sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
9862302819a579f2e826bff4c94f2c6c6ba6d8298a8217b011fab0fa6127654f | Python | 8,604 | 206 | import numpy as np
import paddle
import paddle.nn as nn
import paddle.nn.functional as F
import pgl
from pgl.nn import GraphPool
from pahelix.networks.gnn_block import GIN
from pahelix.networks.compound_encoder import AtomEmbedding, AtomFloatEmbedding, BondEmbedding, \
BondFloatRBF, BondAngleFloatRBF
from pah... |
0ea636ffcd748718bcdf6c279eb1f47c6710b96657b3a69e955404bcd23b872a | Python | 8,606 | 241 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Tickformatstop(_BaseTraceHierarchyType):
_parent_path_str = "scatterternary.m... |
b690fe22b470638c18d5f8ecffdc9ac222522a0d53e20eee9d745f671cf828aa | Python | 8,606 | 241 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Tickformatstop(_BaseTraceHierarchyType):
_parent_path_str = "scatterpolargl.m... |
6df4468eb25d69148a147a5ce64b6c2d4af3068efa3fac353cab1f20a2e51142 | Python | 8,607 | 237 | from os.path import abspath, join, dirname
import SimpleITK as sitk
import numpy as np
from Image import Image
import gc
import os
class ImageRegistration():
"""Docstring for ImageRegistration.
Class for imageRegistration object, has the funtions
and atributes the registration of MRI and CT images
... |
b82d9cb6acba6908b0d886335a8d822c0b0a4a8c592692c53d628cc38ac30037 | Python | 8,608 | 235 | """Helper functions."""
import os
import random
import sys
from typing import Dict
from typing import List
from typing import Tuple
from typing import Union
import gymnasium as gym
import numpy
import numpy as np
import tensorflow as tf
from gymnasium import spaces
from gymnasium.spaces import Box
from gymnasium.space... |
fc58b4260ec044ce9c07cea181e475f6612434261c3834cb79c111e4bfeb614e | Python | 8,612 | 300 | import sys
import argparse
import logging
import time
callset = {1: "cuteSV", 2: "Sniflles", 3: "PBSV", 4: "SVIM"}
USAGE="""\
Evaluate SV callset on NA19240 dataset
"""
def parseArgs(argv):
parser = argparse.ArgumentParser(prog="NA19240_eval", description=USAGE, formatter_class=argparse.RawDescriptionHelpFormatter... |
c60cce271be65c27e9e928f532049dbce4b20dc7ce1ea9840d7929a9baca6f82 | Python | 8,613 | 261 | """Workflows for processing volumetric anatomical data."""
from nipype import logging
from nipype.interfaces import utility as niu
from nipype.pipeline import engine as pe
from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from templateflow.api import get as get_template
from xcp_d import config
fr... |
f165ddc1da09ea94b705c7c6063c7e210acd43fb109517fbeb2e06455d0e5b5f | Python | 8,614 | 267 | # -*- coding: utf-8 -*-
#
# ImFun documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 23 13:17:03 2012.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All c... |
41db2dab06ddcac57c3467f49ef20c9ac506a9c4695f3d85320b23cfa763c09a | Python | 8,615 | 221 | """Utility class to manage a list of filenames.
Use the `add` method to add new filenames. You specify a short "alias" for
them, which you can use to retrieve the full filename later:
>>> fname = FileNames()
>>> fname.add('my_file', '/path/to/file1')
>>> fname.my_file
'/path/to/file1'
Filenames can also be templates th... |
576f1dd37afca0c371f133bba6f52a450a87b25b329c01afb8f1785fcce14b7d | Python | 8,617 | 199 | import unittest
import pickle
import os
import numpy as np
from rdkit import Chem
from rdkit.Chem import (
Atom,
Bond,
RingInfo)
from bioconfpred.conf_ensemble import ConfEnsembleLibrary
from sklearn.preprocessing import OneHotEncoder
from tqdm import tqdm
class MoleculeEncoders(object) :
... |
02417e94cf483d62e38606b8488f15f7c0a75e3233fcee6438266d4403cff1a6 | Python | 8,618 | 225 | """Keypoint-based object detectors: CenterNet (DLA-34) and CornerNet (stacked hourglass).
CenterNet -- Zhou et al., 2019, "Objects as Points", arXiv:1904.07850.
Source: github.com/xingyizhou/CenterNet.
DISTINCTIVE: detect objects as the CENTER POINT of their box. A DLA-34 backbone (deep
layer aggregation -- iterat... |
173b11c81775e019619f30ad25464581cb6472deb7de7db39c38985bdd7a5da5 | Python | 8,618 | 176 | import numpy as np
import pandas as pd
import geopandas as gpd
from datetime import datetime
from operator import itemgetter
from ...utils import constants
from ...utils.constants import UID, DATETIME, LATITUDE, LONGITUDE, GEOLIFE_SAMPLE
from ...core.trajectorydataframe import TrajDataFrame
from ...core.flowdataframe i... |
bc118ccf0e9f898899c9c64a565bf7209a95dbed2ac674b9ae0ec06791ce46e7 | Python | 8,620 | 208 | from contextlib import AbstractContextManager
from typing import List
from uuid import UUID, uuid4
import sqlalchemy
from dependency_injector.providers import Callable
from fastapi import HTTPException
from sqlalchemy import and_, func
from carbonserver.api.domain.organizations import Organizations
from carbonserver.... |
5eca2582def8ff87516f29040d720c7dce0195808ff66d1123dcc615faabe07a | Python | 8,622 | 235 | # Copyright (c) 2024 PaddleHelix Authors. All Rights Reserved.
