93c60219e6fde18de00754329 | Python | 38,702 | 779 | # Copyright 2023 Susung Hong and The HuggingFace Team. 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 requi... |
8a2b25ccbae3c6dafb850b14d1b6ed4b3e131da9301588472687aa0f4c31f0e0 | Python | 38,744 | 1,059 | import base64
import collections
import copy
import hashlib
import json
import logging
import os
import sys
import threading
from dataclasses import dataclass
from datetime import datetime
from io import StringIO
from numbers import Number, Real
from typing import Any, Dict, List, Optional, Tuple, Union
import ray
imp... |
abf6bfe2fe36c9ebf820404a0006418cac1c93405422813725ff61a805316887 | Python | 38,760 | 818 | # -*- coding: utf-8 -*-
"""
LeicaCamWater - is a script for using the built in overhead microtome microscope camera to
watch the cutting of serial sections and monitor the water level.
"""
# based on PyAGTUM_210216.py
# Import Packages
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui, QtW... |
be8feb55adf6ce5526caef5805aaf6fa1a57848496f0ed99da1c85c24d19dc54 | Python | 38,868 | 941 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2023 The HuggingFace Inc. team. 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/LI... |
3befee9839f601c30d4eb0dd406f24f96e327f4ca5d87c6184688b564b00b3e3 | Python | 38,880 | 787 | # Copyright 2023 TIME Authors and The HuggingFace Team. 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 requi... |
320788a9e8cf3915c1cd6e6c9d8b2ca614bfbb8f7e6dee8d5934192782a78919 | Python | 38,973 | 1,095 | from collections import Counter, defaultdict
from copy import deepcopy
from datetime import datetime
from enum import Enum
from itertools import chain
from typing import Any, Dict, List, Optional, Tuple
import ray
from ray._common.utils import binary_to_hex
from ray._raylet import GcsClient
from ray.autoscaler._privat... |
7f2757d7cdc187e9a274d36863b400ac827dfa397eeaf21ec447f4633f574f49 | Python | 39,010 | 874 | import scanpy as sc
import os
import torch
import numpy as np
from scipy.sparse import issparse, csr_matrix
import matplotlib.pyplot as plt
from tqdm import tqdm
from .._settings import add_reference
from .._registry import register_function
def _get_gaston_modules():
from ..external.gaston import cluster_plottin... |
2d3511b7d8518188d5ea3b8c470efb308ad0220fb52f2074dfe14a0c8aa0eda4 | Python | 39,098 | 927 | import math
import os
from argparse import Namespace
from omegaconf import OmegaConf
from typing import Optional
from time import time
from pathlib import Path
import numpy as np
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
import pytorch_lightning as pl
import wandb
from torch_... |
5c31e5c52f3be338c40a495bf11d38c52429b7e5bf239e9fa35c6417b1d647e8 | Python | 39,110 | 1,045 | import gc
import math
from typing import Dict, Mapping, Optional, Tuple, Any, Union
import torch
import numpy as np
from torch import nn, Tensor
import torch.distributed as dist
import torch.nn.functional as F
from torch.nn import TransformerEncoder, TransformerEncoderLayer
from torch.distributions import Bernoulli
fr... |
529564845516786f22ad33b36cf7e8f755a6cf55356dc9f2e27eacbccb7dab05 | Python | 39,165 | 27 | chrs_refseq = {'NC_000001.11': 248956422, 'NC_000002.12': 242193529, 'NC_000003.12': 198295559, 'NC_000004.12': 190214555, 'NC_000005.10': 181538259, 'NC_000006.12': 170805979, 'NC_000007.14': 159345973, 'NC_000008.11': 145138636, 'NC_000009.12': 138394717, 'NC_000010.11': 133797422, 'NC_000011.10': 135086622, 'NC_0000... |
3d2fa6a11811e79d8a0b6aa788995f7b297a8a1f84ca05635c89da2884d35d16 | Python | 39,168 | 1,125 | """Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
End-to-end conformer generation for FastCSP
"""
from __future__ import annotations
import argparse
import json
import math
import shutil
impor... |
