sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
a8e68704d16f8a7a71cbf3ced7efb40c05b4eee79193a4417d8895fa1d18a34d | Python | 37,972 | 962 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium Solvation AFE Protocol --- :mod:`openfe.protocols.openmm_afe.equil_solvation_afe_method`
================================================================================... |
b02c634868adc7869df57467ab540607aaa1122754aebd70aed2ec6b0b23f175 | Python | 38,208 | 1,081 | """End-to-end training workflows for GNN and VAE models.
Wraps the full workflow — test set holdout, Optuna hyperparameter search
with k-fold CV, final model retraining, holdout evaluation, and artifact
saving — into single function calls.
"""
import json
import logging
import random
from dataclasses import dataclass... |
feae8818b6ccc43f5bbbb5ffc9208d99a268451c5fcb4eee30b1b6106a032b5c | Python | 38,208 | 783 | """
SlotDeconv Validation v3 - 改进配色版本
========================================
改进:
1. 使用scanpy风格的配色 (更好看)
2. 优化UMAP可视化
3. 添加legend
"""
from wsgiref.validate import validator
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib.colors import ListedColormap
import m... |
c9f023f64da67a4cf42492022c80090b03bf937673278cb0563f3114dc2162e4 | Python | 38,321 | 1,040 | # Copyright (c) Facebook, Inc. and its affiliates.
import collections
import copy
import functools
import logging
import numpy as np
import os
from typing import Any, Callable, Dict, List, Optional, Tuple, Union
from unittest import mock
import caffe2.python.utils as putils
import torch
import torch.nn.functional as F... |
662b7da369767ef1974e37a459921287f00e4e48f491f32905d9c04c063600ae | Python | 38,343 | 755 | # Garnet model to assign force field parameters
# License is MIT
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import Data
from torch_geometric.nn.conv import SAGEConv
from openmm.app import ForceField, PDBFile, PDBxFile, NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald... |
d2c09ca732318e69b833e2d805efbcac8495d30869f06f4d4bc51d33d31e53b3 | Python | 38,344 | 907 | """
synth_b0 - Synthetic Undistorted B0 Generation using Deep Learning
Part of the micaflow processing pipeline for neuroimaging data.
This module generates synthetic undistorted B0 images from T1-weighted anatomical
images and distorted B0 images using the SynB0-DISCO deep learning framework. The
approach uses an ... |
7d604afc71bc5a53ed6f34f7b60646054b69b1e1cadc68dd6d919de657f0ed44 | Python | 38,388 | 885 | """
python benchmarkProteomics.py --mq-dda "L:\promec\Animesh\nDDA\MaxQuant\DDA\combined\txt\proteinGroups.txt" --mq-dia "L:\promec\Animesh\nDDA\MaxQuant\DIA\combined\txt\proteinGroups.txt" --diann-dda "L:\promec\Animesh\nDDA\DIANN\DDA\report.DDA9.2p6.pg_matrix.tsv" --diann-dia "L:\promec\Animesh\nDDA\DIANN\DIA\report.... |
f6773e158b88fe0a53b26e69de760a6677ecb2908380e04539c58cf35d34d7d4 | Python | 38,450 | 920 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Harder Surrogate Models for Making Competition More Difficult
This module implements surrogate models that make the hide-the-label competition
harder for Bayesian optimizers by using non-GP models and adding noise.
Methods implemented:
1. Non-GP Type 1 Models (Random... |
a7ee8150abfc7eafb32a50aaa6b6fa50b3930c37eb0246423f44a16e63745ba2 | Python | 38,550 | 1,222 | """ Created on Tue Aug 8 13:23:29 2025
@author: dcupolillo """
from __future__ import annotations
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
from matplotlib.animation import FuncAnimation
from matplotlib.gridspec import GridSpec
from matplotlib.transforms import Affine2D
from scipy... |
3dbfa666ed97fdecb0dd13f84edeabe1e172bedd7d8fd256b3250a15219618e0 | Python | 38,573 | 706 | #!/usr/bin/env python
"""
run_analysis.py
---------------
Unified MEA analysis pipeline.
Supports 3Brain (.bxr), Maxwell (.h5), MCS (.h5), Cortical Labs (.h5),
and Axion BioSystems (.csv) files.
Adding a new manufacturer = write one new loader in loaders/ only.