#
# Licensed under Creative Commons Attribution-NonCommercial-ShareAlike 4.0
# International License (the "License"); you may not use this file except
# in compliance with the License. You may obtain a copy of the License at
#
# http://creativecommo... |
c84d7d357a6f88fbb7c3b35cc030d968621545d98cec5624aef32d07cfca9958 | Python | 8,623 | 247 | from pathlib import Path
import importlib.util
import sys
import warnings
import pytest
import tempfile
from face_rhythm import helpers, util, h5_handling, pipelines
_torchcodec_skip_reason = None
if sys.platform.startswith('win'):
_torchcodec_skip_reason = 'torchcodec has no Windows wheels'
elif importlib.util... |
06fd2b1fc9732d490a96aa34431eb813bdeca4eb357f32efba4cd58a2562a840 | Python | 8,624 | 251 | """
Created in March 2024
@author: Laurène David <laurene.david@ip-paris.fr>
@author: Thomas Bonald <bonald@enst.fr>
"""
from typing import Union
import numpy as np
from scipy import sparse
from sknetwork.clustering import BaseClustering
from sknetwork.ranking import PageRank
from sknetwork.clustering import get_mod... |
230761a6cf1fd6512d93cde1d0b14cfae19dafe44fcd9bdf568adc2952d00580 | Python | 8,624 | 278 | from array_api_compat import array_namespace as get_namespace, device
import numpy as np
import pytest
from conftest import approx, to_backend
from pyriemann.geometry.distance import distance_thompson
from pyriemann.geometry.geodesic import (
geodesic,
geodesic_chol,
geodesic_euclid,
geodesic_logchol,
... |
7755fe63ef1addc1fbdb4f4037e19ccd4bae982947fc43c1768253b7ae038133 | Python | 8,624 | 227 | # Copyright (c) 2025, Siyu Wang, Shengbin Di, Yuxi Chi, Johnsonms, Linfeng Zheng, Haoyan Huang, Lanbo Li, Yun Zhong, Man Yuan, Minmin Sun, Yong Li, Wei Lin.
"""Fused multi-head attention (FMHA) backward for the SM100 architecture using CUTE DSL.
Constraints:
* Supported head dimensions: 256 only
* mma_tiler_mn must ... |
81b55a4bbcdefab826420840ec5d6e0b761acae4ecd6776fd351619133e4aebc | Python | 8,625 | 237 | from collections import defaultdict
import time
from PIL import Image
import pprint
import numpy as np
import torch
from torch import optim
from torchvision.utils import save_image, make_grid
import torchsummary
import src.models as models
import src.objectives as objectives
from src.utils import Logger, Timer, save_... |
e0ba38e3a0bf6e7d90f420994f5281492f5d9293f407c44ca6b5c2d720f50619 | Python | 8,625 | 185 | from __future__ import print_function, division, absolute_import
import os
import argparse
from tqdm import tqdm
import torch
from torch.autograd import Variable
from torch.utils import model_zoo
# http://scikit-learn.org
from sklearn.metrics import accuracy_score
from sklearn.metrics import average_precision_score
f... |
055805a446ae6fedd0658f72235dcf9e4f1e3cab105cd099f46deb246cd522c6 | Python | 8,626 | 219 | '''
TNS class : Tree
'''
import copy
import json
import logging
from collections import namedtuple
import numpy as np
from morphio import PointLevel, SectionType
from tns.utils import TNSError
from tns.generate.algorithms import basicgrower, tmdgrower
from tns.generate.section import (SectionGrower, SectionGrowerPath... |
68bd270638a7916f42ed1a3a1b9a8e86667585778f368ccedeca69c6dcf6faf0 | Python | 8,631 | 266 | """Unit tests for flash_attn.cute.utils module."""
import functools
from flash_attn.cute import utils as cute_utils
from flash_attn.cute.utils import hash_callable
def with_positional_default(value):
def inner(arg=value):
return arg
return inner
def with_keyword_default(value):
def inner(*, a... |
fa4f6b713a40d6ca7e1d1d451abd0eb0adcc09105f7007cb33c49feb1ed2c2af | Python | 8,633 | 268 | """Tests for the shared bounded-run / playback engine."""
