An empirical study of ensemble-based semi-supervised learning approaches for imbalanced splice site datasets

Advances in biochemical technologies over the past decades have given rise to Next Generation Sequencing platforms that quickly produce genomic data at much lower costs than ever before. Such overwhelmingly large volumes of sequenced DNA remain difficult to annotate. As a result, numerous computational methods for genome annotation have emerged, including machine learning and statistical analysis approaches that practically and efficiently analyze and interpret data. Supervised machine learning algorithms typically perform well when large amounts of labeled data are available. In bioinformatics and many other data-rich disciplines, the process of labeling instances is costly; however, unlabeled instances are inexpensive and readily available. For a scenario in which the amount of labeled data is relatively small and the amount of unlabeled data is substantially larger, semi-supervised learning represents a cost-effective alternative to manual labeling.

Because semi-supervised learning algorithms use both labeled and unlabeled instances in the training process, they can produce classifiers that achieve better performance than completely supervised learning algorithms that have only a small amount of labeled data available for training [1–3]. The principle behind semi-supervised learning is that intrinsic knowledge within unlabeled data can be lever-aged in order to strengthen the prediction capability of a supervised model that only uses labeled instances, thereby providing a potential advantage for semi-supervised learning. Model parameters learned by a supervised classifier from a small amount of labeled data may be steered towards a more realistic distribution (which more closely resembles the distribution of the test data) by the unlabeled data.

Unfortunately, unlabeled data can also drive the model parameters away from the true distribution if misclassification errors reinforce themselves. Thus, in practice, semi-supervised learning does not always work as intended [4–6]. Moreover, under incorrect assumptions, e.g., regarding the relationship between marginal and conditional distributions of data, semi-supervised learning models risk to perform worse than their supervised counterparts. Given that for many prediction problems the assumptions made by learning algorithms cannot be easily verified without considerable domain knowledge [7] or data exploration, semi-supervised learning is not always "safe" to use. Advantageous utilization of the unlabeled data is problem-dependent, and more research is needed to identify algorithms that can be used to increase the effectiveness of semi-supervised learning [8, 9], in general, and for bioinformatics problems, in particular. At a high level, we aim to identify semi-supervised algorithms that can be used to learn effective classifiers for genome annotation tasks.

In this context, a specific challenge that we address is the "data imbalance" problem, which is prevalent in many domains, including bioinformatics. The data imbalance phenomenon arises when one of the classes to be predicted is underrepresented in the data because instances belonging to that class are rare (noteworthy cases) or hard to obtain. Ironically, minority classes are typically the most important to learn, because they may be associated with special cases. In general, anomaly or novelty detection problems exhibit highly imbalanced distributions. Specific applications outside the bioinformatics area include credit card fraud, cyber intrusions, medical diagnosis, face recognition, defect detection in error-prone software modules, etc. As established in the literature (e.g., [10]), the existence of a major unevenness between the prior class probabilities leads to impartial learning. As a result, classifiers that produce good classification results under normal circumstances (i.e., in the presence of balanced or mildly imbalanced distributions) can be seriously compromised when faced with skewed distributions, as classifiers become strongly biased towards the majority class. In bioinformatics, problems such as promoter recognition, splice site detection, and protein classification are especially difficult because these problems naturally exhibit highly imbalanced distributions.

Resampling datasets in order to reach balanced distributions is a common practice that sometimes improves classification performance, as the model encounters an equal number of instances from each class, thereby producing a more appropriate discriminative function as opposed to a function obtained from skewed distributions. However, it is not well understood what is the most appropriate balancing method. Context-dependent conclusions are usually driven by empirical observations concerning both the classifier used and the imbalance degree. The most straightforward method is under-sampling, in which instances that belong to the majority class are eliminated until a balanced distribution is reached. As a consequence, information is lost, which is obviously not desirable, given the value of labeled instances, yet this is a good way to speed up the computation. Moreover, studies have shown the effectiveness of under-sampling [11] despite its obvious limitations. Over-sampling is another popular resampling method in which instances of the minority class are generated artificially to counterbalance majority instances. These synthetic instances can potentially improve the classifier, as it gains access to more labeled data. The trade-off between longer computation times associated with larger datasets and better classification performance is usually worthwhile. However, with oversampling, classifiers are prone to overfitting, due to duplicate instances.

