sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4d231bc83d433b92b1eafd34d41e60dbc52067e32795f7decbe38d59b3fc0942 | Python | 26,533 | 685 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("../dpeb final check points/robustness results/alphafold_feat_gat_lr_1e-3_checkpoint_inference_output", "w")
import dgl
import dgl.function ... |
f7d9bcf3eae981b303285220ae84d69f4c5d4591345f28f2f0220da0190953a2 | Python | 26,535 | 684 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("../dpeb final check points/robustness results/bioembed_feat_gat_lr_1e-4_checkpoint_r1_inference_output", "w")
import dgl
import dgl.functio... |
2dd667fbb2e1db53dac54d3529d47aa54cce807a4a616eddecd8ff0f1e8bc482 | Python | 26,544 | 535 | import importlib.resources
import numpy as np
import pytest
import torch
from numpy.testing import assert_allclose
from openff.units import unit
from openff.toolkit.topology import Molecule
from openff.nagl.nn.gcn._sage import SAGEConvStack
from openff.nagl.nn._containers import ConvolutionModule, ReadoutModule
from ... |
32a8664725267330595f77289777da77a1b3f9f08cbd8257c16cfbbab8d52b16 | Python | 26,581 | 737 | """ Graph tools. """
import copy
import itertools
import numpy as np
import pandas as pd
import networkx as nx
import matplotlib.pyplot as plt
import neuprint
from neuprint import Client
import Figure4_neurons as neurons
MY_TOKEN = 'eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJlbWFpbCI6InBnaXplbW96ZGlsQGdtYWlsLmNvbSIsI... |
eefcd1f3c1c816384b4c315ff58f61c995641f9f126c4a72bfb394f6d3c57723 | Python | 26,602 | 746 | '''
Utitlity funcitons for analsing children's motion patterns with the Jupyter
noteboks 'Matrix_Extraction.ipynb' and 'Motion_Patterns.ipynb'
'''
import os
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
import scipy.io
import glob
from transforms3d.affines import decompose
from transforms3d... |
054c6306ed2baaf80c6bec89bad269ec74a563a0ae2e0ae9bad3ae0f7f47dc54 | Python | 26,675 | 729 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="3"
os.environ["DGLBACKEND"] = "pytorch"
import sys
concat_type= "_Bio_ESM_Prot_" # Alpha_Prot_Bio_ESM
models_name = "SAGE_GAT_GCN_GTN_GIN" # SAGE_GAT_GCN_GTN_GIN
print("Running Combination: ", concat_type)
... |
5275d4b23fbbb28358313581e22dad28b1b9e6f6a693d81d61531e7ad54794a3 | Python | 26,707 | 609 | import fnmatch
import logging
from collections import defaultdict
from typing import Dict, List, Optional, Tuple, Union, cast
from multiqc import Plot, config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.modules.qualimap.QM_BamQC import genome_fraction_helptext
from multiqc.plot... |
c73fda7e2212b8e0450aa2824e591de1c6b5f754c38f2cdb2f45c1fca540bd9b | Python | 26,785 | 617 | import os
import glob
import threading
import tkinter as tk
from tkinter import ttk, filedialog, messagebox
import mne
import torch
import torch.nn.functional as F
import numpy as np
import matplotlib
matplotlib.use('TkAgg') # Use TkAgg backend
import matplotlib.pyplot as plt
from matplotlib.backends.backend_tkagg impo... |
30247987abc6540a40c433cc6dec8af40ee2a0da25f17f99075819d294ca1441 | Python | 26,817 | 697 | # Imports
from torch.nn.functional import normalize
import os
# import os
os.environ["CUDA_VISIBLE_DEVICES"]="7"
os.environ["DGLBACKEND"] = "pytorch"
import sys
sys.stdout = open("../dpeb final check points/robustness results/protvec_feat_gin_lr_1e-4_checkpoint_run2_inference_output", "w")
import dgl
import dgl.functi... |
5c27b19180db9b3e07f9069340df4e79de0d1c6a1bea1e5463b349bddfd73b8e | Python | 26,823 | 646 | import sys
#from PyQt4.QtWidgets import *
#from PyQt4.QtCore import *
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtWidgets, QtGui
import numpy as np
import cv2
import math
import os
VERSION = (0, 2, 0)
class ControlWindow(QtWidgets.QWidget):
def __init__(self):
QtWidgets.QWidget.__init__(self... |
e8dbe8e30419b3645a417dd36c1de17bd5f40c38682f6e6d296642097e573244 | Python | 26,872 | 704 | """
Unit tests for Adaptive PSO implementation.
Tests cover:
- Basic optimization on benchmark functions
- Opposition-based learning
- Diversity-adaptive parameters
- Dynamic multi-swarm
- Intelligent restart
- Reproducibility
- Edge cases and error handling
- Performance comparisons
Run with: pytest test_adaptive_ps... |
e6768009b1ac17ae044f6cb403e083ff754aa5fbd1d330fe071eb55fbd777dc0 | Python | 26,892 | 562 |
# -*- coding: utf-8 -*-
import glob, os, json
import numpy as np
from scipy.io import loadmat
import pandas as pd
import mat73
import nibabel as nib
import scipy
#statistics
from statistics import mean, stdev
from scipy.ndimage import center_of_mass,label,find_objects
# plotting
import matplotlib.pyplot as plt
impor... |
9baa069a40619060279f69d5e83e2113bf12099e961272bdaca759077b970487 | Python | 26,897 | 916 | """Deprecated from html5lib 1.1.
