LANL Earthquake Prediction

This repository presents an approach used for solving Kaggle LANL Earthquake Prediction Challenge.

For feature engineering we used this kernel, slightly modified for adding some spectral features. The initial training set /data/train.csv contains 4194 rows (one row for each segment) and 1496 columns (features). We applied genetic algorithm with CatboostRegressor for fitness evaluation to implement a feature selection. Based on the GA's results, we selected 15 features and trained the model using CatboostRegressor with default parameters.

Project structure

.
├── ...
├── data                    
    ├── train.csv           # Original training set decomposed into feature set
    ├── test.csv            # Testing signal decomposed into feature set
    └── results.csv         # Modeling results prepared for submission
│── notebooks
    └── earthquake.ipynb    # Misc
├── earthquake
    ├── config.py           # Configuration parameters    
    ├── ga.py               # GA for feature selection
    ├── generator.py        # Feature engineering
    ├── submission.py       # Make prediction and prepare file for submission
    └── utils.py            # Helpers
└── ...

Note, that train and test sets in data directory contain only 200 of 1496 features to reduce the file size.

How to run

First, clone the repository and install it from setup file:

    $ git clone https://github.com/viktorsapozhok/earthquake-prediction.git
    $ cd earthquake-prediction
    $ pip install --editable .

To start the genetic algorithm implementing feature selection, launch ga.py script from project's root directory:

    $ python earthquake/ga.py

Feature engineering

The initial acoustic signal is decomposed into segments with 150000 rows per segment, which suggests that the training dataset has 4194 rows. Features are calculated as aggregations over segments. For more details see, for example, here and here.

Baseline model

Before we start with the feature selection, we calculate feature importance as it is explained here and train the baseline model on the 15 most important features.

from earthquake import config, utils

# load training set
data = utils.read_csv(config.path_to_train)
# create list of features
features = [column for column in data.columns if column not in ['target', 'seg_id']]
# display importance
best_features = utils.feature_importance(data[features], data['target'], n_best=15, n_jobs=8)

List of 15 most important features.

  Imp | Feature
 0.11 | mfcc_5_avg
 0.09 | mfcc_15_avg
 0.07 | percentile_roll_std_5_window_50
 0.06 | percentile_roll_std_10_window_100
 0.06 | mfcc_4_avg
 0.03 | percentile_roll_std_20_window_500
 0.03 | percentile_roll_std_25_window_500
 0.02 | percentile_roll_std_25_window_100
 0.02 | percentile_roll_std_20_window_1000
 0.02 | percentile_roll_std_20_window_10
 0.02 | percentile_roll_std_25_window_1000
 0.01 | percentile_roll_std_10_window_500
 0.01 | percentile_roll_std_10_window_50
 0.01 | percentile_roll_std_50_window_50
 0.01 | percentile_roll_std_40_window_1000

We train the model using CatboostRegressor with default parameters and evaluate the performance with a stratified KFold (5 folds) cross-validation.

import numpy as np
from sklearn.model_selection import cross_val_score
from catboost import CatBoostRegressor

# set output float precision 
np.set_printoptions(precision=3)
# init model
model = CatBoostRegressor(random_seed=0, verbose=False)
# calculate mae on folds
mae = cross_val_score(model, data[best_features], data['target'], 
    cv=5, scoring='neg_mean_absolute_error', n_jobs=8)
# print the results
print('folds: {}'.format(abs(mae)))
print('total: {:.3f}'.format(np.mean(abs(mae))))

CatboostRegressor (without any tuning) trained on 15 features having highest importance score demonstrates mean average error 2.064.

folds: [1.982 2.333 2.379 1.266 2.362]
total: 2.064

Feature selection

To avoid a potential overfitting, we employ a genetic algorithm for feature selection. The genetic context is pretty straightforward. We suppose that the list of features (without duplicates) is the chromosome, whereas each gene represents one feature. n_features is the input parameter controlling the amount of genes in the chromosome.

import random

class Chromosome(object):
    def __init__(self, genes, size):
        self.genes = random.sample(genes, size)

We generate the population with 50 chromosomes, where each gene is generated as a random choice from initial list of features (1496 features). To accelerate the performance, we also add to population the feature set used in the baseline model.

from deap import base, creator, tools
    

def init_individual(ind_class, genes=None, size=None):
    return ind_class(genes, size)    
    

genes = [
    column for column in train.columns
    if column not in ['target', 'seg_id']
]

