Improving protein-protein interactions prediction accuracy using XGBoost feature selection and stacked ensemble classifier

Background and objective The X-ray screening is one of the most popular methodologies in detection of respiratory system diseases. Chest organs are screened on the film or digital file which go to the doctor for evaluation. However, the analysis of x-ray images requires much experience and time. Clinical decision support is very important for medical examinations. The use of Computational Intelligence can simulate the evaluation and decision processes of a medical expert. We propose a method to provide a decision support for the doctor in order to help to consult each case faster and more precisely. Methods We use image descriptors based on the spatial distribution of Hue, Saturation and Brightness values in x-ray images, and a neural network co-working with heuristic algorithms (Moth-Flame, Ant Lion) to detect degenerated lung tissues in x-ray image. The neural network evaluates the image and if the possibility of a respiratory disease is detected, the heuristic method identifies the degenerated tissues in the x-ray image in detail based on the use of the proposed fitness function. Results The average accuracy is 79.06% in pre-detection stage, similarly the sensitivity and the specificity averaged for three pre-classified diseases are 84.22% and 66.7%, respectively. The misclassification errors are 3.23% for false positives and 3.76% for false negatives. Conclusions The proposed neuro-heuristic approach addresses small changes in the structure of lung tissues, which appear in pneumonia, sarcoidosis or cancer and some consequences that may appear after the treatment. The results show high potential of the newly proposed method. Additionally, the method is flexible and has low computational burden.

A neuro-heuristic approach for recognition of lung diseases from X-ray images

Stacking-based multi-objective evolutionary ensemble framework for prediction of diabetes mellitus

Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development.

Circulating microRNAs (miRNA) are small noncoding RNA molecules that can be detected in bodily fluids without the need for major invasive procedures on patients. miRNAs have shown great promise as biomarkers for tumors to both assess their presence and to predict their type and subtype. Recently, thanks to the availability of miRNAs datasets, machine learning techniques have been successfully applied to tumor classification. The results, however, are difficult to assess and interpret by medical experts because the algorithms exploit information from thousands of miRNAs. In this work, we propose a novel technique that aims at reducing the necessary information to the smallest possible set of circulating miRNAs. The dimensionality reduction achieved reflects a very important first step in a potential, clinically actionable, circulating miRNA-based precision medicine pipeline. While it is currently under discussion whether this first step can be taken, we demonstrate here that it is possible to perform classification tasks by exploiting a recursive feature elimination procedure that integrates a heterogeneous ensemble of high-quality, state-of-the-art classifiers on circulating miRNAs. Heterogeneous ensembles can compensate inherent biases of classifiers by using different classification algorithms. Selecting features then further eliminates biases emerging from using data from different studies or batches, yielding more robust and reliable outcomes. The proposed approach is first tested on a tumor classification problem in order to separate 10 different types of cancer, with samples collected over 10 different clinical trials, and later is assessed on a cancer subtype classification task, with the aim to distinguish triple negative breast cancer from other subtypes of breast cancer. Overall, the presented methodology proves to be effective and compares favorably to other state-of-the-art feature selection methods.

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Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification.

Understanding the chemical-disease relations (CDR) is a crucial task in various biomedical domains. Manual mining of these information from biomedical literature is costly and time-consuming. To address these issues, various researches have been carried out to design an efficient automatic tool. In this paper, we propose a multi-view based deep neural network model for CDR task. Typically, multiple representations (or views) of the datasets are not available for this task. So, we train multiple conceptually different deep neural network models on the dataset to generate different abstract features, treated as different views. A novel loss function, “Penalized LF” , is defined to address the problem of imbalance dataset. The proposed loss function is generic in nature. The model is designed as a combination of Convolution Neural Network (CNN) and Bidirectional Long Short Term Memory (Bi-LSTM) network along with a Multi-Layer Perceptron (MLP). To show the efficacy of our proposed model, we have compared it with six baseline models and other state-of-the-art techniques, on “chemicals-and-disease-DFE” dataset, a free text dataset created by Li et al. from BioCreative V Chemical Disease Relation dataset. Results show that the proposed model attains highest $F1-score$ for individual classes, proving its efficiency in handling class imbalance problem in the dataset. To further demonstrate the efficacy of the proposed model, we have presented results on BioCreative V dataset and two Protein-Protein Interaction Identification (PPI) datasets, viz., AiMed and BioInfer. All these results are also compared with the state-of-the-art models.