Usage examples
--------------
# 3Brain file:
python run_a... |
49ddb0242fac89b33d21ca8a286a44bf778fc1e51010a19ae720998d3288f246 | Python | 38,599 | 980 | # -*- coding: utf-8 -*-
"""neu_efficient_multiclass
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1iDtIqB-DBtdb1wcgQDe7C6jSr8cy8-Ox
Transfer-learning EfficientNetV2B0 multiclass pipeline for microstructure
image classification, with stratified evaluation, r... |
607b707fc7a91213191cdb70aa07f4b84137e51c1083f1b4e351999aac19ec7e | Python | 38,960 | 1,003 | from __future__ import annotations
import functools as ft
import itertools as it
import textwrap
import warnings
from collections.abc import Iterable, Mapping
from math import inf
from pathlib import Path
from typing import Any, NoReturn, overload
import attr
import more_itertools as itx
from bids import BIDSLayout
f... |
ff64cf57f0bc5b9366f0357aef0e2051ca6f7675e9d5d07be7b18c635304e701 | Python | 39,008 | 423 | import pytest
@pytest.fixture
def min_result_json():
"""The minimal information a results json must have to be loaded by `openfe gather`."""
result = {
"estimate": {},
"uncertainty": {},
"protocol_result": {
"data": {
"22940961": [
{
... |
2d759adb90abcd46c67fc06a40bc69be67f82ba8e16d4c6bb8bf3ec0e8b55d98 | Python | 39,086 | 831 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
from collections import defaultdict
import numpy as np
import pandas as pd
from six import ensure_str
import cellranger.constants as cr_constants
import cellranger.library_constants as lib_const... |
7d2d981200e1732f3912567eb7bba152e7c65d5a5e57bbcee2692a9c8a3b2a9d | Python | 39,157 | 1,082 | """Molecular fingerprint computation.
Provides a unified interface for computing molecular fingerprints using
both RDKit (Morgan fingerprints) and scikit-fingerprints (skfp) for a
comprehensive library of 2D and 3D fingerprint types.
Includes a disk-backed conformer cache (`_ConformerCache`) so that
expensive 3D conf... |
ecc7f5fbe96d9bfbf270f9910ec70850ff9c526c847cc62a3c0b1abf41252994 | Python | 39,369 | 1,069 | import numpy as np
import networkx as nx
import pandas as pd
from matplotlib import pyplot as plt
import matplotlib as mpl
import matplotlib.animation as animation
from matplotlib.ticker import MaxNLocator, LinearLocator
import os
import math
from sklearn.cluster import KMeans
def formatter(x, pos):
# Keep one d... |
3937eddda44ecf22fe76e7cbede79d76f5c5acb9a408c955f4e9202c109341c0 | Python | 39,414 | 20 | # Copyright (c) Facebook, Inc. and its affiliates.
# Autogen with
# with open("lvis_v1_train.json", "r") as f:
# a = json.load(f)
# c = a["categories"]
# for x in c:
# del x["name"]
# del x["instance_count"]
# del x["def"]
# del x["synonyms"]
# del x["frequency"]
# del x["synset"]
# LVIS_CATEGORY_IMAGE_COUNT = repr... |
65e2d21901a7cb45008829b2187c209fa25c3f02b610f84847ac7509085c9a6d | Python | 39,420 | 1,015 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
327c3480e5c92e03a7446388bca4cd0d48a063ab64123f43456f0ba00991e26b | Python | 39,510 | 890 | """
Created on 18/10/2023
@author: Marc Schneider
AG Neuroimaging and Neuroengineering of Experimental Stroke
Department of Neurology, University Hospital Cologne
This script automates the conversion from the raw bruker data format to the NIfTI
format for the whole dataset using brkraw. The raw
data needs to be store... |
3a4087d7f193b4e613835e98c97b2a12d05d675a3ce559d77405c6a3a1ac4dc5 | Python | 39,550 | 1,104 | """Reset AIDAmri modality folders using runtime-generated output manifests."""
