sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
7f659a8e3873c995870b009e6e7e52d5ca220a9d45f2e177bb5385554ad1ca86 | Python | 5,580 | 159 | from __future__ import annotations
from collections.abc import Hashable
from functools import lru_cache
import pandas as pd
from skbase.base import BaseObject
from skbase.lookup import all_objects
from pgmpy.utils import build_state_names, get_dataset_type, preprocess_data
class BaseStructureScore(BaseObject):
... |
aee38492328fbb65ccee90e609387c444f7c95d4be82dd68f4064d4e5555c3c4 | Python | 5,583 | 135 | import streamlit as st
import glob
import os
import json
import sys
import numpy as np
import time
import joblib
from collections import defaultdict
from pathlib import Path
from argparse import Namespace
from PIL import Image
from st_pages import show_pages_from_config, add_page_title
import importlib
fr... |
4687351fae48919dd9195255ebc7384800c0cf6559ef70817afc87eb4cbfa4f8 | Python | 5,584 | 156 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
from typing import Any, Dict, Optional
import torch.nn as nn
from fairseq.models.fairseq_encoder import EncoderOut
from fairseq.models.transf... |
bf2def11aa306ef0d84c0cedb3961e7664eb0039d4340acd2c7b3f35a476fffa | Python | 5,586 | 199 | #!/usr/bin/env python
# Author_and_contribution:
# Niklas Mueller-Boetticher; created template
# Peiying Cai; implemented method
import argparse
parser = argparse.ArgumentParser(
description="""STAGATE (https://www.nature.com/articles/s41467-022-29439-6)
"""
)
parser.add_argument(
"-c", "--coordinates", h... |
5ea4d3004fdbaf0a35e82a3eb4c79c516ce4616aa297b897ff6ed21dca01138b | Python | 5,587 | 115 | from typing import Sequence
import jax
import jax.numpy as jnp
from joblib import Parallel, delayed
from tqdm import tqdm
from ...geom import masked_pairwise_diffs
from ...molecule import Molecule
from ...types import ElectronConfiguration, ModelDimensions, MolecularConfiguration, Psi, ScfParams
from ...utils import ... |
467b13ba914c15871b5f4343585836145c49fbc2463547fdbe34e168536a8e69 | Python | 5,589 | 186 | # %%
"""Plot Fig. 3 noise-robustness curves from saved experiment data."""
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from scipy.stats import t, ttest_ind
from statsmodels.stats.multitest import multipletests
# ================================
# Settings
# ===========================... |
998c9c869b2695d2be7bed4211663205f98817ced2ded2b8815c3fb41bb00989 | Python | 5,592 | 165 | #
# 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 ... |
b1fd4f9466484556add2491936173a2ea0410adfea13cc2cec802befd0d91a49 | Python | 5,597 | 166 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 21 15:56:25 2024
@author: tower2
"""
from pathlib import Path
import os
import torch
import pandas as pd
import scanpy as sc
from sklearn import metrics
import multiprocessing as mp
from GraphST import GraphST
from GraphST.utils import clustering
im... |
6cf034909247709f57d868a7aafa804e19e76e88d4abe770831015f96d13e83c | Python | 5,599 | 155 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Nov 25 05:36:17 2025
@author: vbp
Figure S2G only: correlation between a trial's post-outcome dopamine
response and the following trial's anticipatory licking, per region, vs.
a trial-shuffled control.
IMPORTANT: the original version of this analysis ... |
7d9b8787bad825983cc122319a8ffea0995adadb30fa08a53456c8a71b62b0ba | Python | 5,602 | 170 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
from __future__ import annotations
from dataclasses import dataclass, field
from functools import cached_property
from typing import (
Any,
Callable,
Dict,
Generic,
Iterable,
List,
Mapping,
Optional,
Tuple,
... |
c55f8cd4ba89b17b84ce42032cb703276fa6cb54cf6884e61b421e6c2d8890dd | Python | 5,602 | 157 | # Original work Copyright 2018 The Google AI Language Team Authors.
# Modified work Copyright 2019 Rowan Zellers
#
# 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/... |
76179dd70b30c503b55099d295950277c694399c4845763221ea7f22a135cfbe | Python | 5,607 | 130 | """Example of how to add a task in tape.
In order to add a new task to TAPE, you must do a few things:
1) Serialize the data into different splits (e.g. train, val, test) and place
them in an appropriate folder inside the tape data directory.
