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bio-experiments's Introduction

bio-experiments

Trying to learn bioinformatics

bio-experiments's People

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bio-experiments's Issues

Keep Track of Experiments

We're trying to gain an intuition and surface-level understanding of what Transformer models can do. Open questions:

  • What are they good at? What are they bad at?
  • Can they operate with small vocabularies?
  • How resistant to noise are they?
  • How do they work with out-of-sample input sizes?

Things We've Learned

  • Use RAdam not Adam. Or use learning rate warmup.

Reverse a Sequence

  • We need to use RAdam
  • We can reverse short sequences
  • We can reverse long sequences
  • We can reverse short sequences with large vocabularies
  • We can reverse large sequences with large vocabularies

Finding Adjacent Duplicates

  • We need ~10,000+ examples to generalize on a sequence length of 10 (Vocab of 10,000)
  • It's hard to train long sequences with sparse outputs directly
    • We tried FocalLoss but couldn't get it to work
  • We can train on short sequences and scale them up until we have a model that can predict on long sequences:
    1. Train on sequence length 10
    2. Train on sequence length 50
    3. Train on sequence length 100

Finding Adjacent Repeats

  • We used 10,000+ training examples based off our previous investigation
  • It's also hard to train long sequence with sparse outputs directly
  • Since the outputs aren't "quite" as sparse, we can get away with:
    1. Train on sequence of length 10
    2. Train on sequence of length 100

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