90c96d4eea3d45ed61bcf8a6cb69f7513b8d4ab0c1f1d9810db686e7170c1077 | Python | 39,212 | 1,031 | """
Copyright (c) Meta Platforms, Inc. and 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 pytest
import torch
import torch.nn as nn
from src.fairchem.core.models.uma.nn.layer_norm import (
get_l_to_all_m_e... |
0fc02c78ef201a766480f5f3e634fa8f046b5b84c59f931d3589cc13e9fa261f | Python | 39,339 | 975 | from __future__ import annotations
from pathlib import Path
from typing import Sequence, Mapping, Literal, Union, Optional, Tuple, Dict
import numpy as np
import pandas as pd
import marsilea as ma
import marsilea.plotter as mp
import inspect
import warnings
from matplotlib.colors import Normalize, Colormap
from matplo... |
ee861e7df4fd63044298e147c28d70cc9661e8ca5cf1bf47221e94b952bcb3f5 | Python | 39,354 | 851 | # masking validation
# coding: utf-8
import argparse
import time
import math
import os
import copy
import sys
import torch
import torch.onnx
import torch.nn as nn
import torch.optim as optim
import torchvision
import torchvision.transforms as transforms
import torch.nn.functional as F
import numpy as np
import logging
... |
6938ef7080b7efca6a3311b5c34f1756214b6076a631f60e78fb5cc34b1b970d | Python | 39,418 | 1,170 | """Tests for scoring"""
import re
from functools import partial
from unittest.mock import Mock
from unittest.mock import patch
import numpy as np
from sklearn.metrics import accuracy_score, make_scorer
import pytest
from skorch.utils import to_numpy
class TestEpochScoring:
@pytest.fixture(params=[{'use_caching... |
a480888b4297da6c399162b3a47c65e97fbd28b5d09825c64e432256be21c710 | Python | 39,431 | 823 | import os
from decimal import Decimal
import utility
import torch.nn.utils as utils
import imageio
from utility import savecolorim
from div2k import normalize, PercentileNormalizer, np, torch
from tifffile import imsave
from tqdm import tqdm
class Trainer():
def __init__(self, args, loader_train, loader_test, dat... |
05d5e378ed55e3ddee4bd0a1dedcd6b1e4c8b786e6d1e0792af476842047412c | Python | 39,494 | 990 | """Marker gene identification and retrieval utilities.
Native re-implementation of the scanpy rank_genes_groups pipeline
(t-test, Wilcoxon, logreg) — no scanpy dependency required.
Ported from:
github.com/scverse/scanpy/blob/af57cffc6eb7fa77618b2ab026231f72cd029c12
/src/scanpy/tools/_rank_genes_groups.py
"""
from ... |
2f418fbf96c3919152a7fd3ee735abac8ed51c62cdc748e19e8daf602255838c | Python | 39,530 | 1,340 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# pylint: disable=broad-except
# pylint: disable=invalid-name
# pylint: disable=line-too-long
# pylint: disable=multiple-statements
# pylint: disable=too-many-lines
#-------------------------------------------------------------------------------
'''
This source defines t... |
bbac7dd1ca2cdb69bdd67f177e6a7c16a02e6665a0c86ede0fbaf306ac9263cb | Python | 39,567 | 925 | import numpy as np
from .gradient_conversions import (
g_from_b, q_from_b, b_from_q, g_from_q, b_from_g, q_from_g)
from ..utils import utils
from ..utils.spherical_convolution import real_sym_rh_basis
from dipy.reconst.shm import real_sym_sh_mrtrix
from scipy.cluster.hierarchy import fcluster, linkage
from dipy.cor... |
b92b2228a7bdf6307d68df0e15204526378160a2432f634a100aa89394a3e1a8 | Python | 39,593 | 797 | #!/usr/bin/env python
"""
Example script to train a VoxelMorph model.
You will likely have to customize this script slightly to accommodate your own data. All images
should be appropriately cropped and scaled to values between 0 and 1.
If an atlas file is provided with the --atlas flag, then scan-to-atlas training i... |
6b7c75e5eee0cc505a163e3bd9980719d9ae36036a64da346d151ae5c3524238 | Python | 39,594 | 1,141 | #!/usr/bin/env python
"""Classify Ray Sphinx/MyST doc-build warnings against a rules table.
