sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c0f9e28502a547875b09a4df25c826d9349e6ffbf7c9175b609e435917e743b0 | Python | 14,147 | 400 | import json
from transformers import (
T5ForConditionalGeneration,
)
import transformers
from transformers import AutoConfig, AutoModel, AutoTokenizer, AutoModelForCausalLM
import re
from transformers import LlamaForCausalLM, LlamaTokenizer
from typing import Any, Dict, List, Mapping, Optional
import numpy as np
im... |
d50fab8c36529217bcd70e97a5cdb5b8f3aa6bf5fcca5e414282520a980a1ba1 | Python | 14,147 | 411 | """Tests for specparam.models.model, including the model object and it's methods.
NOTES
-----
The tests here are not strong tests for accuracy.
They serve rather as 'smoke tests', for if anything fails completely.
"""
import numpy as np
from pytest import raises
from specparam.utils.select import groupby
from specpa... |
e0d28467993f352378f073d6cc44164d55c2a828321b525afc35861516738458 | Python | 14,147 | 390 | import torch
from torch import nn
from torch.utils.model_zoo import load_url as load_state_dict_from_url
__all__ = [
"ResNet",
"resnet18",
"resnet34",
"resnet50",
"resnet101",
"resnet152",
"resnext50_32x4d",
"resnext101_32x8d",
"wide_resnet50_2",
"wide_resnet101_2",
]
MODEL_URL... |
751f6c2dca4d2c3596c4aef06ceecee2809e0291920e272b468e9267b624e58a | Python | 14,150 | 432 | """L5 M3 pins: rank (stacking) channel — stack_by (a), explicit + licensed auto.
Covers the design-memo 4.1 contract: THE LOCKSTEP LICENSE adversarial matrix
(the case list IS the predicate — every globally monotone trace accepts,
every non-monotone trace refuses), the typed refusals, caption/legend
disclosure, rank=s... |
3bc479486fe062f5a79072c25b183169db2444f8f1d8e36377f44705162a494c | Python | 14,152 | 287 | # -*- coding: utf-8 -*-
import brainpy as bp
import brainpy.math as bm
import matplotlib.pyplot as plt
print(bp.__version__)
# bm.set_platform('cpu')
class PoissonStim(bp.NeuGroup):
def __init__(self, size, freq_mean, freq_var, t_interval):
super(PoissonStim, self).__init__(size=size)
# parameters
... |
1ec81338f4319d88a02267345c8bfb963e0326de70174b21fdf91d8a47829b15 | Python | 14,157 | 281 | # 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... |
e77e969ebe04e1783fdc34c47b88d5fdcb0b7c77b1b18da439d8d58822a4e20c | Python | 14,157 | 404 | from abc import ABC, abstractmethod
from typing import Optional, Tuple
import pytest
import torch
from pytest_mock import MockerFixture
from torch import Tensor
from torch.nn import Parameter
from lightly.models import utils
from lightly.models.modules.masked_vision_transformer import MaskedVisionTransformer
class ... |
f1bc23c51dfde8df54bcacc8bef4c5cd90d7daaeebb068ba97050c224173ca15 | Python | 14,159 | 437 | import pytest
from pyrosm import get_data
from pyrosm.config import Conf
# The values used to determine oneway road in OSM
oneway_values = Conf.oneway_values
oneway_col = "oneway"
@pytest.fixture
def test_pbf():
pbf_path = get_data("test_pbf")
return pbf_path
@pytest.fixture
def walk_nodes_and_edges():
... |
2e6ea92fe03dce336898c63c1f4e40ce4d0463c0e0c820770973a63e588b9bea | Python | 14,161 | 340 | from keras.src import backend
from keras.src import ops
from keras.src.api_export import keras_export
from keras.src.backend import KerasTensor
from keras.src.backend.common import standardize_dtype
from keras.src.layers.layer import Layer
@keras_export("keras.layers.Attention")
class Attention(Layer):
"""Dot-pro... |
54ea3dc814a2e4a1b7e854408dc93819ce86a14561a26e0fd7f01b3b197e8db9 | Python | 14,168 | 345 | ######################################################
# This file converts raw HIVdb data files (PI, NRTI, #
# NNRTI) into easy-to-use fasta files for #
# classification. #
# #
# Author: Jonas Ditz ... |
7aeb70b82923ef22877f963a22264ac87808f6181081f88d2fdd95a6f761fb36 | Python | 14,169 | 400 | """
----------------------------------------------------------------------------------------------------
Utility for applying settings to device, from a loaded config
----------------------------------------------------------------------------------------------------
Simply call `config_apply_to_device(... |
9627ce5404ad4d39418186a55d73ce578b1c508ca37e1fdc49288047026d6280 | Python | 14,174 | 378 | """Ancestry/reachability invariants and the label surfaces they guard (B3 L4).