# setting individual creator
creator.create('FitnessMin', base.Fitness, weights=(-1,))
creator.create('Individual', Chromosome, fitness=creator.FitnessMin)

# register callbacks
toolbox = base.Toolbox()
toolbox.register(
    'individual', init_individual, creator.Individual,
    genes=genes, size=n_features)
toolbox.register(
    'population', tools.initRepeat, list, toolbox.individual)

# raise population
pop = toolbox.population(50)

Standard two-point crossover operator is used for crossing two chromosomes.

toolbox.register('mate', tools.cxTwoPoint)

To implement a mutation, we first generate a random amount of genes (> 1), which needs to be mutated, and then mutate these genes in order that the chromosome doesn't contain two equal genes.

Note, that mutation operator must return a tuple.

def mutate(individual, genes=None, pb=0):
    # maximal amount of mutated genes
    n_mutated_max = max(1, int(len(individual) * pb))
    # generate the random amount of mutated genes
    n_mutated = random.randint(1, n_mutated_max)
    # select random genes which need to be mutated
    mutated_indexes = random.sample(
        [index for index in range(len(individual.genes))], n_mutated)
    # mutation
    for index in mutated_indexes:
        individual[index] = random.choice(genes)
    return individual,

toolbox.register('mutate', mutate, genes=genes, pb=0.2)

For fitness evaluation we use lightened version of CatboostRegressor with decreased number of iterations and increased learning rate. Note, that fitness evaluator must also return a tuple.

from catboost import CatBoostRegressor
from sklearn.model_selection import cross_val_score

model = CatBoostRegressor(
    iterations=60, learning_rate=0.2, random_seed=0, verbose=False)

def evaluate(individual, model=None, train=None, n_splits=5):
    mae_folds = cross_val_score(
        model, 
        train[individual.genes], 
        train['target'], 
        cv=n_splits, 
        scoring='neg_mean_absolute_error')
    return abs(mae_folds.mean()),

toolbox.register(
    'evaluate', evaluate, model=model, train=train, n_splits=5)

We register elitism operator to select best individuals to the next generation. The amount of the best individuals is controlling by the parameter mu in the algorithm. To prevent populations with many duplicate individuals, we overwrite the standard selBest operator.

from operator import attrgetter

def select_best(individuals, k, fit_attr='fitness'):
    return sorted(set(individuals), key=attrgetter(fit_attr), reverse=True)[:k]

toolbox.register('select', select_best)

To keep track of the best individuals, we introduce a hall of fame container.

hof = tools.HallOfFame(5)

Finally, we put everything together and launch eaMuPlusLambda evolutionary algorithm. Here we set cxpb=0.2, the probability that offspring is produced by the crossover, and mutpb=0.8, the probability that offspring is produced by mutation. Mutation probability is intentionally increased to prevent a high occurrence of identical chromosomes produced by the crossover.

As a result, we get the list of 15 best features selected into the model.

from deap import algorithms

# mu: the number of individuals to select for the next generation
# lambda: the number of children to produce at each generation
# cxpb: the probability that offspring is produced by crossover
# mutpb: the probability that offspring is produced by mutation
# ngen: the number of generations
algorithms.eaMuPlusLambda(
    pop, toolbox,
    mu=10, lambda_=30, cxpb=0.2, mutpb=0.8,
    ngen=50, stats=stats, halloffame=hof, verbose=True)

Here is the list of 15 features accumulated in the best chromosome after 50 generations.

1. ffti_av_change_rate_roll_mean_1000
2. percentile_roll_std_30_window_50
3. skew
4. percentile_roll_std_10_window_100
5. percentile_roll_std_30_window_50
6. percentile_roll_std_20_window_1000
7. ffti_exp_Moving_average_30000_mean
8. range_3000_4000
9. max_last_10000
10. mfcc_4_avg
11. fftr_percentile_roll_std_80_window_10000
12. percentile_roll_std_1_window_100
13. ffti_abs_trend
14. av_change_abs_roll_mean_50
15. mfcc_15_avg

Training

We again apply default CatboostRegressor to the found feature set and obtain mean average error 2.048.

folds: [1.973 2.313 2.357 1.262 2.334]
total: 2.048

The observed results are used for submission.

Submission results

Cross-validation MAE: 2.048, public score: 1.509, private score: 2.425 (31 place).