sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c7ca2a7072ac7ea2c3be9313521f81af34fc1a5797fb13287d10568f9cc5ae24 | Python | 4,192 | 125 | """BaseEmbeddings"""
# Copyright (c) 2020. Lightly AG and its affiliates.
# All Rights Reserved
import os
from typing import Any, List, Optional, Sequence, Tuple, Union
from omegaconf import DictConfig
from pytorch_lightning import LightningModule, Trainer
from pytorch_lightning.callbacks import Callback
from torch i... |
1fe628057ef49382c869ea01c4501278c6b99e433798ee9e7f838f24ad37dfe6 | Python | 4,193 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
27f188d2f79623e23c62ab9f1244732dad8a7001abd16f5b8cabfa6f1d9287fb | Python | 4,193 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
8f9dc5e68fd838524a2eca5d576a064674b68c4beb626e1d88f906ed77295022 | Python | 4,193 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
28662cad40cdffa11b54ef307f6b5b1c9d0acbb2be518d3c03143ab3a6c45695 | Python | 4,194 | 154 | """Utils for PFAM."""
import xml.etree.ElementTree as ET
from math import ceil
from time import sleep
from xml.etree.ElementTree import ParseError
import fasta_utils
import pandas as pd
import requests
__author__ = "Gianluca Corrado"
__copyright__ = "Copyright 2016, Gianluca Corrado"
__license__ = "MIT"
__maintainer... |
38e1d1cc3ab2da01c88230144fc7f006c93d5730c994cfd34e0642eb0c207265 | Python | 4,194 | 85 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
767587a00c8e7f17fb79ca6d3b117693de1c54412d0a6aa8c8a15a9e2a3daf39 | Python | 4,194 | 146 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
class ResidualUnit(nn.Module):
"""
Residual unit proposed in "Identity mappings in Deep Residual Networks"
by He et al.
"""
def __init__(self, l1, l2, w):
super().__init__()
self.normalize1 = nn.... |
3fdbd5f2f084e4821c820e02b4ac5b09988a1656302ce4845789238e5f415bdd | Python | 4,195 | 127 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import pandas as pd
from sklearn.model_selection import train_test_split, TimeSeriesSplit
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_percentage_error
from sklearn import preprocessing
import ... |
8b72d8b0da666f87e262e35fbab0c082081afc93dc9dc068ac3f6f5a44cc9497 | Python | 4,195 | 85 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
203c08e5daa63c0e0511d475297b2a2e8651d42cc16b98ac2d0d50cb2fc13965 | Python | 4,196 | 127 | from mne.datasets.sample import data_path
from mne.channels import find_ch_adjacency
from ..ari import all_resolutions_inference
from scipy.stats import ttest_1samp
import numpy as np
from os.path import join
import mne
N_PERMS = 50
def custom_statfun_example_1samp(X):
_, p_obs = ttest_1samp(X, 0, axis = 0)
retur... |
a22772b90857a16ec883c272805e87aa2803338e4be4247f7c8a59d16f5351da | Python | 4,198 | 113 | import posixpath
import shutil
from fsspec import AbstractFileSystem
from pydantic import field_validator
from galaxy.exceptions import MessageException
from galaxy.files.models import FilesSourceRuntimeContext
from galaxy.files.sources._defaults import DEFAULT_SCHEME
from galaxy.files.sources._fsspec import (
Ca... |
c75f419e47ed81c1a66562edf540764054a392ffbfa0c9db4880f180943cb9f4 | Python | 4,199 | 169 | #TimesVector
#
#Created by Inuk Jung on 2016-08-3.
#Copyright (c) 2016 Inuk Jung. All rights reserved.
#
#This program is free software: you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation, either version 3 of the License, or
#(at you... |
ad8d21ceb70c958b937eb677cd4f49804e1ce06f6e3c37b4464433132c703726 | Python | 4,200 | 117 | """AST regression tests banning retired TorchLens host-object attributes."""
from __future__ import annotations
import ast
import re
from pathlib import Path
import pytest
ROOT = Path(__file__).resolve().parents[1]
SOURCE_ROOT = ROOT / "torchlens"
LEGACY_ATTR_RE = re.compile(r"^tl__?[a-z]")
RETIRED_NAMES = {
"t... |
66de52439d0752ce54674ae538ee710c109b24a29584734ec4ba07c8ac20089d | Python | 4,201 | 110 | # This current file represents a more-or-less identical experiment to the one