Four defects, one gap:
* The whole derived ancestry class had NO tripwire. Between two labs, eleven planted
corruptions across ``input_ancestors``, ``output_descendants``, ``root_ancestors``,
``internal_source_ancestors``, ``internal_s... |
cace832d3403b40d0f7463eee0d85198c30cadbe68df3d3a3a7a4ce4ae9a6749 | Python | 14,175 | 249 | """
GloDyNE (or previous called DynWalks)
https://github.com/houchengbin/GloDyNE
STEP1: prepare data
STEP2: learn node embeddings
STEP3: evaluate downstream tasks
GloDyNE hyper-parameters:
limit=0.1 # limited computational resources i.e. the upper limit # of selected nodes
... |
e63badf3677bc9791c9425a4e7c7ea03d835ce68dc1aa19350204f06b364bdd4 | Python | 14,175 | 364 | # MIT License
# Copyright (c) 2018 Adrian Wolny (https://github.com/wolny/pytorch-3dunet)
# 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 t... |
5b0fa23c9ce18ab0bfabb3de4ae259a96d9577bd6e20851726eeed74b0fff0eb | Python | 14,181 | 372 | import sys
import argparse
from Bio import SeqIO
from Bio.Seq import Seq
import pandas as pd
import os
import numpy as np
from seqtools import SequenceTools
from collections import Counter
########################
## HARD CODED THINGS ##
#######################
# Firmly set the indexing of nucleotides and amino acid... |
c4c2c85b2a6606164f718abc6e8483a8eaa73305d30de2ec4e26323db87fba0c | Python | 14,184 | 326 | import hashlib
import json
import logging
import os
import sys
from functools import cache, partial
from pathlib import Path
import torch
import yaml
from llama_index.core import Document, SimpleDirectoryReader, VectorStoreIndex
from llama_index.embeddings.huggingface import HuggingFaceEmbedding
from llama_index.embed... |
3c75b76b4522beda3a110750de5bef70b29b0c2eecf17431300046a6b3dea3b0 | Python | 14,192 | 386 | # 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... |
0a68b2226dddf4b8cea10c5fc7734872965114ae8607cc9c97e519c4e5824928 | Python | 14,195 | 344 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 14 15:13:14 2020
@author: Audrey Mazancieux
This script performes "event-related" analyses for one subject that has
performed the local-global task on signal extracted from an ROI in native or
standardised space (using the extract_timeSerie scri... |
00ea699255a754a163efc31c325c92b6a1e533e5af896114eae0359cf1d0183e | Python | 14,196 | 309 | # FAITHFUL PORT of https://github.com/hqyyqh888/DeepUnfolding_WMMSE @ main
# (original: untyped procedural numpy/numpy.matrix script with module-level global
# state -- `DeepUnfolding/train_main.py` `forward()`/`test_model.py` `forward_test()`
# -- not a runnable nn.Module, and not torch)
#
# Ported functions: `t... |
4cc942eb89143a02db864be8ecda294e357359c5ed7d48daeca6c246be5262ff | Python | 14,200 | 432 | # --- 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 Contours(_BaseTraceHierarchyType):
_parent_path_str = "contourcarpet"
_pa... |
33857b01ea704109aa0dd12b4f03e0aeb8a2b6be5e92a98e9b1d58a4d624668b | Python | 14,203 | 316 | """Round-47 security regression (finding secE_1): a POSITIVE forward-dunder allowlist on
the run-path callable-reattach gate, closing the ``torch.Tensor.__setstate__`` storage-
REBIND class (and its non-forward dunder siblings) the r43/r45 belts miss.
secE_1: ``torch.Tensor.__setstate__`` passed ``is_pure_forward_call... |
d07c9707f605c6baba41fc60a61393a817394e0f3e6f2f5b7a6d5b3bfebd2d04 | Python | 14,204 | 344 | """Mech-interp kit core suite (lane F05; mikit Gate 1 identities on R0).
R0 realism: real upstream HF model classes (GPT2LMHeadModel fused-Conv1D,
LlamaForCausalLM rotary/RMS/GQA) with constructed weights, zero network.
Capture-bearing tests share module-scoped traces and are tiered ``heavy``
(the traces cost seconds)... |
f67f06dcf431c916a78097ef87beb477b19e5702a121f22393aa9aa3158ad922 | Python | 14,209 | 578 | # Copyright 2023 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 agree... |
e739b319effde3b37809b2c86a5bc4b8a6a46fdf25ec401ae68b74c5e1eff920 | Python | 14,211 | 424 | import pickle
import numpy as np
from absl.testing import parameterized
from keras.src import backend
from keras.src import layers
from keras.src import saving
from keras.src import testing
from keras.src.layers.core.input_layer import Input
from keras.src.models.functional import Functional
from keras.src.models.mod... |
4235f7089ee4cc9ea7ddf5633f1615956e4d379ec87f6dabd05a29253707c4e5 | Python | 14,214 | 441 | """Static buffers returned from ``forward()`` must yield real output layers.
Regression coverage for the buffer-sole-output bug (raised 2026-06-05): a model
whose ONLY output is a static registered buffer (``def forward(self, x): return
self.buf``) used to capture no output layer at all -- ``tl.trace`` "succeeded"
wit... |
91529adf19103f3cd83e18983d1a0006c8874fc7b7db5e88f75130667e227ba8 | Python | 14,219 | 318 | """Round-45 immunizer: exhaustive classification of Tensor getset-descriptor properties.
The safe pure-read tensor-property surface (``x.T`` / ``x.mT`` / ``x.H`` / ``x.mH`` /
``x.real`` / ``x.imag``) is the single canonical set
``torchlens.utils._callable_safety._PURE_TENSOR_PROPERTY_NAMES``, shared by the capture-sid... |
3ac16f2cb5bedbdd7899d9ae108160ea82193684889ed8517c1c800bfa66d6f1 | Python | 14,223 | 321 | """Committed R0 expectations: floors, diffs, manifests (build rows A4/A5).
