sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
583c4520a7d2150d37a5e485395430c5194a10c92c6d406e07839f553c57e63c | Python | 3,629 | 113 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
import torch.nn.functional as F
from ..ops import emulate_int
class IntLinear(nn.Module):
"""
Qu... |
c80581e73d2c56bc9cd6a17a6140187218dfeb4b6f8b5e4322d92e26718643f5 | Python | 3,629 | 92 | # 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 unittest
import tests.utils as test_utils
import torch
from fairseq.data import TokenBlockDataset
class TestTokenBlockDataset(unitte... |
fc7643272d9690d8e3b738d5aa883d69267198c9f740f9c9e7e5dfd3eded4fe6 | Python | 3,629 | 91 | from model.builders.prostate_models import build_pnet2
#
# current_dir = split(dirname(__file__)[])
# print current_dir
# ind= current_dir.index('pnet_prostate')
# print '/'.join(current_dir[0:ind+1])
# base_dirname= dirname(dirname(__file__))
# print base_dirname
# filename = os.path.basename(__file__)
task = 'classi... |
c323c976a3c14a7bf1203bb6fb6ef77c83a3ff8d7e74a2721520ac00ad94ef36 | Python | 3,632 | 81 | """Standardized on-disk I/O for the Zenodo bundle.
- Parcel data dictionaries <-> HDF5 (nested groups cond/sub/phase/stim).
- Report/consensus embeddings <-> npz (vectors) + parquet (metadata).
The HDF5 parcel store returns exactly the same nested-dict object the original
pickles did, so analysis code is format-a... |
f4ceb0afce2655f2e6ce890293f637539c813282ece2962a9e1d6034cc66802c | Python | 3,635 | 87 | import os, sys
import numpy as np
import torch
from sklearn import metrics
import torch
from torch.optim.lr_scheduler import _LRScheduler
from torch.optim.lr_scheduler import ReduceLROnPlateau
def param_num(model):
num_param0 = sum(p.numel() for p in model.parameters())
num_param1 = sum(p.numel() for p in mo... |
0a04efcec0e2c5cfdd23473b484e1dd3bd6c3f935fe96af3b29888b4461611bc | Python | 3,636 | 94 | """Functions to parse toml config files."""
from __future__ import annotations
import pathlib
import tomlkit
import tomlkit.exceptions
def _tomlkit_to_popo(d):
"""Convert tomlkit to "popo" (Plain-Old Python Objects)
From https://github.com/python-poetry/tomlkit/issues/43#issuecomment-660415820
We nee... |
17ec3e59382ebc78c256991bcb00c7c9fbd00b02ab5fa30aa85e379c2fdb0516 | Python | 3,637 | 95 | from argparse import Namespace
import torch
import torch.nn as nn
from fairseq.models.text_to_speech.fastspeech2 import VariancePredictor
from fairseq.models.text_to_speech.hifigan import Generator
class CodeGenerator(Generator):
def __init__(self, cfg):
super().__init__(cfg)
self.dict = nn.Embed... |
ddb7eface997dbb372d06309dcbe6a929a922dfc20fe294bd7da8148f63a1bea | Python | 3,637 | 105 | """Pick 100 perovskites for SIESTA validation, stratified.
Composition target:
24 endmembers (5-atom primitives, all (A,B,X) combinations)
76 supercells (40 atom 2x2x2) — proportional across kind × (A,B)
split: 40 mixed-X / 18 mixed-A / 12 mixed-B / 6 strained
Only includes records that succeeded under GFN... |
de84694832b0662c0d4e02e4fa92c41f8a20351c2b3dcee926f0f593644ee727 | Python | 3,638 | 135 | import argparse
import sys
from datetime import datetime
from pathlib import Path
import h5py
import numpy as np
from spacestream.analyses.hvm_fitter import HvmFitter
from spacestream.core.paths import HVM_PATH
from spacestream.utils.general_utils import log
from spacestream.utils.get_utils import get_mapping
STREAM... |
1c4bdf7b2e14bcf443e5a2fbfb5da9809e25c9bfa84b984c02b40f91f2582335 | Python | 3,639 | 137 | # Copyright (C) 2025 ETH Zurich, Moritz Thürlemann, and other AMP contributors
from typing import Iterable, Dict, List, Any
import json
import yaml
def get_atom_ids(residue_names:Iterable[str], pdbfile)->Dict[str, list[int]]:
#starts counting from 1 (not from 0 as are indices in openmm)
resnames_in_topology ... |
da88c02505b322c8bc24ef9e5653323373db36bb20fd5215ee0f887e76eb7b71 | Python | 3,639 | 125 | import h5py
import numpy as np
import torch
import scipy.io as sio
from scipy.signal import find_peaks
from TraditionalMatchedFilter import TraditionalMatchedFilter
def compute_metrics(detected_peaks, target_peaks, tolerance=20):
detected_peaks = sorted(detected_peaks)
target_peaks = sorted(target_peaks)
... |
07a03d2e8356f05a1427c4e0e0165b086f3804dd1d69497c852a966fa3eea456 | Python | 3,642 | 104 | """Reading the relation head's own rows back, with no gold to align against.