An algorithmic approach to handle imbalanced data distributions is based on ensembles of classifiers. Limited amounts of labeled data naturally lead to "weaker" classifiers, but ensembles of "weak" classifiers tend to surpass the performance of any single constituent classifier. Moreover, ensembles typically improve the prediction accuracy obtained from a single classifier by a factor that validates the effort and cost associated with learning multiple models. Intuitively, "bagging" several classifiers leads to better overfitting control, since averaging the high variability of individual classifiers also averages the classifiers' overfitting. The first effective model ensemble surfaced in the mid 1990s [12], under the name "bootstrap aggregating" (bagging), which is a meta-algorithm that performs model averaging over models trained on multiple subsets, i.e., bootstrap replicates of the training set. The predictions of the models are combined by voting (in the case of classification) or averaging (in the case of regression) in order to output a single final verdict that reflects the ensemble decision. Originally applied to decision trees, bagging can be used with any classification or regression model and it is especially effective in conjunction with utilization of unstable nonlinear models (i.e., a small change in the training set can cause a significant change in the model's learned parameters). Ensembles of classifiers that utilize bagging, boosting, and hybrid-approaches for imbalanced datasets in the supervised framework were reviewed by Galar et al. [13].

For a comprehensive survey of data resampling and algorithmic approaches to the imbalanced data problem in the supervised learning framework, the reader is referred to [14]. As opposed to supervised learning, fewer efforts have been aimed at the data imbalance problem in the semi-supervised learning framework, with some notable exceptions. In particular, in a previous study [15], we experimented with data resampling and algorithmic solutions and observed that dynamically balancing the classifiers during the semi-supervised iterations of the algorithm is a useful solution that works better than under- and SMOTE (Synthetic Minority Over-sampling Technique) over-sampling for splice site prediction in the context of single semi-supervised classifiers. We also found that ensembles usually tend to perform better than resampling techniques, except for extreme cases when the imbalance degree is 1-to-99, in which case oversampling performs slightly better than the ensemble-based approach. In a subsequent study [16], we empirically evaluated ensembles of self-training semi-supervised classifiers and found that maintaining diversity during the process of semi-supervised learning is an important requirement for the ensemble. In the current study, we experiment with both self-training and co-training, utilizing a different feature representation than the one we used in [16], to accommodate co-training, which requires two views (representations) of the data.

Similar to our prior work, the current study is performed on the problem of predicting splice sites, a challenging but important task in genome annotation [17]. Splice sites are located at the boundaries between exons and introns. At the 3' end of an intron, the "AG" dimer denotes an acceptor splice site; at the 5' end of the intron, the "GT" dimer denotes a donor splice site. Other non-consensus splice sites exist, but they are not considered in this work. We formulate the task of predicting acceptor splice sites as a binary classification problem in which the positive class represents true acceptor splice sites and the negative class is comprised by decoy "AG" sites. We use five relatively large datasets from five organisms. The distribution of the data (ratio of the size of the minority class to majority class) is very skewed - approximately 1% of "AG" dimers are actually acceptor splice sites.

Among others, Sonnenburg et al. [18] previously addressed the splice site prediction problem, in the supervised framework, using Support Vector Machines (SVM) and specialized kernels. As opposed to prior work, in this work, our goal is to investigate ensemble-based semi-supervised learning as a potential solution for splice site prediction and to study the effects of imbalanced distributions on semi-supervised algorithms when labeled data is sparse. Given the large datasets of our case study and the numerous models that needed to be trained to simulate different imbalanced degrees for different ensemble variants, we chose Naïve Bayes as the base classifier in co-training and self-training, because of its computation speed and to avoid tuning hyper-parameters (that many other classifiers require in order to perform well). Although theoretically, the i.i.d. assumption (that the observed features are identically and independently distributed) does not hold for many problems (including for the problem studied in this work), generative models such as Naïve Bayes can show superior performance to discriminative models such as SVM, especially when small amounts of labeled data are available [19, 20].

The rest of this paper is organized as follows. We continue with a review of related work in the next section, where we also contrast our study with other similar studies. In Methods, we describe our approaches, namely the semi-supervised learning ensembles based on self-training and co-training. The Data section is dedicated to describing the datasets and the feature representation used with our classifiers. The experimental setting is described in Experimental setup, starting with the research questions that motivated the study and continuing with details of the evaluation procedure. We discuss the performance of our approaches in Results, and finally, in the Conclusion section, we conclude the study and suggest directions for future work.