from __future__ import annotations
from threading import Event
import pytest
from bokeh.document import Document
from larvaworld.portal.canvas_widgets.environment_models import LarvaPreviewFrame
from larvaworld.portal.simulation.run_playback import (
DEF... |
7c8c7779a4c6fc02c83a2855a5a1679204a50485565b495c95e034df939a89f6 | Python | 8,634 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
8c1e5c8c62000af96057f62bdcc444201fba79bf8a41f35d4a2d923d4a6edd71 | Python | 8,634 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
c282164922ffab035499fcebf4af8a2d76d17b2c26bab58a1d71f9811d79f1d2 | Python | 8,634 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
c297d54df9c2e1f8b6e3d19352813dfd3ff1a981c732ebc4a9206d61d0def173 | Python | 8,636 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
e9f05d20d31100726557a72aef806084e969cb1f5b14823eab7036c05eeb4557 | Python | 8,636 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
f78f0d4e3ca5b5300244087f3a079cd419d5a8e168cf08617b2af550b3414314 | Python | 8,637 | 276 | # -*- coding: utf-8 -*-
#
# Wyrm documentation build configuration file, created by
# sphinx-quickstart on Fri Jun 28 11:37:55 2013.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All co... |
4ff0a7a5ec085d4e1cffb3fb8de501fb33a87a756a9c0813729774c3be705adb | Python | 8,638 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
ccf90e078bf8282a8de3c550ec7a668683706400897ca8929a79b13a106f5c30 | Python | 8,638 | 197 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import os
from pathlib import Path
from typing import Any
import numpy as np
import torch
import torch.distributed as dist
import torch.nn.functional as F
from PIL import Image
from ultralytics.data.dataset import... |
7bcd1ce85311408def695fa7d731098c3fcc8a6c7c5cf2b29cf996dcde3f4a80 | Python | 8,639 | 290 | """dictTool: merge/split/flatten/unflatten dict
Author:
Jin Lee (leepc12@gmail.com) at ENCODE-DCC
"""
import re
from collections import defaultdict
try:
from collections.abc import MutableMapping
except AttributeError:
from collections import MutableMapping
def merge_dict(a, b):
"""Merges b into a ... |
cbacdb74968e6b0135464d3210b688f0ed5649b708276c7eba2b1091c4d68333 | Python | 8,641 | 215 | from __future__ import annotations
from typing import Dict, List, Optional, Tuple
import torch
import torch.nn.functional as F
from pytorch_lightning import LightningModule
from torch import Tensor
from torch.nn import Module
from lightly.utils.benchmarking import knn_predict
from lightly.utils.benchmarking.topk imp... |
60bed75e0da8a01e6e0f5ffdc86192c919d66f9c4bb8b84d139595f6936660eb | Python | 8,645 | 211 | # Copyright 2022 Deepfold 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 law or agreed to in writin... |
c5030f241a0844a6ee7e7a5556bdf2a6e72e0ab67d7fc76d59fe3d46da95eaa3 | Python | 8,645 | 229 | # -*- coding: utf-8 -*-
# Copyright (C) 2020 [COMET-ML]
#
# 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 use, copy, modify,
#... |
2b9892f7e4780278fcec09fb3e3b2bff548cdc4941f44c5d1e6f0df328da43be | Python | 8,646 | 222 | """Run a command in its own process and measure its wall-clock time and peak memory.
The memory of the process and of its child processes is sampled every 50 ms and summed: on
macOS their physical footprint (what Activity Monitor shows; resident memory leaves out the
compressed and swapped pages of a large read), else... |
381f3c7398f213afb2a52b67c3a09560d2077d8c361d4754ab83089f5822fe24 | Python | 8,647 | 235 | import pkg_resources
import logging
from PyQt6 import QtWidgets, uic
from matplotlib.widgets import SpanSelector
import numpy as np
from bmlab.session import Session
from bmlab.controllers import EvaluationController
from bmicro.gui.mpl import MplCanvas
import warnings
logger = logging.getLogger(__name__)
MODE_DE... |
b17fa7055d8aa02b43282f2e53ed0ad5fb7fa8bbfd70ca980de16758ee9eba1b | Python | 8,647 | 244 | model = dict(
type='FasterRCNN',
backbone=dict(
type='ResNet',
depth=50,
num_stages=4,
out_indices=(0, 1, 2, 3),
frozen_stages=0,
norm_cfg=dict(type='SyncBN', requires_grad=True),
norm_eval=False,
style='pytorch',
init_cfg=dict(type='Pretra... |
ebba1d43738cd6e3ded845631f1a5fdff848a75d73050e9c8a7d13324c32fd9d | Python | 8,647 | 155 | # Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.pfam as pfam
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_rnn
import plus.mo... |
810f2f6e62105a0df777cfd1c1fc13a83f6976f70e26edee231c0ff01e315615 | Python | 8,648 | 199 | """Prepare data for segmentation"""
import os
from os.path import join as opj
import shutil
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from scripts.utils.io_utils import write_h5
from scripts.utils.constants import MRI_IMG_DIR, MRI_ORG_LOC_GT_DIR, MRI_CYST_LOC_GT_DIR, ... |
2ce762edee8ee4491f33f34e88137fc3f87b9e34efc620307b840cdee66271e9 | Python | 8,651 | 267 | from functools import lru_cache
from typing import Generator
import numpy as np
from mirp._features.ngtdm_matrix import MatrixNGTDM
from mirp._images.generic_image import GenericImage
from mirp._masks.base_mask import BaseMask
from mirp._features.histogram import get_discretisation_parameters
from mirp._features.text... |
dcf4a754a19ec4b2532575ac6045f5694a246d5fff609ae15b0a782187e9f4e1 | Python | 8,654 | 204 | """Band-edge lockstep: claim -> named leg -> executable evidence (memo D3/B3).
