One Ecosystem : Review Article

Corresponding author: Anne E Thessen (annethessen@gmail.com)
Academic editor: Benjamin Burkhard
Received: 24 Mar 2016  Accepted: 20 Jun 2016  Published: 27 Jun 2016
© 2016 Anne E Thessen.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation: Thessen A (2016) Adoption of Machine Learning Techniques in Ecology and Earth Science. One Ecosystem 1: e8621. doi: 10.3897/oneeco.1.e8621

The natural sciences, such as ecology and earth science, study complex interactions between biotic and abiotic systems in order to understand and make predictions. Machinelearningbased methods have an advantage over traditional statistical methods in studying these systems because the former do not impose unrealistic assumptions (such as linearity), are capable of inferring missing data, and can reduce longterm expert annotation burden. Thus, a wider adoption of machine learning methods in ecology and earth science has the potential to greatly accelerate the pace and quality of science. Despite these advantages, the full potential of machine learning techniques in ecology and earth science has not be fully realized.
This is largely due to 1) a lack of communication and collaboration between the machine learning research community and natural scientists, 2) a lack of communication about successful applications of machine learning in the natural sciences, 3) difficulty in validating machine learning models, and 4) the absence of machine learning techniques in a natural science education. These impediments can be overcome through financial support for collaborative work and the development of graduatelevel educational materials about machine learning. Natural scientists who have not yet used machine learning methods can be introduced to these techniques through Random Forest, a method that is easy to implement and performs well. This manuscript will 1) briefly describe several popular machine learning tasks and techniques and their application to ecology and earth science, 2) discuss the limitations of machine learning, 3) discuss why ML methods are underutilized in natural science, and 4) propose solutions for barriers preventing wider ML adoption.
ecology, machine learning, earth science, statistical learning
Machine Learning (ML) is a discipline of computer science that develops dynamic algorithms capable of datadriven decisions, in contrast to models that follow static programming instructions. The very first mention of ‘machine learning’ in the literature occurred in 1930 and use of the term has been growing steadily since 1980 (
Use of the phrase ‘machine learning’ in the Google Books Ngram Viewer: This plot shows the use of the phrase ‘machine learning’ by decade as percentage of total words in the Google English Corpus. http://books.google.com/ngrams
The advantage of ML over traditional statistical techniques, especially in earth science and ecology, is the ability to model highly dimensional and nonlinear data with complex interactions and missing values (
The exact division between ML methods and traditional statistical techniques is not always clear and ML methods are not always better than traditional statistics. For example, a system may not be linear, but a linear approximation of that system may still yield the best predictor. The exact method(s) must be chosen based on the problem at hand. A meta approach that considers the results of multiple algorithms may be best. This manuscript will discuss four types of ML tasks and seven important limitations of ML methods. These tasks and limitations will be related to six types of ML techniques and their relative strengths and weaknesses in ecology and earth science will be discussed. Specific applications of ML in ecology and earth science will be briefly reviewed with the reasons ML methods are underutilized in natural sciences. Potential solutions will be proposed.
The basic premise of ML is that a machine (i.e., algorithm or model) is able to make new predictions based on data. The basic technique behind all ML methods is an iterative combination of statistics and error minimization or reward maximization, applied and combined in varying degrees. Many ML algorithms iteratively check all or a very high number of possible outcomes to find the best result, with “best” defined by the user for the problem at hand. The potentially high number of iterations is prohibitive of manual calculations and is a large part of why these methods are only now widely available to individual researchers.
Computing power has increased such that ML methods can be implemented with a desktop or even a laptop. Before the current availability of computing power, ecologists and earth scientists had to settle for statistical methods that assumed linearity (
The first step in applying ML is teaching the algorithm using a training data set. The training data set is a collection of independent variables with the corresponding dependent variables. The machine uses the training data to “learn” how the independent variables (input) relate to the dependent variable (output). Later, when the algorithm is applied to new input data, it can apply that relationship and return a prediction. After the algorithm is trained, it needs to be tested to get a measure of how well it can make predictions from new data. This requires another data set with independent and dependent variables, but the dependent variables (target) are not provided to the learner. The algorithm predictions (output) are compared to the withheld data (target) to determine the quality of the predictions and thus the utility of the algorithm. This comparison is an important difference between ML and traditional statistical techniques that use p values for validation.