See `here <https://github.com/html5lib/html5lib-python/issues/443>`_ for
information about its deprecation; `Bleach <https://github.com/mozilla/bleach>`_
is recommended as a replacement. Please let us know in the aforementioned issue
if Bleach is unsuitable for your needs.
"""
from __... |
c726a4d3efc57fa764926534cd0d984107473286c3405b02dbf7bee05b9bf09a | Python | 26,897 | 757 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
CORRELATION BETWEEN EEG AND DNN PEAK LATENCIES
This script creates plots for the encoding analyses.
@author: Agnessa Karapetian
"""
# -----------------------------------------------------------------------------
# STEP 1: Import modules & Define Variables
# --------... |
0ac3bbe9fcbaed38cb55051bd493a87eaef44eb9b5376e38ebdefb050915599f | Python | 26,919 | 727 | """Model factory for creating different types of models."""
import contextlib
import logging
import os
import sys
from abc import ABC, abstractmethod
from typing import Any
import numpy as np
import xgboost as xgb
from sklearn.ensemble import RandomForestClassifier
from sklearn.linear_model import LogisticRegression
... |
3375527fa1c52b7e4084c6b617a919d13babde8bb7c18d70759019983687edf1 | Python | 26,967 | 509 | import logging
import math
import os
import traceback
import itertools
import multiprocessing
from copy import deepcopy
import pandas as pd
import nibabel as nib
import numpy as np
from typing import List, Tuple
# from medpy.metric.binary import hd95, volume_correlation, assd, ravd, obj_assd
from sklearn.metrics import... |
5b43c17fe4a4d4c14a12f767fd62d4ca62afd0f91ee0708c91064b9fe4fa1769 | Python | 27,033 | 716 | import numpy as np
from scipy.cluster import hierarchy
from scipy.spatial import distance
from scipy import stats
import seaborn as sns
import matplotlib.pyplot as plt
from matplotlib.legend_handler import HandlerBase
from anndata import AnnData
from upsetplot import plot as UpSet
import networkx as nx
import sca... |
a6d0c5a1059619f432a6f9a8b37cf5f3a2f34cd62da7cb02ee0c6b5e684a2ca3 | Python | 27,041 | 731 | """AVITI Run Watcher for MosaiCatcher pipeline.
Monitors a sequencing directory for new AVITI runs, detects completion via
dual-snapshot stability, reorganises FASTQs into pipeline-compatible structure,
and launches MosaiCatcher via the Snakemake v9 Python API.
Usage:
# Continuous watcher (in screen/tmux):
py... |
e33d07985db05a6cba38ecaa82d14c29f77f1de66581605921252b7023367aff | Python | 27,090 | 922 | import time
from pathlib import Path
import pickle
import pandas as pd
import numpy as np
import h5py
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
from scipy.signal import savgol_filter
import networkx as nx
from mycolorpy import colorlist as mcp
# Dictionary of colors
COLORS = {
"orange":... |
c4f2c40304b9d9fa983a3a45e0523c0f3549a1687c54f56c4317552619f8efb1 | Python | 27,095 | 720 | import numpy as np
from src.microcircuit import *
#import time
import logging
import warnings
import matplotlib
import matplotlib.pyplot as plt
from matplotlib.pyplot import cm
import matplotlib.gridspec as gridspec
from matplotlib.ticker import FormatStrFormatter
try:
plt.style.use('matplotlib_style.mplstyle')
excep... |
9e17daceead71911f5d29b989caae227a7f86333fbba41fd7fe43a3f1cf7f8ce | Python | 27,116 | 724 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 22 23:43:58 2026
@author: saiful
"""
# Imports
from torch.nn.functional import normalize
import os
import sys
os.environ["DGLBACKEND"] = "pytorch"
#gct
os.environ["CUDA_VISIBLE_DEVICES"]="6"
concat_type= "Bio_Prot_" # Alpha_Prot_Bio_ESM
checkpoin... |
685bd941f3eb32b1c36fa8e36e6ad5972bc3c4c21e5f765c64a490bd8e9cd0a2 | Python | 27,135 | 740 | import errno
import logging
import operator
import os
import shutil
import site
from optparse import SUPPRESS_HELP, Values
from typing import Iterable, List, Optional
from pip._vendor.packaging.utils import canonicalize_name
from pip._internal.cache import WheelCache
from pip._internal.cli import cmdoptions
from pip.... |
bb977c225a5b5ee642c12ea78df942c9b1bc1f7b25a3e9763f99623a8ce841d0 | Python | 27,141 | 704 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
90f322b76085c43d4c8c6cf78ea3b510230c5d8d230e461338a493c3dfa5c6de | Python | 27,145 | 775 | """Set-theoretic operations on geometry objects."""