A Multi-View Deep Neural Network Model for Chemical-Disease Relation Extraction From Imbalanced Datasets

We present a new multiview clustering approach based on multiobjective optimization. In contrast to existing clustering algorithms based on multiobjective optimization, it is generally applicable to data represented by two or more views and does not require specifying the number of clusters a priori. The approach builds upon the search capability of a multiobjective simulated annealing based technique, AMOSA, as the underlying optimization technique. In the first version of the proposed approach, an internal cluster validity index is used to assess the quality of different partitionings obtained using different views. A new way of checking the compatibility of these different partitionings is also proposed and this is used as another objective function. A new encoding strategy and some new mutation operators are introduced. Finally, a new way of computing a consensus partitioning from multiple individual partitions obtained on multiple views is proposed. As a baseline and for comparison, two multiobjective based ensemble clustering techniques are proposed to combine the outputs of different simple clustering approaches. The efficacy of the proposed clustering methods is shown for partitioning several real-world datasets having multiple views. To show the practical usefulness of the method, we present results on web-search result clustering, where the task is to find a suitable partitioning of web snippets.

Exploring Multiobjective Optimization for Multiview Clustering

Recent high throughput omics technology has been used to assemble large biomedical omics datasets. Clustering of single omics data has proven invaluable in biomedical research. For the task of patient sub-classification, all the available omics data should be utilized combinedly rather than treating them individually. Clustering of multi-omics datasets has the potential to reveal deep insights. Here, we propose a late integration based multiobjective multi-view clustering algorithm which uses a special perturbation operator. Initially, a large number of diverse clustering solutions (called base partitionings) are generated for each omic dataset using four clustering algorithms, viz., k means, complete linkage, spectral and fast search clustering. These base partitionings of multi-omic datasets are suitably combined using a special perturbation operator. The perturbation operator uses an ensemble technique to generate new solutions from the base partitionings. The optimal combination of multiple partitioning solutions across different views is determined after optimizing the objective functions, namely conn-XB, for checking the quality of partitionings for different views, and agreement index, for checking agreement between the views. The search capability of a multiobjective simulated annealing approach, namely AMOSA is used for this purpose. Lastly, the non-dominated solutions of the different views are combined based on similarity to generate a single set of non-dominated solutions. The proposed algorithm is evaluated on 13 multi-view cancer datasets. An elaborated comparative study with several baseline methods and five state-of-the-art models is performed to show the effectiveness of the algorithm.

A multiobjective multi-view cluster ensemble technique: Application in patient subclassification.

In real world applications, data sets are often comprised of multiple views, which provide consensus and complementary information to each other. Embedding learning is an effective strategy for nearest neighbour search and dimensionality reduction in large data sets. This paper attempts to learn a unified probability distribution of the points across different views and generates a unified embedding in a low-dimensional space to optimally preserve neighbourhood identity. Probability distributions generated for each point for each view are combined by conflation method to create a single unified distribution. The goal is to approximate this unified distribution as much as possible when a similar operation is performed on the embedded space. As a cost function, the sum of Kullback-Leibler divergence over the samples is used, which leads to a simple gradient adjusting the position of the samples in the embedded space. The proposed methodology can generate embedding from both complete and incomplete multi-view data sets. Finally, a multi-objective clustering technique (AMOSA) is applied to group the samples in the embedded space. The proposed methodology, Multi-view Neighbourhood Embedding (MvNE), shows an improvement of approximately 2−3% over state-of-the-art models when evaluated on 10 omics data sets.

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Sayantan Mitra

Papers

A Multi-View Deep Neural Network Model for Chemical-Disease Relation Extraction From Imbalanced Datasets

Exploring Multiobjective Optimization for Multiview Clustering

A multiobjective multi-view cluster ensemble technique: Application in patient subclassification.

Multi-view clustering for multi-omics data using unified embedding.

A Stack-based Ensemble Framework for Detecting Cancer MicroRNA Biomarkers.