2) Define a dataset as a subclass of a torch Dataset. This s... |
569a52699a8c0974bdbbd4dabc4063bb491ec023b797474a26e0797b333785e5 | Python | 5,613 | 127 | from dataclasses import dataclass
from typing import List, Optional
import numpy as np
import pandas as pd
from kanfood._paths import data_path, first_existing
# Open dataset ships under data/tahini/; also resolves a repo-root copy for backward compatibility.
TAHINI_PATH = first_existing("KANFOOD_TAHINI_PATH",
... |
97f18289c01f990facf87c1758fe85ba37debad2dc65fe179ddfa3a04e5faf48 | Python | 5,613 | 146 | import torch
import torch.nn as nn
import torch.nn.functional as F
from core.Attention import RTModule, SelfModule, STAFM
class FlowHead(nn.Module):
def __init__(self, input_dim=128, hidden_dim=256):
super(FlowHead, self).__init__()
self.conv1 = nn.Conv2d(input_dim, hidden_dim, 3, padding=1)
... |
b5fca4b3e96bf67f8310b76f781b7a8b0b1e49694b0c65545914da6b52499d58 | Python | 5,614 | 196 | #!/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 logging
import os
import shutil
from typing import List, Optional
logger = logging.getLogger(__file__)
try:... |
bb265f00e613c198795459e6808b0f9b805327428399b0b21cad98c932f2ef69 | Python | 5,620 | 156 | __author__ = 'heroico'
import gzip
import io
import logging
from .DataSet import DataSet
class KeyedDataSet(DataSet):
def __init__(self, name=None, index=None, data=[], keys=[]):
super(KeyedDataSet, self).__init__(name, index, data)
self.keys = keys
self.values_by_key = {}
if len(k... |
b0c47d3481f562ea00cc2380af67be7200e6d83f0f722fd1c2089b146b80caf3 | Python | 5,621 | 135 | # utils/gui_utils.py
import os
from moove.qt_helpers import set_combo_items
def zoom(app_state):
"""Zoom in by reducing the x-axis range by 30%."""
x_start, x_end = app_state.ax1.get_xlim()
x_center = (x_start + x_end) / 2
x_diff = x_end - x_start
new_diff = x_diff * 0.7
app_sta... |
01a141bfbce8bec3ef5e1fe0f82fb1766513c591eb607bb5755847970525b158 | Python | 5,623 | 185 | 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 collections.abc import Iterable
from cleo.testers.command_tester import CommandTester
from poetry.p... |
fd4f1e030e94f91bbd28aed7f64c03015300cd9a7ed3c992a3b8624ce05fd0d4 | Python | 5,623 | 174 | #!/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.
"""
Sample from a trained LM; hacked fairseq-interactive
"""
from collections import namedtuple
import os
import ast
... |
06bbc95aee5e86120a3d10d77510fa326ca5a5aaf52756c9a760aa4c1fe12d66 | Python | 5,626 | 166 | #!/usr/bin/env python
"""Draw BRENDA's training, validation and test splits and write them as CSV.
Rare entities that share no surface form with any other are held out of
training, so the unseen bucket of detection recall measures surface forms the
tagger was never trained on. The splits page of the documentation says... |
83da631300b449df48c0bd940d362c3735d7c756d01c5c3f2d081bb0fc64f64c | Python | 5,626 | 107 | # 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... |
dd15fef73c5a634d166912a83c64d4fca3190936d87865c12c9f2a9851a46d55 | Python | 5,626 | 169 | import argparse
from pathlib import Path
from typing import Any
import anndata
import h5py
import numpy as np
import pandas as pd
from anndata import AnnData
def convert_to_h5ad(dataset_dir: Path):
res_path = dataset_dir / "adata.h5ad"
if res_path.exists():
print(f"File {res_path} already existing."... |
8a11bc41afe03fb99e4fd8bb911a248a962e26614d51dc1be761fd30009c9a52 | Python | 5,627 | 112 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import os
from pathlib import Path
from typing import Literal
import fire
from pymatgen.core.structure import Structure
from mattergen.common.data.types import TargetProperty
from mattergen.common.utils.data_classes import PRETRAINED_MODEL_NAME... |
62c2f4a130a8e4227d143213f5a55a05b058824a43c576fca186f24ad347b8f8 | Python | 5,630 | 134 | import time
import psutil
import matplotlib.pyplot as plt
import os
import numpy
import threading
from typing import Union, Tuple, List, Dict
class PerformanceObserver:
def __init__(self, image: Union[str, None] = None, model: Union[str, None] = None, polling_rate: float = 0.1):
self.monitoring = False
... |
a0ded8e4c49243780a967fb4b004d3ea0b69a03530abb83645be39d09e364a34 | Python | 5,631 | 156 | #!/usr/bin/env python
# ENCODE DCC cross-correlation analysis wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
log, ls_l, mkdir_p, pdf2png, rm_f, run_shell_cmd,
strip_ext_ta)
from encode_lib_genomic import (
subsample_ta_pe, subsample_ta_se... |
63c6fb47991f77e5d364ff790278d7a63aac93e57f6f041da02f73c72ed0d19a | Python | 5,632 | 159 | # scSGL - a python package for fene regulatory network inference using graph signal processing based
# signed graph learning
# Copyright (C) 2021 Abdullah Karaaslanli <evdilak@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... |
b736d37bdae4151f70e31d12c2e419c82e9e6be7367716cefe10eceb57f43e2c | Python | 5,633 | 144 | import torch
import torchvision.transforms as transforms
from torch.utils.data import DataLoader, Subset
from pipelines.dataloader import JacquardDataset
from modules.vgg16_baseline_longer import VGG16Baseline
from grasping_pvgg16_longer_bb import PVGG16SeparateHP as PVGG16
import toml
from modules.loss_functions impor... |
051374940624400aaa0271f698ce57a6a6c4b4b413411d0470661b613e464e60 | Python | 5,638 | 94 | import numpy as np
from nnunetv2.training.dataloading.base_data_loader import nnUNetDataLoaderBase
from nnunetv2.training.dataloading.nnunet_dataset import nnUNetDataset
class nnUNetDataLoader2D(nnUNetDataLoaderBase):
def generate_train_batch(self):
selected_keys = self.get_indices()
# preallocate... |
f0d38602482463accdb76ed34bacf0ae98a37ddadfb718258a33df6b3a1be3e9 | Python | 5,638 | 149 | """Define the ConvNet architecture (standard pytorch ANN)."""