``expectations_r0.json`` is the REVIEWED measured golden (generated against
transformers 5.18.0 / torch 2.13.0 on 2026-10-04 by tracing the committed
``families.py`` builders; regenerate deliberately, never with ``--fix``).
The fingerprint and ... |
a01a0801263920381717bd2105e01b876eb213becd2562c57366c7efc7ee45dd | Python | 14,223 | 328 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 9 11:33:54 2022
@author: yihaoy
"""
#%% loading libraries
import matplotlib.pyplot as plt
from scipy.spatial import distance
from scipy import signal
import numpy as np
import jsonpickle
import json
from Neuro2Nets import Neuro2Nets
from datetime i... |
92a8a73e11aaad471dc2723aef3804e5baa03901b019071b042af04c010ea3f0 | Python | 14,226 | 319 | from typing import Iterable, Optional, Tuple
import argparse
import collections
import os
import random
import pickle
import torch
import torch.nn as nn
import tqdm
import transformers
from .utils import device, PrefixLoss, PrefixModel
VERBOSE = False # whether to print grads, etc.
TOP_K = 20 # for printing grads,... |
b28131abd5510b33ebee9621fbc3a170b0af703c6703368c3c8063156f5f801f | Python | 14,232 | 269 | import random
import os
from envs.tunl_2d import Tunl, Tunl_nomem
from agents.model_2d import *
import numpy as np
import torch
import matplotlib.pyplot as plt
from datetime import datetime
import argparse
from tqdm import tqdm
import re
import sys
sys.path.insert(1,'/home/mila/l/lindongy/deeprl-timecells')
from analys... |
624ccb9036e629183a36f66fce6876d77b52298d9665dbb7147a34bbc5017234 | Python | 14,235 | 467 | """Tests for the Phase 13 ``torchlens.compat.report`` API."""
from __future__ import annotations
import warnings
from collections.abc import Iterator
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.backends.tf._tf_compat import get_tf_capability_snapshot
from torchlens.compat i... |
8be4074c8376b4baa5187135f53c23af60caccb297ec1e00d64ecd063672653d | Python | 14,235 | 344 | '''
Util functions and classes for neural system identification
Author: Santiago Cadena
Last update: April 2019
'''
import numpy as np
import os
from scipy import stats
import tensorflow as tf
import tensorflow.contrib.slim as slim
import hashlib
import inspect
import random
from tensorflow.contrib import layers
fro... |
d2fccb6337160185ff0cad94ae13610fb3d45e8273576002682f4134267c5914 | Python | 14,241 | 292 | """
bids_retro main script
author: Lucie Chalet
"""
# import packages
import argparse
import os
import pandas as pd
from database_overview import database_overview
from quality_testing import *
from utils import *
def bids_retro(args):
"""
Formats DICOM database to BIDS standards for PET and MRI pre-clini... |
45bf67fafd97b0a7e1d8ca6cf07fb7aedd34dd79b128d37de8e3e796031796c1 | Python | 14,242 | 364 | from telnetlib import Telnet
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision.transforms as transforms
import numpy as np
from optical_unit import *
from electric_unit import *
from optical_layer import FourierConv
class DDNN_w_PhaseNL_NP_1ch_3layer_readout(nn.Module):
def __in... |
d6aa6b69a2d4c130ec47f05cdcc0a3349c5f81c5266c49d62c7313497b32289e | Python | 14,242 | 394 | import logging
from autouri import AutoURI
from .caper_base import CaperBase
from .caper_labels import CaperLabels
from .caper_wdl_parser import CaperWDLParser
from .caper_workflow_opts import CaperWorkflowOpts
from .cromwell import Cromwell
from .cromwell_rest_api import CromwellRestAPI, has_wildcard, is_valid_uuid
... |
b3dbd0ed82b9fa4555e7a0b2d60d5353e75adb6d71b7111ddb918e6b7eee61a7 | Python | 14,251 | 329 | '''
funkcija za RNN model:
stavljaju se nekolko stacked RNN layera
'''
# osnovne biblioteke
import numpy as np
import pandas as pd
import math
# set to run on CPU
# Early stopping
from keras.callbacks import EarlyStopping
# Evaluation
from sklearn import metrics
# import funkcije za eval... |
12f87068a1ba974ddd194f68113e210177f059c1e74fb2a4db7e42da6f8bf7b5 | Python | 14,252 | 363 | import theano
import theano.tensor as T
from scipy.optimize import minimize
from scipy.ndimage.filters import gaussian_filter as gf
from numpy import fft
import numpy as np
def setup_graph():
"""Setup the theano graph for all possible operations."""
n_x = T.lscalar('n_x')
n_y = T.lscalar('n_y')
pos_x... |
bdbcfd8c9e5d41b6880686d2dd1910ba7ed408d41af57ad1ca95876593b694f9 | Python | 14,255 | 403 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
import argparse
import json
import os
import time
from collections import defaultdict
import numpy as np
import torch
from cpa.data import load_dataset_splits
from cpa.model import CPA, MLP
from sklearn.metrics import r2_score
from torch.autograd ... |
c660f9471706ab338d8aa41ef66701aae126ee4126d25a78b1965df68c21e133 | Python | 14,260 | 383 | import numpy as np
from keras.src import backend
from keras.src import testing
from keras.src.backend.common import keras_tensor
from keras.src.ops import numpy as knp
from keras.src.ops import operation
from keras.src.utils import traceback_utils
class OpWithMultipleInputs(operation.Operation):
def call(self, x... |
d393367b099057007a0698407e903989b7480575d013ef871eedbc3448d0884b | Python | 14,262 | 437 | """Interfaces for the concatenation workflow."""