import warnings
import numpy as np
from shapely import Geometry, GeometryType, lib
from shapely.decorators import (
deprecate_positional,
requires_geos,
)
__all__ = [
"coverage_union",
"coverage_union_all",
"difference",
"disjoint_subset_un... |
b28285d95ed122ce4f46c266196de9bf4be5e51d7523d0d728acfaaf51ba8d53 | Python | 27,244 | 579 | import pandas as pd
import numpy as np
import glob, os, yaml, itertools, subprocess, sys, argparse, shutil
import Bio.SeqUtils
import Bio.Data
from Bio import SeqIO
from Bio.Seq import Seq
import warnings, pickle
warnings.filterwarnings("ignore")
data_utils_dir = "./data_processing/data_utils"
# load all utils funct... |
6aea8dd20aad7602adde06ff34a89718ebc9df258554d62a6a800c7e0e99f0e1 | Python | 27,274 | 723 | # Copyright 2022 Google LLC.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
d4e9869f4cb0f2a6615fec7c3bd304f186522e08b62e96e9bdccfaf19d577899 | Python | 27,279 | 738 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
_____ _______ _______ ____ _ _
/ ____|__ __|/\|__ __| | _ \ | | (_)
| | | | / \ | | ______ | |_) | ___ ___ ___| |_ _ _ __ __ _
| | | | / /\ \ | | ... |
638d50ced23c97285047bd307459dbabc100ac4a22e6d4029aabdbfb604114bc | Python | 27,363 | 786 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Atika Syeda.
"""
import os
import sys
import time
import numpy as np
import torch
from scipy.interpolate import interp1d
from scipy.linalg import eigh
from scipy.ndimage import gaussian_filter1d
from scipy.stats import zscore
from skl... |
059d5d87a0d3546b3e336be9cd5455f0adc2d3e4c77839028a816251f4c3e7a3 | Python | 27,367 | 588 | #!/usr/bin/env python3
import argparse
import os
import sys
import shutil
import json
import pickle
from multiprocessing import Pool, cpu_count
from scipy.spatial.distance import cdist
import numpy as np
import sqlite3
import subprocess
import timeit
import tempfile
import yaml
import logging
from math import cos, si... |
8a50dca714b44bd55d34c1118b9ef9c4ff39b5e0403281bc59ea63302e5949c7 | Python | 27,382 | 896 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
fdeef970a5c94f0fdc6d42107a4d03cf6274623a65615affb1e02b9fd5157c59 | Python | 27,396 | 719 | # This code is in parts based on TopologyProposal in perses
# (https://github.com/choderalab/perses)
# The eventual goal is to move this to the OpenFE alchemical topology
# building toolsets.
# LICENSE: MIT
from copy import deepcopy
import itertools
import logging
from typing import Union, Optional
import warnings
im... |
76961240d0e331b0dfcf95fef78e12ad70a9f222e44af9319d2b0dfdff108715 | Python | 27,422 | 643 | #
# Xmaze.py
#
# Tool for analyzing rat movement in an elevated plus maze experiment.
#
# Originally written by Abel Torres-Espin.
#
# Updates for Python 3 and packaging by Callum Doolin.
#
import sys
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtWidgets, QtGui
import numpy as np
import cv2
import math
... |
49ef938c6701196d04155567bbc13fdb1b0710313f35dae89ad08c8aae7fa98e | Python | 27,423 | 777 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import sys
from math import sqrt
from unittest import mock
import gufe
import mdtraj as mdt
import numpy as np
import pytest
from numpy.testing import assert_allclose
from openff.units impor... |
2ea8f29af9878d57f759e0023609433c87ff5ee387b7cd66b0b94c792ddde0bb | Python | 27,456 | 585 | #!/usr/bin/env python3
"""
Integrate Gene Body MeCP2 Binding with RNA-seq Data
This script integrates the enhanced gene body MeCP2 binding analysis results
with RNA-seq differential expression data to understand the relationship between
MeCP2 binding patterns in gene bodies and gene expression changes.
Features:
- In... |
a0e336ac3ee5fd28250113550e68999fcbba0c07e2757445ff2139412df6f01e | Python | 27,482 | 677 | """distutils.command.install
Implements the Distutils 'install' command."""
import sys
import os
from distutils import log
from distutils.core import Command
from distutils.debug import DEBUG
from distutils.sysconfig import get_config_vars
from distutils.errors import DistutilsPlatformError
from distutils.file_util ... |
1d9f9f2a964f0a9acc9d3f39572258fb773a5a8337d77923e7afddf8af65b7d0 | Python | 27,505 | 643 | import pandas as pd
import numpy as np
import scanpy as sc
import anndata as ad
import scipy.sparse
import os
from sklearn.metrics import pairwise_distances
from sklearn.metrics import silhouette_score
from sklearn.metrics.cluster import adjusted_rand_score
from sklearn.metrics.cluster import normalized_mutual_info_sco... |
c8bf96a552c4b65445100dd94d8d519d09e29546aaf3debeab4c1d26de85df4d | Python | 27,538 | 712 | #!/bin/env python
"""
Module simtk.unit.quantity
Physical quantities with units, intended to produce similar functionality
to Boost.Units package in C++ (but with a runtime cost).
