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[WIP][HEP3] Implement convolution for DNA sequence #16

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[WIP][HEP3] Implement convolution for DNA sequence #16

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Commits on Jun 5, 2013

  1. basic convolution routines for sequences

    Hannes Bretschneider committed Jun 5, 2013
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  2. use dynamic memory in convolve_sequence_gradient

    Hannes Bretschneider committed Jun 5, 2013
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Commits on Jun 6, 2013

  1. convolution gradient now working for all filter sizes that are multip… 

    …les of 4
    Hannes Bretschneider committed Jun 6, 2013
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Commits on Jun 7, 2013

  1. reorder output of max pooling layer

    Hannes Bretschneider committed Jun 7, 2013
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  2. implemented SequenceConvolutionNet

    Hannes Bretschneider committed Jun 7, 2013
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Commits on Jun 8, 2013

  1. factor choice of activation function into method subclassed from Hidd… 

    …enLayer
    Hannes Bretschneider committed Jun 8, 2013
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  2. implemented bias for filters, changed max pooling to use argmax

    Hannes Bretschneider committed Jun 8, 2013
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  3. remove compile-time constants from kernels, make more compatible with… 

    … HiddenLayer
    Hannes Bretschneider committed Jun 8, 2013
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Commits on Jun 9, 2013

  1. adapted new interface for updating parameters

    Hannes Bretschneider committed Jun 9, 2013
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  2. fixed idiotic parameter updating scheme from last night

    Hannes Bretschneider committed Jun 9, 2013
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Commits on Jun 10, 2013

  1. compatibility for double and float, gradient check

    Hannes Bretschneider committed Jun 10, 2013
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Commits on Jul 25, 2013

  1. fixed convolution gradients (debug code remains)

    Hannes Bretschneider committed Jul 25, 2013
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  2. removed debug code

    Hannes Bretschneider committed Jul 25, 2013
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  3. fixed tests, removed loop over filters

    Hannes Bretschneider committed Jul 25, 2013
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  4. removed unnecessary conditional

    Hannes Bretschneider committed Jul 25, 2013
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  5. fix gradient check

    Hannes Bretschneider committed Jul 25, 2013
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  6. fixed memory layout in max-pooling functions

    Hannes Bretschneider committed Jul 25, 2013
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  7. all tests pass!!!

    Hannes Bretschneider committed Jul 25, 2013
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Commits on Jul 26, 2013

  1. L1 and L2 weight decay

    Hannes Bretschneider committed Jul 26, 2013
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Commits on Jul 28, 2013

  1. add dropout

    Hannes Bretschneider committed Jul 28, 2013
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Commits on Jul 29, 2013

  1. Switched input encoding to using just a single byte per nucleotide

    Hannes Bretschneider committed Jul 29, 2013
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  2. Gradients work on new bit-encoding; all tests pass

    Hannes Bretschneider committed Jul 29, 2013
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Commits on Jul 31, 2013

  1. convert sequences to upper case before encoding

    Hannes Bretschneider committed Jul 31, 2013
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Commits on Aug 1, 2013

  1. modified all kernel functions to work on a subarray

    Hannes Bretschneider committed Aug 1, 2013
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  2. changed data layout

    Hannes Bretschneider committed Aug 1, 2013
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  3. removed unused variables

    Hannes Bretschneider committed Aug 1, 2013
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Commits on Aug 5, 2013

  1. Implemented convolutions on separate subregions

    Hannes Bretschneider committed Aug 5, 2013
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Commits on Aug 6, 2013

  1. got MultiSequenceConvolutionLayer working

    Hannes Bretschneider committed Aug 6, 2013
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Commits on Aug 13, 2013

  1. fixed some bugs in MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Aug 13, 2013
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Commits on Aug 14, 2013

  1. enable multiple fully connected layers in MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Aug 14, 2013
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Commits on Aug 18, 2013

  1. refactored models.py into module

    Hannes Bretschneider committed Aug 18, 2013
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  2. restrict dropout to subregion layers in MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Aug 18, 2013
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Commits on Aug 19, 2013

  1. pep8, added license, fixed tests

    Hannes Bretschneider committed Aug 19, 2013
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  2. more pep8

    Hannes Bretschneider committed Aug 19, 2013
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Commits on Aug 21, 2013