import itertools
import os
import re
import pandas as pd
from nipype import logging
from nipype.interfaces.base import (
BaseInterfaceInputSpec,
File,
SimpleInterface,
TraitedSpec,
Undefined,
isdefined,
traits,
)
from xcp_d.utils.concatenat... |
d23dd794ecf7120b984706689c60a1010500a4cd1082ed4e25ed6835f6313477 | Python | 14,266 | 369 | from os import path
# from threading import Thread
import traceback
import logging
import time
from ethoscope.web_utils.control_thread import ControlThread, ExperimentalInformation
from ethoscope.utils.description import DescribedObject
import os
import tempfile
import shutil
import multiprocessing
import glob
import d... |
6379a12e9af4ead48e88018618c0e8f09cecfa18583e6a370521978258c94d1f | Python | 14,272 | 275 | import json
import random
from copy import deepcopy
from pathlib import Path
import numpy as np
import open3d as o3d
import torch
from scipy.spatial.distance import cdist
from tqdm.contrib.concurrent import process_map # or thread_map
from external_src.group_free_3D.pointnet2.pointnet2_utils import furthest_point_sa... |
f44c00fe9980467e13b2e8bcede897f7ab127ff953339f0f4314da1e6675ab2f | Python | 14,275 | 337 | # FAITHFUL PORT of https://github.com/IDEALLab/airfoil-opt-gan @ master (original framework: TensorFlow 1.x)
#
# BezierGAN for airfoil-manifold capture / aerodynamic shape optimization
# (Chen, Chiu & Fuge, "Aerodynamic Design Optimization and Shape
# Exploration using Generative Adversarial Networks", AIAA SciTech 201... |
7ffbbeecacc2159e615723d5b3dc680ddb40b0738d26f33b7509c2acf62941cd | Python | 14,276 | 373 | """``.data``-alias intermediate-layout fail-open closure (r75 F1).
Round-74 (hon1 + free-roam, cross-lab) confirmed the r73 intermediate-layout net FAIL-OPENED
on unlabeled receivers: the C-level ``.data`` getter destroyed labels and ``_base``, so
``(x * 2).data.is_contiguous(channels_last)`` recorded nothing and a ch... |
f546f07c42f9418e37ea8308d4bb455a8861a19f94cf01ef1b2663507fea864c | Python | 14,276 | 491 | import os
import sys
import tempfile
import operator
import functools
import itertools
import re
import contextlib
import pickle
import textwrap
from setuptools.extern import six
from setuptools.extern.six.moves import builtins, map
import pkg_resources.py31compat
if sys.platform.startswith('java'):
import org.p... |
6ada0b163dce0f929f5ec6b975804c0bf988d3a974ebc179c99845e2395ed490 | Python | 14,280 | 355 | """Prepares a distribution for installation
"""
import logging
import os
from pip._vendor import pkg_resources, requests
from pip._internal.build_env import BuildEnvironment
from pip._internal.download import (
is_dir_url, is_file_url, is_vcs_url, unpack_url, url_to_path,
)
from pip._internal.exceptions import (... |
d43e8747281c0ea5671fdc157064fccd344f1bc09c83f1491a7530cfa8bd4216 | Python | 14,280 | 440 | """
sess_trace_util.py
This module contains functions for processing ROI trace data from files
generated by the Allen Institute OpenScope experiments for the Credit
Assignment Project.
Authors: Colleen Gillon
Date: August, 2018
Note: this code uses python 3.7.
"""
"""
sess_trace_util.py
This module contains fu... |
01503850f387884629a1bc95e4846828ffcaef80473ff4e2360e629099267428 | Python | 14,286 | 467 | import collections
import enum
import logging
import os
import sys
import typing
import warnings
from rpy2.rinterface_lib import openrlib
from rpy2.rinterface_lib import callbacks
from typing import Protocol
logger = logging.getLogger(__name__)
ffi = openrlib.ffi
# Container for module-level C objects needing to be ... |
a3ba98a8c1eeac661286cd0768c663990e0eb4e22922a82a7280d29baded4257 | Python | 14,290 | 358 | """Benchmarking module for AlignmentFile functionality"""
import os
import pysam
import sys
import pytest
from TestUtils import make_data_files, BAM_DATADIR, force_str, flatten_nested_list
import PileupTestUtils
def setUpModule():
make_data_files(BAM_DATADIR)
class TestPileupReadSelection:
'''test pileup f... |
a4dea346a7a1f6168391da70043a60bad92df33d192168ab7d49cf3c30e32589 | Python | 14,290 | 358 | import numpy as np
from sncda import SNCDA
from gates import get_ros, ros_inf
from gates import get_parkinsons_rotenone
from gates import get_parkinsons_type2
from mitochondria import Mito
from utils import Recorder, Q_nak
from steady_state import get_steady_state
import figure_properties as fp
import matplotlib.pypl... |
f7aad4707386e8680a7a4e10a5d30cfe91a521f104d12271fe61056baf6ca39b | Python | 14,290 | 363 | """Helpers + fitted-projection contract tests (memo B7/P6/B8; lane F19).
