José C. Riquelme-Santos

Evolutionary feature selection to estimate forest stand variables using LiDAR

Abstract Light detection and ranging (LiDAR) has become an important tool in forestry. LiDAR-derived models are mostly developed by means of multiple linear regression (MLR) after stepwise selection of predictors. An increasing interest in machine learning and evolutionary computation has recently arisen to improve regression use in LiDAR data processing. Although evolutionary machine learning has already proven to be suitable for regression, evolutionary computation may also be applied to improve parametric models such as MLR. This paper provides a hybrid approach based on joint use of MLR and a novel genetic algorithm for the estimation of the main forest stand variables. We show a comparison between our genetic approach and other common methods of selecting predictors. The results obtained from several LiDAR datasets with different pulse densities in two areas of the Iberian Peninsula indicate that genetic algorithms perform better than the other methods statistically. Preliminary studies suggest that a lack of parametric conditions in field data and possible misuse of parametric tests may be the main reasons for the better performance of the genetic algorithm. This research confirms the findings of previous studies that outline the importance of evolutionary computation in the context of LiDAR analisys of forest data, especially when the size of fieldwork datatasets is reduced.

On the evolutionary optimization of k-NN by label-dependent feature weighting

Different approaches of feature weighting and k-value selection to improve the nearest neighbour technique can be found in the literature. In this work, we show an evolutionary approach called k-Label Dependent Evolutionary Distance Weighting (kLDEDW) which calculates a set of local weights depending on each class besides an optimal k value. Thus, we attempt to carry out two improvements simultaneously: we locally transform the feature space to improve the accuracy of the k-nearest-neighbour rule whilst we search for the best value for k from the training data. Rigorous statistical tests demonstrate that our approach improves the general k-nearest-neighbour rule and several approaches based on local weighting.

An evolutionary-weighted majority voting and support vector machines applied to contextual classification of LiDAR and imagery data fusion

Data classification is a critical step to convert remotely sensed data into thematic information. Environmental researchers have recently maximized the synergy between passive sensors and LiDAR (Light Detection and Ranging) for land cover classification by means of machine learning. Although object-based paradigm is frequently used to classify high resolution imagery, it often requires a high level of expertise and time effort. Contextual classification may lead to similar results with a decrease in time and costs for non-expert users. This work shows a novel contextual classifier based on a Support Vector Machine (SVM) and an Evolutionary Majority Voting (SVM-EMV) to develop thematic maps from LiDAR and imagery data. Subsequently, the performance of SVM-EMV is compared to that achieved by a pixel-based SVM as well as to a contextual classified based on SVM and MRF. The classifiers were tested over three different areas of Spain with well differentiated environmental characteristics. Results show that SVM-EMV statistically outperforms the rest (SVM, SVM-MRF) for the three datasets obtaining a 77%, 91% and 92% of global accuracy for Trabada, Huelva and Alto Tajo, respectively.

Automatic environmental quality assessment for mixed-land zones using lidar and intelligent techniques

Research highlights? LiDAR can provide excellent information to improve thematic maps in especially interesting areas. ? Intelligent techniques are a key factor to provide fast and accurate results when lidar is applied to the study of the natural environment. ? Our experimentation on real data from a riparian area in the south of Spain shows decision trees (C4.5) provide the best results with the highest level of clarity for the final model. Human impact on the natural environment is an evident global fact. Natural, industrial and touristic areas coexist in a more than delicate balance. In Andalusia, in the south of Spain, the Regional Ministry for the Environment is responsible for the control and preservation of natural resources. This task bears a high cost in time and money. Remote sensing and the use of intelligent techniques are excellent tools to reduce such costs. This work explores the joint use of the lidar sensor, which provides a great quantity of information describing three dimensional space, and the application of intelligent techniques for rapid and efficient land use and land cover classification with the objective of differentiating urban land from natural ground close to protected areas of Huelva province. For this, seven types of land use and land cover have been studied for a riparian area next to the mouth of the rivers Tinto and Odiel, extracting 33 distinct features from the lidar point cloud. Subsequently, a supervised learning algorithm is applied to construct a model which, with a resolution of 4m2, obtained relative precision between 71% and 100% and an average total precision of 85%.

A comparative study between two regression methods on LiDAR data: a case study

Airborne LiDAR (Light Detection and Ranging) has become an excellent tool for accurately assessing vegetation characteristics in forest environments. Previous studies showed empirical relationships between LiDAR and field-measured biophysical variables. Multiple linear regression (MLR) with stepwise feature selection is the most common method for building estimation models. Although this technique has provided very interesting results, many other data mining techniques may be applied. The overall goal of this study is to compare different methodologies for assessing biomass fractions at stand level using airborne Li-DAR data in forest settings. In order to choose the best methodology, a comparison between two different feature selection techniques (stepwise selection vs. genetic-based selection) is presented. In addition, classical MLR is also compared with regression trees (M5P). The results when each methodology is applied to estimate stand biomass fractions from an area of northern Spain show that genetically-selected M5P obtains the best results.