from __future__ import annotations
import argparse
import os
import shutil
import sys
import tempfile
from pathlib import Path, PurePosixPath
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir)))
from co... |
9b75921b7dbc51f31615ebc0afeb5e0f41315c9f11f43569baf3a7aa747bfde3 | Python | 39,658 | 1,129 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
f8ba081b623ce32eada36c960d97094e557d78daf3f761c7eb12fd6bf55b8e23 | Python | 39,862 | 859 | import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import streamlit as st
import gc
from datetime import datetime
from nmj_master_dashboard import (
BTX_CLASS_EARLY_NMJ,
BTX_CLASS_MUSCLE,
BTX_CLASS_NEURON,
BTX_CLASS_ORPHANED,
DENSITY_COL_EARLY_NMJ,
DENSITY_COL_MUSC... |
9fd1d95e5b4acfaf80988d776f0a94531a93a012aacf96c5781c56719b4770fa | Python | 39,875 | 1,141 | from __future__ import annotations
from abc import ABC, abstractmethod
from itertools import permutations
import sys
import os
from collections import Counter
from concurrent.futures import ProcessPoolExecutor
from typing import (
Generic,
Hashable,
Iterator,
Mapping,
Optional,
Sequence,
Cal... |
52956a4cb6a084ab2d43cfae3be9b141aae47856b6c9a265d19f85e0869cbc90 | Python | 40,104 | 1,109 | # -*- coding: utf-8 -*-
"""neu_cnn_binary
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1iJFezLknVDomErI1A2ogWtHn2n2dqN-3
"""
!pip install tf-keras-vis
"""End-to-end deterministic CNN pipeline for binary frost vs non-frost image
classification with optiona... |
3ff8e5460fe811f8a8f6c6c25ab8f04ced12eb9a6f27b88fde1fc1cf8aabb09f | Python | 40,135 | 938 | """
motion_correction - Diffusion MRI Motion and Eddy Current Artifact Correction
Part of the micaflow processing pipeline for neuroimaging data.
This module corrects for subject motion and eddy current distortions in diffusion-weighted
images (DWI) by registering each volume to a reference B0 image. Subject m... |
37250f605cf02a02c67beccacded6720e992e404e3b61dfcc96776b547e34009 | Python | 40,412 | 1,251 | """AgentSet.py related tests."""
import copy
import pickle
from random import Random
import numpy as np
import pytest
from mesa.agent import Agent
from mesa.agentset import AgentSet, _HardKeyAgentSet
from mesa.model import Model
class AgentTest(Agent):
"""Agent class for testing."""
def get_unique_identif... |
460790379ec49e55e33743ddd8c9b1974557ffa476e61fecda5168fc561f8bc9 | Python | 40,549 | 918 | """Tests for `navis.ml` - machine-learning input helpers."""
import navis
import numpy as np
import pandas as pd
import pytest
@pytest.fixture
def skeleton():
return navis.example_neurons(1, kind="skeleton")
def _coords(n):
if isinstance(n, navis.Skeleton):
return n.nodes[["x", "y", "z"]].values
... |
bc545322d9031f8f29c4dd7c5920a0168972adcde40071caf7beb10f614106c3 | Python | 40,798 | 803 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2019-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
57d2e784875383041640fb7d47c71d16428c00dbcd4607ca43ae312c9e46d430 | Python | 41,088 | 958 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
d88ffcdca80fe818a8a8cc75a367cc9d28e094b66eeb02662ee837a85eb7e08d | Python | 41,289 | 833 | '''
Created on Oct 30, 2024
@author: voodoocode
'''
import numpy as np
import matplotlib
matplotlib.use("Qtagg")
import matplotlib.pyplot as plt
import misc.meta_reader # @UnresolvedImport
SUBJ_META_PATH = "/mnt/data/Professional/LMU/data/Beta-prevalence/beta_pictures/0_per_file_lfp_beta.txt"
PEAK_META_PATH = "/m... |
c5cb057fb9642966b4e64cde8fb69561fa56f098f7c291acc664ba4545d6b182 | Python | 41,371 | 970 |
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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-... |
07834241c19b2d9acd352f0315737bcf39266c9d157fa8d680ea56a306fc6a30 | Python | 41,579 | 973 | import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.ticker as mticker
from matplotlib.colors import TwoSlopeNorm
def plot_capacities(capacity_train, capacity_test, model="10"):
plt.figure()
degrees = [1, 2, 3, 4]
ax = sns.heatmap(capacity_tra... |
b115b62181697d14e347d308f717236fbeefc097a61b66debc6b5fbfccb7a98d | Python | 41,912 | 1,158 | """
Modular prediction pipelines for molecular property prediction.
Provides configurable, multi-step prediction workflows that chain
classification and regression models. Supports any scalar molecular
property: phase classification, transition temperatures, melting points,
birefringence, dielectric anisotropy, etc.
... |
ac43a05c902b3e203ded973eead69788d7b4bc100777cbddc3856f4f84586c12 | Python | 41,957 | 1,255 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
12b0a22b53c3a1a59e37431e9e6b4ce7ff12820636d41075b61dd0d87956e2e6 | Python | 41,978 | 740 | """ Crete network model """
import numpy as np
import matplotlib.pyplot as plt
import nest
from utils import netGen_utils
import PARAMETERS
net_params = getattr(PARAMETERS, "network_params")
class BaseNetwork:
""" Superclass for all network models. """
def __init__(self, Ne, Ni, conn_prob, use_fac, dep2fac_... |
40c97431ea3253386e5b559d3d54ccfc0e5aba6f1f2a24d9fbd1c239c47a3f8f | Python | 41,989 | 978 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Open Race Competition Framework
This module implements the Open Race Game algorithm where optimization strategies
compete to find the global maximum of a black box function with a limited number
of function evaluations in continuous space.