Covers ``srp_dims_for`` (the honestly-labeled dense-JL heuristic),
``srp_fidelity_probe`` (the T-C12 provenance-bearing report), the P6
``tl.stats.PCA`` additive upgrade (mean/n_samples/n_features/digest,
deterministic sign canonicalization, the ... |
86f28207c0a6aefbdbc6bffc092554bd72923917ed773f0a94f9fc0bddd2008a | Python | 14,295 | 320 | '''
funkcija za RNN attention model:
stavljaju se nekolko stacked RNN layera
i na kraju samo ide attention layer, nakon svih RNN layera
'''
# osnovne biblioteke
import numpy as np
import pandas as pd
import math
from attention import Attention
# set to run on CPU
# Early stopping
from keras.callba... |
cff0915e431de43a7c99068fba7a5baa6b65b86172b8d0ba6b0a49208a4a4491 | Python | 14,301 | 366 | import json
import pathlib
import pkg_resources
import numpy as np
from PyQt6 import uic, QtCore, QtWidgets
from .. import formats
from .colocalize_pgrois import StructureCompositeGroupedROIs
class Colocalize(QtWidgets.QWidget):
def __init__(self, *args, **kwargs):
super(Colocalize, self).__init__(*arg... |
bd5d26dcf71066fbe1325b587644ebcd856711709046af4f0b6c18cdf238501e | Python | 14,302 | 374 | import argparse
from typing import Any, List, Tuple
import torch
from pytorch_lightning import LightningModule, Trainer, seed_everything
from torch import Tensor
from torch.optim.optimizer import Optimizer
from torch.utils.data import DataLoader
from pl_bolts.datamodules import ExperienceSourceDataset
from pl_bolts.m... |
23f3bd9ab1edfcc70cf90e2040f108b98e87200df53eef60f171eca6ee47c4d7 | Python | 14,303 | 416 | """
ROI Template Manager for organizing and managing ROI template files.
This module provides utilities for managing ROI template files, including
loading builtin templates, validating templates, and converting legacy
ROI builders to template format.
"""
import json
import os
import warnings
from typing import Any
f... |
68bb16a3dc3fc18d315469fd34f97ea2597d945f39a98870cd6efb5b136b1f47 | Python | 14,306 | 333 | """P0-1 · Exhaustive sign-flip permutation for the GSE169148 paired cohort.
Why this script exists
----------------------
The manuscript's central quantity is the *distribution of signs* of the paired
delta -- "12 of 18 mortality outputs decline against 7 of 18 chronological
ones" -- and until now it was reported with... |
2fdf7cb51151b431c61acb6d45cfd22ad250207c2284e87b9e52460d4b422ade | Python | 14,308 | 411 | # -*- coding: utf-8 -*-
"""
Created on Mon Feb 15 13:24:28 2021
@author: KEPetousakis
"""
import Code_General_utility_spikes_pickling as util
import numpy as np
import Code_General_Nassi_functions as nf
import matplotlib.pyplot as plt
from copy import deepcopy as dcp
import scipy.stats as stats
import matplotlib
impo... |
c5dcaabba0c9b81012888b1c896cf18c1d255f1c0e249468c394815fe7562356 | Python | 14,308 | 405 | #!/usr/bin/env python
import argparse
import glob
from pathlib import Path
# try to set cache/config as early as possible (for clusters)
from util import gen_util
gen_util.CC_config_cache()
from matplotlib import pyplot as plt
import torch
import pandas as pd
import numpy as np
gen_util.extend_sys_path(__file__, p... |
f04341fd3da133229b2b099f26d8582f6d844a909502215e003879defcf9ac87 | Python | 14,313 | 354 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in May 2018
@author: Nathan de Lara <nathan.delara@polytechnique.org>
@author: Thomas Bonald <bonald@enst.fr>
"""
from typing import Union
import numpy as np
from scipy import sparse
from sknetwork.embedding.base import BaseEmbedding
from sknetwork.linalg imp... |
a7ff7f573fcaf90e4f2a25ad1dd920d76cbf5efe168c7f2b929c57a51ef4acee | Python | 14,315 | 352 | # -*- coding: utf-8 -*-
# Generated by the protocol buffer compiler. DO NOT EDIT!
# source: bream/platform_qc_results.proto
"""Generated protocol buffer code."""
from google.protobuf import descriptor as _descriptor
from google.protobuf import message as _message
from google.protobuf import reflection as _reflection
f... |
3b3daa38e1a49508f5b07e8f8b25364bf467eeba1bb7f3cb30db3f891ab91801 | Python | 14,321 | 376 | import tensorflow as tf
from tensorflow import keras
import numpy as np
import time
from matplotlib import pyplot as plt
import pandas as pd
import random
#%% select a portion of data from database
from gemmi import cif
number = []
I = []
for i in range(0, 1000000):#1667834
try:
doc = cif.re... |
cf5c9a8cb1e69fe1836feaf367988794a98f6430db3bd7cda8fda35dff33dca1 | Python | 14,324 | 369 | # -*- coding: utf-8 -*-
"""
Grammar to parse headers in Amira files
"""
import sys
import re
import time
import collections
from pprint import pprint
TOKEN_NAME = 'name'
TOKEN_NUMBER = 'number'
TOKEN_STRING = 'string'
TOKEN_OP = 'op'
TOKEN_COMMENT = 'comment'
TOKEN_NEWLINE = 'newline'
TOKEN_COMMA = 'comma'
TOKEN_COL... |
b1bdbf8e2001f79d9e4a33a110d096c41fca66ef237f9c5008bca215d807feff | Python | 14,330 | 374 | # Copyright (c) 2024, Tri Dao.
import pytest
import torch
import torch.nn.functional as F
from einops import rearrange, repeat
from flash_attn.ops.triton.layer_norm import (
layer_norm_fn,
layer_norm_ref,
rms_norm_ref,
layer_norm_linear_fn,
)
is_sm8x = torch.cuda.get_device_capability("cuda")[0] >= ... |
d6fde3e2f765136458e93273d8b819dc3ed43943375c5ab2f28ddb8fb94d50c7 | Python | 14,334 | 401 | """Round-10 security regression: RCE via output-container reconstruction + member traversal.