Read-only diagnostic. Reads a Sphinx warning stream (a file, stdin, or pasted
text -- either the `/rtd-build-logs warnings` output or a raw `sphinx-build`
log / `-w` warnings file), parses each warning into a record, classifies... |
21b85e00c778ef41f1bb060e3a784c195e5b394d2e15b9e6ff441c237cf837c7 | Python | 39,610 | 979 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
e68abf6502fcdfc99f0afd11ca1b7fadb3ad980dad4b4a78895d9d071be23ce5 | Python | 39,638 | 1,000 | # coding=utf-8
# Copyright 2023 HuggingFace Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... |
247a737ef31e574e4447196d255ac0ecedb8e9b5dc7927fcbe31e8f1644e35d1 | Python | 39,714 | 1,024 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""High level analog tiles (base)."""
# pylint: disable=too-few-public-methods, abstract-method, too-many-instance-attributes
from collections import OrderedDic... |
c9e90e478aaf90dafce7423f4d85127d1dd9f9582726744d1ad66f063b8b8022 | Python | 39,737 | 1,030 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
36db55a02c5812c4608662547260869ab138822885629547b62115cd5c6140bc | Python | 39,791 | 999 | # built-in dependencies
from typing import List, Union, Optional, Dict, Any, Set, IO, cast, Callable, TYPE_CHECKING
import io
import time
# 3rd party dependencies
import numpy as np
from numpy.typing import NDArray
from tqdm import tqdm
# project dependencies
from deepface.commons import image_utils, package_utils
fr... |
a39d74abe98b7d069005fd241cb21565dfa525d4c3a648ccd7818e78345bc498 | Python | 39,828 | 515 | """Training data from the .cc files of mapped projects: each run's model inputs as CandyCrunch builds them (pooled spectra of MS1-refined precursors, one per
candidate composition), labelled from the project's map with pipeline_labels.label_run, one file per run, merged into a training and a pretraining table.
Usage (... |
bc1f141c2c71a259b5feb0e42e259648da21a73886af2a1f93864c2d0758aef7 | Python | 39,889 | 1,151 | """Semisupervised multimodal VAEs for metagenomics binning, this files contains the implementation of the VAEVAE for MMSEQ predictions"""
__cmd_doc__ = """Encode depths and TNF using a VAE to latent representation"""
import numpy as _np
from functools import partial
from math import log as _log
from typing import Op... |
e72ec8f097e2e93c7a3b4478e631b0cab93bf3794a4e47b2145406eecd4244c8 | Python | 39,906 | 1,185 | # Copyright 2023 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
ade7aac83dedb4820970266cf8061874928c465fee248659cd12d7fd1abded0d | Python | 39,907 | 1,202 | """Tests for callbacks/logging.py"""
from functools import partial
import os
import tempfile
import unittest.mock
from unittest.mock import Mock
from unittest.mock import call, patch
import numpy as np
import pytest
import torch
from torch import nn
from skorch.tests.conftest import neptune_installed
from skorch.tes... |
2163ae34e39a5bb4f2dc23542b5da6aac32f1dda3ade783ad0bd11e0e0a63155 | Python | 40,019 | 1,124 | # Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under th... |
abbdbc4e99724102545db3438f01ad7146cd4b4c090158182db7864fea7938fe | Python | 40,069 | 644 | # -*- coding: utf-8 -*-
"""
# SCRIPT: CREATE EVENT.TSV FILES FROM THE BEHAVIORAL DATA FOR BIDS AND ANALYZE THE BEHAVIORAL DATA
# PROJECT: FMRIREPLAY
# WRITTEN BY QI HUANG, 2022-2023
# CONTACT: STATE KEY LABORATORY OF COGNITIVE NEUROSCIENCE AND LEARNING, BEIJING NORMAL UNIVERSITY
"""
# In[1]: load packages, fun... |
c22720190dc045713d6ba08ebed7489c0dbc8df030efe2d21e5d7acb3b59982e | Python | 40,082 | 977 | r"""
Monocle2-style trajectory analysis for AnnData.
Pure-Python re-implementation of Monocle 2 (Qiu et al. 2017), exposed as
a single `Monocle` class for convenient use within omicverse.