import math
from typing import Generator
import torch.nn as nn
from torch import Tensor
from torch.nn import Parameter
from .layers import Conv2dFA, LinearFA, LinearKP, LinearSCFA
def conv2d_outsize(insize: int, kernel_size: int) -> int:
return insi... |
9f11cf5acfc6ecb740012786f80df21bf26a2f7797064c31f3f72315b4c30996 | Python | 5,640 | 117 | # -*- coding: utf-8 -*-
"""
.. _tutorial05_ref:
Tutorial 5: Colors and colorbars
================================
This tutorial demonstrates how to configure the colorbar(s) with ``surfplot``.
Layer color maps and colorbars
------------------------------
The color map can be specified for each added plotting layer... |
2d11706efd063367cb602599873336bef07260ad8fad8ae58da53b54889dc2c4 | Python | 5,642 | 129 | import pandas as pd
import gc
from preprocessor.utils.preprocess_intrinsic import preprocess_intrinsic
from preprocessor.utils.preprocess_synaptic import preprocess_synaptic
class MembraneCurrentPreprocessor:
"""
Preprocesses intrinsic and synaptic currents and combines them into membrane currents.
"""
... |
86acd754900b77508b39cab31c2dbda7cfe62ad7129990e7c52590b02bbff8ef | Python | 5,642 | 114 | import torch
from torch import autocast
from nnunetv2.training.loss.compound_losses import DC_and_BCE_loss, DC_and_CE_loss
from nnunetv2.training.loss.dice import get_tp_fp_fn_tn, MemoryEfficientSoftDiceLoss
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
from nnunetv2.utilities.helpers import ... |
3b0f1171dc9b0db3262e477bb0baf6c1a4e20e02fb641bf8389819a96b8f5994 | Python | 5,643 | 129 | import logging
from typing import Callable, cast
import pandas as pd
import scanpy as sc
from anndata import AnnData
from ..._constants import Keys
log = logging.getLogger(__name__)
def load_dataset(
pattern: str | None = None,
tissue: list[str] | str | None = None,
species: list[str] | str | None = No... |
48ccbc9348d20b00aef844f9835ad15bec7d362f8ff993f1cbccee5a6e47b9b5 | Python | 5,643 | 129 | from typing import (
Any,
Callable,
Iterable,
List,
Mapping,
Optional,
Sequence,
Tuple,
Union,
)
from . import options as opts
from .options import ThumbnailOpts
from .options.charts_options import BaseGraphic, GlobeLayersOpts
from .options.series_options import JsCod... |
2805fbd0e27a9fbbbf0add0f82691783ee27f3e5dda2f75aa1fe030c4b14ec02 | Python | 5,646 | 160 | #!/usr/bin/env python3
"""Strip a DGR training checkpoint down to inference-only weights for release.
Training checkpoints carry optimizer state, which roughly triples their size and has no
use at inference. This writes ``model.safetensors`` plus a ``config.json`` recording the
architecture hyperparameters needed to r... |
a780da36e9160245d72397e1ce91f98dbc9df33beec45dc7a3ef4941a49f18cb | Python | 5,646 | 107 | # 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... |
e0865dce08f2220ddcc83660ab9c012c1ef90acf7ddc78de0d8c064e44d9bb07 | Python | 5,648 | 179 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import Conv1d, ConvTranspose1d
from torch.nn.utils import remove_weight_norm, weight_norm
LRELU_SLOPE = 0.1
def init_weights(m, mean=0.0, std=0.01):
classname = m.__class__.__name__
if classname.find("Conv") != -1:
m.wei... |
b8148a96f6158542a60d2081bca1d0ac4d702cdcaf2beadbcdce53255e75a032 | Python | 5,649 | 175 | import glob
import logging
import os
import pandas as pd
logger = logging.getLogger("gsMap.utils.regression_read")
def _read_sumstats(fh, alleles=False, dropna=False):
"""Parse GWAS summary statistics."""
logger.info(f"Reading summary statistics from {fh} ...")
# Determine compression type
compress... |
36b5563667dc097779240613cd8083e63d564a745807c0a85b34effbef90603d | Python | 5,651 | 132 | import torch
import numpy as np
from pathlib import Path
from tqdm import tqdm
from compute_energy import compute_energy
class EarlyStopping:
'''
If the relative decrease in the loss is < min_delta for # of consecutive steps = tolerance,
then the training is stopped.