FINDING 1 (CRITICAL RCE): the portable output ``ContainerSpec`` (torchlens-owned, so the
safe unpickler correctly admits it) carries ``type_module`` / ``type_qualname`` as plain
KEEP strings plus literal constructor args. Reco... |
7f7b4544daf065e045f39bd6930c5ecc96a661de6675ee537c5f1bb0ecf75849 | Python | 14,336 | 391 | """Round-5 security regression: load-time / run-time ``torch.from_file`` file-I/O.
``torch.from_file`` is a ``_VariableFunctionsClass`` factory that CREATES/TRUNCATES
an arbitrary file (``shared=True``) or READS an arbitrary file into a tensor
(``shared=False``). Its real ``__module__`` is plainly ``"torch"``, so the
... |
a333561849a9fa004e83ddd19bea46cb5baf3d85048a7e4ee5d5870faaf4cccd | Python | 14,336 | 388 | from __future__ import annotations
import importlib.metadata as im
from larvaworld.gui_v2.registry_bridge import (
GuiEntry,
GuiNavigationModel,
build_navigation_model,
)
from larvaworld.gui_v2.tabs.home import build_home_text, build_home_widget
from larvaworld.gui_v2.tabs.placeholder import (
build_e... |
776accde322d76eb0404482883ff9395beb39afc76d8ce0cd4bd9a7ab7f52965 | Python | 14,337 | 300 | #!/usr/bin/python
#-*-coding:utf-8-*-
# Copyright (c) 2022 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use... |
534351d7b9f8fa4e16c26794a78bdbe89b8322ad0f6e14366c79649a0e3b56ad | Python | 14,338 | 354 | #!/usr/bin/env python
"""
Automated state annotation using a combination of linear
discriminant analysis (LDA) and hidden Markov model (HMM).
"""
import pickle
import numpy as np
from pomegranate import (
MultivariateGaussianDistribution,
HiddenMarkovModel,
)
from sklearn.discriminant_analysis import LinearDi... |
b8aca0fae46382446efc3e4a694d6dc32cb59e204aa509f5e8f8992d39b86134 | Python | 14,339 | 408 | # Author: Christian Brodbeck <christianbrodbeck@nyu.edu>
"""Statistical Parametric Mapping"""
from operator import mul
import numpy as np
from .. import _info, fmtxt
from .._data_obj import Dataset, Factor, Var, NDVar, Case, asmodel, asndvar, assub, combine, dataobj_repr
from .._exceptions import DimensionMismatchErr... |
dfb3c48a4c63d7829437599e6a35ce8bf99ed4f0895e658e1153e587b4063297 | Python | 14,340 | 363 | """r55 CLASS 1 + r57 immunizer -- portable device strings are closed-gate data.
r54 ``sec_2`` (HIGH): a tinygrad ``.tlspec`` carries per-blob ``logical_device``
/ ``device_at_save`` strings in plaintext ``manifest.json``; the codec passed
them straight into ``tinygrad.Tensor(device=<attacker str>)`` where the
``disk:<... |
7ea44147a7da748c84e4cedd8827644cd236061b4a3ae068e457070fca29b42a | Python | 14,346 | 358 | # pylint: disable=missing-function-docstring, missing-class-docstring, unused-argument
"""R2Plus1D, https://arxiv.org/abs/1711.11248. Code adapted from
https://github.com/pytorch/vision/blob/master/torchvision/models/video/resnet.py."""
import torch
import torch.nn as nn
from torch.nn import BatchNorm3d
__all__ = ['R2... |
db22de0fd927c98abdaa73ab6c38ca83d49670cd129fd6f17550f1feb8b116b4 | Python | 14,346 | 300 | """
Module containing all the supported datasets, which are subclasses of the
abstract class :class:`robustness.datasets.DataSet`.
Only includes the Dataset classes that used in Feather et al. 2022.
Currently supported datasets:
- ImageNet (:class:`robustness.datasets.ImageNet`)
- Word-Speaker-Noise: (:class:`robu... |
23f7abed1a172158c55b6f1f486db093012fe8cfeb1c17c1a5226eab71fac2e2 | Python | 14,347 | 389 | """tviz typed-record contract rows (memo D2/D5/D6/D12/D13/D16/D19).
Construction validation, honesty metadata, the closed annotation-kind
vocabulary, receipt attachment validation, and the sum-to-score invariant --
every ``tv_*`` refusal class is provoked here or in the render/bridge suites.
