sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7199d387c0ade9c0f8a1c0b0b4dbd3f6f0c1e305d2f70f1c115e81546c6fce09 | Python | 3,504 | 112 | #!/usr/bin/env python3
"""Train a spiking microcircuit student network from a YAML experiment config.
This script implements the two-phase training procedure:
1. **Teacher phase** — runs a fixed teacher network (no weight updates) over the
combined training and validation inputs to generate target membrane potent... |
22ebd462ad0493489fb0813fbb5392c4b26cca8807598c8ca12cf10e2ffa991d | Python | 3,505 | 88 | # 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... |
3a91bc6d7151fbe232f6617fc1e1e44295dc76b10ae0507fdafd46c3ab0a47d4 | Python | 3,505 | 100 | # /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... |
3b196b0f3487bb2970e2a8b15914f0f03c9a64afc667085884712a8a58207630 | Python | 3,507 | 94 | from argschema import ArgSchemaParser
import os
import logging
import subprocess
import time
import numpy as np
from ...common.utils import load_kilosort_data
from .postprocessing import remove_double_counted_spikes
def run_postprocessing(args):
print('ecephys spike sorting: kilosort postprocessing module')
... |
0005b8031dbbaaceee9828cbc205466fa54991c6b9d057431f1fd449ac77de97 | Python | 3,508 | 107 | import numpy as np
import pandas as pd
import pytest
from src.dfer import df_dual, df_single, run_analysis
from src.dfer.df_common import read_analysis_output, save_analysis_output
def test_save_analysis_output_records_selected_option(tmp_path):
output_path = tmp_path / "recording_Data.csv"
save_analysis_ou... |
94638069b48fb85b3eda42e6b00c94d8e7ad29507cd942cb9686bce9f82cb158 | Python | 3,509 | 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.
from fairseq.utils import safe_getattr
from fairseq.modules import TransformerEncoderLayer, TransformerDecoderLayer
from ..modules.multihead_a... |
9a02431832f06513376ad8230f5b270610009e811536145250738a81edd4be62 | Python | 3,511 | 100 | # /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... |
c2e3705991c04a8c57f608138760d3df72c3dd6b24593784aebaf90224ac278f | Python | 3,511 | 116 | import subprocess
three_to_one = {'CYS': 'C', 'ASP': 'D', 'SER': 'S', 'GLN': 'Q', 'LYS': 'K',
'ILE': 'I', 'PRO': 'P', 'THR': 'T', 'PHE': 'F', 'ASN': 'N',
'GLY': 'G', 'HIS': 'H', 'LEU': 'L', 'ARG': 'R', 'TRP': 'W',
'ALA': 'A', 'VAL':'V', 'GLU': 'E', 'TYR': 'Y', 'MET': 'M'}
one_to_three = {value : key ... |
d9d394fcc749716705065cd05d6b0d5d0573a2dd7bcde2cd1e9c4128c5053276 | Python | 3,511 | 127 | # 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 os
from typing import Optional, Callable, Set
import torch
from torchvision.datasets.vision impor... |
c7105ca3c2d11fea8ea145448f3383484698e5435f86bce153bbc2050a86be55 | Python | 3,512 | 109 | import torch
import numpy as np
from typing import List, Callable
import numpy as np
import cv2
class PerturbationConfidenceMetric:
def __init__(self, perturbation):
self.perturbation = perturbation
def __call__(self, input_tensor: torch.Tensor,
cams: np.ndarray,
ta... |
9f25b3e989f82726c426ce2f696fd1e730c03a063058ee5bf5aa97262d70e184 | Python | 3,513 | 100 | # @license
# Copyright 2020 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... |
7b2cf99677d568fc04509b69d3d92232d56cb985ccedf96d6211e7c71b59202a | Python | 3,514 | 79 | import polars as pl
from src.utils import gtf_to_SJ, read_gtf
import os
def get_CSSs(predicted_cds_gtf, out, novel=True, feature="exon"):
"""
Get novel canonical splice sites present in the predicted GTF but not the GENCODE GTF.