# we have been using, with the exception being it uses dynamic accuracy bar
# instead of static accuracy bar.
# I think in general this tends to have a slightly negative effect on the
# performance of the model, but within 0.5-1% in accuracy... |
aa3b2c5fa3b9adb08bd63cf631fd4b06bbefc514d68c1b848c58e34829069fc6 | Python | 4,201 | 128 | from xml.dom.minidom import Identified
import torch
from learning.train import collate_MIL as collate_MIL
from models.attention_model import Attention_MB
from learning.train import MIL_Dataset as MIL_Dataset
from learning.train import calculate_error as calculate_error
from torch.utils.data import DataLoader, Sequen... |
f2bd53c1c1f4e0d5145b5230621ead46d88698156464f7cc6d5f655cbd5f108e | Python | 4,201 | 113 | import os
import re
import time
from carbontracker import exceptions
from carbontracker.components.handler import Handler
from typing import List, Union
# RAPL Literature:
# https://www.researchgate.net/publication/322308215_RAPL_in_Action_Experiences_in_Using_RAPL_for_Power_Measurements
RAPL_DIR = "/sys/class/power... |
6622fcd6b8e6354c0c69fefedc819b538695bc036157f5463dbbeada7cf6114d | Python | 4,202 | 85 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
8b98e6f237f67329f7456cf6a39fc698afa9556dc5660991d9d7ac404400dcf7 | Python | 4,202 | 147 | import numpy as np
import pandas as pd
import io
from PIL import Image
import matplotlib
from anndata import AnnData
import networkx as nx
from typing import Optional, Union, Mapping # Special
from typing import Sequence, Iterable # ABCs
from typing import Tuple # Classes
from textwrap import dedent
from enum imp... |
183dfe8a7f79cbe5dcf6414241ba7da3d974c1addab597dd04a8920865ba9bba | Python | 4,203 | 126 | from pathlib import Path
import geopandas as gpd
import pandas as pd
import pytest
from shapely.geometry import box
import pyrosm
import pyrosm.data.extract_index as ei
import pyrosm.data.geofabrik_index as gi
from pyrosm import get_data_by_bbox
HELSINKI = [24.93, 60.16, 24.96, 60.18]
BBBIKE_URL = "https://download.... |
57bf7851a9b8f20f0c1d821bde3ca9d56c35db896a4f63a37377ea3d7a4ac1fe | Python | 4,203 | 117 | """
Tools for parsing MSMC and smc++ output
Functions:
read_msmc: Parses MSMC format files.
read_smcpp: Parses smc++ format files.
decimate_sizes: Simplifies size histories.
"""
import numpy as np
import pandas as pd
def read_msmc(fname, mut_rate):
"""
Parses an MSMC format file into sizes and ti... |
8931d6ce60c1656dc4befd6aab6c5c8696fcda1a67efcc1d67dd1bfa03fc46c5 | Python | 4,203 | 107 | #! /usr/bin/env python
from setuptools import setup, Extension
from distutils.command.build import build
import os
import subprocess
import sys
def main():
try:
import numpy
try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_n... |
3170c200dd1f4bb350bb912871bd71ba54053c2340836fe09114946e37fd1b14 | Python | 4,204 | 94 | """9. Inference on your own videos using pre-trained models
===========================================================
In this tutorial, we provide a script for you to make human activity predictions on your own videos.
The only thing you need to prepare is a text file containing the information of your videos (e.g.,... |
3423b5a85a41c2028b9adadc7b2ee5c81de09d1d8476a2c6894fc6881d379d1b | Python | 4,204 | 107 |
import glob, os, shutil
from eppy.modeleditor import IDF
def replace_in_textfile(filename_source, filename_target, text, replace_text):
with open(filename_source, 'r') as file :
filedata = file.read()
filedata = filedata.replace(text, replace_text)
with open(filename_target, 'w') as file:
... |
e409214382a8595540aa452d40b8127125b74ec86769ab77b2f3dc9bd567a208 | Python | 4,204 | 134 | """
Credit: https://github.com/nhartland/KL-divergence-estimators/blob/master/src/knn_divergence.py
"""
import warnings
import numpy as np
from scipy.spatial import KDTree
from sklearn.neighbors import NearestNeighbors
def knn_distance(point, sample, k):
"""Euclidean distance from `point` to it's `k`-Nearest
... |
def40ab266966430c3d406cabc81aac7db08b6b9bfe47d352f0686811c8781aa | Python | 4,205 | 107 |
import glob, os, shutil
from eppy.modeleditor import IDF
def replace_in_textfile(filename_source, filename_target, text, replace_text):
with open(filename_source, 'r') as file :
filedata = file.read()
filedata = filedata.replace(text, replace_text)
with open(filename_target, 'w') as file:
... |
d242e5417414107ad34cd1c6db26c30e2de6b863c8002ffece5b0cf28f19f266 | Python | 4,206 | 105 | #!/usr/bin/env python
import argparse
import sys
import textwrap
def main(args):
"""
Extract the protein and coding section from an augustus gff, gtf file
Example file:
HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1
HS04636 AUGUSTUS tra... |
2829510e6887f53f8ffa72434ae3c9215e315e5370d5a8701a47554c818db3ec | Python | 4,207 | 122 | """
The evaluation metrics.