ONE support-policy table (tests/support/proofnet/support_policy.tsv) is the
authority; this suite holds pyproject's declared bands, the per-leg
constraints files, the installed environment, and the HF_5_CANDIDATE
enumerated-red manifest in ... |
8123ba2016d67bef862d1b537f9b096e83f48b9821b2a3dec1c02e187ea952b2 | Python | 8,656 | 276 | import math
from typing import Any, Tuple
import numpy as np
import torch
from pytorch_lightning import LightningDataModule
from torch import Tensor
from torch.utils.data import DataLoader, Dataset
from pl_bolts.utils import _SKLEARN_AVAILABLE
from pl_bolts.utils.warnings import warn_missing_pkg
if _SKLEARN_AVAILABL... |
1c805139d9de7a44faca8da2937466c358e25767d0101c5f9062e206559553f0 | Python | 8,658 | 285 | '''ML models'''
__all__ = []
import copy
from itertools import product
from bdpy.preproc import select_top
import numpy as np
from numpy.linalg import norm
from scipy import stats
from sklearn.svm import SVC
from tqdm import tqdm
import warnings
class EnsembleClassifier(object):
'''Ensemble classifier.'''
... |
a02b281405bc75057f2e3f079284bedeb99329bbfe638672d68e1c732a7f2fd5 | Python | 8,658 | 208 | import sys
import os
import gc
sys.path.append('../TM2_segmentation')
import SimpleITK as sitk
import numpy as np
import pandas as pd
import nibabel as nib
from skimage.transform import resize, rescale
from scipy.ndimage import rotate
from scipy import ndimage
import matplotlib.pyplot as plt
from numpy import median
i... |
037599b42c91626d00278df9f865aa4bf3c29628a6d2b7b99461239e77d56ee5 | Python | 8,659 | 231 | import os
import os, sys
from config import *
sys.path.append(where_am_i())
from pathlib import Path
from utilities import dataloading_utilities as dlutils
from scipy.signal import correlate
from torch.utils.data import DataLoader
from utilities.folders import *
import pandas as pd
import numpy as np
import pickle
i... |
dff5c6f1ed3dbd2e3a60cc10af7f015df84c4462018f76149aa18450a27dbe55 | Python | 8,660 | 173 | #!/usr/bin/env python3
"""
File: prepare_metabrain_phenotype_matrix.py
Created: 2021/10/13
Last Changed: 2021/12/06
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directo... |
f4baa9d9611ef983f2416cde489d26a0cda0f7eb67885d5c377cff15493c1456 | Python | 8,661 | 220 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test objects and function in the module ``tfep.potentials.mimic``.
"""
# =====================================... |
4ddba5bb478fe1c18e44923ded98725fd3bceae874b5ea5fbfeda886e265da73 | Python | 8,666 | 240 | import torch
from strategy_obj import (
strategy_proba,
strategy_weight,
strategy_proba_post_scale_temp_tunning,
strategy_BMA,
strategy_BMC,
strategy_Learn_weights,
)
import torch
import pandas as pd
from itertools import combinations
import logging
# Delete the padding in order to compare the ... |
5caedab2abb0f8fca74a1f8379aafc2d06ea1f6ccada2e62dbe3d52aee854707 | Python | 8,667 | 284 | """Bounding boxes transformation functions."""
from __future__ import division
import numpy as np
__all__ = ['crop', 'flip', 'resize', 'translate', 'affine_transform', 'get_affine_transform']
def crop(bbox, crop_box=None, allow_outside_center=True):
"""Crop bounding boxes according to slice area.
This method... |
c78cb7b884273949489cc48067b9656205b18137c6bd1922cad84040993a0fe5 | Python | 8,667 | 199 | '''
Implements the import-export blueprint.
'''
import pandas as pd
import datetime
from dash import ctx, dcc, html
import dash_bootstrap_components as dbc
from dash_extensions.enrich import DashBlueprint, PrefixIdTransform, Output, Input, State
from dash.exceptions import PreventUpdate
from utils.utils import cust... |
c15cfc3490c9b496e8b9503dcaf875eceded479337301c67e3c02c99292b22c9 | Python | 8,669 | 228 | #!/usr/bin/env python
# coding: utf-8
# This script has kindly been provided by Julia Schessner.
from io import BytesIO
from reportlab.pdfgen import canvas
from reportlab.lib.utils import ImageReader
from reportlab.platypus import Paragraph
from pdfrw import PdfReader, PdfDict
from pdfrw.buildxobj import pagexobj
f... |
c94cf32a2163cafd971d59095a18cea790d41e90df44f3c86ef4e03a8822e9d0 | Python | 8,669 | 246 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# spateo documentation build configuration file, created by
# sphinx-quickstart on Tue April 5 13:47:02 2022.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# au... |
4059d52e4981a7bfaffd6bb69b441c47500fc305d33d90b4110c0e189191eef6 | Python | 8,673 | 198 | """
cnn_numpy.py -- pure numpy forward pass for SongCNN (see
song-feature-analysis/scripts/cnn_model.py), loading weights from a plain
.npz file exported from a trained PyTorch checkpoint (see that repo's
scripts/export_npz.py).