`evaluate_model` puts the head's rows through `align_relation_predictions`,
which needs gold. Inference has none, so the only thing left is the argmax
and the batch's interning table — and the table is what says which
candidate sets the two a... |
0f2bc5e58994107802b039ef4449f1d245a37bea47cd1797f6da1deeb597e43e | Python | 3,643 | 100 | import unittest
from pyecharts import options as opts
from pyecharts.charts import Geo, AMap, BMap, LMap, GMap
from pyecharts.exceptions import NonexistentCoordinatesException
BAIDU_MAP_API_PREFIX = "https://api.map.baidu.com/api?v=2.0"
FAKE_API_KEY = "fake_application_key"
class TestException(unittest.TestCase):
... |
3a43dbebdb2aea399a2eb9858c24e85eb868c0a7ce14bda478a410b8c478c1bf | Python | 3,644 | 116 | """The HDF5 resume loop must not re-append documents already stored.
`generate_embeddings.py` keys its resume set off `pubmed_ids[:]`, which h5py
hands back as `bytes`, and compares it against `str(row_id)` — a membership
test that is always `False`, so an unfixed script silently duplicates every
document at new offse... |
13d20d9046dcd57e08cc74437dc14acac8f3203847b49d09cf2a76746255bb68 | Python | 3,646 | 118 | #!/usr/bin/env python
# ENCODE DCC MACS2 call peak wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
assert_file_not_empty, human_readable_number,
log, ls_l, mkdir_p, rm_f, run_shell_cmd, strip_ext_ta)
def parse_arguments():
parser = argpa... |
2fe7311c7e110eec3fd3092ff7accf6f9ce083322ba60322ec615b94b948fc23 | Python | 3,646 | 113 | import numpy as np
from rich import print
from scipy.sparse import csr_matrix
from scvi.utils import dependencies
def adjusted_nearest_neighbors(
cell_samples: np.ndarray,
cell_coordinates: np.ndarray,
cell_labels: np.ndarray,
radius: int | None = None,
k_nn: int | None = None,
return_sparse:... |
7baebd175faa3d6697f0c89811e8b743a7415685e068c56fcf429376ec709cc4 | Python | 3,649 | 83 | #!/usr/bin/env python3
"""R1 ponto 3 (MAE e R2 na Fig. 1a) e R1 ponto 4 (definicao de misto_F).
Reproduz EXATAMENTE as predicoes out-of-fold do painel (a) de fig_manuscrito.py --
mesmo GroupKFold por familia, mesma grade de alpha, mesma normalizacao por atomo --
e acrescenta MAE e R2 ao RMSE ja publicado. Nada aqui re... |
5748d6fbf799d511c540c200d7c3d9ed2ba46bb92c514ff6270f99b5ed8d372c | Python | 3,651 | 113 | from __future__ import annotations
import logging
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import scipy
from anndata import AnnData
from mudata import MuData
if TYPE_CHECKING:
from typing import Literal
from scvi._types import AnnOrMuData
logger = logging.getLogger(__name__)
... |
150fc07f4f325d0fd80c9e1155d2e4951796bf06971cb93ce8603aa2be0a8946 | Python | 3,653 | 118 | import numpy as np
import torch
from utils.data.dataholder import DataHolder
@torch.no_grad()
def sample_noise(self, batch: DataHolder) -> torch.Tensor:
"""
Samples noise z_t from the noise model based on the node features and other batch information.
Parameters:
batch (DataHolder): Batch data co... |
63b45f891596466d434daef2817d10b816cbce5133385b7556609b61355ef3dd | Python | 3,653 | 104 | # 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 argparse import Namespace
from typing import Union
from fairseq.dataclass import FairseqDataclass
from fairseq.dataclass.utils import me... |
172c8c61b35771bb948e942956b4311ec8553e4349adc59ae1d6a2336ba3537d | Python | 3,654 | 154 | """
This module contains methods to deliver reward at different situations.
"""
"""
Copyright (c) 2019, 2022 [copyright holders here]
This file is part of NoSeMaze.
NoSeMaze is free software: you can redistribute it and/or
modify it under the terms of GNU General Public License as
published by the Free Software Fou... |
105164a6ba24f0c73f6a5d1e3baa48d41438f7f81870e5b07c65f5fcea05e72a | Python | 3,655 | 90 | import pytest
from pgmpy.factors import FactorSet
from pgmpy.factors.discrete import DiscreteFactor
@pytest.fixture
def phi1():
return DiscreteFactor(["x1", "x2", "x3"], [2, 3, 2], range(12))
@pytest.fixture
def phi2():
return DiscreteFactor(["x3", "x4", "x1"], [2, 2, 2], range(8))
@pytest.fixture
def ph... |
c02adb2f49f5826027002fcf1a0fe751a856f6f5a0b03187b2d88f0aeb36e361 | Python | 3,655 | 105 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 1 13:40:02 2024
@author: tower2
"""
import torch
import torch.nn as nn
import torch.optim as optim
from torch_geometric.nn import GCNConv
import torch_geometric.nn as pyg_nn
import torch.nn.functional as F
from tqdm import tqdm
from torchviz impor... |
02890b65163a300ded89bb6bbb29ae5b51be115ac77a3afeb6f12e0302191b5b | Python | 3,656 | 124 | # 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 functools
import sys
import unittest
import torch
from fairseq.distributed import utils as dist_utils
from .utils import objects_are... |
285eed4eccd4c9f3d234215366f3e9e28f4fb832332c1155c296c53f2c6d4b77 | Python | 3,656 | 133 | """
Simple non-parametric forecasting baselines for fMRI ROI windows.