  1. changed nucleotide representation to ASCII codes; implemented SeqArra… 

    …yDataProvider
    Hannes Bretschneider committed Aug 21, 2013
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Commits on Aug 23, 2013

  1. implemented receptive fields (still untested)

    Hannes Bretschneider committed Aug 23, 2013
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Commits on Aug 25, 2013

  1. debugged fully_connected_layer

    Hannes Bretschneider committed Aug 25, 2013
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Commits on Aug 30, 2013

  1. Fully connected layer working

    Hannes Bretschneider committed Aug 30, 2013
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Commits on Sep 11, 2013

  1. enable SeqArrayDataProvider to copy data to and from GPU

    Hannes Bretschneider committed Sep 11, 2013
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Commits on Jan 10, 2014

  1. Made compatible with recent changes in Hebel

    Hannes Bretschneider committed Jan 10, 2014
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Commits on Jan 22, 2014

  1. Refactored MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Jan 22, 2014
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Commits on Jan 24, 2014

  1. Refactored convolve_sequence_gradient and gradient_reduce. Memory-ali… 

    …gned first-stage reduce operation
    Hannes Bretschneider committed Jan 24, 2014
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  2. Slightly improve computation of convolution gradient

    Hannes Bretschneider committed Jan 24, 2014
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Commits on Feb 4, 2014

  1. Re-enabled dropout for MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Feb 4, 2014
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Commits on May 12, 2014

  1. Converted "and" to "&&" in kernel to work on Windows

    Michael committed May 12, 2014
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Commits on May 13, 2014

  1. Force pool_size to be a divisor of sequence length. Allow pool_size=N… 

    …one for no pooling
    Hannes Bretschneider committed May 13, 2014
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Commits on May 23, 2014

  1. Refactored max-pooling; switched to unsigned long for indices

    Hannes Bretschneider committed May 23, 2014
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  2. Modify models to use new max-pooling kernels

    Hannes Bretschneider committed May 23, 2014
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  3. Reverted indices to unsigned int, because unsigned long is crazy slow… 

    …. Results in crashes with double input.
    Hannes Bretschneider committed May 23, 2014
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Commits on May 27, 2014

  1. Enable trim on HDF5SeqArrayDataProvider

    Hannes Bretschneider committed May 27, 2014
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  2. Fix gradients with L1/L2 regularization

    Hannes Bretschneider committed May 27, 2014
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Commits on Jun 5, 2014

  1. Started big kernel rewrite. convolve_dna_sequence_done.

    Hannes Bretschneider committed Jun 5, 2014
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Commits on Jun 12, 2014

  1. Implemented new convolve_dna_sequence_gradient and gradient_reduce ke… 

    …rnels.
    Hannes Bretschneider committed Jun 12, 2014
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  2. Use float4 type for filter_shared in convolve_dna_sequence

    Hannes Bretschneider committed Jun 12, 2014
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  3. Remove unnecessary typecast

    Hannes Bretschneider committed Jun 12, 2014
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Commits on Jun 13, 2014

  1. Fixed several bad memory access patterns in convolve_dna_sequence kernel

    Hannes Bretschneider committed Jun 13, 2014
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  2. Wrappers and tests for convolve_dna_sequence_gradient

    Hannes Bretschneider committed Jun 13, 2014
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Commits on Jun 14, 2014

  1. Implemented max-pooling kernel

    Hannes Bretschneider committed Jun 14, 2014
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Commits on Jun 16, 2014

  1. Docstring for max_pool kernel.

    Hannes Bretschneider committed Jun 16, 2014
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  2. Typo

    Hannes Bretschneider committed Jun 16, 2014
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Commits on Jun 17, 2014

  1. Implemented max_pool_gradient; use macros for basic CUDA variables.

    Hannes Bretschneider committed Jun 17, 2014
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  2. Some fixes to max_pool_gradient

    Hannes Bretschneider committed Jun 17, 2014
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  3. Extra assert in max_pool_gradient.

    Hannes Bretschneider committed Jun 17, 2014
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  4. sum_pool kernel and tests.

    Hannes Bretschneider committed Jun 17, 2014
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  5. Docstring for sum_pool kernel.

    Hannes Bretschneider committed Jun 17, 2014
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  6. Implemented sum_pool_gradient kernel and tests.