Examples
--------
>>> import omicverse as ov
>>> mono = ov.single.Monocle(adata)
>>> mono.preprocess()
>>> mono.select_ordering_ge... |
e8e7bb52e503492ea994ed3002c490595097ab8f932b85a953ed22a62d2b7137 | Python | 40,098 | 929 | #!/usr/bin/env python3.7
"""Defines FiberSet class.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing
instructions. The source code can be found on the following GitHub
repository: https://github.com/wmglab-duke/ascent
"""
import csv
import os... |
543d9d4f2616852ddda970a0553f3241d5cbbc467ed676b1023186b0119547a8 | Python | 40,128 | 776 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
541ccc94196ea2b436c8fbb26349b631a5a354743e6f1f17663a5c503380e28f | Python | 40,129 | 1,072 | """
QC of surface topology and mesh quality.
The hippocampal (and dentate) surface should be a compact, orientable
2-manifold with boundary, homeomorphic to a closed disk: one connected
component, genus g = 0 and b = 1 boundary loop, so the Euler characteristic
chi = V - E + F = 2c - 2g - b = 1 (c = number of c... |
9e53d7da1dbec5420881f40c694849592c3cbd3a2d6fbe0f050abd95c341b107 | Python | 40,185 | 949 | """Module for integrating spatial transcriptomics data across different conditions.
This module implements STAligner, a method for integrating spatial transcriptomics data
across different experimental conditions, technologies, and developmental stages. The
integration preserves both gene expression patterns and spati... |
1037eb82af321948295a48ee7961a77836e23bf8b36537d6e3ab9b8091ed03d5 | Python | 40,277 | 997 | r"""Time-to-event plots: Kaplan-Meier curves and competing-risk incidence.
Both estimators are implemented here directly on top of NumPy/SciPy rather
than pulled from ``lifelines``, so survival plotting works in a bare
``omicverse`` install. The implementations follow the standard references and
are checked against ``... |
662ad78b72289019fbbfc15bee196e4555b719794496be0ffd18e606644cc7d3 | Python | 40,325 | 1,157 | import logging
import warnings
from typing import Callable, Dict, List, Optional, Tuple
import keras
import numpy as np
import tensorflow as tf
from keras import layers, ops
from sklearn.metrics import (
accuracy_score,
average_precision_score,
r2_score,
roc_auc_score,
)
from ml4h.models.Block import ... |
82fccd782baeb8d3415a2e9fd72fa7dea795109555bb9bf207942c49d1989f30 | Python | 40,330 | 1,118 | r"""
AnnData Rust backend compatibility patches.
"""
from __future__ import annotations
import os
from types import MethodType
from typing import Iterable
import numpy as np
from .._settings import Colors
def _ov_debug_enabled() -> bool:
try:
val = os.environ.get("OV_DEBUG") or os.environ.get("OMICVER... |
e480171a6ab37a81c16961a6f072f341623116fed314447bf62c20fed42a5e37 | Python | 40,398 | 1,072 | """Data-prep helpers for ``ov.genetics`` — genetics-specific wrangling.
The post-GWAS pipeline strings together several methods that each want
their inputs shaped a particular way: genotype PCA needs a scaled
matrix, locus definition needs LD clumping, colocalization wants a
summary-statistics dict, TWAS wants a predi... |
806b45e3325c9716da3377fd99a27056553484657913ff58a49e4f04eae3e677 | Python | 40,431 | 1,058 | from mozaik.experiments.vision import VisualExperiment
from parameters import ParameterSet
import mozaik.stimuli.vision.topographica_based as topo
import numpy
import numpy as np
import mozaik
class MapSimpleGabor(VisualExperiment):
r"""
Map RF with a Gabor patch stimuli.
This experiment presents a serie... |
036d452ea4f42a6121d005174dcb97a708c9a9af6455f00b1e85e047625b5121 | Python | 40,482 | 893 | import visionloader as vl
import numpy as np
from typing import List, Dict, Tuple, Sequence, Union, Optional, Any
from collections import namedtuple
import itertools
import statsmodels.robust as robust
from scipy import interpolate
from scipy import ndimage
import shapely.affinity as affinity
from shapely.geometry ... |
cb3a01e4071677e88b78ddec31a8fec519ba08a4c84ba61cc19dcec805c9d4b1 | Python | 40,495 | 1,193 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
""" A set of utilities, mostly for post-processing and visualization
We put arrays on disk as raw bytes, extending along the first dimension.