"""
from __future__ impor... |
7e843b45c49b5b0d061608ceca70500993765e18a0509ce5449586d71f0c9e41 | Python | 14,350 | 359 | import mne
from mne.io import Raw
from mne.preprocessing import read_ica
from .constants import *
from .data_types import Epochs, FrequencyBands
from .modeling import CrossValidation, EEGmodel, RTmodel, Tuner
from os import path, makedirs
import pickle as pkl
import logging
import shap
import matplotlib.pyplo... |
ac0ecde90cdc28ba18ae73f8165e578c1c88a8fd0df76a51a38478707e612c7f | Python | 14,356 | 352 | """Tests for xcp_d.ingression.abcdbids."""
from pathlib import Path
from unittest.mock import patch
import nibabel as nb
import numpy as np
import pandas as pd
import pytest
from xcp_d.ingression import abcdbids
# Small imaging grid: 5x5x5 = 125 voxels; 5x5x5x4 = 500 voxels (under limit)
_SHAPE_3D = (5, 5, 5)
_SHAP... |
12fbcd5a1af2915de54e46473a08687f07a667efec8b1286f7b5d4c906d2f437 | Python | 14,361 | 416 | """Message migration tools (Broker <-> Broker)."""
import socket
from functools import partial
from itertools import cycle, islice
from kombu import Queue, eventloop
from kombu.common import maybe_declare
from kombu.utils.encoding import ensure_bytes
from celery.app import app_or_default
from celery.utils.nodenames i... |
c9216e35ef4dec2767d5676f9aa859ac0974fc2c55988ad3990c13b300882954 | Python | 14,368 | 466 | from contextlib import contextmanager
from unittest.mock import Mock, PropertyMock, patch, sentinel
import pytest
from celery import canvas, group, result, uuid
from celery.canvas import Signature
from celery.exceptions import ChordError, Retry
from celery.result import AsyncResult, EagerResult, GroupResult
def pas... |
1b05181cfe37d1d9b2630eca8adab39432307f61cef0e6daf30ca3224afb8967 | Python | 14,369 | 342 | """Implicit-boundary tightening pins (L9 memo 1.2).
The close routine is a journal/scavenge/finalize split whose FINALIZE guard
lives INSIDE ``_close_implicit_backward_pass_if_open`` so no caller can
bypass it: JOURNAL + SCAVENGE run on every close on any thread; FINALIZE
(the R36-1 D2H fence + full projection) runs o... |
49a8680e7990c5ac2b3285c044d677917d6fdf49435d859962388155da2a14eb | Python | 14,369 | 347 | """Round-49 hon2_1 immunizer -- cross-thread captured-operand consumption over the PATCHABLE
private-C free-function modules (`torch._C._{nn,special,fft,linalg,sparse,nested}`).
r47 closed the `torch.ops.*` class surface. But a private-C FREE function
(`torch._C._nn.gelu(gate)`) is a THIRD op surface: it bypasses BOTH... |
f006971f690f7d74aa934d87e4afb9d8fd78731e5a50e5c35cfecaa12e00e1f2 | Python | 14,371 | 405 | import numpy as np
import scipy
import brian2.only as br
from tqdm import tqdm
import matplotlib as mpl
import matplotlib.pyplot as plt
import pandas as pd
import network
import analysis
from functools import partial
from multiprocessing import Manager, Pool
import sys
from time import time
import os
... |
78814b70614536b3492905693c403c231ef6632d4bbc4bcc049aee721bc5526c | Python | 14,376 | 461 | #!/usr/bin/env python
#
# Copyright 2020 Google Inc. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
81c71e07c394ebcfa24809176d3bbd137a1b1ac766087af06aab351e6a087c8e | Python | 14,376 | 403 | """Extended image transformations to `mxnet.image`."""
from __future__ import division
import random
import numpy as np
import mxnet as mx
from mxnet import nd
from mxnet.base import numeric_types
__all__ = ['imresize', 'resize_long', 'resize_short_within',
'random_pca_lighting', 'random_expand', 'random_fl... |
f685b4142c4f057e4dcf5c220fce8e6c890b58091e3fbe9fbcb81088125e1e43 | Python | 14,377 | 384 | # -*- coding: utf-8 -*-
from __future__ import print_function, unicode_literals, absolute_import, division
from six.moves import range, zip, map, reduce, filter
from six import string_types
import numpy as np
from collections import namedtuple
import sys, os, warnings
from ..utils import _raise, consume, axes_check_a... |
338a29799df1445dc66390f31db4aa8252617c306a92429458b060d80667da28 | Python | 14,386 | 344 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 19 10:30:02 2019
@author: Sebastien M. Popoff
Based on https://openreview.net/forum?id=H1T2hmZAb
"""
import torch
from torch.nn import Module, Parameter, init
from torch.nn import Conv2d, Linear, BatchNorm1d, BatchNorm2d
from torch.nn import Conv... |
59c435da630a408a4a28dfb03eab8ba5e98eb16927ae1a861fdbbb5f9923b0ea | Python | 14,388 | 390 | """Single-parameter popup content: the Inspect/Add-Parameter view, shared
between read-only display and editable clone-and-save. Standalone from
`parameter_db_app.py`, which owns the popup *shell*
(`_DraggableResizablePopup`) and database-wide actions (Remove
confirmation, the table itself) -- these builders only produ... |
527f44c6cb99b836b3fce71c761ee7b848e686035bbf2aae8a172433616e5b1a | Python | 14,389 | 320 | # This code shows the process of extracting features from a PyTorch model
# developed by Meta researchers
# For details about the model or paper, see https://github.com/facebookresearch/ConvNeXt
# https://arxiv.org/abs/2201.03545
# Ref: Islam et al, Revealing Hidden Patterns in Deep Neural Network Feature Space... |
b73850b3c396415f957c246f6177ff71cece5bda57314908cc97da06aeda627c | Python | 14,398 | 354 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""Functions for converting ABCD-BIDS-format derivatives to fMRIPrep format.
