Deep Neural Architectures for Highly Imbalanced Data in Bioinformatics

Machine and Deep Learning Methods for Predicting 3D Genome Organization

Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers and transcription factor binding site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, and TAD boundaries) and analyze their pros and cons. We also point out obstacles to the computational prediction of 3D interactions and suggest future research directions.

Class imbalance on medical image classification: towards better evaluation practices for discrimination and calibration performance

PURPOSE

This work aims to assess standard evaluation practices used by the research community for evaluating medical imaging classifiers, with a specific focus on the implications of class imbalance. The analysis is performed on chest X-rays as a case study and encompasses a comprehensive model performance definition, considering both discriminative capabilities and model calibration.

MATERIALS AND METHODS

We conduct a concise literature review to examine prevailing scientific practices used when evaluating X-ray classifiers. Then, we perform a systematic experiment on two major chest X-ray datasets to showcase a didactic example of the behavior of several performance metrics under different class ratios and highlight how widely adopted metrics can conceal performance in the minority class.

RESULTS

Our literature study confirms that: (1) even when dealing with highly imbalanced datasets, the community tends to use metrics that are dominated by the majority class; and (2) it is still uncommon to include calibration studies for chest X-ray classifiers, albeit its importance in the context of healthcare. Moreover, our systematic experiments confirm that current evaluation practices may not reflect model performance in real clinical scenarios and suggest complementary metrics to better reflect the performance of the system in such scenarios.

CONCLUSION

Our analysis underscores the need for enhanced evaluation practices, particularly in the context of class-imbalanced chest X-ray classifiers. We recommend the inclusion of complementary metrics such as the area under the precision-recall curve (AUC-PR), adjusted AUC-PR, and balanced Brier score, to offer a more accurate depiction of system performance in real clinical scenarios, considering metrics that reflect both, discrimination and calibration performance.

CLINICAL RELEVANCE STATEMENT

This study underscores the critical need for refined evaluation metrics in medical imaging classifiers, emphasizing that prevalent metrics may mask poor performance in minority classes, potentially impacting clinical diagnoses and healthcare outcomes.

KEY POINTS

Common scientific practices in papers dealing with X-ray computer-assisted diagnosis (CAD) systems may be misleading. We highlight limitations in reporting of evaluation metrics for X-ray CAD systems in highly imbalanced scenarios. We propose adopting alternative metrics based on experimental evaluation on large-scale datasets.

Single-Cell RNA-Seq Debiased Clustering via Batch Effect Disentanglement

A variety of single-cell RNA-seq (scRNA-seq) clustering methods has achieved great success in discovering cellular phenotypes. However, it remains challenging when the data confounds with batch effects brought by different experimental conditions or technologies. Namely, the data partitions would be biased toward these nonbiological factors. Meanwhile, the batch differences are not always much smaller than true biological variations, hindering the cooperation of batch integration and clustering methods. To overcome this challenge, we propose single-cell RNA-seq debiased clustering (SCDC), an end-to-end clustering method that is debiased toward batch effects by disentangling the biological and nonbiological information from scRNA-seq data during data partitioning. In six analyses, SCDC qualitatively and quantitatively outperforms both the state-of-the-art clustering and batch integration methods in handling scRNA-seq data with batch effects. Furthermore, SCDC clusters data with a linearly increasing running time with respect to cell numbers and a fixed graphics processing unit (GPU) memory consumption, making it scalable to large datasets. The code will be released on Github.

Meta Learning With Graph Attention Networks for Low-Data Drug Discovery

Finding candidate molecules with favorable pharmacological activity, low toxicity, and proper pharmacokinetic properties is an important task in drug discovery. Deep neural networks have made impressive progress in accelerating and improving drug discovery. However, these techniques rely on a large amount of label data to form accurate predictions of molecular properties. At each stage of the drug discovery pipeline, usually, only a few biological data of candidate molecules and derivatives are available, indicating that the application of deep neural networks for low-data drug discovery is still a formidable challenge. Here, we propose a meta learning architecture with graph attention network, Meta-GAT, to predict molecular properties in low-data drug discovery. The GAT captures the local effects of atomic groups at the atom level through the triple attentional mechanism and implicitly captures the interactions between different atomic groups at the molecular level. GAT is used to perceive molecular chemical environment and connectivity, thereby effectively reducing sample complexity. Meta-GAT further develops a meta learning strategy based on bilevel optimization, which transfers meta knowledge from other attribute prediction tasks to low-data target tasks. In summary, our work demonstrates how meta learning can reduce the amount of data required to make meaningful predictions of molecules in low-data scenarios. Meta learning is likely to become the new learning paradigm in low-data drug discovery. The source code is publicly available at: https://github.com/lol88/Meta-GAT.