Genome annotation is an ample task that requires machine learning and statistical methods to assist experimental approaches, especially given the large amount of genomic data being generated at unprecedented rates. Supervised machine learning approaches have been widely used in bioinformatics for many tasks, including splice site prediction [18, 21–24]. For example, human splice site detection was explored in [25] using SVM classifiers with a Gaussian kernel, and in [21] using a combination of Markov Models and SVM classifiers with polynomial kernels. The work in [22] proposed a Markov Model approach for splice site detection in a human dataset with imbalance degrees of 1-to-96 for acceptors and 1-to-116 for donors.

Semi-supervised learning has generally been used in bioinformatics to solve protein classification problems [26–31], with a few notable exceptions focused on DNA classification [2, 3]. A small number of studies [32, 26, 33] have explored the data imbalance problem in the semi-supervised context and proposed effective solutions, but the imbalance degrees were moderate. For example, in [32], the authors addressed the problem of molecule activity prediction and experimented with transductive SVM classifiers on datasets with relatively small sizes (3K instances), exhibiting imbalance degrees no higher than 1-to-40.

As opposed to that, we focus on datasets with higher degrees of imbalance (up to 1-to-99) and study the behavior of semi-supervised learning algorithms when the available labeled data is less than 1% of the total amount of training data. In general, such a small amount of labeled data is expected to lead to weak classifiers, but an ensemble of classifiers could help overcome this shortcoming to some extent. Galar et al. [13] showed that, in supervised frameworks, ensembles perform better than single learners trained on resampled data. Lusa and Blagus [34] found that balancing the class prior in the training set via "multiple down-sizing", in other words, training an ensemble of subclassifiers on balanced subsets, is particularly useful for high-dimensional representations. They showed this using a simulated set and a genuine, publicly available dataset from a breast cancer gene expression microarray study. Another study by Li et al. [11] also concluded that an ensemble of co-training classifiers is suitable for imbalanced datasets.

Our objective in this study was to adapt existing semi-supervised learning ensembles to datasets with high degrees of imbalance. Towards this goal, we used the approach from [11] as inspiration for two of the methods presented in this work. In [11], the authors proposed that, as the co-training sub-classifiers iterate, the balanced labeled subsets are augmented with the same instances, specifically, the most confidently labeled positive instances and the most confidently labeled negative instances. In our previous work on the problem of splice site prediction [16], we found that adding different instances to each self-training subsets leads to improved prediction because diversity is maintained. However, it was not clear what was the best way to manipulate the original distribution to ensure the largest diversity among ensemble members. Motivated by the results of our dynamic balancing technique, where only positive instances are added to the training set during the self-training iterations [15], and also by our preliminary results on ensemble approaches based on self-training classifiers [16], in the current study, we further analyze various combinations of ensembles and dynamic balancing, with focus on how the augmentation of labeled data should be managed during the semi-supervised iterations. We also experiment with co-training, in addition to self-training, and investigate how ensembles of self-training and co-training Naïve Bayes classifiers behave in the semi-supervised framework when dealing with various imbalance ratios.

A study from Wei and Dunbrack [35] that explored the effects of various distributions on supervised learning was centered around classification of human missense mutations as deleterious or neutral. By systematically varying the ratio of deleterious to neutral mutations in the training set, the authors concluded that balancing the training dataset improves the performance of SVM as evaluated by several accuracy measures, even when the distribution of the data is just mildly imbalanced. The study in [35] was performed under the assumption that the real distribution of deleterious versus neutral mutations is unknown. In the datasets used in our work [36], the proportion of true splice sites was assumed to be approximately 1% of the total number of occurrences of the "AG" dimer throughout the genome, and thus this was the highest imbalance degree that we experimented with (i.e., 1-to-99). However, we varied the ratio of splice site to non-splice site "AG"s from 1-to-5 to 1-to-99, to perform a systematic study of the performance obtained using ensemble-based semi-supervised approaches as a function of the imbalance ratio.

This section describes the algorithms studied. As we focus on ensemble-based semi-supervised learning from imbalanced class distributions, specifically ensembles of self-training and co-training classifiers, we will first provide background on self-training and co-training, and also on ensemble learning. Then, we will describe the supervised ensemble approach used as a baseline in our evaluation, and finally, our proposed self-training and co-training ensemble variants.

