README.md

ST2 (Game Theory) - EI Genetic Algorithms

Introduction

Presentation

The aim of this Python project is to circularize a plasmid by optimizing the values of a table calculating the plasmid's 3D trajectory.

_"In microbiology and molecular biology, a plasmid is a DNA molecule distinct from chromosomal DNA.

For this purpose, 2 meta-heuristic algorithms are used and compared:

• Simulated annealing
• Genetic algorithm.

Cost function

A well-defined cost function is essential to ensure the convergence of meta-heuristic algorithms.

It is defined to minimize the distance between the beginning and the end of the chain and to minimize the angle to ensure coherent junction:

The parameters are :

• $dist$ : the distance between node $n-1$ and $0$.
• $dot_1$: the scalar product between $V_{end}$ and $V_{middle}$.
• $dot_1$: the scalar product between $V_{middle}$ and $V_{begin}$.

Initialization

• Create a Python virtual environment

python -m venv venv

• Activate environment

  • Windows

  .\venv\Scripts\activate

  • Linux / macos

  source ./venv/Scripts/activate

• Install Python libraries

pip install -r requirements.txt

Finding a solution

• Simulated annealing algorithm

python 3dna <directory of the file .fasta> recuit

Example

python 3dna ./data/plasmid_8k.fasta recuit

• Genetic algorithm

python 3dna <directory of the file .fasta file> genetics <selection strategy>

List of selection strategies

elitisme (défaut)
roulette
rang
tournoi

Example

python 3dna ./data/plasmid_8k.fasta genetique tournoi

Returned value

At the end of an algorithm's execution, several values are printed:

• The 3D rotation table in json format

• The difference between the values of Twist and Wedge and their maximum threshold for each pair of nucleotides (the value of Direction is constant)

• The distance between the start and end dinucleotide centers.

• Noting

  • $p_i$ the position of the center of the ith dinucleotide
  • $n$ the number of nucleotides in the sequence
  • $v_{end} = p_{n - 1} - p_{n - 2}$$
  • $v_{middle} = p_0 - p_{n - 1}$$
  • $v_{begin} = p_1 - p_0$

  The cosine similarity between the vectors $v_{end}$ and $v_{middle}$, and $v_{middle}$ and $v_{begin}$.

Algorithm configuration

The internal values used for the algorithm can be modified in the 3dna/__main__.py file.

• Simulated annealing algorithm

recuit = Recuit(
    seq=seq,
    k_max=1000,
    e_min=0.1,
    temp_init=300,
    refroidissement=0.99,
    dist_min=0.,
    relier=1
)

argument	type	description
seq	str	The nucleotide sequence
k_max	int	Maximum number of iterations
e_min	float	Energy threshold
temp_init	float	Initial temperature
refroidissement	float	cooling coefficient
dist_min	float	The distance threshold
Relier	int	The number of nucleotides linked between the end and the beginning of the sequence

• Genetic algorithm

genetique = Genetique(
    seq=seq,
    methode_utilisee=args.methode_utilisee,
    nbr_generation_max=150,
    N=50,
    probabilite_mutation_initiale=0.05,
    probabilite_mutation_finale=0.05,
    relier = 1
)

argument	type	description
seq	str	The nucleotide sequence
methode_utilisee	str	The name of the selection strategy
nbr_generation_max	int	Maximum number of generations
N	int	Population size
probabilite_mutation_initiale	float	The probability of initial mutation
probabilite_mutation_finale	float	The probability of final mutation
Relier	int	The number of nucleotides linked between the end and the beginning of the sequence

Note: The mutation probability evolves linearly from the initial value to the final value.

Test

A test has been implemented using the pytest library.

It can be run with

cd 3dna
pytest

A coverage report in html format can be generated with

python -m pytest --cov=. --cov-report html

Statistics

The algorithms can be tested with several hundred iterations to obtain a distribution of the distance between the center of the first and last dinucleotide, and of the minimum cosine similarity.

python 3dna/stat.py
python 3dna/plot.py