"""
import math
from typing import List, Callable, Union
from sklearn.metrics import accuracy_score, mean_squared_error, roc_auc_score, mean_absolute_error, r2_score, \
precision_recall_curve, auc, recall_score, confusion_matrix
def accuracy(targets: List[int], preds: List[float], thr... |
6b844385d6723e54382b723d91ee14d05d7440a6c61e183516dff489cde31716 | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
7109df46fb29028a8fa21f1a6795c3faef2eb134ae52c60b4e7481e06506779e | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
b9f93dcdd47fd32fa94ee146a1b7e80a14ce6b87ebad996431c30a7462aa5612 | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
e1166b17bc31060da05a0c92ad243bb80f54f2725af2648ce98fdc2fa259b4a8 | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
e5e665fb49003f179326d3e2b52bd58034f60a27134c6173d7072e76f82dc55d | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
e71ade1dc99a5b3782dd0e7ea6f454b586b448b72193e656bae6518e23d1d0ca | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
ede0c67b3b624f3cb2a1536861f491d316b53562f5a4d48fc95b91cf75398120 | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
fd13fb9078a9a07be24859b35faf837ea77a252faa49e651ade09cad816fa293 | Python | 4,208 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
7219350db5775ed5b7451cd8d3b2ef59ab6439344906e91ed778ae1f4120a292 | Python | 4,209 | 111 | import math
import time
from threading import Event, Lock, Thread, current_thread
from codecarbon.external.logger import logger
# Longest stop() waits for the in-flight call, a guess at "a measurement should
# never take longer than this", so a wedged one cannot hang the caller for long.
STOP_JOIN_TIMEOUT_SECONDS = 5... |
79c4c80c3319656f20306f66a856e1b3e4efb4b4a336ce0e6403cacbccdf7db0 | Python | 4,209 | 141 | from flask_login import login_required, current_user
from flask_restplus import Namespace, Resource, reqparse
from werkzeug.security import generate_password_hash
from database import UserModel
from ..util.query_util import fix_ids
api = Namespace('admin', description='Admin related operations')
users = reqparse.Req... |
b685ac4552f5634ae738f02a1af1c6ec4f84882faa95d491d694946976c9f9de | Python | 4,209 | 106 | """Fixwave-2 FW2-POLISH regression pins for the R47 dead-config debloat.
Three families of silent no-op configuration killed in grind b7 R47:
- R47-1: nine write-only "future" option fields (declared, validated, read by
NOTHING). The fields and their keywords are deleted outright (shim-removal
lane, 2026-08-19: t... |
7e7c3baeaf04e7b557dd649b83a0a1a12a5319a7ca421e7f2e3f8cb85f4e0828 | Python | 4,210 | 117 | # SOURCE: vendored from https://github.com/Thijsvanede/DeepLog @ master
#
# Source: deeplog/deeplog.py, class DeepLog -- the CCS 2017 DeepLog log-key anomaly
# detection model: one-hot encodes an integer log-key sequence, feeds it through a
# stacked LSTM, and predicts a distribution over the next log key via a linear ... |
8eb400d926e72e45283abe9987aafc0422c470f01fe513c78fb8dccdab915ee0 | Python | 4,210 | 137 | #!/home/ubuntu/miniconda2/bin/python
from __future__ import division
import sys
import glob, os, gc
import uuid
import os.path
import csv
import numpy as np
from time import time
from subprocess import (call, Popen, PIPE)
from itertools import product
import shutil
import re
import pickle
from boto3.session import Ses... |
58ecbafce4185bb4cea5b99519fab0bee34d6520259016148394d71754033621 | Python | 4,211 | 141 | """
====================================================================
One Way manova
====================================================================
One way manova to compare Left vs Right.