A splice site is considered novel if it is not present in the GENCODE GTF, whe... |
c31cdc0545c12606da11b230704f7122eeb9087455cd02c03c89ed40304e12cc | Python | 3,514 | 178 | import subprocess
import tarfile
import urllib.request
from pathlib import Path
GSMAP_RESOURCE_URL = "https://yanglab.westlake.edu.cn/data/gsMap/gsMap_resource.tar.gz"
GSMAP_EXAMPLE_URL = "https://yanglab.westlake.edu.cn/data/gsMap/Visium_example_data.tar.gz"
def run_command(cmd):
result = subprocess.run(cmd, c... |
29d0d8103dd9aae6b2b8f967a0757fd8a5bb5e9a9429545079e77a5d6b24d44f | Python | 3,515 | 88 | 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... |
776c0d0d8553dbaf216d4a71ceb112471d3ab4a07f2cba70435dd44b4afef775 | Python | 3,518 | 108 | # coding=utf-8
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_scatter import scatter_mean, scatter_add, scatter_max
from torch_sparse import coalesce
from torch_geometric.utils import to_dense_adj, dense_to_sparse
from math import pi
class FourierFeatures(nn.Module):
"""From VDM"""
... |
31d7a5bab2de64b3c80690736b20403c9fc0b2a2f9134bd052f14a31257be0ca | Python | 3,519 | 99 | import os
import pandas as pd
import numpy as np
from .metrics import compare_templates, make_interp_temp, compute_isi_score, compute_isi_score
from .merges import compute_overall_score, ID_merge_groups, make_merges
from ...common.spike_template_helpers import find_depth
def automerging(spike_times, spike_clusters, c... |
e7c574badaa075f95be3927f3f02a5208f862ae8e0a6707fffcac912d7775742 | Python | 3,520 | 135 | # 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 os
import torch
from torchvision import datasets, transforms
from timm.data import create_transf... |
a156481004de22c84a6c396c2a6faee78f0f8ff30b4edb1a0a2a4faecac65a73 | Python | 3,524 | 92 | """Runs stats describe on data. Prints data in a markdown table."""
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import math
import numpy as np
import scipy.stats as stats
class StatsDescribe(object):
"""Describe summary statis... |
bbd3779e6e0a1616a1122e40caed00259643b9d29d8b49e59812fae5ce0a4fe7 | Python | 3,525 | 94 | #!/usr/bin/env python3
"""Download a C4 database H5 file via the npyx helper.
The C4 database (https://www.c4-database.com) hosts the H5 files needed by
the NEMO and WF-RF baselines (and by HIPPIE_WF3DACG retraining). The download
URLs are XOR-encrypted inside npyx and require a password issued by the C4
authors — reg... |
0ec088a6cd5eb55b5df681abacf497a67c3ccd8b66b15d2a162d195b53803ffc | Python | 3,527 | 121 | #
# 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 sys
import numpy as np
sys.path.append("../..")
from simulator.algorithms.dsp.dft import DF... |
a71d7220c58f5bf60cd5cd118ab8b24d614dd82db143b4b3eab4b96deb44497e | Python | 3,527 | 83 | import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from unittest.mock import patch
from GMXMMPBSA.gbnsr6_topology import _compact_equivalent_lj_types, prepare_gbnsr6_topology
class GBNSR6TopologyTest(unittest.TestCase):
def test_compaction_preserves_solty_length(self):
class... |
0c438523e880ae89f0810211fd1d0646282d6edfd7dacd6a6078b3d14ef3cb90 | Python | 3,532 | 118 | """Figure 2 panel A primitive — architectural ablation + hyperparameter tuning pipeline.
Draws a horizontal flowchart describing the methodology used to arrive at the
locked HIPPIE configuration for downstream benchmarks:
1. baseline VAE on Hausser
2. architectural ablation ladder (8 rungs of conditioning / n... |
a7641a73e0e1705d12c1d08299abb5707fe30830b61080d6af3572362e60bae0 | Python | 3,532 | 93 | # 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 fairseq.models import register_model, register_model_architecture
from fairseq.models.transformer import (
TransformerModel,
base... |
003f71aaf14929b39157bf53c3441adc1251defdbf042cdcf4535101c0bd9ef3 | Python | 3,535 | 90 | import pytest
from anndata import AnnData
from scvi import REGISTRY_KEYS
from scvi.data import AnnDataManager, fields, synthetic_iid
from scvi.data._utils import _get_adata_minify_type
from scvi.model.base import BaseModelClass
class TestModelClass(BaseModelClass):
__test__ = False
@classmethod
def setu... |
280f2ab97ea8a7220df6a035503abddb8638a1ff0d810eb763aef1c98fd0c18e | Python | 3,536 | 88 | import json
import os
from pathlib import Path
import sys
import unittest
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
MODULE_DIR = Path(__file__).resolve().parents[1]
REPO_DIR = MODULE_DIR.parent
if str(MODULE_DIR) not in sys.path:
sys.path.insert(0, str(MODULE_DIR))
from PyQt6.QtWidgets import QApplic... |
7ef6436dd807b5a536840ba386938093ced5b3c021717432bf5e8ee8966e2154 | Python | 3,536 | 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.
import logging
import torch
from fairseq import optim
from omegaconf import DictConfig
logger = logging.getLogger(__name__)
class AMPOptim... |
939d8a61c3b17a954d82cc0bb04800891f62f91e403c1f4f1edd405e1515c7a9 | Python | 3,536 | 120 | from __future__ import annotations
import sys
import types
import pandas as pd
import pytest
from matplotlib.figure import Figure
def _install_pyside_stub(monkeypatch):
try:
import PySide6 # noqa: F401
return
except ModuleNotFoundError:
pass
pyside_module = types.ModuleType("Py... |
95ed25ca75809fc7caff845523cb0c41a9526d6aa7252d596bf21e1029f06eb0 | Python | 3,536 | 90 | """
02_genomewide_screen.py
Genome-wide co-expression screen and epigenetic regulator enrichment (Table 2, Figure 1).