These estimators are compatible with the shared forecasting pipeline and expect
unflattened input windows shaped ``(N, M, ROI)``. They provide useful reference
models for interpreting whether learned forecasters beat basic persistence or
window-aver... |
b6dfbecc643f8bf7831903b4eacba20bccebbb8b8274464f920ab6815aedeb40 | Python | 3,656 | 126 | """Fetch the BRENDA data blobs from the Hugging Face Hub and verify them.
Paths are resolved from ``__file__`` rather than through
``resources.files("brenda_references")`` on purpose: this is a bootstrap
script, so it has to run before the package is necessarily importable.
"""
from __future__ import annotations
imp... |
379cf175d29c8e9d2d013807a60d556a4fbebfda9193ba53b878685caf4cb747 | Python | 3,659 | 94 | from ... import options as opts
from ... import types
from ...charts.chart import RectChart
from ...globals import ChartType
class Kline(RectChart):
"""
<<< K-line >>>
K-line shows the highest value, the lowest value,
the starting value and the ending value of the data on the day,
whi... |
1642b9357513244ddfaa2cc954ba0564cc7efb3496e075e342d29abf3846400f | Python | 3,661 | 110 | #!/usr/bin/env python3
"""G1 — cross-modal imputation.
For each checkpoint, iterate over its own modality set: mask one modality at
the encoder input (zero tensor), run forward, measure MSE + 1-D Wasserstein
against the real modality for every reconstructed output.
HIPPIE has three modalities (wave, isi, acg) → 3×3 c... |
b8f1bc187de60baedfc89fd1e1a6c4c91bdaa10b343f79d55229fe62a47d2b8f | Python | 3,661 | 113 | import os
import numpy as np
import pytest
from scvi.data import synthetic_iid
from scvi.external import SOLO
from scvi.model import SCVI
@pytest.mark.parametrize("soft", [True, False])
@pytest.mark.parametrize("return_logits", [True, False])
def test_solo(soft: bool, return_logits: bool):
n_latent = 5
adat... |
9c8606d3ade18f21eb7bb5da52dd2471dfeb5dcf0d481c7c73318f1410c5a840 | Python | 3,662 | 92 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Sankey(Chart):
"""
<<< Sankey >>>
Sankey diagram is a special flow diagram, which is mainly used to
express how raw materials, energy and so on from the initial fo... |
ef970a1e4c36e79da53df89c7829dab6b470069bf59a7ea0d04d3b071ab9d622 | Python | 3,662 | 92 | """Validate OCE on test set: per-isomer-group hierarchization + global metrics."""
from __future__ import annotations
from collections import defaultdict
from pathlib import Path
import numpy as np
from scipy.stats import spearmanr, kendalltau
from oce.atomic_table import load_table
from oce.dataset import load_data... |
29eb6ddd9aeef55ffd6d92e00284f0ea5434e55bbfd0f39f970e9847a6880020 | Python | 3,663 | 115 | #!/usr/bin/env python
# ENCODE DCC blacklist filter wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
get_ext, get_num_lines, gunzip, log, mkdir_p,
rm_f, run_shell_cmd, strip_ext, strip_ext_bam)
def parse_arguments():
parser = argparse.Arg... |
910b4c73bbe444ac641979d7a921500dd72507c88413a56c6f7a4d6e091c2692 | Python | 3,664 | 118 | import matplotlib.pyplot as plt
import matplotlib.image as mpimg
from PIL import Image
import numpy as np
import pandas as pd
import seaborn as sns
# Create main figure with 4 rows × 2 cols
fig, axes = plt.subplots(4, 2, figsize=(14, 22))
axes = axes.reshape(4, 2)
from matplotlib.gridspec import GridSpec
import matpl... |
b4f5945fc87c44299665988aab507acd8f292a121a3a1dec54de64ecbabbca6b | Python | 3,664 | 102 | """Deprecated compatibility shim for :class:`pgmpy.causal_discovery.GES`."""