'''
def __init__(self, tol_st... |
e982fe5bf5f9f26deb49e9693c6f80933d74b1bdfa665ba55ce41675011ebc65 | Python | 5,651 | 134 | """Phase 3/4: oils per-food benchmark + shared-chemistry transfer.
(1) Does oils show nonlinearity (KAN/MLP vs PLS)? (2) Do tahini-KAN and oils-KAN, trained
independently, flag the SAME FTIR bands on a common cm-1 axis -> transferable chemistry.
Run: python -m kanfood.phase3_transfer"""
import sys, os
from pathlib imp... |
02ae327e89410c23e5d2149d15792bee4a889be1c2c7d0c2e7f14abd17ba3e90 | Python | 5,652 | 146 | import torch
import torch.nn as nn
import torch_geometric
import numpy as np
import os
import copy
import pandas as pd
from tqdm import tqdm
from sklearn.metrics import roc_auc_score
import warnings
warnings.filterwarnings('ignore')
from .encode_structure import *
from .model import *
from .utils import *
def get_gr... |
93159c5f8d2c91a87d14e77b85d2e5f4b027e837294197e39d305cf388de042e | Python | 5,652 | 155 | import argparse
def main(args):
from dateutil import parser
import numpy as np
import os, time, gzip, json
import glob
folder_with_pdbs_path = args.input_path
save_path = args.output_path
alpha_1 = list("ARNDCQEGHILKMFPSTWYV-")
states = len(alpha_1)
alpha_3 = ['ALA','ARG... |
818d1c650b0ea247b07c2d0d7cfe4a4da3cea9459b897d590712cd2446c4905b | Python | 5,653 | 165 | import os
import numpy as np
import random
def print_file(str_, save_file_path=None):
print(str_)
if save_file_path != None:
f = open(save_file_path, 'a')
print(str_, file=f)
class Metrictor_PPI:
def __init__(self, pre_y, truth_y, is_binary=False):
self.TP = 0
self.FP = 0
... |
c8a3f30eb55fcaac7b5b71939adf473cf2ec42092082186a52f7872deb621d2e | Python | 5,656 | 176 | import re
import os
import torch
import tempfile
import math
from dataclasses import dataclass
from torchaudio.models import wav2vec2_model
# iso codes with specialized rules in uroman
special_isos_uroman = "ara, bel, bul, deu, ell, eng, fas, grc, ell, eng, heb, kaz, kir, lav, lit, mkd, mkd2, oss, pnt, pus, rus, srp,... |
d3be334efd7a18503b77b8d6e4c8d77cd3b9f5d4520eb5ec035cc54a9936b9cc | Python | 5,659 | 154 | import os
import platform
import shutil
import subprocess
import warnings
from pathlib import Path
from shutil import copyfileobj
from typing import Literal, Union
from urllib.request import urlopen
import tenacity
from rnalysis.utils import io
try:
import jdk
except ImportError: # pragma: no cover
warnings... |
b2e0b893134dc2286b478fcd27280a2b63051aa1c8a7a57aeec64166735bc2ae | Python | 5,661 | 159 | """Utility functions for joint embedding loss."""
from __future__ import annotations
import torch
def variance_loss(z: torch.Tensor, target_std: float = 1.0) -> torch.Tensor:
"""Compute variance regularization loss (VICReg-style).
Penalizes dimensions with standard deviation below target_std.
This prev... |
d7c13f052ac9c8173aeb24b331052e75baaae2e5e495932b7bbac67344bf3789 | Python | 5,661 | 129 | # 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... |
0b04206863b2e762e80011c6b1d8557cfc0e4cfd5de7c63c309b602ca49edbb0 | Python | 5,662 | 113 | from typing import Tuple
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunetv2.evaluation.evaluate_predictions import load_summary_json
from nnunetv2.paths import nnUNet_results
from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name, conve... |
1ba702ab054665af7cefb592094b9f3cc51ff278c1f45427a205493bfe080282 | Python | 5,663 | 144 | import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column WMD existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
Parameters
-----... |
4f70c403c7520aa329aa6f142715ad4e34d869a5914992dae2f88be1039bad33 | Python | 5,664 | 145 |
import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column WMD existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
Parameters
----... |
21068f84e6f9ceb8619455951f4172a6af684cd23818925dcffb1ca86317badb | Python | 5,670 | 146 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
From Uchida Takumi https://github.com/uchida-takumi/CustomizedLinear/blob/master/CustomizedLinear.py
extended torch.nn module which cusmize connection.
This code base on https://pytorch.org/docs/stable/notes/extending.html
"""
import math
import torch
import torch.nn a... |
bddad0ff63523030b3304b4f9033355bbc974a69bfe42bc8ac541f9034b5472f | Python | 5,675 | 141 | from ... import options as opts
from ... import types
from ...charts.chart import Chart
from ...globals import ChartType
class Graph(Chart):
"""
<<< Graph >>>
The graph is used to represent the relational data.