Ranks all brain-expressed genes by PCDH coordination score in GTEx BA9.
Tests enrichment of epigenetic regulators in top 5%.
Replicates in putamen, hippocampus, and nucleus accumbens.
Harbert D. (2026... |
646609d4e1c3bbeaac3f9bb6e10b66a78ef254125bb0f68164f24b272b9ca997 | Python | 3,537 | 110 | import json
import os
from typing import Callable
import haiku as hk
import jax.numpy as jnp
import joblib
from huggingface_hub import hf_hub_download
from nucleotide_transformer.bulk_rna_bert.config import BulkRNABertConfig
from nucleotide_transformer.bulk_rna_bert.model import build_bulk_rna_bert_forward_fn
from nu... |
3f9e187b37c53bafce74df53d5215b3100832865b16d1b6d28fb825be240b487 | Python | 3,539 | 125 | # 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
def prob_check(tensor, eps=1e-10):
assert not torch.isnan(tensor).any(), (
"Nan in a probability tensor."
)
... |
8bdd692e7f941fdd42aae81ec3e44077fcf3cf4cba529fd36a1f88bc202c1232 | Python | 3,541 | 113 | import json
import os
from typing import Callable
import haiku as hk
import jax.numpy as jnp
import joblib
from huggingface_hub import hf_hub_download
from nucleotide_transformer.bulk_rna_bert.tokenizer import BinnedOmicTokenizer
from nucleotide_transformer.mojo.config import MOJOConfig
from nucleotide_transformer.mo... |
9cd3ca4c8f1930b959d4aa65de2d07140eb1fc0a6149fa938b6c1163d150bf0f | Python | 3,541 | 122 | from __future__ import annotations
from typing import TYPE_CHECKING
import pytest
from poetry.console.commands.env.activate import EnvActivateCommand
from poetry.console.commands.env.activate import ShellNotSupportedError
from poetry.utils._compat import WINDOWS
if TYPE_CHECKING:
from cleo.testers.application_... |
25945aaca584e5b0f466c5162c1038ff923a6c0b4fd61f4ff2e3f12576474789 | Python | 3,543 | 114 | #!/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 numpy as np
import tqdm
import torch
import random
from shuti... |
c426ec3ecb7ad0d4f12fa3a16ee83fadb91618d621bf51dbbf6738bfcbdf560e | Python | 3,544 | 100 | import sys
from pathlib import Path
import pandas as pd
sys.path.insert(0, str(Path(__file__).parent))
import correct_and_normalize
ROOT = Path("__MS_GEO_ROOT__")
WORKBOOK = ROOT / "Used_Methylation_and_RNAseq_Dataset_Inventory.xlsx"
EXPR_DIR = ROOT / "Expression_Data"
EXPR_META = EXPR_DIR / "Combined_Metadata.csv"... |
c938f4507ee864c323f7e2e91ccff42de3aec24329cbff4db97b9cf3acb3dbd5 | Python | 3,544 | 97 | #!/usr/bin/env python3
"""
Parse GeneMark .lst file and extract protein-coding nucleotide sequences
from the corresponding FASTA file.
"""
import re
import sys
from pathlib import Path
def reverse_complement(seq):
comp = str.maketrans('ACGTacgtNn', 'TGCAtgcaNn')
return seq.translate(comp)[::-1]
def parse_lst... |
d957894486974f1f55b2ca2cfee0835daca7da53b3a74d2f51b461bdbd41d187 | Python | 3,544 | 113 | """The frozen base model stays in eval mode whatever the heads are doing.
`no_grad` does not disable dropout, so a base model carried along by
`model.train()` would hand a fresh draw of a document's activations to every
epoch while the CPU cache and the precomputed store, each written once, served
one draw forever. Re... |
3c5d611e9ab1af58646f76dea2169e224f361d8988a4695a8f5f9a6381f6008e | Python | 3,545 | 109 | import pytest
from brenda_references.docdb import BrendaDocDB
import pathlib
TESTDB_PATH = pathlib.Path(__file__).parent / "test_files/testdb.json"
def test_strain_search():
with BrendaDocDB(path=TESTDB_PATH) as docdb:
assert docdb.strain_by_designation("ATCC 51142") is None
designations = ("S... |
5f439450b12f9fd784a3da6b3a123b94ac8d35e83e3295d2016ba61c88d480c4 | Python | 3,546 | 93 | #!/usr/bin/env python
# PYTHON_ARGCOMPLETE_OK
"""Evaluate an expression on a protocol.
This is meant to quickly change a protocol using mathematical expressions. The expressions
can be any valid python string separated if needed with the semicolon (;).
