Changelog

0.5.0 - 2022-02-08

Added

  • Cropping1D Support
  • User specified stop layers (undocumented)
  • Support for MultiHeadAttention layers

Changed

  • Refinements to segmenting
  • Segment starting with see-through layers followed by Conv1Ds with valid padding are kept in one segment
  • Layers are duplicated with from_config and get_config
  • Generalized pooling layers and added ability to add custom pooling layers

Fixed

  • Runs for batch size 1
  • Multi-input layers that had the same input twice (e.g. Add()([x,x])) would not run, fixed this
  • Support for newer versions of tensorflow which changed sub-models class from keras to tf.keras (in flatten_model)
  • Stop layers were traversed redundantly

0.4.0 - 2020-09-16

Added

  • Sequences for benchmarking in notebooks dir and a notebook to process the sequence
  • Benchmarking notebooks
  • Notebook to time Basset conv and fc separately
  • Ability to specify custom mutations
  • For each mutation, models only run on input sequences for which character is different from mutation. As a result, each batch usually has a different size. This is slow for the first few batches as it entails a one-time cost.
  • Lots of documentation and a logo!

Changed

  • Models updated:
    • Activation added to Basset
    • Num output for Basset and Factorized Basset
    • For BPNet, only one channel output and one counts instead of two

Fixed

  • FastISM object would keep intermediate outputs of a batch even after it was used, as a result it would occupy extra memory. Get rid of such objects now through a cleanup() function. This has stopped GPU Resource errors that popped up after running a few batches

0.3.0 - 2020-08-24

Added

  • Support for multi-input models where alternate input does not merge with primary sequence input before a stop layer.
  • Support for layers that dependend on exact order of inputs, e.g. Subtract and Concat.

0.2.0 - 2020-08-22

Added

  • Support for recursively defined networks with 3 test cases
  • This Changelog file.

Changed

  • BPNet test cases atol changed to 1e-5 so they pass deterministically

0.1.3 - 2020-08-21

Added

  • First PyPI release and tagged version
  • Tested and working on non-recursively defined single-input, single and multi-output architectures
  • Tested and working on arcitectures with skip connections

The format is based on Keep a Changelog.