Algorithm Implementation:
1... |
2f954257e1797f71e6f9d36a74f347601f7cdf8f6897b6c6bc047e202913965a | Python | 42,115 | 913 | # Copyright (c) Facebook, Inc. and its affiliates.
import copy
import math
from typing import List
import torch
import torch.nn.functional as F
from fvcore.nn import sigmoid_focal_loss_star_jit, smooth_l1_loss
from torch import nn
from detectron2.layers import ShapeSpec, batched_nms, cat, paste_masks_in_image
from det... |
b65b8c7dc6d9fe68701fa02867214ea4188cc825e4622845a8f49bf453b9a3c6 | Python | 42,140 | 990 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
b237282621519ad37bf33a51caeedda3b0b6a8d9bd424e557112e5e37eb7c92d | Python | 42,420 | 1,127 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
f2e29548f044e641ece158d3556d5516bd95e86abcab26cf6d825e114fcec5d1 | Python | 42,639 | 939 | #!/usr/bin/env python
# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
c73766ab9e60c42150b10536ac4a0ef232a88b952db21fb07b9534de658c0f4f | Python | 42,657 | 975 | # AUTOGENERATED! DO NOT EDIT! File to edit: 01_rnamap.ipynb (unless otherwise specified).
__all__ = ['bed2splicesiteinfo', 'MapBase', 'RNAmap', 'reshape_into_bins']
# Cell
import numpy
import scipy
from matplotlib import pyplot
import seaborn
import pandas as pd
import pyfastx
from tqdm import tqdm
import pyBigWig
fr... |
636ec71c4a063ecd5c5ac9f03c54653e1f0a437aef5f93d0772c40cb627e70f9 | Python | 42,734 | 1,102 | ############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Tests for universal barcode extraction.
Tests the univers... |
63ec7daf96f76c043f98074336367d55b55922204c77787fcffa2d2d27b66600 | Python | 42,946 | 792 | import os
import json
import numpy as np
import sys
import scanpy as sc
import scvelo as scv
import anndata as ad
import torch
from torch.nn.parameter import Parameter
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import scipy
from sklearn.neighbors import NearestNeighbors
from sklearn.metrics.pa... |
2afae12521bcb3f0726dffab193242b77b70ed86a59104ff6d50ffec8f1a0add | Python | 42,978 | 1,174 | from statsmodels.stats.multitest import multipletests
from scipy.stats import sem, mannwhitneyu
from scipy.stats import mannwhitneyu
from pop_coupling.shared_plotting import apply_global_style, PALETTE
import seaborn as sns
from collections import defaultdict
import traceback
import pop_coupling.fig_utils as fig... |
07e9a5182fd99a4019552b521f6de39d8abd9acd84d0e64eb7dbbd4be6d6c03b | Python | 43,559 | 1,176 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from torchvision import transforms
from torchvision.transforms import functional as TF
from PIL import Image, ImageEnhance
from tqdm import tqdm
from torch.utils.data import Dataset, DataLoader
import random
import matplotli... |
a67bf3dbe79bf0fa685c4dc4d332dcbfbc7b71f4cd11dc8d42c18ed7f6f12dc9 | Python | 44,073 | 1,258 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
db992413de089b320dfd069f99e4adcadfc86c50d310f986cf85ab5ad9d73fb4 | Python | 44,290 | 979 | #!/usr/bin/env python
# Copyright 2016-2024 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
1c2042de102b6b86cbba58c75a7924bd29d05775cb653589a9f49cabf128eadb | Python | 44,414 | 1,167 | """Tests for the CMTK/elastix transform backends.
navis runs CMTK and elastix point transforms through navis-fastcore's in-process
Rust implementation. The deprecated `"binary"` backend shells out to the external
binaries (`streamxform`, `transformix`) instead, and is kept until 3.0.
Two kinds of test live here:
* B... |
eb0e63cc9b017946d3d254c17eab2000d7d198f754c6226f3c0e3b12ec33808d | Python | 44,492 | 1,182 | """
bias_correction - N4 Bias Field Correction for MRI Data
Part of the micaflow processing pipeline for neuroimaging data.
This module corrects intensity non-uniformity (bias field) in MR images using the
N4ITK algorithm from Advanced Normalization Tools (ANTs). Bias field artifacts appear
as smooth, spatia... |
93c1bf0b17c3ce7ac19a7cb6aec11cd1c1db658f7e13228eb210243ba664c9a5 | Python | 44,556 | 1,160 | """AgentSet related classes.