from collections.abc import Iterable
from typing import Any
import pandas as pd
from pgmpy.base import PDAG
from pgmpy.causal_discovery import GES as _GES
from pgmpy.estimators import StructureEstimator
from pgmpy.structure_score import Bas... |
be4e95e4ceea747845093645132d4bf191d7945406a50b133a24549c6579bde1 | Python | 3,667 | 116 | from __future__ import annotations
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import argument
from cleo.helpers import option
from cleo.io.null_io import NullIO
from tomlkit import table
from tomlkit.items import AoT
from poetry.config.source import Source
from poetry.console.comm... |
e62b876e1e118791a75a9e1b089ab9f00822b99bfd7056854dc69847bd602532 | Python | 3,668 | 98 | # coding=utf-8
# Copyright 2020 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
2c433cfabfdfd8866edc699a08332d419ad8f29331fa02eec04317ecdd61000e | Python | 3,669 | 102 | from __future__ import annotations
from itertools import product
from math import gcd
import numpy as np
import pandas as pd
REQUIRED_FEATURE_COLUMNS = ("phi_local", "phi_uncertainty", "phi_stability")
def zscore(values: np.ndarray) -> np.ndarray:
values = np.asarray(values, dtype=float)
std = values.std()... |
4da1c0e4f472e50c3528932b79e4603755e7dc4d5a0a1b0b1156a696a5d43a02 | Python | 3,669 | 98 | """Subprocess wrapper around xtb for ground-state energies."""
from __future__ import annotations
import re
import shutil
import subprocess
import tempfile
from pathlib import Path
from ase import Atoms
from ase.io import write as ase_write
XTB_BIN = "/home/xtb/bin/xtb"
EH_TO_EV = 27.211386245988
import os as _os
... |
64430561d35c8bb1cb464970dc11cc8e60c74490e62c194d04a7f87a18ac8209 | Python | 3,670 | 100 | # coding=utf-8
# Copyright 2020 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
31a6935d956a45cb85db9a8b4edc149eaa5284423e92a42d93166bd0cd86aacb | Python | 3,671 | 102 | from __future__ import annotations
import re
from typing import TYPE_CHECKING
from typing import ClassVar
from cleo.helpers import argument
from cleo.helpers import option
from packaging.utils import canonicalize_name
from poetry.console.commands.installer_command import InstallerCommand
if TYPE_CHECKING:
fro... |
185868b1dfa34ff666aa88f100e22792c84b1eea24eaf9de3fcfaccfd02676eb | Python | 3,672 | 95 | import logging
from argparse import ArgumentParser
from transformers.commands import BaseTransformersCLICommand
from transformers.pipelines import SUPPORTED_TASKS, Pipeline, PipelineDataFormat, pipeline
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
def try_infer_format_from_ext(path: str):
... |
1b37c65b5763cd0054f84f6f754b88aacbafc07aa0a3bbe0acdf6ac43dca30bc | Python | 3,672 | 65 | #!/usr/bin/env python3
"""Numeros laterais da Sec. 4.3 no protocolo final (sem copias; CV interna agrupada).
(1) metalicidade: AUC do 1F e do wave15 com a MESMA maquinaria da varredura
(run_classification do sweep_targets, features brutas, GroupKFold por familia),
completo (controle: tem de dar o +0,012 ... |
5a7efd78a8bf885c5410e5cdf223bb5b758da7557ef0b870682ee61e9579020e | Python | 3,672 | 128 | from typing import Sequence, TypeVar, Callable, Generator, Optional
import functools
import torch
import numpy as np
import contextlib
from tqdm.auto import trange
TensorLike = TypeVar("TensorLike", np.ndarray, torch.Tensor)
T = TypeVar("T")
@contextlib.contextmanager
def numpy_seed(seed):
"""Context manager wh... |
055c8c14b9c2be94f32205a62f47ae21a49f1547b99b04e10c450cf7d38f0790 | Python | 3,673 | 96 | import logging
from argparse import ArgumentParser
from transformers.commands import BaseTransformersCLICommand
from transformers.pipelines import SUPPORTED_TASKS, Pipeline, PipelineDataFormat, pipeline
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
def try_infer_format_from_ext(path: str):
... |
3ea6e780d986de337c0c42a7c6c056ea4fb0a5584ecbc2780263afbbce64bdae | Python | 3,673 | 119 | #!/usr/bin/env python3 -u
# 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 os
import os.path as osp
import tqdm
import torch
import torch.nn.functional as F
from shutil... |
8945795b93763ebbd7807d4b9a4fec6281f6e6bbe64520e5c08c093600fd26e4 | Python | 3,673 | 128 | from __future__ import annotations
import functools
from pathlib import Path
from typing import TYPE_CHECKING
from poetry.core.packages.utils.link import Link
from poetry.config.config import Config
from poetry.inspection.info import PackageInfo
from poetry.inspection.info import PackageInfoError
from poetry.utils.... |
0561ce2b0006140ed84be7827bb67f0da9c7948fbcef183c19cdd3e862eea906 | Python | 3,674 | 80 | #!/usr/bin/env python3
from collections import defaultdict
import numpy as np
import pytest
from pgmpy.factors.discrete import DiscreteFactor, TabularCPD
from pgmpy.inference import Inference
from pgmpy.models import DiscreteBayesianNetwork, DiscreteMarkovNetwork
@pytest.fixture
def inference_data():
bayesian =... |
a7cde2b3209499ebf465604bb1c0c3cebb1deef75ae0fe4bdec0e2d6e20ede7c | Python | 3,677 | 119 | # 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 numpy as np
import torch
from fairseq.data import Dictionary, FairseqDataset
from fairseq.tasks import LegacyFairseqTa... |
ae6d73ec104170ca52de622329beb72087cf74b4acc50d767f0f244369a781ec | Python | 3,678 | 95 | """The StrainInfo write-back must not join on a generic designation.
