Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Fast differentiable DNA and protein sequence optimization for molecular
  design   Designing DNA and protein sequences with improved function has the potential
to greatly accelerate synthetic biology. Machine learning models that
accurately predict biological fitness from sequence are becoming a powerful
tool for molecular design. Activation maximization offers a simple design
strategy for differentiable models: one-hot coded sequences are first
approximated by a continuous representation which is then iteratively optimized
with respect to the predictor oracle by gradient ascent. While elegant, this
method suffers from vanishing gradients and may cause predictor pathologies
leading to poor convergence. Here, we build on a previously proposed
straight-through approximation method to optimize through discrete sequence
samples. By normalizing nucleotide logits across positions and introducing an
adaptive entropy variable, we remove bottlenecks arising from overly large or
skewed sampling parameters. The resulting algorithm, which we call Fast
SeqProp, achieves up to 100-fold faster convergence compared to previous
versions of activation maximization and finds improved fitness optima for many
applications. We demonstrate Fast SeqProp by designing DNA and protein
sequences for six deep learning predictors, including a protein structure
predictor.

13
The categories of this paper are: quant-ph
17
The categories of this paper are: q-fin
23
The categories of this paper are: solv-int
2
The categories of this paper are: math
15
The categories of this paper are: nucl-ex
4
The categories of this paper are: cond-mat
28
The categories of this paper are: alg-geom
27
The categories of this paper are: comp-gas
18
The categories of this paper are: econ
7
The categories of this paper are: hep-th
3
The categories of this paper are: physics
35
The categories of this paper are: mtrl-th
31
The categories of this paper are: ao-sci
12
The categories of this paper are: nucl-th
34
The categories of this paper are: chem-ph
9
The categories of this paper are: nlin