Uses similar API as Scientific.Physics.PhysicalQuantities
but different internals to satisfy our local requirements.
In particular, there i... |
89ffa3797d59cae144842593461dbf0b43f762f45c877b87636465e4b9407dfb | Python | 27,543 | 257 | from truesight.experiment.services import (
EvaluationRef,
)
from truesight.evaluation import evals
one_word_freeform = EvaluationRef(
slug="Animal Preference",
n_samples=100,
notes=None,
cfg=evals.FreeformCfg(
prompts=[
"Name your favorite animal using only one word.",
... |
b6b9d4508c4ee1ec0427be0e4f4205a5e91d4743c0918e13b8fbc6be6e297b74 | Python | 27,552 | 713 | #!/usr/bin/env python3
"""
Statistical testing framework for weights and cell response.
"""
import sys
import torch
import numpy as np
import scipy.stats as stats
from scipy import optimize
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from typing import Dict, List, Tuple, Optional
import w... |
1f173f5bf3de4b879a006a01fafa351452f780550e16c052583bceb22d67c9ec | Python | 27,563 | 672 | # src/plot.py
import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import matplotlib as mpl
from scipy.signal import butter, filtfilt
# Set font embedding for SVG export
mpl.rcParams['svg.fonttype'] = 'none'
# Append src/ path for local imports
sys.path.ap... |
447c7e178e657f86f8776358d4dde8c0c9ad6cfda00317888df1dbbaec461713 | Python | 27,703 | 719 | import csv
import logging
import random
from collections import defaultdict
from math import isinf, isnan
import spectra
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, heatmap, scatter, table
from multiqc.utils import mqc_colour
log = logging.getLogger(__n... |
2c7df2953ed174dd44743632fba13da06af5664b23d2adb30c30dc4c8336a69c | Python | 27,720 | 932 | """Default parameter values for analysis of trajectories."""
from pathlib import Path
from typing import TypedDict
import numpy
import pandas
from openff.units import unit
from proteinbenchmark.utilities import package_data_directory
class KarplusDict(TypedDict, total=False):
dihedral: str
delta: float
... |
367aebcbf332239cdfa7325f7cacb85f7410ca9326f483da603b33fe08040bd0 | Python | 27,767 | 633 | import logging
import re
from html import escape
from typing import Union
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import linegraph, table
log = logging.getLogger(__name__)
# Maps each per-cell QC value column to its companion "cell rank" column in checkatlas qc/*.t... |
68731f881cbe8d9d581d16af6f8824f4c7a84238dae40931d3d0c9575515a13e | Python | 27,955 | 690 | """
相关性可视化：C-index vs XAI 稳定性
仅生成：Kuncheva Index vs C-index 的扇形热图 + 对应CSV（相关矩阵/显著性矩阵等）
"""
import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from matplotlib.colors import LinearSegmentedColormap
from scipy import stats
from typing import Optional, Dict, Set
from pa... |
215048af2c74713ca570f282bcf3abc8a6232d831c17eb8d92afb4e710a69af1 | Python | 27,971 | 797 | '''
NeuroBED_ML
Python helper functions used for data preprocessing,
outlier detection, correlation analysis, SHAP computation,
ROC visualization, and model bookkeeping within the NeuroBED_ML framework.
'''
import pandas as pd
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
from ... |
dd7b474d5e46b9ccf5b92430507154228264e985a64969d91111c7d1c5385ec2 | Python | 28,038 | 683 | """
RNV-T empirical validation reference implementation.
This script implements the five phases described in the manuscript:
1) Local Vascular Extraction (LVE)
2) Global Transformer-based Encoding (GTE)
3) Graph-based Convolutional Attention Network (G-CAN)
4) Local-Global Attention Fusion (LGAF)
5) Optimized training... |
1c8075034a8fe2791f22d762b8858b8d3a0cc37c4e87b933687aab5ca944de64 | Python | 28,051 | 674 | #!/usr/bin/env python3
"""
SAMMY-seq Chromatin State Analysis Pipeline
This script processes SAMMY-seq data to identify heterochromatin and euchromatin regions
by comparing the S2S (accessible) and S3 (inaccessible) fractions.