Deep learning-based prediction of post-pancreaticoduodenectomy pancreatic fistula

Postoperative pancreatic fistula is a life-threatening complication with an unmet need for accurate prediction. This study was aimed to develop preoperative artificial intelligence-based prediction models. Patients who underwent pancreaticoduodenectomy were enrolled and stratified into model development and validation sets by surgery between 2016 and 2017 or in 2018, respectively. Machine learning models based on clinical and body composition data, and deep learning models based on computed tomographic data, were developed, combined by ensemble voting, and final models were selected comparison with earlier model. Among the 1333 participants (training, n = 881; test, n = 452), postoperative pancreatic fistula occurred in 421 (47.8%) and 134 (31.8%) and clinically relevant postoperative pancreatic fistula occurred in 59 (6.7%) and 27 (6.0%) participants in the training and test datasets, respectively. In the test dataset, the area under the receiver operating curve [AUC (95% confidence interval)] of the selected preoperative model for predicting all and clinically relevant postoperative pancreatic fistula was 0.75 (0.71-0.80) and 0.68 (0.58-0.78). The ensemble model showed better predictive performance than the individual ML and DL models.

Challenges in the real world use of classification accuracy metrics: From recall and precision to the Matthews correlation coefficient

The accuracy of a classification is fundamental to its interpretation, use and ultimately decision making. Unfortunately, the apparent accuracy assessed can differ greatly from the true accuracy. Mis-estimation of classification accuracy metrics and associated mis-interpretations are often due to variations in prevalence and the use of an imperfect reference standard. The fundamental issues underlying the problems associated with variations in prevalence and reference standard quality are revisited here for binary classifications with particular attention focused on the use of the Matthews correlation coefficient (MCC). A key attribute claimed of the MCC is that a high value can only be attained when the classification performed well on both classes in a binary classification. However, it is shown here that the apparent magnitude of a set of popular accuracy metrics used in fields such as computer science medicine and environmental science (Recall, Precision, Specificity, Negative Predictive Value, J, F1, likelihood ratios and MCC) and one key attribute (prevalence) were all influenced greatly by variations in prevalence and use of an imperfect reference standard. Simulations using realistic values for data quality in applications such as remote sensing showed each metric varied over the range of possible prevalence and at differing levels of reference standard quality. The direction and magnitude of accuracy metric mis-estimation were a function of prevalence and the size and nature of the imperfections in the reference standard. It was evident that the apparent MCC could be substantially under- or over-estimated. Additionally, a high apparent MCC arose from an unquestionably poor classification. As with some other metrics of accuracy, the utility of the MCC may be overstated and apparent values need to be interpreted with caution. Apparent accuracy and prevalence values can be mis-leading and calls for the issues to be recognised and addressed should be heeded.

MicroRNAs as powerful tool against COVID-19: Computational perspective

Severe acute respiratory syndrome coronavirus 2 is the virus that is responsible for the current pandemic, COVID-19 (SARS-CoV-2). MiRNAs, a component of RNAi technology, belong to the family of short, noncoding ssRNAs, and may be crucial in the battle against this global threat since they are involved in regulating complex biochemical pathways and may prevent viral proliferation, translation, and host expression. The complicated metabolic pathways are modulated by the activity of many proteins, mRNAs, and miRNAs working together in miRNA-mediated genetic control. The amount of omics data has increased dramatically in recent years. This massive, linked, yet complex metabolic regulatory network data offers a wealth of opportunity for iterative analysis; hence, extensive, in-depth, but time-efficient screening is necessary to acquire fresh discoveries; this is readily performed with the use of bioinformatics. We have reviewed the literature on microRNAs, bioinformatics, and COVID-19 infection to summarize (1) the function of miRNAs in combating COVID-19, and (2) the use of computational methods in combating COVID-19 in certain noteworthy studies, and (3) computational tools used by these studies against COVID-19 in several purposes. This article is categorized under: Infectious Diseases > Computational Models.