    Hannes Bretschneider committed Jun 17, 2014
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Commits on Jun 19, 2014

  1. Implemented 1D convolution on floating point inputs.

    Hannes Bretschneider committed Jun 19, 2014
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Commits on Jun 20, 2014

  1. Implement option to use process only some of the input channels at on… 

    …ce. This reduces shared memory requirements.
    Hannes Bretschneider committed Jun 20, 2014
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Commits on Jul 17, 2014

  1. Implemented gradients of 1D convolution with respect to filters.

    Hannes Bretschneider committed Jul 17, 2014
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Commits on Jul 18, 2014

  1. Don't read more input than necessary; allow block sizes that don't di… 

    …vide number of filters and width.
    Hannes Bretschneider committed Jul 18, 2014
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  2. Docstring for convolve_1d_grad_kernel

    Hannes Bretschneider committed Jul 18, 2014
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Commits on Jul 22, 2014

  1. Refactored some calculations into macros

    Hannes Bretschneider committed Jul 22, 2014
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Commits on Jul 23, 2014

  1. Implemented 1D convolution gradient wrt to the input.

    Hannes Bretschneider committed Jul 23, 2014
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Commits on Jul 30, 2014

  1. Replace temp objects with device memory pool

    Hannes Bretschneider committed Jul 30, 2014
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Commits on Aug 13, 2014

  1. Use memory pools; implement deep multi-sequence layers

    Hannes Bretschneider committed Aug 13, 2014
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Commits on Aug 14, 2014

  1. Some optimizations, replace C arguments with constants

    Hannes Bretschneider committed Aug 14, 2014
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Commits on Aug 27, 2014

  1. Finally made it work

    Hannes Bretschneider committed Aug 27, 2014
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Commits on Sep 15, 2014

  1. Add global pooling option

    Hannes Bretschneider committed Sep 15, 2014
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  2. Some changes to slaved layers

    Hannes Bretschneider committed Sep 15, 2014
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Commits on Oct 2, 2014

  1. Fix a bug in HDF5SeqArrayDataProvider that caused the same same data … 

    …to be repeatedly returned
    Hannes Bretschneider committed Oct 2, 2014
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Commits on Nov 14, 2014

  1. Replaced backend with cuDNN.

    Hannes Bretschneider committed Nov 14, 2014
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Commits on Nov 26, 2014

  1. Change HDF5SeqArrayDataProvider interface

    Hannes Bretschneider committed Nov 26, 2014
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Commits on Nov 28, 2014

  1. Add ConvolutionDummyLayer and fix bug inSeqArrayDataProvider

    Hannes Bretschneider committed Nov 28, 2014
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  2. Bug in SlavedConvolution1DLayer

    Hannes Bretschneider committed Nov 28, 2014
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  3. Bug in MultiSequenceConvolutionLayer

    Hannes Bretschneider committed Nov 28, 2014
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Commits on Jan 22, 2015

  1. Include cuDNN wrapper.

    Hannes Bretschneider committed Jan 22, 2015
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  2. Make FlatteningLayer 4D

    Hannes Bretschneider committed Jan 22, 2015
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  3. Subclass from ParameterfreeLayer; clean up imports and some other things

    Hannes Bretschneider committed Jan 22, 2015
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  4. Switched from Markdown to RST for README to make PyPi a little happier.

    Hannes Bretschneider committed Jan 22, 2015
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  5. Remove unneccesary assert statement in DummyLayer.

    Hannes Bretschneider committed Jan 22, 2015
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  6. Add 'hebel/sequence_convolution/' from commit '92f45e53c58f76e0763058… 

    …9603cd30016efb3c78'

git-subtree-dir: hebel/sequence_convolution
git-subtree-mainline: 318aed3
git-subtree-split: 92f45e5
    Hannes Bretschneider committed Jan 22, 2015
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  7. Move src directory to root

    Hannes Bretschneider committed Jan 22, 2015
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  8. Moved sequence convolution layers to hebel/layers

    Hannes Bretschneider committed Jan 22, 2015
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Commits on Jan 23, 2015

  1. Merge pycuda_ops into hebel

    Hannes Bretschneider committed Jan 23, 2015
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  2. Make data_providers a package; move seq_array

    Hannes Bretschneider committed Jan 23, 2015
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