Based on the methodology described in the SAMMY-seq paper where:
- Euchromatin: regions wit... |
fd2ccd38f6877f985061aa9b272dab5b04a378d1c660c075913caf9be34b9c53 | Python | 28,134 | 717 | """
:mod:`alchemiscale.strategist.service` --- strategist service
=============================================================
"""
import logging
import multiprocessing as mp
import os
import time
import traceback
from concurrent.futures import ProcessPoolExecutor, as_completed
import datetime
from pathlib import Pa... |
6a70c3f54ca2a68c0de07ec1215e9f1cc4098ea93959a99d250e5054054f8169 | Python | 28,168 | 680 | # Example Models
import os # to handle path information
import numpy as np
import matplotlib.pyplot as plt
import nibabel as nb
from nilearn import plotting
from decimal import Decimal
from torch import exp,log,sqrt
from model import Model
import torch as pt
from arrangements import *
import sys
class PottsModel_old(... |
846846061ed3904921fc8420e42d56ff1b8f36b8082afe415173f213eab42ee1 | Python | 28,203 | 821 | from __future__ import absolute_import
import io
import logging
import zlib
from contextlib import contextmanager
from socket import error as SocketError
from socket import timeout as SocketTimeout
try:
import brotli
except ImportError:
brotli = None
from ._collections import HTTPHeaderDict
from .connection ... |
085330f741d221145e2b8972a2a2a8fffa022a00ad347676bbe1be0829f5d23e | Python | 28,213 | 719 | """
:mod:`alchemiscale.strategist.service` --- strategist service
=============================================================
"""
import logging
import multiprocessing as mp
import os
import time
import traceback
from concurrent.futures import ProcessPoolExecutor, as_completed
import datetime
from pathlib import Pa... |
7fde2e949fd9ae087fe2c6103a6ca4e1b2b86e8b4c73c0e437a6a0c1497ec5d1 | Python | 28,265 | 584 | import argparse, subprocess, glob, os, vcf, tracemalloc, pickle
import numpy as np
import pandas as pd
from Bio import SeqIO
# starting the memory monitoring
tracemalloc.start()
#################################### STEP 0: READ IN FILES AND INITIALIZE VARIABLES ####################################
########... |
3112a46d95bd004fefa79a3f9ae4478159accd51e19f63b5a0d3beafc4c2e3f9 | Python | 28,425 | 735 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import pandas as pd
import torch.nn as nn
from scipy.signal import welch, butter, filtfilt, iirnotch, stft, resample, resample_poly, medfilt as median_filter
from math import gcd
def bandpass_filter(data, lowcut, ... |
98f9b9207acd0ad16f18aa71a5bb3349f6ed1e46933797f28ff6b4b5bdfa3adf | Python | 28,455 | 702 | #!/usr/bin/env python3
"""
Ablation study — Isolating SAM's contributions.
Three ablation studies on a subset of 6 representative architectures:
1. SAM ρ sensitivity: ρ ∈ {0, 0.01, 0.02, 0.05, 0.10, 0.20}
2. Augmentation strategy: {None, Basic, Strong} × {Adam, SAM+Adam}
3. Training strategy... |
c6ea45d0f9c02c2622d7697a7b3a4131a066ebeba54414d79830153dbe5066d6 | Python | 28,526 | 633 | import os
import glob
import threading
import tkinter as tk
from tkinter import ttk, filedialog, messagebox
import mne
import torch
import torch.nn.functional as F
import numpy as np
import matplotlib
matplotlib.use('TkAgg') # Use TkAgg backend
import matplotlib.pyplot as plt
from matplotlib.backends.backend_tkagg impo... |
70dc533ae791ec39024c7a94f6699bf8aa3a90779dc23a5cc37ec15d201a742d | Python | 28,535 | 661 | # Imports
from neuron import h, rxd
import numpy as np
import json
from matplotlib import pyplot
from neuron.units import mM, mV, nM, uM
from neuron.rxd import v
from neuron.rxd.rxdmath import vtrap, exp, log, tanh, fabs
import os
from tqdm import tqdm
import csv
# Add necessary .hoc to Neuron h backbone
h.load_file('... |
cc114adc6b3601d54666ee001c7c0cf48eeb7bf2982b643d5773e6feb18d4077 | Python | 28,617 | 721 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import mdtraj as mdt
import numpy as np
import openfe
import pytest
from openff.units import unit
from openff.units.openmm import ensure_quantity
from openmm import (
CustomAngleForce,
... |
a73bed39c9edb3858508256f2b3e506476e3c8c5cc9bc7d18b62f89d58dcdc26 | Python | 28,627 | 686 | import datetime
import logging
import os
import traceback
from copy import deepcopy
from glob import glob
import SimpleITK as sitk
from utils.utilities import folder_eligibility_check
class PatientDICOM:
_gender = ""
_birth_date = ""
def __init__(self, dicom_folder):
self.__reset()
self.di... |
8602b2efcf8d4c95dd4ddba48032f8329744e51cf7ad907182871bbdb7c5bac6 | Python | 28,654 | 614 | import pandas as pd
import nibabel as nib
import numpy as np
import os.path
import os, glob
from joblib import Parallel, delayed
import time
from scipy.stats import zscore, iqr
import brsc_utils as util
# plotting
import seaborn as sns
import matplotlib.pyplot as plt
# Nipype
from nipype.interfaces.fsl.maths import S... |
aa87fa88381032fdb1917418a11531bb871ac368408309b8bb08a8a192d50d9d | Python | 28,701 | 624 | from dataclasses import dataclass
import numpy as np
import pandas as pd
# flake8: noqa: E501
@dataclass
class HRpQCT_Dataset:
"""
Class to hold the dataset and its metadata
Args: (pandas.DataFrame) dataset: the dataset from REDCap
Output: (dataclasses_hrpqct.Dataset) dataset: the dataset that can b... |
f590699a0b5abd8b94c181056236aed816fea7a2f4dc723556211d7dc3d006f0 | Python | 28,711 | 784 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Restraint Geometry classes
TODO
----
* Add relevant duecredit entries.