These functions are specifically designed to work with abcd-hcp-pipeline version 0.1.3.
https://github.com/DCAN-Labs/abcd-hcp-pi... |
a2a91db4ab9344f72cd428d18239a032298a16ad78308b8725cc17d02ebff23b | Python | 14,404 | 384 | """
SETUP.py — Run this ONCE from your eeg_wheelchair/ folder.
It writes all the correct source files directly to src/
so there are no version mismatch issues.
Usage:
cd /Users/ariachadha/Desktop/eeg_wheelchair
python SETUP.py
"""
import os, sys
ROOT = os.path.dirname(os.path.abspath(__file__))
SRC = os.pat... |
2ff4e25f90bcab068a2725359314afa71400e517a7de92eb60f3b7c5638bfba0 | Python | 14,405 | 360 | # Copyright (c) 2025, Jay Shah, Ganesh Bikshandi, Ying Zhang, Vijay Thakkar, Pradeep Ramani, Tri Dao.
import math
from typing import Optional
import torch
from einops import rearrange, repeat
from flash_attn.bert_padding import pad_input, unpad_input
def generate_random_padding_mask(max_seqlen, batch_size, device, ... |
5d4e57d1f3342c68665a32dba54c20298d51012c4ecae153ef10e76109e875d0 | Python | 14,408 | 392 | # 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... |
0975cf1728591eb2c5d3b9537a10bdd94a0c319c2946c91d4125c4479910493e | Python | 14,409 | 386 | # 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... |
8728fe0c9bf1914b1939e070a64af3c1505c2f94e3620553619a235791174ded | Python | 14,409 | 396 | """
Functions to compute phases and envelopes
"""
import numbers
import numpy as np
import pynapple as nap
def apply_hilbert_transform(data):
"""
Apply the Hilbert transform to a time-series.
This function wraps :func:`scipy.signal.hilbert` to compute the analytic signal,
which represents the orig... |
37ae624982851d627a296600215aaaf5ce59f9f761e2b8bd88a3b70fb5f9f058 | Python | 14,415 | 423 | import os
import warnings
import torch
from tlib import tutils
from ..utils.data import read_batch, get_random_subset, plot_grid
from .datasets import Dataset, ImageDataset, ImageDatasetFromFiles
class DataModule(tutils.classes.StateAndArgsSaver):
"""
DataModule combining all datasets.
:param train_dat... |
4000f4a2b0ec2e9f12a841d1e1e098b571c4826f32ee8b1bd725a356f7e0a697 | Python | 14,420 | 415 | # SOURCE: vendored from https://github.com/automl/RNAformer @ main
#
# RNAformer (automl group) -- a scalable axial-attention transformer for RNA secondary-
# structure / base-pair prediction, operating directly on an LxL pairwise "contact map"
# latent built from the sequence via an outer-sum sequence-to-matrix embedd... |
bee3a863c8474aa887b94960138983c8f40bc754d1c760f7255d20caeaa5fb69 | Python | 14,420 | 304 | import os
import logging
import shutil
import argparse
import numpy as np
from tqdm import tqdm
import mxnet as mx
from mxnet import gluon, autograd
from mxnet.gluon.data.vision import transforms
import gluoncv
gluoncv.utils.check_version('0.6.0')
from gluoncv.loss import *
from gluoncv.utils import makedirs, LRSched... |
efd2be0c13f3c64ab14b28d2e181ba086291a3586563fcbc5366bb9e01eda570 | Python | 14,420 | 358 | # 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... |
f7567f7899e5ad477631d4a63d0842059a68de0c41fcaf9978c120483ea32436 | Python | 14,422 | 306 | """Perform transfer-learning for offset stratification with a provided COVID-Net
From the trained weights of a COVID-Net for COVID-19 identification in radiographs,
this tool performs transfer learning to re-use these weights for stratification of
patient offset (# of days since symptoms began *)
Steps to use this:
1... |
080d8b3831a31fc75413d5fc97a9c899a4c04b513516ca975ff6e2a174af3152 | Python | 14,429 | 360 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 28 19:17:40 2022
@author: fcheng
"""
'''Feature-to-Generator reconstruction.'''
import glob
import os
import sys
from bdpy.dl.torch.models import AlexNetGenerator
from bdpy.dataform import Features, DecodedFeatures
from bdpy.feature import norma... |
e29f5594392d9d8c2be746c61c24b10c02f76b9b2882acd809ad3752c838ec5c | Python | 14,430 | 356 | """Acceptance test of st.tl.cci.run on a synthetic Visium HD sample.
Checks the results match a stored baseline, and records time and memory so
they can be followed over time. It takes minutes, so pytest deselects it by default:
# Baselines from the code checked out, e.g. master:
pytest -m acceptance --accept... |
cad5e49f3ef1bcf470610ae03dc64cee05b7dcde820a8e13af41128cdc02d080 | Python | 14,437 | 341 | from typing import Optional
import numpy as np
from anndata import AnnData
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
def _generate_vf_class(
adata: AnnData,
vf_key: str,
method: str = "gaussian_process",
nonrigid_only: bool = False,
):
if v... |
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