Core Objects: AgentSet, AbstractAgentSet, _HardKeyAgentSet, GroupBy.
"""
# Postpone annotation evaluation to avoid NameError from forward references (PEP 563). Remove once Python 3.14+ is required.
from __future__ import annotations
import contextlib
import copy
import itertools
import m... |
c1d2e361bb0688b76052bbb1df223c0ce7a067e0595dfed9a7aa5339fa058feb | Python | 44,680 | 1,057 | #!/usr/bin/env python3
"""
Ultimate Proteomics Batch Correction Pipeline
=============================================
A state-of-the-art batch correction pipeline for proteomics data combining:
- Advanced missing value imputation
- Ultra-robust ComBat with hierarchical modeling
- Next-generation adaptive BBKNN
- AI-d... |
77431766bd1ea071c9a856eeb980dd7f265947dec139a50f36b2eff6a2aedd1a | Python | 44,709 | 913 | import importlib # <--- ADD THIS
import gzip
import os
from pathlib import Path
import sys
import numpy as np
import torch.backends.cudnn as cudnn
import yaml
import torch
import torch.nn as nn
import nibabel as nib
import glob
# Ensure main_hdf5 is accessible if instantiate_from_config is used elsewhere,
... |
f4f0e518fa3c6cdc7472dee0d3b49a72c1ecc110c436f28974e329a1b4793412 | Python | 44,727 | 830 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
e167f22345aadd4246b48dbc9527755cf6b1afb797019edacc0f552a45581e3b | Python | 44,809 | 1,251 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
0c0e183bdaf1e84cb30a304abb1b07435ddfd88927b41742c08990606d0f61ed | Python | 44,974 | 1,157 | # -*- coding: utf-8 -*-
"""neu_mobile_binary
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1bI5kKH1HzPCR-tVNKocZjQv9ztwnp9rR
Transfer-learning MobileNetV2 pipeline for binary frost vs non-frost
classification, with detailed error analysis and custom Score-C... |
df1a9e304df16e53e43fea8ef739664dc756962c74583c2681f3242cc9e815af | Python | 45,189 | 1,051 |
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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-... |
b5a658952bfe45f3d9ca5698fef521bb6276df59b909b2ac193889c5c907d361 | Python | 45,273 | 1,195 | import pandas as pd
data = pd.read_table('L:/promec/TIMSTOF/LARS/2021/November/SIGRID/combined/txtNoNQd/proteinGroupsWT_CosLS.txt')
data.head(2)
data.columns
data["N: q-value"].hist()
data["N: Phase"].hist()
data['row_num'] = data.reset_index().index
data['Name']=data['T: Protein IDs']+';'+data['T: Gene names']+';'+dat... |
860057f28a966dc1ad7dc8ffb68ef6273bcbbb93b0faa30e5d90d53bd2bb1153 | Python | 45,534 | 1,250 | """
If you use this code, please cite one of the SynthSeg papers:
https://github.com/BBillot/SynthSeg/blob/master/bibtex.bib
Copyright 2020 Benjamin Billot
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 Lice... |
15231402f77e24f32446fc1bacf363a6d59cc82cec03b0eae5c300c6ec82ba4e | Python | 45,922 | 1,175 | import math
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.axes import Axes
from matplotlib.animation import FuncAnimation, PillowWriter
from pathlib import Path
from . import color
from ..figure.utils import plot_ellipse, plot_arrow, plot_contours
from ..fig_utils import erase_al... |
5affba74b17b252582fab60162f4fe2ce0aa97084f45c2496a8b82cb6fb463de | Python | 45,990 | 1,762 | import sys
from functools import partial
from pathlib import Path
import pandas as pd
from scipy.io import loadmat
import scipy.signal
import numpy as np
from sklearn.cluster import SpectralClustering
from sklearn.metrics import silhouette_score
from scipy.stats import circmean
from scipy.ndimage import gaussian_filte... |
594e4f58c549409538b43e8cbba6175f3b171051fc56e7606f3654b5f5131d10 | Python | 46,846 | 660 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
from collections import namedtuple
import pytest
import gffu... |
327eb88c79abaf1190aa23e1916c9fd68879b5414b697178d4d1bef794165153 | Python | 47,209 | 1,531 | """Tests for mesa.experimental.actions."""
# ruff: noqa: D101, D102, D103, D107
import logging
import pytest
from mesa import Agent, Model
from mesa.experimental.actions import Action, ActionState, HasActions
# --- Helpers ---
class ActionAgent(HasActions, Agent):
"""Agent with action support, as models combi... |
02c5bc7b5a6905d4dcad16f37e2e2c596b832f2610d67e5930e6acd0c19867b0 | Python | 47,272 | 1,280 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium AFE Protocol base classes
===============================================
Base classes for the equilibrium OpenMM absolute free energy ProtocolUnits.