**A Note on Terms: The interdisciplinary nature of ML and its application has resulted in a confusing collection of terms for similar concepts. Below are groups of functional synonyms describing the major concepts discussed in this manuscript.
There are four different types of tasks that will be discussed in the context of available ML techniques and natural science problems. Most ML techniques can be used to perform multiple tasks and several tasks can be used in combination to address the same problem; therefore, it can be difficult to draw firm boundaries around categories of tasks and techniques. Many of the natural science problems discussed in the latter half of this paper have been addressed using all of the tasks and techniques discussed. The list below is not meant to be comprehensive. Only the tasks most relevant to the natural science applications are discussed here. Each ML technique mentioned here is more thoroughly discussed in its own section.
Task 1) Function Approximation. In this task, the machine inferrs a function from (x,y) data points, which are real numbers (
Task 2) Classification. This process assigns a new observation to a category based on training data (
Task 3) Clustering. This task is similar to classification, but the machine is not given training data to learn what the classes are (
Task 4) Rule Induction. This task extracts a set of formal rules from a set of observations, which can be used to make predictions about new data. Fuzzy Inference and some Treebased ML techniques use rule induction to make predictions. Genetic Algoriothms can be used to infer rules (
As with any technique, a working knowledge of the limitations of ML is necessary for proper application (
1) Demanding Perfection. Algorithms that perfectly model training data are not very useful. This is due to overfitting and it happens when an algorithm is so good at modeling the training data that it does not perform well in the "real world" (
Comparison of performance of two algorithms (grey lines) on hypothetical training (A) and test (B) data (black points).
As algorithm performance on training data increases, performance on test data increases only to a certain point (dashed line). Increases in performance on training data beyond this point results in overfitting.
2) Favoring Complexity Over Simplicity. It is important for a problem to be addressed with just the right amount of complexity and this varies according to the nature of the problem and the data (e.g.
3) Including As Many Features As Possible. It can be difficult to know a priori which features are important predictors in a given problem, but including a large number of features in a model (i.e. a shotgun approach), especially features that are not relevant, can make a model a poor predictor
The second type of limitation results from not recognizing imperfections in data sets (
1) Class imbalance. This problem occurs when one or more classes are underrepresented compared to the others (
2) Too many categories. This problem is related to the Curse of Dimensionality and it occurs when a category has a high number of distinct values (i.e. high cardinality,
3) Missing data. Different types of learners and problems have different levels of tolerance for missing data during training, testing, and prediction (see discussion of ML techniques below). There are several methods for applying ML techniques to data with missing values (
4) Outliers. If the observations are real and not the result of human error, outliers can be an important source of insight. They only become a problem when they go unnoticed and models are applied to a data set as though outliers are not present. There are many methods for outlier detection that are recommended as a preprocessing step before ML (
Treebased Methods
Treebased ML methods include decision trees, classification trees, and regression trees (
Decision and Classification Tree Schematic: Treebased machine learning methods infer rules for splitting a data set into more homogeneous data sets until a specified number of terminal classes or maximum variance within the terminal classes is reached. The inferred splitting rules can give additional information about the system being studied.
Random Forest is a relatively new treebased method that fits a userselected number of trees to a data set and then combines the predictions from all trees (
Ensemble treebased methods, especially Random Forest, have been demonstrated to outperform traditional statistical methods and other ML methods in earth science and ecology applications (
For a more detailed description of treebased methods see
Artificial Neural Networks
An Artificial Neural Network (ANN) is a ML approach inspired by the way neurological systems process information (
Artificial Neural Network Schematic: A neural network is made up of three layers (input, hidden, output). Each layer contains interconnected units (neurons). Each connection has an assigned connection weight. The number of hidden units and the connection weights are iteratively improved to minimize the error between the output and the target.