"""
import seaborn as sns
from time import time
from matplotlib import pyplot as plt
from mne import Epochs, pick_types... |
d6855d60e2328f7a54a1804d770854b5d753ede450383bf683239cc6194c0614 | Python | 4,211 | 126 | #!/usr/bin/env python
# coding: utf-8
# In[4]:
import pandas as pd
from sklearn.model_selection import train_test_split, TimeSeriesSplit
from sklearn.linear_model import LinearRegression
from sklearn.metrics import mean_squared_error, r2_score, mean_absolute_percentage_error
from sklearn import preprocessing
import... |
280eb46de56722ae845c3e323c07d52e722dfc218da7a8d7ae65694d9981a6d6 | Python | 4,212 | 125 | import argparse
import itertools
from dataclasses import dataclass
from pathlib import Path
from typing import List, Optional
DTYPE_MAP = {
"fp16": "cutlass::half_t",
"bf16": "cutlass::bfloat16_t",
}
SM = [80] # Sm80 kernels support up to
HEAD_DIMENSIONS = [32, 64, 96, 128, 192, 256]
IS_CAUSAL = ["false", "t... |
b5f27429ab0ef94ec7ec4e044ed47c39fac8a2124aa9dc091720fa93786efe7a | Python | 4,212 | 142 | import datetime
try:
import zoneinfo
except ImportError:
from backports import zoneinfo
import pytest
import time
from rpy2 import robjects
import rpy2.robjects.vectors
_dateval_tuple = (1984, 1, 6, 6, 22, 0, 1, 6, 0)
_zones_str = (None, 'America/New_York', 'Australia/Sydney')
def test_POSIXlt_from_invalid... |
767a2c97893d3cb64dfd1d5287247000ddfbe9b76dd8f24d443807537236d5bc | Python | 4,213 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
01b3fe1f4f17adf9a2abb208a7e446d671d0b6679f6c60ee67527cdfed4378f4 | Python | 4,214 | 84 | # Asteroid Impact (c) Media Neuroscience Lab, Rene Weber
# Authored by Nick Winters
#
# Asteroid Impact is licensed under a
# Creative Commons Attribution-ShareAlike 4.0 International License.
#
# You should have received a copy of the license along with this
# work. If not, see <http://creativecommons.org/lic... |
4373801bb8f0c035587368fe51b07cbf1019b71cc3b279e01a241e8c2e1fdc20 | Python | 4,214 | 133 | r"""
Port of DEBtool_M/animal/get_tm_mod_habp.m — mean lifespan for holometabolous insects.
Integrates the aging/survival ODE from emergence to death, computing mean lifespan.
See get_tm_mod_habp.m source at:
G:\Το Drive μου\DEB projects\Drosophila DEB model\code\Drosophilla_DEB_Evridiki\get_tm_mod_habp.m
Citation... |
fac07db3e79db9931a63ebc1d0190d180f3c3b5c8b78b5effc11428e14c766e3 | Python | 4,215 | 125 | from collections import Counter
from permacache import permacache
import numpy as np
import pandas as pd
def load_interactions():
"""
Loads the interactions from the Lang Paper. Specifically, supplementary
table 9.
Returns
-------
dictionary from interaction type to a table guaranteed to... |
8530baf83b2216cd64200ef1777ac36257865446481d98688534e213d9535ae1 | Python | 4,216 | 153 | """
From Niklas Wilming et al. Nature Communications 2020
https://github.com/DonnerLab/2020_Large-scale-Dynamics-of-Perceptual-Decision-Information-across-Human-Cortex
"""
from numpy import asarray, iscomplexobj, zeros, newaxis, zeros_like, real
import multiprocessing
import os
import pickle
import socket
import warnin... |
9669dbb3661478673271210dc5f3b7cb8e5e3beb64bcc328d1cd75c0af64af05 | Python | 4,216 | 110 | import unittest
from unittest import mock
import datetime
from carbontracker.emissions.intensity.fetchers import energidataservice
from carbontracker import exceptions
class TestEnergiDataService(unittest.TestCase):
def setUp(self):
self.logger = mock.MagicMock()
self.fetcher = energidataservice.E... |
0eb67de59de672e31960f9dc67249c2362faa12fdd60aa8e6661232c5bfaf005 | Python | 4,217 | 154 |
# LICENSE
#
# _This file is Copyright 2018 by the Image Processing and Analysis Group (BioImage Suite Team). Dept. of Radiology & Biomedical Imaging, Yale School of Medicine._
#
# BioImage Suite Web is licensed under the Apache License, Version 2.0 (the "License");
#
# - you may not use this software except in complia... |
194a812461119ca47c9d281bdddec294a185b61efc4d5c07e4d0a6404094bb02 | Python | 4,217 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
475371d4a155a75342b13e761bcc418054736c09823371e2bee0645e43e447d4 | Python | 4,217 | 107 | """Записать настоящий прогон движка в компактный JSON для веб-проигрывателя.
Пишет позиции/энергию агентов, поле ресурса (даунсемпл), метки и живые
метрики покадрово. Байты пакуются в base64, чтобы страница-артефакт была
самодостаточной (без внешних запросов).
"""
import base64
import json
import numpy as np
from sim ... |
ebd0402bff1d3164dbce2727a9bac6be17e2e546b671bbcd538d8fa95b9ea4ae | Python | 4,217 | 116 | from keras.src import activations
from keras.src import backend
from keras.src.api_export import keras_export
from keras.src.backend.common import standardize_dtype
from keras.src.layers.layer import Layer
def _large_negative_number(dtype):
"""Return a Large negative number based on dtype."""
if standardize_d... |
5279336e4d7b6ee5e8541ce52e7b517e3e4993641f93c182fba66ecf46098a98 | Python | 4,218 | 109 | """C02 detached SummaryReport layer pins (summary memo item 10 / sumfam 10).