"""
def add(
self,
series_name: str,
nodes: t... |
1c1ed652a41b48804730ffd5012e04bae02b7a9e763806c2cd8d115b4994340c | Python | 5,677 | 124 | """Payload I/O for dynamic-segmentation visualize panels."""
from __future__ import annotations
import json
import os
from dataclasses import dataclass
from typing import Dict, Optional
import numpy as np
@dataclass
class SegEvalPayload:
"""Serializable payload for six-panel visualization."""
... |
6633aaa91ba0f53f2f422f44d792872877a524a213d53395f68108ad04a82e1b | Python | 5,678 | 117 | # Source code:
# https://github.com/zbmed-semtec/doc2vec-doc-relevance-training/blob/main/code/train_model/main.py
# This file includes the modifications to the source codes according to this project!
import os
import time
import yaml
import argparse
import logging
import utilities
import precision
import calculate_g... |
fa7658922dd18f174d2295a7f73f5e296b35eb7694f03f52881bbe5443fd0b56 | Python | 5,678 | 167 | # 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 os
import nu... |
22e37c6f2dd564966b9b36a7f60fd2fc63b9436897d085490c02d3bd590615b7 | Python | 5,682 | 161 | """Every tracked script under `scripts/` must name modules that exist.
`scripts/` is the one corner no other gate covers: mypy runs against `src/`
only and nothing executes these files, so a script can name a module that has
not existed for years and stay green. The module part is checked statically
with `ast` and `fi... |
8134eb4a3d830dfd5ee54acb1c9daacac6c0af21522567d96988691eb6284f9d | Python | 5,682 | 157 | """"code to fit learning curves
adapted from
https://github.com/NickleDave/learning-curves/"""
import numpy as np
from scipy import optimize
def residual_two_functions(params, x, y1, y1err, y2, y2err):
"""
returns residuals
between two lines, specified by parameters in variable params,
an... |
d09c28cb7c2014eaca8ae71da9a855b974595c3a1dd99b6bdb9a16a470aefd32 | Python | 5,682 | 139 | """Define the architecture of the spiking RDD net."""
import numpy as np
import numpy.typing as npt
import torch
import torch.nn as nn
from .rdd_layers import SpikingFA
class RDDNetBase:
"""Base class for RDD-based spiking networks of arbitrary depth.
Builds a chain of SpikingFA layers and implements the s... |
eb13dd9fde8ac5db690fb9563757a7621a304a5da3daccded1078b4954b6605f | Python | 5,684 | 152 | #!/usr/bin/env python
# ENCODE DCC Naive overlap wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
from encode_lib_common import (
assert_file_not_empty, gunzip, log, ls_l, mkdir_p, rm_f, run_shell_cmd)
from encode_lib_genomic import peak_to_bigbed, peak_to_hammock
from encode_lib... |
4467e6c87a3019d4ef281c0c4fdab2da8d29d7393d97897c0a85405b4a0017cb | Python | 5,686 | 138 | import torch
from torch import nn
from torch.nn import functional as F
class SelfTrans(nn.Module):
def __init__(self, in_channels, inter_channels=None, mode='dot', dimension=2, bn_layer=True):
# def __init__(self, in_channels, inter_channels=None, mode='dot', dimension=2, bn_layer=True, n_mix, d_k):
su... |
cfd47d9778a46e8dedbc914cb7a9522d7937dc2e51d192d73588498d279faff5 | Python | 5,688 | 152 | # import torch
# import torch.nn as nn
#
# def autopad(k, p=None, d=1):
# """
# Pads kernel to 'same' output shape, adjusting for optional dilation; returns padding size.
#
# `k`: kernel, `p`: padding, `d`: dilation.
# """
# if d > 1:
# k = d * (k - 1) + 1 if isinstance(k, int) els... |
1bb8501f52636318d9d10d6085d4330c83bab94a4f9e29c39b9c41e04fdf35f0 | Python | 5,693 | 136 | """Manages GO Term fill colors and bordercolors."""
__copyright__ = "Copyright (C) 2016-2017, DV Klopfenstein, H Tang, All rights reserved."
__author__ = "DV Klopfenstein"
import sys
import collections as cx
class GoeaResults(object):
"""Manages GOEA Results for plotting."""
kws_set = set(['id2symbol', 'st... |
833e256a4026d041f0871550b2fa737d49f828587bd9c31e86b0817b11a15675 | Python | 5,695 | 166 | import torch
import pytest
from neurovfm.models import (
AggregateThenClassify,
ClassifyThenAggregate,
)
import neurovfm.models.mil as mil_mod
class _LinearDense(torch.nn.Module):
"""CPU-friendly stand-in for flash_attn FusedDense used in MIL modules."""
def __init__(self, in_features: int, out_feat... |
1ab17cc79a9bb5ca17a9d1ab74503b769eaeb8c5d904402f668f22fe284e6a4a | Python | 5,696 | 114 | from typing import Tuple
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunetv2.evaluation.evaluate_predictions import load_summary_json
from nnunetv2.paths import nnUNet_results
from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name, conve... |
a4af2548f9945532f1dd48b9a500b96f5416f01b3261ddfc7a9a9df1c034df9e | Python | 5,696 | 175 | from pathlib import Path
import sys
import pandas as pd
import re
import math
BASE_DIR = Path(".")