The columns of the input protocol are loaded and stored as arrays... |
9f5a0a6eecbc36a0ea5a9710b565356bb0b529a5b850e42f96db829f379130b0 | Python | 3,546 | 78 | # Copyright 2021 HIP Applied Computer Vision Lab, Division of Medical Image Computing, German Cancer Research Center
# (DKFZ), Heidelberg, Germany
#
# 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... |
d8dfb59b0b7a8610ceb7196310df9f99e0d26ed5479516bd9b12b80adf69a5b3 | Python | 3,548 | 87 | import numpy as np
import tqdm
import math
from msi_visual.extract import timsdata
import sqlite3
from msi_visual.extract.base_msi_to_numpy import BaseMSIToNumpy
import time
class BrukerTimsToNumpy(BaseMSIToNumpy):
def get_regions(self, input_path: str):
td = timsdata.TimsData(input_path)
... |
09be7194c3a3ff02cca9f6a3003f594362d8e6e8f90ec1210909fcfefb8c8424 | Python | 3,549 | 112 | #!/usr/bin/env python3
"""
Run MSMC2 baseline on existing tree sequences.
This script reads existing simulated tree sequences and runs MSMC2
to provide a baseline for comparison with neural network approaches.
All outputs go to baselines/results/. Existing comparison-results.pkl
files are never modified.
Usage:
... |
8a1780928fe26adec974837f233f9023e51f933dfa0e0ab72667b417faed4eba | Python | 3,549 | 102 | """Deprecated compatibility shim for :class:`pgmpy.causal_discovery.HillClimbSearch`."""
from types import SimpleNamespace
import pandas as pd
from pgmpy.base import DAG
from pgmpy.causal_discovery import HillClimbSearch as _HillClimbSearch
from pgmpy.estimators import StructureEstimator
from pgmpy.estimators.Expert... |
0abac9473b2d61062b3f7c6e473081e5f5a107fbafacd326c3494b80a66f0903 | Python | 3,550 | 89 | from math import ceil
from torch.utils.data import Dataset, DistributedSampler
class BatchDistributedSampler(DistributedSampler):
"""``EXPERIMENTAL`` Sampler that restricts to loading from a subset of the dataset.
In contrast to :class:`~torch.utils.data.distributed.DistributedSampler`,
retrieves a mini... |
a1a21b85e02a3e8612b74ce3331eaf661d1d15db50d7bde4405b1a317759a4f1 | Python | 3,550 | 96 | from __future__ import annotations
from collections import defaultdict
from functools import cached_property
from functools import partial
from typing import TYPE_CHECKING
from typing import Any
from poetry.core.packages.utils.link import Link
from poetry.core.packages.utils.utils import splitext
from poetry.reposit... |
3c3dafed336c6536fc442c4227df15a7e48a4a08ce080c01d542b6b12a577d5e | Python | 3,551 | 94 | """Post-training ``summary.log`` adapter payload for dynamic segmentation (``dlbase.summary_log``).
Mirrors ``tasks/classification/post_train_eval.classification_eval_splits``: split names must be
``train`` / ``val`` / ``test`` (``val`` only when distinct val metrics exist in stat history).
"""
from __future__ ... |
f8799619e84a0599adfdca1033b605cad51312334bc3cb5c941bfde6c0443d6a | Python | 3,554 | 114 | #!/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 soundfile as sf
from tqdm import tqdm
import pandas as ... |
1074b6242df81dd63ca207f088e0a3752e22eeb25a52abf6ae09f808b67e8e5a | Python | 3,555 | 65 | from batchgenerators.utilities.file_and_folder_operations import *
import shutil
from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
from nnunetv2.paths import nnUNet_raw
def convert_amos_task2(amos_base_dir: str, nnunet_dataset_id: int = 219):
"""
AMOS doesn't say anything abo... |
86b6700da298c2e58a315f7f3911f9a9ee75b2e73996f5d8b04cc5794b6b9338 | Python | 3,556 | 102 | import os
from os import listdir
from os.path import join
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from sklearn import metrics
from config_path import PROSTATE_LOG_PATH, PLOTS_PATH
from utils.evaluate import evalualte
from utils.plots import plot_roc, plot_prc
from utils.stats_utils... |
cc3d84427e132afc8e380e1fd17687d892293828d9dd69736d96489f5c6bfee4 | Python | 3,556 | 101 | # @license
# Copyright 2016 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... |
1d8dd9f437d3c3e94b3083a09ab4c62f1c546a77498649a262ace2c1f7098c5a | Python | 3,558 | 91 | import os
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
df_volume = pd.read_csv("../meta_results_volume/meta_analysis_without_covars.csv")
df_area = pd.read_csv("../meta_results_area/meta_analysis_without_covars.csv")
df_thickness = pd.read_csv("../meta_results_thickness/meta_analysis_witho... |
86a6575aa5c089d992871b9704168ccb9a24057a88a6dbcfcecf84c67ce409a0 | Python | 3,560 | 114 | """Unit tests for telemetry refactor helpers and settings persistence."""
from __future__ import annotations
from pathlib import Path
from uuid import uuid4
import pandas as pd
from src.features.telemetry_alignment.io.static_input_builders import (
build_opto_cluster_entries,
build_photometry_cluster_entrie... |
76d49ccdc4ecfac4a033b2640f24f31730bbc5fa3904535c816d8b2c6eaf8ee0 | Python | 3,561 | 88 | import os
import pandas as pd
import numpy as np
from BLRun.runner import Runner
class JUMP3Runner(Runner):
"""Concrete runner for the JUMP3 GRN inference algorithm."""
def generateInputs(self):
'''
Function to generate desired inputs for JUMP3.