`apiadapters.straininfo.StrainInfoAdapterBase.retrieve_strain_models` (not
editable here) pairs a returned record with whichever BRENDA strain shares
its *first* matching designation, with no organism constraint. `A2` is short
enough that StrainInfo ... |
f441077ef739634ef3a37fe6617e7c8b628dd718f8c03c0de74039ece9d626ff | Python | 3,678 | 110 | import numpy as np
import itertools
def weighted_quantiles(values, weights=None, quantiles=0.5, interpolate=True):
#set interpolate to False for better performance but less acurate result
if type(weights)==type(None):
weights=np.repeat(1,values.size)
... |
e7de204ab7c40badb28a7f24e14a5132addf0cdd968c8ec9b06f6ea50afccdbd | Python | 3,682 | 108 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
# import matplotlib.pyplot as plt
# import pytorch_lightning.callbacks
# get_ipython().run_line_magic('load_ext', 'autoreload')
# get_ipython().run_line_magic('autoreload', '2')
# get_ipython().run_line_magic('matplotlib', 'widget')
# In[2]:
print('=========Loading imp... |
f1f69749addb545af65146c33c981e2f0eda9345b559cb851668c2d037345c4a | Python | 3,682 | 96 | import pandas as pd
import numpy as np
import os, sys, logging
def read_bim(bimFile, logger=None, sep='\t'):
'''
Read PLINK bim file.
Input:
------
bimFile, PLINK bim file path
logger, python logger for process information
sep, separator of bim file
Return:
------
... |
ab8de30f71ec704a997c90f51d15c62835ad7d42bd316dda9cd65c705c72b7ad | Python | 3,683 | 112 | # coding=utf-8
# Copyright 2018 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
b3ddfc84a360c5924d146fd53df759ad2728066d0d6b948dc47a1b3e2633e916 | Python | 3,685 | 114 | # coding=utf-8
# Copyright 2018 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
d43694972c437c3e48fee74544596a28bd8ba89a5c03b1e88ae26a5e51cc856f | Python | 3,685 | 98 | import torch
from tqdm import tqdm
from torch.nn.functional import normalize
from transformers import EsmConfig, EsmForMaskedLM, EsmTokenizer
class ProteinEncoder(torch.nn.Module):
def __init__(self,
config_path: str,
out_dim: int,
load_pretrained: bool = True,
... |
b9705d57ce02968b10c0c6c8e3b4c08e609706608bd89204ec2c0c54dea91e94 | Python | 3,686 | 106 | # 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.
"""isort:skip_file"""
from .adaptive_input import AdaptiveInput
from .adaptive_softmax import AdaptiveSoftmax
from .base_layer import BaseLaye... |
2af082b38c1c5c4ab9dc97fc30011808d3e119e64ce53698cf736352b487f162 | Python | 3,690 | 76 | import torch
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
class nnUNetTrainer_5epochs(nnUNetTrainer):
def __init__(self, plans: dict, configuration: str, fold: int, dataset_json: dict, unpack_dataset: bool = True,
device: torch.device = torch.device('cuda')):
"... |
29bf2a4faf291f62af27f83a951d5ba75aa4226b6a086b410ce0d6fc8b01c03f | Python | 3,691 | 104 | # @license
# Copyright 2022 Google Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... |
4718c005f8a7cf18e5adbffbfc920ef6af61f8049905b1c84d157c517b21e247 | Python | 3,691 | 95 | def run_surf_cmd(
input_seg,
cmd,
cfg,
singularity_path=None,
singularity_mount=None,
singularity_home=None,
):
"""
Run a segmentation command with the given input SRR.
Args:
input_seg (str or list): Path to the input segmentation file or a list
... |
40f8a59dcfdbc808cd701a8ec252ec36f24c3c7783a9c27ec7f099066fb894fc | Python | 3,692 | 122 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
import numpy as np
import warnings
def get_target_sequences(manifest, ground_truth, to_take=1000):
import json
import ... |
5e37237d357c38d42e5ea273a966ee39d8d58cf4f28424c6fd62eed76ffe8def | Python | 3,692 | 104 | # 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... |
608b511c2a378ba6fb0e7744711203ec4dc787b47898825821904c2d5e9798cf | Python | 3,692 | 90 | #!/usr/bin/env python
# Author_and_contribution: Jieran Sun; created script
import argparse
parser = argparse.ArgumentParser(description="Aggregate the results into a single tsv file. Notice that the folder structure should be input_folder/*/results_files")
parser.add_argument(
"-i", "--input_folder", help="Inp... |
4ccc24c2cb5d6f47fed44dff5c2455239bcbe32c55dcb00a0d782a8a6db4d53e | Python | 3,693 | 103 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_test_desikan_main(gpu_index=0):
torch.cuda.set_device(gpu_inde... |
3823bea581a68438eee50bf461a901d2e417430ad2b9128b23b143f6477d326a | Python | 3,694 | 103 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def CBIG_mfm_test_desikan_main(gpu_index=0):
torch.cuda.set_device(gpu_inde... |
890187a3bebf4e71e62d475948ce8472867aac31e619f1be72c22c2bd666a71c | Python | 3,694 | 132 | import numpy as np
import pandas as pd
from st_risk.eval.reference_eval import (
marker_subset_discordance_mean,
random_subset_markers,
reference_signature_residual_proxy,
reference_subsampling_instability,
)
def test_random_subset_markers_respects_fraction_and_minimum():
markers = {
"A":... |
549ec846e7630f50f823b47a59cedffefc0ffb8bbfe6912d4ec39a3c144d1a66 | Python | 3,695 | 103 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
import glob
import argparse
from utils.dedup import deup
import sys
WORKDIR_ROOT = os.environ.get('WORKDIR_ROOT', None)
if WORKDI... |
92138cb367fcebeb3ef50dd1b04fce48a436f07ad0d46b0ae480d3edacf9a02a | Python | 3,696 | 112 | """Figure sizing and filesystem export helpers."""