Why not onnxruntime: checked 2026-09-22 -- the fleet's Pi image is
32-bit ARM (armv7/armhf... |
c6d0c617dc414a7b01085e456374f12cf58c65a2519c53c31711692010824ec3 | Python | 8,674 | 237 | """Explorer memo item-3 riders (lane F25).
- P3 pin: input ops receive activation transforms on the TRACE path (the
fastlog pin lives in test_explorer_watch_p1_summary_role.py).
- P4: retained-memory truth on reduce-only captures plus the two
``total_transformed_*`` read-time totals.
- Fused spine kernel: exact-co... |
97ccee032771c63d3b3994a77bc71f33a32ff502c0e5ab8366b2e9c614f570c9 | Python | 8,675 | 207 | # model
from ast import Global
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch_geometric as tg
import torch_scatter
import e3nn
from e3nn import o3
from typing import Dict, Union
# crystal structure data
from ase import Atom, Atoms
from ase.neighborlist import neighbor_list
from ase.vis... |
a68ef82afd301f5ad8ecf97ff1439cb453b77bb13aa40d309bc13e69bbc3c18b | Python | 8,675 | 226 | """P5 outcome-matrix cells and lockstep proofs.
The remaining design-matrix cells not covered by the P0-P3 suites:
raise_on_nan's honest raw-tensor-only scope, the no-frontier halt failure
class, cooked-halted gate arming (N4/N5 on ``Recording.to_trace()``
products), the OOM double-fault, the never-fired halt predicat... |
5acbe40e6313c9dd8ee59ab3a04a9eb7b8e803685b7c108137a36f858d8d1762 | Python | 8,676 | 230 | import os
import time
import numpy as np
import pandas as pd
import nibabel as nib
from os.path import join as pjoin
from matplotlib import pyplot as plt
from magicbox.io.io import CiftiReader, save2cifti
from cxy_visual_dev.lib.predefine import All_count_32k, proj_dir
anal_dir = pjoin(proj_dir, 'analysis')
work_dir =... |
c6afa8dbec3198a4c49aaba3fdff430072d9fe4dd8c7d55fd65733aa02226215 | Python | 8,676 | 159 | # encoding=utf-8
import os
import dataset.data_act as data_act
import pandas as pd
import dataset.data_weather as data_weather
import datetime
from ourmodel.loss_transfer import TransferLoss
import torch
import math
from dataset import data_process
def load_act_data(data_folder, batch_size=64, domain="1_20"):
x_t... |
f7e20fab1940dbb8b5d751618b6333c6c906af6ecf0f1c8e98bf10244320e2ae | Python | 8,677 | 210 | # Copyright (c) 2022 PaddlePaddle Authors. 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 app... |
03ffc4143e556d1657656d32bea6078c68befa146ed53b1ce0f8f1e9621f5aaa | Python | 8,679 | 298 | """Custom ResNet Implementation
Note that the architecture we present here differs from the one used in
torchvision. We replace the first 7x7 convolution by a 3x3 convolution to make
the model faster and run better on smaller input image resolutions.
Furthermore, we introduce a resnet-9 variant for extra small models... |
ed7e342f529478d180a46d3e64ea2d8b7ff809a2fe70b894540ed9085a92aa2d | Python | 8,681 | 230 | # Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed ... |
03c908668f18731ef879802a9effae6a8a7cbd4da0f938bb8b03fcbc207fd3db | Python | 8,682 | 197 | import logging
from sqlalchemy import select
from sqlalchemy.sql.expression import func
# Cannot import galaxy.model b/c it creates a circular import graph.
import galaxy
from galaxy.util import unicodify
log = logging.getLogger(__name__)
class UsesItemRatings:
"""
Mixin for getting and setting item rating... |
970d5a9167fecee474af140c3034c40f9e464e15a210fd9d5cfccd0809d02cca | Python | 8,686 | 220 | """MS COCO keypoints dataset."""
from __future__ import absolute_import
from __future__ import division
import os
import copy
import numpy as np
import mxnet as mx
from .utils import try_import_pycocotools
from ..base import VisionDataset
from ...utils.bbox import bbox_xywh_to_xyxy, bbox_clip_xyxy
class COCOKeyPoints... |
889e2f8ac9dd447fd58bb88fb542e165de7c6148ef12691be137c7195bbeec62 | Python | 8,692 | 212 | """Counterfactual-harvest schema (leverage B17 / D-13): fields land NOW.