INDEX_2016_PATH = BASE_DIR / "dataset" / "index" / "v2016" / "INDEX_general_PL_data.2016"
INDEX_2020_PATH = BASE_DIR / "dataset" / "index" / "v2020.R1" / "INDEX_general_PL.2020R1.lst"
SPLIT_DIR = BASE_DIR / "processed_... |
db84543101016f932e4c27fce6ac388983ba4d704c4ff74e5fbe8894a14cfe11 | Python | 5,701 | 125 | # ##############################################################################
# GPLv3 LICENSE INFO #
# #
# Copyright (C) 2020 Mario S. Valdés-Tresanco and Mario E. Valdés-Tresanco ... |
0fec56f86cd8edd97f48c93e00753bda5989e9e29a90c8613fcbd45d9c14f948 | Python | 5,703 | 198 | from __future__ import annotations
import json
import os
import re
from pathlib import Path
from typing import TYPE_CHECKING
from typing import Any
import pytest
from poetry.config.config import Config
from poetry.config.config import PackageFilterPolicy
from poetry.config.config import boolean_normalizer
from poet... |
3cf20bf605a277143c8045ae418380a62a5065795f1f3b22605366f2dc154aa8 | Python | 5,703 | 149 | import pickle
import tkinter as tk
from tkinter import filedialog
from tkinter import ttk
from src.align_photometry_behaviour import DataProcessingSingleInstance
from src.align_telemetry_opto_photom import MenopauseDataProcessingApp
from src.window_utils import center_window_on_screen
class AppDashboard(tk.Tk):
... |
ad707ae1c2909a09c5318173167ed8b2129278a23230d42df768f9c09540822b | Python | 5,704 | 154 | #!/usr/bin/env python3
"""
@file train_pc.py
@author Simon Yu
@date 02/11/2024
@brief Script for training PC models.
"""
import argparse
import header
import logger
import math
import pc
import test_pc
import torch
import tqdm
import utility
import wandb
def processArguments():
parser = argparse.ArgumentPar... |
39f2deee7649d0eaa01e76b66daed110811e42c5c3d9034f2e3144cd91361ab3 | Python | 5,705 | 157 | import os
import tempfile
import unittest
from unittest.mock import MagicMock, patch
from PIL import Image
from simulation_encoder.loader import PNGLoader
def _write_images(directory, filenames):
"""Save real 10×10 greyscale PNGs to directory."""
for filename in filenames:
Image.new("L", (10, 10)).s... |
5a985e6cb70fc7cd39d5c012898517fa6e9bebfb76de1aca658e0a1dc3a2b7d0 | Python | 5,706 | 115 | #!/usr/bin/env python3
"""O gap com descritores de DOS: oraculo, circularidade e o que sobra de util.
ADVERTENCIA DE CIRCULARIDADE, declarada antes de qualquer numero. O gap E uma
propriedade da DOS -- e a largura da regiao vazia em torno de E_F -- e o
`DOS_VBM` so pode ser avaliado sabendo onde esta o VBM, isto e, sa... |
bb86929e1e63196e2cd801e59f083b90f0e5d0a62a144adb2fe207aed6781ef3 | Python | 5,707 | 129 | # 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... |
76598a7d9bff35cf32469a4db72a1fb2d27c34959ccb62d3b9c38b39de2af541 | Python | 5,708 | 153 | import copy
from io import StringIO
import re
import tempfile
import unittest
from pathlib import Path
from GMXMMPBSA.exceptions import InputError
from GMXMMPBSA.input_parser import input_file
class InputParserTest(unittest.TestCase):
def _parse(self, contents):
with tempfile.TemporaryDirectory() as tmpd... |
c7c0a9a92952cd6777e11aa0341aed6d8836e67db6c33de80e31158d2b827be6 | Python | 5,710 | 158 | import pandas as pd
import numpy as np
import random
from itertools import combinations
from scipy.stats import norm
import matplotlib.pyplot as plt
from tqdm import tqdm
from collections import Counter, defaultdict
"""
This script measures how often pairs of chromatophores co-occur in the same
cluster and compares th... |
1560310b88c12a55f25014b84d4b7b5353f3f9d332f2e64bd32d9ce605af0ef8 | Python | 5,718 | 128 | from typing import Union
import torch
from torch._dynamo import OptimizedModule
from nnunetv2.training.lr_scheduler.warmup import Lin_incr_LRScheduler, PolyLRScheduler_offset
from nnunetv2.training.nnUNetTrainer.nnUNetTrainer import nnUNetTrainer
from torch.nn.parallel import DistributedDataParallel as DDP
from nnun... |
209f2dd17adc3c60ede7f0dcb05fef6abadbfef6a0b75f1566811b598d0c8bcd | Python | 5,719 | 158 | """graph_utils.py
https://github.com/RexYing/gnn-model-explainer
Utility for sampling graphs from a dataset.