"""
import warnings
from typing import Optional
import MDAnalysis as mda
import numpy as np
import numpy.typing a... |
7030e0bc6e26600eb6840fcee20c430bac15d01c105acc4857252051bbd34426 | Python | 28,721 | 783 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Restraint Geometry classes
TODO
----
* Add relevant duecredit entries.
"""
import warnings
from typing import Optional
import MDAnalysis as mda
import numpy as np
import numpy.typing as... |
550c19ba7dd734a96b214b1367560a4500cec07feea96989f33b98b8c0079eb9 | Python | 28,752 | 659 | """Makes design matrices for a subject list and first-level model names.
"""
from os import system
from os.path import exists
import traceback
import warnings
import sys
from ast import literal_eval
from pathlib import Path
import numpy as np
import pandas as pd
from nilearn import image
from nilearn.glm.first_level... |
21ebdae700a04fae0fd3ebdd4f5c31aa6279739ccee84dc15fa699f5ed808da3 | Python | 28,763 | 715 | # -*- coding: utf-8 -*-
"""DEPRECATED / OUTDATED — legacy pure-Python GSEA engine.
This module is the original NumPy implementation of the enrichment-score and
permutation machinery. It has been superseded by the Rust extension
``gseapy.gse`` (see ``src/stats.rs`` / ``src/algorithm.rs``) and is no longer
imported by a... |
ac506d175049c9975de47a1c9b3c466d66b94228a4477b48e612d7b39a49697b | Python | 28,774 | 722 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
ProtocolUnit implementations for the HybridTopProtocol.
"""
import logging
import os
import pathlib
import warnings
from itertools import chain
from typing import Any
import mdtraj
impo... |
b594605d198485373a5c2d353626d39fd53d3b743de8fc170d6cc2cdf97f50ba | Python | 28,795 | 871 |
import os
import random
import numpy as np
import pandas as pd
import torch
import scipy
import scipy.sparse as sps
import logging
import torch.nn.functional as F
import scanpy as sc
from natsort import natsorted
from scipy.sparse import coo_matrix
from sklearn.preprocessing import LabelEncoder
from sklearn.neighbors ... |
42742848f8bfe6e52cfbbb9f0793e5e3ff3c4d0292f11320802c2f2077bf4ef6 | Python | 28,808 | 561 | from __future__ import absolute_import
from . import parallel_task_manager
import os
import numpy as np
import subprocess
from scipy import sparse
import random
import time
import warnings
from collections import Counter, deque
import numpy.core.numeric as numeric
from scipy.optimize import curve_fit
import multiproce... |
2463b5ff81e2223bdca71e0ea6bd4a01a31427240308781fae1984363dae3546 | Python | 28,825 | 663 | import json
import pathlib
from ..data_gathering import (
get_lomap_score,
get_transformation_network_map,
parse_ligand_network,
get_shape_score,
get_volume_score,
get_mapping_RMSD_score,
get_number_heavy_dummy_heavy_core_atoms,
gather_transformation_scores,
get_number_rotatable_bon... |
d4c16b3e377c618bfee309deb4e4a0f36a57d7f7e70d066c85e9698c88967b3f | Python | 28,872 | 683 | import os
import imageio
import yaml
import numpy as np
import pandas as pd
from typing import List
from magicgui.widgets import Container, FileEdit, LineEdit, ComboBox, Label, CheckBox, PushButton
from qtpy.QtWidgets import QListWidget, QListWidgetItem, QMessageBox, QSizePolicy
from qtpy.QtGui import QFont, QImage, QP... |
0332e1ad7d38dbf17bf30641620d5ebf71a7e112b1e5553f01ac9742c885c255 | Python | 28,896 | 767 | # This code is in parts based on TopologyProposal in perses
# (https://github.com/choderalab/perses)
# The eventual goal is to move this to the OpenFE alchemical topology
# building toolsets.
# LICENSE: MIT
# turn off formatting since this is mostly vendored code
# fmt: off
import itertools
import logging
import warn... |
cbc86016a7d5d0aae2a3e1de80f0770f4a7f01e898704f17c0094476612b0ded | Python | 28,937 | 852 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import
import distutils.util
try:
from importlib.machinery import EXTENSION_SUFFIXES
except ImportErr... |
e76248c8fe42eb24fc0e94f53b666c78063ebccbcb4dbf05a8ed20f3938560cb | Python | 28,999 | 1,024 | """
shared options and groups
The principle here is to define options once, but *not* instantiate them
globally. One reason being that options with action='append' can carry state
between parses. pip parses general options twice internally, and shouldn't
pass on state. To be consistent, all options will follow this de... |
91a1c766343c42fb11c66604ad7974817da0aed4b4ff844fd011246df3c88bce | Python | 29,010 | 895 | import warnings
import contextlib
import copy
import functools
from typing import TYPE_CHECKING, Tuple, List, Union, Dict, NamedTuple, Any, Optional
import numpy as np
from openff.units import unit
from openff.utilities import requires_package
from openff.utilities.exceptions import MissingOptionalDependencyError
i... |
d387570e68d95152c7c228076fb99351462e53698a4cc70272c76f0dfd64fe88 | Python | 29,096 | 621 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Author: Caro Nettekoven
"""
import numpy as np
import TaskRest.paths as indiv_paths
import Functional_Fusion.dataset as ds
from TaskRest.preprocessing.hcp_dataset_class import get_hcprest_dataset
import Functional_Fusion.atlas_map as am
import itertools
import numpy as... |
f8e600b1c8512ab43e3e146b27e1102fad592d66cebcc20247e13218a7412b4e | Python | 29,110 | 668 | """Sample based data generators.