SummaryReport(str) with __repr__ == __str__, _repr_html_, to_dict(), and
sections; typed SummaryRow/SummaryTotals/CaptureFacts; the five-value
evidence enum; the raw-numbers pin; the detach pin (survives del model /
del trace / cleanup); prof... |
6efd69b96a679d5194b6ce0ee86ab57ea5238b3b978875da4ef2a28c82c9566f | Python | 4,218 | 138 | """Tests for bdpy.dl.torch.domain.core."""
import unittest
from bdpy.dl.torch.domain import core as core_module
class DummyAddDomain(core_module.Domain):
def send(self, num):
return num + 1
def receive(self, num):
return num - 1
class DummyDoubleDomain(core_module.Domain):
def send... |
57e37c319f6f594061e6fdbe2641e1dd622e85aeeeca71920a04cfd2e00a1981 | Python | 4,219 | 120 | """
====================================================================
Data transformations in the Riemannian Procrustes Analysis
====================================================================
Use the SpectralEmbedding module to plot in 2D the transformations on the
matrices from source and target domains when... |
40a827f7f5f4afb6ca78f51dad9a7433f00f06c7473ebb62efa74f80a95e253e | Python | 4,220 | 91 | """This script estimates TRFs for several models and saves them"""
from pathlib import Path
import re
import eelbrain
import mne
import numpy
STIMULI = [str(i) for i in range(1, 13)]
DATA_ROOT = Path("~").expanduser() / 'Data' / 'Alice'
PREDICTOR_DIR = DATA_ROOT / 'predictors'
EEG_DIR = DATA_ROOT / 'eeg'
SUBJECTS = ... |
99595a47f616123ea144b0a65b666074c3b7eabc1df5bd0f61381dedb464197a | Python | 4,221 | 103 | """
Neural Network implementation for image segmentation
Copyright (c) 2022 Giansalvo Gusinu <profgusinu@gmail.com>
Code adapted from TensorFlow Tutorial
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Softw... |
d0ca907c8e1d3dd7cd3eb90d17fabc7f4d05597842368b1eadffcd0467850126 | Python | 4,221 | 136 | from datetime import datetime, timedelta
from typing import List, Optional
import dateutil.relativedelta
from dependency_injector.wiring import Provide, inject
from fastapi import APIRouter, Depends
from starlette import status
from carbonserver.api.schemas import Project, ProjectCreate, ProjectPatch, ProjectReport
f... |
51bb82676bd7b18b7a704be7351163e0fb9e6b4eeda8cfefa54ccd79dd81f98a | Python | 4,222 | 112 | import numpy as np
from rdkit import Chem
from rdkit.Chem.Scaffolds import MurckoScaffold
import tensorflow as tf
from tensorflow.keras.layers import Embedding, Dropout, Dense
class AFMPConfig():
def __init__(self, embedding_size: int=256, dropout_rate: float=0.3,
propegation_factor: float=0.4... |
9f4379334d68dfea9be250a8fb11c912053f2b554e1af84af3c9f199b57fd1f9 | Python | 4,223 | 108 | import torch.nn as nn
try:
from torchvision.models.utils import load_state_dict_from_url
except:
from torch.hub import load_state_dict_from_url
from .custom_modules import FakeReLUM, ConvHPool2d, HannPooling2d
__all__ = ['AlexNet_reduced_aliasing', 'alexnet_reduced_aliasing']
model_urls = {
}
class AlexNet_... |
523c4d150a2cac038f5e40c7675bd2bc1f49e04e42ece7c2704b4a537b3fcdac | Python | 4,225 | 121 | #! /usr/bin/env python3
from MarkovModels import common
from MarkovModels.BeattieModel import BeattieModel
from MarkovModels.KempModel import KempModel
from MarkovModels.ClosedOpenModel import ClosedOpenModel
import argparse
import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
import multi... |
986f6e3b7b3cf7e7e9da64333439403a6d9a14db8989bbfeffdaa6868577b643 | Python | 4,225 | 127 | import numpy as np
import dgl
import torch
import torch.nn.functional as F
import h5py
import sys
sys.path.append('../pkgs/graph-sc/')
import train
import models
device = train.get_device()
import warnings
warnings.filterwarnings("ignore", category=FutureWarning)
import scanpy as sc
from scbig.utils import read_data,se... |
86882bff8881b495028ccb22f3bd9fdbba842376d4ef160d7e91eb9065acb133 | Python | 4,226 | 115 | """Fork capture-outcome derivation (the anti-masquerade contract).