For our empirical evaluation, we used five imbalanced and relatively large datasets, originally published in [36] and used for a domain adaptation study. The datasets belong to five organisms, C. elegans, which contains approximately 120K instances, and C. remanei, P. pacificus, D. melanogaster, and A. thaliana, which contain approximately 160K instances each. In each of these datasets, the true acceptor splice sites represent 1% of the total number of instances, hence the datasets exhibit a 1-to-99 imbalance ratio. The class label of each instance is either positive to indicate a true acceptor splice site, or negative to indicate a decoy splice site.

Algorithm 4 Ensembles that distribute only positive instances - CTEPD/STEPD

1: Given: a training set comprised of labeled and unlabeled data D = (D _l , D _u ), |D _l | ≪ |D _u |

2: Create U by picking S random instances from D _u and update D _u = D _u - U , S = sample size

3: Generate N balanced subsets from D _l : D _{l 1}, . . ., D _ln

4: repeat

5:     for i = 1 to N do

6:         CT: Train subclassifiers C_i1 on view₁ and C_i2 on view₂ of balanced subset D _li

            ST: Train subclassifier C _i on combined views of balanced subset D _li

7:         CT: Classify instances in U using subclassifiers C_i1 and C_i2

            ST: Classify instances in U using subclassifier C _i

8:         CT: Use C_i1 and C_i2 to select 2 positive instances and add them to P

            ST: Use C _i to select 2 positive instances and add them to P

9:         Augment the current balanced subset with positive and negative instances

10:     end for

11:     Discard remaining unused instances from U

12:     Create a new unlabeled sample U and update D _u = D _u - U

13: until U is empty (i.e., the unlabeled data is exhausted)

In our previous work [15, 16], we used 141-dimensional feature vectors to represent instances, $x=\left(x_1,x_2,...,x_N\right)\in {ℝ}^N$ (N = 141). Each dimension corresponds to a position in the original sequences, and takes as values one of the four nucleotides {A, C, G, T }, as shown in Figure 1. Specifically, feature x _i indicates the nucleotide found at the corresponding position i. In the current work, because the co-training algorithm requires two views of the data, we use the nucleotide/position representation as the first view and the 3-nucleotide/position representation from [40] as the second view. As the name suggests, 3-nucleotides are sequences of length 3 (also referred to as 3-mers or "codons"). Intuitively, 3-nucleotides can capture more context information, as compared to single nucleotides. The 3-nucleotide/position representation, thus, captures additional correlations between nucleotides, while maintaining a low number of features (specifically, 139 features for our sequences which have length 141), thereby making the two views comparable. Given that nucleotide/position and 3-nucleotide/position features have shown to be effective in a domain adaptation scenario [40], we hypothesize that semi-supervised learning could also benefit from these feature representations. For self-training, we used the two views together and trained the classifiers on the complete set of features.

1 Which ensembles are more affected by imbalanced distributions, supervised ensembles or semi-supervised ensembles? The supervised baseline remains somewhat constant irrespective of the imbalance degree, showing that additional labeled data can help alleviate problems caused by extreme cases of imbalance. Note that experiments with milder degrees of imbalance contain less instances than experiments with higher degrees of imbalance, given the way we constructed our datasets. When the imbalance degree is the highest, 1-to-99, we used the entire dataset. Compared to supervised learning, semi-supervised learning ensembles show a slow decrease in performance as the imbalance degrees become more prominent, most probably due to the fact that additional unlabeled data is more difficult to label correctly.

2 How does the performance of the approaches vary with the imbalance degree? As can be seen from the table, for lower degrees of imbalance (1-to-5 to 1-to-40), semi-supervised ensembles are considerably surpassing the supervised baselines. As the experiments become increasingly difficult (the imbalance degree becomes more prominent), some semi-supervised ensembles deteriorate as a result of unlabeled data being incorrectly classified with high confidence, and they are surpassed by the supervised baselines.