from __future__ import annotations
import datetime
import math
from pathlib import Path
def apply_figure_size_and_fonts(
fig,
axis_width_cm: float,
axis_height_cm: float,
font_settings: dict,
current_xlabel: str,
current_ylabel: str,
) -> No... |
9d49b7703c7ac6b542284aed66eee2765523a03fbfc44dbd7c2fe7fbd8705611 | Python | 3,696 | 109 | #!/usr/bin/env python3
import polars as pl
import argparse
def main():
parser = argparse.ArgumentParser("Get best_orf.tsv")
parser.add_argument("--final_sample_classification", action='store', type=str, required=True)
parser.add_argument("--final_sample_fasta", action='store', type=str, required=True)
... |
a1dcef0926c8abb457386ded344ef25eda8ea0e7c380463d75239cb47dd0953c | Python | 3,696 | 160 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from poetry.config.source import Source
from poetry.repositories.repository_pool import Priority
if TYPE_CHECKING:
from poetry.poetry import Poetry
from tests.types import CommandTesterFactory
from tests.types import Proj... |
33a8d42ff9bf78e162b35321c5cbd4d4ec12fb46e3f53b9857016797e0133e8b | Python | 3,697 | 126 | import json
from pathlib import Path
from typing import Dict, Tuple, List
import numpy as np
import pytest
import torch
from neurovfm.data.metadata import DatasetMetadata
@pytest.fixture
def create_dataset_dir(tmp_path) -> Path:
"""
Create a dataset directory structure with raw/ and processed/ and return its path... |
315ba0fadcd9c175a17cad5cd38e81dee2f4a08489fb84cbfb0c51e0abcefca3 | Python | 3,698 | 105 | import os
import zarr
import tskit
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
from tqdm import tqdm
from multiprocessing import Pool
import ts_simulators
# Get information from config
simulator_config = snakemake.params.simulator_config
simulator = getattr(ts_sim... |
c061d6d958a159582b9d0ab5c9927c1efe5b049a8c7af9d7d11e5356ea028bce | Python | 3,698 | 123 | """Local whole-genome MSA access for GPN-Star training and inference."""
from typing import Any
import numpy as np
import zarr
from gpn.data import ReverseComplementer, Tokenizer, slice_alignment
class GenomeMSA:
def __init__(
self,
path: str,
n_species: int,
subset_chroms: list... |
b384828da6309acda90529d1c976fc26a5b46a18c126012fbcd496bcb2f1c0b8 | Python | 3,701 | 126 | from unittest.mock import MagicMock
import anndata
import numpy as np
import pytest
import novae
from novae._constants import Keys
from novae.utils._validate import log
N_PANELS = 2
N_SLIDES_PER_PANEL = 3
adatas = novae.data.toy_dataset(n_panels=N_PANELS, n_slides_per_panel=N_SLIDES_PER_PANEL)
single_adata = adat... |
f3e8f7e2276d8fcd6ebe4321895a64120dbc395510cda9818366f5c795877bc4 | Python | 3,701 | 92 | import os
import pandas as pd
from BLRun.runner import Runner
class GRNVBEMRunner(Runner):
"""Concrete runner for the GRN-VBEM GRN inference algorithm."""
def generateInputs(self):
'''
Function to generate desired inputs for GRNVBEM.
It will create the input folder at self.working_di... |
41cc5691001907b8169e0c9c7b809f386a3cfc55edf53bba98bd4ad67e73a56a | Python | 3,702 | 106 | """The shipped pooling default is length-invariant, on the class head.
`logsumexp` is `max + log(T)` to within a bounded correction, so on
~8,000-token documents it hands every column about nine nats of length bias and
the cheapest answer to the pooled objective becomes a channel that never fires.
The assertion turns ... |
20554fe9aac2db06a6ff43c554a3fc898a2b1cc162fa870596cae91f2477d279 | Python | 3,703 | 90 | """
Logits-based knowledge distillation.
"""
from __future__ import annotations
from typing import Dict, Tuple, Union
import torch
import torch.nn.functional as F
from .base import DistillationMethod
class LogitsDistillation(DistillationMethod):
"""
KL divergence on segmentation logits.