If the folder/files under self.input_d... |
96e7e38969fd9e6c9a9eb09588f758826d2567ca7c0c5d9fc0648e904f4b16f2 | Python | 3,565 | 114 | #!/usr/bin/env python
# ENCODE DCC FRiP wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
get_num_lines, gunzip, log, ls_l, mkdir_p, rm_f,
run_shell_cmd, strip_ext, write_txt)
def parse_arguments():
parser = argparse.ArgumentParser(prog='E... |
8dc9f4ff0c57eb709a6198a2feeda4bc23dfbb48d16e799024db94be691ab8d6 | Python | 3,569 | 95 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from functools import cached_property
from typing import Iterable, Iterator, Mapping
import numpy as np
from pymatgen.entries.computed_entries import ComputedStructureEntry
from mattergen.evaluation.utils.symmetry_analysis import (
DefaultS... |
9e79e4061844956a583e8af8765240ea31a6ffb3699a02dffa558613b5f07c40 | Python | 3,570 | 117 | import argparse
import yaml
from BLEval.AUPRC import AUPRC
from BLEval.AUROC import AUROC
from BLEval.data import EvaluationData
from BLEval.EarlyPrecision import EarlyPrecision
from BLEval.SignedEarlyPrecision import SignedEarlyPrecision
from BLEval.BLTime import BLTime
from BLEval.Borda import Borda
from BLEval.Jac... |
1b36a6549e5e5898062945280ee3a5c856fa0f1f536eaf0fb93f4e4e590283d7 | Python | 3,571 | 111 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import copy
import logging
import unittest
import torch
from fairseq.optim.fp16_optimizer import FP16Optimizer, MemoryEfficientFP16Optimizer
... |
7ffec0ae9b14806ced129ec5ecb99bfb0b23f44246a2c437d8e30168a409c995 | Python | 3,572 | 99 | from collections.abc import Sequence
import torch
import torch.nn as nn
class ConditionalDenseNN(nn.Module):
"""Dense neural network with multiple outputs, optionally conditioned on a context variable.
(Derived from pyro.nn.dense_nn.ConditionalDenseNN with some modifications [1])
Parameters
-------... |
8911646827542bb3bc6c23fa341de054fe5f4b1d128e1e9eff3017fcd0a516a3 | Python | 3,573 | 95 | from typing import Iterable, List, Sequence
import numpy as np
import torch
from torch.utils.data import Sampler, SubsetRandomSampler, BatchSampler
class SubsetSequentialSampler(Sampler):
"""Samples elements sequentially from a given list of indices, without replacement.
Arguments:
indices (sequence... |
d2c4296371477041875e613dbb1bfdd7b73b072eccaa01b74e8e3ac3e0cbce7d | Python | 3,575 | 98 | '''
This script implements ICA on image patches from natural videos.
Author: Jonathan Gant
Date: 29.01.2025
'''
import numpy as np
from decord import VideoReader, cpu
import glob
import os
import cv2
import multiprocessing
from joblib import Parallel, delayed
from sklearn.decomposition import FastICA
from sklearn.de... |
19bcb079383df003ae57e1f9b0774830ea38abb255e21246ba5e25cec88ab898 | Python | 3,579 | 108 | # Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... |
f66613d618584663a1b6a083b4730005b6d24fba9a6b7a4216670c22dd27b68c | Python | 3,581 | 109 | """The linker contract: longest match, set-valued answers, NIL, nesting.
Everything runs off small in-memory indexes; the real `SurfaceFormIndex`
implementation is used throughout, so these pin the linker against the same
lookup machinery the labelling pipeline matches with.
"""
import pytest
from d3text import surfa... |
91e2847de6a65e981dc1d0e4cbc1588f542506544a4c5397ead06722673b4e50 | Python | 3,582 | 102 | """Map GO terms or associations to GO slim terms."""
from __future__ import print_function
__copyright__ = "Copyright (C) 2010-present, H Tang et al. All rights reserved."
__author__ = "various"
import argparse
import os
import sys
from ..associations import read_associations
from ..mapslim import mapslim
from ..ob... |
08b39a9578530e79b7f478fbb63bbe8f5e960531db9dbf19cbb84dd8a9594058 | Python | 3,584 | 129 | """
This module contains the model of the table in Schedule Generator 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 Found... |
0d6173af5e515e259d50487fbd80ed110043dd62136a9943e19ce451a577cd1c | Python | 3,584 | 118 | from typing import Literal
import numpy as np
import torch
from anndata import AnnData
import scvi
from scvi import REGISTRY_KEYS
from scvi.data import AnnDataManager, fields
from scvi.train import TrainRunner
class TestSparseDataSplitter(scvi.dataloaders.DataSplitter):
def __init__(self, *args, expected_sparse... |
9b4ed4a03348c2752378644ece682a3c10b1183cbf82a7982631f1bc3ce2d615 | Python | 3,584 | 110 | """Opening a `LayerBoundaryStore` enables blosc2's process-global GIL release.