Thist mostly impl... |
13ec524d8f73c7579a1c7d575d0f94c0ce725dc53e6159666a7635539689c7a7 | Python | 47,511 | 1,301 | #!/usr/bin/env python
#
# Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
#
# pylint: disable=not-an-iterable
from __future__ import annotations
import json
import math
import pickle
from collections import OrderedDict, defaultdict
from collections.abc import Callable, Generator
from typing import Any, Nam... |
151d0ad59df280abbcdc5a57be9278865448c09ff1da0308a1582b13274ec328 | Python | 47,565 | 1,402 | import copy
import glob
import json
import math
import os
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
import torch
import torch.nn.functional as F
import tqdm
from Bio.PDB import PDBParser
from Bio.PDB.Polypeptide import is_aa
fro... |
6ca28c3b7d3dd730ad04b6a68f4e8283e178a2e9b97467b05e7c042fb8b5b6bd | Python | 47,982 | 1,237 | #!/usr/bin/env python
#
# Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
#
"""Here, you could find everything shown in the summary tab."""
from __future__ import annotations
import os.path
from typing import TYPE_CHECKING
import cellranger.constants as cr_constants
import cellranger.molecule_counter as... |
2a3e690c937f7e9ae69e001f59a63fc497abb6966869900cbd1fa508bf06ccf8 | Python | 48,110 | 905 | """
s-opNMF (stochastic opNMF) implemented in python
* 2 Methods of sampling is available for stochastic optimization
* Uniform Sampling
* Uniform Sampling
* without replacement
* DPP Sampling
* with Gaussian Kernel
* with Linear Kernel
"""
## Module Imports
import sys #check p... |
4db4e353f4dbe7f4742d5f14e32fa86eff7df7df121b90baae96beed8d4e9d52 | Python | 48,204 | 1,250 | from Bio import SeqIO, AlignIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from glob import glob
import logging
import math
import multiprocessing as mp
import numpy as np
import os
import random
import re
import subprocess
from scipy.stats import skewnorm
import pandas as pd
from pathlib import Path
im... |
78fe28fbaad2a6c23899d49b3dae0c68b919ab8608f925a01fd01ce0b6457002 | Python | 48,388 | 1,154 | from .unionfind import UnionFind
import sys
from tqdm.autonotebook import tqdm
from .pipelines_utils import save_plots, compute_scores_table, compute_pvalues_table
from .stacked_generalization import stacked_multi_omic
from .metrics import jaccard_matrix
from .stabl import save_stabl_results
from .preprocessing import ... |
75ba08e4ae90baed603a48350ff95b9b4b6a8040977e47dd191a9ac01c6f9769 | Python | 48,480 | 1,057 | """
This file contains all the utilities used in that project. They are classified in 5 categories:
1- loading/saving functions:
-load_volume
-save_volume
-get_volume_info
-get_list_labels
-load_array_if_path
-write_pickle
-read_pickle
-write_model_summary
2- reformatting functions
-... |
73fad73a99587e94781510f83d4208610e90bad2eaa7d2eb13cda241893aef38 | Python | 48,650 | 1,350 | import numpy as np
import pandas
import matplotlib.pyplot as plt
from matplotlib import rcParams
import scipy
from scipy.optimize import basinhopping, minimize
import argparse
import os
from utils import general
print(scipy.__version__)
rcParams['text.usetex'] = True
rcParams['pgf.texsystem'] = 'pdflatex'
rcParams['t... |
a1e2e80f3870fee20b42df462680fa744f8838b959f95fb15931e0a3bf5dfc42 | Python | 49,254 | 1,364 | # -*- coding: utf-8 -*-
"""
Created on Wed Apr 6 21:27:55 2022
@author: Joseph Vermeil
MainPlotter_##.py - Script to plot graphs.
Please replace the "_NewUser" in the name of the file by "_##",
a suffix corresponding to the user's name (ex: JV for Joseph Vermeil)
Joseph Vermeil, 2022
This program is free software:... |
e289787385d95abb27c10264efd9b42653a176f64444b305d7ef904fd96ec16e | Python | 49,739 | 1,118 | """RAVEN 3D autoencoder training entry point.