DeepSMOTE: Fusing Deep Learning and SMOTE for Imbalanced Data

Despite over two decades of progress, imbalanced data is still considered a significant challenge for contemporary machine learning models. Modern advances in deep learning have further magnified the importance of the imbalanced data problem, especially when learning from images. Therefore, there is a need for an oversampling method that is specifically tailored to deep learning models, can work on raw images while preserving their properties, and is capable of generating high-quality, artificial images that can enhance minority classes and balance the training set. We propose Deep synthetic minority oversampling technique (SMOTE), a novel oversampling algorithm for deep learning models that leverages the properties of the successful SMOTE algorithm. It is simple, yet effective in its design. It consists of three major components: 1) an encoder/decoder framework; 2) SMOTE-based oversampling; and 3) a dedicated loss function that is enhanced with a penalty term. An important advantage of DeepSMOTE over generative adversarial network (GAN)-based oversampling is that DeepSMOTE does not require a discriminator, and it generates high-quality artificial images that are both information-rich and suitable for visual inspection. DeepSMOTE code is publicly available at https://github.com/dd1github/DeepSMOTE.

Class-Imbalanced Deep Learning via a Class-Balanced Ensemble

Class imbalance is a prevalent phenomenon in various real-world applications and it presents significant challenges to model learning, including deep learning. In this work, we embed ensemble learning into the deep convolutional neural networks (CNNs) to tackle the class-imbalanced learning problem. An ensemble of auxiliary classifiers branching out from various hidden layers of a CNN is trained together with the CNN in an end-to-end manner. To that end, we designed a new loss function that can rectify the bias toward the majority classes by forcing the CNN's hidden layers and its associated auxiliary classifiers to focus on the samples that have been misclassified by previous layers, thus enabling subsequent layers to develop diverse behavior and fix the errors of previous layers in a batch-wise manner. A unique feature of the new method is that the ensemble of auxiliary classifiers can work together with the main CNN to form a more powerful combined classifier, or can be removed after finished training the CNN and thus only acting the role of assisting class imbalance learning of the CNN to enhance the neural network's capability in dealing with class-imbalanced data. Comprehensive experiments are conducted on four benchmark data sets of increasing complexity (CIFAR-10, CIFAR-100, iNaturalist, and CelebA) and the results demonstrate significant performance improvements over the state-of-the-art deep imbalance learning methods.

Robust and efficient COVID-19 detection techniques: A machine learning approach

The devastating impact of the Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) pandemic almost halted the global economy and is responsible for 6 million deaths with infection rates of over 524 million. With significant reservations, initially, the SARS-CoV-2 virus was suspected to be infected by and closely related to Bats. However, over the periods of learning and critical development of experimental evidence, it is found to have some similarities with several gene clusters and virus proteins identified in animal-human transmission. Despite this substantial evidence and learnings, there is limited exploration regarding the SARS-CoV-2 genome to putative microRNAs (miRNAs) in the virus life cycle. In this context, this paper presents a detection method of SARS-CoV-2 precursor-miRNAs (pre-miRNAs) that helps to identify a quick detection of specific ribonucleic acid (RNAs). The approach employs an artificial neural network and proposes a model that estimated accuracy of 98.24%. The sampling technique includes a random selection of highly unbalanced datasets for reducing class imbalance following the application of matriculation artificial neural network that includes accuracy curve, loss curve, and confusion matrix. The classical approach to machine learning is then compared with the model and its performance. The proposed approach would be beneficial in identifying the target regions of RNA and better recognising of SARS-CoV-2 genome sequence to design oligonucleotide-based drugs against the genetic structure of the virus.

Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine

Precision medicine uses genetic, environmental and lifestyle factors to more accurately diagnose and treat disease in specific groups of patients, and it is considered one of the most promising medical efforts of our time. The use of genetics is arguably the most data-rich and complex components of precision medicine. The grand challenge today is the successful assimilation of genetics into precision medicine that translates across different ancestries, diverse diseases and other distinct populations, which will require clever use of artificial intelligence (AI) and machine learning (ML) methods. Our goal here was to review and compare scientific objectives, methodologies, datasets, data sources, ethics and gaps of AI/ML approaches used in genomics and precision medicine. We selected high-quality literature published within the last 5 years that were indexed and available through PubMed Central. Our scope was narrowed to articles that reported application of AI/ML algorithms for statistical and predictive analyses using whole genome and/or whole exome sequencing for gene variants, and RNA-seq and microarrays for gene expression. We did not limit our search to specific diseases or data sources. Based on the scope of our review and comparative analysis criteria, we identified 32 different AI/ML approaches applied in variable genomics studies and report widely adapted AI/ML algorithms for predictive diagnostics across several diseases.

Hybrid Deep Neural Network for Handling Data Imbalance in Precursor MicroRNA

Over the last decade, the field of bioinformatics has been increasing rapidly. Robust bioinformatics tools are going to play a vital role in future progress. Scientists working in the field of bioinformatics conduct a large number of researches to extract knowledge from the biological data available. Several bioinformatics issues have evolved as a result of the creation of massive amounts of unbalanced data. The classification of precursor microRNA (pre miRNA) from the imbalanced RNA genome data is one such problem. The examinations proved that pre miRNAs (precursor microRNAs) could serve as oncogene or tumor suppressors in various cancer types. This paper introduces a Hybrid Deep Neural Network framework (H-DNN) for the classification of pre miRNA in imbalanced data. The proposed H-DNN framework is an integration of Deep Artificial Neural Networks (Deep ANN) and Deep Decision Tree Classifiers. The Deep ANN in the proposed H-DNN helps to extract the meaningful features and the Deep Decision Tree Classifier helps to classify the pre miRNA accurately. Experimentation of H-DNN was done with genomes of animals, plants, humans, and Arabidopsis with an imbalance ratio up to 1:5000 and virus with a ratio of 1:400. Experimental results showed an accuracy of more than 99% in all the cases and the time complexity of the proposed H-DNN is also very less when compared with the other existing approaches.

Deep Learning for the discovery of new pre-miRNAs: Helping the fight against COVID-19

The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has been recently found responsible for the pandemic outbreak of a novel coronavirus disease (COVID-19). In this work, a novel approach based on deep learning is proposed for identifying precursors of small active RNA molecules named microRNA (miRNA) in the genome of the novel coronavirus. Viral miRNA-like molecules have shown to modulate the host transcriptome during the infection progression, thus their identification is crucial for helping the diagnosis or medical treatment of the disease. The existence of the mature miRNAs derived from computationally predicted miRNA precursors (pre-miRNAs) in the novel coronavirus was validated with small RNA-seq data from SARS-CoV-2-infected human cells. The results demonstrate that computational models can provide accurate and useful predictions of pre-miRNAs in the SARS-CoV-2 genome, underscoring the relevance of machine learning in the response to a global sanitary emergency. Moreover, the interpretability of our model shed light on the molecular mechanisms underlying the viral infection, thus contributing to the fight against the COVID-19 pandemic and the fast development of new treatments. Our study shows how recent advances in machine learning can be used, effectively, in response to public health emergencies. The approach developed in this work could be of great help in future similar emergencies to accelerate the understanding of the singularities of any viral agent and for the development of novel therapies. Data and source code available at: https://sourceforge.net/projects/sourcesinc/files/aicovid/.