`_resolve_layer_boundary_cached` reads a batch's hits from a single
background thread while the main thread replays an earlier hit, so
`blosc2.decompress2` must not hold the GIL during that read -- otherwise the
background thread just queue... |
325930411203584c3c99078aeafad00d0294acad3a7a18f79c714c88e1518d23 | Python | 3,587 | 94 | import os
import pandas as pd
import numpy as np
from BLRun.runner import Runner
class LEAPRunner(Runner):
"""Concrete runner for the LEAP GRN inference algorithm."""
def generateInputs(self):
'''
Function to generate desired inputs for LEAP.
If the folder/files under self.input_dir ... |
cba72cda4bdc7dd427e3f2c5dc2a5cc5c2b08694072f8af2feb539e291e94709 | Python | 3,587 | 60 | #04
import sys
sys.path.append("..")
import torch.nn as nn
from modelR.backbones.mobilenetv3 import MobileNetV3
from modelR.backbones.shufflenetv2 import ShuffleNet2_Det
# from modelR.backbones.ghostnet import GhostNet_Det
from modelR.backbones.mobilenetv2 import MobilenetV2
from modelR.necks.Three_Head import... |
f8c974614d4fb54029bf221d92faec7b0f559d13e2b7b311b43130721eca11d6 | Python | 3,590 | 117 | """Polisher module for polishing and stitching consensus sequences."""
import tempfile
import medaka.common
import medaka.medaka
import medaka.prediction
class Polisher:
"""Responsible for polishing and stitching consensus sequences.
Uses subparsers to handle different sets of arguments for each step.
... |
79399b3b16cd0b711497bea3e2a5825159b899343b06809ca0f7840a24d5dba8 | Python | 3,592 | 89 | #!/usr/bin/env python3
# distinguish trunc versus novel for tx nic/nnc
# read in gencode gtf, only exons from protein-coding genes, and make a merged bed
# then find out if protruding 5' end is within intron or exons to determine if
# an nic/nnc is subset (and creating an ntrunc) or protruding (and creating a novel atg... |
6f7c63c541ea314d7d8e9b3a04b21dff7a2bad8b50b43b1032002e7016b6bf47 | Python | 3,593 | 63 | """Tiny synthetic data; never use these synthetic variants to estimate performance."""
import io
import json
from pathlib import Path
import zipfile
import nibabel as nib
import numpy as np
def case_bytes(index=0, channels=1, negative=False, shape=(12, 10, 6), spacing=(0.7, 0.9, 2.0), mutate=None):
case_id = f"S... |
22c72bb46a33b30e7ef8b15bb2fa52ed1950f92140b0a39160650e6545226930 | Python | 3,594 | 114 | # prepare_pairs_c3_temporal.py
# Option B: temporal split (NOT shuffled) for C3, per task.
#
# Reads: OUT_DIR from extraction, where you have:
# sub-XX__...task-BI...__timeseries.npy
# sub-XX__...task-Film...__timeseries.npy
# sub-XX__...task-React...__timeseries.npy
#
# Writes: data_c3... |
b161588cd0ffbd633f0ba61d8603ae7602ebeb5b35d8caf099c6e398db56144f | Python | 3,595 | 101 | import h5py
import numpy as np
import torch
from torch.utils.data import TensorDataset, DataLoader
from DeepMathedFilterModel import EncoderDecoder, DeepMatchedDetector
use_templates = False
use_He = False
device = torch.device("mps" if torch.backends.mps.is_available() else "cpu")
# Load pretrained model
pretrained_m... |
18081a6614e19b0227cffd9bef46a99f2d4a4ed2aebc938cae3388b6779ec100 | Python | 3,596 | 108 | """Fixtures having to do with source files, i.e.,
the "raw" files that go into a data set
used with neural networks
"""
import pandas as pd
import pytest
from .test_data import GENERATED_TEST_DATA_ROOT
# copied from vaktestdata.constants; could we add this to that with sys.path? or vice versa
GENERATED_SOURCE_FILES_C... |
b455698bee99d2764e6c74c8f8ba73c1b54a9e2b3d4d8c52cfe9cf7fd8556bf0 | Python | 3,597 | 95 | from itertools import cycle
import numpy as np
from torch.utils.data import DataLoader
from scvi.data import AnnDataManager
from ._ann_dataloader import AnnDataLoader
class ConcatDataLoader(DataLoader):
"""DataLoader that supports a list of list of indices to load.