``Trace.fork()`` is the sanctioned mutation surface, so a fork must never
carry its parent's blessed settle stamp by identity: pre-fix, a hand-edited
fork saved (and re-loaded) as a bit-identical ATTESTED COMPLETE product.
Forks now settle a DERIVED ou... |
eda1cfbba2a4e80b4c6388f4c39cf3db041a1b2c00a79397a9c59af283cecdb9 | Python | 4,226 | 129 | """Phase 5a tests for taps, record spans, and report values."""
from __future__ import annotations
import torch
import torchlens as tl
from torchlens.report import log_value
class MetricModel(torch.nn.Module):
"""Model that records a report value during capture."""
def forward(self, x: torch.Tensor) -> to... |
317c251a1cb6599c840dbe534ee2aa8f16fe7004b211c119a1e46e5ca043db91 | Python | 4,227 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
913502a19f9f43f5afa4b69fdee387458b33302538b2dffe38dad276da5bb85b | Python | 4,227 | 141 | import sys
sys.path.insert(1, '/u/home/r/ryo10244/Xiao_lab/dsRNA_pred/script/utils')
import re
import pysam
import argparse as ap
import pandas as pd
import numpy as np
from utils import *
from sklearn.linear_model import LogisticRegression
from sklearn.model_selection import train_test_split, cross_val_scor... |
7114534a682b7997439d474b247a9003d454f88b277e708ee803b576fe84353f | Python | 4,228 | 119 | '''
Code to generate state space labels from a binary labeled peptide annotation sequence.
States are hardcoded.
'''
from typing import List, Tuple
import numpy as np
def parse_coordinate_string(coordinate_string: str, merge_overlaps: bool=True) -> List[Tuple[int,int]]:
peptides = []
coordinates = coord... |
a82978583024a173a8ca3e6fbabbc43ac527ff5df8004b3218f3ba863e36544e | Python | 4,228 | 142 | """PyanNet speaker diarization network from pyannote.audio.
Paper: pyannote.audio: neural building blocks for speaker diarization, Bredin et al. 2019.
The original PyanNet is an end-to-end sequence-labeling model over raw audio:
SincNet-like learnable band-pass filters, temporal convolutional context, recurrent
seque... |
135a0f4fb8a48a8dc4c507881025b20f4e95384c4178344814072464c376fda3 | Python | 4,229 | 88 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
995bbf408cc84595e2e0026eec8c06a906ed959947f109752de44836ef38ee2b | Python | 4,229 | 119 | """Loss functions for the RL models."""
from typing import List, Tuple
import numpy as np
import torch
from torch import Tensor, nn
def dqn_loss(batch: Tuple[Tensor, Tensor], net: nn.Module, target_net: nn.Module, gamma: float = 0.99) -> Tensor:
"""Calculates the mse loss using a mini batch from the replay buff... |
9eb14bf6b3311d651e305d7f9b96987b11d1e476fddf0b9d000102ca7e0acd4c | Python | 4,229 | 145 | """ESCM2: Entire Space Counterfactual Multi-Task Model for post-click CVR.
Paper: Wang et al. 2022, "ESCM2: Entire Space Counterfactual Multi-Task Model
for Post-Click Conversion Rate Estimation" (SIGIR), arXiv:2204.05125.
The compact reconstruction keeps the defining ESMM-style shared embedding with
three towers: em... |
177367b46d73a5db2bad1addf84154dd460ab0c10a2714cf0525544543724842 | Python | 4,230 | 124 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Uniformtext(_BaseLayoutHierarchyType):
_parent_path_str = "layout"
_pat... |
1b5eb4c92eb59959c8a2deeb44338545140d11a33b8667d7af179dcb0113c332 | Python | 4,230 | 159 | 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 .utils import normalize
def plot_history(history,*keys,**kwargs):
"""Plot (Keras) training history returned by :func:`CAR... |
36df082dea9e45f405a2b915e16800d7885c700f1580cb97914a6412542b0ba9 | Python | 4,230 | 118 | try:
# When using torch and tensorflow, torch needs to be imported first,
# otherwise it will segfault upon import. This should force the torch
# import to happen first for all tests.
import torch # noqa: F401
except ImportError:
torch = None
import os # noqa: E402
import pytest # noqa: E402
f... |
4f58424dcada78f6f6274aeff2f68e1bfa2282c19974d51ac0877edd92806340 | Python | 4,230 | 106 | # -*- coding: utf-8 -*-
# Copyright (c) 2016-2018 Braintech Sp. z o.o. [Ltd.] <http://www.braintech.pl>
# All rights reserved.
"""Mixin for SmartTagsManager to create MNE.Epochs objects."""