"""
import networkx as nx
import numpy as np
import torch
import torch.utils.data
class GraphSampler(torch.utils.data.Dataset):
""" Sample graphs and nodes in graph
"""
def __init__(
... |
3a7c82a7de4afaec5e91fb81b66c1128b255ed22f9681c5a32c859769ca21521 | Python | 5,720 | 120 | import numpy as np
from sklearn.decomposition import PCA
from enigmatoolbox.datasets.base import load_summary_stats
def cross_disorder_effect(disorder='all_disorder', measure=None,
additional_data_cortex=None, additional_name_cortex=None, additional_data_subcortex=None,
... |
7453844126caca306e18c7bbc0d5071bf7859a29bcbef1f9b6d025eed3e3a8c5 | Python | 5,720 | 149 | # analysis script for the results from the BEM simulation
#%% Imports
import numpy as np
import matplotlib.pyplot as plt
font = { 'size' : 20}
plt.rc('font', **font)
#%% Plot parameters
legendfontsize = 15
linewidth = 2.5
#%% The parameters used in the simulation
jitlevels = np.array((1e-3,3e-3,1e-2)) #jitter l... |
f9db325acce69c4d4899bdc4f397cc6513a1182933dc87713cae3111e0b647d7 | Python | 5,720 | 114 | from typing import Tuple
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunetv2.evaluation.evaluate_predictions import load_summary_json
from nnunetv2.paths import nnUNet_results
from nnunetv2.utilities.dataset_name_id_conversion import maybe_convert_to_dataset_name, conve... |
081b650881d8c78f9c7cdf4e737734157f9c96c59f69bad1002c7f61b9d35060 | Python | 5,722 | 191 | """
This module contains data readers for the training of Garfield model.
"""
import os
import numpy as np
import pandas as pd
import scipy
from scipy.sparse import issparse, csr
from glob import glob
from anndata import AnnData
from muon import MuData
import muon as mu
import scanpy as sc
def read_mtx(path):
"... |
36799bec00ad4bef53bab5b9c50e13a828a77a33ec61cbee4f93b1a9ae5481eb | Python | 5,723 | 169 | import logging
from pathlib import Path
import anndata
import numpy as np
import pandas as pd
import scanpy as sc
import scipy
import zarr
from scipy.stats import gmean, rankdata
from tqdm import tqdm
from gsMap.config import CreateSliceMeanConfig
# %% Helper functions
logger = logging.getLogger(__name__)
def get_... |
3d160eb7c1123a4e969830b01b1f33bd094454559b3e0aeee17cc649af687a46 | Python | 5,724 | 169 | import os
import time
import math
import json
import random
import numpy as np
import argparse
import torch
import torch.nn as nn
from tqdm import tqdm
from gnn_data import GNN_DATA
from gnn_model import GIN_Net2, GIN_Net3
from utils import Metrictor_PPI, print_file
def boolean_string(s):
if s not in {'False', '... |
846816e6b9d0cc65a1575ceace61b15c2082c20bacf6f4bc91f79098a4e107b7 | Python | 5,726 | 149 | import json
import numpy as np
import cv2
from sklearn.preprocessing import LabelEncoder
from msi_visual.normalization import total_ion_count, spatial_total_ion_count
import numpy as np
from PIL import Image
import cv2
import xgboost as xgb
import cv2
from sklearn.preprocessing import LabelEncoder
from colle... |
8ec384b9ea7cabb437070d363010b4ae8cc1c3d96d44952db19d7396d3ead592 | Python | 5,728 | 106 | import vtk, qt, slicer
import numpy as np
from .Effect import AbstractEffect
from ..Helpers import GridNodeHelper
import WarpDrive
class AbstractPointerEffect(AbstractEffect):
def __init__(self, sliceWidget):
AbstractEffect.__init__(self, sliceWidget)
self.parameterNode = WarpDrive.WarpDriveLogic().getPa... |
0c020524284e26cb15ee7ea485649cbfc8ff4b1dca2908c30854a064028b6f33 | Python | 5,731 | 175 | from datetime import datetime
import numpy as np
from sklearn.decomposition import PCA
from spacestream.core.feature_extractor import get_features_from_layer
from spacestream.datasets.imagenet import imagenet_validation_dataloader
from spacestream.datasets.nsd import nsd_dataloader
from spacestream.utils.get_utils im... |
990b37ec769e1fe1a9103e9e6d060a8b7de39e89c50955cee03f3d7620b3a860 | Python | 5,733 | 238 | #!/usr/bin/python
# Copyright (c) 2014 Kyle Lutz <kyle.r.lutz@gmail.com>
# Distributed under the Boost Software License, Version 1.0
# See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt
#
# See http://boostorg.github.com/compute for more information.
# driver script for boost.comp... |
e810019460320b7860b413ed08cd6d91e545d914e28adcb552600fd638462757 | Python | 5,733 | 144 | import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column cosine similarity existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
Parame... |
328380e78bc9aba086c7acd0983ea714485562c958909e77d06dd0dcdc794965 | Python | 5,735 | 135 | """
@file dataset.py
@author Simon Yu
@date 02/15/2023
@brief NPC dataset class.
