2,193 research outputs found
Machine learning-guided directed evolution for protein engineering
Machine learning (ML)-guided directed evolution is a new paradigm for
biological design that enables optimization of complex functions. ML methods
use data to predict how sequence maps to function without requiring a detailed
model of the underlying physics or biological pathways. To demonstrate
ML-guided directed evolution, we introduce the steps required to build ML
sequence-function models and use them to guide engineering, making
recommendations at each stage. This review covers basic concepts relevant to
using ML for protein engineering as well as the current literature and
applications of this new engineering paradigm. ML methods accelerate directed
evolution by learning from information contained in all measured variants and
using that information to select sequences that are likely to be improved. We
then provide two case studies that demonstrate the ML-guided directed evolution
process. We also look to future opportunities where ML will enable discovery of
new protein functions and uncover the relationship between protein sequence and
function.Comment: Made significant revisions to focus on aspects most relevant to
applying machine learning to speed up directed evolutio
Discovering Representations for Black-box Optimization
The encoding of solutions in black-box optimization is a delicate,
handcrafted balance between expressiveness and domain knowledge -- between
exploring a wide variety of solutions, and ensuring that those solutions are
useful. Our main insight is that this process can be automated by generating a
dataset of high-performing solutions with a quality diversity algorithm (here,
MAP-Elites), then learning a representation with a generative model (here, a
Variational Autoencoder) from that dataset. Our second insight is that this
representation can be used to scale quality diversity optimization to higher
dimensions -- but only if we carefully mix solutions generated with the learned
representation and those generated with traditional variation operators. We
demonstrate these capabilities by learning an low-dimensional encoding for the
inverse kinematics of a thousand joint planar arm. The results show that
learned representations make it possible to solve high-dimensional problems
with orders of magnitude fewer evaluations than the standard MAP-Elites, and
that, once solved, the produced encoding can be used for rapid optimization of
novel, but similar, tasks. The presented techniques not only scale up quality
diversity algorithms to high dimensions, but show that black-box optimization
encodings can be automatically learned, rather than hand designed.Comment: Presented at GECCO 2020 -- v2 (Previous title 'Automating
Representation Discovery with MAP-Elites'
Discrete and fuzzy dynamical genetic programming in the XCSF learning classifier system
A number of representation schemes have been presented for use within
learning classifier systems, ranging from binary encodings to neural networks.
This paper presents results from an investigation into using discrete and fuzzy
dynamical system representations within the XCSF learning classifier system. In
particular, asynchronous random Boolean networks are used to represent the
traditional condition-action production system rules in the discrete case and
asynchronous fuzzy logic networks in the continuous-valued case. It is shown
possible to use self-adaptive, open-ended evolution to design an ensemble of
such dynamical systems within XCSF to solve a number of well-known test
problems
Neo: A Learned Query Optimizer
Query optimization is one of the most challenging problems in database
systems. Despite the progress made over the past decades, query optimizers
remain extremely complex components that require a great deal of hand-tuning
for specific workloads and datasets. Motivated by this shortcoming and inspired
by recent advances in applying machine learning to data management challenges,
we introduce Neo (Neural Optimizer), a novel learning-based query optimizer
that relies on deep neural networks to generate query executions plans. Neo
bootstraps its query optimization model from existing optimizers and continues
to learn from incoming queries, building upon its successes and learning from
its failures. Furthermore, Neo naturally adapts to underlying data patterns and
is robust to estimation errors. Experimental results demonstrate that Neo, even
when bootstrapped from a simple optimizer like PostgreSQL, can learn a model
that offers similar performance to state-of-the-art commercial optimizers, and
in some cases even surpass them
Born to learn: The inspiration, progress, and future of evolved plastic artificial neural networks
Biological plastic neural networks are systems of extraordinary computational
capabilities shaped by evolution, development, and lifetime learning. The
interplay of these elements leads to the emergence of adaptive behavior and
intelligence. Inspired by such intricate natural phenomena, Evolved Plastic
Artificial Neural Networks (EPANNs) use simulated evolution in-silico to breed
plastic neural networks with a large variety of dynamics, architectures, and
plasticity rules: these artificial systems are composed of inputs, outputs, and
plastic components that change in response to experiences in an environment.
These systems may autonomously discover novel adaptive algorithms, and lead to
hypotheses on the emergence of biological adaptation. EPANNs have seen
considerable progress over the last two decades. Current scientific and
technological advances in artificial neural networks are now setting the
conditions for radically new approaches and results. In particular, the
limitations of hand-designed networks could be overcome by more flexible and
innovative solutions. This paper brings together a variety of inspiring ideas
that define the field of EPANNs. The main methods and results are reviewed.
Finally, new opportunities and developments are presented
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