Alongside each array x we ensure the value x.dtype which stores the string
description of the array's dtype.
See Also:
----------... |
0c0e5986be719b5b607974bdae983939c213cb4ef04966d9fe298fa4d1ed6d7f | Python | 40,535 | 1,212 | # +
import warnings
import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import ListedColormap
from matplotlib.gridspec import GridSpec
from .._registry import register_function
from ._plotdata import get_values
def to_rgb_grayscale(img, p_low: float = 1.0, p_high: float ... |
8597e7b01d9506b61bc6c7c257f506df09c9b9a064ba756a993dfbd1c5cb5a50 | Python | 40,561 | 1,126 | # coding=utf-8
# =============================================================================
# Copyright (c) 2001-2021 FLIR Systems, Inc. All Rights Reserved.
#
# This software is the confidential and proprietary information of FLIR
# Integrated Imaging Solutions, Inc. ("Confidential Information"). You
# shall not di... |
087bcb88860f68d127fcccbceead163b4134096e17e3bbf09e1d5eb94af7a101 | Python | 40,568 | 1,051 | import pdb
import time
import copy
import logging
import numpy as np
import scipy.sparse
import scipy.integrate
from scipy.optimize import minimize
from tqdm.auto import tqdm, trange
import progressbar
from numba import jit, njit, prange
from connectivity import Connectivity, SparseConnectivity, BilinearPlasticityRule,... |
5ac2ebb01cb5afbd1b32c805eb594afebb234e3f60f2b41ccc6b30d504ea5a70 | Python | 40,568 | 1,115 | #!/usr/bin/env python3
import argparse
import os
import sys
import re
import math
import warnings
import time
import struct
from collections import defaultdict
import pandas as pd
import numpy as np
import hicstraw
import cooler
from scipy.stats import expon
from scipy.ndimage import gaussian_filter
from scipy.ndimag... |
eac5600547f7bb6e522bf99cb9ca3c03ada9eef74a9f81babd16fcaccddaa3aa | Python | 40,622 | 1,134 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
Tests for Wigner D matrix computation.
Tests verify:
1. Mathematical correctness (orthogonality, determinant, edge -> +Y)
2. Agreement between... |
cd0ac689ebf234be9f176ae200566e6f2b51a604c60239b723aaa23a7119e498 | Python | 40,783 | 829 | import CLEAR_settings
import csv
import os
import cv2
import numpy as np
import matplotlib.pyplot as plt
from tqdm.auto import tqdm
import copy
import pandas as pd
import CLEAR_regression
import torch
import torch.nn.functional as F
import torchvision
from PIL import Image
from skimage import measure
fro... |
552aeed3351432b69bf9d235e9456ecf2e598540ee79e94bb9956de782f2d2a0 | Python | 40,813 | 1,072 | ###########################################################################################
# Implementation of Geometric-Complete Perceptron layers
#
# Papers:
# (1) Geometry-Complete Perceptron Networks for 3D Molecular Graphs,
# by A Morehead, J Cheng
# (2) Geometry-Complete Diffusion for 3D Molecule Generation,... |
f24ba02d47b90d7aec2bb0dfcbfaf4ef3415fab88554d605be1aa6abcbe4c72e | Python | 40,917 | 1,149 | """ Callbacks for printing, logging and log information."""
import sys
import time
import tempfile
from contextlib import suppress
from numbers import Number
from itertools import cycle
from pathlib import Path
import numpy as np
import tqdm
from tabulate import tabulate
from skorch.utils import Ansi
from skorch.dat... |
648e261c914dd59e5d6ddeb870ec6605f1983d933dc6337abc7bf133edd803be | Python | 41,005 | 975 | r"""Measure-then-place panel layout: the axes box is the size you asked for.