Config paramet... |
d888dab58537b4d1b6683f6b0934a90914c41cd209d0b4316961d5394cdd5232 | Python | 3,705 | 87 | #!/usr/bin/env python3
"""SET-AFTER-USE check: an option SET below the line that already consumed it.
usage: set_after_use.py <script dir>
Distinct from use-before-definition and invisible to it. The variable IS
defined before use - typically by a guarded default near the top - so nothing
errors. The problem is t... |
fbd32f61524c5b68ac2c7e7c409e52a8abeead9f63e1e323853e86b86d9f98f9 | Python | 3,706 | 105 | import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
def load_relevance_matrix(input_path: str) -> pd.DataFrame:
data = pd.read_csv(input_path, delimiter='\t')
return data
def random_cosine_similarities(data: pd.DataFrame) -> pd.DataFrame:
splits = data["Group"].value_cou... |
1b8be0edff02892b53492008a3353a59eefda62daba9a420cea8c3c279d005a2 | Python | 3,707 | 100 | #!/usr/bin/env python3
# MIT License
#
# Copyright 2025 Broad Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to u... |
5f662f5b95706236316acd2d7bb8da79f2304cd2d99145ee0c61fcb908e1acc5 | Python | 3,707 | 98 | from umap.parametric_umap import ParametricUMAP
from msi_visual.utils import normalize, segment_visualization
import tensorflow as tf
import numpy as np
import os
import cv2
from pathlib import Path
import joblib
class UMAPVirtualStain:
def __init__(self, n_components=1, start_bin=0, end_bin=None):
... |
a0c65a0783fe6e7bd2dedb188bd2d7318708123de091735efc0bac33ffef6cd5 | Python | 3,710 | 118 | #
# Copyright 2017-2023 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with
# Sandia Corporation, the U.S. Government retains certain rights in this software.
#
# See LICENSE for full license details
#
import numpy as np
from scipy.optimize import minimize
import time
import os
# Use th... |
94e79ae2eb42b8875f1696e8d7b371385f680f8d1dbb3fb44b8818f250fd2fcd | Python | 3,711 | 77 | #! /usr/bin/env python
__author__ = 'heroico'
import metax
__version__ = metax.__version__
import logging
import os
import copy
from metax import Exceptions
from metax import Logging
from metax.gwas import Utilities as GWASUtilities
import M03_betas
import M04_zscores
def run(args):
if not args.overwrite and ... |
0cd1eb3870e6051083c53b1572ff1f51af75eedd26a2279bc49ed387bad0fa77 | Python | 3,713 | 125 | import re
import shlex
from pathlib import Path
import pytest
from gsMap.main import create_parser
# Import your original functions
def extract_bash_blocks(markdown_text):
bash_block_pattern = r"""
(?:
(?:```|~~~)(?:bash|shell|sh){1,}\s*\n
(.*?)
(?:```|~~~)
)
... |
68396364a58c64b2c8d0fab0186534db9d7dab38a6b478017a4ba4f5f1906d07 | Python | 3,713 | 123 | #!/usr/bin/env python
# Author_and_contribution: Niklas Mueller-Boetticher; created script
# Author_and_contribution: Qirong Mao; Implemented feature selection with Moran's I
import argparse
# TODO adjust description
parser = argparse.ArgumentParser(description="SVG selection using Squidpy (Moran's I)")
parser.add_... |
b9729f100bfa0c96f82335977b1b7a8003bdac2f99bd5b4c0bc297ed239a425f | Python | 3,713 | 124 | import json
from os import getenv
from typing import Any
from .._constants import Keys
PROVIDERS = ["openai", "anthropic"]
def api_request(
api_key: str | None,
provider: str,
model: str,
messages: list[dict[str, str]],
output_schema: dict[str, Any],
max_tokens: int,
seed: int | None = N... |
c2f473a76f584900050f6865236017e3a262ad34ed4a6f7970bbf799387d1d73 | Python | 3,715 | 166 | from __future__ import annotations
import packaging.tags
GET_PLATFORMS = f"""
import importlib.util
import json
import sys
from pathlib import Path
spec = importlib.util.spec_from_file_location(
"packaging", Path(r"{packaging.__file__}")
)
packaging = importlib.util.module_from_spec(spec)
sys.modules[spec.name... |
370866713f7195c0352a354cb62772a0545585359ab771b90489ae267aa9349c | Python | 3,717 | 97 | #
# estimate.py
# Copyright (c) 2020 Daisuke Endo
# This software is released under the MIT License.
# http://opensource.org/licenses/mit-license.php
#
#----------------------------------
# This is a function for estimating synaptic connectivity.
# if __name__ == "__main__"
# "spikefile": a set of spike trains.
# Repla... |
4f5282d4df3ceb52a55429fe497ed09ac658cba701885ed24c0c000c6afcfc74 | Python | 3,719 | 107 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
import torch.nn.functional as F
class PQEmbedding(nn.Module):
"""
Quantized counterpart of nn.Emb... |
a7831cd3f198a47cefe066a0e3634d28ea2f21e26d521fa6b68424db6308a734 | Python | 3,719 | 87 | #!/usr/bin/env python3
"""R1 ponto 3 (MAE e R2 na Fig. 1a) e R1 ponto 4 (definicao de misto_F).