ANN can be a powerful modeling tool when the underlying relationships are unknown and the data are imprecise and noisy (
For a more detailed description of a multilayer, feedforward ANN with back propagation see section 4.1 in
Support Vector Machines
A Support Vector Machine (SVM) is a type of binary classifier. Data are represented as points in space and classes are divided by a straight line "margin". The SVM maximizes the margin by placing the largest possible distance between the margin and the instances on both sides (
Support Vector Machine Schematic
SVM is well suited for problems with many features compared to instances (Curse of Dimensionality) and is capable of avoiding problems with local minima (
For a more detailed description of SVMs see section 6 in
Genetic Algorithm
Genetic Algorithms (GA) are based on the process of evolution in natural systems in that a population of competing solutions evolves over time to converge on an optimal solution (
Genetic Algorithm Schematic: In this simplified schematic of a genetic algorithm, the five potential solutions, or “chromosomes”, undergo mutation and recombination. Then the best performing solutions are selected for another iteration of mutation and recombination. This cycle is repeated until an optimal solution is found.
An advantage of GA is the removal of the often arbitrary process of choosing a model to apply to the data (
For a more detailed discussion of GA see
Fuzzy Inference Systems
Fuzzy inference methods, such as Fuzzy Logic and Inductive Logic Programming, provide a practical approach to automating complex analysis and inference in a long workflow (
Fuzzy Inference Rule Set. This is a simplified example of an "if/then" rule set derived from data (in the table) using fuzzy inference. The inferred rules can be used to predict when an allowanced with be dispensed.
Fuzzy inference systems perform a rule induction task. The resulting rules can be easy to understand and interpret, as long as the rule sets are not too large, but overfitting can be a problem (
For more information about fuzzy inference systems and rule induction see
Bayesian Methods
Bayesian ML methods are based on Bayesian statistical inference, which started in the 18th century with the development of Bayes’ theorem (
Bayesian Classifier Schematic: This diagram shows a simplified schematic of a Bayesian classifier working to assign a new datum (white triangle) to one of two classes (grey and black).
A Bayesian classifier gives good results in most cases and requires fewer training data compared to other ML methods (
For a more detailed discussion of Bayesian Classifiers and Bayesian Networks see section 5.1 in
For many researchers, machine learning is a relatively new paradigm that has only recently become accessible with the development of modern computing. While the adoption of ML methods in earth science and ecology has been slow, there are several published studies using ML in these disciplines (e.g.,
Habitat Modeling and Species Distribution
Understanding the habitat requirements of a species is important for understanding its ecology and managing its conservation. Habitat modelers are interested in using multiple data sets to make predictions and classifications about habitat characteristics and where taxa are likely to be located or engaging in a specific behavior (e.g., nesting
Species Identification
Identifying taxa can require specialized knowledge only possessed by a very few and the data set requiring expert curation can be large (e.g., automated collection of images and sounds). Thus, the expert annotation step is a major bottleneck in biodiversity studies. In order to increase throughput, algorithms are trained on images, sounds, and other types of data labeled with taxon names. (For more information about automated taxon identification specifically, see
Remote Sensing
Satellite images and other data gathered from sensors at great elevation (e.g., LIDAR) are an excellent way to gather large amounts of data about Earth over broad spatial scales. In order to be useful, these data must go through some minimum level of processing (
Resource Management
Making decisions about conservation and resource management can be very difficult because there is often not enough data for certainty and the consequences of being wrong can be disastrous. ML methods can provide a means of increasing certainty and improving results, especially techniques that incorporate Bayesian probabilities. Several algorithms have been applied to water (
Forecasting
Discovery of deterministic chaos in meteorological models (
Environmental Protection and Safety
Just as ML can help resource managers make important decisions with or without adequate data coverage, environmental protection and safety decisions can be aided with ML methods when data are sparse. ML has been used to classify environmental samples into inferred quality classes in situations where direct analyses are too costly (
Climate Change Studies
One of the more pressing societal problems is the mitigation of and adaptation to climate change. Policymakers require wellformed predictions in order to make decisions, but the complexity of the climate system, the interdisciplinary nature of the problem, and the data structures prevents the effective use of linear modeling techniques. ML is used to study important processes such as El Niño, the Quasi Biennial Oscillation, the MaddenJulian Oscillation, and monsoon modes (
The application of ML methods in ecology and earth science has already demonstrated the potential for increasing the quality and accelerating the pace of science. One of the more obvious ways ML does this is by coping with data gaps. The Earth is undersampled, despite spending hundreds of millions of dollars on earth and environmental science (e.g.,
ML can accelerate the pace of science by quickly performing complex classification tasks normally performed by a human. A bottleneck in many ecology and earth science workflows are the manual steps performed by an expert, usually a classification task such as identifying a species. Expert annotation can be even more time consuming when the expert must search through a large volume of data, like a sensor stream, for a desired signal (
As discussed above, ML techniques can perform better than traditional statistical methods in some systems, but a direct comparison of performance between ML techniques and traditional statistical methods is difficult because there is no universal measure of performance and results can be very situationspecific (
Even though ML can outperform traditional statistics in some applications (
Another barrier to using ML techniques is the need for adequate amounts of training and test data within the desired range of prediction. This places an important constraint on the application of ML to problems that have appropriate, annotated data sets available. For example, the Google image recognition algorithm was developed using 1.2 million annotated images (
This combination of lack of formal education and important data restrictions can lead to naive applications of ML techniques, which can increase resistence to their adoption.