The manifest/resume schema for intervened dataset extraction lands at launch
unconditionally — adding a resume-compared policy field to a RELEASED
artifact is exactly the migration this schema exists to prevent. Execution
ships per ADDRESS CLASS ... |
959615a911e53f72a77a96cece1f1c65d90fd58fa4c2e78e7e413224072eaa2e | Python | 8,692 | 211 | from functools import reduce
import mudata as md
import numpy as np
import pytest
from anndata import AnnData
from anndata.tests.helpers import assert_equal
from mudata import MuData
import muon as mu
@pytest.fixture
def mdata() -> MuData:
return MuData(
{
"mod1": AnnData(np.arange(0, 100, 0... |
44255e7a2a269463642de403f06e9476f7b1f8d0c8ff1283e398578e067695b4 | Python | 8,693 | 216 | # Copyright (c) 2022, Tri Dao.
import torch
import torch.nn as nn
from einops import rearrange
from torch import Tensor
from flash_attn.utils.distributed import all_reduce, reduce_scatter
class GPT2Embeddings(nn.Module):
def __init__(
self,
embed_dim,
vocab_size,
max_position_emb... |
ceddf697fc0f200a0bfbc73c9a08dc0fc8ec1d0ce86f921e5f3d44083b0874b8 | Python | 8,693 | 221 | import numpy as np
import pytest
from seqpro.rag import Ragged
from seqpro.rag._utils import lengths_to_offsets
def to_py(x):
"""Universal, layout-agnostic materialization to nested python lists/bytes.
Recurses by peeling the outer (always-int) axis; never calls to_packed, so it
works on string and string... |
8bcece46354cfa4980cbe5ff6682d3801cc330cff2b0d499487f79ac96696f96 | Python | 8,694 | 207 | #!/usr/bin/python3
# -*- coding: utf-8 -*-
"""Gridsearching on the Columbia yeti cluster.
"""
import time
import sys
import os
import stat
import subprocess
import logging
import crf_util
from gridsearch_train_crfs import GridsearchTrial
class GridsearchTrialYeti(GridsearchTrial):
"""Adaptation of GridsearchTria... |
a2fba1383fb707f1be94e317d35c48bbd66393cb02de56230a3ffe5751fe8313 | Python | 8,694 | 182 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
5241a2731a824557606ef77e3f59b014da0d437f1575f4be93093ee18b5b65bd | Python | 8,695 | 243 | """Integration testing utilities."""
import socket
import sys
from collections import defaultdict
from functools import partial
from itertools import count
from typing import Any, Callable, Dict, Sequence, TextIO, Tuple # noqa
from kombu.exceptions import ContentDisallowed
from kombu.utils.functional import retry_ove... |
994971fc7530c190250dee6c3355e16d291531ba646ac5cd7904a8991392423a | Python | 8,695 | 236 | from importlib import resources
import logging
from PyQt6 import QtWidgets, uic
from matplotlib.widgets import SpanSelector
import numpy as np
from bmlab.session import Session
from bmlab.controllers import EvaluationController
from bmicro.gui.mpl import MplCanvas
import warnings
logger = logging.getLogger(__name_... |
c6597206ab59ebbd52a47895b0807b59be2614212a5e76b82f382844911d9562 | Python | 8,695 | 262 | #!/usr/bin/env python3
# flake8: noqa: E402
"""
Demonstration script for the new sleep restriction functionality.
This script shows how to use the new DailyScheduler and mAGOSleepRestriction classes.
"""
import datetime
import os
import sys
import time
from unittest.mock import Mock
# Add the ethoscope package to th... |
f608b3643659feb5a6a0c0b22670ed65f6bc3f1c563d7a0fc28b10fe03f290b3 | Python | 8,695 | 267 | from __future__ import annotations
import pytest
from pytest import approx # noqa: PT013
from pybind11_tests import ConstructorStats
from pybind11_tests import sequences_and_iterators as m
def test_slice_constructors():
assert m.make_forward_slice_size_t() == slice(0, -1, 1)
assert m.make_reversed_slice_ob... |
167a6b0066d61f4aa3f790ce4240459debdc962e1ca73d2dd00f37e44ff2520f | Python | 8,697 | 238 | """
Replay of a recorded dataset in the simulation viewer.
Drives agents from stored coordinates rather than from a brain, so that
experimental and simulated behaviour can be inspected with the same renderer.
