anna-hope

# Based on https://arxiv.org/pdf/1404.2188.pdf
# Anton Melnikov

import torch
from torch import nn
import torch.nn.functional as F
import numpy as np

class DynamicKMaxPooling(nn.Module):
    def __init__(self, k_top, L):

bayesian_neural_network.ipynb

kastnerkyle

# Alec Radford, Indico, Kyle Kastner
# License: MIT
"""
Convolutional VAE in a single file.
Bringing in code from IndicoDataSolutions and Alec Radford (NewMu)
Additionally converted to use default conv2d interface instead of explicit cuDNN
"""
import theano
import theano.tensor as T
from theano.compat.python2x import OrderedDict

isaacs

# Hello, and welcome to makefile basics.
#
# You will learn why `make` is so great, and why, despite its "weird" syntax,
# it is actually a highly expressive, efficient, and powerful way to build
# programs.
#
# Once you're done here, go to
# http://www.gnu.org/software/make/manual/make.html
# to learn SOOOO much more.

Newmu

"""
The MIT License (MIT)

Copyright (c) 2015 Alec Radford

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is

syhw

"""
A deep neural network with or w/o dropout in one file.

License: Do What The Fuck You Want to Public License http://www.wtfpl.net/
"""

import numpy, theano, sys, math
from theano import tensor as T
from theano import shared
from theano.tensor.shared_randomstreams import RandomStreams

davfre

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)