Finally, communication between the ML research community and natural science research community is poor (
How can the use of ML methods in ecology and earth science be encouraged? One barrier that has been partially lowered is the lack of tools and services to support the application of ML in these domains. Use of ML algorithms built with user infrastructure, such as GRASSGIS (
Research scientists want to have a good understanding of the algorithms they use, which makes adoption of a new method a nontrivial investment. Reducing the cost of this investment for ML techniques is an important part of encouraging adoption. One way to do this is through a trusted collaborator who can simultaneously guide the research and transfer skills. These collaborators can be difficult to find, but many potential partners can be found in industry. A useful tool would be a publiclyavailable repository of annotated data sets to act as a sandbox for researchers wanting to learn and experiment with these methods, similar to Kaggle (https://www.kaggle.com/) but with natural science data. Random Forest is easier for a beginner to implement, gives easy to interpret results, and has high performance on ecology and earth science classification problems (
Finally, ML successes and impacts in ecology and earth science need to be more effectively communicated and the results from ML analyses need to be easily interpreted for decisionmakers (
Funding agencies can facilitate this process by specifically soliciting new collaborative projects (research projects, workshops, hackathons, conference sessions) that apply ML methods to ecology and earth science in innovative ways and initiatives to develop education materials for natural science students. Proper implementation of ML methods requires an understanding of the data science and the discipline that can best be achieved through interdisciplinary collaboration.
ML methods offer a diverse array of techniques, now accessible to individual researchers, that are well suited to the complex data sets coming from ecology and earth science. These methods have the potential to improve the quality of scientific research by providing more accurate models and accelerate progress in science by widening bottlenecks, filling data gaps, and enhancing understanding of how systems work. Application of these methods within the ecology and earth science domain needs to increase if society is to see the benefit. Adoption can be promoted through interdisciplinary collaboration, increased communication, increased formal and informal education, and financial support for ML research. Partnerships with companies interested in environmental issues can be an excellent source of knowledge transfer. A good introductory ML method is Random Forest, which is easy to implement and gives good results. However, ML methods have limitations and are not the answer to all problems. In some cases traditional statistical approaches are more appropriate (
There are many more types of ML methods and subtly different techniques than what has been discussed in this paper. Implementing ML effectively requires additional background knowledge. A very helpful series of lectures by Stanford Professors Trevor Hastie and Rob Tibshirani called “An Introduction to Statistical Learning with Applications in R” can be accessed online for free and gives a general introduction to traditional statistics and some ML methods. Kaggle (https://www.kaggle.com/) is an excellent source of independent, handson data science lessons. A suggested introductory text is "Machine Learning Methods in the Environmental Sciences", by William Hsieh (
The author would like to acknowledge NASA for financial support and the Boston Machine Learning Meetup Group for inspiration. This paper was greatly improved by comments from Ronny Peters (reviewer), Christopher W. Lloyd, Holly A. Bowers, Alan H. Fielding, and Joseph Gormley.