"""
import argparse, os, sys, datetime, glob, importlib
from omegaconf import OmegaConf
import numpy as np
from PIL import Image
import torch
import torchvision
from torch.utils.data import DataLoader, Dataset
import pytorch_lightning as pl
from pytorch_lightning import se... |
c42fec0b3847feb8cf4537e0cf2a7a058c290c33d453eb26ea85290deabc25a4 | Python | 49,746 | 1,599 | """ Created on Mon Nov 6 14:41:00 2023
@author: dcupolillo """
from __future__ import annotations
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
import matplotlib.colors as colors
import matplotlib.patches as patches
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkit... |
5be4db7a42183103d7648effc0fd3ff4d5fe35a4b0b9f07d864c569c39a25bd2 | Python | 49,756 | 1,115 | import argparse, os, sys, datetime, glob, importlib
from omegaconf import OmegaConf
import numpy as np
from PIL import Image
import torch
import torchvision
from torch.utils.data import DataLoader, Dataset
import pytorch_lightning as pl
from pytorch_lightning import seed_everything, Trainer
from pytorch_lightning.callb... |
4a43649c4f4a30aa4b51832985c431d33443989ab94d767b4d0e87c92714c438 | Python | 49,821 | 1,376 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium SepTop Protocol base classes
==================================================
Base classes for the equilibrium OpenMM SepTop free energy ProtocolUnits.
Thist mostly ... |
a243cd56cae3c586de37b42e848c6c34ab71bd36e01a763289606f7aff29b8ba | Python | 49,987 | 1,386 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 1 11:21:02 2022
@authors: Joseph Vermeil, Anumita Jawahar
UtilityFunctions.py - contains all kind of small functions used by CortExplore programs,
to be imported with "import UtilityFunctions as ufun" and call with "cp.my_function".
Joseph Vermeil, Anumita Jawahar, 2022... |
d411f31bbde137e4625711b3307cb951eb2acd772049f6d3c8f9f610486ceda2 | Python | 50,162 | 1,129 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
ba1232aa33118d514e0a04054c3268eb08127678fc10252fee1e8769ea751753 | Python | 50,377 | 1,281 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
103fadd103ed3765be035ceb71d86b7a9601362a3f96d864d34b47dafc230d4e | Python | 50,927 | 938 | import os
import json
import numpy as np
import sys
import scanpy as sc
import scvelo as scv
import anndata as ad
import torch
from torch.nn.parameter import Parameter
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import scipy
from sklearn.neighbors import NearestNeighbors
from sklearn.metrics.pa... |
df7d97042d173f1682456d86f4bddbfe9a7f6cb10f41e8b1e16b128892d514ae | Python | 50,935 | 1,280 | # -*- coding: utf-8 -*-
"""neu_resnet_binary
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1OfI0i2Ub4YgAlFT8z2dFOBmbJAbPa2S7
Transfer-learning ResNet50 pipeline for binary frost vs non-frost classification,
with cross-validation, detailed misclassification ... |
42085be96d685cff2a50997ae282ec7fca90fdd194cb3fd19ccb57a1f6a1a70b | Python | 50,952 | 939 | import os
import json
import numpy as np
import sys
import scanpy as sc
import scvelo as scv
import anndata as ad
import torch
from torch.nn.parameter import Parameter
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import scipy
from sklearn.neighbors import NearestNeighbors
from sklearn.metrics.pa... |
5433a22d9e07da4bb73687ff25b6a08fa4375e3262e42261e3ee1624f319ff60 | Python | 51,433 | 1,114 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
1c236685f2b114fd43789b2b4c954535bcd74d47c9e9e9021cc81745409029f9 | Python | 51,599 | 1,334 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM Equilibrium Binding AFE Protocol --- :mod:`openfe.protocols.openmm_afe.equil_binding_afe_method`
====================================================================================... |
14ccb034756a16ee74febbf4347f7bfcf8e80208c7a9d3b896e25ce48f550e79 | Python | 51,980 | 1,551 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import collections
import copy
import csv
import math
import random
import re
import sys
from collections.abc import Sequence
from typing import Any # pylint: disable=unused-import
import numpy ... |
1dd628efb58102c4d5c08cfdef674c192f9da3b09862ec21fc8dd0d7319006f6 | Python | 52,044 | 1,289 | # Copyright (c) Facebook, Inc. and its affiliates.
import colorsys
import logging
import math
import numpy as np
from enum import Enum, unique
import cv2
import matplotlib as mpl
import matplotlib.colors as mplc
import matplotlib.figure as mplfigure
import pycocotools.mask as mask_util
import torch
from matplotlib.back... |
145e1d3cfa935f0b8d65c1700e50c90885dfe878c717bb8f23e4aa5e648b6bcf | Python | 52,313 | 1,499 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import itertools
import json
import math
import pathlib
from unittest import mock
import gufe
import mdtraj as md
import numpy as np
import numpy.typing as npt
import openmm
import openmm.ap... |
0ca3640ef0ef9bce73cbb875864ce455ab2f5d53522684405b042750ba715d3c | Python | 52,375 | 1,323 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Relative Free Energy methods using OpenMM and OpenMMTools in a
Perses-like manner.