"""
import header
import json
import logger
import os
import PIL.Image
import torch
import utility
def getIndicesFromLabelsAttribute(labels_attribute):
labels_to_indices = {}
for attribute in labels_attribute.keys():
... |
448b784a30e1bb2b2201baa9fda9fe7b0d415301f2a1f8bef36df4fce8ad1c5d | Python | 5,737 | 148 | #!/usr/bin/env python3
import pandas as pd
import numpy as np
import csv
import argparse
import gtfparse
import multiprocessing
REQUIRED_COLUMNS = [
"seqname",
"source",
"feature",
"start",
"end",
"score",
"strand",
"frame",
]
def make_attribute_column(row):
attribute = ''
fo... |
91b97a16010c77665996592dee40dfcaf39900b540399a8053e317f3d84d1fa3 | Python | 5,738 | 153 | """
Medical Image I/O Module
This module provides a unified interface for loading and preprocessing medical images
from various formats (NIfTI, DICOM) with automatic format detection.
The main entry point is the `load_image()` function, which automatically detects
the image format based on file extension or directory... |
f2afe1a8de94b95e3451249555e2a40e164d36cafa6bb40b2e1d37c12555ec6e | Python | 5,740 | 147 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import signal
import threading
import torch
import torch.nn as nn
from torch.nn.parallel import DistributedDataParal... |
44cca8a73fd72750078ef59a9762dec677066350fd13ccc8fe98dd8d70305ab9 | Python | 5,742 | 144 | import argparse
import pandas as pd
import numpy as np
from typing import List, Tuple
def read_file(tsv_file: str) -> Tuple[List, pd.DataFrame]:
"""
Reads the input 4-column cosine similarity existing pairs TSV file in a pandas dataframe, generates all the unique PMIDs
and returns the dataframe.
Parame... |
766d4a2b9d25eadeb72d1921a5df3cd2576c3608b55fbd84ee13964adc1b2a45 | Python | 5,742 | 156 | import logging
import matplotlib.pyplot as plt
import numpy as np
import scanpy as sc
import seaborn as sns
from anndata import AnnData
from lightning import Trainer
from lightning.pytorch.callbacks import Callback
from .._constants import Keys
from ..model import Novae
from .eval import heuristic, mean_fide_score
fr... |
2de9bb7a73a4778effc9e8456a2d45f6cb7ed8e303d94eef29762c34ce19d11e | Python | 5,745 | 188 | import json
import os
import tqdm
from fairseq.data import Dictionary, data_utils
def load_dictionary(dict_path):
return Dictionary.load(dict_path)
def load_dataset(split_path, src_dict):
dataset = data_utils.load_indexed_dataset(
split_path,
src_dict,
combine=False, # set to true fo... |
70ff24d31b5c9ecc30e4284ca6281f2e187aa0efde8ba3e51a0e498395fd0355 | Python | 5,745 | 187 | import os
import subprocess
from pathlib import Path
import pytest
class OneQMCProcessError(Exception):
pass
@pytest.fixture(scope="class")
def project_root():
return Path(os.path.realpath(os.path.dirname(__file__))) / "../.."
@pytest.fixture(scope="class")
def train_workdir(tmp_path_factory):
return... |
35476c615357f40f2bbfe3858414f17be694becab703c33d5395b565e6e2a2ef | Python | 5,751 | 144 | """Cross-element variance analysis for C, Si, Ge phase17 SZP campaigns.
Tests the "carbon's privileged status" hypothesis: among group-14 elements,
does the AIREBO/Tersoff vs DFT cross-lattice spread depend systematically
on bonding flexibility (sp²/sp³ in C vs sp³ only in Si/Ge)?
Inputs combined:
C : phase 12 + 1... |
8b7130fd7d720e78576712a24747ddf99072f378b3709699a4d1200b46da1bf5 | Python | 5,751 | 157 | # 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... |
e3ed2af77407dc2f144c28c030751bc17f9c93293a7f4e31fd25df8cd62eb395 | Python | 5,752 | 180 | import os
from utils.mpr import MultipleProcessRunner
from tqdm import tqdm
class Downloader(MultipleProcessRunner):
"""
Download files that has unified resource locator
"""
def __init__(self, base_url, save_path, overwrite=False, skip_error_info=False, **kwargs):
"""
Args:... |
8dd71dda24e830db3b362296b267d38a4ce0aec1197c7d11cf2fa5df59c1749f | Python | 5,753 | 146 | import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
# Define paths
base_dir = Path('/egor2/egor/MovieProject2')
bttf_dir = 'backtothefuture'
fd_file_pattern = 'motion_{subject_id}_enorm.1D'
plots_dir = base_dir / "bids_data/derivatives/group_analysis"
plots_dir.mkdir(parents=True, exist_ok=Tr... |
4a8418d330f016cd61a70710ac65b70cb2282d086c46a0bb85c2250401d6b5ab | Python | 5,754 | 158 | import numpy
from numpy import dot as _d
from .. import MatrixManager2
from .. import MatrixManager
###############################################################################
class GeneExpressionMatrixManager(object):
def __init__(self, snp_covariance, model_manager):
self.snp_covariance_manager = Ma... |
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