Sample data generators yield data from a sliding window in order to categorize
the pixel of the center of the window using the data closest to it. These
generators can be helpful when there is limited training data.
"""
import os
import numpy as np
from tensorflow.keras import back... |
caecc4ecd5861a64fc0e07d0f754231b04395286c823e5c4f72e09acac01a0dd | Python | 29,163 | 723 | #!/usr/bin/env python
from __future__ import division
import pandas as pd
import numpy as np
import itertools as it
import os
import sys
import traceback
import gzip
import bz2
import argparse
from scipy.stats import chi2
from ldsc_thin import MASTHEAD, Logger, sec_to_str
import time
np.seterr(invalid='ignore')
try:
... |
e7195eb3f59231de6b03842f56d8f828a52e6472591e6389cda017008da35e8c | Python | 29,261 | 1,213 | #!/usr/bin/env python3
# ----------------------------------------------------------------------------
# Copyright (c) 2020--, Qiyun Zhu.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------... |
8838b699d9505dd88d166ffe041135a3ff539443aa2564aac50aab0b67186cf4 | Python | 29,275 | 923 | import pandas as pd
from experiments import quick_plot
from experiments.open_model_p2_2025_07_01 import (
build_mcq_animal_preference_evaluation,
get_ft_cfg,
)
from experiments import quick_calculate
from refs.llm_base_refs import llama, qwen25_7b, gpt41_nano
from refs.paper.animal_preference_code_refs import G... |
da992b752fc5b7cd078a41044b0ca427e027804c80011b36ae1e2a4e842082a2 | Python | 29,303 | 578 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import, unicode_literals
import time
import numpy as np
from scipy import optimize, stats
from deepdish import io as dio
from . import utils, math
def basis_vanBergen2015(s, n_channels=8, power=5):
'''
Para... |
be596a1a1081becca4989d98eb374bb9d2175d3c9353c63f0969b9cd145b86ee | Python | 29,351 | 719 | ##############################################################################
# pymbar: A Python Library for MBAR
#
# Copyright 2016-2017 University of Colorado Boulder
# Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center
# Portions of this software are Copyright 2010-2016 University of Virginia
#
# Authors: M... |
c3c65de80e99f35c0aa56e45ff46e98710559562fc8a1caba5644140b02d8d8e | Python | 29,353 | 719 | ##############################################################################
# pymbar: A Python Library for MBAR
#
# Copyright 2016-2017 University of Colorado Boulder
# Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center
# Portions of this software are Copyright 2010-2016 University of Virginia
#
# Authors: M... |
bbae5d363ec4e2e988d1fea101fd5bd0d16c4ba6f36253f1afb9f22a90ac5a4c | Python | 29,435 | 743 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import Callable
import pytest
import openfe
from ..conftest import mol_from_smiles
class BadMapper(openfe.setup.atom_mapping.LigandAtomMapper):
@classmethod
def _defa... |
4083be4bedd4e274b43fb8a0e50770c32aa3a8a587af8ed3b4b3a4a89114e1c0 | Python | 29,490 | 712 | #!/usr/bin/env python3
"""
SAMMY-seq Chromatin State Analysis Pipeline
This script processes SAMMY-seq data to identify heterochromatin and euchromatin regions
by comparing the S2S (accessible) and S3 (inaccessible) fractions.
Based on the methodology described in the SAMMY-seq paper where:
- Euchromatin: regions wit... |
04c10bff75b713c9d72bf017016aa695871cb2fa339c52a44c19133d1e3c0c1f | Python | 29,561 | 866 | # This file is dual licensed under the terms of the Apache License, Version
# 2.0, and the BSD License. See the LICENSE file in the root of this repository
# for complete details.
from __future__ import absolute_import
import distutils.util
try:
from importlib.machinery import EXTENSION_SUFFIXES
except ImportErr... |
c2f9ecfc43ab02e2f0bb61ef62a1a790220abb136512f2c1a8fd5f9321fe1f2d | Python | 29,573 | 832 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import os
import pathlib
import sys
from typing import List, Literal
import click
import pandas as pd
from openfecli import OFECommandPlugin
from openfecli.clicktypes import HyphenAwareCho... |
75153269c2a2521d1e4d5e9d4660dbd28cf500e178368670064780a6b99e6c8a | Python | 29,581 | 911 |
from time_fidelity import *
from frequency_fidelity import *
from time_frequency_fidelity import *
from complexity_fidelity import *
from spatial_fidelity import *
from diversity import *
from privacy import *
def _sim(a, b, eps=1e-12):
"""Normalised absolute-difference similarity in [0,1]."""
return 1.0 - np... |
799a10e032748bc7ea8587d05cc3f3ab1f5338f87284dfb099a413f7ac405306 | Python | 29,646 | 782 | """Main module for training and evaluating connectivity models.