"""
from __future__ import annotations
from typing import Any
import copy
import numpy as np
from .. impor... |
5bbe5a6ce624e888505d33d599262e29fc76e8f15a557cd5c0957d578cef5da3 | Python | 8,697 | 274 | from typing import Optional
from itertools import chain
from functools import partial
import torch
import torch.nn as nn
from .gin import GIN
from .gat import GAT
from .gcn import GCN
from .dot_gat import DotGAT
from .loss_func import sce_loss
from graphmae.utils import create_norm, drop_edge
def setup_module(m_typ... |
376396a89cb38c69822e3f98fdcc1670c132421961fd2894ff2a75dae68b6a48 | Python | 8,701 | 270 | import h5py
import numpy as np
from tqdm import tqdm
import torch
from torch.utils.data import DataLoader
import torch.nn as nn
import torch.nn.functional as F
import os
from random import shuffle
import itertools, operator
from load_psam_motif import *
from map_protein_name import *
import random
from utils impor... |
eae013958c4d2b290f7bf524629c78660ee70c3e83954a9e07f34d2271082f46 | Python | 8,705 | 193 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import logging
import time
import numpy as np
import os
import torch
from voxelpose_lib.utils.vis import save_debug_3d_cubes
from voxelpose_lib.utils.vis import save_debug_3d_images
from voxelpose_lib.utils.v... |
08d4d2324e121c1039bd9fe10d6a86166b43ee36d85725898c3a57bb09ee591c | Python | 8,706 | 197 | # FAITHFUL REIMPLEMENTATION from Zhang, Xu, Yu, Zhang, Chen, Yu, "ADL-MVDR: All
# Deep Learning MVDR Beamformer for Target Speech Separation" (ICASSP 2021,
# arXiv:2008.06994) -- no public code. The official repo
# (https://github.com/zzhang68/adlmvdr) is a demo-only page (audio/video/image
# assets, no model source), ... |
a931008d2871a6e878fbb29a02d9323c2f1e716dde9e94f90a83861372fd5c2f | Python | 8,711 | 272 | """Integration tests for the TorchLens portable I/O flow."""
from __future__ import annotations
import importlib.util
from pathlib import Path
from typing import Any
import pytest
import safetensors # noqa: F401
import torch
from torch import nn
pd = pytest.importorskip("pandas")
import torchlens as tl # noqa: E... |
f8262895da186ab13e2ca1d93b371aae38cffdd1fa85d0ed46a0b5bef6c965fe | Python | 8,712 | 287 | import numpy as np
import h5py
from scipy import signal
from scipy.stats.stats import pearsonr
from scipy.stats import zscore
import os
def columnwise_correlation(ypred, y, zscorea=True, zscoreb=True, axis=0):
r'''Compute correlations efficiently
Examples
--------
>>> x = np.random.randn(100,2)
>... |
0aeef49d897bdbccfa61b2ac5256b0c9c04e01e972321b7543f44fe44300b030 | Python | 8,716 | 253 | import math
import torch
import torch.distributed as dist
import torch.nn as nn
import torch.nn.functional as F
from torch import Tensor
def prototype_probabilities(
queries: Tensor,
prototypes: Tensor,
temperature: float,
) -> Tensor:
"""Returns probability for each query to belong to each prototype... |
40c3d301a77641543e575ddea720804cf23959268a37f852bb3e286a211c4c39 | Python | 8,719 | 265 | from abc import ABC, abstractmethod
from permacache import permacache, stable_hash
import numpy as np
import tqdm.auto as tqdm
from shelved.hsmm.gene_dataset import (
get_from_genes,
run_on_all_genes,
run_on_all_genes_with_threshold,
run_on_entire_gene,
)
from modular_splicing.utils.construct import ... |
73dc9461ea36a8be9309250bb41f81b5c6bbdd84d330b50e6bc6b87e83694882 | Python | 8,720 | 240 | import os
from typing import Union, Optional, List, Dict, Any, Literal, Tuple
import numpy as np
import xarray as xr
import torch.nn as nn
from tqdm.auto import tqdm
from seqexplainer import get_layer_outputs
from seqexplainer import get_activators_max_seqlets, get_activators_n_seqlets, get_pfms
from seqdata import g... |
806cb06e68f8385eca3e4a80a8f3490c421a2220ed10bcd0be6b15f86e2b2243 | Python | 8,720 | 230 | """PointASNL: Robust Point Clouds Processing using Nonlocal Spatial Correlations.
Yan, Zheng, Li, Wang, Cui, Qi & Tian (Meituan / Stanford), CVPR 2020, arXiv:2003.00492.
Source: https://github.com/yanx27/PointASNL
PointASNL has two distinctive primitives:
1. Adaptive Sampling (AS) module: instead of fixed FPS centr... |
a412142c2aa43f920f0d6fc7d75d5fc669c3547dc25a9359678e47fe20e33b24 | Python | 8,720 | 269 | #!/usr/bin/env python
"""
boxplot:
- box: first quartile and third quartile
- line inside the box: median
- outlier: 1.5 IQR higher than the third quartile or 1.5 IQR lower than the first quartile
IQR = third quartile - first quartile
- The smallest/largest value that is not an outlier is connected to the bo... |
ae9220a3623024eb107d7e0f484f267262bb90d63eb6cdd86748228bcdb2c3ab | Python | 8,721 | 267 | # This example requires the following dependencies to be installed:
# pip install lightly
# Note: The model and training settings do not follow the reference settings
# from the paper. The settings are chosen such that the example can easily be
# run on a small dataset with a single GPU.
import copy
from functools im... |
0fa933bbea04cbe652654a429e5fa0f0ffba56c1df38816fff15f6a617d1782e | Python | 8,722 | 253 | # Copyright (c) 2021 PaddlePaddle Authors. 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 app... |
ed328bed3adac84a4c71f22b9b8a640efa4cf07934d9514c919460174c710346 | Python | 8,722 | 225 | #####
# Function to perform outlier analysis and compute descriptive metrics
# Francesca Grisoni, TU/e April 2021
#####
import numpy as np
def curate_dataframe(df, outlier_test=True, alpha=0.05, convert_to_log=False, rm_high_std=True):
"""
:param df:
:param outlier_test:
:param alpha:
:param con... |
369ec393b8e90513a0c4517ac0b1b9b271d6f220ab0c176ccd80b84edfc63c84 | Python | 8,726 | 298 | # -*- coding: utf-8 -*-
# @Author: gviejo
# @Date: 2022-01-02 23:30:51
# @Last Modified by: gviejo
# @Last Modified time: 2023-11-16 13:17:59
"""
BaseLoader is the general class for loading session with pynapple.