Reproduz EXATAMENTE as predicoes out-of-fold do painel (a) de fig_manuscrito.py --
mesmo GroupKFold por familia, mesma grade de alpha, mesma normalizacao por atomo --
e acrescenta MAE e R2 ao RMSE ja publicado. Nada aqui re... |
d19868b6eeb0ae11741e3df4234fae0d24a7cdb6e983c418a95bd0f2ddedff02 | Python | 3,719 | 120 | """
Training script for the hybrid transformer model.
Step-by-step and well-commented for GitHub and IEEE-style reproducibility.
"""
import os
import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from configs.config import Config
from datasets.kvasir_dataset import KvasirDataset, collect_image_p... |
22e0b0efe7f71f043f5c7fe5fe7c3311371dfba1621305a3a1db7a442b5fce26 | Python | 3,722 | 73 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'autonomouse-control(BEAST)/UI/ControlWindowGraphicsView.ui'
#
# Created by: PyQt5 UI code generator 5.9.2
#
# WARNING! All changes made in this file will be lost!
from pyqtgraph import PlotWidget
from PyQt5 import QtCore, QtGui, QtWidgets
... |
50b93cd3fdee8b8d5ebc7b3909523ac3ad91fce0958705816c78e4a50ea991a3 | Python | 3,724 | 105 | from torch.utils.data import DataLoader
import torch
import lightning.pytorch as pl
from typing import Union, Optional
from pathlib import Path
from rinalmo.data.alphabet import Alphabet
from rinalmo.data.constants import *
from rinalmo.data.downstream.ncrna_classification.dataset import ncRNADataset
from rinalmo.ut... |
b08f8abe011b33856a818013fdbd231396a4cf15f0ff4f26fd8f797f20c100cc | Python | 3,726 | 97 | """Download the Visual Genome dataset."""
import json
import os
# Imports
import click
import datasets
from datasets import load_dataset
from compositionality_study.constants import COCO_A_ANNOT_FILE, COCO_DIR, LARGE_DATASET_STORAGE_PATH
@click.command()
@click.option("--hf_coco_name", type=str, default="Multimoda... |
0267b9213aee9f036065ffcbd82f0ad3553287fc524f8483bfda4b567604b56b | Python | 3,729 | 102 | '''
By K. Butenko
These functions allow to retrieve data about simulated pathways
(after Kuncel pre-filtering, but keeping original number of tracts!) and stimulation protocol
'''
import matplotlib.pyplot as plt
import numpy as np
import os
import h5py
#import seaborn as sns
#sns.set()
import sys
os.enviro... |
21ea48e33f2b4d953bd73130d82fceaf4d847ccfa5cd8d6c7420ecc5ef88fd93 | Python | 3,731 | 133 | # Copyright 2026 Hongyu Sun
# Licensed under the Apache License, Version 2.0
import argparse
import time
from pathlib import Path
import numpy as np
import torch
from torch.utils.data import DataLoader
import pytorch_lightning as pl
from pytorch_lightning.callbacks import ModelCheckpoint
from pytorch_lightning import... |
338dcd9478dd200ea372280c1001187acc7ed3b77a43358d8b3b4ddb21b99674 | Python | 3,731 | 111 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from collections.abc import Collection
from dataclasses import dataclass, field
from typing import List
import torch
from fairseq.dataclass i... |
7da252741e9c46abb99b96446184a14702972cb332b8c9a0d0ec1dc8a1e11620 | Python | 3,732 | 118 | import logging
from sklearn import svm, linear_model
from sklearn.ensemble import AdaBoostRegressor, RandomForestRegressor
from sklearn.ensemble import RandomForestClassifier, AdaBoostClassifier
from sklearn.gaussian_process import GaussianProcessClassifier
from sklearn.linear_model import Ridge, ElasticNet, Lasso, SG... |
aaf439728d341024f132496055452d05888b7fb28bb21c160e68a92cece5368b | Python | 3,734 | 89 | """SIESTA-PBE textbook validation: does periodic DFT rank perovskite polymorphs
correctly, before committing to the full 100-structure pipeline?
Relaxes all 5 polymorphs (variable cell) for 4 compositions whose experimental
ground-state structure is unambiguous, and checks that the lowest-energy
polymorph matches expe... |
3e2674952eb9f25bccf776c499233c2878598ea6bf86eb7246313533cafa7881 | Python | 3,738 | 114 | # 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 unittest
import torch
from fairseq.modules.sparse_multihead_attention import SparseMultiheadAttention
class TestSparseMultiheadAtten... |
537ddf9f0d1d76840f4a05d65f92b54dfd3027fbd467df1222f10dcfdd57f6a8 | Python | 3,738 | 131 | """
This module contains the model of the table shown in controller UI.
"""
"""
Copyright (c) 2019, 2022 [copyright holders here]
This file is part of NoSeMaze.
NoSeMaze is free software: you can redistribute it and/or
modify it under the terms of GNU General Public License as
published by the Free Software Foundat... |
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