Can Boosted Randomness Mimic Learning Algorithms of Geometric Nature? Example of a Simple Algorithm That Converges in Probability to Hard-Margin SVM

In the light of the general question posed in the title, we write down a very simple randomized learning algorithm, based on boosting, that can be seen as a nonstationary Markov random process. Surprisingly, the decision hyperplanes resulting from this algorithm converge in probability to the exact hard-margin solutions of support vector machines (SVMs). This fact is curious because the hard-margin hyperplane is not a statistical solution, but a purely geometric one-driven by margin maximization and strictly dependent on particular locations of some data points that are placed in the contact region of two classes, namely the support vectors. The proposed algorithm detects support vectors probabilistically, without being aware of their geometric definition. We give proofs of the main convergence theorem and several auxiliary lemmas. The analysis sheds new light on the relation between boosting and SVMs and also on the nature of SVM solutions since they can now be regarded equivalently as limits of certain random trajectories. In the experimental part, correctness of the proposed algorithm is verified against known SVM solvers: libsvm, liblinear, and also against optimization packages: cvxopt (Python) and Wolfram Mathematica.

High precision in microRNA prediction: A novel genome-wide approach with convolutional deep residual networks

MicroRNAs (miRNAs) are small non-coding RNAs that have a key role in the regulation of gene expression. The importance of miRNAs is widely acknowledged by the community nowadays and computational methods are needed for the precise prediction of novel candidates to miRNA. This task can be done by searching homologous with sequence alignment tools, but results are restricted to sequences that are very similar to the known miRNA precursors (pre-miRNAs). Besides, a very important property of pre-miRNAs, their secondary structure, is not taken into account by these methods. To fill this gap, many machine learning approaches were proposed in the last years. However, the methods are generally tested in very controlled conditions. If these methods were used under real conditions, the false positives increase and the precisions fall quite below those published. This work provides a novel approach for dealing with the computational prediction of pre-miRNAs: a convolutional deep residual neural network (mirDNN). This model was tested with several genomes of animals and plants, the full-genomes, achieving a precision up to 5 times larger than other approaches at the same recall rates. Furthermore, a novel validation methodology was used to ensure that the performance reported in this study can be effectively achieved when using mirDNN in novel species. To provide fast an easy access to mirDNN, a web demo is available at http://sinc.unl.edu.ar/web-demo/mirdnn/. The demo can process FASTA files with multiple sequences to calculate the prediction scores and generates the nucleotide importance plots. FULL SOURCE CODE: http://sourceforge.net/projects/sourcesinc/files/mirdnn and https://github.com/cyones/mirDNN. CONTACT: gstegmayer@sinc.unl.edu.ar.

Novel SARS-CoV-2 encoded small RNAs in the passage to humans

Motivation

The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has recently emerged as the responsible for the pandemic outbreak of the coronavirus disease (COVID-19). This virus is closely related to coronaviruses infecting bats and Malayan pangolins, species suspected to be an intermediate host in the passage to humans. Several genomic mutations affecting viral proteins have been identified, contributing to the understanding of the recent animal-to-human transmission. However, the capacity of SARS-CoV-2 to encode functional putative microRNAs (miRNAs) remains largely unexplored.

Results

We have used deep learning to discover 12 candidate stem-loop structures hidden in the viral protein-coding genome. Among the precursors, the expression of eight mature miRNAs-like sequences was confirmed in small RNA-seq data from SARS-CoV-2 infected human cells. Predicted miRNAs are likely to target a subset of human genes of which 109 are transcriptionally deregulated upon infection. Remarkably, 28 of those genes potentially targeted by SARS-CoV-2 miRNAs are down-regulated in infected human cells. Interestingly, most of them have been related to respiratory diseases and viral infection, including several afflictions previously associated with SARS-CoV-1 and SARS-CoV-2. The comparison of SARS-CoV-2 pre-miRNA sequences with those from bat and pangolin coronaviruses suggests that single nucleotide mutations could have helped its progenitors jumping inter-species boundaries, allowing the gain of novel mature miRNAs targeting human mRNAs. Our results suggest that the recent acquisition of novel miRNAs-like sequences in the SARS-CoV-2 genome may have contributed to modulate the transcriptional reprogramming of the new host upon infection.

Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning

MOTIVATION

The genome-wide discovery of microRNAs (miRNAs) involves identifying sequences having the highest chance of being a novel miRNA precursor (pre-miRNA), within all the possible sequences in a complete genome. The known pre-miRNAs are usually just a few in comparison to the millions of candidates that have to be analyzed. This is of particular interest in non-model species and recently sequenced genomes, where the challenge is to find potential pre-miRNAs only from the sequenced genome. The task is unfeasible without the help of computational methods, such as deep learning. However, it is still very difficult to find an accurate predictor, with a low false positive rate in this genome-wide context. Although there are many available tools, these have not been tested in realistic conditions, with sequences from whole genomes and the high class imbalance inherent to such data.