@author: Guillaume Viejo
"""
import importlib
import os
import warnings
from pathlib import Path
im... |
44fbb6bae07434bb09203d67cc6aebdc3060453b449b153030af3b061457317a | Python | 8,727 | 261 | # -*- coding: utf-8 -*-
#
# 20/20 Permutation Test documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 28 13:53:42 2014.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerate... |
5465478a86dc07403ad7b92ea86018d8362222c96b7845d5a68d6903404b66e1 | Python | 8,729 | 329 | """Deterministic model zoo used by the capture characterization oracle."""
from __future__ import annotations
from typing import Any
import torch
from torch import nn
class PlainCNN(nn.Module):
"""Small convolutional network for ordinary feed-forward capture."""
def __init__(self) -> None:
"""Init... |
cfe4164a4359411f4f2badcd5b803f885531983c26183e8c83333402f30fbff5 | Python | 8,729 | 243 | from dataclasses import dataclass
from pathlib import Path
from typing import Dict, List, Tuple
import numpy as np
import xarray as xr
from tqdm import tqdm
from hobj.benchmarks.common import (
compare_msen,
simulate_sessions,
summarize_bootstrap_score,
)
from hobj.benchmarks.binary_classification.estimat... |
6aa2b8d002a1c933995dac7e32f653d2e7cf347c7ded23c1b26c3bbc11fe0868 | Python | 8,731 | 223 | import os
import zipfile
from unittest import mock
import h5py
import numpy as np
import pytest
import keras
from keras.src import testing
from keras.src.saving import saving_lib
from keras.src.saving.file_editor import KerasFileEditor
def get_source_model():
inputs = keras.Input((2,))
x = keras.layers.Dens... |
f72126f499f471cba2544a374993c0c47d57115e4bfdc362fa0304bb2d00dac4 | Python | 8,732 | 220 | import os.path
import numpy as np
import pytest
CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
GENERIC_KWARGS = dict([
("write_features", False),
("export_features", True),
("image", os.path.join(CURRENT_DIR, "data", "sts_images_raw", "STS_001", "MR_T1", "image")),
("mask", os.path.join(CURR... |
f07dd7d4aacf1b10f75110f0a9ef4d9ee0a764fe2a1177745ced9d86b921a77e | Python | 8,733 | 214 | """
navigation plugin - UI load and handling
QOL add-ons for easily traversing through the trace plot
SimplyFire - Customizable analysis of electrophysiology data
Copyright (C) 2022 Megumi Mori
This program comes with ABSOLUTELY NO WARRANTY
This program is free software: you can redistribute it and/or modify
it under... |
24e29b5a048b366b8393a4ba8157ee5ebbe64cde12473e2f92c7d2b605dcc2e4 | Python | 8,734 | 209 | """Closed host-input-metadata-read witness class for sparse runnable execution (r29-C1).
r27-H2 witnessed only ``is_contiguous`` / ``stride`` / ``requires_grad`` reads on a model
input. The confirming hunt found MANY more host-reading tensor accessors that steer control
flow on facts the shape+dtype input contract nev... |
81fd8d54631868456d73e8f36955df42596967aadb95b10abada94d5ec596973 | Python | 8,734 | 213 | """Vizmech wave-3 items 18-19: the widened, indexed geometry audit.
Calibration discipline (memo s6): every metric is proven in BOTH directions
-- a known-bad must fail and a known-good must pass with headroom, never
tuned-tight. The known-bad is a PINNED hand-built DOT reproducing the
historic 12-way fan-in head-labe... |
3f89b3e12b13427582a06e4d7e749c46ce497d3a94f8783c61567efce2f588fa | Python | 8,735 | 225 | """Anti-recurrence tests for the non-torch tensor-display crash (cert10 follow-on).
Round-10 fix ``d2bfca03`` correctly made ``finalize_single_pass_trace`` flip
every preview-backend (MLX/tinygrad/TF/JAX/Paddle) op's ``_tracing_finished``
to ``True``. That newly routes finalized preview-backend ops with a *saved*
acti... |
681133e453cf441040c9a7d37871d224aa4f36e55f06c5940fdc58bde4e680f1 | Python | 8,737 | 212 | #!/usr/bin/env python3
"""
Dx AI — training set sub-sampling sensitivity.
Question for clinical deployment: how many subjects does the tool need
to maintain its accuracy? The Dx AA canonical was trained/evaluated on
131 AD + 367 HC across six cohorts. A new clinical site might only have
30-50 AD subjects available f... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.