In the original study [11] that inspired our CTEO and STEO variants, the ensemble approach was used to predict the sentiment polarity of Amazon reviews with imbalance degrees ranging between 1-to-5 and 1-to-8, and proved to be superior to supervised baselines. Our variants, CTEO and STEO, also produced good results for experiments with relatively low imbalance degrees, 1-to-5 and 1-to-10. From 1-to-20 onwards, however, the CTEO and STEO semi-supervised ensembles performed worse than their supervised baselines, but, surprisingly, the self-training ensembles more effectively utilized the unlabeled data as compared to the co-training ensembles. For approaches that employ the "dynamic balancing" technique [39] in which only positive instances are used, the ensemble based on co-training CTEP leveraged the unlabeled data and surpassed the supervised counterpart for experiments with up to 1-to-60 imbalance degree, after which point no discernible difference was observed between CTEP and the baseline. The ensemble based on self-training, STEP, is more sensitive and was deteriorated by the unlabeled data beginning with Experiment 1-to-10. The "pseudo" positive instances could have been misclassified, thereby misleading the classifiers, which all use the same newly labeled positive instances. In general, the ensembles that do not distribute the instances among their subclassifiers deteriorate and fall below the baseline for moderate and high degrees of imbalance. Variants of the algorithms where instances are distributed tend to outperform the other approaches. When both positive and negative instances are used to augment the labeled data, CTEOD and STEOD outperformed the not-distributed versions CTEO and STEO. The self-training based approach STEOD still falls below the supervised baseline for experiments over 1-to-50, but the co-training based approach CTEOD is surpassing the baseline for all experiments. The variants CTEPD and STEPD, which add only positive instances and distribute them, surpassed the baseline for all experiments. No significant difference in performance between CTEOD and CTEPD was observed, but STEPD out-performed STEOD and surpassed the baseline in all experiments. Thus, the "dynamic" balancing approach proved to be more useful for the self-training based ensemble.

3 What is the best strategy for utilizing newly labeled instances when using ensembles of semi-supervised classifiers trained on highly imbalanced data? One important observation that can be made based on our results is that the distribution of the newly labeled instances among subclassifiers in order to ensure subclassifier diversity is a useful approach for semi-supervised ensembles. Variants that distribute the newly labeled instances (either positive and negative for CTEOD and STEOD, or solely positive for CTEPD and STEPD) achieved overall better performance than the classifiers that receive all the newly labeled instances (CTEO, STEO, CTEP, and STEP). Therefore, the conclusion is that diversity in this case is more useful than the addition of substantially more "pseudo" (newly) labeled instances during the semi-supervised iterations.

Our results for the paired t-test showed no particular consistency, specifically some experiments and results were statistically significant and others were not.

In this work, we proposed and studied several ensemble-based variants of two popular semi-supervised learning algorithms, self-training and co-training, and tested their performance on the task of predicting splice sites. The task was formulated as a binary classification problem and the models' performance was tested on five large acceptor splice site datasets from five organisms. We adapted the ensembles to address the highly imbalanced datasets of our case study, and we used various approaches to augment the labeled data during the semi-supervised iterations. Our results showed that one important constraint of any ensemble (based on self-training or co-training) is to maintain diversity of the ensemble's subclassifiers, by augmenting the labeled subsets of subclassifiers with unique newly labeled instances. Maintaining the ensemble diversity by adding less but unique instances to each sub-classifier is a better approach than adding the same (larger sets of) instances to all subclassifiers.

In order to address highly skewed distributions, we found that dynamically balancing of ensembles by utilizing only positive instances during semi-supervised iterations to augment the labeled data and distributing them among constituent subclassifiers is a useful technique that benefits both types of ensembles, but especially the self-training-based approaches. For co-training-based approaches, whether instances from both classes are added (CTEOD) or just positives (CTEPD), the performance variations are negligible. Both approaches CTEPD and CTEOD surpass the other semi-supervised ensembles studied.

In general, our results show that ensembles based on self-training are surpassed by the ensembles based on co-training, a trend that has been reported many times in the literature for single classifiers, e.g., in the prediction of alternatively spliced exons [3], or text classification [5].

As part of future work, we consider exploring other base learners (e.g., large margin classifiers) for self-training and co-training algorithms. Given that aggregated stacking produced the best results for protein function prediction and genetic interactions prediction in [44], it would be interesting to explore meta-learning and ensemble selection for the splice site prediction problem. Transductive approaches demonstrated great potential for protein classification from imbalanced datasets [32], and SVM has previously been shown to successfully identify splice sites [18]. Therefore, the behavior of SVM in a transductive context is of interest in relation to splice site prediction.