RESULTS

In this work, we review six recent methods for tackling this problem with machine learning. We compare the models in five genome-wide datasets: Arabidopsis thaliana, Caenorhabditis elegans, Anopheles gambiae, Drosophila melanogaster, Homo sapiens. The models have been designed for the pre-miRNAs prediction task, where there is a class of interest that is significantly underrepresented (the known pre-miRNAs) with respect to a very large number of unlabeled samples. It was found that for the smaller genomes and smaller imbalances, all methods perform in a similar way. However, for larger datasets such as the H. sapiens genome, it was found that deep learning approaches using raw information from the sequences reached the best scores, achieving low numbers of false positives.

AVAILABILITY

The source code to reproduce these results is in: http://sourceforge.net/projects/sourcesinc/files/gwmirna Additionally, the datasets are freely available in: https://sourceforge.net/projects/sourcesinc/files/mirdata.

DL4papers: a deep learning approach for the automatic interpretation of scientific articles

Motivation

In precision medicine, next-generation sequencing and novel preclinical reports have led to an increasingly large amount of results, published in the scientific literature. However, identifying novel treatments or predicting a drug response in, for example, cancer patients, from the huge amount of papers available remains a laborious and challenging work. This task can be considered a text mining problem that requires reading a lot of academic documents for identifying a small set of papers describing specific relations between key terms. Due to the infeasibility of the manual curation of these relations, computational methods that can automatically identify them from the available literature are urgently needed.

Results

We present DL4papers, a new method based on deep learning that is capable of analyzing and interpreting papers in order to automatically extract relevant relations between specific keywords. DL4papers receives as input a query with the desired keywords, and it returns a ranked list of papers that contain meaningful associations between the keywords. The comparison against related methods showed that our proposal outperformed them in a cancer corpus. The reliability of the DL4papers output list was also measured, revealing that 100% of the first two documents retrieved for a particular search have relevant relations, in average. This shows that our model can guarantee that in the top-2 papers of the ranked list, the relation can be effectively found. Furthermore, the model is capable of highlighting, within each document, the specific fragments that have the associations of the input keywords. This can be very useful in order to pay attention only to the highlighted text, instead of reading the full paper. We believe that our proposal could be used as an accurate tool for rapidly identifying relationships between genes and their mutations, drug responses and treatments in the context of a certain disease. This new approach can certainly be a very useful and valuable resource for the advancement of the precision medicine field.

Availability and implementation

A web-demo is available at: http://sinc.unl.edu.ar/web-demo/dl4papers/. Full source code and data are available at: https://sourceforge.net/projects/sourcesinc/files/dl4papers/.

Contact

lbugnon@sinc.unl.edu.ar

Supplementary information

Supplementary data are available at Bioinformatics online.

Complexity measures of the mature miRNA for improving pre-miRNAs prediction

Motivation

The discovery of microRNA (miRNA) in the last decade has certainly changed the understanding of gene regulation in the cell. Although a large number of algorithms with different features have been proposed, they still predict an impractical amount of false positives. Most of the proposed features are based on the structure of precursors of the miRNA only, not considering the important and relevant information contained in the mature miRNA. Such new kind of features could certainly improve the performance of the predictors of new miRNAs.

Results

This paper presents three new features that are based on the sequence information contained in the mature miRNA. We will show how these new features, when used by a classical supervised machine learning approach as well as by more recent proposals based on deep learning, improve the prediction performance in a significant way. Moreover, several experimental conditions were defined and tested to evaluate the novel features impact in situations close to genome-wide analysis. The results show that the incorporation of new features based on the mature miRNA allows to improve the detection of new miRNAs independently of the classifier used.

Availability and implementation

https://sourceforge.net/projects/sourcesinc/files/cplxmirna/.

Supplementary information

Supplementary data are available at Bioinformatics online.