:func:`~omicverse.pl.multipanel` is a gridspec. A gridspec divides the canvas
into cells and the *axes box* is whatever survives after matplotlib has fitted
the decorations into the cell — so a column shares one width, a row shares one
height... |
17c0b24e627eb29af6ab3ca01a473ad7709c1cf4c4890ae8e257ff5278ff343d | Python | 41,059 | 919 | # coding=utf-8
# Copyright 2023 HuggingFace Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... |
eb6bd0a381fe1a07153b58d41b1cd489d696f6f4f698dfbf2669a5d5e2f39511 | Python | 41,077 | 975 | import json
import logging
import os
import pathlib
import re
import sys
from datetime import datetime
from dataclasses import is_dataclass
from typing import Any, Dict
import sphinx
from docutils import nodes
from sphinx.util.matching import compile_matchers
logger = logging.getLogger(__name__)
sys.path.insert(0, o... |
a447c6517c21432edc9e6a1f2b9302ba549516a3010cf451a1054ce4c4dfdd09 | Python | 41,085 | 1,024 | """
Implements the pre-processing of edges into blocks of nodes (modules) for future
creation of DynapcnnLayer objects.
"""
from typing import Deque, Dict, List, Optional, Set, Tuple, Type, Union
from torch import Size, nn
from sinabs.layers import SumPool2d
from .connectivity_specs import VALID_SINABS_EDGE_TYPES
f... |
cf1b5478b49421524c7f7b6821ffa10d9b2ca25976c9da79c6ec6908bbd5169f | Python | 41,085 | 1,055 | """Paired microbe ↔ metabolite integration.
Three analysis layers that all consume a pair of AnnDatas sharing
``obs_names`` (i.e. the same samples measured on both platforms):
- :func:`paired_spearman` — Spearman rank correlation between each
CLR-transformed microbe and each log1p-transformed metabolite,
FDR-corr... |
850581ce234402e89c341e21f629c78b4889b6361337153f426e8ba4829687a5 | Python | 41,097 | 876 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 1 16:14:53 2022
@author: joern
"""
# https://coderzcolumn.com/tutorials/machine-learning/scikit-learn-sklearn-feature-selection
# %% imports
import os
os.chdir("/home/joern/Aktuell/PaclitaxelPainLipidomics/08AnalyseProgramme/PaclitaxelNeuropathyPr... |
0472ea7f665d2b5aa7d1285c99bfd5aaa855d992164db11988a3877982522ac4 | Python | 41,101 | 876 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 1 16:14:53 2022
@author: joern
"""
# https://coderzcolumn.com/tutorials/machine-learning/scikit-learn-sklearn-feature-selection
# %% imports
import os
os.chdir("/home/joern/Aktuell/PaclitaxelPainLipidomics/08AnalyseProgramme/PaclitaxelNeuropathyPr... |
0f4e59bf32ec7a67fa800367f17b7d4b8f48c4f2b30210f910207e0a2bff5c27 | Python | 41,201 | 1,022 | """Implements multi-node-type autoscaling.
This file implements an autoscaling algorithm that is aware of multiple node
types (e.g., example-multi-node-type.yaml). The Ray autoscaler will pass in
a vector of resource shape demands, and the resource demand scheduler will
return a list of node types that can satisfy the... |
1d2afed323fdbc68e94017e5c1b4b91f3d19b6ef6cd6c47b096b0403601612e9 | Python | 41,212 | 1,238 | from __future__ import print_function
import numpy as np
import pandas as pd
import os
import random
#os.environ['CUDA_LAUNCH_BLOCKING'] = "1"
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import constraints, Distribution, Normal, Gamma, Poisson, Dirichlet
from torch.dis... |
0c2af3aa9146c424157861b41a2210fc6bdcfb9480d44678d7aece8c41be7b8a | Python | 41,257 | 752 |
"""
Functions for CLEAR to create local regressions
Outstanding work - perform_regression() accuracy & decision boundaries for multi-class
"""
from datetime import datetime
import numpy as np
import pandas as pd
import statsmodels.api as sm
import copy
from sklearn.preprocessing import PolynomialFeat... |
03ba6722394e3b7456e1b0f678913dacf8697e36cb3f234378557e4f67856c19 | Python | 41,273 | 860 | import torch.autograd.functional as F
from modnn.Dataset import DataCook
import pickle
import os
import time
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
import numpy as np
import torch
import matplotlib.dates as dates
import matplotlib.pyplot as plt
from modnn.Models import ModNN_phy, BaseNN, ModNN_dat... |
a13bd96a24caecbc72c9e671e5e81a7d10b083d19fb4ff1341f74036d7b5c2c8 | Python | 41,297 | 843 | # -*- coding: utf-8 -*-
from __future__ import print_function, unicode_literals, absolute_import, division
import warnings
from .config import Config
from .base_model import BaseModel, suppress_without_basedir
from ..utils import _raise, axes_check_and_normalize, axes_dict
from ..utils.six import Path
from ..utils.t... |
7d753212f20cce9a456df55f10ff30ce38eacc6f7e0785afd5cc477bd1bbb0bf | Python | 41,300 | 1,175 | """Utils for plotting whole network graph."""