import mne
import numpy
from ..read_manager import ReadManager
from .utils import requires_mne
class SmartTagManagerMNEMixin:
... |
46f56f0f0e627743c3e9e1fba238f1fa2ad518ac969273dc874327db2cecdb9f | Python | 4,231 | 128 | """ Point cloud class for synapses
"""
import logging
import numpy as np
from scipy.spatial import cKDTree
from tns.astrocyte.math_utils import norm as vectorial_norm
L = logging.getLogger(__name__)
MIN_EPS = -1e-6
# pylint: disable=unsubscriptable-object
class PointCloud:
""" Point cloud data structure wit... |
2436b39d69f19dadf2cf4d386a24234ebd03c5ee767fbf81e22dd7b186c32719 | Python | 4,232 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
285d3906dab601638f1b36ff39496668856d1675cc5f90f794e4d07cd3fbecd9 | Python | 4,233 | 111 | import torch
import torch
from torch import nn
import torch_geometric as tg
from torch_geometric.loader import DataLoader
import torch.utils.data
import shutil
import sys
import rdkit
sys.path.insert(1, '~/egnn_cof/models/egnn_clean')
sys.path.insert(1, '~/egnn_cof')
# from easydict import EasyDict as edict
import tor... |
68b63ebc42533336e0c99e586907a272ea1b416086c5303747eef4eb8ced565e | Python | 4,233 | 111 | # -*- coding: utf-8 -*-
"""Average Attention module."""
import torch
import torch.nn as nn
from bioseq2seq.modules.position_ffn import PositionwiseFeedForward
class AverageAttention(nn.Module):
"""
Average Attention module from
"Accelerating Neural Transformer via an Average Attention Network"
:cite... |
72558a393f29ab7c01c42c429fbd9e87ce6a4de6ef094383c567a98a64e364ab | Python | 4,233 | 129 | # converter for ldreduced rgenetics datatype
# used for grr and eigenstrat - shellfish if we get around to it
import os
import subprocess
import sys
import tempfile
import time
prog = "pbed_ldreduced_converter.py"
galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0... |
f0f824527616be5a5e6f34176141894b7d4039ad8be87d68d39413ee0a1e60e1 | Python | 4,233 | 110 | import numpy as np
from scipy.optimize import curve_fit
from Metrics.src.utils import mtr_asym_curve, LorentzianPool, multi_lorentzian
def mtr_asym(
Z: np.ndarray, mask: np.ndarray, mtr_asym_ppm: tuple, ppm: float
) -> tuple[np.ndarray, np.ndarray]:
"""
Calculate MTR asymmetry and MTR asymmetry image.
... |
d6fd7988403d306e293abc1dea2d47128c0a0dc1edea623d76dfde5ba18d618f | Python | 4,235 | 112 | """Implementation of the CNN Decoder part of
"Convolutional Sequence to Sequence Learning"
"""
import torch
import torch.nn as nn
from bioseq2seq.modules import ConvMultiStepAttention
from bioseq2seq.utils.cnn_factory import shape_transform, GatedConv
from bioseq2seq.decoders.decoder import DecoderBase
SCALE_WEIGHT =... |
4d7e117f7c3bab8dbe3de9876be7aff306b198b1cfca26b9812bc61f3a696493 | Python | 4,236 | 105 | """Mask Target Generator."""
from __future__ import absolute_import
from mxnet import gluon, autograd
class MaskTargetGenerator(gluon.HybridBlock):
"""Mask RCNN target encoder to generate mask targets.
Parameters
----------
num_images : int
Number of input images.