EVOR-STACK: A label-dependent evolutive stacking on remote sensing data fusion

Land use and land covers (LULC) maps are remote sensing products that are used to classify areas into different landscapes. Data fusion for remote sensing is becoming an important tool to improve classical approaches. In addition, artificial intelligence techniques such as machine learning or evolutive computation are often applied to improve the final LULC classification. In this paper, a hybrid artificial intelligence method based on an ensemble of multiple classifiers to improve LULC map accuracy is shown. The method works in two processing levels: first, an evolutionary algorithm (EA) for label-dependent feature weighting transforms the feature space by assigning different weights to every attribute depending on the class. Then a statistical raster from LIDAR and image data fusion is built following a pixel-oriented and feature-based strategy that uses a support vector machine (SVM) and a weighted k-NN restricted stacking. A classical SVM, the original restricted stacking (R-STACK) and the current improved method (EVOR-STACK) are compared. The results show that the evolutive approach obtains the best results in the context of the real data from a riparian area in southern Spain.

A SVM and k-NN restricted stacking to improve land use and land cover classification

Land use and land cover (LULC) maps are remote sensing products that are used to classify areas into different landscapes The newest techniques have been applied to improve the final LULC classification and most of them are based on SVM classifiers In this paper, a new method based on a multiple classifiers ensemble to improve LULC map accuracy is shown The method builds a statistical raster from LIDAR and image fusion data following a pixel-oriented strategy Then, the pixels from a training area are used to build a SVM and k-NN restricted stacking taking into account the special characteristics of spatial data A comparison between a SVM and the restricted stacking is carried out The results of the tests show that our approach improves the results in the context of the real data from a riparian area of Huelva (Spain).

Machine learning techniques to discover genes with potential prognosis role in Alzheimer’s disease using different biological sources

Abstract Alzheimer’s disease is a complex progressive neurodegenerative brain disorder, being its prevalence expected to rise over the next decades. Unconventional strategies for elucidating the genetic mechanisms are necessary due to its polygenic nature. In this work, the input information sources are five: a public DNA microarray that measures expression levels of control and patient samples, repositories of known genes associated to Alzheimer’s disease, additional data, Gene Ontology and finally, a literature review or expert knowledge to validate the results. As methodology to identify genes highly related to this disease, we present the integration of three machine learning techniques: particularly, we have used decision trees, quantitative association rules and hierarchical cluster to analyze Alzheimer’s disease gene expression profiles to identify genes highly linked to this neurodegenerative disease, through changes in their expression levels between control and patient samples. We propose an ensemble of decision trees and quantitative association rules to find the most suitable configurations of the multi-objective evolutionary algorithm GarNet, in order to overcome the complex parametrization intrinsic to this type of algorithms. To fulfill this goal, GarNet has been executed using multiple configuration settings and the well-known C4.5 has been used to find the minimum accuracy to be satisfied. Then, GarNet is rerun to identify dependencies between genes and their expression levels, so we are able to distinguish between healthy individuals and Alzheimer’s patients using the configurations that overcome the minimum threshold of accuracy defined by C4.5 algorithm. Finally, a hierarchical cluster analysis has been used to validate the obtained gene-Alzheimer’s Disease associations provided by GarNet. The results have shown that the obtained rules were able to successfully characterize the underlying information, grouping relevant genes for Alzheimer Disease. The genes reported by our approach provided two well defined groups that perfectly divided the samples between healthy and Alzheimer’s Disease patients. To prove the relevance of the obtained results, a statistical test and gene expression fold-change were used. Furthermore, this relevance has been summarized in a volcano plot, showing two clearly separated and significant groups of genes that are up or down-regulated in Alzheimer’s Disease patients. A biological knowledge integration phase was performed based on the information fusion of systematic literature review, enrichment Gene Ontology terms for the described genes found in the hippocampus of patients. Finally, a validation phase with additional data and a permutation test is carried out, being the results consistent with previous studies.

An evolutionary voting for k-nearest neighbours

We optimize the voting system for the k nearest neighbours.We use evolutionary computation.We study the influence of the closeness of neighbours on the search process.The results are statistically validated. This work presents an evolutionary approach to modify the voting system of the k-nearest neighbours (kNN) rule we called EvoNN. Our approach results in a real-valued vector which provides the optimal relative contribution of the k-nearest neighbours. We compare two possible versions of our algorithm. One of them (EvoNN1) introduces a constraint on the resulted real-valued vector where the greater value is assigned to the nearest neighbour. The second version (EvoNN2) does not include any particular constraint on the order of the weights. We compare both versions with classical kNN and 4 other weighted variants of the kNN on 48 datasets of the UCI repository. Results show that EvoNN1 outperforms EvoNN2 and statistically obtains better results than the rest of the compared methods.

An Approach to Silhouette and Dunn Clustering Indices Applied to Big Data in Spark

K-Means and Bisecting K-Means clustering algorithms need the optimal number into which the dataset may be divided. Spark implementations of these algorithms include a method that is used to calculate this number. Unfortunately, this measurement presents a lack of precision because it only takes into account a sum of intra-cluster distances misleading the results. Moreover, this measurement has not been well-contrasted in previous researches about clustering indices. Therefore, we introduce a new Spark implementation of Silhouette and Dunn indices. These clustering indices have been tested in previous works. The results obtained show the potential of Silhouette and Dunn to deal with Big Data.