Parameters
----------
adata_mana... |
6459b5ed5d1e80dd0fdc23726401b82744378ddf181e5cf44a60f8e300e03613 | Python | 3,599 | 97 | #!/usr/bin/env python3
import unittest
from pgmpy.base import UndirectedGraph
from pgmpy.tests import help_functions as hf
class TestUndirectedGraphCreation(unittest.TestCase):
def setUp(self):
self.graph = UndirectedGraph()
def test_class_init_without_data(self):
self.assertIsInstance(self... |
b1fc98005cabad2048df2b2844d2370c2f5a2ea2ace09e8a50dd2db05cb90b33 | Python | 3,599 | 131 | import math
from functools import partial
from typing import Callable, Optional, TypeVar
import haiku as hk
import jax
import jax.numpy as jnp
T = TypeVar("T", covariant=True)
Constructor = Callable[..., T]
class Identity(hk.Module):
def __init__(self, **kwargs):
super().__init__()
def __call__(se... |
eb535bcc5bbd9e4f1f8f60741a0764aab6a56a5a77444c362721d0b868347e14 | Python | 3,599 | 93 |
from typing import Union, List
import lmdb
import os
import pickle as pkl
from tqdm import tqdm
from pathlib import Path
import warnings
warnings.filterwarnings("ignore", module="tensorflow")
warnings.filterwarnings("ignore", module="numpy")
from tape import data_utils # noqa: E402
import tensorflow as tf # noqa: E... |
aa8f4760c5ac36440a660ead13b4e9a1b568c76af4770091087798f74bfdd8f3 | Python | 3,600 | 98 | # 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 unittest
from tempfile import TemporaryDirectory
from fairseq import options
from fairseq.binarizer import FileBinarizer, Vo... |
716235ef6382b1647355bebfdce125e3574262b42fd2ac5a0f3c71b0c211ab3e | Python | 3,601 | 107 | # 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... |
2c353bb35f051a4b7e75abe4ca6c4288f497b853744e780a8198299fa4f9d888 | Python | 3,603 | 102 | #!/usr/bin/env python
# ENCODE DCC cross-correlation analysis wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_common_genomic import *
from encode_common_log_parser import parse_xcor_score
def parse_arguments():
parser = argparse.ArgumentParser(prog='ENCODE DCC cross... |
a2284560433159dad5429d30c81644e57ccc990f36ec152b9dcfdf84c7734758 | Python | 3,603 | 86 | from copy import deepcopy
import numpy as np
def merge(dict1, dict2):
keys = np.unique(list(dict1.keys()) + list(dict2.keys()))
keys = np.unique(keys)
res = {}
for k in keys:
all_configs = []
if dict1.get(k) is not None:
all_configs += list(dict1[k])
if dict2.get(k)... |
f45d0375425ad5cf865e7d3c428242ae15e6e8aace113769e182901c62235eff | Python | 3,604 | 93 | from lightning import LightningModule
from lightning.pytorch.callbacks import BaseFinetuning
from torch.optim.optimizer import Optimizer
import re
import yaml
def _collect_leaf_module_names(pl_module: LightningModule):
leaf_module_names = set()
for module_name, _ in pl_module.named_modules():
# Ignor... |
525431a4314cdce8c1c54bd01ed3a4de50971ce99235bf32b0cef1a86ec0b50c | Python | 3,606 | 129 | """tests for vak.cli.prep module"""
from unittest import mock
import pandas as pd
import pytest
import vak.config
import vak.common.constants
import vak.common.paths
@pytest.mark.parametrize(
"config_type, audio_format, spect_format, annot_format",
[
("eval", "cbin", None, "notmat"),
("learn... |
7f2ea482724c4cada6f64864d89541529ca94e89e8410848313ac909fcc5a0b2 | Python | 3,606 | 94 | from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import scanpy as sc
from sklearn.cluster import KMeans
from sklearn.decomposition import PCA
from sklearn.model_selection import ParameterGrid
if TYPE_CHECKING:
from anndata import AnnData
def select_genes(
adata: AnnDat... |
e951e8b82f03596576538a7321ce2b3cd9d6853fc4b1814c3a4f036b60b5281d | Python | 3,609 | 102 | """
Convert a trk streamline file to a binary map.
Arguments:
trk_file_in
mask_file_out
reference_file (file with same affine as DWI file, e.g. brain mask)
Example:
python trk_2_binary.py CST_right.trk CST_right.nii.gz nodif_brain_mask.nii.gz
"""
import os, sys, inspect
from dipy.tracking import util... |
94bf1f54f7c77641ead3dcedaef049fb9cf5efcea26efe14ec6bcb64d7de9a36 | Python | 3,611 | 72 | """Corrected leave-one-BRAND-out, using the paper's own loaders / preprocessing / tuned params."""
import sys, os, re, json, numpy as np, pandas as pd
sys.stdout.reconfigure(encoding="utf-8")
sys.path.insert(0, r"C:\kan")
os.chdir(r"C:\kan")
os.environ.setdefault("KAN2_DIR", r"C:\Users\abdulhamid batayhi\Desktop\kan2")... |
08abcb37fb4c039ac12ba30db98b22adfb200be6d42a200e26e7ec213855af8a | Python | 3,613 | 109 | #!/usr/bin/env python
"""
Author: Ken Chen
Email: chenkenbio@gmail.com
"""
import os
import sys
import json
import pickle
import gzip
from glob import glob
from tqdm import tqdm
import numpy as np
import pandas as pd
from importlib import reload
from collections import defaultdict, OrderedDict
import torch
import tor... |
0a0985e4061bed827cc986fad9b90160684eebdcce2f06a3a07c57795e0aacfa | Python | 3,617 | 91 | """Small ORCA textbook test: can a molecular DFT engine (ORCA, no PBC) order
perovskite polymorphs correctly on a cluster?