Designed to work together with Functional_Fusion package.
Dataset, session, and parcellation names are as in Functional_Fusion.
The main work is being done by train_model and eval_model functions.
@authors: Ladan Shahshahani, Maedbh King, Jörn ... |
23a5c9c5a16d83e913306385767d664b4526d0bfbd53a1826b1a339d679bc010 | Python | 29,647 | 778 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Test utility functions in utils.py.
"""
import abc
import copy
# =============================================... |
2dc2cb76dbeb33365bbfd8a0cb333758666be51aa4c0ed860b908927e4f1c32b | Python | 29,656 | 708 | #!/usr/bin/env python
"""
@package npt_lipid
Runs a simulation to compute condensed phase properties (for example, the density
or the enthalpy of vaporization) and compute the derivative with respect
to changing the force field parameters. This script is a part of ForceBalance.
All code in this repository is rele... |
20541b1c1c7931b41d6e81c2773db821006be75c569ba97dbcf266376e23a083 | Python | 29,745 | 674 | import cv2
import numpy as np
from functools import partial
import json
from scipy.interpolate import interp1d
from scipy.ndimage import binary_dilation
import shapely.geometry as shpgeo
from shapely.ops import unary_union
import os
import tensorstore as ts
import time
from feabas.concurrent import submit_to_workers
f... |
e5548dd1292be6a084879aa168da678029aaa403d12acf5752fc719e269ef373 | Python | 29,854 | 703 | import json
import logging
import re
from collections import Counter, defaultdict
from typing import Any, Dict, Optional, Tuple
from multiqc import config
from multiqc.base_module import BaseMultiqcModule, ModuleNoSamplesFound
from multiqc.plots import bargraph, linegraph, table
from multiqc.types import ColumnKey
lo... |
3844aa6b53287957e1c250c28274f3a029e3f16b0b4f37281166b40bb0395677 | Python | 29,872 | 830 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from math import sqrt
from unittest import mock
import gufe
import mdtraj as mdt
import numpy as np
import openmm
import pytest
from numpy.testing import assert_allclose
from openff.units im... |
5b6a93413c137ef00c469f6630499d0b6b81786ee00a885ea4e70ac825d134a6 | Python | 29,905 | 817 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Free Energy Protocols input settings.
This module implements base settings necessary to run
free energy calculations using OpenMM +/- Tools, such
as :mod:`openfe.protocols.ope... |
d605761bea30940da2c1c6f160073804e4e23d144607c4f3a6e534c2e84cd954 | Python | 29,960 | 819 | """Support for installing and building the "wheel" binary package format.
"""
import collections
import compileall
import contextlib
import csv
import importlib
import logging
import os.path
import re
import shutil
import sys
import warnings
from base64 import urlsafe_b64encode
from email.message import Message
from i... |
e06f275f3b0bd8d654c604f9de061e7e25b39a4c9c93811c901ea42d66f211c3 | Python | 29,985 | 520 | from __future__ import absolute_import
from builtins import zip
from builtins import range
import re
import subprocess
import pytest
from packaging.version import Version
from forcebalance.nifty import *
from forcebalance.gmxio import GMX
from forcebalance.tinkerio import TINKER
from forcebalance.openmmio import OpenMM... |
48fc636cfb283a6bca0a0fb97f1cc2ae832bf56df4a34e7083e13a3736b354f1 | Python | 29,987 | 765 | #!/usr/bin/env python3
"""
Peak-Based MeCP2 Enrichment vs Gene Expression Correlation Analysis (DEA genes with significant MeCP2 enrichment)
This script analyzes the correlation between peak-based MeCP2 enrichment and gene expression changes.
It uses the peak enrichment data generated by peak_based_enrichment_analysis... |
92c526d93e36f19118d9cddf6a21d0cc34a6b7d60d6c77ae1f669ab7c928642b | Python | 29,997 | 769 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Hybrid Topology Protocols using OpenMM and OpenMMTools in a Perses-like manner.
Acknowledgements
----------------
These Protocols are based on, and leverages components originating from
... |
3d71ae48842607ea64d633600be0c94a3eaf45b1829089ab15a4bc294924c13c | Python | 30,037 | 583 | import traceback
import shutil
from aenum import Enum, unique
import logging
from typing import Union, Any, Tuple, List
import numpy as np
import nibabel as nib
from nibabel.processing import resample_to_output
from copy import deepcopy
import os
from pathlib import PurePath
import re
from utils.utilities import get_t... |
3c16a128c511bdfed595b2a17eb207618a4509758c2472d65bbdde1474af88be | Python | 30,038 | 621 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2018 herrlich10@gmail.com
#
# 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 ... |
b0e4a2470d6c11e5fdfb83c5b18f2cd9d1c92d0a234b8f6442dc30f84f79ec2e | Python | 30,072 | 879 | # Copyright 2017 Google Inc.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... |
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