This module implements the necessary methodology toolking to run calculate a
ligand relative... |
bd8fabbc631da83ac9ba50c87cdfbd0e02b18743c5241e898ca0ce7abf6ffaaa | Python | 52,408 | 1,466 | import os
from pathlib import Path
from warnings import warn
import sys
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from knockpy.knockoffs import GaussianSampler
from sklearn.base import BaseEstimator, clone
from sklearn.feature_selection import SelectorM... |
a38a9b9faca263069a6ebb1b79e7433a2f022dd3e27e2a7faddaa49015c480ca | Python | 52,862 | 1,098 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
0e4f88decc8a544157d41a7a909046c83d0496a328c8fc8ad1f83a02351175be | Python | 53,042 | 1,343 | # -*- coding: utf-8 -*-
"""neu_mobile_multiclass
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1N9jVg6AtP9qvZb5heee1C9fX6szDN8vE
Transfer-learning MobileNetV2 multiclass pipeline for microstructure image
classification, with stratified evaluation, per-class... |
eb8a3f48f24d1a2b459a2f83a629d87f959308cf46ca2c9fd307d332c72de7ea | Python | 53,307 | 1,058 | '''
Created on Oct 28, 2024
@author: voodoocode
'''
import os
import finnpy.file_io.data_manager as dm
import numpy as np
import matplotlib
matplotlib.use("Qtagg")
import matplotlib.pyplot as plt
import scipy.signal
import functools
import PyQt6.QtWidgets
import multiprocessing
import pyqtgraph
pyqtgraph.setConfi... |
a8283b38b32388671fe9e1d31efd381c93c35e487af007a4306208a433a40f9b | Python | 54,161 | 1,277 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 19 17:09:52 2022
@author: walte
"""
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Li... |
467a557702ef786de6ea4afff4dd42bc3dc6b690e20c0ef9d8e78583f15e9e99 | Python | 54,924 | 1,664 | import sys
from functools import partial
from pathlib import Path
import pandas as pd
from scipy.io import loadmat
import scipy.signal
import numpy as np
from sklearn.cluster import SpectralClustering
from sklearn.metrics import silhouette_score
from scipy.stats import circmean
from scipy.ndimage import gaussian_filte... |
20ec83f0a5fb8a22e8ea8168ec341c948d08c2ef81ffc3fabde350eebca89847 | Python | 54,967 | 1,549 | """XGBoost training routines: k-fold CV, Optuna search, and final training.
Mirrors the structure of the GNN training routines but uses XGBoost's
native training API instead of PyTorch's epoch-based training loop.
Fingerprint type is included as a categorical hyperparameter in the
Optuna search for joint fingerprint-h... |
1e65f1c7cc50c66cd3443fda02f4ae0860c624be1be1e2c30c22cf2b0dca272c | Python | 55,467 | 1,317 | # Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
from __future__ import annotations
import enum
import itertools
from collections import Counter
from collections.abc import Collection, Container, Iterable, Mapping
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any, NamedTuple
import m... |
1a3e7b460ba3aa347323d806c3271a5233fbfb23f7202c292427bc94c2eb543c | Python | 55,774 | 1,503 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# 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... |
4884156f19d4e10675553d3d71daed1770d053093349c84a4407ffd60f6c9a4f | Python | 56,119 | 1,511 | """Tests for links between representations (`navis.core.schema`).
A link is an array aligned to one axis whose values name elements of another,
so the tests come in three groups:
- that a selection *carries* it - the mesh/skeleton cascade, which is what stops
a masked mesh from throwing its skeleton away and re-ske... |
0350a1cdf081a71380a9cde7518088106239c912880f32ee2966413bb790c534 | Python | 56,984 | 1,309 | # Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
# This is a modified version of cocoeval.py where we also have the densepose evaluation.
# pyre-unsafe
__author__ = "tsung... |
4e5b8c87eef2c130fa0bd016049f996bea21a53304136730da350ce38ccbbd0c | Python | 57,094 | 1,660 | """Test cell spaces."""
import copy
import pickle
import random
import random as stdlib_random
import sys
import networkx as nx
import numpy as np
import pytest
from mesa import Model
from mesa.discrete_space import (
Cell,
CellAgent,
CellCollection,
FixedAgent,
Grid2DMovingAgent,
HexGrid,
... |
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