On Restricting Real-Valued Genotypes in Evolutionary Algorithms
- URL: http://arxiv.org/abs/2005.09380v1
- Date: Tue, 19 May 2020 11:58:40 GMT
- Title: On Restricting Real-Valued Genotypes in Evolutionary Algorithms
- Authors: J{\o}rgen Nordmoen, T{\o}nnes Frostad Nygaard, Eivind Samuelsen and
Kyrre Glette
- Abstract summary: We will illustrate the challenge of limiting the parameters of real-valued genomes and analyse the most promising method to properly limit these values.
The proposed method requires minimal intervention from Evolutionary Algorithm practitioners and behaves well under repeated application of variation operators.
- Score: 1.290382979353427
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: Real-valued genotypes together with the variation operators, mutation and
crossover, constitute some of the fundamental building blocks of Evolutionary
Algorithms. Real-valued genotypes are utilized in a broad range of contexts,
from weights in Artificial Neural Networks to parameters in robot control
systems. Shared between most uses of real-valued genomes is the need for
limiting the range of individual parameters to allowable bounds. In this paper
we will illustrate the challenge of limiting the parameters of real-valued
genomes and analyse the most promising method to properly limit these values.
We utilize both empirical as well as benchmark examples to demonstrate the
utility of the proposed method and through a literature review show how the
insight of this paper could impact other research within the field. The
proposed method requires minimal intervention from Evolutionary Algorithm
practitioners and behaves well under repeated application of variation
operators, leading to better theoretical properties as well as significant
differences in well-known benchmarks.
Related papers
- Semantically Rich Local Dataset Generation for Explainable AI in Genomics [0.716879432974126]
Black box deep learning models trained on genomic sequences excel at predicting the outcomes of different gene regulatory mechanisms.
We propose using Genetic Programming to generate datasets by evolving perturbations in sequences that contribute to their semantic diversity.
arXiv Detail & Related papers (2024-07-03T10:31:30Z) - VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling [60.91599380893732]
VQDNA is a general-purpose framework that renovates genome tokenization from the perspective of genome vocabulary learning.
By leveraging vector-quantized codebooks as learnable vocabulary, VQDNA can adaptively tokenize genomes into pattern-aware embeddings.
arXiv Detail & Related papers (2024-05-13T20:15:03Z) - Seeing Unseen: Discover Novel Biomedical Concepts via
Geometry-Constrained Probabilistic Modeling [53.7117640028211]
We present a geometry-constrained probabilistic modeling treatment to resolve the identified issues.
We incorporate a suite of critical geometric properties to impose proper constraints on the layout of constructed embedding space.
A spectral graph-theoretic method is devised to estimate the number of potential novel classes.
arXiv Detail & Related papers (2024-03-02T00:56:05Z) - Efficient and Scalable Fine-Tune of Language Models for Genome
Understanding [49.606093223945734]
We present textscLingo: textscLanguage prefix ftextscIne-tuning for textscGentextscOmes.
Unlike DNA foundation models, textscLingo strategically leverages natural language foundation models' contextual cues.
textscLingo further accommodates numerous downstream fine-tune tasks by an adaptive rank sampling method.
arXiv Detail & Related papers (2024-02-12T21:40:45Z) - Predicting loss-of-function impact of genetic mutations: a machine
learning approach [0.0]
This paper aims to train machine learning models on the attributes of a genetic mutation to predict LoFtool scores.
These attributes included, but were not limited to, the position of a mutation on a chromosome, changes in amino acids, and changes in codons caused by the mutation.
Models were evaluated using five-fold cross-validated averages of r-squared, mean squared error, root mean squared error, mean absolute error, and explained variance.
arXiv Detail & Related papers (2024-01-26T19:27:38Z) - DNA Sequence Classification with Compressors [0.0]
Our study introduces a novel adaptation of Jiang et al.'s compressor-based, parameter-free classification method, specifically tailored for DNA sequence analysis.
Not only does this method align with the current state-of-the-art in terms of accuracy, but it also offers a more resource-efficient alternative to traditional machine learning methods.
arXiv Detail & Related papers (2024-01-25T09:17:19Z) - Conditionally Invariant Representation Learning for Disentangling
Cellular Heterogeneity [25.488181126364186]
This paper presents a novel approach that leverages domain variability to learn representations that are conditionally invariant to unwanted variability or distractors.
We apply our method to grand biological challenges, such as data integration in single-cell genomics.
Specifically, the proposed approach helps to disentangle biological signals from data biases that are unrelated to the target task or the causal explanation of interest.
arXiv Detail & Related papers (2023-07-02T12:52:41Z) - Neural-Network-Directed Genetic Programmer for Discovery of Governing
Equations [0.0]
faiGP is designed to leverage the properties of a function algebra that have been encoded into a grammar.
We quantify the impact of different types of regularizers, including a diversity metric adapted from studies of the transcriptome.
arXiv Detail & Related papers (2022-03-15T21:28:05Z) - Multi-modal Self-supervised Pre-training for Regulatory Genome Across
Cell Types [75.65676405302105]
We propose a simple yet effective approach for pre-training genome data in a multi-modal and self-supervised manner, which we call GeneBERT.
We pre-train our model on the ATAC-seq dataset with 17 million genome sequences.
arXiv Detail & Related papers (2021-10-11T12:48:44Z) - Understanding Overparameterization in Generative Adversarial Networks [56.57403335510056]
Generative Adversarial Networks (GANs) are used to train non- concave mini-max optimization problems.
A theory has shown the importance of the gradient descent (GD) to globally optimal solutions.
We show that in an overized GAN with a $1$-layer neural network generator and a linear discriminator, the GDA converges to a global saddle point of the underlying non- concave min-max problem.
arXiv Detail & Related papers (2021-04-12T16:23:37Z) - Complexity-based speciation and genotype representation for
neuroevolution [81.21462458089142]
This paper introduces a speciation principle for neuroevolution where evolving networks are grouped into species based on the number of hidden neurons.
The proposed speciation principle is employed in several techniques designed to promote and preserve diversity within species and in the ecosystem as a whole.
arXiv Detail & Related papers (2020-10-11T06:26:56Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.