Probe = the ferroelectric off-centering sign, which is robust to cluster
surface effects (identical atoms in cubic vs distorted polymorph, so the
under-coordinated surface cancels in the energy di... |
c76d5822fdb8ea06be993067c30c9bc810ec85df0d0374144d182543e0a47a41 | Python | 3,617 | 116 | # ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.16.4
# kernelspec:
# display_name: Python 3 (ipykernel)
# language: python
# name: python3
# ---
# %% vscode={"languageId": "plaintext"}
... |
d19027f2d5d2ae78150cbd6745225b577e223f5e662d8d6aa4c14c6fa505498b | Python | 3,617 | 119 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.
import logging
import sys
from ty... |
e91095c79213ec6e146c721e04805ce7dc6517513fb32f8182a2b8881b7d5f13 | Python | 3,617 | 121 | import numpy as np
from sklearn.linear_model import LogisticRegression
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import make_pipeline
from sklearn.metrics import confusion_matrix, f1_score, balanced_accuracy_score
from imblearn.over_sampling import SMOTE, RandomOverSampler
import seaborn ... |
afae092fe90ce03b710a8ffd07777d73d2dbe52a4a963f89fbc597f8734d0d08 | Python | 3,619 | 116 | from collections.abc import Callable, Mapping, Sequence
from functools import wraps
from typing import Any
import torch
from torch.nn import Module
def auto_move_data(fn: Callable) -> Callable:
"""Decorator for :class:`~torch.nn.Module` methods to move data to correct device.
Input arguments are moved autom... |
f55cd5a589d0ded1f7993d12834ff804de19fdab21310775e5e9b0f158b78d6e | Python | 3,619 | 120 | import logging
import anndata
import numpy as np
from scipy import sparse
logger = logging.getLogger(__name__)
class ArrayFakerSparse(sparse.csr_matrix):
"""Create a wrapper around a sparse matrix layer in an AnnCollection.
This wrapper ensures compatibility with the typical AnnData API when
accessing ... |
15780521b8916b844cabf67c3a9633b61de9cca0c1050c6d91dd4c2ef28bd2a9 | Python | 3,620 | 102 | import os
import json
import logging
from pathlib import Path
from typing import Optional, Dict, Any
try:
from openai import OpenAI # type: ignore[import]
except ImportError:
OpenAI = None
API_DEFAULT_KWARGS = {
"model": "gpt-5-2025-08-07",
"max_output_tokens": 5120,
"text": {"verbosity": "low"}... |
18b3215f91bfb93520e4643c57b4054fd455260dad9f29d105cd3aac149e08dd | Python | 3,623 | 82 | import numpy as np
import torch
import skimage.io as skio
from tqdm import tqdm
from src.utils.dataset import DatasetSUPPORT_test_stitch
from model.SUPPORT import SUPPORT
def validate(test_dataloader, model):
"""
Validate a model with a test data
Arguments:
test_dataloader: (Pytorch DataLoad... |
ddfdf2b7c6fbe21204753bb58b14f5a138853803d1bad3a3f304f4003b7a623d | Python | 3,623 | 119 | #!/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
import p... |
213af46cf2535afdb17d2de254703bf0c85be3a71971b0121886966ef0e76e94 | Python | 3,624 | 90 | import numpy as np
from matplotlib import pyplot as plt
import matplotlib as mpl
import pandas as pd
import seaborn as sns
import scipy.ndimage as filters#changed from scipy.ndimage.filters as the namespace was deprecated 05/24/2023
import scipy.stats as stats
rc_pub={'font.size': 8, 'axes.labelsize': 8, 'lege... |
5fbda1555c8ca0e52bece37314b03a1b3b1904661e64a0411193d1b0e0590981 | Python | 3,624 | 86 | """Given GO ids and an obo, creates a small sub-graph DAG.
Sub-graphs can be used to create shortcut paths and eliminate nodes.
"""
from collections import defaultdict
from goatools.godag_small import GODagSmall
__copyright__ = "Copyright (C) 2016-2018, DV Klopfenstein, H Tang, All rights reserved."
__author__ = ... |
3456b6aca10f7376dd4ee905b92d8d6c32b346b332db966320d52b46d58f3290 | Python | 3,628 | 117 | """Figure/table notes for outputs.
Each script calls `build_notes()` with a list of legends, producing
a plain text file with captions and footnotes for each output.
"""
from __future__ import annotations
from datetime import datetime, timezone
from typing import Any, Dict, List, Optional
import textwrap
def _ts_is... |
33ca207ce0c24c62c598472bad3e4d97bd790904bb17e421ffd18b2aeb0fe1d5 | Python | 3,629 | 105 | #
# 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
#
from __future__ import annotations
from types import ModuleType, NoneType
class ComputeBackend:... |
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