num_rois : int
... |
e5f552caf0e6f2ab710041631ee439898d8adffe1d2e32c9ac0f31a15e71b070 | Python | 4,236 | 142 | #!/usr/bin/env python
# encoding: utf-8
from __future__ import (absolute_import, division,
print_function, unicode_literals)
import os, sys, re
import logging
import TGraph
import TNode
import TGLOBALS
logger = logging.getLogger(__name__)
class Compact_graph_pruner:
def __init__(sel... |
865ce92ba14a0a6ce513db7c513726f680d8ee1ebfee66d78c714da12cb39205 | Python | 4,237 | 130 | import numpy as np
from numpy.random import default_rng
import pathlib
from mpi4py import MPI
from causal_optoconnectics.tools import conditional_probability, joint_probability, roll_pad
from causal_optoconnectics.generator import (
construct_connectivity_filters,
construct_connectivity_matrix,
simulate,
... |
4bc81f06b39b7b61947a2bc57dfad1be15d565d262c977913fea2d6ace76b428 | Python | 4,238 | 109 | import os
from mirp.extract_features_and_images import extract_features
CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
def test_adc_conversion_multi_frame():
# Multi-frame ADC image - micrometers^2/s
feature_data = extract_features(
adc_conversion="um2/s",
image=os.path.join(CURRENT... |
92469f6ed7f6dbf031b98b19930ea014731f2e5345648f8923cb98389f23c974 | Python | 4,238 | 142 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 23 11:12:06 2022
@author: cjquinn, yididiya
"""
#from click import confirm
import os
from pathlib import Path
import pickle
import pandas as pd
from config import Configuration
import argparse
'''
Preprocessing
'''
def get_recording_detail... |
6dd25be14d583959d509291b11e35848620a31de134c1543c5cafd0e22822116 | Python | 4,239 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
3a11cbf370d0029d174c1b905cfdba94e0bababa3a94ea6c42222d09358e9133 | Python | 4,240 | 139 | from typing import Optional
import numpy as np
import pytest
from gym import core, spaces
from gym.wrappers import OrderEnforcing, TimeLimit
class ArgumentEnv(core.Env):
observation_space = spaces.Box(low=0, high=1, shape=(1,))
action_space = spaces.Box(low=0, high=1, shape=(1,))
calls = 0
def __in... |
d1d3620cbfac0c2957c24e28115a8f92ac3e550a6253650503671bc7e74bd837 | Python | 4,240 | 129 | # SPDX-License-Identifier: LGPL-2.1-or-later
#!/usr/bin/env python
#-*- coding: utf-8 -*-
import sys
import numpy as np
class DataBase(object):
def __init__(self, data, mask):
self.mask = None
self._mask_slice = None
self.data = data
if mask:
self._cut_out_data(mask)
... |
99781cf561331dc01ec8f5d1849fbcfa89b6a2e0c1e17e5d7ebfc14938e874c2 | Python | 4,241 | 104 | # Copyright (c) 2023, Tri Dao.
import time
import pytest
import torch
from flash_attn.models.gpt import GPTLMHeadModel
from flash_attn.models.gpt_neox import gpt_neox_config_to_gpt2_config, remap_state_dict_hf_gpt_neox
from flash_attn.utils.pretrained import state_dict_from_pretrained
from transformers import AutoTok... |
4bbf3eeebab0612c9248f8cc76805194871530fb4340ed8452538f6e697f5d0a | Python | 4,242 | 120 | """
====================================================================
Plot the data transformations in the Riemannian Procrustes Analysis
====================================================================
Use the SpectralEmbedding module to plot in 2D the transformations on the data
points from source and target ... |
7fed1f6c764eeca4f70bd466ffa0f8ff59c47a1dc5b7cfc9c5a9ce452b7066d6 | Python | 4,242 | 127 | import cv2
import numpy
import time
from skimage.metrics import structural_similarity as ssim
from propagation_ASM import *
import model
import tools
from scipy import io
imgpath='E:/DIV2K/DIV2K_valid_HR/0887.png'
pitch=0.0036
wavelength=0.000520
n = 2160
m = 3840
z0=160 #juli
layernum=6
interval=10
t... |
fd3968bd12e34c59a1a689777b5dd1ae277826c344dd8212eaa9c1469fe94701 | Python | 4,242 | 118 | def pca(mtx, n_comp=30, index_name='index', new_index=None):
"""
Function to perform scaling and PCA on an input matrix
Parameters
----------
mtx : sample by feature
n_comp : number of pcs to return
index_name : name of index if part of input
Returns
sklearn pca object and pca datafr... |
ea91a245bd00d13e56d35394315ef6e26ee6fba4bbbae8406701f123848dd3e9 | Python | 4,243 | 121 | """C02 stats_table substrate + health-scan sync batching (sumfam 17-18)."""
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.report import STATS_ROW_STATES, StatsTable
def _model() -> nn.Module:
return nn.Sequential(nn.Linear(4, 4), nn.ReLU(), nn.Linear(4, 2)).eval()
def t... |
d2810e011d16cb08e5b5caf63487f9f7c663547b69595ed396ed4563c7a2c8fe | Python | 4,244 | 98 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
from pathlib import Path
from types import MethodType
from typing import Any
import torch
from ultralytics.engine.model import Model
from ultralytics.utils import DEFAULT_CFG_DICT
from ultralytics.utils.checks imp... |
bc001dfc519f4e4b46b60afc7e38e62e626f04f0ca82a3c70be0658d01ea918a | Python | 4,245 | 106 | """Experimental bounding box transformations."""
from __future__ import division
import random
import numpy as np
from ..bbox import crop as bbox_crop
from ....utils import bbox_iou
def random_crop_with_constraints(bbox, size, min_scale=0.3, max_scale=1,
max_aspect_ratio=2, constraints... |
2989bbb85a99d9674b138971cff80fc1f74256b640c6dad629864a7e5320b84e | Python | 4,247 | 79 | #==============================================================================#
# Author: Dominik Müller #
# Copyright: 2024 IT-Infrastructure for Translational Medical Research, #
# University of Augsburg ... |
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