import collections
import itertools
from numbers import Number
from typing import Dict, List, Optional, Tuple, Union
import matplotlib
import matplotlib.pyplot as plt
import networkx as nx
import numpy as np
from toolz import valfilter
from . import plt_utils
class Who... |
008765dc5ab6bbc043b13e63640a90cacde6eab3dd5eef844f5df71d8d4d6af7 | Python | 41,432 | 1,158 | # coding=utf-8
# =============================================================================
# Copyright (c) 2001-2021 FLIR Systems, Inc. All Rights Reserved.
#
# This software is the confidential and proprietary information of FLIR
# Integrated Imaging Solutions, Inc. ("Confidential Information"). You
# shall not di... |
83dc677db76aedcfe6594eee708a3a979b73dc47d22abc668b6e3f623ebcd3eb | Python | 41,471 | 999 | __all__ = ['ADRDModel']
import wandb
import torch
from torch.utils.data import DataLoader
import numpy as np
import tqdm
import multiprocessing
from sklearn.base import BaseEstimator
from sklearn.utils.validation import check_is_fitted
from sklearn.model_selection import train_test_split
from scipy.special import expi... |
33a9ab7a291981b4f6bee1f8f18939eddfb859cfdb967b461379c0f3316ab0ac | Python | 41,532 | 1,052 | # encoding: utf-8
r"""
This file contains the API for direct stimulation of neurons.
By direct stimulation here we mean a artificial stimulation that
would happen during electrophisiological experiment - such a injection
of spikes/currents etc into cells. In mozaik this happens at population level - i.e.
each direct ... |
d52f2db8f65a8fd0bfccc41386166d8ff2926ba1993f0d52b3b847ae2dd84aba | Python | 41,677 | 885 | # Ultralytics YOLO 🚀, GPL-3.0 license
"""
Export a YOLOv8 PyTorch model to other formats. TensorFlow exports authored by https://github.com/zldrobit
Format | `format=argument` | Model
--- | --- | ---
PyTorch | - ... |
33202ebf0498e4a08a5bd25d6721fdc8f0976efc54f52d5f210c49d2d9c14ddf | Python | 41,687 | 1,159 | import argparse
import tempfile
import torch
from accelerate import load_checkpoint_and_dispatch
from transformers import CLIPTextModelWithProjection, CLIPTokenizer
from diffusers import UnCLIPPipeline, UNet2DConditionModel, UNet2DModel
from diffusers.models.prior_transformer import PriorTransformer
from diffusers.pi... |
c1f73955db7fbf0cdd9b2f06f9c304a77167d7ae12c5b92bcda9d68ce7f4aae8 | Python | 41,715 | 833 | """
SV de novo filtering script
"""
import argparse
import yaml
import numpy as np
import pandas as pd
import pybedtools
import collections
import time
from subprocess import Popen, PIPE
pd.options.mode.chained_assignment = None # default='warn'
def verbose_print(msg, verbose):
if verbose == "True":
p... |
6125017ffa29749de342950464b1e4bdac3c260fe67ebb60f501d241e1f8ee30 | Python | 41,770 | 890 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 1 16:14:53 2022
@author: joern
"""
# https://coderzcolumn.com/tutorials/machine-learning/scikit-learn-sklearn-feature-selection
# %% imports
import os
os.chdir("/home/joern/Aktuell/PaclitaxelPainLipidomics/08AnalyseProgramme/PaclitaxelNeuropathyPr... |
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